Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 90 of 335
Found at i:29278493 original size:32 final size:32
Alignment explanation
Indices: 29278456--29278527 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
29278446 AAATTTTATG
29278456 AAATATTTT-CAGGAAATT-TTCCAAACAATAGA
1 AAATATTTTACA-GAAATTATT-CAAACAATAGA
* *
29278488 AAATATTTTACATAAATTCATTCAAACACTAGA
1 AAATATTTTACAGAAATT-ATTCAAACAATAGA
29278521 AAATATT
1 AAATATT
29278528 AGCTTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 14 0.40
33 19 0.54
34 2 0.06
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (32 bp):
AAATATTTTACAGAAATTATTCAAACAATAGA
Found at i:29281204 original size:32 final size:33
Alignment explanation
Indices: 29281105--29281218 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
29281095 GGTGTACACT
**
29281105 CCTTTCCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTCCAAGTGGTACACACAAAGTATACCTAA
* * *
29281138 TCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACCTAA
* *
29281171 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTCCAAGTGGTACACACAAAGTATACCTAA
* *
29281203 CCTTTTCAAGTTGTAC
1 CCTTTCCAAGTGGTAC
29281219 CATTTGGGTA
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
32 29 0.43
33 37 0.55
34 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.32
Consensus pattern (33 bp):
CCTTTCCAAGTGGTACACACAAAGTATACCTAA
Found at i:29284669 original size:28 final size:28
Alignment explanation
Indices: 29284604--29284702 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
29284594 CATGAGATTG
* * *
29284604 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
29284633 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
29284661 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
29284689 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
29284703 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:29288800 original size:44 final size:45
Alignment explanation
Indices: 29288710--29288838 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 45
29288700 GACAGAACGA
* *
29288710 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGGGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
29288756 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
29288800 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29288839 CAGGATATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.51
45 1 0.01
46 33 0.48
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:29291941 original size:20 final size:20
Alignment explanation
Indices: 29291916--29291954 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
29291906 CTAGCCCCAC
29291916 GGCCATGTCCCAGGCCACAT
1 GGCCATGTCCCAGGCCACAT
29291936 GGCCATGTCCCAGGCCACA
1 GGCCATGTCCCAGGCCACA
29291955 CGAGCGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.41, G:0.26, T:0.13
Consensus pattern (20 bp):
GGCCATGTCCCAGGCCACAT
Found at i:29296755 original size:32 final size:33
Alignment explanation
Indices: 29296656--29296769 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 33
29296646 GGTGTACATT
* **
29296656 CCTTTCCAAATGGTACACACAAAGTATACATTT
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
** * *
29296689 CCTTTTTATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACATAA
*
29296722 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
* *
29296754 CCTTTTCAAGTTGTAC
1 CCTTTCCAAGTGGTAC
29296770 CATTTGGGTA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
32 29 0.44
33 36 0.55
34 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (33 bp):
CCTTTCCAAGTGGTACACACAAAGTATACATAA
Found at i:29299831 original size:136 final size:137
Alignment explanation
Indices: 29299587--29299872 Score: 511
Period size: 136 Copynumber: 2.1 Consensus size: 137
29299577 CATTGGGCCT
** * *
29299587 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
29299652 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATGAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
29299716 CATATGC
131 CATATGC
29299723 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
29299788 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
29299853 CATATGC
131 CATATGC
29299860 AAGCCCATTTGGG
1 AAGCCCATTTGGG
29299873 GAGACTACTC
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 121 0.85
137 22 0.15
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:29300157 original size:25 final size:26
Alignment explanation
Indices: 29300120--29300172 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
29300110 TCAAACATGC
29300120 ATTTAGGTCAATTTAACC-CTAGGGGT
1 ATTTAGGTCAATTT-ACCACTAGGGGT
*
29300146 ATTTCGGT-AATTTACCTACTAGGGGT
1 ATTTAGGTCAATTTACC-ACTAGGGGT
29300172 A
1 A
29300173 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.12
25 5 0.21
26 16 0.67
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (26 bp):
ATTTAGGTCAATTTACCACTAGGGGT
Found at i:29301692 original size:26 final size:26
Alignment explanation
Indices: 29301656--29301791 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
29301646 CATGAAATTC
29301656 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29301682 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29301708 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29301734 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
29301760 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29301786 TTATCA
1 TTATCA
29301792 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29304709 original size:46 final size:44
Alignment explanation
Indices: 29304605--29304712 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
29304595 TGTCTTTGAC
** * * *
29304605 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
29304649 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29304695 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29304713 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29310662 original size:46 final size:44
Alignment explanation
Indices: 29310558--29310665 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
29310548 TGTCTTTGAC
** * * *
29310558 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
29310602 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29310648 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29310666 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29313718 original size:22 final size:22
Alignment explanation
Indices: 29313693--29313736 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29313683 GAACCATATG
29313693 TAAATGATTTTTCCTCTTTTGA
1 TAAATGATTTTTCCTCTTTTGA
29313715 TAAATGATTTTTCCTCTTTTGA
1 TAAATGATTTTTCCTCTTTTGA
29313737 ACAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (22 bp):
TAAATGATTTTTCCTCTTTTGA
Found at i:29319462 original size:10 final size:10
Alignment explanation
Indices: 29319429--29319471 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
29319419 CGTAACATTT
*
29319429 TAAATATAAA
1 TAAATAAAAA
*
29319439 TGAATAAAATA
1 TAAATAAAA-A
*
29319450 TAATTAAAAA
1 TAAATAAAAA
29319460 TAAATAAAAA
1 TAAATAAAAA
29319470 TA
1 TA
29319472 CTATTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:29319715 original size:2 final size:2
Alignment explanation
Indices: 29319708--29319742 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29319698 TTGTGCCTTT
29319708 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
29319743 TAATTTATAA
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:29320057 original size:13 final size:13
Alignment explanation
Indices: 29320032--29320071 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
29320022 AAAATAATTT
29320032 AAAT-TTAATTATA
1 AAATATTAA-TATA
29320045 AAATATTAATATA
1 AAATATTAATATA
29320058 AAATATTTAATATA
1 AAATA-TTAATATA
29320072 TATATTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATTAATATA
Found at i:29320067 original size:14 final size:14
Alignment explanation
Indices: 29320034--29320071 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
29320024 AATAATTTAA
29320034 ATTTAATTATAAAAT
1 ATTTAA-TATAAAAT
29320049 A-TTAATATAAAAT
1 ATTTAATATAAAAT
29320062 ATTTAATATA
1 ATTTAATATA
29320072 TATATTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 12 0.55
15 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTAATATAAAAT
Found at i:29320792 original size:22 final size:22
Alignment explanation
Indices: 29320767--29320809 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
29320757 CATTAAGGGC
*
29320767 TAAA-TTTATCTTTATGTTTTTT
1 TAAAGTTTAT-TTTATATTTTTT
29320789 TAAAGTTTTATTTTATATTTT
1 TAAAG-TTTATTTTATATTTT
29320810 AGGGCAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 9 0.50
24 5 0.28
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
TAAAGTTTATTTTATATTTTTT
Found at i:29324243 original size:25 final size:23
Alignment explanation
Indices: 29324215--29324264 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29324205 GTATAGAACT
*
29324215 TTTTTATAAATTTTTATAAATATAA
1 TTTTTAT-AATATTT-TAAATATAA
*
29324240 TTTTTATAGTATTTTAAATATAA
1 TTTTTATAATATTTTAAATATAA
29324263 TT
1 TT
29324265 ATAGTTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.48
24 5 0.22
25 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTATAATATTTTAAATATAA
Found at i:29328914 original size:2 final size:2
Alignment explanation
Indices: 29328907--29328931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29328897 CATAAAAAGC
29328907 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
29328932 TGTAAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29329857 original size:29 final size:31
Alignment explanation
Indices: 29329777--29329860 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
29329767 AATCAAAATT
**
29329777 AAAGTTTCATGTATA-AATTTAAACCACAATC
1 AAAGTTTCATGTATAGAA-TTGCACCACAATC
*
29329808 AAAGTTTCATGTATATAATTGCACCA-AATC
1 AAAGTTTCATGTATAGAATTGCACCACAATC
*
29329838 AAAGTTT-ATGTATCGAATTGCAC
1 AAAGTTTCATGTATAGAATTGCAC
29329861 AATGACTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.29
30 11 0.23
31 21 0.44
32 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.33
Consensus pattern (31 bp):
AAAGTTTCATGTATAGAATTGCACCACAATC
Found at i:29336760 original size:31 final size:29
Alignment explanation
Indices: 29336690--29336781 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 29
29336680 GATTCCATAG
* *
29336690 GTCCCTGTATGTTTCATAAATTTAATATTTA
1 GTCCCTTTAT-TTTTATAAATTTAA-ATTTA
29336721 GTCCCTTTATTTTTTATAAATTTGAAATTTA
1 GTCCCTTTA-TTTTTATAAATTT-AAATTTA
*
29336752 GTCTCTTTATTTTTA-AAATTTTAAAATTTA
1 GTCCCTTTATTTTTATAAA-TTT-AAATTTA
29336782 ATTCTAATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.06
30 16 0.30
31 32 0.59
32 3 0.06
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (29 bp):
GTCCCTTTATTTTTATAAATTTAAATTTA
Found at i:29339630 original size:54 final size:54
Alignment explanation
Indices: 29339511--29339620 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 54
29339501 GGAATTGGGT
*
29339511 TTGGAATAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
1 TTGGAACAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
* * * *
29339565 TTGGAACAGAATAATGGGATGGAGA-CTCAAATTTCGGAGGGTATTGAAGTGGGC
1 TTGGAACAGAATAATGGGATGGAAATC-CAAATTTCAGAGGGTAATGAAGTAGGC
29339619 TT
1 TT
29339621 TAATGAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (54 bp):
TTGGAACAGAATAATGGGATGGAAATCCAAATTTCAGAGGGTAATGAAGTAGGC
Found at i:29341222 original size:48 final size:48
Alignment explanation
Indices: 29341166--29341266 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 48
29341156 TTTGAGAAGT
*
29341166 GTTAAAATTTAAAGAATCTATTTGGCGGCAGAAATCAAGGATGACATG
1 GTTAAAATTTAAAGAATCTATTTGGCGACAGAAATCAAGGATGACATG
29341214 GTTAAAATTTAAAGAATCTATTTGGCGACAGAAATCAAGGATGACATG
1 GTTAAAATTTAAAGAATCTATTTGGCGACAGAAATCAAGGATGACATG
29341262 GTTAA
1 GTTAA
29341267 GGGAAAGGGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (48 bp):
GTTAAAATTTAAAGAATCTATTTGGCGACAGAAATCAAGGATGACATG
Found at i:29347748 original size:43 final size:43
Alignment explanation
Indices: 29347700--29347846 Score: 138
Period size: 43 Copynumber: 3.4 Consensus size: 43
29347690 ATCGAGATGT
* *
29347700 GATTACATGTAAGACCATGTTTGGGACATTGGCATTGTATTGA
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
* * * * *
29347743 GATTACGTGTAATACCATGTCTGAGACATTGGCATCGTTAAT-C
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TATTGA
* * * * *
29347786 GATTTCATGTAAGACCCTGTCTGGGACAGTAGCATCG-ATATGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-TGA
29347829 G-TTAACATGTAAGACCAT
1 GATT-ACATGTAAGACCAT
29347847 ATTTGGGATA
Statistics
Matches: 82, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.01
42 3 0.04
43 75 0.91
44 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:29358838 original size:16 final size:16
Alignment explanation
Indices: 29358819--29358864 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
29358809 ACTATAATGG
29358819 AATAGGGCTGTAATTA
1 AATAGGGCTGTAATTA
29358835 AATAGGGCTGTAATTA
1 AATAGGGCTGTAATTA
*
29358851 AATAGAGCTGTAAT
1 AATAGGGCTGTAAT
29358865 CAGTAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.30
Consensus pattern (16 bp):
AATAGGGCTGTAATTA
Found at i:29359108 original size:58 final size:58
Alignment explanation
Indices: 29359044--29359165 Score: 174
Period size: 58 Copynumber: 2.1 Consensus size: 58
29359034 TTAATAAGAG
* *
29359044 TATTATTAAAAATAATTTAATAAAAATAATAAATAGTTTAACCAAATT-TTAACATAAT
1 TATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATAAT
* * * *
29359102 TATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATAAT
1 TATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATAAT
29359160 TATTAT
1 TATTAT
29359166 ATGAATTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.39
58 35 0.61
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (58 bp):
TATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATAAT
Found at i:29363270 original size:19 final size:19
Alignment explanation
Indices: 29363234--29363270 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29363224 TAATTAGGCT
* *
29363234 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
29363253 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
29363271 GAAAAAGGGC
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:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:29363819 original size:15 final size:15
Alignment explanation
Indices: 29363799--29363851 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
29363789 GTCTATGATA
29363799 AACAAATTAAGTGGT
1 AACAAATTAAGTGGT
*
29363814 AACAAATATAA-TGAT
1 AACAAAT-TAAGTGGT
29363829 AAACAAATTAAGTGGT
1 -AACAAATTAAGTGGT
29363845 AACAAAT
1 AACAAAT
29363852 GTAATGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 20 0.61
16 13 0.39
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.25
Consensus pattern (15 bp):
AACAAATTAAGTGGT
Found at i:29363828 original size:31 final size:31
Alignment explanation
Indices: 29363793--29363861 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
29363783 ATTTTCGTCT
29363793 ATGATAAACAAATTAAGTGGTAACAAATATA
1 ATGATAAACAAATTAAGTGGTAACAAATATA
*
29363824 ATGATAAACAAATTAAGTGGTAACAAATGTA
1 ATGATAAACAAATTAAGTGGTAACAAATATA
29363855 ATG-TAAA
1 ATGATAAA
29363862 TATGTGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (31 bp):
ATGATAAACAAATTAAGTGGTAACAAATATA
Found at i:29363835 original size:16 final size:15
Alignment explanation
Indices: 29363793--29363861 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
29363783 ATTTTCGTCT
29363793 ATGATAAACAAATTA
1 ATGATAAACAAATTA
*
29363808 AGTGGT-AACAAATATA
1 A-TGATAAACAAAT-TA
29363824 ATGATAAACAAATTA
1 ATGATAAACAAATTA
*
29363839 AGTGGT-AACAAATGTA
1 A-TGATAAACAAAT-TA
29363855 ATG-TAAA
1 ATGATAAA
29363862 TATGTGTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
14 1 0.02
15 25 0.56
16 19 0.42
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.26
Consensus pattern (15 bp):
ATGATAAACAAATTA
Found at i:29364414 original size:17 final size:18
Alignment explanation
Indices: 29364392--29364425 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29364382 TAAATGAGTT
29364392 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
29364409 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
29364426 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:29364915 original size:13 final size:14
Alignment explanation
Indices: 29364894--29364933 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
29364884 ATTTGATTGG
29364894 AAAATGAATTAAA-
1 AAAATGAATTAAAT
*
29364907 AATATGAATTAAAT
1 AAAATGAATTAAAT
29364921 AAAAGTGAATTAA
1 AAAA-TGAATTAA
29364934 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAT
Found at i:29365332 original size:21 final size:22
Alignment explanation
Indices: 29365296--29365357 Score: 92
Period size: 21 Copynumber: 2.9 Consensus size: 22
29365286 TAAGCACTTT
29365296 ATGTGTCGTATATCAGGCACCTC
1 ATGTGTCGT-TATCAGGCACCTC
29365319 ATGTGTC-TTATCAGGCACCTC
1 ATGTGTCGTTATCAGGCACCTC
*
29365340 GTGTGTCGTT-TCAGGCAC
1 ATGTGTCGTTATCAGGCAC
29365358 TTATTTGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 27 0.73
22 3 0.08
23 7 0.19
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (22 bp):
ATGTGTCGTTATCAGGCACCTC
Found at i:29368182 original size:31 final size:31
Alignment explanation
Indices: 29368146--29368263 Score: 130
Period size: 31 Copynumber: 3.7 Consensus size: 31
29368136 ATCACATTAT
29368146 TATTAAATTAATAAAATATTATCAAGATAAA
1 TATTAAATTAATAAAATATTATCAAGATAAA
* * *
29368177 TATTAAATTAAATTAAATA-TATCATATATATTAG
1 TATTAAATT-AATAAAATATTATCA-AGATA--AA
* *
29368211 TATTAAATTAATAAAATACTATCTAGATAAA
1 TATTAAATTAATAAAATATTATCAAGATAAA
*
29368242 TATTAAATTAATATTAATATTA
1 TATTAAATTAATA-AAATATTA
29368264 ATATTAATAT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
31 28 0.39
32 18 0.25
33 12 0.17
34 14 0.19
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (31 bp):
TATTAAATTAATAAAATATTATCAAGATAAA
Found at i:29368259 original size:6 final size:6
Alignment explanation
Indices: 29368240--29368289 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
29368230 TATCTAGATA
*
29368240 AATATT AA-ATT AATATT AATATT AATATT AATATT AATATT AATACT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
29368287 AAT
1 AAT
29368290 TATTTCTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (6 bp):
AATATT
Found at i:29368779 original size:52 final size:50
Alignment explanation
Indices: 29368704--29368810 Score: 153
Period size: 52 Copynumber: 2.1 Consensus size: 50
29368694 AAAAGCTAAA
*
29368704 TAAATAAAAATGAAATTCTATTAGATTAATTATCTTTTTGAAATTAAAAATC
1 TAAATAAAAATAAAATTCTATTAGATTAATTAT-TTTTT-AAATTAAAAATC
* *
29368756 TAAATAAAAATAAAATT-TAATTAGATTAATTATTTTTTAACTTATAAATC
1 TAAATAAAAATAAAATTCT-ATTAGATTAATTATTTTTTAAATTAAAAATC
29368806 TAAAT
1 TAAAT
29368811 TTGACTCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 15 0.29
51 6 0.12
52 30 0.59
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (50 bp):
TAAATAAAAATAAAATTCTATTAGATTAATTATTTTTTAAATTAAAAATC
Found at i:29381332 original size:19 final size:19
Alignment explanation
Indices: 29381310--29381349 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29381300 TTATTAAAAT
29381310 ATTATAATAAAAT-TAGAAA
1 ATTATAA-AAAATATAGAAA
*
29381329 ATTATAAAAATTATAGAAA
1 ATTATAAAAAATATAGAAA
29381348 AT
1 AT
29381350 ATATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTATAAAAAATATAGAAA
Found at i:29384323 original size:21 final size:22
Alignment explanation
Indices: 29384299--29384341 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29384289 GTATTGCTAT
29384299 AATAATT-ATAATTA-TAATCAA
1 AATAATTAAT-ATTATTAATCAA
29384320 AATAATTAATATTATTAATCAA
1 AATAATTAATATTATTAATCAA
29384342 CAATCTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAATATTATTAATCAA
Found at i:29389289 original size:16 final size:16
Alignment explanation
Indices: 29389268--29389303 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
29389258 ATTTAAATCA
29389268 AATTTAAATTCGAA-AT
1 AATTTAAATTC-AATAT
29389284 AATTTAAATTCAATAT
1 AATTTAAATTCAATAT
29389300 AATT
1 AATT
29389304 AAAACCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTAAATTCAATAT
Found at i:29390558 original size:14 final size:14
Alignment explanation
Indices: 29390535--29390569 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29390525 TACAATATTC
*
29390535 AAATAATAACAACA
1 AAATAGTAACAACA
29390549 AAATAGTAACAACA
1 AAATAGTAACAACA
*
29390563 TAATAGT
1 AAATAGT
29390570 GAAATGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:29390902 original size:18 final size:18
Alignment explanation
Indices: 29390879--29390913 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29390869 TGGTCGAGGG
29390879 TTCAATCCTCGCCTTGGT
1 TTCAATCCTCGCCTTGGT
*
29390897 TTCAATCTTCGCCTTGG
1 TTCAATCCTCGCCTTGG
29390914 GTATGAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.17, T:0.40
Consensus pattern (18 bp):
TTCAATCCTCGCCTTGGT
Found at i:29391225 original size:23 final size:23
Alignment explanation
Indices: 29391174--29391225 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
29391164 TCATTTAAAC
*
29391174 AAATACTCATATTTATATAATTA
1 AAATATTCATATTTATATAATTA
*
29391197 AAATATTCATATTT-TATACTATA
1 AAATATTCATATTTATATAAT-TA
29391220 AAATAT
1 AAATAT
29391226 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATATTCATATTTATATAATTA
Found at i:29394947 original size:30 final size:29
Alignment explanation
Indices: 29394907--29394968 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
29394897 ACTCCATTTT
*
29394907 TTTTTTAATTTTTATGAACT-TTTTATAAGA
1 TTTTTAAATTTTTATGAA-TATTTTATAA-A
*
29394937 TTTTTAAATTTTTTTGAATATTTTATAAA
1 TTTTTAAATTTTTATGAATATTTTATAAA
29394966 TTT
1 TTT
29394969 AAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTTAAATTTTTATGAATATTTTATAAA
Found at i:29394950 original size:21 final size:21
Alignment explanation
Indices: 29394916--29394968 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
29394906 TTTTTTTAAT
* *
29394916 TTTTATGAACTTTTTAT-AAGA
1 TTTTAT-AAATTTTTTTGAAGA
*
29394937 TTTT-TAAATTTTTTTGAATA
1 TTTTATAAATTTTTTTGAAGA
29394957 TTTTATAAATTT
1 TTTTATAAATTT
29394969 AAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 8 0.30
21 11 0.41
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTTATAAATTTTTTTGAAGA
Found at i:29396090 original size:26 final size:26
Alignment explanation
Indices: 29396052--29396111 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
29396042 TGTCGTCATC
* * * *
29396052 TTCTATTCGTTTCTTTCTTTTTGTTG
1 TTCTTTTCGTTTCCTTCATTTTCTTG
*
29396078 TTCTTTTCTTTTCCTTCATTTTCTTG
1 TTCTTTTCGTTTCCTTCATTTTCTTG
29396104 TCTCTTTT
1 T-TCTTTT
29396112 TGATTCTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.03, C:0.20, G:0.07, T:0.70
Consensus pattern (26 bp):
TTCTTTTCGTTTCCTTCATTTTCTTG
Found at i:29406957 original size:23 final size:23
Alignment explanation
Indices: 29406912--29406958 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29406902 TATATCAAAC
*
29406912 AAACAACACTTAATAACATTATA
1 AAACAACACTTAATAACAATATA
*
29406935 AAACTAACATTTAATAA-AATATA
1 AAAC-AACACTTAATAACAATATA
29406958 A
1 A
29406959 CAATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
AAACAACACTTAATAACAATATA
Found at i:29409236 original size:87 final size:87
Alignment explanation
Indices: 29409145--29409639 Score: 324
Period size: 87 Copynumber: 5.6 Consensus size: 87
29409135 GGATGCCAAA
*
29409145 TCATCTTGGATTTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTACTCTCCGTC
1 TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTACTCTCCGTC
* *
29409210 GAATATGGAGACGTCAAATCTG
66 GAATATGGAGATGCCAAATCTG
* * *
29409232 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTGTCTACTCTCCGT
*
29409296 CGAA-ATGGAGATGCCAGATCTG
65 CGAATATGGAGATGCCAAATCTG
* ** * * * * * * * * *
29409318 TTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTT
1 TCATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATGT-GTCTA-CT-CT
* * ** *
29409383 CCTTGT-AAACATAAAAATGCCAAA----
61 CC--GTCGAATATGGAGATGCCAAATCTG
* * *
29409407 TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTC
1 TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTACTCTCCGTC
* * *
29409472 GAATATGGAGAAGTCAGATCTG
66 GAATATGGAGATGCCAAATCTG
* * * * * * * * *
29409494 TTATCTTGGATCTACTTTGATGTGAAAAACATCTGGAA-GTCAAATCTGCTATGTCTTCGATTTA
1 TCATCTTGGATCTGC-TTCA-GT-ATAAACATCT-GAAGGTTAGATCTGCTATGT-GTCTA-CT-
* * * *
29409558 CTCCTTGTTGAAGATAGAGAAGCCAAATCTTG
59 CTCC--GTCGAATATGGAGATGCCAAATC-TG
* * * **
29409590 TTATCTTGGATCTGCTTTAGTGTAAACA-CGTGAAGGCCAGATCTGCTATG
1 TCATCTTGGATCTGCTTCAGTATAAACATC-TGAAGGTTAGATCTGCTATG
29409640 CTTTGGTCTG
Statistics
Matches: 311, Mismatches: 70, Indels: 48
0.72 0.16 0.11
Matches are distributed among these distances:
82 2 0.01
83 10 0.03
84 3 0.01
86 38 0.12
87 97 0.31
88 25 0.08
89 24 0.08
90 24 0.08
91 8 0.03
92 6 0.02
93 35 0.11
94 2 0.01
95 21 0.07
96 16 0.05
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (87 bp):
TCATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTACTCTCCGTC
GAATATGGAGATGCCAAATCTG
Found at i:29409416 original size:175 final size:177
Alignment explanation
Indices: 29409232--29409565 Score: 521
Period size: 175 Copynumber: 1.9 Consensus size: 177
29409222 GTCAAATCTG
* *
29409232 TCATCTTGGATCTGCTTCAGTA-AAATCATCTGAAGGCTAGATCTGCTATGTATCTGCTCTCCGT
1 TCATCTTGGATCTACTTCAGTATAAA-CATCTGAAGGCTAGATCTGCTATGTATCTGCCCTCCGT
* * * *
29409296 CGAA-ATGGAGATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTG-AGAACATCCGAAAGTCA
65 CGAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCA
**
29409359 AATCTGCTATGTCTTCGATTTGTTCCTTGTAAACATAAAAATGCCAAA
130 AATCTGCTATGTCTTCGATTTACTCCTTGTAAACATAAAAATGCCAAA
* *
29409407 TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTCCGTC
1 TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGCTAGATCTGCTATGTATCTGCCCTCCGTC
* * *
29409472 GAATATGGAGAAGTCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCTGGAAGTCAA
66 GAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
29409537 ATCTGCTATGTCTTCGATTTACTCCTTGT
131 ATCTGCTATGTCTTCGATTTACTCCTTGT
29409566 TGAAGATAGA
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
175 60 0.42
176 41 0.29
177 42 0.29
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (177 bp):
TCATCTTGGATCTACTTCAGTATAAACATCTGAAGGCTAGATCTGCTATGTATCTGCCCTCCGTC
GAATATGGAGAAGCCAGATCTGTTATCTTGGATCTACTTTGATGTGAAAAACATCCGAAAGTCAA
ATCTGCTATGTCTTCGATTTACTCCTTGTAAACATAAAAATGCCAAA
Found at i:29415796 original size:47 final size:47
Alignment explanation
Indices: 29415687--29415797 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
29415677 CCGGGATAAG
*
29415687 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
29415734 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
29415781 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
29415798 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:29416552 original size:4 final size:4
Alignment explanation
Indices: 29416536--29416570 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
29416526 AAATTTCCCT
29416536 TTTC TTT- TTTC TTTC TTTC TTTC -TTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
29416571 CACGTTTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:29416552 original size:11 final size:12
Alignment explanation
Indices: 29416536--29416570 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
29416526 AAATTTCCCT
29416536 TTTCTTT-TTTC
1 TTTCTTTCTTTC
29416547 TTTCTTTCTTTC
1 TTTCTTTCTTTC
29416559 -TTCTTTCTTTC
1 TTTCTTTCTTTC
29416570 T
1 T
29416571 CACGTTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTTTCTTTC
Found at i:29416556 original size:15 final size:15
Alignment explanation
Indices: 29416536--29416570 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
29416526 AAATTTCCCT
*
29416536 TTTCTTTTTTCTTTC
1 TTTCTTTCTTCTTTC
29416551 TTTCTTTCTTCTTTC
1 TTTCTTTCTTCTTTC
29416566 TTTCT
1 TTTCT
29416571 CACGTTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTCTTCTTTC
Found at i:29423004 original size:47 final size:47
Alignment explanation
Indices: 29422895--29423005 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
29422885 CCGGGATAAG
*
29422895 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
29422942 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
29422989 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
29423006 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:29423755 original size:4 final size:4
Alignment explanation
Indices: 29423742--29423778 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
29423732 TCAAATTTCC
29423742 CTTT -TTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
29423779 CACGTTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:29430214 original size:17 final size:18
Alignment explanation
Indices: 29430192--29430225 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29430182 GTATCAGAAT
*
29430192 ATAC-AACATATGTAATA
1 ATACAAACACATGTAATA
29430209 ATACAAACACATGTAAT
1 ATACAAACACATGTAAT
29430226 GCAAAGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (18 bp):
ATACAAACACATGTAATA
Found at i:29430534 original size:21 final size:21
Alignment explanation
Indices: 29430486--29430537 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
29430476 AACTTCTTGA
* *
29430486 TGAGTTAGGGCAGTAGGTATC
1 TGAGTTGGGGCAGTAGGTAAC
29430507 TGAGTTGGGGCAGTAGGTAAC
1 TGAGTTGGGGCAGTAGGTAAC
29430528 TGAGTTGGGG
1 TGAGTTGGGG
29430538 TACCTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.08, G:0.44, T:0.27
Consensus pattern (21 bp):
TGAGTTGGGGCAGTAGGTAAC
Found at i:29430569 original size:21 final size:21
Alignment explanation
Indices: 29430527--29430571 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29430517 CAGTAGGTAA
* *
29430527 CTGAGTTGGGGTACCTTTTTG
1 CTGACTTGGGGTACCTTGTTG
29430548 CTGACTTGGGGTAGCC-TGTTG
1 CTGACTTGGGGTA-CCTTGTTG
29430569 CTG
1 CTG
29430572 GGTTCGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.09, C:0.18, G:0.36, T:0.38
Consensus pattern (21 bp):
CTGACTTGGGGTACCTTGTTG
Found at i:29431801 original size:46 final size:46
Alignment explanation
Indices: 29431620--29431801 Score: 240
Period size: 46 Copynumber: 4.0 Consensus size: 46
29431610 TTTGACATGA
* * * * * *
29431620 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* *** *
29431666 TACCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
29431712 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
29431758 TGCCATGGTATCTATCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
29431802 AGAGCACACT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
45 4 0.03
46 117 0.97
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:29433934 original size:3 final size:3
Alignment explanation
Indices: 29433913--29433948 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
29433903 GTTTATATAT
*
29433913 ATA ATA TATA ATA ACA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
29433949 GACTTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29435015 original size:42 final size:43
Alignment explanation
Indices: 29434897--29435073 Score: 220
Period size: 42 Copynumber: 4.2 Consensus size: 43
29434887 AAAAAAAAAC
* * *
29434897 TCATTGCATGCATATTAAAAAATAGGCAGC-AC--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
*
29434937 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
* *
29434980 TCATTGCATGTATATT-AAAAATAGTCAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
* * * *
29435022 TCATTGCATACATATTAAAAGA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
*
29435064 TCACTGCATG
1 TCATTGCATG
29435074 TAATCAGCAA
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 28 0.24
41 1 0.01
42 63 0.53
43 26 0.22
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAACAA
Found at i:29436733 original size:11 final size:11
Alignment explanation
Indices: 29436719--29436774 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
29436709 AGATAAATAT
29436719 TATTTTATTAA
1 TATTTTATTAA
*
29436730 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
29436743 TATTTTATTAT
1 TATTTTATTAA
*
29436754 TATTTTATTAT
1 TATTTTATTAA
29436765 TATTTTATTA
1 TATTTTATTA
29436775 GTATATAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 27 0.68
12 6 0.15
13 7 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:29439076 original size:46 final size:46
Alignment explanation
Indices: 29438890--29439073 Score: 323
Period size: 46 Copynumber: 4.0 Consensus size: 46
29438880 AGTGTGCTCT
29438890 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29438936 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
29438982 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
29439028 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
29439074 GTGCCATATG
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:29440415 original size:15 final size:15
Alignment explanation
Indices: 29440395--29440424 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29440385 ATGCATCACT
29440395 ATCACTACCAGACAC
1 ATCACTACCAGACAC
29440410 ATCACTACCAGACAC
1 ATCACTACCAGACAC
29440425 GTTTTCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:29440780 original size:62 final size:62
Alignment explanation
Indices: 29440709--29440943 Score: 344
Period size: 62 Copynumber: 3.8 Consensus size: 62
29440699 TAGGAGCTTG
*
29440709 GATACAAACAATGACAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATCGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
* * *
29440771 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATTGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
* * * * ** *
29440833 GATACAAACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATG-TA-TAATTTAATCGCA
*
29440897 GATACAAACAATGACAGATATACACAATAAACATCAATTTGATAATG
1 GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATG
29440944 ACATTCATAC
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
62 105 0.65
63 1 0.01
64 55 0.34
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (62 bp):
GATACAAACAATGACAGATATACACAATAAACATCAATTTAATAATGTATAATTTAATCGCA
Found at i:29440954 original size:34 final size:34
Alignment explanation
Indices: 29440852--29440954 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 34
29440842 AATGGCAGAT
29440852 ATACACAATAAACATCAATTTGATAATGACATTC
1 ATACACAATAAACATCAATTTGATAATGACATTC
** * * *
29440886 AT--ACAATGGCAGATACAA----ACAATGACAGAT-
1 ATACACAAT-AAACAT-CAATTTGATAATGACA-TTC
29440916 ATACACAATAAACATCAATTTGATAATGACATTC
1 ATACACAATAAACATCAATTTGATAATGACATTC
29440950 ATACA
1 ATACA
29440955 ATGGCAGATA
Statistics
Matches: 49, Mismatches: 10, Indels: 20
0.62 0.13 0.25
Matches are distributed among these distances:
30 13 0.27
31 4 0.08
32 10 0.20
33 4 0.08
34 18 0.37
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (34 bp):
ATACACAATAAACATCAATTTGATAATGACATTC
Found at i:29440969 original size:112 final size:115
Alignment explanation
Indices: 29440840--29441100 Score: 375
Period size: 112 Copynumber: 2.3 Consensus size: 115
29440830 GCAGATACAA
**
29440840 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGGCAGATACAAA
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATAACAGATACAAA
29440905 CAAT-G-A-CAGATATACACAATAAACATCAATTTGATAATGACATTCAT
66 CAATGGAAGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* * *
29440952 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAATAACAGATACAAA
1 ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATAACAGATACAAA
* * *
29441017 CAATGGCAAATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCAT
66 CAATGG--AA--GCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* *
29441071 ACAATGGCAGATACAAACAATAAACATCAA
1 ACAATGGCAGATATACACAATAAACATCAA
29441101 AATCAAAATC
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
112 64 0.49
113 1 0.01
116 1 0.01
119 64 0.49
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (115 bp):
ACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATAACAGATACAAA
CAATGGAAGCAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:29440973 original size:48 final size:48
Alignment explanation
Indices: 29440904--29441012 Score: 173
Period size: 48 Copynumber: 2.3 Consensus size: 48
29440894 GCAGATACAA
29440904 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
1 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* * *
29440952 ACAATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCAT
1 ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
* *
29441000 ATAATAACAGATA
1 ACAATGACAGATA
29441013 CAAACAATGG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (48 bp):
ACAATGACAGATATACACAATAAACATCAATTTGATAATGACATTCAT
Found at i:29441070 original size:71 final size:71
Alignment explanation
Indices: 29440954--29441091 Score: 240
Period size: 71 Copynumber: 1.9 Consensus size: 71
29440944 ACATTCATAC
*
29440954 AATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATATAATAACAGATACAAACA
1 AATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATAACAGATACAAACA
29441019 ATGGCA
66 ATGGCA
* **
29441025 AATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGGCAGATACAAACA
1 AATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATAACAGATACAAACA
29441090 AT
66 AT
29441092 AAACATCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (71 bp):
AATGGCAGATATACACAATAAAGATCAGTTTGATAATGACATTCATACAATAACAGATACAAACA
ATGGCA
Found at i:29441260 original size:18 final size:18
Alignment explanation
Indices: 29441233--29441315 Score: 70
Period size: 18 Copynumber: 4.9 Consensus size: 18
29441223 AAATAACCCT
* *
29441233 AAATCGAAATCTAAATCG
1 AAATCAAAATCTAAATTG
*
29441251 AAATCAAAATC-AAATTC
1 AAATCAAAATCTAAATTG
*
29441268 TAATC-----CTAAATTG
1 AAATCAAAATCTAAATTG
* *
29441281 AGATCAAAATCGAAATTG
1 AAATCAAAATCTAAATTG
29441299 AAATCAAAATCTAAATT
1 AAATCAAAATCTAAATT
29441316 AGAATCAGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.02
13 8 0.16
17 8 0.16
18 32 0.65
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (18 bp):
AAATCAAAATCTAAATTG
Found at i:29441314 original size:12 final size:12
Alignment explanation
Indices: 29441231--29441270 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
29441221 CGAAATAACC
29441231 CTAAATCGAAAT
1 CTAAATCGAAAT
29441243 CTAAATCGAAAT
1 CTAAATCGAAAT
*
29441255 CAAAATC-AAATT
1 CTAAATCGAAA-T
29441267 CTAA
1 CTAA
29441271 TCCTAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 22 0.88
ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25
Consensus pattern (12 bp):
CTAAATCGAAAT
Found at i:29441321 original size:18 final size:17
Alignment explanation
Indices: 29441273--29441322 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
29441263 AATTCTAATC
29441273 CTAAATTGAGATCAAAAT
1 CTAAATTGA-ATCAAAAT
*
29441291 CGAAATTGAAATCAAAAT
1 CTAAATTG-AATCAAAAT
29441309 CTAAATTAGAATCA
1 CTAAATT-GAATCA
29441323 GTGAGTGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 26 0.93
19 2 0.07
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (17 bp):
CTAAATTGAATCAAAAT
Found at i:29441374 original size:12 final size:12
Alignment explanation
Indices: 29441332--29441374 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
29441322 AGTGAGTGTT
* *
29441332 TCAAAATTGTAA
1 TCAAAATCGAAA
29441344 TCAAAATCGAAA
1 TCAAAATCGAAA
29441356 T-AGAAATCGAAA
1 TCA-AAATCGAAA
29441368 TCAAAAT
1 TCAAAAT
29441375 TAAATTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (12 bp):
TCAAAATCGAAA
Found at i:29441940 original size:31 final size:29
Alignment explanation
Indices: 29441901--29441973 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
29441891 GGCAACTGTT
*
29441901 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
*
29441931 ACGTTAGTGA-TCGTTTTGTTACTTTTTGAA
1 A-GTTAGTGACT-GTTTTGTCACTTTTTGAA
29441961 AGTTAAGTGACTG
1 AGTT-AGTGACTG
29441974 AAATGAAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 24 0.65
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:29443301 original size:11 final size:10
Alignment explanation
Indices: 29443276--29443341 Score: 78
Period size: 10 Copynumber: 6.4 Consensus size: 10
29443266 AGAAATTTTT
*
29443276 AATTTTTTAA
1 AATTTTTTAG
29443286 AATTTTTTATG
1 AATTTTTTA-G
*
29443297 TATTTTTTAG
1 AATTTTTTAG
29443307 AATTTTTTAG
1 AATTTTTTAG
*
29443317 AATTTTTTTAT
1 AA-TTTTTTAG
*
29443328 AATTTTTTAA
1 AATTTTTTAG
29443338 AATT
1 AATT
29443342 ATAAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
10 32 0.65
11 17 0.35
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:29443303 original size:21 final size:20
Alignment explanation
Indices: 29443276--29443341 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
29443266 AGAAATTTTT
29443276 AATTTTTTAAAATTTTTTATG
1 AATTTTTTAAAATTTTTTA-G
* *
29443297 TATTTTTTAGAATTTTTTAG
1 AATTTTTTAAAATTTTTTAG
* *
29443317 AATTTTTTTATAATTTTTTAA
1 AA-TTTTTTAAAATTTTTTAG
29443338 AATT
1 AATT
29443342 ATAAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
AATTTTTTAAAATTTTTTAG
Found at i:29443314 original size:31 final size:31
Alignment explanation
Indices: 29443276--29443341 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
29443266 AGAAATTTTT
* *
29443276 AATTTTTTA-AAATTTTTTATGT-ATTTTTTAG
1 AATTTTTTAGAAA-TTTTT-TATAATTTTTTAA
*
29443307 AATTTTTTAGAATTTTTTTATAATTTTTTAA
1 AATTTTTTAGAAATTTTTTATAATTTTTTAA
29443338 AATT
1 AATT
29443342 ATAAAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 2 0.07
31 26 0.87
32 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (31 bp):
AATTTTTTAGAAATTTTTTATAATTTTTTAA
Found at i:29443471 original size:9 final size:9
Alignment explanation
Indices: 29443457--29443487 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29443447 TACCAATCTG
29443457 TTATTCGAA
1 TTATTCGAA
29443466 TTATTCGAA
1 TTATTCGAA
*
29443475 TTTTTCGAA
1 TTATTCGAA
29443484 TTAT
1 TTAT
29443488 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (9 bp):
TTATTCGAA
Found at i:29451294 original size:3 final size:3
Alignment explanation
Indices: 29451286--29451332 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
29451276 TAGATAAATA
29451286 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29451333 AGATAAAACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29451510 original size:18 final size:17
Alignment explanation
Indices: 29451489--29451529 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
29451479 AAAAAATAAT
29451489 AATAAAATAAATCAAACA
1 AATAAAATAAAT-AAACA
* *
29451507 AATAACATAAATAAATA
1 AATAAAATAAATAAACA
29451524 AATAAA
1 AATAAA
29451530 TAAGACGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAATAAATAAACA
Found at i:29451520 original size:4 final size:4
Alignment explanation
Indices: 29451493--29451532 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
29451483 AATAATAATA
*
29451493 AAAT AAAT CAAAC AAAT AACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AA
29451533 GACGAGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 25 0.78
5 7 0.22
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:29453537 original size:21 final size:21
Alignment explanation
Indices: 29453513--29453552 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29453503 CCAATCCCAT
29453513 GCAT-CAGATAATAACAACATG
1 GCATGCAG-TAATAACAACATG
29453534 GCATGCAGTAATAACAACA
1 GCATGCAGTAATAACAACA
29453553 GTCAAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.17
Consensus pattern (21 bp):
GCATGCAGTAATAACAACATG
Found at i:29455140 original size:26 final size:26
Alignment explanation
Indices: 29455105--29455188 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
29455095 CATGAAATTC
*
29455105 TTATTATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
29455131 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
29455157 TTATCATGGAACATTTATCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
29455183 TTATCA
1 TTATCA
29455189 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:29458363 original size:12 final size:12
Alignment explanation
Indices: 29458346--29458378 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
29458336 CGGCCTGCCC
29458346 ATATTAATTTTT
1 ATATTAATTTTT
29458358 ATATT-ATTTTT
1 ATATTAATTTTT
29458369 ATA-TAATTTT
1 ATATTAATTTT
29458379 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:29463612 original size:15 final size:16
Alignment explanation
Indices: 29463591--29463651 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 16
29463581 TATATAAAGG
29463591 GTAATAAATAATAAAA
1 GTAATAAATAATAAAA
29463607 -TAATAATAGATAATAAAA
1 GTAAT-A-A-ATAATAAAA
29463625 TTGTAAT-AATAATAAAA
1 --GTAATAAATAATAAAA
29463642 GT-ATAAATAA
1 GTAATAAATAA
29463652 AATAAATAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 15
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.05
15 11 0.29
16 1 0.03
17 10 0.26
18 10 0.26
21 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
GTAATAAATAATAAAA
Found at i:29463631 original size:21 final size:17
Alignment explanation
Indices: 29463592--29463641 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
29463582 ATATAAAGGG
29463592 TAATAAATAATAAAATAA
1 TAAT-AATAATAAAATAA
**
29463610 TAATAGATAATAAAATTG
1 TAATA-ATAATAAAATAA
29463628 TAATAATAATAAAA
1 TAATAATAATAAAA
29463642 GTATAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATAATAATAAAATAA
Found at i:29463650 original size:18 final size:17
Alignment explanation
Indices: 29463597--29463657 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
29463587 AAGGGTAATA
29463597 AATAATAAAATA-ATAAT
1 AATAATAAAATATA-AAT
*
29463614 AGATAATAAAAT-TGTAAT
1 A-ATAATAAAATAT-AAAT
29463632 AATAATAAAAGTATAAAT
1 AATAATAAAA-TATAAAT
29463650 AA-AATAAA
1 AATAATAAA
29463658 TAACAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 16 0.43
18 20 0.54
19 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAATAAAATATAAAT
Found at i:29472404 original size:26 final size:26
Alignment explanation
Indices: 29472367--29472450 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
29472357 TGATACAAAT
* *
29472367 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
29472393 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
29472419 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
29472445 TGATAA
1 TGATAA
29472451 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:29477251 original size:30 final size:30
Alignment explanation
Indices: 29477216--29477273 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
29477206 CATAGCCATG
*
29477216 ACACACGGGCGTGTGGCCTACCCGTGTATC
1 ACACACGGGCGTGTGGACTACCCGTGTATC
*
29477246 ACACACGGGCGTGTGGATTACCCGTGTA
1 ACACACGGGCGTGTGGACTACCCGTGTA
29477274 GAAGTGCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGGACTACCCGTGTATC
Found at i:29479370 original size:19 final size:19
Alignment explanation
Indices: 29479346--29479383 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29479336 TCAGACTATC
*
29479346 ACCCTTCTCTCGTTGTGTT
1 ACCCTTATCTCGTTGTGTT
29479365 ACCCTTATCTCGTTGTGTT
1 ACCCTTATCTCGTTGTGTT
29479384 TACTCGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.29, G:0.16, T:0.47
Consensus pattern (19 bp):
ACCCTTATCTCGTTGTGTT
Found at i:29480837 original size:33 final size:32
Alignment explanation
Indices: 29480800--29480878 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 32
29480790 AAAGGGTGAT
29480800 ACTTGAAAAGGACTTATGTAC-CCAAGTG-GTAC
1 ACTTGAAAAGG--TTATGTACACCAAGTGTGTAC
**
29480832 AACTTGAAAAGGTTATGTACACCTTGTGTGTAC
1 -ACTTGAAAAGGTTATGTACACCAAGTGTGTAC
29480865 ACTTGAAAAGGTTA
1 ACTTGAAAAGGTTA
29480879 GGTATACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
31 8 0.19
32 19 0.45
33 15 0.36
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (32 bp):
ACTTGAAAAGGTTATGTACACCAAGTGTGTAC
Found at i:29480941 original size:33 final size:33
Alignment explanation
Indices: 29480828--29480943 Score: 119
Period size: 33 Copynumber: 3.5 Consensus size: 33
29480818 TACCCAAGTG
* ** * * *
29480828 GTACAACTTGAAAAGGTTATGTACACCTTGTGT
1 GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
**
29480861 GTA-CACTTGAAAAGGTTAGGTATACTTTGTGT
1 GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
*
29480893 ATACCA-TATGAAAAGGAAAGGTATACTTTGTGT
1 GTACCACT-TGAAAAGGAAAGGTATACTTTGTGT
*
29480926 GTACCACTTGGAAAGGAA
1 GTACCACTTGAAAAGGAA
29480944 TGTAGACCTC
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 28 0.39
33 42 0.59
34 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (33 bp):
GTACCACTTGAAAAGGAAAGGTATACTTTGTGT
Found at i:29481826 original size:3 final size:3
Alignment explanation
Indices: 29481812--29481857 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
29481802 TAGATGAATA
**
29481812 AAT AAT AA- AAT AAT AAT AAT AGAT AAT AA- AAT GTT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
29481856 AA
1 AA
29481858 AAGTATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:29481849 original size:21 final size:20
Alignment explanation
Indices: 29481812--29481857 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
29481802 TAGATGAATA
29481812 AATAATAAAATAATAATAAT
1 AATAATAAAATAATAATAAT
**
29481832 AGATAATAAAATGTTAATAAT
1 A-ATAATAAAATAATAATAAT
29481853 AATAA
1 AATAA
29481858 AAGTATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AATAATAAAATAATAATAAT
Found at i:29483563 original size:22 final size:19
Alignment explanation
Indices: 29483518--29483574 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 19
29483508 TAATAATGTT
29483518 ATAATATAATTTTATAAATTAA
1 ATAATAT-A-TTTATAAA-TAA
* *
29483540 TATACTATACTTTATAACTAA
1 -ATAATATA-TTTATAAATAA
29483561 ATAATATATTTATA
1 ATAATATATTTATA
29483575 TACTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 3 0.10
22 8 0.27
23 6 0.20
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATATATTTATAAATAA
Found at i:29485333 original size:20 final size:20
Alignment explanation
Indices: 29485308--29485345 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29485298 TTTAATAAAA
29485308 ATTAAAAAATATAAAATATT
1 ATTAAAAAATATAAAATATT
* *
29485328 ATTAAAAATTATGAAATA
1 ATTAAAAAATATAAAATA
29485346 CATAAAAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
ATTAAAAAATATAAAATATT
Found at i:29489684 original size:15 final size:16
Alignment explanation
Indices: 29489666--29489695 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29489656 AAATTATCCA
29489666 AAAAAAAAGT-AAAAG
1 AAAAAAAAGTGAAAAG
29489681 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
29489696 TTAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAAAAAGTGAAAAG
Found at i:29496338 original size:10 final size:10
Alignment explanation
Indices: 29496313--29496345 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29496303 TCTTAATTTT
*
29496313 TAAAAATTTA
1 TAAAAATATA
29496323 -AAAAATATA
1 TAAAAATATA
29496332 TAAAAATATA
1 TAAAAATATA
29496342 TAAA
1 TAAA
29496346 TATTTTCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAAATATA
Found at i:29496381 original size:30 final size:31
Alignment explanation
Indices: 29496347--29496423 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
29496337 ATATATAAAT
* *
29496347 ATTTTCTA-AAAAATATAATAATAAATTTTA
1 ATTTTATATAAAAATATAATAATAAATTTAA
* * *
29496377 ATTTTATATTAATATATATTAATAAATTTAA
1 ATTTTATATAAAAATATAATAATAAATTTAA
*
29496408 ATTTTATTATTAAAAT
1 ATTTTA-TATAAAAAT
29496424 TTTGAGAGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 7 0.18
31 24 0.62
32 8 0.21
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTTTATATAAAAATATAATAATAAATTTAA
Found at i:29496389 original size:21 final size:21
Alignment explanation
Indices: 29496360--29496399 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29496350 TTCTAAAAAA
*
29496360 TATAATAATAAATTTTAATTT
1 TATAATAATAAATATTAATTT
* *
29496381 TATATTAATATATATTAAT
1 TATAATAATAAATATTAAT
29496400 AAATTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TATAATAATAAATATTAATTT
Found at i:29496400 original size:31 final size:32
Alignment explanation
Indices: 29496359--29496420 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
29496349 TTTCTAAAAA
*
29496359 ATATAATAATAAATTTTAATTTTA-TATTAAT
1 ATATAATAATAAATTTAAATTTTATTATTAAT
*
29496390 ATATATTAATAAATTTAAATTTTATTATTAA
1 ATATAATAATAAATTTAAATTTTATTATTAA
29496421 AATTTTGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATAATAATAAATTTAAATTTTATTATTAAT
Found at i:29500360 original size:104 final size:104
Alignment explanation
Indices: 29500158--29500348 Score: 321
Period size: 104 Copynumber: 1.8 Consensus size: 104
29500148 AGCCATTTAA
*
29500158 TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATTTCTTTTAACATAA
1 TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATCTCTTTTAACATAA
* **
29500223 TTTTTTTATATTTTCATTATATATATTCTTTTAATTTTC
66 TTTTTTTATATTTTCATTATAAATATTAATTTAATTTTC
*
29500262 TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTTCTCCCTTCTACATCTCTTTTAACATAA
1 TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATCTCTTTTAACATAA
*
29500327 TTTTTTTATATTTTTATT-TAAA
66 TTTTTTTATATTTTCATTATAAA
29500349 ATGATAATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 3 0.04
104 80 0.96
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (104 bp):
TTTTTATTTTATTTTATTTTACTTCTCCCTCTATTTTCCTCCCTTCTACATCTCTTTTAACATAA
TTTTTTTATATTTTCATTATAAATATTAATTTAATTTTC
Found at i:29503895 original size:19 final size:19
Alignment explanation
Indices: 29503871--29503914 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
29503861 TTAAAAAAAC
*
29503871 TTAAAATAA-ATATAAATTA
1 TTAAAATAATAT-TAAAATA
*
29503890 TTAAAATTATATTAAAATA
1 TTAAAATAATATTAAAATA
29503909 TTAAAA
1 TTAAAA
29503915 ACTATGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATAATATTAAAATA
Found at i:29503915 original size:20 final size:19
Alignment explanation
Indices: 29503883--29503930 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
29503873 AAAATAAATA
* *
29503883 TAAATTATTAAAATTATAT
1 TAAAATATTAAAACTATAT
*
29503902 TAAAATATTAAAAACTATGT
1 TAAAATATT-AAAACTATAT
29503922 TAAAATATT
1 TAAAATATT
29503931 TTAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAATATTAAAACTATAT
Found at i:29508172 original size:26 final size:24
Alignment explanation
Indices: 29508140--29508189 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 24
29508130 TAAATAAAAA
29508140 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAATATAA-AAA-CAAATAT
29508166 ATTTAAAAATATAAAAACAAATAT
1 ATTTAAAAATATAAAAACAAATAT
29508190 TAAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.29
25 3 0.12
26 14 0.58
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
ATTTAAAAATATAAAAACAAATAT
Found at i:29508187 original size:12 final size:12
Alignment explanation
Indices: 29508172--29508204 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
29508162 ATATATTTAA
29508172 AAATATAAAAAC
1 AAATATAAAAAC
*
29508184 AAATATTAAAAC
1 AAATATAAAAAC
29508196 AAATA-AAAA
1 AAATATAAAA
29508205 TGATACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAATATAAAAAC
Found at i:29508199 original size:24 final size:25
Alignment explanation
Indices: 29508144--29508205 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 25
29508134 TAAAAAATTT
**
29508144 AAAAATATAATAAATCAAATATATTT
1 AAAAATATAA-AAATCAAATATATAA
29508170 AAAAATATAAAAA-CAAATAT-TAA
1 AAAAATATAAAAATCAAATATATAA
*
29508193 AACAA-ATAAAAAT
1 AAAAATATAAAAAT
29508206 GATACTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 7 0.22
23 5 0.16
24 7 0.22
25 3 0.09
26 10 0.31
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (25 bp):
AAAAATATAAAAATCAAATATATAA
Found at i:29516002 original size:16 final size:16
Alignment explanation
Indices: 29515981--29516011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29515971 GATATTTTAA
29515981 TATATTATATTAATAT
1 TATATTATATTAATAT
*
29515997 TATATTATGTTAATA
1 TATATTATATTAATA
29516012 AAATAATAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:29516108 original size:12 final size:12
Alignment explanation
Indices: 29516091--29516121 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29516081 GAAGCAGGGG
29516091 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
29516103 AGAAAAAGGGAA
1 AGAAAAAGAGAA
29516115 AGAAAAA
1 AGAAAAA
29516122 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:29518497 original size:17 final size:18
Alignment explanation
Indices: 29518466--29518500 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29518456 GAAAATACTA
29518466 ATAAAAAGTAAAATTTAG
1 ATAAAAAGTAAAATTTAG
*
29518484 ATAAAAA-TAGAATTTAG
1 ATAAAAAGTAAAATTTAG
29518501 GAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
ATAAAAAGTAAAATTTAG
Found at i:29520923 original size:23 final size:22
Alignment explanation
Indices: 29520897--29520946 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
29520887 AATTTTAAAA
**
29520897 ATTTGAAATGTTTTATAATATAT
1 ATTTGAAAAATTTTA-AATATAT
*
29520920 ATTTTTAAAAATTTTAAATATAT
1 A-TTTGAAAAATTTTAAATATAT
29520943 ATTT
1 ATTT
29520947 TTGGAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.13
23 9 0.39
24 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTTGAAAAATTTTAAATATAT
Found at i:29520968 original size:36 final size:35
Alignment explanation
Indices: 29520919--29521012 Score: 134
Period size: 36 Copynumber: 2.6 Consensus size: 35
29520909 TTATAATATA
* *
29520919 TATTTTTAAAAATTTTAAATATATATTTTTGGAAT
1 TATTTTTATAAATTTTAAATATATATTTTTGAAAT
*
29520954 TATTTCTTATAAATTTTAAAAATATATTTTTGAAAT
1 TATTT-TTATAAATTTTAAATATATATTTTTGAAAT
*
29520990 TAATTTTTCTAAATTTTAAATAT
1 T-ATTTTTATAAATTTTAAATAT
29521013 TGTTTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
35 5 0.10
36 43 0.83
37 4 0.08
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (35 bp):
TATTTTTATAAATTTTAAATATATATTTTTGAAAT
Found at i:29521018 original size:21 final size:20
Alignment explanation
Indices: 29520993--29521038 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
29520983 TTGAAATTAA
*
29520993 TTTTTCTAAATTTTAAATAT
1 TTTTTCTAAATATTAAATAT
*
29521013 TGTTTTTTAAATATTAAATAT
1 T-TTTTCTAAATATTAAATAT
29521034 TTTTT
1 TTTTT
29521039 AATAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTCTAAATATTAAATAT
Found at i:29521049 original size:28 final size:27
Alignment explanation
Indices: 29521025--29521092 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
29521015 TTTTTTAAAT
* *
29521025 ATTAAATATTTTTTAATAATATTTAATA
1 ATTAAA-ATTTTTAAATAAAATTTAATA
*
29521053 ATTAAAATTTTTAAATAAAATTT-GT-
1 ATTAAAATTTTTAAATAAAATTTAATA
*
29521078 ATAAAAATTTTTAAA
1 ATTAAAATTTTTAAA
29521093 AAGGTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 14 0.39
26 1 0.03
27 15 0.42
28 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTAAAATTTTTAAATAAAATTTAATA
Found at i:29521050 original size:21 final size:20
Alignment explanation
Indices: 29520994--29521050 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
29520984 TGAAATTAAT
*
29520994 TTTTCTAAATTTTAAATATTG
1 TTTTATAAA-TTTAAATATTG
*
29521015 TTTTTTAAATATTAAATATT-
1 TTTTATAAAT-TTAAATATTG
29521035 TTTTAATAATATTTAA
1 TTTT-ATAA-ATTTAA
29521051 TAATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 5 0.16
21 24 0.77
22 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTATAAATTTAAATATTG
Found at i:29521071 original size:13 final size:13
Alignment explanation
Indices: 29521027--29521092 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
29521017 TTTTAAATAT
*
29521027 TAAATATTTTTTAA
1 TAAA-ATTTTTAAA
* * *
29521041 TAATATTTAATAAT
1 TAAAATTT-TTAAA
29521055 TAAAATTTTTAAA
1 TAAAATTTTTAAA
* *
29521068 TAAAATTTGTATA
1 TAAAATTTTTAAA
29521081 -AAAATTTTTAAA
1 TAAAATTTTTAAA
29521093 AAGGTTTAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
12 10 0.25
13 18 0.45
14 12 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAAAATTTTTAAA
Found at i:29521342 original size:20 final size:20
Alignment explanation
Indices: 29521313--29521418 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 20
29521303 ATATTATTAA
*
29521313 AAAAATATATTT-AATTTTT
1 AAAAATATATTTAAAATTTT
29521332 AAAAATAATATTTAAAATTTT
1 AAAAAT-ATATTTAAAATTTT
*
29521353 AAAAA-ATTAGTTT-CAA----
1 AAAAATA-TA-TTTAAAATTTT
* *
29521369 AAATATATATTTAAAATTTA
1 AAAAATATATTTAAAATTTT
*
29521389 AAAAACA-ATTTTAAAATTTT
1 AAAAATATA-TTTAAAATTTT
*
29521409 AAAAAAATAT
1 AAAAATATAT
29521419 ATATTATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 23
0.68 0.08 0.23
Matches are distributed among these distances:
15 3 0.04
16 8 0.12
17 1 0.01
19 8 0.12
20 32 0.48
21 15 0.22
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (20 bp):
AAAAATATATTTAAAATTTT
Found at i:29521358 original size:22 final size:19
Alignment explanation
Indices: 29521312--29521359 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
29521302 CATATTATTA
29521312 AAAAAATATATTTAATTTT
1 AAAAAATATATTTAATTTT
*
29521331 TAAAAATAATATTTAAAATTTT
1 AAAAAAT-ATATTT--AATTTT
29521353 AAAAAAT
1 AAAAAAT
29521360 TAGTTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 6 0.25
22 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAAATATATTTAATTTT
Found at i:29521370 original size:22 final size:21
Alignment explanation
Indices: 29521313--29521357 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29521303 ATATTATTAA
*
29521313 AAAAAT-ATATTT-AATTTTT
1 AAAAATAATATTTAAAATTTT
29521332 AAAAATAATATTTAAAATTTT
1 AAAAATAATATTTAAAATTTT
29521353 AAAAA
1 AAAAA
29521358 ATTAGTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAATAATATTTAAAATTTT
Found at i:29521477 original size:23 final size:22
Alignment explanation
Indices: 29521446--29521488 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29521436 AAATTTTTTA
*
29521446 AAATTAATAATAAAAAATAAATT
1 AAATAAATAA-AAAAAATAAATT
*
29521469 AAATAAATAAACAAAATAAA
1 AAATAAATAAAAAAAATAAA
29521489 ATAAGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAATAAAAAAAATAAATT
Found at i:29521490 original size:23 final size:19
Alignment explanation
Indices: 29521444--29521490 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 19
29521434 TCAAATTTTT
29521444 TAAAATTAATAATAAAAAA
1 TAAAATTAATAATAAAAAA
29521463 T-AAATTAAATAAATAAACAAAA
1 TAAAATT-AAT-AAT-AA-AAAA
29521485 TAAAAT
1 TAAAAT
29521491 AAGGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 3 0.13
21 2 0.09
22 5 0.22
23 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAATTAATAATAAAAAA
Done.