Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 45 of 120
Found at i:12143200 original size:35 final size:35
Alignment explanation
Indices: 12143154--12143221 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
12143144 TGGAGCAGAC
*
12143154 AAAAGAAACCAATCCTATCTCTCTGAAGTTGCAAT
1 AAAAGAAACCAATCCTATCTCTCTAAAGTTGCAAT
12143189 AAAAGAAACCAATCCTATCTCTCTAAAGTTGCA
1 AAAAGAAACCAATCCTATCTCTCTAAAGTTGCA
12143222 TAGAGCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (35 bp):
AAAAGAAACCAATCCTATCTCTCTAAAGTTGCAAT
Found at i:12144817 original size:23 final size:24
Alignment explanation
Indices: 12144776--12144826 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
12144766 TGTATTTGTT
* * *
12144776 TTTAAATCTAGCATTA-TTTAATA
1 TTTAAATCTAACATAATTTTAAAA
*
12144799 TTTAAATTTAACATAATTTTAAAA
1 TTTAAATCTAACATAATTTTAAAA
12144823 TTTA
1 TTTA
12144827 TCATTAGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
TTTAAATCTAACATAATTTTAAAA
Found at i:12155738 original size:39 final size:39
Alignment explanation
Indices: 12155679--12155788 Score: 166
Period size: 39 Copynumber: 2.8 Consensus size: 39
12155669 TTAGTAGAAA
12155679 ACTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCC
1 ACTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCC
* * *
12155718 ACTGTTGTACTTCGGCACCCCTGATCACACTTACGTGCC
1 ACTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCC
* * *
12155757 CCTGTTGTACTTCGGTACTCCTGATAGCACTT
1 ACTGTTGTACTTCGGTACCCCTGATCGCACTT
12155789 TCGTGCCGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.32
Consensus pattern (39 bp):
ACTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCC
Found at i:12158835 original size:23 final size:23
Alignment explanation
Indices: 12158801--12158851 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12158791 TCGTTGAGCT
*
12158801 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
12158824 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
12158847 AGTAA
1 TGTAA
12158852 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:12159318 original size:3 final size:3
Alignment explanation
Indices: 12159300--12159338 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
12159290 TTTTAAATGA
12159300 TAT T-T TAT TAT T-T TAT TAT T-T TAT TAT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12159339 CTATTTAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.25
3 24 0.75
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TAT
Found at i:12159343 original size:8 final size:8
Alignment explanation
Indices: 12159300--12159335 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
12159290 TTTTAAATGA
12159300 TATTTTAT
1 TATTTTAT
12159308 TATTTTAT
1 TATTTTAT
12159316 TATTTTAT
1 TATTTTAT
12159324 TATTTTAT
1 TATTTTAT
12159332 TATT
1 TATT
12159336 ATTCTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:12159343 original size:16 final size:16
Alignment explanation
Indices: 12159300--12159344 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12159290 TTTTAAATGA
*
12159300 TATTTTATTATTTTAT
1 TATTTTACTATTTTAT
*
12159316 TATTTTATTATTTTAT
1 TATTTTACTATTTTAT
12159332 TATTATT-CTATTT
1 TATT-TTACTATTT
12159345 AGTATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 25 0.93
17 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTACTATTTTAT
Found at i:12161792 original size:15 final size:15
Alignment explanation
Indices: 12161772--12161800 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12161762 GTATTGTTGC
12161772 TTGATAACACGGTGA
1 TTGATAACACGGTGA
12161787 TTGATAACACGGTG
1 TTGATAACACGGTG
12161801 TGTGAGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:12164175 original size:36 final size:36
Alignment explanation
Indices: 12164132--12164202 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
12164122 CTCGCTTTAG
* *
12164132 GATTTGTAATTAACTTCAAATTAGGGTTTTAGGATA
1 GATTTGTAACTAACTTCAAATTAAGGTTTTAGGATA
*
12164168 GATTTGTAACTAACTTCGAATTAAGGTTTTAGGAT
1 GATTTGTAACTAACTTCAAATTAAGGTTTTAGGAT
12164203 GAAACAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (36 bp):
GATTTGTAACTAACTTCAAATTAAGGTTTTAGGATA
Found at i:12168951 original size:3 final size:3
Alignment explanation
Indices: 12168943--12168981 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
12168933 TATTAGAAGT
12168943 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
12168982 TTTGTAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:12179718 original size:2 final size:2
Alignment explanation
Indices: 12179711--12179739 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12179701 CACCCTCTGC
12179711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12179740 ATTTTCAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12188498 original size:195 final size:195
Alignment explanation
Indices: 12188161--12188548 Score: 686
Period size: 195 Copynumber: 2.0 Consensus size: 195
12188151 ATGACAATAT
*
12188161 GGATATTTTGGCCTTGTGACTTAATGAGACCATTGGATATAGTTGACATTTCATAGGATTGTGAG
1 GGATATTTTGGCCTTGTGACTTAATGAGACCATTGGATATAGTTGACATTTCATAAGATTGTGAG
* *
12188226 TTCTCATATATATGTGTTATGATATATGGGGTGATGAGGCCTAGGGACAGTCTTGGAAAGATAAG
66 TTCTCATATATATGTGTTATGATATATGAGGCGATGAGGCCTAGGGACAGTCTTGGAAAGATAAG
* *
12188291 GGAATGTGAGCCAAGCTCCATTCACTGGGATATATATGTGTGGTGTGTTGGAGAGCATTAGCTAA
131 GGAATATGAGCCAAGCTCCATTCACTGGGATATATATGTGTGGTGTGTTGGACAGCATTAGCTAA
* *
12188356 GGATATTTTGGCCTTGTGACTTAATGAGACCATTGGATATAGTTGGCATTTCATAAGATTGTGGG
1 GGATATTTTGGCCTTGTGACTTAATGAGACCATTGGATATAGTTGACATTTCATAAGATTGTGAG
* * *
12188421 TTCTCATATATATGTGTTGTGATATATGAGGCGATGAGGCCTAGGGACAGTTTTGGAGAGATAAG
66 TTCTCATATATATGTGTTATGATATATGAGGCGATGAGGCCTAGGGACAGTCTTGGAAAGATAAG
12188486 GGAATATGAGCCAAGCTCCATTCACTGGGATATATATGTGTGGTGTGTTGGACAGCATTAGCT
131 GGAATATGAGCCAAGCTCCATTCACTGGGATATATATGTGTGGTGTGTTGGACAGCATTAGCT
12188549 TTATGTTTCG
Statistics
Matches: 183, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 183 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (195 bp):
GGATATTTTGGCCTTGTGACTTAATGAGACCATTGGATATAGTTGACATTTCATAAGATTGTGAG
TTCTCATATATATGTGTTATGATATATGAGGCGATGAGGCCTAGGGACAGTCTTGGAAAGATAAG
GGAATATGAGCCAAGCTCCATTCACTGGGATATATATGTGTGGTGTGTTGGACAGCATTAGCTAA
Found at i:12191502 original size:14 final size:13
Alignment explanation
Indices: 12191479--12191521 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
12191469 TAATATTTGA
12191479 TTTATTATTTTAT
1 TTTATTATTTTAT
12191492 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
12191505 TTTAATTTATTTTAT
1 TTT-A-TTATTTTAT
12191520 TT
1 TT
12191522 GACTTGGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 12 0.46
14 7 0.27
15 7 0.27
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:12192489 original size:17 final size:17
Alignment explanation
Indices: 12192463--12192499 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12192453 GAATTCACCA
12192463 TTTGGAGAACTCTAAGG
1 TTTGGAGAACTCTAAGG
* *
12192480 TTTGGTGAACTCTAGGG
1 TTTGGAGAACTCTAAGG
12192497 TTT
1 TTT
12192500 AAAAGACTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (17 bp):
TTTGGAGAACTCTAAGG
Found at i:12202673 original size:24 final size:24
Alignment explanation
Indices: 12202645--12202690 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12202635 ATCATTTTTT
* *
12202645 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
12202669 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
12202691 GGAATGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:12207941 original size:15 final size:15
Alignment explanation
Indices: 12207921--12207952 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
12207911 GGGTATTACA
12207921 AACCCGATGTATGTC
1 AACCCGATGTATGTC
12207936 AACCCGATGTATGTC
1 AACCCGATGTATGTC
12207951 AA
1 AA
12207953 ACAAATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (15 bp):
AACCCGATGTATGTC
Found at i:12214288 original size:36 final size:35
Alignment explanation
Indices: 12214241--12214360 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 35
12214231 CCGAATATGC
*
12214241 CAATAGCATGTTTTTGATCTATTAAACTATATGTG
1 CAATAGTATGTTTTTGATCTATTAAACTATATGTG
* * * * * * *
12214276 CAATTAGTATG-TTATGATATGTTTTATCTAAATATG
1 CAA-TAGTATGTTTTTGATCT-ATTAAACTATATGTG
* *
12214312 CCAATAGCATGTTTTTGATCTGTTAAACTATATGTG
1 -CAATAGTATGTTTTTGATCTATTAAACTATATGTG
*
12214348 GAACTAGTATGTT
1 CAA-TAGTATGTT
12214361 CTGATTTGTT
Statistics
Matches: 62, Mismatches: 18, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
35 12 0.19
36 40 0.65
37 10 0.16
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (35 bp):
CAATAGTATGTTTTTGATCTATTAAACTATATGTG
Found at i:12214356 original size:72 final size:72
Alignment explanation
Indices: 12214234--12214376 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
12214224 GTGATGGCCG
*
12214234 AATATGCCAATAGCATGTTTTTGATCTATTAAACTATATGTGCAATTAGTATGTTATGATATGTT
1 AATATGCCAATAGCATGTTTTTGATCTATTAAACTATATGTGCAACTAGTATGTTATGATATGTT
*
12214299 TTATCTA
66 TAATCTA
* * * *
12214306 AATATGCCAATAGCATGTTTTTGATCTGTTAAACTATATGTGGAACTAGTATGTTCTGATTTGTT
1 AATATGCCAATAGCATGTTTTTGATCTATTAAACTATATGTGCAACTAGTATGTTATGATATGTT
12214371 TAATCT
66 TAATCT
12214377 GCATATAGGC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (72 bp):
AATATGCCAATAGCATGTTTTTGATCTATTAAACTATATGTGCAACTAGTATGTTATGATATGTT
TAATCTA
Found at i:12222046 original size:30 final size:29
Alignment explanation
Indices: 12222010--12222071 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 29
12222000 AATGTGAAAC
12222010 TGTTATGGCTTTGGTGTAATTCAAAATTTA
1 TGTTATGGCTTTGGTGTAATTC-AAATTTA
12222040 TGTTATGGCTTTGGTGTAATTCAAATTTA
1 TGTTATGGCTTTGGTGTAATTCAAATTTA
12222069 TGT
1 TGT
12222072 GGTCAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.48
Consensus pattern (29 bp):
TGTTATGGCTTTGGTGTAATTCAAATTTA
Found at i:12223485 original size:25 final size:26
Alignment explanation
Indices: 12223446--12223508 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
12223436 GTGAAATATA
* *
12223446 ATAAATATTTATGTATATATATAAATT
1 ATAAA-ATGTATGTACATATATAAATT
* **
12223473 AT-AAATGTATGTACATCTATGTATT
1 ATAAAATGTATGTACATATATAAATT
12223498 ATAAAATGTAT
1 ATAAAATGTAT
12223509 ATAAGTATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 18 0.60
26 10 0.33
27 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (26 bp):
ATAAAATGTATGTACATATATAAATT
Found at i:12223808 original size:3 final size:3
Alignment explanation
Indices: 12223790--12223836 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
12223780 TAAATACGAA
* *
12223790 AAT ATT AAT GAT 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
12223837 CATCAAACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12224666 original size:17 final size:18
Alignment explanation
Indices: 12224644--12224683 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12224634 AAAAAACAAT
*
12224644 AATAAAAATAAAGA-TAA
1 AATAAAAAGAAAGATTAA
*
12224661 AATAAATAGAAAGATTAA
1 AATAAAAAGAAAGATTAA
12224679 AATAA
1 AATAA
12224684 GAAAAACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAAAAAGAAAGATTAA
Found at i:12226333 original size:159 final size:159
Alignment explanation
Indices: 12226044--12226334 Score: 422
Period size: 159 Copynumber: 1.8 Consensus size: 159
12226034 CGATAGCAAA
* * *
12226044 GAGATAGGATTCGCTACCTTCAACTTTAATCGGCTCCACTTCAGCTTTAATCAATTCCACTGCAA
1 GAGATAAGATTCGCTACCTTCAACTTTAATCGACTCCACTTCAGCTTTAATCAATTCCACTACAA
* ** *
12226109 CACCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCGCTACAACGTCAAGGAAATAA
66 CACCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCAACTACAACGCCAAGGAAATAA
12226174 GACTTGCTGCTATTATTCTTAACGCCAGG
131 GACTTGCTGCTATTATTCTTAACGCCAGG
* * * * * *
12226203 GAGATAAGATTCGCTGCCTTCAGCTTTAATCTACTCCGCTTTAGCTTTAATCTATTCCACTACAA
1 GAGATAAGATTCGCTACCTTCAACTTTAATCGACTCCACTTCAGCTTTAATCAATTCCACTACAA
* * *
12226268 CGCCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCAACTACCATGCC-AGAGAAATA
66 CACCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCAACTACAACGCCAAG-GAAATA
12226332 AGA
130 AGA
12226335 TTCGCTATTG
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
158 2 0.02
159 113 0.98
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (159 bp):
GAGATAAGATTCGCTACCTTCAACTTTAATCGACTCCACTTCAGCTTTAATCAATTCCACTACAA
CACCAAGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCAACTACAACGCCAAGGAAATAA
GACTTGCTGCTATTATTCTTAACGCCAGG
Found at i:12226335 original size:51 final size:51
Alignment explanation
Indices: 12226241--12226364 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 51
12226231 ATCTACTCCG
*
12226241 CTTTAGCTTTAATCTATTCCACTACAACGCCAAGGAAACAAGATTCGCTAC
1 CTTTAGCTTTAATCTATTCAACTACAACGCCAAGGAAACAAGATTCGCTAC
* * * *
12226292 CTTTAGCTTTAATCTGTTCAACTACCATGCC-AGAGAAATAAGATTCGCTA-
1 CTTTAGCTTTAATCTATTCAACTACAACGCCAAG-GAAACAAGATTCGCTAC
* *
12226342 -TTGTAGCTTCAATCTATTTAACT
1 CTT-TAGCTTTAATCTATTCAACT
12226365 GCAATGTCGG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
49 2 0.03
50 19 0.30
51 42 0.67
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (51 bp):
CTTTAGCTTTAATCTATTCAACTACAACGCCAAGGAAACAAGATTCGCTAC
Found at i:12226385 original size:50 final size:50
Alignment explanation
Indices: 12226331--12226606 Score: 329
Period size: 50 Copynumber: 5.5 Consensus size: 50
12226321 CCAGAGAAAT
* *
12226331 AAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * ** * * * *
12226381 AAGATTCACTGTTGTAGCTTCAATTTGTTCCACTACACTG-CTAGTGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
*
12226431 AAGATTTGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* ** * ** * * *
12226481 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGAGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
*
12226531 AAGATTCACTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
*
12226581 AAGATTCGCTATTGTAGCTTCAATCT
1 AAGATTCGCTGTTGTAGCTTCAATCT
12226607 GTTCCGCTGC
Statistics
Matches: 181, Mismatches: 43, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
49 1 0.01
50 179 0.99
51 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (50 bp):
AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
Found at i:12226435 original size:100 final size:100
Alignment explanation
Indices: 12226295--12226611 Score: 501
Period size: 100 Copynumber: 3.2 Consensus size: 100
12226285 TCGCTACCTT
* * * *
12226295 TAGCTTTAATCTGTTCAACTAC-CATGCCAGAGAAATAAGATTCGCTATTGTAGCTTCAATCTAT
1 TAGCTTCAATCTGTTCCACTACAC-TGCCAGAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTAT
* *
12226359 TTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTG
65 TTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* * * *
12226395 TAGCTTCAATTTGTTCCACTACACTGCTAGTGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATT
1 TAGCTTCAATCTGTTCCACTACACTGCCAGAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATT
12226460 TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
66 TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* *
12226495 TAGCTTCAATCTGTTCCACTACACCGCCAGAGAAGTAAGATTCACTGTTGTAGCTTCAATCTATT
1 TAGCTTCAATCTGTTCCACTACACTGCCAGAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATT
*
12226560 TAACTGCAATGTCAGGGAAGCAAGATTCGCTATTG
66 TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
12226595 TAGCTTCAATCTGTTCC
1 TAGCTTCAATCTGTTCC
12226612 GCTGCGACTT
Statistics
Matches: 199, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 198 0.99
101 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (100 bp):
TAGCTTCAATCTGTTCCACTACACTGCCAGAGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATT
TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
Found at i:12226585 original size:150 final size:150
Alignment explanation
Indices: 12226244--12226606 Score: 361
Period size: 150 Copynumber: 2.4 Consensus size: 150
12226234 TACTCCGCTT
* * * * * * * *
12226244 TAGCTTTAATCTATTCCACTACAACGCCAAGGAAACAAGATTCGCTACCTT-TAGCTTTAATCTG
1 TAGCTTCAATCTATTCAACTACAATGCTAGGGAAGCAAGATTCGCTA--TTGTAGCTTCAATCTA
* * * * * ** * * * *
12226308 TTCAACTACCATGCCAGAGAAATAAGATTCGCTATTGTAGCTTCAATCTATTTAACTGCAATGTC
64 TTTAACTGCAATGTCAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCTATTCAACTACAACGCC
* *
12226373 GGGGAAGCAAGATTCACTGTTG
129 AGAGAAGCAAGATTCACTGTTG
* * * * * * * *
12226395 TAGCTTCAATTTGTTCCACTACACTGCTAGTGAAGTAAGATTTGCTGTTGTAGCTTCAATCTATT
1 TAGCTTCAATCTATTCAACTACAATGCTAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCTATT
* * * *
12226460 TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCAG
66 TAACTGCAATGTCAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCTATTCAACTACAACGCCAG
*
12226525 AGAAGTAAGATTCACTGTTG
131 AGAAGCAAGATTCACTGTTG
* *
12226545 TAGCTTCAATCTATTTAACTGCAATG-TCAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCT
1 TAGCTTCAATCTATTCAACTACAATGCT-AGGGAAGCAAGATTCGCTATTGTAGCTTCAATCT
12226607 GTTCCGCTGC
Statistics
Matches: 168, Mismatches: 42, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
149 3 0.02
150 130 0.77
151 35 0.21
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (150 bp):
TAGCTTCAATCTATTCAACTACAATGCTAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCTATT
TAACTGCAATGTCAGGGAAGCAAGATTCGCTATTGTAGCTTCAATCTATTCAACTACAACGCCAG
AGAAGCAAGATTCACTGTTG
Found at i:12227870 original size:18 final size:18
Alignment explanation
Indices: 12227830--12227871 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12227820 TTGGCCTCTC
*
12227830 CTTT-TTCTTTTTTCTTT
1 CTTTCTTCTTCTTTCTTT
12227847 -TCTTCTTCTTCTTTCTTT
1 CT-TTCTTCTTCTTTCTTT
12227865 CTTTCTT
1 CTTTCTT
12227872 ATTTTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 2 0.10
18 17 0.81
19 1 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTCTTCTTCTTTCTTT
Found at i:12227879 original size:18 final size:18
Alignment explanation
Indices: 12227837--12227879 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12227827 CTCCTTTTTC
*
12227837 TTTTTTCTTTTCTTCTTC
1 TTTTTTCTTTTCTTCTTA
*
12227855 TTCTTTC-TTTCTTTCTTA
1 TTTTTTCTTTTC-TTCTTA
12227873 TTTTTTC
1 TTTTTTC
12227880 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTTTCTTCTTA
Found at i:12233209 original size:72 final size:72
Alignment explanation
Indices: 12233058--12233200 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
12233048 TCTCAGATTT
* * * * *
12233058 AAAAAAGGGATCATGCCCAGTAAGTTATGACACGATCTTTTCTTAATTCTCAAGATCGTTTAAAA
1 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCAAGATCATTTAAAA
12233123 CTTGAGA
66 CTTGAGA
*
12233130 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGAT-TTCTTCTTAATTCCCGAGATCATTTAAA
1 AAAAAAAGGATCATGCCCAATAAGTTAGGACACGATCTT-TTCTTAATTCCCAAGATCATTTAAA
12233194 ACTTGAG
65 ACTTGAG
12233201 TTTGAAAAGA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.03
72 62 0.97
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (72 bp):
AAAAAAAGGATCATGCCCAATAAGTTAGGACACGATCTTTTCTTAATTCCCAAGATCATTTAAAA
CTTGAGA
Found at i:12233685 original size:25 final size:26
Alignment explanation
Indices: 12233655--12233708 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
12233645 AACAAATATA
*
12233655 TATGTATATATATAAATTAT-AAATG
1 TATGTACATATATAAATTATAAAATG
* **
12233680 TATGTACATCTATGTATTATAAAATG
1 TATGTACATATATAAATTATAAAATG
12233706 TAT
1 TAT
12233709 ATAAGTATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (26 bp):
TATGTACATATATAAATTATAAAATG
Found at i:12234009 original size:3 final size:3
Alignment explanation
Indices: 12233991--12234026 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
12233981 TAAATACGAA
* *
12233991 AAT ATT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12234027 GAGCCTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:12242072 original size:37 final size:37
Alignment explanation
Indices: 12242022--12242093 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
12242012 TATATTTTAT
*
12242022 AGTATTATATATT-ATAATTTTAGTAAATTCATATAAG
1 AGTATTATATATTAATAACTTTAGTAAATT-ATATAAG
*
12242059 AGTATTGAT-TATTAATAACTTTATTAAATTATATA
1 AGTATT-ATATATTAATAACTTTAGTAAATTATATA
12242094 TTTTAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 15 0.48
38 16 0.52
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
AGTATTATATATTAATAACTTTAGTAAATTATATAAG
Found at i:12242110 original size:16 final size:16
Alignment explanation
Indices: 12242089--12242134 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12242079 TTATTAAATT
12242089 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
12242105 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
12242120 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
12242135 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:12242143 original size:107 final size:108
Alignment explanation
Indices: 12242029--12242239 Score: 361
Period size: 107 Copynumber: 2.0 Consensus size: 108
12242019 TATAGTATTA
* * * *
12242029 TATATTATAATTTTAGTAAATTCATATAAGAGTATTGATTATTAATAACTTTATTAAATTATATA
1 TATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAACTTTATTAAATTATATA
12242094 TTTTAATTATAATATATTTAATAATAATTATG-TTAAATTATC
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
* *
12242136 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAACTTTATTAAATTATATA
12242201 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
12242240 ATGATTAAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
107 91 0.94
108 6 0.06
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (108 bp):
TATATTATAATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAACTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
Found at i:12242217 original size:16 final size:16
Alignment explanation
Indices: 12242196--12242237 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12242186 TTATTAAATT
*
12242196 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12242212 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12242227 AT-TATGTTTAA
1 ATATAT-TTTAA
12242238 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12242222 original size:15 final size:15
Alignment explanation
Indices: 12242187--12242228 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12242177 TTAAGAATTT
*
12242187 TATTAAATTAT-ATA
1 TATTTAATTATAATA
12242201 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
12242215 TATTTAATAATAAT
1 TATTTAATTATAAT
12242229 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:12242408 original size:39 final size:40
Alignment explanation
Indices: 12242365--12242469 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
12242355 TTCCATTATG
12242365 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
12242404 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
12242449 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
12242470 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:12242463 original size:45 final size:44
Alignment explanation
Indices: 12242363--12242472 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
12242353 TTTTCCATTA
12242363 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
12242402 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
12242447 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
12242473 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:12242472 original size:16 final size:16
Alignment explanation
Indices: 12242453--12242504 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
12242443 GATTTGCTAT
* *
12242453 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
12242469 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12242485 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12242501 TACA
1 TACA
12242505 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12243048 original size:14 final size:14
Alignment explanation
Indices: 12243029--12243069 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12243019 CTAGTTTCCA
*
12243029 GTTTAGAATTTATT
1 GTTTAGGATTTATT
*
12243043 GTTTAGGATTTAAT
1 GTTTAGGATTTATT
*
12243057 GCTTAGGATTTAT
1 GTTTAGGATTTAT
12243070 ATTGAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (14 bp):
GTTTAGGATTTATT
Found at i:12246520 original size:39 final size:39
Alignment explanation
Indices: 12246432--12246601 Score: 162
Period size: 39 Copynumber: 4.4 Consensus size: 39
12246422 CATATTCACT
* * * * *
12246432 TTTAAGCATATATCCTATTACACATATAATCACCTAACA
1 TTTAAGCATATATCATAATACTCAAATAATCACATAACA
*** *
12246471 TACCATCATATATCATAATACTCAAATAATCACATAACA
1 TTTAAGCATATATCATAATACTCAAATAATCACATAACA
* ** *
12246510 TTTAAGCATATATCACAATACTTTTAA-ACTCACATAACA
1 TTTAAGCATATATCATAATAC-TCAAATAATCACATAACA
** *
12246549 TTTAAGCATATATCATAATACTCGTATAATCGCATAACA
1 TTTAAGCATATATCATAATACTCAAATAATCACATAACA
* *
12246588 TTCAAGAATATATC
1 TTTAAGCATATATC
12246602 CCAATATTCA
Statistics
Matches: 104, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
38 2 0.02
39 99 0.95
40 3 0.03
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCATAATACTCAAATAATCACATAACA
Found at i:12246522 original size:78 final size:77
Alignment explanation
Indices: 12246432--12246607 Score: 183
Period size: 78 Copynumber: 2.2 Consensus size: 77
12246422 CATATTCACT
* * * *
12246432 TTTAAGCATATATCCTATTACACATATAA-TCACCTAACATACCATCATATATCATAATACTCAA
1 TTTAAGCATATATCC-AATACACATA-AACTCACATAACATACAAGCATATATCATAATACTCAA
12246496 ATAATCACATAACA
64 ATAATCACATAACA
*** ** **
12246510 TTTAAGCATATATCACAATACTTTTAAACTCACATAACATTTAAGCATATATCATAATACTCGTA
1 TTTAAGCATATATC-CAATACACATAAACTCACATAACATACAAGCATATATCATAATACTCAAA
*
12246575 TAATCGCATAACA
65 TAATCACATAACA
* *
12246588 TTCAAGAATATATCCCAATA
1 TTTAAGCATATAT-CCAATA
12246608 TTCAAAAACA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
77 2 0.02
78 77 0.95
79 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (77 bp):
TTTAAGCATATATCCAATACACATAAACTCACATAACATACAAGCATATATCATAATACTCAAAT
AATCACATAACA
Found at i:12246525 original size:22 final size:22
Alignment explanation
Indices: 12246499--12246563 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
12246489 TACTCAAATA
12246499 ATCACATAACATTTAAGCATAT
1 ATCACATAACATTTAAGCATAT
*
12246521 ATCACA-ATAC-TTTTA--A-A-
1 ATCACATA-ACATTTAAGCATAT
*
12246538 CTCACATAACATTTAAGCATAT
1 ATCACATAACATTTAAGCATAT
12246560 ATCA
1 ATCA
12246564 TAATACTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 7 0.22
18 6 0.19
19 1 0.03
20 1 0.03
21 6 0.19
22 11 0.34
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (22 bp):
ATCACATAACATTTAAGCATAT
Found at i:12251386 original size:25 final size:26
Alignment explanation
Indices: 12251352--12251425 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
12251342 TTTCTCACCC
* * *
12251352 CAATTTTACCCC-AGTAAGATTTTGA
1 CAATTTTACCCCTAATAAAATTTTAA
12251377 CAATTTTACCCCTAATAAAATTTTAA
1 CAATTTTACCCCTAATAAAATTTTAA
* *
12251403 CGATTTTACCCCCAATAAAATTT
1 CAATTTTACCCCTAATAAAATTT
12251426 CAAGAAAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 12 0.28
26 31 0.72
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.36
Consensus pattern (26 bp):
CAATTTTACCCCTAATAAAATTTTAA
Found at i:12251621 original size:35 final size:36
Alignment explanation
Indices: 12251513--12251621 Score: 211
Period size: 36 Copynumber: 3.1 Consensus size: 36
12251503 AAACAGTCCG
12251513 AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
1 AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
12251549 AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
1 AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
12251585 AAAACATAAACTCATTCTTCCATCA-TTTTTTAAGT
1 AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
12251620 AA
1 AA
12251622 TCCTATATAG
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
35 12 0.16
36 61 0.84
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (36 bp):
AAAACATAAACTCATTCTTCCATCATTTTTTTAAGT
Found at i:12265569 original size:20 final size:20
Alignment explanation
Indices: 12265546--12265595 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
12265536 CATGGACACT
12265546 GAAGTGTATACAGAGGCACC
1 GAAGTGTATACAGAGGCACC
* *
12265566 GAAGTGCAAACAGAGGCACC
1 GAAGTGTATACAGAGGCACC
12265586 GAAGTGTATA
1 GAAGTGTATA
12265596 TCTCGTACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.30, T:0.14
Consensus pattern (20 bp):
GAAGTGTATACAGAGGCACC
Found at i:12280542 original size:18 final size:18
Alignment explanation
Indices: 12280519--12280571 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
12280509 TTCAGTGGAG
12280519 ACAAAAAAAACCAAAA-AC
1 ACAAAAAAAA-CAAAAGAC
*
12280537 ACAAAAAAAGAACAAAAGAG
1 AC-AAAAAA-AACAAAAGAC
12280557 ACAAAAAAAACAAAA
1 ACAAAAAAAACAAAA
12280572 CAAAAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 9 0.29
19 17 0.55
20 5 0.16
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (18 bp):
ACAAAAAAAACAAAAGAC
Found at i:12280543 original size:9 final size:9
Alignment explanation
Indices: 12280519--12280576 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
12280509 TTCAGTGGAG
12280519 ACAAAAAAA
1 ACAAAAAAA
* *
12280528 ACCAAAAAC
1 ACAAAAAAA
12280537 ACAAAAAAAGA
1 AC-AAAAAA-A
* *
12280548 ACAAAAGAG
1 ACAAAAAAA
12280557 ACAAAAAAA
1 ACAAAAAAA
12280566 ACAAAACAAA
1 ACAAAA-AAA
12280576 A
1 A
12280577 AACCTCTACA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
9 22 0.58
10 14 0.37
11 2 0.05
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:12280560 original size:20 final size:19
Alignment explanation
Indices: 12280516--12280571 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
12280506 CGGTTCAGTG
*
12280516 GAGACAAAAAAAACCAAAA
1 GAGACAAAAAAAAACAAAA
*
12280535 -ACACAAAAAAAGAACAAAA
1 GAGACAAAAAAA-AACAAAA
12280554 GAGAC-AAAAAAAACAAAA
1 GAGACAAAAAAAAACAAAA
12280572 CAAAAAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 17 0.53
19 12 0.38
20 3 0.09
ACGTcount: A:0.77, C:0.14, G:0.09, T:0.00
Consensus pattern (19 bp):
GAGACAAAAAAAAACAAAA
Found at i:12282149 original size:44 final size:43
Alignment explanation
Indices: 12282096--12282278 Score: 233
Period size: 43 Copynumber: 4.2 Consensus size: 43
12282086 GCGTGAAATA
* * *
12282096 GATCGAAGATAGTAGGTCCTGTCTTCCTATATTGGTAGGAAGTG
1 GATCGAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGGAAGTG
* * **
12282140 GATCAAAGATGCAGATCTTGTTTTCCTATATTGGTAAAAAGTG
1 GATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGGAAGTG
* *
12282183 GATCAAAGATGCAGATCTTGTTTTCCTATATTGGTAGGAAGTG
1 GATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGGAAGTG
* *
12282226 GATCGAAGATGCAGATCTTGTCTTCCCATACTGGT-GGCAAAGTG
1 GATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGG--AAGTG
12282270 GATCGAAGA
1 GATCGAAGA
12282279 AAACAGATCT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 2 0.02
43 99 0.80
44 23 0.19
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.31
Consensus pattern (43 bp):
GATCGAAGATGCAGATCTTGTCTTCCTATATTGGTAGGAAGTG
Found at i:12282543 original size:26 final size:26
Alignment explanation
Indices: 12282507--12282558 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12282497 AATTAAAAAG
12282507 ATTGAAGCCGCAACAGTGAATCTTAC
1 ATTGAAGCCGCAACAGTGAATCTTAC
12282533 ATTGAAGCCGCAACAGTGAATCTTAC
1 ATTGAAGCCGCAACAGTGAATCTTAC
12282559 TTCCTTGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (26 bp):
ATTGAAGCCGCAACAGTGAATCTTAC
Found at i:12282858 original size:43 final size:43
Alignment explanation
Indices: 12282809--12283485 Score: 181
Period size: 44 Copynumber: 15.4 Consensus size: 43
12282799 TCTAAGATTA
* *
12282809 CAGTGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
* * * *
12282852 CAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGT--AGTTC-TATCTCCCTGAGCAG
* * * ** * * * *
12282896 TAGTGGAGCAGATCGAAGATAACGGA-TTTTACCTCCCTGAG-ATTA
1 CAGTGGAGTAGATTGAAG-CCA-GTAGTTCTATCTCCCTGAGCA--G
* * *
12282941 CAGTGGAGTACATTGAAGCCAGCAGTTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
* * * * *
12282984 TAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGT--AGTTC-TATCTCCCTGAGCAG
* * * *** ** * * *
12283028 TAGTGAAGTAGATCGAAGATGGCGGATTTTACCTCCCTGAG-ATTA
1 CAGTGGAGTAGATTGAAGCCAGTAG-TTCTATCTCCCTGAGCA--G
* * * *
12283073 CAGTGGAGTACATTGAAGCCAGTAGTTCTATCTTCCTGAGAAA
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
* * * * * *
12283116 CAGTGGAATAGATTGAAAACCA-CAGATCTTATCTCCCTAAACAG
1 CAGTGGAGTAGATTG-AAGCCAGTAGTTC-TATCTCCCTGAGCAG
* * * * * * * *
12283160 TAGTGAAGCAGATCGAAGATGGCA-TA-TTTTACCTCCCTGAG-ATTA
1 CAGTGGAGTAGATTG-A-A-GCCAGTAGTTCTATCTCCCTGAGCA--G
* * * *
12283205 CAGTGGAGTACATTGAAGCTAGTAGTTCTATCTTCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
* * * *
12283248 TAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCT-AGGCAG
1 CAGTGGAGTAGATTGAAGCCAGT--AGTTC-TATCTCCCTGA-GCAG
* * * * * * *
12283292 TAATGGAGCAGATCGAAG--ATGTCAGATTTTACCTCCCTGAG-ATTA
1 CAGTGGAGTAGATTGAAGCCA-GT-AG-TTCTATCTCCCTGAGCA--G
* *
12283337 CAGTGGAGTACATTGAAGCCAGTAG-CCTCATCTCCCTGAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCT-ATCTCCCTGAGCAG
* * * * * *
12283380 CAGTGGAGTAGGTCGAAG--ATGACAGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCA-G-TAG-TTCTATCTCCCTGA-G-CAG
* *
12283425 CAGTGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
* *
12283468 CAGTAGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
12283486 ATTACAGATC
Statistics
Matches: 443, Mismatches: 140, Indels: 102
0.65 0.20 0.15
Matches are distributed among these distances:
41 6 0.01
42 4 0.01
43 119 0.27
44 218 0.49
45 85 0.19
46 8 0.02
47 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
CAGTGGAGTAGATTGAAGCCAGTAGTTCTATCTCCCTGAGCAG
Found at i:12282914 original size:132 final size:132
Alignment explanation
Indices: 12282747--12283417 Score: 1020
Period size: 132 Copynumber: 5.1 Consensus size: 132
12282737 AACCACCAAA
* *
12282747 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTAAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
12282812 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
12282877 AT
131 AT
**
12282879 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAACGGATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* *
12282944 TGGAGTACATTGAAGCCAGCAGTTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
12283009 AT
131 AT
* *
12283011 CTTATCTCCCTAAGCAGTAGTGAAGTAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* * * * * **
12283076 TGGAGTACATTGAAGCCAGTAGTTCTATCTTCCTGAGAAACAGTGGAATAGATTGAAAACCACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
12283141 AT
131 AT
* * **
12283143 CTTATCTCCCTAAACAGTAGTGAAGCAGATCGAAGATGGCATATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* * *
12283208 TGGAGTACATTGAAGCTAGTAGTTCTATCTTCCTGGGCAGTAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
12283273 AT
131 AT
* * * *
12283275 CTTATCTCCCTAGGCAGTAATGGAGCAGATCGAAGATGTCAGATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* * * * * *
12283340 TGGAGTACATTGAAGCCAGTAG-CCTCATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATGACA
66 TGGAGTACATTGAAGCCAGTAGTTCT-ATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACA
12283404 GAT
130 GAT
* *
12283407 TTTACCTCCCT
1 CTTATCTCCCT
12283418 GAGGTTACAG
Statistics
Matches: 490, Mismatches: 48, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
131 2 0.00
132 488 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (132 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
AT
Found at i:12282973 original size:88 final size:88
Alignment explanation
Indices: 12282881--12283285 Score: 246
Period size: 88 Copynumber: 4.6 Consensus size: 88
12282871 TTACAGATCT
* *
12282881 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAACGGATTTTACCTCCCTGAGATTACAGTG
1 TATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCTGAGATTACAGTG
12282946 GAGTACATTGAAGCCAGCAGTTC
66 GAGTACATTGAAGCCAGCAGTTC
* ** * * * * * *
12282969 TATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT--AGT
1 TATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCTGAG-ATTACAGT
* * * *** * *
12283032 GAAGTAGATCGAAGATGGCGGATTT
65 GGAGTACATTGAAGCCAGCAG-TTC
* * * * * ** ** * * * *
12283057 TACCTCCCTGAG-ATTACAGTGGAGTACATTGAAGCCAGTAG-TTCTATCTTCCTGAGA-AACAG
1 TATCTCCCTGAGCAGT--AGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCTGAGATTACAG
* * * *
12283119 TGGAATAGATTGAAAACCA-CAGATC
64 TGGAGTACATTG-AAGCCAGCAGTTC
* * * ** *
12283144 TTATCTCCCTAAACAGTAGTGAAGCAGATCGAAGATGGCATATTTTACCTCCCTGAGATTACAGT
1 -TATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCTGAGATTACAGT
* *
12283209 GGAGTACATTGAAGCTAGTAGTTC
65 GGAGTACATTGAAGCCAGCAGTTC
* * ** * * * *
12283233 TATCTTCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT
1 TATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCT
12283286 AGGCAGTAAT
Statistics
Matches: 225, Mismatches: 80, Indels: 24
0.68 0.24 0.07
Matches are distributed among these distances:
87 36 0.16
88 148 0.66
89 41 0.18
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (88 bp):
TATCTCCCTGAGCAGTAGTGGAGCAGATCGAAGATAACAGATTTTACCTCCCTGAGATTACAGTG
GAGTACATTGAAGCCAGCAGTTC
Found at i:12283399 original size:88 final size:88
Alignment explanation
Indices: 12283277--12283505 Score: 291
Period size: 88 Copynumber: 2.6 Consensus size: 88
12283267 TTACAGATCT
* * *
12283277 TATCTCCCT-AGGCAGTAATGGAGCAGATCGAAGATGTCAGATTTTACCTCCCTGAGATTACAGT
1 TATCTCCCTGA-GCAGCAGTGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGATTACAGT
12283341 GGAGTACATTGAAGCCAGTAGC-C
65 GGAGTACATTGAAGCCAGTAGCTC
* * *
12283364 TCATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATGACAGATTTTACCTCCCTGAGGTTACAGT
1 T-ATCTCCCTGAGCAGCAGTGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGATTACAGT
*
12283429 GGAGTACATTGAAGCCAGTAGTTC
65 GGAGTACATTGAAGCCAGTAGCTC
* * ** * * * *
12283453 TATCTCCCTGGGCAGCAGTAGAATAGATTGAAGATTACAGATCTTATCTCCCT
1 TATCTCCCTGAGCAGCAGTGGAGCAGATCGAAGATGACAGATTTTACCTCCCT
12283506 AGGCAGTAGT
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
87 1 0.01
88 120 0.97
89 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTGGAGCAGATCGAAGATGACAGATTTTACCTCCCTGAGATTACAGTG
GAGTACATTGAAGCCAGTAGCTC
Found at i:12283513 original size:264 final size:260
Alignment explanation
Indices: 12282747--12283559 Score: 935
Period size: 264 Copynumber: 3.1 Consensus size: 260
12282737 AACCACCAAA
* *
12282747 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCTCTAAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* *
12282812 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATCACAG
* * * ** *
12282877 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAACGGATTTTACCTCCCTGAGATTAC
131 ATCTTATCTCCCTAGGTA-CAGTGGAGCAGATCGAAG-CCA-GTATTTTACCTCCCTGAGA-TAC
*
12282942 AGTGGAGTACATTGAAGCCAGCAGTTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTAC
192 AGTGGAGTACATTGAAGCTAGCAGTTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTAC
12283007 AGAT
257 AGAT
* *
12283011 CTTATCTCCCTAAGCAGTAGTGAAGTAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* * * * *
12283076 TGGAGTACATTGAAGCCAGTAGTTCTATCTTCCTGAGAAACAGTGGAATAGATTGAAAACCACAG
66 TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATCACAG
* *
12283141 ATCTTATCTCCCTA--AACAGTAGTGAAGCAGATCGAAGATGGCA-TATTTTACCTCCCTGAGAT
131 ATCTTATCTCCCTAGGTACAGT-G-G-AGCAGATCG-A-A-GCCAGTATTTTACCTCCCTGAGA-
* *
12283203 TACAGTGGAGTACATTGAAGCTAGTAGTTCTATCTTCCTGGGCAGTAGTGGAATAGATTGAAGAT
189 TACAGTGGAGTACATTGAAGCTAGCAGTTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGAT
12283268 TACAGAT
254 TACAGAT
* * * *
12283275 CTTATCTCCCTAGGCAGTAATGGAGCAGATCGAAGATGTCAGATTTTACCTCCCTGAGATTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
* * * * *
12283340 TGGAGTACATTGAAGCCAGTAG-CCTCATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAGATGACA
66 TGGAGTACATTGAAGCCAGTAGTTCT-ATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATCACA
* * * * * * * * *
12283404 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGGGCA-G
130 GATCTTATCTCCCT-AGG-TACAGTGGAGCAGATCGAAGCCAGTA-TTTTACCTCCCTGAG-ATA
* * * * * * ** * *
12283468 CAGTAGAATAGATTGAAGATTA-CAGATCTTATCTCCCTAGGCAGTAGTGGAGCAGATCG--CAT
191 CAGTGGAGTACATTGAAG-CTAGCAGTTC-TATCTCCCTGGGCAGTAGTGGAATAGATTGAAGAT
*
12283530 CA-AG-T
254 TACAGAT
12283535 CTTATCTCCCTAAGCAGTAGTGGAG
1 CTTATCTCCCTAAGCAGTAGTGGAG
12283560 TAGACGGAAA
Statistics
Matches: 472, Mismatches: 61, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
260 24 0.05
261 5 0.01
262 8 0.02
263 25 0.05
264 391 0.83
265 9 0.02
266 3 0.01
267 2 0.00
268 5 0.01
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (260 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGATTACAG
TGGAGTACATTGAAGCCAGTAGTTCTATCTCCCTGAGCAGCAGTGGAATAGATTGAAGATCACAG
ATCTTATCTCCCTAGGTACAGTGGAGCAGATCGAAGCCAGTATTTTACCTCCCTGAGATACAGTG
GAGTACATTGAAGCTAGCAGTTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGAT
Found at i:12285042 original size:32 final size:32
Alignment explanation
Indices: 12285001--12285064 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
12284991 GCAGCATTTT
12285001 AGGGATGGGGATTATTGCCCAGTTAGTCCCTA
1 AGGGATGGGGATTATTGCCCAGTTAGTCCCTA
12285033 AGGGATGGGGATTATTGCCCAGTTAGTCCCTA
1 AGGGATGGGGATTATTGCCCAGTTAGTCCCTA
12285065 TCTCTCTGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (32 bp):
AGGGATGGGGATTATTGCCCAGTTAGTCCCTA
Found at i:12290573 original size:43 final size:42
Alignment explanation
Indices: 12290525--12290609 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
12290515 CACTTTTACC
*
12290525 GGCGCTTGGACAAAAAACGCCAGTAAAAATCGAGCATTAGCGG
1 GGCGCTT-GACAAAAAACGCCACTAAAAATCGAGCATTAGCGG
* *** * *
12290568 GGCGCTTTATGGAAATCGCCACTAAAGATCGAGCATTAGCGG
1 GGCGCTTGACAAAAAACGCCACTAAAAATCGAGCATTAGCGG
12290610 CATTTTTTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
42 28 0.80
43 7 0.20
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (42 bp):
GGCGCTTGACAAAAAACGCCACTAAAAATCGAGCATTAGCGG
Found at i:12290652 original size:39 final size:40
Alignment explanation
Indices: 12290598--12290675 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
12290588 ACTAAAGATC
*
12290598 GAGCATTAGCGGCATTTTTT-GAAAAACGCCGCAAAAAAT
1 GAGCATTAGCGGCATTTTTTGGAAAAACGCCGAAAAAAAT
12290637 GAGCATTAGCGGCATTTTTTGGAAAAACGCCGAAAAAAA
1 GAGCATTAGCGGCATTTTTTGGAAAAACGCCGAAAAAAA
12290676 CTAAAGCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 20 0.54
40 17 0.46
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (40 bp):
GAGCATTAGCGGCATTTTTTGGAAAAACGCCGAAAAAAAT
Found at i:12290782 original size:41 final size:41
Alignment explanation
Indices: 12290732--12291071 Score: 334
Period size: 41 Copynumber: 8.3 Consensus size: 41
12290722 CATTTTCAAA
*
12290732 AAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAG
1 AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
* * * *
12290773 AATGTGCCGCTAATGCTCTGGGATTTAGCGGCGTTTTTG-G
1 AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
** * * * *
12290813 AAAAGCGTAGCTAATGCTCTGTGTTTTAGCGGCGTTTTTTAA
1 -AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
*
12290855 AAAGCGCCTCTAATGCTCGGGGTTTTAGCGGCGTTTTTG-G
1 AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
* * * *
12290895 AAAAGCGCCGCTAATGCTCTGTGTTTTAGCGGCGTTTTTTAA
1 -AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
* * * * * *
12290937 AAAGAGCAGCTAATGCTCGGTGTTTTAGTGGCATCTTTT-AA
1 AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGT-TTTTGAG
* * *
12290978 AAAGCGCTGCTAATGCT-GGAGGCTTTAGCGGCATTTTTG-G
1 AAAGCGCCGCTAATGCTCGG-GGTTTTAGCGGCGTTTTTGAG
*
12291018 AAAAGCGCCGCTAATGCT--GGGTCTTTAGCGGCGTTTTTGAA
1 -AAAGCGCCGCTAATGCTCGGGGT-TTTAGCGGCGTTTTTGAG
*
12291059 AAAGCGTCGCTAA
1 AAAGCGCCGCTAA
12291072 AAACATTTTA
Statistics
Matches: 249, Mismatches: 40, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
39 2 0.01
40 35 0.14
41 208 0.84
42 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (41 bp):
AAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCGTTTTTGAG
Found at i:12290851 original size:82 final size:82
Alignment explanation
Indices: 12290730--12291071 Score: 372
Period size: 82 Copynumber: 4.2 Consensus size: 82
12290720 AGCATTTTCA
* * * *
12290730 AAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAGAATGTGCCGCTAATGCTCTGGG
1 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGG
*
12290795 ATTTAGCGGCGTTTTTG
66 TTTTAGCGGCGTTTTTG
* * * * * * * *
12290812 GAAAAGCGTAGCTAATGCTCTGTGTTTTAGCGGCGTTTTTTAAAAAGCGCCTCTAATGCTCGGGG
1 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGG
12290877 TTTTAGCGGCGTTTTTG
66 TTTTAGCGGCGTTTTTG
* * * * * * * *
12290894 GAAAAGCGCCGCTAATGCTCTGTGTTTTAGCGGCGTTTTTTAAAAAGAGCAGCTAATGCTC-GGT
1 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGG-
* *
12290958 GTTTTAGTGGCATCTTTT-
65 GTTTTAGCGGCGT-TTTTG
* *
12290976 AAAAAGCG-CTGCTAATGCT-GGAGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATG--CTG
1 AAAAAGCGTC-GCTAATGCTCGG-GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTG
12291037 GGTCTTTAGCGGCGTTTTTG
64 GGT-TTTAGCGGCGTTTTTG
12291057 AAAAAGCGTCGCTAA
1 AAAAAGCGTCGCTAA
12291072 AAACATTTTA
Statistics
Matches: 221, Mismatches: 31, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
80 7 0.03
81 28 0.13
82 182 0.82
83 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (82 bp):
AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGG
TTTTAGCGGCGTTTTTG
Found at i:12290933 original size:123 final size:123
Alignment explanation
Indices: 12290730--12291071 Score: 469
Period size: 123 Copynumber: 2.8 Consensus size: 123
12290720 AGCATTTTCA
* * *
12290730 AAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCGTTTTT-GAGAATGTGCCGCTAATGCTCTGG
1 AAAAAGCGCCTCTAATGCTCGGGGCTTTAGCGGCGTTTTTGGA-AAAGCGCCGCTAATGCTCTGG
* * * * *
12290794 GATTTAGCGGCGTTTTTGGAAAAGCGTAGCTAATGCTCTGTGTTTTAGCGGCGTTTTTT
65 GTTTTAGCGGCGTTTTTGAAAAAGCGTAGCTAATGCTCGGTGTTTTAGCGGCATCTTTT
* *
12290853 AAAAAGCGCCTCTAATGCTCGGGGTTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGTG
1 AAAAAGCGCCTCTAATGCTCGGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGG
* * * *
12290918 TTTTAGCGGCGTTTTTTAAAAAGAGCAGCTAATGCTCGGTGTTTTAGTGGCATCTTTT
66 TTTTAGCGGCGTTTTTGAAAAAGCGTAGCTAATGCTCGGTGTTTTAGCGGCATCTTTT
*
12290976 AAAAAGCG-CTGCTAATGCT-GGAGGCTTTAGCGGCATTTTTGGAAAAGCGCCGCTAATG--CTG
1 AAAAAGCGCCT-CTAATGCTCGG-GGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTG
*
12291037 GGTCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAA
64 GGT-TTTAGCGGCGTTTTTGAAAAAGCGTAGCTAA
12291072 AAACATTTTA
Statistics
Matches: 194, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
121 5 0.03
122 31 0.16
123 156 0.80
124 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (123 bp):
AAAAAGCGCCTCTAATGCTCGGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGG
TTTTAGCGGCGTTTTTGAAAAAGCGTAGCTAATGCTCGGTGTTTTAGCGGCATCTTTT
Found at i:12291501 original size:21 final size:21
Alignment explanation
Indices: 12291413--12291501 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
12291403 GAGTTACAAT
*
12291413 TTTAAGGTTTAGGGAGTATGGG
1 TTTAAGGTTTAGGG-GTAAGGG
* ** * *
12291435 TTTAAGGATTATAGATTAGGG
1 TTTAAGGTTTAGGGGTAAGGG
* * * * *
12291456 ATTATGGTTCAAGGGT-TGGG
1 TTTAAGGTTTAGGGGTAAGGG
12291476 ATTTAAGGTTTAGGGGTAAGGG
1 -TTTAAGGTTTAGGGGTAAGGG
12291498 TTTA
1 TTTA
12291502 GGGGTTAGAC
Statistics
Matches: 46, Mismatches: 19, Indels: 5
0.66 0.27 0.07
Matches are distributed among these distances:
20 3 0.07
21 29 0.63
22 14 0.30
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.37
Consensus pattern (21 bp):
TTTAAGGTTTAGGGGTAAGGG
Found at i:12291751 original size:21 final size:20
Alignment explanation
Indices: 12291717--12291757 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
12291707 TATGGATTTA
*
12291717 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
12291737 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
12291758 ATGAGTTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:12291787 original size:22 final size:22
Alignment explanation
Indices: 12291746--12291793 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12291736 TGGGATTTAA
* *
12291746 GGTTTAGGGGTTATGAGTTATG
1 GGTTTAGGGGTTATAAGTTAGG
12291768 GGTTTAGGGGTTA-AACGTTAGG
1 GGTTTAGGGGTTATAA-GTTAGG
12291790 GGTT
1 GGTT
12291794 AAGAGTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTATAAGTTAGG
Found at i:12291788 original size:14 final size:14
Alignment explanation
Indices: 12291771--12291804 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12291761 AGTTATGGGT
12291771 TTAGGGGTTAA-ACG
1 TTAGGGGTTAAGA-G
12291785 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
12291799 TTAGGG
1 TTAGGG
12291805 ATTTAGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.41, T:0.29
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:12292289 original size:40 final size:40
Alignment explanation
Indices: 12292245--12292350 Score: 140
Period size: 42 Copynumber: 2.6 Consensus size: 40
12292235 AAAATAAAAG
* *
12292245 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTATAGATCGA
1 GCATTAGCGGCGCTTTTTAAAAAACGCCACTATAAATCGA
* *
12292285 GCATTAGCGGCGCTTCTTAAAAAAAACGCCACTATAAATTGA
1 GCATTAGCGGCGCTT-TT-TAAAAAACGCCACTATAAATCGA
*
12292327 GCTTTAGCGGCGCTATTTTAAAAA
1 GCATTAGCGGCGCT-TTTTAAAAA
12292351 TGCCGCAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
40 15 0.26
41 7 0.12
42 34 0.60
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTAAAAAACGCCACTATAAATCGA
Found at i:12295643 original size:43 final size:41
Alignment explanation
Indices: 12295555--12295696 Score: 169
Period size: 43 Copynumber: 3.3 Consensus size: 41
12295545 AAAGCATGTT
* * *
12295555 TTTAGTGGCGTTTGTGAAAAAGCGTCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTG-AAAAGCGCCGCTAAAGGTCATGATC
* *
12295597 TTTAGCGGCGTTTGTAGTATAAA-CGCCGCTAAAGGCCGTGATC
1 TTTAGCGGCGTTTGT-G-A-AAAGCGCCGCTAAAGGTCATGATC
12295640 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGT-G-AAAAGCGCCGCTAAAGGTCATGATC
*
12295683 TTTAGCGGGGTTTG
1 TTTAGCGGCGTTTG
12295697 CGTTAAAGCG
Statistics
Matches: 86, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
42 17 0.20
43 66 0.77
44 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTGTGAAAAGCGCCGCTAAAGGTCATGATC
Found at i:12302019 original size:5 final size:5
Alignment explanation
Indices: 12302009--12302044 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
12301999 TGAGCATTCG
12302009 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
12302045 AATTTTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:12303080 original size:9 final size:9
Alignment explanation
Indices: 12303066--12303102 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12303056 TATAGTTTGA
12303066 TATTCGAAT
1 TATTCGAAT
12303075 TATTCGAAT
1 TATTCGAAT
*
12303084 TATTCGAGT
1 TATTCGAAT
12303093 TATTCGAAT
1 TATTCGAAT
12303102 T
1 T
12303103 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12303173 original size:9 final size:9
Alignment explanation
Indices: 12303156--12303186 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12303146 TTGAGTTGAT
12303156 TCGAATAAC
1 TCGAATAAC
*
12303165 TCGATTAAC
1 TCGAATAAC
12303174 TCGAATAAC
1 TCGAATAAC
12303183 TCGA
1 TCGA
12303187 TTCGTTTAAC
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:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:12326151 original size:27 final size:28
Alignment explanation
Indices: 12326094--12326151 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
12326084 ATTTTTTTTA
*
12326094 ATATAATGTAATTATTTTTTAAAATTTT
1 ATATAATGTAATTATTTTTTAAAATTCT
*
12326122 ATAT-ATGTAATTATATTTTTATAA-TCT
1 ATATAATGTAATTAT-TTTTTAAAATTCT
12326149 ATA
1 ATA
12326152 CGTATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (28 bp):
ATATAATGTAATTATTTTTTAAAATTCT
Found at i:12330067 original size:14 final size:15
Alignment explanation
Indices: 12330041--12330073 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12330031 TCCCAAGCTA
*
12330041 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
12330056 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
12330070 GGAA
1 GGAA
12330074 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:12331830 original size:88 final size:88
Alignment explanation
Indices: 12331580--12332159 Score: 623
Period size: 88 Copynumber: 6.7 Consensus size: 88
12331570 GCAGTAGCGG
* * * * * * * * *
12331580 AGCAGATCGAAGACACTAGCCTTGCCTCACTCGGTGGCAGCGGAGCAGGTTAAAGATAGCAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
* *
12331645 TTGCCTTCCTGTACTGACAATGA
66 TTGCCTTCCTGTACCGACAGTGA
* *** * ** * ** * *
12331668 AGCAGATCAAAGATTGTGAATCCTAT--CTCCCT-GGACAGCAGTGGAATAGGTTAAAAATTA-C
1 AGCAGATCGAAGA-T-ACCAGCCT-TGCCTCCCTAGG-TTGTAGTGGAGCAGGTTGAAGA-TAGC
* * *
12331729 AGATCTTGCCTTCCTGCATCGACAGTGA
61 AAATCTTGCCTTCCTGTACCGACAGTGA
* * * **
12331757 AGCAGATTGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATTGCGGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
* *
12331822 TTGCCTTCCTATATCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
* *
12331845 AGCAGATCGAAGATACCAGCCTTGCCTTCCTAGGTTGTAGTGGAGCA-G--GCAGAT--C---T-
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
12331901 TT-CCTTCCTGTACCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
* * * *
12331923 AGCAGATCGAAGATAGCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAACAAATA
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
*
12331988 TTGCCTTCCTAG-ACTGACAGTGA
66 TTGCCTTCCT-GTACCGACAGTGA
12332011 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
*
12332076 CTGCCTTCCTGTACCGACAGTGA
66 TTGCCTTCCTGTACCGACAGTGA
*
12332099 AGCAGAGCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCA
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCA
12332160 GATGTTGTCT
Statistics
Matches: 419, Mismatches: 52, Indels: 42
0.82 0.10 0.08
Matches are distributed among these distances:
78 62 0.15
79 3 0.01
80 1 0.00
81 5 0.01
83 2 0.00
85 5 0.01
86 2 0.00
87 9 0.02
88 263 0.63
89 60 0.14
90 6 0.01
91 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (88 bp):
AGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATC
TTGCCTTCCTGTACCGACAGTGA
Found at i:12332009 original size:166 final size:168
Alignment explanation
Indices: 12331728--12332156 Score: 621
Period size: 166 Copynumber: 2.5 Consensus size: 168
12331718 TTAAAAATTA
* * *
12331728 CAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATTGAAGATACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTT
** ** * *
12331793 GTAGTGGAGCAGGTTGAAGATTGCGGATCTTGCCTTCCTATATCGACAGTGAAGCAGATCGAAGA
66 GTAGTGGAGCAGGTTGAAGATAACAAATATTGCCTTCCTAGATCGACAGTGAAGCAGATCGAAGA
*
12331858 TACCAGCCTTGCCTTCCTAGGTTGTAGTGGAGCA-G-G
131 TACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTG
* *
12331894 CAGATCTTTCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATAGCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTT
12331959 GTAGTGGAGCAGGTTGAAGATAACAAATATTGCCTTCCTAGA-CTGACAGTGAAGCAGATCGAAG
66 GTAGTGGAGCAGGTTGAAGATAACAAATATTGCCTTCCTAGATC-GACAGTGAAGCAGATCGAAG
12332023 ATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTG
130 ATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGG-TG
* *
12332063 AAGATAGCAAATCCTGCCTTCCTGTACCGACAGTGAAGCAGAGCGAAGATACCAGCCTTGCCTCC
1 CAGAT--C---T--TGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCC
*
12332128 CTAGGTTGTAGTGGAGCAGGTTGAAGATA
59 CTGGGTTGTAGTGGAGCAGGTTGAAGATA
12332157 GCAGATGTTG
Statistics
Matches: 235, Mismatches: 17, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
165 1 0.00
166 150 0.64
167 1 0.00
169 5 0.02
171 1 0.00
174 1 0.00
176 76 0.32
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.24
Consensus pattern (168 bp):
CAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTT
GTAGTGGAGCAGGTTGAAGATAACAAATATTGCCTTCCTAGATCGACAGTGAAGCAGATCGAAGA
TACCAGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTG
Found at i:12332023 original size:45 final size:45
Alignment explanation
Indices: 12331897--12332113 Score: 122
Period size: 44 Copynumber: 4.9 Consensus size: 45
12331887 GAGCAGGCAG
* * *
12331897 ATCTTTCCTTCCT-GTACCGACAGTGAAGCAGATCGAAGATAGC-A
1 ATCTTGCCTTCCTAG-ACTGACAGTGAAGCAGATCGAAGATAACAA
** * * ** * * * *
12331941 GCCTTGCCTCCCTGGGTTG-TAGTGGAGCAGGTTGAAGATAACAA
1 ATCTTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGATAACAA
* *
12331985 ATATTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGAT-ACCA
1 ATCTTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGATAACAA
** * ** * * * * *
12332029 GCCTTGCCTCCCTAGGTTG-TAGTGGAGCAGGTTGAAGATAGCAA
1 ATCTTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGATAACAA
* * *
12332073 ATCCTGCCTTCCT-GTACCGACAGTGAAGCAGAGCGAAGATA
1 ATCTTGCCTTCCTAG-ACTGACAGTGAAGCAGATCGAAGATA
12332114 CCAGCCTTGC
Statistics
Matches: 119, Mismatches: 48, Indels: 11
0.67 0.27 0.06
Matches are distributed among these distances:
43 35 0.29
44 51 0.43
45 33 0.28
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.24
Consensus pattern (45 bp):
ATCTTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGATAACAA
Found at i:12332256 original size:44 final size:44
Alignment explanation
Indices: 12332186--12332334 Score: 185
Period size: 44 Copynumber: 3.4 Consensus size: 44
12332176 ACTGGTGGCT
* * *
12332186 AAGTAGATCGAAGAAAGCAGACCTTGTCTTCATGCCTTGGCGTG
1 AAGTAGATCGAAGATAGCAGATCTTGTCTTCATGCATTGGCGTG
* * *
12332230 AAGTAGATCAAAGATAGCAAATCTTGTCTTCATGTATTGGCGTG
1 AAGTAGATCGAAGATAGCAGATCTTGTCTTCATGCATTGGCGTG
* *
12332274 AAGTAGATCGAAGATAGCAGATCTTGTCTTCCCAT--ACTGGTGGTG
1 AAGTAGATCGAAGATAGCAGATCTTGTCTT--CATGCATTGG-CGTG
12332319 AAGTAGATCGAAGATA
1 AAGTAGATCGAAGATA
12332335 CAAGTCTTAT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
44 70 0.76
45 19 0.21
46 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
AAGTAGATCGAAGATAGCAGATCTTGTCTTCATGCATTGGCGTG
Found at i:12332288 original size:176 final size:176
Alignment explanation
Indices: 12331903--12332289 Score: 420
Period size: 176 Copynumber: 2.2 Consensus size: 176
12331893 GCAGATCTTT
* * *
12331903 CCTTCCTGTACCGACAGTGAAGCAGATCGAAGATAGCAGCCTTGCCTCCCTGGGTTGTAGTGGAG
1 CCTTCATGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAG
* *
12331968 CAGGTTGAAGATAACAAATATTGCCTTCCTAGACTGACAGTGAAGCAGATCGAAGATACCAGCCT
66 CAGGTTGAAGATAACAAATATTGCCTTCCCAGACTGACAGTGAAGCAGATCGAAGAAACCAGCCT
* * * * * **
12332033 TGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAAATCCTG
131 TGCCTCCATAGCTTGGAGTGAAGCAGATCAAAGATAGCAAATCCTG
* *
12332079 CCTTCCTGTACCGACAGTGAAGCAGAGCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAG
1 CCTTCATGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAG
* * * * * *** * *
12332144 CAGGTTGAAGATAGCAGATGTTGTCTTCCCATACTGGTGGCT-AAGTAGATCGAAGAAAGCAGAC
66 CAGGTTGAAGATAACAAATATTGCCTTCCCAGACTGACAG-TGAAGCAGATCGAAGAAACCAG-C
* * * * *
12332208 CTTGTCTTCAT-GCCTTGGCGTGAAGTAGATCAAAGATAGCAAATCTTG
129 CTTGCCTCCATAG-CTTGGAGTGAAGCAGATCAAAGATAGCAAATCCTG
* ** * *
12332256 TCTTCATGTATTGGC-GTGAAGTAGATCGAAGATA
1 CCTTCATGTACCGACAGTGAAGCAGATCGAAGATA
12332290 GCAGATCTTG
Statistics
Matches: 174, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
176 128 0.74
177 46 0.26
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (176 bp):
CCTTCATGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTAGGTTGTAGTGGAG
CAGGTTGAAGATAACAAATATTGCCTTCCCAGACTGACAGTGAAGCAGATCGAAGAAACCAGCCT
TGCCTCCATAGCTTGGAGTGAAGCAGATCAAAGATAGCAAATCCTG
Found at i:12334208 original size:2 final size:2
Alignment explanation
Indices: 12334168--12334200 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12334158 ACCAATGTTT
12334168 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 T
12334201 GAATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12336661 original size:41 final size:41
Alignment explanation
Indices: 12336615--12336711 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
12336605 TGTCTCATCC
* *
12336615 CGTGTCTTAAGCCGTGTAACTCACTGACTTAGGTACATGGT
1 CGTGTCGTAGGCCGTGTAACTCACTGACTTAGGTACATGGT
**
12336656 CGTGTCGTAGGTTGTGTAACTCACTGACTTAGGTACATGGT
1 CGTGTCGTAGGCCGTGTAACTCACTGACTTAGGTACATGGT
12336697 CGTGTCGTAGGCCGT
1 CGTGTCGTAGGCCGT
12336712 ATGCTAGACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.32
Consensus pattern (41 bp):
CGTGTCGTAGGCCGTGTAACTCACTGACTTAGGTACATGGT
Found at i:12336814 original size:25 final size:25
Alignment explanation
Indices: 12336780--12336831 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
12336770 TGCTCACACC
*
12336780 TGAAATAATAAGTGACACGCAGATG
1 TGAAATAATAAGTGACACACAGATG
12336805 TGAAATAATAAGTGACACACAGATG
1 TGAAATAATAAGTGACACACAGATG
12336830 TG
1 TG
12336832 TGTGTCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (25 bp):
TGAAATAATAAGTGACACACAGATG
Found at i:12348550 original size:10 final size:9
Alignment explanation
Indices: 12348513--12348554 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
12348503 TAGTAACATT
12348513 ACAAAATAA
1 ACAAAATAA
*
12348522 ACAAAGTAA
1 ACAAAATAA
*
12348531 ACAAAAGAA
1 ACAAAATAA
12348540 ACAAAATGAA
1 ACAAAAT-AA
12348550 ACAAA
1 ACAAA
12348555 CTACTCCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.74, C:0.12, G:0.07, T:0.07
Consensus pattern (9 bp):
ACAAAATAA
Found at i:12353078 original size:10 final size:10
Alignment explanation
Indices: 12353041--12353082 Score: 54
Period size: 9 Copynumber: 4.5 Consensus size: 10
12353031 TAGTAACATT
12353041 ACAAAATG-A
1 ACAAAATGAA
*
12353050 ACAAAGT-AA
1 ACAAAATGAA
12353059 ACAAAA-GAA
1 ACAAAATGAA
12353068 ACAAAATGAA
1 ACAAAATGAA
12353078 ACAAA
1 ACAAA
12353083 CTGCTCCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.71, C:0.12, G:0.10, T:0.07
Consensus pattern (10 bp):
ACAAAATGAA
Found at i:12371473 original size:91 final size:91
Alignment explanation
Indices: 12371344--12371511 Score: 309
Period size: 91 Copynumber: 1.8 Consensus size: 91
12371334 TTAAATGTAT
* *
12371344 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
12371409 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
*
12371435 AAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
12371500 GAAAATTTATTA
66 GAAAATTTATTA
12371512 GTTATAATTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 74 1.00
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:12371478 original size:47 final size:46
Alignment explanation
Indices: 12371341--12371486 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 46
12371331 TGGTTAAATG
* *
12371341 TATAAATTATATATCATTATTAAATTATATTTAATATTAATTA-TT
1 TATAAATTATATATAATTATTAAATTATATTTAATAATAATTATTT
* * **
12371386 T-TAAATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGAATTT
1 TATAAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-AATTATTT
*
12371431 TATGAAATTATATATTATTATTAAATTATATTTAATAATAATTA-TT
1 TAT-AAATTATATATAATTATTAAATTATATTTAATAATAATTATTT
12371477 T-TAAATTATA
1 TATAAATTATA
12371487 CAAATTCATA
Statistics
Matches: 79, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
43 6 0.08
44 29 0.37
45 9 0.11
46 8 0.10
47 20 0.25
48 7 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (46 bp):
TATAAATTATATATAATTATTAAATTATATTTAATAATAATTATTT
Found at i:12371682 original size:16 final size:16
Alignment explanation
Indices: 12371661--12371706 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12371651 TTATTAAATT
12371661 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
12371677 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
12371692 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
12371707 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:12371726 original size:107 final size:109
Alignment explanation
Indices: 12371596--12371811 Score: 366
Period size: 107 Copynumber: 2.0 Consensus size: 109
12371586 TATTTTATAG
* *
12371596 TATCATATATTATTATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 TATCATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
12371661 ATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
66 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
* *
12371704 TATC-TATATTATGT-TTTGAGTAAATTTATATAAGAATATTAATTATTAATAATTTTATTAAAT
1 TATCATATATTAT-TATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
12371767 TATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
65 TATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
12371812 ATGATTAAAT
Statistics
Matches: 102, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
107 91 0.89
108 11 0.11
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (109 bp):
TATCATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
Found at i:12371788 original size:18 final size:18
Alignment explanation
Indices: 12371742--12371789 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
12371732 TATAAGAATA
*
12371742 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
12371758 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
12371775 TTAATTATAATATAT
1 TTAATTATAATATAT
12371790 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:12371789 original size:16 final size:16
Alignment explanation
Indices: 12371742--12371809 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
12371732 TATAAGAATA
12371742 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
12371758 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
12371775 TTAATTATAATATA-T
1 TTAATTATAATATATT
*
12371790 TTAATAATAAT-TATGT
1 TTAATTATAATATAT-T
12371806 TTAA
1 TTAA
12371810 ATATGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.05
15 14 0.33
16 18 0.42
17 6 0.14
18 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:12372034 original size:45 final size:44
Alignment explanation
Indices: 12371954--12372044 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
12371944 ACCTCTATTC
*
12371954 CATTCAACCAAACATAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACATAAGATTACTATTACGCCTCTATTCCAATA
* *
12371998 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCAATA
1 CATTCAACCAAACATA-AGA-TTACTATTACGCCTCTATTCCAATA
12372043 CA
1 CA
12372045 GCGAACCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACATAAGATTACTATTACGCCTCTATTCCAATA
Found at i:12375585 original size:6 final size:6
Alignment explanation
Indices: 12375574--12375634 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
12375564 GACGTGCTCT
* * * *
12375574 AGATTC AGATTC AGATTC AGATTC AGATTAC ATATAC ACAGTC AGATTC
1 AGATTC AGATTC AGATTC AGATTC AGATT-C AGATTC AGATTC AGATTC
*
12375623 AGATTC ATATTC
1 AGATTC AGATTC
12375635 GGACTTAGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 42 0.91
7 4 0.09
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (6 bp):
AGATTC
Found at i:12375681 original size:13 final size:13
Alignment explanation
Indices: 12375654--12375698 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
12375644 TCCTTTACAG
12375654 ATACAGATACAGAT
1 ATACAGA-ACAGAT
*
12375668 A-ACGGAATCAGAT
1 ATACAGAA-CAGAT
12375681 ATACAGAACAGAT
1 ATACAGAACAGAT
12375694 ATACA
1 ATACA
12375699 AAATCCTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 20 0.74
14 6 0.22
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.18
Consensus pattern (13 bp):
ATACAGAACAGAT
Found at i:12379078 original size:23 final size:23
Alignment explanation
Indices: 12379052--12379095 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12379042 TCTGAGGCCC
*
12379052 GAAATGATAGAATTTG-TAAATGT
1 GAAAGGATA-AATTTGTTAAATGT
*
12379075 GAAAGGTTAAATTTGTTAAAT
1 GAAAGGATAAATTTGTTAAAT
12379096 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (23 bp):
GAAAGGATAAATTTGTTAAATGT
Found at i:12381592 original size:22 final size:22
Alignment explanation
Indices: 12381565--12381607 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12381555 TAATAATAAA
*
12381565 TTTTAATCGATATTTTTAATTT
1 TTTTAATCGATAATTTTAATTT
**
12381587 TTTTAATTTATAATTTTAATT
1 TTTTAATCGATAATTTTAATT
12381608 GAAAGTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAATCGATAATTTTAATTT
Found at i:12386981 original size:18 final size:18
Alignment explanation
Indices: 12386958--12386998 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
12386948 TTGCTGCAGA
12386958 AGCAATAGCTTGCAGGAC
1 AGCAATAGCTTGCAGGAC
12386976 AGCAATAGCTTGCAGGAC
1 AGCAATAGCTTGCAGGAC
12386994 AGCAA
1 AGCAA
12386999 CTCAGATCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.27, T:0.15
Consensus pattern (18 bp):
AGCAATAGCTTGCAGGAC
Found at i:12401840 original size:51 final size:51
Alignment explanation
Indices: 12401778--12401893 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
12401768 TCCAAGTCAT
* * * *
12401778 TTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATTTCATTTC
1 TTCATTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATCTCATTTC
* * **
12401829 TTCATTTTCATTTTGAAGAAAATCATAATCATTTTGAAATGATCTCATTTC
1 TTCATTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATCTCATTTC
*
12401880 TCCATTTTCATTTT
1 TTCATTTTCATTTT
12401894 CATCTTAGAG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.47
Consensus pattern (51 bp):
TTCATTTTCATTTTGAAGAAAACCACAATCATTTCCAAATGATCTCATTTC
Found at i:12401926 original size:57 final size:55
Alignment explanation
Indices: 12401777--12401926 Score: 137
Period size: 51 Copynumber: 2.7 Consensus size: 55
12401767 TTCCAAGTCA
* * * * * *
12401777 TTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTATTTCATTTCTTCAT
1 TTTCATTTTCA-TTTAGAGAAAA-CATAATCATTTCCAAATGATCTCATTTCTCCAT
* * **
12401834 TTTCATTTTGA---AGA-AAATCATAATCATTTTGAAATGATCTCATTTCTCCAT
1 TTTCATTTTCATTTAGAGAAAACATAATCATTTCCAAATGATCTCATTTCTCCAT
*
12401885 TTTCATTTTCATCTTAGAGAAAACTGTAATCATTTCCAAATG
1 TTTCATTTTCAT-TTAGAGAAAAC-ATAATCATTTCCAAATG
12401927 TTTCCCTTTT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
51 36 0.50
52 3 0.04
53 2 0.03
55 3 0.04
56 4 0.06
57 24 0.33
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.44
Consensus pattern (55 bp):
TTTCATTTTCATTTAGAGAAAACATAATCATTTCCAAATGATCTCATTTCTCCAT
Found at i:12402944 original size:13 final size:13
Alignment explanation
Indices: 12402926--12402950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12402916 GAAATCATAA
12402926 TTATAATAATTTT
1 TTATAATAATTTT
12402939 TTATAATAATTT
1 TTATAATAATTT
12402951 CAGTAAACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATAATAATTTT
Found at i:12405304 original size:16 final size:17
Alignment explanation
Indices: 12405272--12405304 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12405262 GTAATGGAAT
12405272 AAGAAAAGCTAAAACAA
1 AAGAAAAGCTAAAACAA
*
12405289 AAGAAAA-CTAATACAA
1 AAGAAAAGCTAAAACAA
12405305 GAGTCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.70, C:0.12, G:0.09, T:0.09
Consensus pattern (17 bp):
AAGAAAAGCTAAAACAA
Found at i:12406769 original size:5 final size:5
Alignment explanation
Indices: 12406755--12406785 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
12406745 GCATTGGAAC
12406755 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
12406786 CTTAGTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:12414165 original size:61 final size:62
Alignment explanation
Indices: 12414087--12414206 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 62
12414077 TATTTCAGAA
* *
12414087 TTTTTAGAATTATAACTAAAGTGACA-AATCTTGTAAACACT-GAAGGCTAAATTTGTTAAAT
1 TTTTTAGAATTAAAACTAAAGTGACAGAAT-ATGTAAACACTGGAAGGCTAAATTTGTTAAAT
* * * * *
12414148 TTTTTAGATTTAAAACTAAATTGATAGAATATGTAAACATTGGAGGGCTAAATTTGTTA
1 TTTTTAGAATTAAAACTAAAGTGACAGAATATGTAAACACTGGAAGGCTAAATTTGTTA
12414207 TTAGATCAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 31 0.62
62 19 0.38
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (62 bp):
TTTTTAGAATTAAAACTAAAGTGACAGAATATGTAAACACTGGAAGGCTAAATTTGTTAAAT
Found at i:12420047 original size:77 final size:76
Alignment explanation
Indices: 12419921--12420069 Score: 210
Period size: 77 Copynumber: 1.9 Consensus size: 76
12419911 TACCAATGCC
*
12419921 AATAAAATAATTTCCATTATTTTATCAATGAAGTTATTTAGATGATGTTTGTTTGAATATGAAGT
1 AATAAAATAATTTCCATTATTTTATCAATGAAGTTATTTAAATGATGTTTGTTTGAA-ATGAAGT
12419986 GTTGAATGCAAT
65 GTTGAATGCAAT
* * ** * *
12419998 AATAAAATAATTTCCATT-TTTTTTTAGATGGTGTTATTTAAATGTTGTTTGTTTGAAATGAATT
1 AATAAAATAATTTCCATTATTTTATCA-ATGAAGTTATTTAAATGATGTTTGTTTGAAATGAAGT
12420062 GTTGAATG
65 GTTGAATG
12420070 ATATTTATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
76 20 0.31
77 44 0.69
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (76 bp):
AATAAAATAATTTCCATTATTTTATCAATGAAGTTATTTAAATGATGTTTGTTTGAAATGAAGTG
TTGAATGCAAT
Found at i:12432769 original size:180 final size:180
Alignment explanation
Indices: 12432463--12432815 Score: 528
Period size: 180 Copynumber: 2.0 Consensus size: 180
12432453 GCTATAATGT
* * ** **
12432463 GGAATGATTTCACTTGCTCATTTGTGCTAATTTCATACAAGATGGATTATTGCCTCTTTTTCCAG
1 GGAATGATTTCACTTACCCATTTGCACTAATTTCATACAAGATGGATTATTAACTCTTTTTCCAG
* * * *
12432528 TAGAACATATGCGAATTACCTTAACAATTATTTTCATTGTGAATTAACGTATAACAGATTGA-TT
66 TAGAACATATGCCAATTACCTTAACAATTACTTTCATTGCGAATTAACGTACAACAGATTGATTT
12432592 CTAGAAAACTCATGCATAGAGATTCACACTTGGAGAATTTTTTTTACAAGC
131 C-AGAAAACTCATGCATAGAGATTCACACTTGGAGAATTTTTTTTACAAGC
*
12432643 GGAATGATTTCGCTTACCCATTTGCACTAATTTCATACAAGATGGATTATTAACTCTTTTTCCAG
1 GGAATGATTTCACTTACCCATTTGCACTAATTTCATACAAGATGGATTATTAACTCTTTTTCCAG
** * * ***
12432708 TAGAACATATGCCAATTACCTTAGTAATTGCTTTCATTGCGGATTAACGTACGGTAGATTGATTT
66 TAGAACATATGCCAATTACCTTAACAATTACTTTCATTGCGAATTAACGTACAACAGATTGATTT
12432773 CAGAAAACTCATGCATAGAGATTCACACTTGGAGAATTTTTTT
131 CAGAAAACTCATGCATAGAGATTCACACTTGGAGAATTTTTTT
12432816 ACATGCAGAT
Statistics
Matches: 154, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 151 0.98
181 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (180 bp):
GGAATGATTTCACTTACCCATTTGCACTAATTTCATACAAGATGGATTATTAACTCTTTTTCCAG
TAGAACATATGCCAATTACCTTAACAATTACTTTCATTGCGAATTAACGTACAACAGATTGATTT
CAGAAAACTCATGCATAGAGATTCACACTTGGAGAATTTTTTTTACAAGC
Found at i:12432997 original size:29 final size:29
Alignment explanation
Indices: 12432964--12433031 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
12432954 ATTCTTAAAT
**
12432964 GATAGTCACT-TCTAAACTCTTGTTTGGCA
1 GATAGTCACTATC-AAACTCTTGTTTAACA
* *
12432993 GATAGTCACTATCAGACTCTTGTTTAACG
1 GATAGTCACTATCAAACTCTTGTTTAACA
12433022 GATAGTCACT
1 GATAGTCACT
12433032 GCGAACTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (29 bp):
GATAGTCACTATCAAACTCTTGTTTAACA
Found at i:12435475 original size:67 final size:68
Alignment explanation
Indices: 12435324--12435691 Score: 358
Period size: 68 Copynumber: 5.5 Consensus size: 68
12435314 GATATGCTGC
* * *
12435324 CATAGTCGAGCTATAGTCTTACA-CATGTAACCCCAAGTTTAATGTCCTGGT-AGACTCTATTGG
1 CATAGTCGAGCTATGGTCTTACACCATGTAAACCCATGTTTAATGTCCTGGTGA-ACTCTATTGG
12435387 TTGT
65 TTGT
* * * * *
12435391 CATAGTTGGGTTATGGTCTTACACCATGTAAACCCATGTTTAATTTCTTGGTGAACTCTATTGG-
1 CATAGTCGAGCTATGGTCTTACACCATGTAAACCCATGTTTAATGTCCTGGTGAACTCTATTGGT
12435455 TGT
66 TGT
* * * * * *
12435458 CATAATCGTGCTATGGTCTTACACCTTGT-AACCTCATGTTTAATGTCCTAGAGGACTCTATTGG
1 CATAGTCGAGCTATGGTCTTACACCATGTAAACC-CATGTTTAATGTCCTGGTGAACTCTATTGG
12435522 TTGT
65 TTGT
* * * * * * *
12435526 CATAGTTGAGCTATGGTTTTACACCTTGT-AACCTTATGTTTAATGTCCTGGCGGACTTTATTGG
1 CATAGTCGAGCTATGGTCTTACACCATGTAAACC-CATGTTTAATGTCCTGGTGAACTCTATTGG
*
12435590 TTGC
65 TTGT
* **
12435594 CATAGTCGAGCTATGGCCTTACACC-T-TATAACCCATGTTTAATGTCCTAATGGAA-TCTATT-
1 CATAGTCGAGCTATGGTCTTACACCATGTA-AACCCATGTTTAATGTCCTGGT-GAACTCTATTG
12435655 GTTCGT
64 GTT-GT
* * * *
12435661 CAAAGTTGAGCTATGGTTTTACACCTTGTAA
1 CATAGTCGAGCTATGGTCTTACACCATGTAA
12435692 CCCCTTTTGA
Statistics
Matches: 250, Mismatches: 41, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
66 8 0.03
67 113 0.45
68 126 0.50
69 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (68 bp):
CATAGTCGAGCTATGGTCTTACACCATGTAAACCCATGTTTAATGTCCTGGTGAACTCTATTGGT
TGT
Found at i:12435541 original size:135 final size:136
Alignment explanation
Indices: 12435321--12435691 Score: 459
Period size: 135 Copynumber: 2.7 Consensus size: 136
12435311 CTCGATATGC
* * * *
12435321 TGCCATAGTCGAGCTATAGTCTTACA-CATGTAACCCCAAGTTTAATGTCCTGGTA-GACTCTAT
1 TGCCATAGTCGAGCTATGGTCTTACACCTTGTAA-CCCATGTTTAATGTCCTAG-AGGACTCTAT
* * * * * * *
12435384 TGGTTGTCATAGTTGGGTTATGGTCTTACACCATGTAAACC-CATGTTTAATTTCTTGGTGAACT
64 TGGTTGTCATAGTTGAGCTATGGTTTTACACCTTGTAAACCTCATGTTTAATGTCCTGGCGAACT
12435448 CTATTGG-
129 CTATTGGT
* * *
12435455 TGTCATAATCGTGCTATGGTCTTACACCTTGTAACCTCATGTTTAATGTCCTAGAGGACTCTATT
1 TGCCATAGTCGAGCTATGGTCTTACACCTTGTAACC-CATGTTTAATGTCCTAGAGGACTCTATT
* * *
12435520 GGTTGTCATAGTTGAGCTATGGTTTTACACCTTGT-AACCTTATGTTTAATGTCCTGGCGGACTT
65 GGTTGTCATAGTTGAGCTATGGTTTTACACCTTGTAAACCTCATGTTTAATGTCCTGGCGAACTC
12435584 TATTGGT
130 TATTGGT
* * *
12435591 TGCCATAGTCGAGCTATGGCCTTACACCTTATAACCCATGTTTAATGTCCTA-ATGGAATCTATT
1 TGCCATAGTCGAGCTATGGTCTTACACCTTGTAACCCATGTTTAATGTCCTAGA-GGACTCTATT
*
12435655 -GTTCGTCAAAGTTGAGCTATGGTTTTACACCTTGTAA
65 GGTT-GTCATAGTTGAGCTATGGTTTTACACCTTGTAA
12435692 CCCCTTTTGA
Statistics
Matches: 205, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
134 33 0.16
135 140 0.68
136 32 0.16
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (136 bp):
TGCCATAGTCGAGCTATGGTCTTACACCTTGTAACCCATGTTTAATGTCCTAGAGGACTCTATTG
GTTGTCATAGTTGAGCTATGGTTTTACACCTTGTAAACCTCATGTTTAATGTCCTGGCGAACTCT
ATTGGT
Found at i:12435693 original size:67 final size:67
Alignment explanation
Indices: 12435324--12435694 Score: 415
Period size: 67 Copynumber: 5.5 Consensus size: 67
12435314 GATATGCTGC
* * * * *
12435324 CATAGTCGAGCTATAGTCTTACA-CATGTAACCCCAAGTTTAATGTCCTGGTAGACTCTATTGGT
1 CATAGTTGAGCTATGGTCTTACACCTTGTAA-CCCATGTTTAATGTCCTGGTGGACTCTATTGGT
12435388 TGT
65 TGT
* * * * * *
12435391 CATAGTTGGGTTATGGTCTTACACCATGTAAACCCATGTTTAATTTCTTGGTGAACTCTATTGG-
1 CATAGTTGAGCTATGGTCTTACACCTTGT-AACCCATGTTTAATGTCCTGGTGGACTCTATTGGT
12435455 TGT
65 TGT
* * * * *
12435458 CATAATCGTGCTATGGTCTTACACCTTGTAACCTCATGTTTAATGTCCTAGAGGACTCTATTGGT
1 CATAGTTGAGCTATGGTCTTACACCTTGTAACC-CATGTTTAATGTCCTGGTGGACTCTATTGGT
12435523 TGT
65 TGT
* * * *
12435526 CATAGTTGAGCTATGGTTTTACACCTTGTAACCTTATGTTTAATGTCCTGGCGGACTTTATTGGT
1 CATAGTTGAGCTATGGTCTTACACCTTGTAACC-CATGTTTAATGTCCTGGTGGACTCTATTGGT
*
12435591 TGC
65 TGT
* * * ** *
12435594 CATAGTCGAGCTATGGCCTTACACCTTATAACCCATGTTTAATGTCCTAATGGAATCTATT-GTT
1 CATAGTTGAGCTATGGTCTTACACCTTGTAACCCATGTTTAATGTCCTGGTGGACTCTATTGGTT
12435658 CGT
66 -GT
* *
12435661 CAAAGTTGAGCTATGGTTTTACACCTTGTAACCC
1 CATAGTTGAGCTATGGTCTTACACCTTGTAACCC
12435695 CTTTTGAGGT
Statistics
Matches: 255, Mismatches: 44, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
66 7 0.03
67 123 0.48
68 123 0.48
69 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (67 bp):
CATAGTTGAGCTATGGTCTTACACCTTGTAACCCATGTTTAATGTCCTGGTGGACTCTATTGGTT
GT
Found at i:12444069 original size:6 final size:6
Alignment explanation
Indices: 12444058--12444085 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12444048 ATCATGTACC
12444058 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
12444086 GCTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:12444186 original size:19 final size:18
Alignment explanation
Indices: 12444154--12444190 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12444144 TCATTGTTTA
12444154 TTTTTTTATGTATATTAG
1 TTTTTTTATGTATATTAG
*
12444172 TTTTATTTATTTATATTAG
1 TTTT-TTTATGTATATTAG
12444191 ACCTGTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTTTTATGTATATTAG
Found at i:12456533 original size:44 final size:44
Alignment explanation
Indices: 12456444--12456866 Score: 280
Period size: 44 Copynumber: 9.6 Consensus size: 44
12456434 CCAATGATCC
* * ** **
12456444 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-TACCTTGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAG-TCT
*
12456488 TATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
* * * *
12456532 TATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGTAAGTCT
* * * * * **
12456577 TATCTCTCTGAAGTTGCAG-AGAGCATA-T-CGCATCT-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
* *
12456617 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGACT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
* * *
12456661 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGAAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGTAAGTCT
* **
12456706 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CCG-ATAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGTA-AGTCT
* * * * * *
12456750 TATCTACCTGAATTTGCAGTGGAGCCGACTCATGAAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGTAAGTCT
* * * * * * *
12456795 TATCCCCCTGAAATTCCAGTGGGGTAGACTAAATAAATGAA-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGT-AAGTCT
12456839 TATCTCCCTGAAGTTGCAGTGGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
12456867 TTAAAGATAG
Statistics
Matches: 294, Mismatches: 63, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
40 22 0.07
41 7 0.02
42 2 0.01
43 10 0.03
44 152 0.52
45 96 0.33
46 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCT
Found at i:12456678 original size:129 final size:132
Alignment explanation
Indices: 12456485--12456872 Score: 473
Period size: 129 Copynumber: 2.9 Consensus size: 132
12456475 ATACCTTGGA
* * *
12456485 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTAAGTCTTATCCTCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
* * ** **
12456550 GTGAGGCAGACTGAAGATGGCAAATCTTATCTCTCTGAAGTTGCAG-AGAGC-A-TATCGCATCT
66 GTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAATTAAAGCAGAT
12456612 AG
131 AG
*
12456614 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGACTTATCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
* *
12456679 GTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGA
66 GTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTAGAGCA-ATTAAAGCAGA
12456744 TAG
130 TAG
* * * * * * * *
12456747 TCTTATCTACCTGAATTTGCAGTGGAGCCGACTCATGAAAGCAAGTCTTATCCCCCTGAAATTCC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
* * * *
12456812 AGTGGGGTAGACT-AA-AT-AAATGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
65 AGTGAGGCAGACTGAAGATGGAA--AATCTTATCTCCCTGAAGTTGCAGTAGAGCA-ATTAAAG
12456873 ATAGCAAATC
Statistics
Matches: 228, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
129 105 0.46
130 4 0.02
131 2 0.01
132 3 0.01
133 78 0.34
134 36 0.16
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (132 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCA
GTGAGGCAGACTGAAGATGGAAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAATTAAAGCAGAT
AG
Found at i:12456796 original size:89 final size:88
Alignment explanation
Indices: 12456444--12456826 Score: 224
Period size: 89 Copynumber: 4.4 Consensus size: 88
12456434 CCAATGATCC
* * * * **
12456444 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-TACCTTGGATCTTAT-CTCTCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAGA-CTTATCCTC-CTGAAGTTGCAG
* *
12456507 TG-GAGCAGACT-AAGTAAGTAAGTCT
63 TGAG-GCAGACTCAAGAAAGAAAGTCT
* *
12456532 TATC-CTCCTAAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA-ATCTTAT-CTCTCTGAAGTTG
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGA-CTTATCCTC-CTGAAGTTG
* * * ***
12456593 CAGAGA-GCATA-TC--G-CATCTAGTCT
60 CAGTGAGGCAGACTCAAGAAAGAAAGTCT
12456617 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGACTTATCCTCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGACTTATCCTCCTGAAGTTGCAGTG
* ** *
12456682 AGGCAGACTGAAGATGGAAAATCT
65 AGGCAGACTCAAGAAAGAAAGTCT
* * *
12456706 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCCGATAGTCTTAT-CTACCTGAATTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGACTTATCCT-CCTGAAGTTGCA
* * *
12456768 GTG-GAGCCGACTCATGAAAGCAAGTCT
62 GTGAG-GCAGACTCAAGAAAGAAAGTCT
* * * * *
12456795 TATCCCCCTGAAATTCCAGTGGGGTAGACTAA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
12456827 ATAAATGAAT
Statistics
Matches: 231, Mismatches: 41, Indels: 44
0.73 0.13 0.14
Matches are distributed among these distances:
84 26 0.11
85 39 0.17
86 8 0.03
87 5 0.02
88 33 0.14
89 117 0.51
90 2 0.01
91 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (88 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGACTTATCCTCCTGAAGTTGCAGTGA
GGCAGACTCAAGAAAGAAAGTCT
Found at i:12458683 original size:21 final size:20
Alignment explanation
Indices: 12458658--12458705 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
12458648 ACCTTTTATT
12458658 TTTATTTTATTTT-TTTTGCTA
1 TTTATTTT-TTTTCTTTTG-TA
12458679 TTTATTTTTTTTCTTTTGTA
1 TTTATTTTTTTTCTTTTGTA
12458699 -TTATTTT
1 TTTATTTT
12458706 GCTCGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.27
20 6 0.23
21 13 0.50
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTATTTTTTTTCTTTTGTA
Found at i:12458834 original size:19 final size:20
Alignment explanation
Indices: 12458793--12458834 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
12458783 ATTTCTATGC
* *
12458793 CATTGTAATATTTATTATCG
1 CATTGTAATATTTAATATAG
*
12458813 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
12458832 CAT
1 CAT
12458835 CACATCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:12460755 original size:18 final size:18
Alignment explanation
Indices: 12460732--12460771 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
12460722 AAATGCAATC
12460732 AGTAAAAGGAACCAACAG
1 AGTAAAAGGAACCAACAG
12460750 AGTAAAAGGAACCAACAG
1 AGTAAAAGGAACCAACAG
12460768 AGTA
1 AGTA
12460772 TTAATCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.15, G:0.23, T:0.07
Consensus pattern (18 bp):
AGTAAAAGGAACCAACAG
Found at i:12464733 original size:23 final size:23
Alignment explanation
Indices: 12464706--12464770 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
12464696 GGATCTACAC
* * *
12464706 AATCTTCTAAGATTATAAAATTA
1 AATCTTATAAAATTACAAAATTA
**
12464729 AATCTTATAAAATTACAAAATGG
1 AATCTTATAAAATTACAAAATTA
*
12464752 AATTTTATAAAATTACAAA
1 AATCTTATAAAATTACAAA
12464771 TCTTCTAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (23 bp):
AATCTTATAAAATTACAAAATTA
Found at i:12467527 original size:27 final size:27
Alignment explanation
Indices: 12467489--12467556 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
12467479 CAGAAGAATG
12467489 ACTGATTAAGGATCCTCGAGTAGTTTA
1 ACTGATTAAGGATCCTCGAGTAGTTTA
*
12467516 ACTGATTAAGGATCCTTGAGTAGTTTA
1 ACTGATTAAGGATCCTCGAGTAGTTTA
12467543 ACTGATTAAGGATC
1 ACTGATTAAGGATC
12467557 ATTTTCACCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (27 bp):
ACTGATTAAGGATCCTCGAGTAGTTTA
Found at i:12468730 original size:16 final size:16
Alignment explanation
Indices: 12468709--12468748 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12468699 TTTGGTTCGC
*
12468709 TGTAATGGAATAGAGG
1 TGTAATAGAATAGAGG
12468725 TGTAATAGAATAGAGG
1 TGTAATAGAATAGAGG
*
12468741 CGTAATAG
1 TGTAATAG
12468749 GTAATCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.03, G:0.33, T:0.25
Consensus pattern (16 bp):
TGTAATAGAATAGAGG
Found at i:12468955 original size:7 final size:7
Alignment explanation
Indices: 12468943--12468975 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12468933 TAATTTAATC
12468943 ATATTAA
1 ATATTAA
12468950 ATATTAA
1 ATATTAA
12468957 ATATTAA
1 ATATTAA
12468964 ATATTAA
1 ATATTAA
12468971 ATATT
1 ATATT
12468976 CTTACATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
ATATTAA
Done.