Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 76 of 78
Found at i:16250799 original size:19 final size:20
Alignment explanation
Indices: 16250752--16250802 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
16250742 GAAATCCCTT
**
16250752 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
16250772 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
16250791 TGAAGATACATG
1 TGAAAATACATG
16250803 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16256697 original size:5 final size:5
Alignment explanation
Indices: 16256687--16256732 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
16256677 ACTCAAAAAG
16256687 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
16256733 GAAGTTGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:16257013 original size:22 final size:22
Alignment explanation
Indices: 16256987--16257028 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16256977 TTTGTGCTGT
*
16256987 AAACAATATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
16257009 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
16257029 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.17
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:16257599 original size:19 final size:21
Alignment explanation
Indices: 16257575--16257626 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
16257565 CGTCCAAGAG
*
16257575 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
16257594 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
16257615 CATGTATTTTCA
1 CATGTATTTTCA
16257627 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:16261802 original size:20 final size:21
Alignment explanation
Indices: 16261779--16261822 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
16261769 TTCTTTTCTT
*
16261779 TGCTTTTTC-TTCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
16261799 TGC--TTTCAATCTTTTTGAG
1 TGCTTTTTCAATCTTTTTGAG
16261818 TGCTT
1 TGCTT
16261823 CTTTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
18 4 0.20
19 13 0.65
20 3 0.15
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (21 bp):
TGCTTTTTCAATCTTTTTGAG
Found at i:16264424 original size:26 final size:26
Alignment explanation
Indices: 16264388--16264454 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
16264378 TAGAACACCT
16264388 ATGTGCCTTGCATATGACCAGCCCCC
1 ATGTGCCTTGCATATGACCAGCCCCC
** * *
16264414 ATGTGTTTTGCATGTGATCAGCCCCC
1 ATGTGCCTTGCATATGACCAGCCCCC
16264440 ATGTGCCTTGCATAT
1 ATGTGCCTTGCATAT
16264455 TGTGCATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.31
Consensus pattern (26 bp):
ATGTGCCTTGCATATGACCAGCCCCC
Found at i:16286749 original size:19 final size:20
Alignment explanation
Indices: 16286702--16286752 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
16286692 GAAACCCCTT
**
16286702 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
16286722 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
16286741 TGAAGATACATG
1 TGAAAATACATG
16286753 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16296542 original size:5 final size:5
Alignment explanation
Indices: 16296525--16296564 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
16296515 ATTCAAAAAG
*
16296525 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA AAG-A AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
16296565 GTTAAAGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.78, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:16306627 original size:13 final size:12
Alignment explanation
Indices: 16306608--16306692 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
16306598 ATATGGGCGT
16306608 GATATGGTGATG
1 GATATGGTGATG
16306620 GAATATGGTGAT-
1 G-ATATGGTGATG
*
16306632 GATATAGGCG-T-
1 GATAT-GGTGATG
16306643 GATAATGGTGATG
1 GAT-ATGGTGATG
16306656 GATATGGTGAT-
1 GATATGGTGATG
*
16306667 GATATAGGCG-T-
1 GATAT-GGTGATG
16306678 GATAATGGTGATG
1 GAT-ATGGTGATG
16306691 GA
1 GA
16306693 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
11 23 0.38
12 22 0.37
13 15 0.25
ACGTcount: A:0.29, C:0.02, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:16306661 original size:35 final size:35
Alignment explanation
Indices: 16306598--16306692 Score: 165
Period size: 35 Copynumber: 2.7 Consensus size: 35
16306588 GTTGGTTATA
*
16306598 ATATGGGCGTGAT-ATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGG-ATATGGTGATG
16306633 ATATAGGCGTGATAATGGTGATGGATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGATATGGTGATG
16306668 ATATAGGCGTGATAATGGTGATGGA
1 ATATAGGCGTGATAATGGTGATGGA
16306693 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 48 0.83
36 10 0.17
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (35 bp):
ATATAGGCGTGATAATGGTGATGGATATGGTGATG
Found at i:16310602 original size:22 final size:23
Alignment explanation
Indices: 16310577--16310621 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
16310567 GTTGGTTATA
*
16310577 ATATGGGCGTGAT-ATGGTGATG
1 ATATAGGCGTGATAATGGTGATG
16310599 ATATAGGCGTGATAATGGTGATG
1 ATATAGGCGTGATAATGGTGATG
16310622 GACTATGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.27, C:0.04, G:0.38, T:0.31
Consensus pattern (23 bp):
ATATAGGCGTGATAATGGTGATG
Found at i:16310614 original size:36 final size:38
Alignment explanation
Indices: 16310589--16310660 Score: 116
Period size: 36 Copynumber: 2.0 Consensus size: 38
16310579 ATGGGCGTGA
16310589 TATGGTGATGATATAGGCGTGAT-A-ATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATATGGTGATGGAC
16310625 TATGGTGATGATATAGGCGTGATAATA--GTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATATGGTGATGGAC
16310661 AGATTGTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 32 0.94
37 1 0.03
38 1 0.03
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.31
Consensus pattern (38 bp):
TATGGTGATGATATAGGCGTGATAATATGGTGATGGAC
Found at i:16312556 original size:19 final size:21
Alignment explanation
Indices: 16312518--16312560 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
16312508 TAATAAAGGG
16312518 AATAAAAAATATAAGTAATGA
1 AATAAAAAATATAAGTAATGA
*
16312539 AATAAAAGA-ATAAG-AATGA
1 AATAAAAAATATAAGTAATGA
16312558 AAT
1 AAT
16312561 GAAATAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (21 bp):
AATAAAAAATATAAGTAATGA
Found at i:16313017 original size:19 final size:21
Alignment explanation
Indices: 16312974--16313025 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
16312964 GAAACCCCTT
16312974 TGAAAATACATGATGTTTAAA
1 TGAAAATACATGATGTTTAAA
*
16312995 TGAAAATACATTAT-TTT-AA
1 TGAAAATACATGATGTTTAAA
*
16313014 TGAAGATACATG
1 TGAAAATACATG
16313026 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATGTTTAAA
Found at i:16321100 original size:24 final size:24
Alignment explanation
Indices: 16321054--16321105 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
16321044 CCTTGGCACT
* * *
16321054 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAACTGTTGGAACA
* *
16321078 TCAAGTGGCATAACTGTTGGAACG
1 TCAAGTGGCACAACTGTTGGAACA
16321102 TCAA
1 TCAA
16321106 AGGACATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAACTGTTGGAACA
Found at i:16323101 original size:318 final size:317
Alignment explanation
Indices: 16322525--16323160 Score: 1137
Period size: 318 Copynumber: 2.0 Consensus size: 317
16322515 GATTACTGCT
* *
16322525 TGATGTAAGGTAATTCTACCTTCTCGTTTGATTGTGGGTCTAGGAAGGAAGAAAACAACCTGCAC
1 TGATGTAAGGTAATTATACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGAAAACAACCTGCAC
* *
16322590 AAGTGAATAGCTCAAAACAGAATGGATAAGGGTGATAAATGTATGGTTTAATAAGTAGGCTATTT
66 AAGTGAATAGCTCAAAACAGAATGGATAAGGGTGATAAACGTATGGTTTAATAAGTAGGATATTT
*
16322655 AATAAATGAGAGATGGAAGTGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAGG
131 AATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAGG
*
16322720 ATGGTTGTGAGGATAGTATATTAAAGAATACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGAC
196 ATGGTTGTGAGGATAGTATATTAAAGAACACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGAC
*
16322785 CCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTA
261 CCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTA
16322842 TGATGTAAGGTAATTATACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCA
1 TGATGTAAGGTAATTATACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAG-AAAACAACCTGCA
* * *
16322907 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGATATT
65 CAAGTGAATAGCTCAAAACAGAATGGATAAGGGTGATAAACGTATGGTTTAATAAGTAGGATATT
*
16322972 TAATAAATGAGATATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
130 TAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
* * *
16323037 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
195 GATGGTTGTGAGGATAGTATATTAAAGAACACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
16323102 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTA
260 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTA
16323160 T
1 T
16323161 ATGAACTAGG
Statistics
Matches: 304, Mismatches: 14, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
317 49 0.16
318 255 0.84
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (317 bp):
TGATGTAAGGTAATTATACCTTCTCGTTTGATTGTGGATCTAGGAAGGAAGAAAACAACCTGCAC
AAGTGAATAGCTCAAAACAGAATGGATAAGGGTGATAAACGTATGGTTTAATAAGTAGGATATTT
AATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAGG
ATGGTTGTGAGGATAGTATATTAAAGAACACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGAC
CCAATCTTTATATTGTTTCTTCAAGGGGTGGTGATAAGTACTTTGACCCACTAGTTA
Found at i:16327479 original size:35 final size:36
Alignment explanation
Indices: 16327431--16327514 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 36
16327421 ATTTATAAGT
* * *
16327431 TGGTGATAATATAGGCGTG-ATATGGTAATGGAATA
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
* * *
16327466 TGGTGATGTTATAGGCGTGAAAATGGTGATGGAAGG
1 TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
16327502 TGGTGATGA-ATAG
1 TGGTGATGATATAG
16327515 ATAGTATCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 21 0.51
36 20 0.49
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGAAAATGGTAATGGAAGA
Found at i:16336950 original size:15 final size:15
Alignment explanation
Indices: 16336917--16336959 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16336907 TGGATAATTA
*
16336917 AGAAA-GAAAAAAAT
1 AGAAATGAAAAGAAT
16336931 AGAAATGAAAAGAAT
1 AGAAATGAAAAGAAT
* *
16336946 TGAAATGGAAAGAA
1 AGAAATGAAAAGAA
16336960 ATGTTATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (15 bp):
AGAAATGAAAAGAAT
Found at i:16337186 original size:13 final size:13
Alignment explanation
Indices: 16337154--16337189 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
16337144 ATAGACGTGC
*
16337154 AATGGTAATGGAA
1 AATGGTGATGGAA
16337167 AATGGTGATGGAA
1 AATGGTGATGGAA
*
16337180 GATGGTGATG
1 AATGGTGATG
16337190 TTTAGGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.25
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:16339091 original size:19 final size:21
Alignment explanation
Indices: 16339041--16339092 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
16339031 GAAACCCCTT
16339041 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
16339062 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
16339081 T-AAAGATACATG
1 TGAAA-ATACATG
16339093 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 4 0.13
21 13 0.43
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:16342477 original size:35 final size:33
Alignment explanation
Indices: 16342426--16342499 Score: 105
Period size: 35 Copynumber: 2.2 Consensus size: 33
16342416 GCTTGCTTTC
16342426 TTTTTGAATTTCTTTTTCTTTTCT-TCTTTTCTT
1 TTTTTGAATTTCTTTTTCTTTT-TGTCTTTTCTT
16342459 TTTTCTGAATTTTCTTTTTCTTTTTGTCTTTTCTT
1 TTTT-TGAA-TTTCTTTTTCTTTTTGTCTTTTCTT
16342494 TCTTTT
1 T-TTTT
16342500 TGTACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
33 4 0.11
34 5 0.14
35 25 0.68
36 3 0.08
ACGTcount: A:0.05, C:0.15, G:0.04, T:0.76
Consensus pattern (33 bp):
TTTTTGAATTTCTTTTTCTTTTTGTCTTTTCTT
Found at i:16342492 original size:19 final size:17
Alignment explanation
Indices: 16342421--16342502 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 17
16342411 CCTTGGCTTG
**
16342421 CTTTCTTTTTGAATTTCT
1 CTTTCTTTTTGTCTTT-T
*
16342439 TTTTCTTTTCT-TCTTTT
1 CTTTCTTTT-TGTCTTTT
* **
16342456 CTTT-TTTCTGAATTTT
1 CTTTCTTTTTGTCTTTT
16342472 CTTTTTCTTTTTGTCTTTT
1 C--TTTCTTTTTGTCTTTT
16342491 CTTTCTTTTTGT
1 CTTTCTTTTTGT
16342503 ACTCCAATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.02
16 8 0.16
17 15 0.31
18 14 0.29
19 11 0.22
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGTCTTTT
Found at i:16343243 original size:19 final size:21
Alignment explanation
Indices: 16343201--16343251 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 21
16343191 AAACCCCTTA
16343201 GAAAATACATGACTTTTAAAT
1 GAAAATACATGACTTTTAAAT
16343222 GAAAATACATGA-TTTT-AAT
1 GAAAATACATGACTTTTAAAT
*
16343241 GAAGATACATG
1 GAAAATACATG
16343252 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (21 bp):
GAAAATACATGACTTTTAAAT
Found at i:16348380 original size:26 final size:27
Alignment explanation
Indices: 16348330--16348386 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
16348320 AAATGTGCAA
*
16348330 AAAGAAAGCAAAAGGAAAGACAAAATC
1 AAAGAAAGCAAAAGGAAAGACAAAAGC
*
16348357 AAAGAAAG-AAAAGTAAAG-CTAAAAGC
1 AAAGAAAGCAAAAGGAAAGAC-AAAAGC
16348383 AAAG
1 AAAG
16348387 GTTGTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 18 0.67
27 8 0.30
ACGTcount: A:0.67, C:0.09, G:0.19, T:0.05
Consensus pattern (27 bp):
AAAGAAAGCAAAAGGAAAGACAAAAGC
Found at i:16352349 original size:36 final size:36
Alignment explanation
Indices: 16352276--16352416 Score: 221
Period size: 36 Copynumber: 3.9 Consensus size: 36
16352266 ATTTATAAGT
*
16352276 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
*
16352311 TGGTGATAATATAAGCGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
*
16352347 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
* * *
16352383 TGGTGATGATATAGGTGTGATAATGTTGATGGAC
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAC
16352417 ATATTGTATC
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.20
36 79 0.80
ACGTcount: A:0.30, C:0.04, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGACTA
Found at i:16352351 original size:13 final size:12
Alignment explanation
Indices: 16352333--16352399 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
16352323 AAGCGTGATA
16352333 ATGGTGATGGACT
1 ATGGTGATGGA-T
16352346 ATGGTGAT-GAT
1 ATGGTGATGGAT
*
16352357 ATAGGCG-T-GAT
1 AT-GGTGATGGAT
16352368 AATGGTGATGGACT
1 -ATGGTGATGGA-T
16352382 ATGGTGAT-GAT
1 ATGGTGATGGAT
16352393 ATAGGTG
1 AT-GGTG
16352400 TGATAATGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
11 13 0.28
12 14 0.30
13 18 0.39
14 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.31
Consensus pattern (12 bp):
ATGGTGATGGAT
Found at i:16352804 original size:19 final size:20
Alignment explanation
Indices: 16352757--16352807 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
16352747 GAAACCCCTT
**
16352757 TGAAAATACATGATTTTGGA
1 TGAAAATACATGATTTTAAA
16352777 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
16352796 TGAAGATACATG
1 TGAAAATACATG
16352808 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16356255 original size:19 final size:20
Alignment explanation
Indices: 16356214--16356264 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
16356204 GAAACCCCTT
*
16356214 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
16356234 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
16356253 TGAAGATACATG
1 TGAAAATACATG
16356265 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:16358108 original size:19 final size:21
Alignment explanation
Indices: 16358084--16358135 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
16358074 CGGCCAAGAG
*
16358084 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
16358103 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
16358124 CATGTATTTTCA
1 CATGTATTTTCA
16358136 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:16358571 original size:19 final size:19
Alignment explanation
Indices: 16358547--16358588 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
16358537 ATCCTTTCTT
16358547 TATTTCATTTCATT-CTTAA
1 TATTTCATTTCATTACTT-A
16358566 TATTTCATTTCATTACTTA
1 TATTTCATTTCATTACTTA
16358585 TATT
1 TATT
16358589 ACTATCCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTCATTTCATTACTTA
Found at i:16366264 original size:19 final size:19
Alignment explanation
Indices: 16366240--16366309 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
16366230 GGCCAAGACT
* *
16366240 ATGTATCTTCATTTAAATC
1 ATGTATTTTCATTAAAATC
*
16366259 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCAT-TAAAATC
*
16366279 ATGTATTTTTATTAAAAATC
1 ATGTATTTTCATT-AAAATC
16366299 ATGTATTTTCA
1 ATGTATTTTCA
16366310 AAGGGGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATC
Found at i:16366279 original size:20 final size:20
Alignment explanation
Indices: 16366254--16366309 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
16366244 ATCTTCATTT
16366254 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
* *
16366274 AAATCATGTATTTTTATTAA
1 AAATCATGTATTTTCATCAA
16366294 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
16366310 AAGGGGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:16367067 original size:19 final size:19
Alignment explanation
Indices: 16367043--16367112 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 19
16367033 GGCCAAGACT
* *
16367043 ATGTATCTTCATTTAAATC
1 ATGTATTTTCATTAAAATC
*
16367062 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCAT-TAAAATC
*
16367082 ATGTATTTTTATTAAAAATC
1 ATGTATTTTCATT-AAAATC
16367102 ATGTATTTTCA
1 ATGTATTTTCA
16367113 AAGGGGTTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
19 11 0.26
20 32 0.74
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (19 bp):
ATGTATTTTCATTAAAATC
Found at i:16367082 original size:20 final size:20
Alignment explanation
Indices: 16367057--16367112 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
16367047 ATCTTCATTT
16367057 AAATCATGTATTTTCATCAA
1 AAATCATGTATTTTCATCAA
* *
16367077 AAATCATGTATTTTTATTAA
1 AAATCATGTATTTTCATCAA
16367097 AAATCATGTATTTTCA
1 AAATCATGTATTTTCA
16367113 AAGGGGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATCATGTATTTTCATCAA
Found at i:16367475 original size:803 final size:803
Alignment explanation
Indices: 16365931--16367538 Score: 3216
Period size: 803 Copynumber: 2.0 Consensus size: 803
16365921 CCATGACACC
16365931 TAGATGCATGTTGGAAGACAAGTCACGCCTAGTTGCTGCCATATTCATTCCATGGACTTCAAGAC
1 TAGATGCATGTTGGAAGACAAGTCACGCCTAGTTGCTGCCATATTCATTCCATGGACTTCAAGAC
16365996 ACCATCCTATGGTTGTAACATCACCAAAGCCTTGCAAGAAGACCCATGTGCATTCACGTAGGCTG
66 ACCATCCTATGGTTGTAACATCACCAAAGCCTTGCAAGAAGACCCATGTGCATTCACGTAGGCTG
16366061 CCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATTGGTGCCAAAACACCAAGGGA
131 CCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATTGGTGCCAAAACACCAAGGGA
16366126 TGCTTCCTATTCGGCCAAAGACTTTTTCCTCTTCATTTTGGCGCCCAAATAACTTCCAAATGCAT
196 TGCTTCCTATTCGGCCAAAGACTTTTTCCTCTTCATTTTGGCGCCCAAATAACTTCCAAATGCAT
16366191 TCAAATCAACCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGACTATGTATCTTCATTTAA
261 TCAAATCAACCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGACTATGTATCTTCATTTAA
16366256 ATCATGTATTTTCATCAAAAATCATGTATTTTTATTAAAAATCATGTATTTTCAAAGGGGTTTCA
326 ATCATGTATTTTCATCAAAAATCATGTATTTTTATTAAAAATCATGTATTTTCAAAGGGGTTTCA
16366321 ACCTTGGCCGAACCATCAAGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGCTATTG
391 ACCTTGGCCGAACCATCAAGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGCTATTG
16366386 CATTTCATTTGTAACTCAACCCTTTGATCAATTAAAAATCCTTTGTGAGATTATTCTCTCTTCAA
456 CATTTCATTTGTAACTCAACCCTTTGATCAATTAAAAATCCTTTGTGAGATTATTCTCTCTTCAA
16366451 GTTCTTTTTAGAACTATATCGATTAAGCAAGTCTTTCTAAAGCTTGTGGCGTCATTCCTTCACCT
521 GTTCTTTTTAGAACTATATCGATTAAGCAAGTCTTTCTAAAGCTTGTGGCGTCATTCCTTCACCT
16366516 TGATACTTTTGGTTCCTAGTTCATATAACTAGAGGGTCAAAGTCCTTACTACCATCCCTTATAGA
586 TGATACTTTTGGTTCCTAGTTCATATAACTAGAGGGTCAAAGTCCTTACTACCATCCCTTATAGA
16366581 ACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTTCCTTCTTAGTTCTATAAGATACTA
651 ACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTTCCTTCTTAGTTCTATAAGATACTA
16366646 TCTATTCATCACCACCTTCCATCACCGTTTTTACGCCTATAACATCACCATATTCCATTACCATA
716 TCTATTCATCACCACCTTCCATCACCGTTTTTACGCCTATAACATCACCATATTCCATTACCATA
16366711 TCACGCCTATATTATCACCAACT
781 TCACGCCTATATTATCACCAACT
16366734 TAGATGCATGTTGGAAGACAAGTCACGCCTAGTTGCTGCCATATTCATTCCATGGACTTCAAGAC
1 TAGATGCATGTTGGAAGACAAGTCACGCCTAGTTGCTGCCATATTCATTCCATGGACTTCAAGAC
16366799 ACCATCCTATGGTTGTAACATCACCAAAGCCTTGCAAGAAGACCCATGTGCATTCACGTAGGCTG
66 ACCATCCTATGGTTGTAACATCACCAAAGCCTTGCAAGAAGACCCATGTGCATTCACGTAGGCTG
16366864 CCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATTGGTGCCAAAACACCAAGGGA
131 CCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATTGGTGCCAAAACACCAAGGGA
16366929 TGCTTCCTATTCGGCCAAAGACTTTTTCCTCTTCATTTTGGCGCCCAAATAACTTCCAAATGCAT
196 TGCTTCCTATTCGGCCAAAGACTTTTTCCTCTTCATTTTGGCGCCCAAATAACTTCCAAATGCAT
16366994 TCAAATCAACCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGACTATGTATCTTCATTTAA
261 TCAAATCAACCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGACTATGTATCTTCATTTAA
16367059 ATCATGTATTTTCATCAAAAATCATGTATTTTTATTAAAAATCATGTATTTTCAAAGGGGTTTCA
326 ATCATGTATTTTCATCAAAAATCATGTATTTTTATTAAAAATCATGTATTTTCAAAGGGGTTTCA
16367124 ACCTTGGCCGAACCATCAAGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGCTATTG
391 ACCTTGGCCGAACCATCAAGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGCTATTG
16367189 CATTTCATTTGTAACTCAACCCTTTGATCAATTAAAAATCCTTTGTGAGATTATTCTCTCTTCAA
456 CATTTCATTTGTAACTCAACCCTTTGATCAATTAAAAATCCTTTGTGAGATTATTCTCTCTTCAA
16367254 GTTCTTTTTAGAACTATATCGATTAAGCAAGTCTTTCTAAAGCTTGTGGCGTCATTCCTTCACCT
521 GTTCTTTTTAGAACTATATCGATTAAGCAAGTCTTTCTAAAGCTTGTGGCGTCATTCCTTCACCT
16367319 TGATACTTTTGGTTCCTAGTTCATATAACTAGAGGGTCAAAGTCCTTACTACCATCCCTTATAGA
586 TGATACTTTTGGTTCCTAGTTCATATAACTAGAGGGTCAAAGTCCTTACTACCATCCCTTATAGA
16367384 ACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTTCCTTCTTAGTTCTATAAGATACTA
651 ACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTTCCTTCTTAGTTCTATAAGATACTA
16367449 TCTATTCATCACCACCTTCCATCACCGTTTTTACGCCTATAACATCACCATATTCCATTACCATA
716 TCTATTCATCACCACCTTCCATCACCGTTTTTACGCCTATAACATCACCATATTCCATTACCATA
16367514 TCACGCCTATATTATCACCAACT
781 TCACGCCTATATTATCACCAACT
16367537 TA
1 TA
16367539 TAAATTTCCA
Statistics
Matches: 805, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
803 805 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (803 bp):
TAGATGCATGTTGGAAGACAAGTCACGCCTAGTTGCTGCCATATTCATTCCATGGACTTCAAGAC
ACCATCCTATGGTTGTAACATCACCAAAGCCTTGCAAGAAGACCCATGTGCATTCACGTAGGCTG
CCATGTGCATCATTCAAGCATGTGCACTCCATGTGACATCAAATTGGTGCCAAAACACCAAGGGA
TGCTTCCTATTCGGCCAAAGACTTTTTCCTCTTCATTTTGGCGCCCAAATAACTTCCAAATGCAT
TCAAATCAACCTTAGGGCCGAACCAACACATAACCATTCGGCCAAGACTATGTATCTTCATTTAA
ATCATGTATTTTCATCAAAAATCATGTATTTTTATTAAAAATCATGTATTTTCAAAGGGGTTTCA
ACCTTGGCCGAACCATCAAGTATCTATTCGGCCTAAACCCTTTGAAAACTATAAATAGGCTATTG
CATTTCATTTGTAACTCAACCCTTTGATCAATTAAAAATCCTTTGTGAGATTATTCTCTCTTCAA
GTTCTTTTTAGAACTATATCGATTAAGCAAGTCTTTCTAAAGCTTGTGGCGTCATTCCTTCACCT
TGATACTTTTGGTTCCTAGTTCATATAACTAGAGGGTCAAAGTCCTTACTACCATCCCTTATAGA
ACTTATAAGAAACGGGTCTTTGCTCCTTTATAGCATTGGTTCCTTCTTAGTTCTATAAGATACTA
TCTATTCATCACCACCTTCCATCACCGTTTTTACGCCTATAACATCACCATATTCCATTACCATA
TCACGCCTATATTATCACCAACT
Found at i:16371512 original size:35 final size:36
Alignment explanation
Indices: 16371432--16371514 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
16371422 AGATACTATC
* *
16371432 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
16371469 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
16371504 TATTATCACCA
1 TATTATCACCA
16371515 ACTTAAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:16376360 original size:318 final size:317
Alignment explanation
Indices: 16375783--16376418 Score: 1155
Period size: 318 Copynumber: 2.0 Consensus size: 317
16375773 CCTAGTTCAT
*
16375783 ATAACTAGTGGGTCAAAGTACTTATCACCACCCCTTGAAGAAACAATATAAAGATTGGGTCTTTG
1 ATAACTAGTGGGTCAAAGTACTTAACACCACCCCTTGAAGAAACAATATAAAGATTGGGTCTTTG
*
16375848 CTCTCTATAGCATTGGTTCTTCTTTGAGCGTTCTTCAAGATACTATCCTCACAACCATCCTTTTG
66 CTCTCTATAGCATTGGTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCTTTTG
* *
16375913 TTTCATCGCCATAACCATAACCATTTCAATCATCTTCCGCTTCCATCTCTCATTTATTAAATATC
131 TTTCATCGCCATAACCATAACCATTTCAATCATCTTCCACTTCCATCTCTCATTTATTAAATAGC
*
16375978 CTACCTATTAAACCATACGTTTACCACCCTTATCCATTCTGTTTTGAGCCATTCACTTGTGCAGG
196 CTACCTATTAAACCATACATTTACCACCCTTATCCATTCTGTTTTGAGCCATTCACTTGTGCAGG
* *
16376043 TTGTTTTGCTTCCTTCCTAGATCCACAATCAAACGAGAAGGTATAATTACCTTACATC
261 TTGTTTT-CTTCCTTCCTAGACCCACAATCAAACGAGAAGGTAGAATTACCTTACATC
16376101 ATAACTAGTGGGTCAAAGTACTTAACACCACCCCTTGAAGAAACAATATAAAGATTGGGTCTTTG
1 ATAACTAGTGGGTCAAAGTACTTAACACCACCCCTTGAAGAAACAATATAAAGATTGGGTCTTTG
* *
16376166 CTCTCTATAGCATTGGTTCTTCTTTGAGCATTCTTTAATATACTATCCTCACAACCATCCTTTTG
66 CTCTCTATAGCATTGGTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCTTTTG
16376231 TTTCATCGCCATAACCATAACCATTTCAATCATCTTCCACTTCCATCTCTCATTTATTAAATAGC
131 TTTCATCGCCATAACCATAACCATTTCAATCATCTTCCACTTCCATCTCTCATTTATTAAATAGC
* * *
16376296 CTACTTATTAAACCATACATTTATCACCCTTATCCATTCTGTTTTGAGCTATTCACTTGTGCAGG
196 CTACCTATTAAACCATACATTTACCACCCTTATCCATTCTGTTTTGAGCCATTCACTTGTGCAGG
16376361 TTGTTTTCTTCCTTCCTAGACCCACAATCAAACGAGAAGGTAGAATTACCTTACATC
261 TTGTTTTCTTCCTTCCTAGACCCACAATCAAACGAGAAGGTAGAATTACCTTACATC
16376418 A
1 A
16376419 AGCAGTAATC
Statistics
Matches: 306, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
317 49 0.16
318 257 0.84
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (317 bp):
ATAACTAGTGGGTCAAAGTACTTAACACCACCCCTTGAAGAAACAATATAAAGATTGGGTCTTTG
CTCTCTATAGCATTGGTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCTTTTG
TTTCATCGCCATAACCATAACCATTTCAATCATCTTCCACTTCCATCTCTCATTTATTAAATAGC
CTACCTATTAAACCATACATTTACCACCCTTATCCATTCTGTTTTGAGCCATTCACTTGTGCAGG
TTGTTTTCTTCCTTCCTAGACCCACAATCAAACGAGAAGGTAGAATTACCTTACATC
Found at i:16376565 original size:40 final size:39
Alignment explanation
Indices: 16376514--16376590 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
16376504 AAAGTGAAAG
**
16376514 AAAGCAAGAAAA-ATCAGCAAAGAAA-TTGAAAGCACTCGA
1 AAAGCAAGAAAAGAAAAG-AAAGAAAGTTG-AAGCACTCGA
16376553 AAAGCAAAGAAAAGAAAAGAAAGAAAGTTGAAGCACTC
1 AAAGC-AAGAAAAGAAAAGAAAGAAAGTTGAAGCACTC
16376591 ATCAACAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 5 0.15
40 22 0.67
41 6 0.18
ACGTcount: A:0.58, C:0.13, G:0.19, T:0.09
Consensus pattern (39 bp):
AAAGCAAGAAAAGAAAAGAAAGAAAGTTGAAGCACTCGA
Found at i:16377865 original size:24 final size:24
Alignment explanation
Indices: 16377838--16377889 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
16377828 GACATGTCCT
* * *
16377838 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
16377862 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
16377886 TTGA
1 TTGA
16377890 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:16378736 original size:24 final size:24
Alignment explanation
Indices: 16378709--16378760 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
16378699 GACATGTCCT
* * *
16378709 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
16378733 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
16378757 TTGA
1 TTGA
16378761 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:16378790 original size:871 final size:872
Alignment explanation
Indices: 16377107--16378848 Score: 3468
Period size: 871 Copynumber: 2.0 Consensus size: 872
16377097 TTTTCCATAC
16377107 AAAATGTAACGTGGGAGATAAAGTTTGTGTGGTGATCATTGATGGAGGAAGTTGTACAAATGTAG
1 AAAATGTAACGTGGGAGATAAAGTTTGTGTGGTGATCATTGATGGAGGAAGTTGTACAAATGTAG
16377172 CAAGTACTCACATGGTGGAAAAGTTAGGTCTCCAGACTTCCAAGCATCCTCATCCTTACAAACTT
66 CAAGTACTCACATGGTGGAAAAGTTAGGTCTCCAGACTTCCAAGCATCCTCATCCTTACAAACTT
16377237 CAATGGCCTAATGATGTGGGTGAAGCCAAGGTAACCAAACAAGTTGTTATACCTTTTGCAATTGG
131 CAATGGCCTAATGATGTGGGTGAAGCCAAGGTAACCAAACAAGTTGTTATACCTTTTGCAATTGG
16377302 AAGATACCAAGATGAAGTCCTTTGTGACATGGTGCCCATGAGTGCAAGCCACCGTATACTCGGAC
196 AAGATACCAAGATGAAGTCCTTTGTGACATGGTGCCCATGAGTGCAAGCCACCGTATACTCGGAC
16377367 GTCCTTGGCAATATGATAAGAAGGCTACTCATGATGGATTCTCTAACAAGTACTCTTTCCAACAT
261 GTCCTTGGCAATATGATAAGAAGGCTACTCATGATGGATTCTCTAACAAGTACTCTTTCCAACAT
16377432 GAAGGAAAGAAAATCATATTGGCACCCTTGCTTCCCAGTCAAGTTCATGAATGCCAAGTGACCCT
326 GAAGGAAAGAAAATCATATTGGCACCCTTGCTTCCCAGTCAAGTTCATGAATGCCAAGTGACCCT
16377497 TAAGTCACACATAGAAGAATGGGAGAAAATGAAGGCCATAAAAAGAAGCTTTGAAGAAGAACGTT
391 TAAGTCACACATAGAAGAATGGGAGAAAATGAAGGCCATAAAAAGAAGCTTTGAAGAAGAACGTT
16377562 TTGTGGAGACAAGAATAATTGGAAATGAATCTGTTGGAGTTGAAAAGGATGTTTTGCAAGTAGTG
456 TTGTGGAGACAAGAATAATTGGAAATGAATCTGTTGGAGTTGAAAAGGATGTTTTGCAAGTAGTG
16377627 GAGCAAATTGAAATTGGCAAATTTGAAAAGGATGAGTATAGAGAAGAAAAGAAGAGTGAAGGATA
521 GAGCAAATTGAAATTGGCAAATTTGAAAAGGATGAGTATAGAGAAGAAAAGAAGAGTGAAGGATA
16377692 ATTTTTTCCTAACAATTCTTCTTCTACTATTTCTTTTTCCTTGCAGGATATTCAAAGAGACATAT
586 ATTTTTTCCTAACAATTCTTCTTCTACTATTTCTTTTTCCTTGCAGGATATTCAAAGAGACATAT
16377757 ATTTTCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAACAGGTGTGACCTTTGGTAAT
651 ATTTTCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAACAGGTGTGACCTTTGGTAAT
16377822 CCACAAGACATGTCCTTTGACGTTCCAACAGTTATGCCACTTGATGTTCAAAAAGATGTGCCACT
716 CCACAAGACATGTCCTTTGACGTTCCAACAGTTATGCCACTTGATGTTCAAAAAGATGTGCCACT
16377887 TGAAGTGCCAAGGAATGGGATCATTGATAATCCAAGTACATTGCACATATTGAAGGGAATTCAGC
781 TGAAGTGCCAAGGAATGGGATCATTGATAATCCAAGTACATTGCACATATTGAAGGGAATTCAGC
16377952 AACCAATGGAGATTTCCATCATTAAGA
846 AACCAATGGAGATTTCCATCATTAAGA
16377979 AAAATGTAACGTGGGAGATAAAGTTTGTGTGGTGATCATTGATGGAGGAAGTTGTACAAATGTAG
1 AAAATGTAACGTGGGAGATAAAGTTTGTGTGGTGATCATTGATGGAGGAAGTTGTACAAATGTAG
16378044 CAAGTACTCACATGGTGGAAAAGTTAGGTCTCCAGACTTCCAAGCATCCTCATCCTTACAAACTT
66 CAAGTACTCACATGGTGGAAAAGTTAGGTCTCCAGACTTCCAAGCATCCTCATCCTTACAAACTT
16378109 CAATGGCCTAATGATGTGGGTGAAGCCAAGGTAACCAAACAAGTTGTTATACCTTTTGCAATTGG
131 CAATGGCCTAATGATGTGGGTGAAGCCAAGGTAACCAAACAAGTTGTTATACCTTTTGCAATTGG
16378174 AAGATACCAAGATGAAGTCCTTTGTGACATGGTGCCCATGAGTGCAAGCCACCGTATACTCGGAC
196 AAGATACCAAGATGAAGTCCTTTGTGACATGGTGCCCATGAGTGCAAGCCACCGTATACTCGGAC
16378239 GTCCTTGGCAATATGATAAGAAGGCTACTCATGATGGATTCTCTAACAAGTACTCTTTCCAACAT
261 GTCCTTGGCAATATGATAAGAAGGCTACTCATGATGGATTCTCTAACAAGTACTCTTTCCAACAT
16378304 GAAGGAAA-AAAATCATATTGGCACCCTTGCTTCCCAGTCAAGTTCATGAATGCCAAGTGACCCT
326 GAAGGAAAGAAAATCATATTGGCACCCTTGCTTCCCAGTCAAGTTCATGAATGCCAAGTGACCCT
*
16378368 TAAGTCACGCATAGAAGAATGGGAGAAAATGAAGGCCATAAAAAGAAGCTTTGAAGAAGAACGTT
391 TAAGTCACACATAGAAGAATGGGAGAAAATGAAGGCCATAAAAAGAAGCTTTGAAGAAGAACGTT
16378433 TTGTGGAGACAAGAATAATTGGAAATGAATCTGTTGGAGTTGAAAAGGATGTTTTGCAAGTAGTG
456 TTGTGGAGACAAGAATAATTGGAAATGAATCTGTTGGAGTTGAAAAGGATGTTTTGCAAGTAGTG
16378498 GAGCAAATTGAAATTGGCAAATTTGAAAAGGATGAGTATAGAGAAGAAAAGAAGAGTGAAGGATA
521 GAGCAAATTGAAATTGGCAAATTTGAAAAGGATGAGTATAGAGAAGAAAAGAAGAGTGAAGGATA
16378563 ATTTTTTCCTAACAATTCTTCTTCTACTATTTCTTTTTCCTTGCAGGATATTCAAAGAGACATAT
586 ATTTTTTCCTAACAATTCTTCTTCTACTATTTCTTTTTCCTTGCAGGATATTCAAAGAGACATAT
16378628 ATTTTCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAACAGGTGTGACCTTTGGTAAT
651 ATTTTCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAACAGGTGTGACCTTTGGTAAT
16378693 CCACAAGACATGTCCTTTGACGTTCCAACAGTTATGCCACTTGATGTTCAAAAAGATGTGCCACT
716 CCACAAGACATGTCCTTTGACGTTCCAACAGTTATGCCACTTGATGTTCAAAAAGATGTGCCACT
16378758 TGAAGTGCCAAGGAATGGGATCATTGATAATCCAAGTACATTGCACATATTGAAGGGAATTCAGC
781 TGAAGTGCCAAGGAATGGGATCATTGATAATCCAAGTACATTGCACATATTGAAGGGAATTCAGC
16378823 AACCAATGGAGATTTCCATCATTAAG
846 AACCAATGGAGATTTCCATCATTAAG
16378849 CAACCAAGGC
Statistics
Matches: 869, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
871 536 0.62
872 333 0.38
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (872 bp):
AAAATGTAACGTGGGAGATAAAGTTTGTGTGGTGATCATTGATGGAGGAAGTTGTACAAATGTAG
CAAGTACTCACATGGTGGAAAAGTTAGGTCTCCAGACTTCCAAGCATCCTCATCCTTACAAACTT
CAATGGCCTAATGATGTGGGTGAAGCCAAGGTAACCAAACAAGTTGTTATACCTTTTGCAATTGG
AAGATACCAAGATGAAGTCCTTTGTGACATGGTGCCCATGAGTGCAAGCCACCGTATACTCGGAC
GTCCTTGGCAATATGATAAGAAGGCTACTCATGATGGATTCTCTAACAAGTACTCTTTCCAACAT
GAAGGAAAGAAAATCATATTGGCACCCTTGCTTCCCAGTCAAGTTCATGAATGCCAAGTGACCCT
TAAGTCACACATAGAAGAATGGGAGAAAATGAAGGCCATAAAAAGAAGCTTTGAAGAAGAACGTT
TTGTGGAGACAAGAATAATTGGAAATGAATCTGTTGGAGTTGAAAAGGATGTTTTGCAAGTAGTG
GAGCAAATTGAAATTGGCAAATTTGAAAAGGATGAGTATAGAGAAGAAAAGAAGAGTGAAGGATA
ATTTTTTCCTAACAATTCTTCTTCTACTATTTCTTTTTCCTTGCAGGATATTCAAAGAGACATAT
ATTTTCAAGTAGAAAATTCAAGAAACATGTCTTTTGAAGAACCAACAGGTGTGACCTTTGGTAAT
CCACAAGACATGTCCTTTGACGTTCCAACAGTTATGCCACTTGATGTTCAAAAAGATGTGCCACT
TGAAGTGCCAAGGAATGGGATCATTGATAATCCAAGTACATTGCACATATTGAAGGGAATTCAGC
AACCAATGGAGATTTCCATCATTAAGA
Found at i:16387390 original size:24 final size:24
Alignment explanation
Indices: 16387358--16387404 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16387348 GATGTAGGAG
16387358 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
16387381 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
16387405 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:16391375 original size:24 final size:24
Alignment explanation
Indices: 16391343--16391389 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
16391333 GATGTAGGAG
16391343 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
16391366 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
16391390 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:16396683 original size:19 final size:21
Alignment explanation
Indices: 16396659--16396709 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
16396649 GGCCAAGAGC
*
16396659 ATGTATCTTCA-TTAAA-ATA
1 ATGTATTTTCATTTAAACATA
*
16396678 ATGTATTTTCATTTAAACATC
1 ATGTATTTTCATTTAAACATA
16396699 ATGTATTTTCA
1 ATGTATTTTCA
16396710 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 5 0.18
21 13 0.46
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAACATA
Found at i:16397150 original size:19 final size:21
Alignment explanation
Indices: 16397126--16397168 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
16397116 TCTTTATTTC
16397126 ATTTCATT-CTTAT-TCTTTT
1 ATTTCATTACTTATATCTTTT
*
16397145 ATTTCATTACTTATATTTTTT
1 ATTTCATTACTTATATCTTTT
16397166 ATT
1 ATT
16397169 CCCTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTCATTACTTATATCTTTT
Found at i:16399081 original size:13 final size:11
Alignment explanation
Indices: 16399040--16399124 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
16399030 ACAATCTGTC
16399040 CATCACCATTAT
1 CATCACCA-TAT
*
16399052 CA-CGCCTATAT
1 CATCACC-ATAT
16399063 CATCACCATAGT
1 CATCACCATA-T
16399075 CCATCACCATTAT
1 -CATCACCA-TAT
*
16399088 CA-CGCCTATAT
1 CATCACC-ATAT
16399099 CATCACCATATT
1 CATCACCATA-T
16399111 CCATCACCATAT
1 -CATCACCATAT
16399123 CA
1 CA
16399125 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:16399084 original size:36 final size:36
Alignment explanation
Indices: 16399037--16399133 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
16399027 GATACAATCT
16399037 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16399073 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
16399109 TTCCATCACCA-TATCACGCCCATAT
1 GTCCATCACCATTATCACGCCTATAT
16399134 TATAACCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16399625 original size:14 final size:15
Alignment explanation
Indices: 16399591--16399637 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
16399581 AATTTGGAGT
16399591 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
16399606 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
16399620 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
16399637 G
1 G
16399638 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:16403054 original size:36 final size:36
Alignment explanation
Indices: 16403014--16403110 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
16403004 GATACAATCT
16403014 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16403050 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
16403086 TTCCATCACCA-TATCACGCCCATAT
1 GTCCATCACCATTATCACGCCTATAT
16403111 TATAACCAAC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 13 0.22
36 46 0.78
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16403058 original size:13 final size:11
Alignment explanation
Indices: 16403017--16403101 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
16403007 ACAATCTGTC
16403017 CATCACCATTAT
1 CATCACCA-TAT
*
16403029 CA-CGCCTATAT
1 CATCACC-ATAT
16403040 CATCACCATAGT
1 CATCACCATA-T
16403052 CCATCACCATTAT
1 -CATCACCA-TAT
*
16403065 CA-CGCCTATAT
1 CATCACC-ATAT
16403076 CATCACCATATT
1 CATCACCATA-T
16403088 CCATCACCATAT
1 -CATCACCATAT
16403100 CA
1 CA
16403102 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:16405004 original size:19 final size:21
Alignment explanation
Indices: 16404966--16405008 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
16404956 TAATAAAGGG
16404966 AATAAAAAATATAAGTAATGA
1 AATAAAAAATATAAGTAATGA
*
16404987 AATAAAAGA-ATAAG-AATGA
1 AATAAAAAATATAAGTAATGA
16405006 AAT
1 AAT
16405009 GAAATAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (21 bp):
AATAAAAAATATAAGTAATGA
Found at i:16405468 original size:19 final size:21
Alignment explanation
Indices: 16405425--16405476 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
16405415 GAAACCCCTT
16405425 TGAAAATACATGATGTTTAAA
1 TGAAAATACATGATGTTTAAA
*
16405446 TGAAAATACATTAT-TTT-AA
1 TGAAAATACATGATGTTTAAA
*
16405465 TGAAGATACATG
1 TGAAAATACATG
16405477 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATGTTTAAA
Found at i:16408440 original size:13 final size:12
Alignment explanation
Indices: 16408421--16408506 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
16408411 ATATGGGCGT
16408421 GATATGGTGATG
1 GATATGGTGATG
16408433 GAATATGGTGAT-
1 G-ATATGGTGATG
*
16408445 GATATAGGCG-T-
1 GATAT-GGTGATG
16408456 GATAATGGTGATG
1 GAT-ATGGTGATG
16408469 GACTATGGTGAT-
1 GA-TATGGTGATG
*
16408481 GATATAGGCG-T-
1 GATAT-GGTGATG
16408492 GATAATGGTGATG
1 GAT-ATGGTGATG
16408505 GA
1 GA
16408507 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:16408476 original size:36 final size:36
Alignment explanation
Indices: 16408405--16408507 Score: 172
Period size: 36 Copynumber: 2.9 Consensus size: 36
16408395 TTATAAGTTA
* * *
16408405 GTGATAATATGGGCGTGAT-ATGGTGATGGAATATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
16408440 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
1 GTGATGATATAGGCGTGATAATGGTGATGGACTATG
16408476 GTGATGATATAGGCGTGATAATGGTGATGGAC
1 GTGATGATATAGGCGTGATAATGGTGATGGAC
16408508 AGATTGTATC
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 47 0.73
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
GTGATGATATAGGCGTGATAATGGTGATGGACTATG
Found at i:16412416 original size:13 final size:12
Alignment explanation
Indices: 16412397--16412482 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
16412387 ATATGGGCGT
16412397 GATATGGTGATG
1 GATATGGTGATG
16412409 GAATATGGTGAT-
1 G-ATATGGTGATG
*
16412421 GATATAGGCG-T-
1 GATAT-GGTGATG
16412432 GATAATGGTGATG
1 GAT-ATGGTGATG
16412445 GACTATGGTGAT-
1 GA-TATGGTGATG
*
16412457 GATATAGGCG-T-
1 GATAT-GGTGATG
16412468 GATAATGGTGATG
1 GAT-ATGGTGATG
16412481 GA
1 GA
16412483 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:16412483 original size:36 final size:36
Alignment explanation
Indices: 16412387--16412483 Score: 169
Period size: 36 Copynumber: 2.7 Consensus size: 36
16412377 GTTGGTTATA
* *
16412387 ATATGGGCGTGAT-ATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
16412422 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
16412458 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
16412484 AGATTGTATC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
35 12 0.20
36 47 0.80
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
Found at i:16415541 original size:34 final size:32
Alignment explanation
Indices: 16415484--16415555 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 32
16415474 CTTGGCTTGC
*
16415484 TTTC-TTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTTGAATTTCTTCTTCTTTT-TATCT
16415515 TTTCTTTTTCTGAATTTTCTTCTTCTTTTTATCT
1 TTTCTTTTT-TGAA-TTTCTTCTTCTTTTTATCT
16415549 TTTCTTT
1 TTTCTTT
16415556 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 23 0.64
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.74
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTCTTCTTTTTATCT
Found at i:16425222 original size:20 final size:21
Alignment explanation
Indices: 16425197--16425249 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
16425187 CGGCCAAGAG
*
16425197 CATGTATCTTCA-TTAAAAAT
1 CATGTATTTTCATTTAAAAAT
16425217 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
16425238 CATGTATTTTCA
1 CATGTATTTTCA
16425250 AAGGGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:16432081 original size:36 final size:36
Alignment explanation
Indices: 16432048--16432181 Score: 205
Period size: 36 Copynumber: 3.7 Consensus size: 36
16432038 TCTTCCATTT
16432048 CCATTATCACGCCTATATCATCACCATAGTCCATCA
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
* *
16432084 CCATTATCACGCCTTTATCATCACCATAGTCCATCT
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
* * *
16432120 CCATTATCACGCCTATATCGTCACCATATTCCACCA
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
* *
16432156 CCATTATCACGCCCATATTATCACCA
1 CCATTATCACGCCTATATCATCACCA
16432182 ACTTATAAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 88 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
CCATTATCACGCCTATATCATCACCATAGTCCATCA
Found at i:16436480 original size:36 final size:36
Alignment explanation
Indices: 16436440--16436580 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
16436430 AACACCATCT
*
16436440 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
16436476 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
16436512 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * * *
16436548 TCCACCACCATTATCATGCCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
16436581 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:16437058 original size:33 final size:32
Alignment explanation
Indices: 16436994--16437058 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
16436984 CTTGTTGATG
*
16436994 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
16437026 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
16437059 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:16444627 original size:19 final size:21
Alignment explanation
Indices: 16444586--16444637 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
16444576 GAAACCCCTT
16444586 TGAAAATACATGATATTTAAA
1 TGAAAATACATGATATTTAAA
*
16444607 TGAAAATATATGAT-TTT-AA
1 TGAAAATACATGATATTTAAA
*
16444626 TGAAGATACATG
1 TGAAAATACATG
16444638 CTCTTGACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATATTTAAA
Found at i:16445187 original size:35 final size:36
Alignment explanation
Indices: 16445140--16445207 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
16445130 ATTTAGAAGT
16445140 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
16445175 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
16445208 TAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:16448414 original size:20 final size:23
Alignment explanation
Indices: 16448375--16448417 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
16448365 AATAAAGGGG
16448375 ATAATAATATATAAGTAATGAAA
1 ATAATAATATATAAGTAATGAAA
16448398 ATAA-AATA-ATAAG-AATGAAA
1 ATAATAATATATAAGTAATGAAA
16448418 TGAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 4 0.20
23 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (23 bp):
ATAATAATATATAAGTAATGAAA
Found at i:16448428 original size:20 final size:22
Alignment explanation
Indices: 16448375--16448429 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
16448365 AATAAAGGGG
*
16448375 ATAATAATATATAAGTAATGAAA
1 ATAA-AATAAATAAGTAATGAAA
16448398 ATAAAAT-AATAAG-AATG-AA
1 ATAAAATAAATAAGTAATGAAA
*
16448417 ATGAAATAAATAA
1 ATAAAATAAATAA
16448430 AGGATAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 9 0.31
21 5 0.17
22 3 0.10
23 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.25
Consensus pattern (22 bp):
ATAAAATAAATAAGTAATGAAA
Found at i:16452051 original size:19 final size:19
Alignment explanation
Indices: 16452027--16452091 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
16452017 TCTTTTTGAA
16452027 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
16452046 TTTCTTTTTCGAAATTTTCTTCT
1 TTTCTTTTTC----TTTTCTTCT
*
16452069 TCTT-TTTATCTTTTCTTTCT
1 T-TTCTTTTTCTTTTC-TTCT
16452089 TTT
1 TTT
16452092 TGTACTCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
19 17 0.44
20 5 0.13
23 15 0.38
24 2 0.05
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:16452072 original size:34 final size:31
Alignment explanation
Indices: 16452015--16452086 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
16452005 CTTGGCTTGC
*
16452015 TTTCTTTTTGAATTTCTTTTTCTTTTCT-TCT
1 TTTCTTTTTGAATTTCTTCTTCTTTT-TATCT
16452046 TTTCTTTTTCGAAATTTTCTTCTTCTTTTTATCT
1 TTTCTTTTT-G-AA-TTTCTTCTTCTTTTTATCT
16452080 TTTCTTT
1 TTTCTTT
16452087 CTTTTTGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
32 1 0.03
33 3 0.08
34 23 0.64
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (31 bp):
TTTCTTTTTGAATTTCTTCTTCTTTTTATCT
Found at i:16452844 original size:19 final size:21
Alignment explanation
Indices: 16452801--16452852 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
16452791 GAAACCCCTT
16452801 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
16452822 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
16452841 TGAAGATACATG
1 TGAAAATACATG
16452853 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:16461455 original size:22 final size:23
Alignment explanation
Indices: 16461430--16461481 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
16461420 ATTTATAAGT
*
16461430 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGAGTGATAA
*
16461452 TGGTGATGATATAGGAGTGATAA
1 TGGTGATAATATAGGAGTGATAA
16461475 TGGTGAT
1 TGGTGAT
16461482 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGAGTGATAA
Found at i:16461473 original size:36 final size:36
Alignment explanation
Indices: 16461450--16461557 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
16461440 ATAGGCGTGA
*
16461450 TATGGTGATGATATAGGAGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
16461486 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
16461522 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
16461558 ATATTGTATC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:16461492 original size:13 final size:12
Alignment explanation
Indices: 16461448--16461556 Score: 56
Period size: 11 Copynumber: 9.2 Consensus size: 12
16461438 ATATAGGCGT
16461448 GATATGGTGAT-
1 GATATGGTGATG
*
16461459 GATATAG-GA-G
1 GATATGGTGATG
16461469 TGATAATGGTGATG
1 -GAT-ATGGTGATG
16461483 GACTATGGTGAT-
1 GA-TATGGTGATG
*
16461495 GATATAGGCG-T-
1 GATAT-GGTGATG
16461506 GATAATGGTGATG
1 GAT-ATGGTGATG
16461519 GACTATGGTGAT-
1 GA-TATGGTGATG
*
16461531 GATATAGGCG-T-
1 GATAT-GGTGATG
16461542 GATAATGGTGATG
1 GAT-ATGGTGATG
16461555 GA
1 GA
16461557 CATATTGTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 28
0.69 0.05 0.25
Matches are distributed among these distances:
10 2 0.03
11 29 0.38
12 19 0.25
13 24 0.31
14 3 0.04
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:16472846 original size:35 final size:36
Alignment explanation
Indices: 16472799--16472866 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
16472789 ATTTATAAGT
16472799 TGGTGATAATATAAGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAAGCGTGATAATGGTGATGGAATA
* *
16472834 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAAGCGTGATAATGGTGATGGA
16472867 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAAGCGTGATAATGGTGATGGAATA
Found at i:16474336 original size:18 final size:18
Alignment explanation
Indices: 16474310--16474353 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16474300 GTGAAGTATG
*
16474310 AATGGTGTTGTCGTGGCA
1 AATGTTGTTGTCGTGGCA
*
16474328 AATGTTGTTGTCGTGGTA
1 AATGTTGTTGTCGTGGCA
*
16474346 AGTGTTGT
1 AATGTTGT
16474354 AAGGTTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.07, G:0.36, T:0.41
Consensus pattern (18 bp):
AATGTTGTTGTCGTGGCA
Found at i:16476745 original size:19 final size:20
Alignment explanation
Indices: 16476721--16476760 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
16476711 TATCCTTTCT
16476721 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
16476740 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
16476760 T
1 T
16476761 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:16481618 original size:35 final size:35
Alignment explanation
Indices: 16481543--16481651 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
16481533 TAAGATACTA
16481543 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
16481578 CCTATAACATCACCATTTTCCATTACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
16481613 TCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
16481648 CCTA
1 CCTA
16481652 AATAATCACC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 43 0.67
36 21 0.33
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:16482067 original size:24 final size:24
Alignment explanation
Indices: 16482046--16482090 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
16482036 AACAAAAGCA
* *
16482046 ACAAAAAGAGAAA-AAAAGAAAGA
1 ACAAAAACAAAAAGAAAAGAAAGA
*
16482069 AGAAAAACAAAAAGAAAAGAAA
1 ACAAAAACAAAAAGAAAAGAAA
16482091 AAGACTCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (24 bp):
ACAAAAACAAAAAGAAAAGAAAGA
Found at i:16482071 original size:17 final size:16
Alignment explanation
Indices: 16482051--16482092 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16482041 AAGCAACAAA
16482051 AAGAGAAAAAAAGAAAG
1 AAGAGAAAAAAA-AAAG
*
16482068 AAGA-AAAACAAAAAG
1 AAGAGAAAAAAAAAAG
*
16482083 AAAAGAAAAA
1 AAGAGAAAAA
16482093 GACTCCTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAGAAAAAAAAAAG
Found at i:16487510 original size:36 final size:36
Alignment explanation
Indices: 16487437--16487541 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
16487427 ATTTATAAGT
* * *
16487437 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
16487472 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
16487508 TGGTAATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
16487542 ATATTATATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:16487628 original size:23 final size:23
Alignment explanation
Indices: 16487601--16487646 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16487591 AGACCCGTTT
16487601 CTTATAAGTTCTATAAGGGATGG
1 CTTATAAGTTCTATAAGGGATGG
16487624 CTTATAAGTTCTATAAGGGATGG
1 CTTATAAGTTCTATAAGGGATGG
16487647 TATGAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (23 bp):
CTTATAAGTTCTATAAGGGATGG
Found at i:16487949 original size:19 final size:20
Alignment explanation
Indices: 16487902--16487952 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
16487892 GAAACCCTTT
**
16487902 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
16487922 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
16487941 TGAAGATACATG
1 TGAAAATACATG
16487953 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16491784 original size:36 final size:36
Alignment explanation
Indices: 16491642--16491769 Score: 222
Period size: 36 Copynumber: 3.6 Consensus size: 36
16491632 TGATAATATG
* * *
16491642 GGCGTGAT-ATGGTGATGGAATATGGTGATGATATA
1 GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
16491677 GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
1 GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
16491713 GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
1 GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
16491749 GGCGTGATAATGGTGATGGAC
1 GGCGTGATAATGGTGATGGAC
16491770 ATATTGTATC
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 8 0.09
36 81 0.91
ACGTcount: A:0.27, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
GGCGTGATAATGGTGATGGACTATGGTAATGTTATA
Found at i:16491784 original size:72 final size:71
Alignment explanation
Indices: 16491642--16491784 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 71
16491632 TGATAATATG
*
16491642 GGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTAAT
1 GGCGTGATATGGTGATGGAATATGGTAATGATATAGGCGTGATAATGGTGATGGACTATGGTAAT
*
16491707 GTTATA
66 CTTATA
* * *
16491713 GGCGTGATAATGGTGATGGACTATGGTAATGTTATAGGCGTGATAATGGTGATGGACATATTGT-
1 GGCGTGAT-ATGGTGATGGAATATGGTAATGATATAGGCGTGATAATGGTGATGGAC-TATGGTA
16491777 ATCTTATA
64 ATCTTATA
16491785 AAACTAAGAA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 8 0.12
72 52 0.80
73 5 0.08
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.34
Consensus pattern (71 bp):
GGCGTGATATGGTGATGGAATATGGTAATGATATAGGCGTGATAATGGTGATGGACTATGGTAAT
CTTATA
Found at i:16495435 original size:36 final size:35
Alignment explanation
Indices: 16495383--16495483 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 35
16495373 ATACTACCTA
16495383 AACATCACCATCTTCCATCACCATTTTCACGTCTAT
1 AACATCACCATCTTCCATCACCA-TTTCACGTCTAT
* * * *
16495419 AACATCACCATTTTCCATTACCATTGCATGTCTAT
1 AACATCACCATCTTCCATCACCATTTCACGTCTAT
* * *
16495454 ATCATTACCATCTTCTATCACCATTTCACG
1 AACATCACCATCTTCCATCACCATTTCACG
16495484 CCTAAATAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
35 33 0.61
36 21 0.39
ACGTcount: A:0.28, C:0.33, G:0.04, T:0.36
Consensus pattern (35 bp):
AACATCACCATCTTCCATCACCATTTCACGTCTAT
Found at i:16497459 original size:2 final size:2
Alignment explanation
Indices: 16497452--16497504 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
16497442 TCGGGCCGAG
* * * *
16497452 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
16497492 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
16497505 TTTAAATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16497559 original size:51 final size:52
Alignment explanation
Indices: 16497457--16497566 Score: 154
Period size: 51 Copynumber: 2.1 Consensus size: 52
16497447 CCGAGTATAT
*
16497457 ATATTTAAATTAAATATATAAATATTATATATATATATATATATATATTTTA
1 ATATTTAAATTAAATATATAAATATTATATATATATAAATATATATATTTTA
* *
16497509 A-ATTTAAATTAAATTTATTAATATTATATATATATAAA-ATA-ATTATTTTTA
1 ATATTTAAATTAAATATATAAATATTATATATATATAAATATATA-TA-TTTTA
16497560 ATATTTA
1 ATATTTA
16497567 TCGGGCCGGG
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.10
51 40 0.77
52 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (52 bp):
ATATTTAAATTAAATATATAAATATTATATATATATAAATATATATATTTTA
Found at i:16497621 original size:13 final size:12
Alignment explanation
Indices: 16497565--16497608 Score: 70
Period size: 12 Copynumber: 3.6 Consensus size: 12
16497555 TTTTAATATT
16497565 TATCGGGCCGGG
1 TATCGGGCCGGG
16497577 TATCGGGCCGGG
1 TATCGGGCCGGG
*
16497589 TATCGGGCCTGG
1 TATCGGGCCGGG
16497601 TAATCGGG
1 T-ATCGGG
16497609 TAATCGGGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.11, C:0.23, G:0.45, T:0.20
Consensus pattern (12 bp):
TATCGGGCCGGG
Found at i:16497669 original size:29 final size:29
Alignment explanation
Indices: 16497636--16497698 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
16497626 ACTAAACCTG
*
16497636 TCCCCGTCCCCATTTAACATAAACGGTTT
1 TCCCCGTCCCCATTTAACATAAACGATTT
* *
16497665 TCCCCGTCCCCGTTTAACTTAAACGATTT
1 TCCCCGTCCCCATTTAACATAAACGATTT
16497694 TCCCC
1 TCCCC
16497699 ATTCCTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.21, C:0.38, G:0.10, T:0.32
Consensus pattern (29 bp):
TCCCCGTCCCCATTTAACATAAACGATTT
Found at i:16497708 original size:29 final size:29
Alignment explanation
Indices: 16497636--16497710 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
16497626 ACTAAACCTG
* * *
16497636 TCCCCGTCCCCATTTAACATAAACGGTTT
1 TCCCCATCCCCGTTTAACATAAACGATTT
* *
16497665 TCCCCGTCCCCGTTTAACTTAAACGATTT
1 TCCCCATCCCCGTTTAACATAAACGATTT
* *
16497694 TCCCCATTCCTGTTTAA
1 TCCCCATCCCCGTTTAA
16497711 TTCGGTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (29 bp):
TCCCCATCCCCGTTTAACATAAACGATTT
Found at i:16498011 original size:19 final size:20
Alignment explanation
Indices: 16497987--16498029 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
16497977 AGCATTTATC
*
16497987 TTCATTAAAATTC-TGTATT
1 TTCATTAAAAATCATGTATT
*
16498006 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
16498026 TTCA
1 TTCA
16498030 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:16498833 original size:13 final size:12
Alignment explanation
Indices: 16498817--16498855 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
16498807 CAACAAAAGG
16498817 AGAAAAAGAAAGA
1 AGAAAAAGAAA-A
*
16498830 AGAAAAACAAAA
1 AGAAAAAGAAAA
16498842 AG-AAAAGAAAA
1 AGAAAAAGAAAA
16498853 AGA
1 AGA
16498856 CTCCTACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 10 0.43
12 3 0.13
13 10 0.43
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:16498853 original size:6 final size:6
Alignment explanation
Indices: 16498817--16498855 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
16498807 CAACAAAAGG
*
16498817 AGAAAA AGAAAGA AGAAAA ACAAAA AG-AAA AGAAAA AGA
1 AGAAAA AGAAA-A AGAAAA AGAAAA AGAAAA AGAAAA AGA
16498856 CTCCTACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:16503429 original size:20 final size:20
Alignment explanation
Indices: 16503393--16503431 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16503383 TCATCACATA
*
16503393 AGGAGCTTAAATTTAGCTGG
1 AGGAGCTTAAATGTAGCTGG
16503413 AGGAGC-TAGAATGTAGCTG
1 AGGAGCTTA-AATGTAGCTG
16503432 AACTTAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (20 bp):
AGGAGCTTAAATGTAGCTGG
Found at i:16504887 original size:6 final size:6
Alignment explanation
Indices: 16504846--16504889 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
16504836 AAAAGCAACA
*
16504846 AAAAGAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
16504890 CTCCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:16505226 original size:17 final size:17
Alignment explanation
Indices: 16505178--16505226 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
16505168 TCCTACCTCT
*
16505178 ACCATAACCATTTCAAG
1 ACCATAACCATTTCTAG
16505195 ACCATAACCATTTCTAG
1 ACCATAACCATTTCTAG
*
16505212 ACCCTAACCATTTCT
1 ACCATAACCATTTCT
16505227 TTTTAAGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.29
Consensus pattern (17 bp):
ACCATAACCATTTCTAG
Found at i:16509886 original size:10 final size:10
Alignment explanation
Indices: 16509871--16509929 Score: 64
Period size: 10 Copynumber: 5.8 Consensus size: 10
16509861 TGCTATTTTT
16509871 AAAAAAAACA
1 AAAAAAAACA
*
16509881 AAAAAAAGCA
1 AAAAAAAACA
**
16509891 AAAAAAGGCA
1 AAAAAAAACA
*
16509901 AAAAAAAAAA
1 AAAAAAAACA
*
16509911 AACAAAAAAGA
1 AA-AAAAAACA
16509922 AAAAAAAA
1 AAAAAAAA
16509930 AGCCAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
10 33 0.79
11 9 0.21
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:16509909 original size:14 final size:14
Alignment explanation
Indices: 16509871--16509927 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
16509861 TGCTATTTTT
16509871 AAAAAAAACAAAAA-
1 AAAAAAAA-AAAAAC
* **
16509885 AAAGCAAAAAAAGGC
1 AAA-AAAAAAAAAAC
16509900 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
16509914 AAAAAAGAAAAAAA
1 AAAAAA-AAAAAAA
16509928 AAAGCCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 20 0.59
15 14 0.41
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:16509910 original size:23 final size:21
Alignment explanation
Indices: 16509874--16509930 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 21
16509864 TATTTTTAAA
16509874 AAAAACAAAAAAAAGCAAAAAAAGG
1 AAAAA-AAAAAAAA-C-AAAAAA-G
16509899 CAAAAAAAAAAAAACAAAAAAG
1 -AAAAAAAAAAAAACAAAAAAG
16509921 AAAAAAAAAA
1 AAAAAAAAAA
16509931 GCCAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 10 0.32
22 1 0.03
23 6 0.19
24 1 0.03
25 8 0.26
26 5 0.16
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAACAAAAAAG
Found at i:16509912 original size:34 final size:34
Alignment explanation
Indices: 16509871--16509937 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
16509861 TGCTATTTTT
* *
16509871 AAAAAAAACAAAAAA-AAGCAAAAAAAGGCAAAAA
1 AAAAAAAACAAAAAAGAA-AAAAAAAAGCCAAAAA
16509905 AAAAAAAACAAAAAAGAAAAAAAAAAGCCAAAA
1 AAAAAAAACAAAAAAGAAAAAAAAAAGCCAAAA
16509938 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (34 bp):
AAAAAAAACAAAAAAGAAAAAAAAAAGCCAAAAA
Found at i:16519629 original size:13 final size:11
Alignment explanation
Indices: 16519588--16519673 Score: 68
Period size: 11 Copynumber: 7.3 Consensus size: 11
16519578 ACAATCTGTC
16519588 CATCACCATTAT
1 CATCACCA-TAT
*
16519600 CA-CGCCTATAT
1 CATCACC-ATAT
16519611 CATCACCATAGT
1 CATCACCATA-T
16519623 CCATCACCATTAT
1 -CATCACCA-TAT
*
16519636 CA-CGCCTATAT
1 CATCACC-ATAT
16519647 CATCACCATATT
1 CATCACCATA-T
16519659 CCATCACCATAT
1 -CATCACCATAT
16519671 CAT
1 CAT
16519674 GCCTATATTA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
11 25 0.41
12 15 0.25
13 19 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:16519632 original size:36 final size:36
Alignment explanation
Indices: 16519585--16519689 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
16519575 GATACAATCT
16519585 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16519621 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
16519657 TTCCATCACCA-TATCATGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
16519690 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16520164 original size:14 final size:15
Alignment explanation
Indices: 16520130--16520176 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
16520120 AATTTGAAGT
16520130 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
16520145 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
16520159 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
16520176 G
1 G
16520177 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:16523790 original size:13 final size:11
Alignment explanation
Indices: 16523768--16523833 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
16523758 TATCACGCCT
16523768 ATATCATCACC
1 ATATCATCACC
16523779 ATAGTCCATCACC
1 ATA-T-CATCACC
*
16523792 ATTATCA-CGCC
1 A-TATCATCACC
16523803 TATATCATCACC
1 -ATATCATCACC
16523815 ATATTCCATCACC
1 ATA-T-CATCACC
16523828 ATATCA
1 ATATCA
16523834 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:16523796 original size:36 final size:36
Alignment explanation
Indices: 16523746--16523850 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
16523736 GATACAATCT
*
16523746 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16523782 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
16523818 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
16523851 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16524316 original size:14 final size:15
Alignment explanation
Indices: 16524293--16524337 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 15
16524283 TTTGGAGTGC
16524293 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
16524308 AAAAG-AAGAAAAGA
1 AAAAGAAAGAAAAGA
16524322 AAAAGCAAAAGAAAAG
1 AAAAG--AAAGAAAAG
16524338 TGAAGAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 14 0.52
15 5 0.19
17 8 0.30
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:16526660 original size:15 final size:15
Alignment explanation
Indices: 16526630--16526677 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
16526620 GATGTAGGAG
16526630 TATTTTTCTTTTCTTTT
1 TATTTTTC--TTCTTTT
16526647 TATTTTTCTTCTTTT
1 TATTTTTCTTCTTTT
16526662 TATTTTT-TCTCTTTT
1 TATTTTTCT-TCTTTT
16526677 T
1 T
16526678 GTTACTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 21 0.70
17 8 0.27
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTCTTCTTTT
Found at i:16533399 original size:19 final size:20
Alignment explanation
Indices: 16533357--16533407 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
16533347 GAAACCCCTT
16533357 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
16533377 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
16533396 TGAAGATACATG
1 TGAAAATACATG
16533408 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:16540498 original size:13 final size:11
Alignment explanation
Indices: 16540457--16540541 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
16540447 ACAATCTGTC
16540457 CATCACCATTAT
1 CATCACCA-TAT
*
16540469 CA-CGCCTATAT
1 CATCACC-ATAT
16540480 CATCACCATAGT
1 CATCACCATA-T
16540492 CCATCACCATTAT
1 -CATCACCA-TAT
*
16540505 CA-CGCCTATAT
1 CATCACC-ATAT
16540516 CATCACCATATT
1 CATCACCATA-T
16540528 CCATCACCATAT
1 -CATCACCATAT
16540540 CA
1 CA
16540542 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:16540501 original size:36 final size:36
Alignment explanation
Indices: 16540454--16540556 Score: 181
Period size: 36 Copynumber: 2.9 Consensus size: 36
16540444 GATACAATCT
16540454 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16540490 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
16540526 TTCCATCACCA-TATCACGCCTATATTATCAC
1 GTCCATCACCATTATCACGCCTATATCATCAC
16540557 TAACTTATAA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16544536 original size:13 final size:11
Alignment explanation
Indices: 16544495--16544579 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
16544485 ACAATCTGTC
16544495 CATCACCATTAT
1 CATCACCA-TAT
*
16544507 CA-CGCCTATAT
1 CATCACC-ATAT
16544518 CATCACCATAGT
1 CATCACCATA-T
16544530 CCATCACCATTAT
1 -CATCACCA-TAT
*
16544543 CA-CGCCTATAT
1 CATCACC-ATAT
16544554 CATCACCATATT
1 CATCACCATA-T
16544566 CCATCACCATAT
1 -CATCACCATAT
16544578 CA
1 CA
16544580 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:16544539 original size:36 final size:36
Alignment explanation
Indices: 16544492--16544596 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
16544482 GATACAATCT
16544492 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
16544528 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
16544564 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
16544597 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:16554009 original size:16 final size:17
Alignment explanation
Indices: 16553985--16554028 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16553975 TTGAAATCTT
*
16553985 TTTCTTTTTCTTCTTTTC
1 TTTCTTTTT-GTCTTTTC
16554003 -TTCTTTTTGTCTTTTC
1 TTTCTTTTTGTCTTTTC
16554019 TTTCTTTTTG
1 TTTCTTTTTG
16554029 CACTCCAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTCTTTTTGTCTTTTC
Found at i:16555695 original size:23 final size:24
Alignment explanation
Indices: 16555639--16555686 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
16555629 ATAGGTATAA
16555639 TATATATATATGAAAATAACTATCT
1 TATA-ATATATGAAAATAACTATCT
*
16555664 TATAATATATG-AAATAAGTATCT
1 TATAATATATGAAAATAACTATCT
16555687 ATAGGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 7 0.32
25 4 0.18
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (24 bp):
TATAATATATGAAAATAACTATCT
Found at i:16556244 original size:34 final size:33
Alignment explanation
Indices: 16556176--16556244 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
16556166 GTTGATGAAT
*
16556176 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* *
16556209 GAAGGATGATGTTATTGGCG-TGATAATGGTGATG
1 GAAGGATGAT-TTAATGGCGATGA-AATGGTAATG
16556243 GA
1 GA
16556245 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:16560597 original size:34 final size:33
Alignment explanation
Indices: 16560529--16560597 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
16560519 GTTGATGAAT
*
16560529 GAAGGATGATTTAATGGTGATGAAATGGTAATG
1 GAAGGATGATTTAATGGCGATGAAATGGTAATG
* *
16560562 GAAGGATGATGTTATTGGCG-TGAAAATGGTGATG
1 GAAGGATGAT-TTAATGGCGATG-AAATGGTAATG
16560596 GA
1 GA
16560598 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.33, C:0.01, G:0.36, T:0.29
Consensus pattern (33 bp):
GAAGGATGATTTAATGGCGATGAAATGGTAATG
Found at i:16563532 original size:24 final size:21
Alignment explanation
Indices: 16563497--16563539 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
16563487 GGCTCATTCT
*
16563497 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
16563520 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
16563540 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:16564783 original size:15 final size:15
Alignment explanation
Indices: 16564748--16564776 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16564738 GTGCTTCAAC
16564748 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
16564762 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
16564777 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:16564825 original size:24 final size:23
Alignment explanation
Indices: 16564771--16564825 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
16564761 TTTCTTTGCT
* * *
16564771 TTTCTTCTTTTTGAGTGCTGGAT
1 TTTCTTTTTTTTGAGTGCTGCAA
* *
16564794 TTTTTTTTTTTTGGAGTGCTTCAA
1 TTTCTTTTTTTT-GAGTGCTGCAA
16564818 TTTCTTTT
1 TTTCTTTT
16564826 CTGATTTTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.09, C:0.11, G:0.16, T:0.64
Consensus pattern (23 bp):
TTTCTTTTTTTTGAGTGCTGCAA
Found at i:16568341 original size:21 final size:21
Alignment explanation
Indices: 16568302--16568341 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16568292 ATGCATCCTT
* * *
16568302 ATTAGCTCATAGACTTTATAC
1 ATTAGCTCACACACATTATAC
16568323 ATTAGCTCACACACATTAT
1 ATTAGCTCACACACATTAT
16568342 GAGATGATAT
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:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (21 bp):
ATTAGCTCACACACATTATAC
Found at i:16568761 original size:34 final size:34
Alignment explanation
Indices: 16568723--16568789 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
16568713 GGCTAGGAAG
16568723 CTTATTCACAAACAACCCATTGCTTGCTAGCTAA
1 CTTATTCACAAACAACCCATTGCTTGCTAGCTAA
* * *
16568757 CTTATTCATAAACAGCCCCTTGCTTGCTAGCTA
1 CTTATTCACAAACAACCCATTGCTTGCTAGCTA
16568790 GCTACACACC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.31
Consensus pattern (34 bp):
CTTATTCACAAACAACCCATTGCTTGCTAGCTAA
Found at i:16581474 original size:17 final size:17
Alignment explanation
Indices: 16581452--16581487 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
16581442 AAGAGATGTA
16581452 TTCTCTCATAAGGGCAC
1 TTCTCTCATAAGGGCAC
16581469 TTCTCTCATAAGGGCAC
1 TTCTCTCATAAGGGCAC
16581486 TT
1 TT
16581488 GAAGTTTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (17 bp):
TTCTCTCATAAGGGCAC
Done.