Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 196 of 205
Found at i:58070960 original size:16 final size:17
Alignment explanation
Indices: 58070919--58070965 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
58070909 GTTCTTGTTT
58070919 TCATTTTATTGTTTTTATC
1 TCATTTTA-T-TTTTTATC
*
58070938 TCTTTTTATTTTTTATC
1 TCATTTTATTTTTTATC
58070955 T-ATTTTATTTT
1 TCATTTTATTTT
58070966 CATTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 9 0.35
18 1 0.04
19 7 0.27
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (17 bp):
TCATTTTATTTTTTATC
Found at i:58075934 original size:12 final size:12
Alignment explanation
Indices: 58075919--58075954 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
58075909 AAAAACAAAT
58075919 GAAAAGAAAAAA
1 GAAAAGAAAAAA
*
58075931 GAAAAGAAAAAT
1 GAAAAGAAAAAA
58075943 GAAAAAGAAAAA
1 G-AAAAGAAAAA
58075955 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:58077278 original size:50 final size:50
Alignment explanation
Indices: 58077218--58077483 Score: 191
Period size: 50 Copynumber: 5.4 Consensus size: 50
58077208 ATTAAAGCTA
*
58077218 CAACGACGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
* * * * ** ** * **
58077268 CAATGGCGAATC-T--TTCCATGGCGA-TGCAGTAGAGCAGATTAAAGCTA
1 CAACGGCGAATCTTGCTTCCCTGAC-ATTGCAATTTAAAAGATTGAAGCCG
* * *
58077315 CAACGGTGAATCTTGCTTCCCCGACATTGTAATTTAAAAGATTGAAGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
* ** * * * ** * * **
58077365 CAACGGTGAATCTTAATTCCATGGCGA-TGCAGTGGAACAGATTAAAGCTA
1 CAACGGCGAATCTTGCTTCCCTGAC-ATTGCAATTTAAAAGATTGAAGCCG
* * * *
58077415 TAACGGCGAATCTTGCTTCCCCGATATTGCAATTTAAAAGATTGAGGCCG
1 CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
*
58077465 CAACGGCGAATCTTACTTC
1 CAACGGCGAATCTTGCTTC
58077484 TTTAGTGGTG
Statistics
Matches: 152, Mismatches: 57, Indels: 14
0.68 0.26 0.06
Matches are distributed among these distances:
47 32 0.21
48 2 0.01
49 3 0.02
50 114 0.75
51 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (50 bp):
CAACGGCGAATCTTGCTTCCCTGACATTGCAATTTAAAAGATTGAAGCCG
Found at i:58077432 original size:100 final size:99
Alignment explanation
Indices: 58077195--58077540 Score: 471
Period size: 100 Copynumber: 3.5 Consensus size: 99
58077185 TCCCTGGCAG
* * *
58077195 TGCAGTGGAGCAGATTAAAGCTACAACGACGAATCTTGCTTCCCTGACATTGCAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
*
58077260 TGAAGCCGCAATGGCGAATC-T-TTCCATGGCGA
66 TGAAGCCGCAACGGCGAATCTTATTCCATGGCGA
* * * *
58077292 TGCAGTAGAGCAGATTAAAGCTACAACGGTGAATCTTGCTTCCCCGACATTGTAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
*
58077357 TGAAGCCGCAACGGTGAATCTTAATTCCATGGCGA
66 TGAAGCCGCAACGGCGAATCTT-ATTCCATGGCGA
* *
58077392 TGCAGTGGAACAGATTAAAGCTATAACGGCGAATCTTGCTTCCCCGATATTGCAATTTAAAAGAT
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
* ** * * *
58077457 TGAGGCCGCAACGGCGAATCTTACTTCTTTAGTGG
66 TGAAGCCGCAACGGCGAATCTTA-TTCCATGGCGA
* * * *
58077492 TGTAATGGAACAGATTAAAGCTACAACAGTGAATCTTGCTTCCCCGACA
1 TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACA
58077541 CCGTAGTTCA
Statistics
Matches: 219, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
97 78 0.36
98 1 0.00
99 1 0.00
100 139 0.63
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (99 bp):
TGCAGTGGAACAGATTAAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTTAAAAGAT
TGAAGCCGCAACGGCGAATCTTATTCCATGGCGA
Found at i:58078450 original size:45 final size:45
Alignment explanation
Indices: 58077577--58078449 Score: 1092
Period size: 45 Copynumber: 19.4 Consensus size: 45
58077567 ACATTGCAGA
* *
58077577 TCTTGTCTTCCTGTATTGGCAGCAAAGTAGA-TCGAAGATAACAAC
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* * *
58077622 TCTTATCTTCCTGTATTGGCACCGAAGTAGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * * * * * *
58077667 TTTTGTCTTCTTGTGTTGGTAGCAAAGTAGACTAAAGATAA-TAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
**
58077711 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCGAAGATAGTAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
58077757 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * *
58077801 ATCTTGTCTTCTTGTATTGGCAGCGAAATAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
58077847 TCTTATCTTCCTGTATTGGCAGCAAAGTAGACTGAAGATAACAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
58077892 TCTTGTCTTCCTGTATTGGCAGCGAAGTATACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * *
58077936 ATCTTATCTTCCTGTATTGGCAGTGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
*
58077982 TCTTGTCTTTCTGTATTGGCAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
58078026 ATCTTGTCTTCCTGTATTGGCAACGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* * * * *
58078072 TCTTATCTTCCTGTTTTAGCAGCGAAATAGACTGAAGATAGCAAG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
58078117 TCTTGTCTTCCTGTATTGACAGCGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
58078161 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
58078207 TCTTGTCTTTCTGTATTGGCAACGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
*
58078251 ATCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
58078297 TCTTGTCTTCCTGTATTAGCAGCAAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* * * *
58078341 ATCTTGTCTTCCTCTATTGCCAGCAAAGTAGA-TCGAAGATAGCAAG
1 -TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACT-GAAGATAACAAG
* *
58078387 TCTTGTCTTCCTGTATTGACAACGAAGTAGACTGAAGATAAC-AG
1 TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
* *
58078431 ATCTTGCCTTCCTATATTG
1 -TCTTGTCTTCCTGTATTG
58078450 ATGGTGAAGC
Statistics
Matches: 720, Mismatches: 80, Indels: 56
0.84 0.09 0.07
Matches are distributed among these distances:
44 22 0.03
45 677 0.94
46 21 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (45 bp):
TCTTGTCTTCCTGTATTGGCAGCGAAGTAGACTGAAGATAACAAG
Found at i:58078630 original size:50 final size:50
Alignment explanation
Indices: 58078541--58078636 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
58078531 GCAGTGGAAC
* * *
58078541 AGATTGAAGCTACAACGGCAAATCTTGTTTCCCCGACATTGTAATTTAAA
1 AGATTGAAGCTACAACGGCAAATCTTCTTTCCCCAACATTGCAATTTAAA
* * * *
58078591 AGATTGAAGCTACGATGGCGAATCTTACTTT-CCTAACATTGCAATT
1 AGATTGAAGCTACAACGGCAAATCTT-CTTTCCCCAACATTGCAATT
58078637 AAACATACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 35 0.92
51 3 0.08
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (50 bp):
AGATTGAAGCTACAACGGCAAATCTTCTTTCCCCAACATTGCAATTTAAA
Found at i:58078801 original size:27 final size:27
Alignment explanation
Indices: 58078763--58078815 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
58078753 GCAGTAGTGG
58078763 AGCAGACAAAAGAAACCAATCCTATCA
1 AGCAGACAAAAGAAACCAATCCTATCA
58078790 AGCAGACAAAAGAAACCAATCCTATC
1 AGCAGACAAAAGAAACCAATCCTATC
58078816 TTCCTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (27 bp):
AGCAGACAAAAGAAACCAATCCTATCA
Found at i:58078860 original size:44 final size:43
Alignment explanation
Indices: 58078812--58079011 Score: 187
Period size: 44 Copynumber: 4.6 Consensus size: 43
58078802 AAACCAATCC
* *
58078812 TATCTTCCTGAAGTTGCAGTTGAGCAGATCAAAACCACAGATCT
1 TATC-TCCTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
* *
58078856 TATCTCTCTGAAGTTGCAGTAGAGCAGATC-ACATC-CAG-TCT
1 TATCTC-CTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
* * ** *
58078897 TATCTCCCTGAAGTTTCAGTGGAGCAG-GCAAAAGAAACCA-ATCC
1 TATCT-CCTGAAGTTGCAGTGGAGCAGATCAAAA-TCA-CAGATCT
*
58078941 TATCTCCTTAAAGTTGCAGTGGAGC-GAATCAAAATCACAGATCT
1 TATCTCC-TGAAGTTGCAGTGGAGCAG-ATCAAAATCACAGATCT
*
58078985 TATCTCTCTAAAGTTGCAGTGGAGCAG
1 TATCTC-CTGAAGTTGCAGTGGAGCAG
58079012 GTTGAAGATA
Statistics
Matches: 127, Mismatches: 16, Indels: 25
0.76 0.10 0.15
Matches are distributed among these distances:
40 1 0.01
41 28 0.22
42 4 0.03
43 10 0.08
44 77 0.61
45 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (43 bp):
TATCTCCTGAAGTTGCAGTGGAGCAGATCAAAATCACAGATCT
Found at i:58079719 original size:19 final size:17
Alignment explanation
Indices: 58079705--58079740 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
58079695 CATTTTATTA
58079705 TTTTTATCTCTTTTTAT
1 TTTTTATCTCTTTTTAT
58079722 TTTTTATCTC-TTTTAT
1 TTTTTATCTCTTTTTAT
58079738 TTT
1 TTT
58079741 CATTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATCTCTTTTTAT
Found at i:58084854 original size:20 final size:20
Alignment explanation
Indices: 58084829--58084866 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58084819 ATTCTGAGAT
58084829 ATATTATTAAAATTCTAATA
1 ATATTATTAAAATTCTAATA
*
58084849 ATATTATTATAATTCTAA
1 ATATTATTAAAATTCTAA
58084867 GATACAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTATTAAAATTCTAATA
Found at i:58086803 original size:7 final size:7
Alignment explanation
Indices: 58086791--58086817 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
58086781 CTCCTTTATT
58086791 TAATTTA
1 TAATTTA
58086798 TAATTTA
1 TAATTTA
58086805 TAATTTA
1 TAATTTA
58086812 TAATTT
1 TAATTT
58086818 TAAAACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TAATTTA
Found at i:58087561 original size:20 final size:21
Alignment explanation
Indices: 58087515--58087561 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
58087505 ATTTAATTTT
*
58087515 TTTTTCTTTTATATCCTTTTA
1 TTTTTCTTTTATATCCCTTTA
** *
58087536 ACTTTCTTTT-TTTCCCTTTA
1 TTTTTCTTTTATATCCCTTTA
58087556 TTTTTC
1 TTTTTC
58087562 ATTCTCTTCT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTTATATCCCTTTA
Found at i:58089891 original size:17 final size:18
Alignment explanation
Indices: 58089869--58089903 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
58089859 TATATGATAG
58089869 GTTAATAAATT-TAAATT
1 GTTAATAAATTATAAATT
*
58089886 GTTAATAATTTATAAATT
1 GTTAATAAATTATAAATT
58089904 TTTATTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
GTTAATAAATTATAAATT
Found at i:58095415 original size:20 final size:19
Alignment explanation
Indices: 58095369--58095419 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
58095359 AAGTCAACTT
58095369 GTATCGATACTTGGATAAA
1 GTATCGATACTTGGATAAA
* *
58095388 GTACCGATTCTTGGACCT-AA
1 GTATCGATACTTGGA--TAAA
58095408 GTATCGATACTT
1 GTATCGATACTT
58095420 TACATTGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 13 0.50
20 12 0.46
21 1 0.04
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (19 bp):
GTATCGATACTTGGATAAA
Found at i:58097205 original size:24 final size:24
Alignment explanation
Indices: 58097175--58097252 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
58097165 TGTATAACAA
58097175 GAAGCTCATAAGAGCCATAATCAG
1 GAAGCTCATAAGAGCCATAATCAG
** *
58097199 GAAGCTCATGTGAGCCAATAA-CGG
1 GAAGCTCATAAGAGCC-ATAATCAG
* **
58097223 GTAGCTCCGAAGAGCCATTAAT-AG
1 GAAGCTCATAAGAGCCA-TAATCAG
58097247 GAAGCT
1 GAAGCT
58097253 TCAGATACCC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
23 1 0.02
24 36 0.88
25 4 0.10
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCAG
Found at i:58097324 original size:25 final size:26
Alignment explanation
Indices: 58097294--58097351 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
58097284 AGCCATATCG
*
58097294 GGAAGCTC-CGGAAAGCCATTAATCA
1 GGAAGCTCACAGAAAGCCATTAATCA
* * *
58097319 GGAAGCTCACAGAGAGCCTTTAATCG
1 GGAAGCTCACAGAAAGCCATTAATCA
58097345 GGAAGCT
1 GGAAGCT
58097352 TTGAAAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACAGAAAGCCATTAATCA
Found at i:58097341 original size:26 final size:25
Alignment explanation
Indices: 58097187--58097351 Score: 76
Period size: 24 Copynumber: 6.8 Consensus size: 25
58097177 AGCTCATAAG
**
58097187 AGCCA-TAATCAGGAAGCT-CATGTG
1 AGCCATTAATCAGGAAGCTCCA-GAA
* * *
58097211 AGCCAATAA-CGGGTAGCTCC-GAA
1 AGCCATTAATCAGGAAGCTCCAGAA
* *
58097234 GAGCCATTAAT-AGGAAGCTTCAGAT
1 -AGCCATTAATCAGGAAGCTCCAGAA
* * * * **
58097259 ACCCA-TATATCGGGAAGTTCAAGCG
1 AGCCATTA-ATCAGGAAGCTCCAGAA
* *
58097284 AGCCA-T-ATCGGGAAGCTCCGGAA
1 AGCCATTAATCAGGAAGCTCCAGAA
*
58097307 AGCCATTAATCAGGAAGCTCACAGAG
1 AGCCATTAATCAGGAAGCTC-CAGAA
* *
58097333 AGCCTTTAATCGGGAAGCT
1 AGCCATTAATCAGGAAGCT
58097352 TTGAAAGCCA
Statistics
Matches: 104, Mismatches: 27, Indels: 18
0.70 0.18 0.12
Matches are distributed among these distances:
23 20 0.19
24 34 0.33
25 30 0.29
26 20 0.19
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
AGCCATTAATCAGGAAGCTCCAGAA
Found at i:58099659 original size:42 final size:42
Alignment explanation
Indices: 58099613--58099712 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
58099603 CCGTGTGACC
*
58099613 AGGCCGTGTGACTCACACGGCCTAGACACACGCCTGTGTCTA
1 AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
* * * * *
58099655 AGGCCGTGTGACTCCCGCGGTCTAGAGACACGCCCGTTTCTA
1 AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
* *
58099697 AAGCCGTGTAACTCAC
1 AGGCCGTGTGACTCAC
58099713 TGACTTGCAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (42 bp):
AGGCCGTGTGACTCACACGGCCTAGACACACGCCCGTGTCTA
Found at i:58100768 original size:20 final size:22
Alignment explanation
Indices: 58100734--58100774 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
58100724 CTTTACTTTC
*
58100734 CACACTCATTCCATATGCATAA
1 CACACTCATTCCATAAGCATAA
58100756 CACAC-CATT-CATAAGCATA
1 CACACTCATTCCATAAGCATA
58100775 TCATTCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (22 bp):
CACACTCATTCCATAAGCATAA
Found at i:58101487 original size:25 final size:25
Alignment explanation
Indices: 58101362--58101490 Score: 79
Period size: 25 Copynumber: 5.2 Consensus size: 25
58101352 AAGCTCTTTC
*
58101362 GAGCCATATAAT-GGGAAGCTCATGA
1 GAGCCAT-TAATAGGAAAGCTCATGA
* * * *
58101387 AAGTCATATAACAGG-AAGCTCATAA
1 GAGCCAT-TAATAGGAAAGCTCATGA
* * * *
58101412 GAGCC-GTAATTGGAAAGTTCATGC
1 GAGCCATTAATAGGAAAGCTCATGA
* * * *
58101436 GAGCCAAT-ATTGGGAAGCTC-CGAA
1 GAGCCATTAATAGGAAAGCTCATG-A
58101460 GAGCCATTAATAGGAAAGCTCATGA
1 GAGCCATTAATAGGAAAGCTCATGA
58101485 GAGCCA
1 GAGCCA
58101491 ATTATCGAGA
Statistics
Matches: 77, Mismatches: 21, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
23 6 0.08
24 29 0.38
25 39 0.51
26 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATAGGAAAGCTCATGA
Found at i:58101489 original size:49 final size:48
Alignment explanation
Indices: 58101400--58101492 Score: 123
Period size: 49 Copynumber: 1.9 Consensus size: 48
58101390 TCATATAACA
* * * *
58101400 GGAAGCTCATAAGAGCCGTAATTGGAAAGTTCATGCGAGCCAATATTG
1 GGAAGCTCAGAAGAGCCGTAATAGGAAAGCTCATGAGAGCCAATATTG
* *
58101448 GGAAGCTCCGAAGAGCCATTAATAGGAAAGCTCATGAGAGCCAAT
1 GGAAGCTCAGAAGAGCC-GTAATAGGAAAGCTCATGAGAGCCAAT
58101493 TATCGAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
48 15 0.39
49 23 0.61
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.19
Consensus pattern (48 bp):
GGAAGCTCAGAAGAGCCGTAATAGGAAAGCTCATGAGAGCCAATATTG
Found at i:58101538 original size:25 final size:24
Alignment explanation
Indices: 58101475--58101641 Score: 95
Period size: 25 Copynumber: 6.7 Consensus size: 24
58101465 ATTAATAGGA
* *
58101475 AAGCTCATGAGAGCCAATTATCGAG
1 AAGCTCAT-AGAGCCAATTAACGGG
* * *
58101500 AAACTCCAGAGAGCCAATTACCGGG
1 AAGCT-CATAGAGCCAATTAACGGG
*
58101525 AAGCTCATACGAGCC-ATAAACGGG
1 AAGCTCATA-GAGCCAATTAACGGG
* *
58101549 AAGCTCAAAAAAGCC-ATTAAATCGGG
1 AAGCTC-ATAGAGCCAATT-AA-CGGG
* * *
58101575 AAGCTCATGAGAGCTAAATAATGGG
1 AAGCTCAT-AGAGCCAATTAACGGG
* * * *
58101600 AACCTTATAAGAGCCAAGTATCGGG
1 AAGCTCAT-AGAGCCAATTAACGGG
*
58101625 AAGCTCGTGAGAGCCAA
1 AAGCTCAT-AGAGCCAA
58101642 ATATTGAGAC
Statistics
Matches: 108, Mismatches: 27, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
24 22 0.20
25 66 0.61
26 18 0.17
27 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (24 bp):
AAGCTCATAGAGCCAATTAACGGG
Found at i:58101550 original size:24 final size:26
Alignment explanation
Indices: 58101521--58101582 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 26
58101511 AGCCAATTAC
**
58101521 CGGGAAGCTCATACGAGCCA-TAAA-
1 CGGGAAGCTCATAAAAGCCATTAAAT
*
58101545 CGGGAAGCTCAAAAAAGCCATTAAAT
1 CGGGAAGCTCATAAAAGCCATTAAAT
58101571 CGGGAAGCTCAT
1 CGGGAAGCTCAT
58101583 GAGAGCTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 17 0.53
25 4 0.12
26 11 0.34
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CGGGAAGCTCATAAAAGCCATTAAAT
Found at i:58105005 original size:17 final size:18
Alignment explanation
Indices: 58104983--58105017 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58104973 AACAAGTAAT
58104983 TTAATATT-TTTATTTTA
1 TTAATATTATTTATTTTA
58105000 TTAATATTATTTATTTTA
1 TTAATATTATTTATTTTA
58105018 AATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTAATATTATTTATTTTA
Found at i:58110148 original size:3 final size:3
Alignment explanation
Indices: 58110140--58110164 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58110130 TATTGTCCCT
58110140 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
58110165 ATTTATCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58112216 original size:19 final size:18
Alignment explanation
Indices: 58112176--58112219 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
58112166 TTTCTCTTTT
58112176 TTGCATTCATTGTATTCA
1 TTGCATTCATTGTATTCA
58112194 TTGCATTCA-TGTATTAACA
1 TTGCATTCATTGTATT--CA
58112213 TTGCATT
1 TTGCATT
58112220 GTATCATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 9 0.38
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (18 bp):
TTGCATTCATTGTATTCA
Found at i:58112233 original size:19 final size:18
Alignment explanation
Indices: 58112177--58112233 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
58112167 TTCTCTTTTT
58112177 TGCATTCATTGTATTCAT-
1 TGCATTCATTGTA-TCATA
58112195 TGCATTCA-TGTAT--TA
1 TGCATTCATTGTATCATA
*
58112210 -ACATTGCATTGTATCATA
1 TGCATT-CATTGTATCATA
58112228 TGCATT
1 TGCATT
58112234 AAGTCTCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 6 0.19
17 4 0.13
18 10 0.32
19 4 0.13
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (18 bp):
TGCATTCATTGTATCATA
Found at i:58114778 original size:22 final size:23
Alignment explanation
Indices: 58114736--58114779 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
58114726 ACTTCACTTT
*
58114736 AAAAAAAAATAATAAATGAAAAC
1 AAAAAAAAATAATAAAAGAAAAC
58114759 AAAAAAAGAA-AA-AAAAGAAAA
1 AAAAAAA-AATAATAAAAGAAAA
58114780 AGAAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAAAAATAATAAAAGAAAAC
Found at i:58115495 original size:15 final size:16
Alignment explanation
Indices: 58115471--58115501 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
58115461 TAAAAATGAC
58115471 AATATGCATTCATACA
1 AATATGCATTCATACA
58115487 AATAT-CATTCATACA
1 AATATGCATTCATACA
58115502 CATCTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32
Consensus pattern (16 bp):
AATATGCATTCATACA
Found at i:58115848 original size:54 final size:52
Alignment explanation
Indices: 58115779--58116337 Score: 203
Period size: 54 Copynumber: 11.4 Consensus size: 52
58115769 TTCCCTGGCA
* * *
58115779 TTGCAGTGAAACAGATTAAAGCTACAAATTATGCCAAATCTTATCTTCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
* * *
58115833 TTGCAGTGGAGCAGATTGAAGCTAC-------C-AACCTTATC-TCTTTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTC-CTGAAG
* * * * **
58115877 TTACAGCGGAGCAGACTGAAG--AC-----ATCGAATCTTAT-TTCCCTGGCG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAAG
* * *
58115922 TTGCAGTGGAACAGATTAAAGCTA-AATATTATAACGGATCTTATCTTCCTAAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAA-ATTAT--CGAATCTTATCTTCCTGAAG
* *
58115976 TTGCAGTTGAGCAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTA-T-CGAATCTTATCTTCCTGAAG
** * *
58116030 TTGCAGTGGAGCAGATTAAAGC--C--ACCA--GCA--TTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
* * * * * **
58116074 TTACAGCGGAGCAGACTGAAG--AC-----AGCGAATCTTAT-TTCCCTGGCG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAAG
* * *
58116119 TTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
* * ** * *
58116173 TTACGGTGGAGCAGATTAAAGC--C--ACCA--GCA--TTATCTCCCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
* * *
58116217 TTGCAGCGGAGCAGACT---G--A-AAA-CATCGAATCTTAT-TTCCCT-AACG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTT-CCTGAA-G
* * * * *
58116262 TTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATTTTATCTTTCTGAAG
1 TTGCAGTGGAGCAGATTAAAGCTACAAATTAT--CGAATCTTATCTTCCTGAAG
*
58116316 TTGCAGTAGAGCAGATTAAAGC
1 TTGCAGTGGAGCAGATTAAAGC
58116338 CACCAGCATT
Statistics
Matches: 374, Mismatches: 76, Indels: 110
0.67 0.14 0.20
Matches are distributed among these distances:
41 4 0.01
42 3 0.01
43 6 0.02
44 92 0.25
45 74 0.20
46 5 0.01
47 3 0.01
48 1 0.00
50 4 0.01
51 3 0.01
52 7 0.02
54 161 0.43
55 11 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (52 bp):
TTGCAGTGGAGCAGATTAAAGCTACAAATTATCGAATCTTATCTTCCTGAAG
Found at i:58115926 original size:143 final size:142
Alignment explanation
Indices: 58115662--58116000 Score: 464
Period size: 143 Copynumber: 2.4 Consensus size: 142
58115652 GATTGAAGTC
* * * * *
58115662 ATTATGACAGATCTTATCTTCTTGAAGTTGTAGTGGAGCAAAGATTGAAGCCACTAGCCTTATCT
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGC--AGATTGAAGCTACCAACCTTATCT
* *
58115727 CCCTGAAGTTGCGCGGAGCAGATTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACA
64 CCCTGAAGTTACGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACA
58115792 GATTAAAGCTACAA-
129 GATTAAAGCTA-AAT
* * *
58115806 ATTATGCCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCT
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCC
* * * *
58115871 TTGAAGTTACAGCGGAGCAGACTGAAGACATCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAG
66 CTGAAGTTAC-GCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACAG
58115936 ATTAAAGCTAAAT
130 ATTAAAGCTAAAT
* * * * *
58115949 ATTATAACGGATCTTATCTTCCTAAAGTTGCAGTTGAGCAGATTAAAGCTAC
1 ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
58116001 AAGTTATTGC
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
142 32 0.19
143 105 0.61
144 35 0.20
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (142 bp):
ATTATGACAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACCAACCTTATCTCC
CTGAAGTTACGCGGAGCAGACTGAAGACATCAAATCTTATTTCCCTGGCATTGCAGTGAAACAGA
TTAAAGCTAAAT
Found at i:58115993 original size:197 final size:197
Alignment explanation
Indices: 58115790--58116194 Score: 634
Period size: 197 Copynumber: 2.1 Consensus size: 197
58115780 TGCAGTGAAA
*
58115790 CAGATTAAAGCTACAAATTA-TGCCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
1 CAGATTAAAGCTACAAATTATTG-CAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAG
* * ** *
58115854 CTACCAACCTTATCTCTTTGAAGTTACAGCGGAGCAGACTGAAGACATCGAATCTTATTTCCCTG
65 CCACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTG
*
58115919 GCGTTGCAGTGGAACAGATTAAAGCTA-AATATTATAACGGATCTTATCTTCCTAAAGTTGCAGT
130 GCGTTGCAGTGGAACAGATTAAAGCTACAA-ATTATAACGGATCTTATCTTCCTAAAGTTACAGT
*
58115983 TGAG
194 GGAG
* *
58115987 CAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
1 CAGATTAAAGCTACAAATTATTGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
*
58116052 CACCAGCATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
66 CACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
** * * *
58116117 CGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTCTTGAAGTTACGGTGG
131 CGTTGCAGTGGAACAGATTAAAGCTACAAATTATAACGGATCTTATCTTCCTAAAGTTACAGTGG
58116182 AG
196 AG
58116184 CAGATTAAAGC
1 CAGATTAAAGC
58116195 CACCAGCATT
Statistics
Matches: 190, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
197 186 0.98
198 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (197 bp):
CAGATTAAAGCTACAAATTATTGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGC
CACCAACATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGG
CGTTGCAGTGGAACAGATTAAAGCTACAAATTATAACGGATCTTATCTTCCTAAAGTTACAGTGG
AG
Found at i:58116071 original size:44 final size:45
Alignment explanation
Indices: 58116016--58116374 Score: 183
Period size: 44 Copynumber: 7.6 Consensus size: 45
58116006 ATTGCGAATC
*
58116016 TTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCA-
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* * * * * * *
58116060 TTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGC-GAAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* ** * **
58116104 CTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGAT
1 -TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C--ACCA--GC--AT
* * * *
58116158 CTTATCTTCTTGAAGTTACGGTGGAGCAGATTAAAGCCACCAGCA-
1 -TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
* * * * *
58116203 TTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAA-ACATC-GAAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCCACCAGCAT
* * * **
58116247 CTTATTTCCCT-AACGTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATT
1 -TTATCTCCCTGAA-GTTGCAGTGGAGCAGATTAAAGC--C--ACCA--GC--A-T
** *
58116302 TTATCTTTCTGAAGTTGCAGTAGAGCAGATTAAAGCCACCAGCA-
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
*
58116346 TTATCTCCCTGAAGTTGCAGCGGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
58116375 CTGAAGACAG
Statistics
Matches: 229, Mismatches: 59, Indels: 54
0.67 0.17 0.16
Matches are distributed among these distances:
43 4 0.02
44 91 0.40
45 53 0.23
46 2 0.01
47 2 0.01
48 4 0.02
49 3 0.01
50 4 0.02
52 4 0.02
54 59 0.26
55 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAGCAT
Found at i:58116433 original size:143 final size:143
Alignment explanation
Indices: 58115975--58116419 Score: 712
Period size: 143 Copynumber: 3.1 Consensus size: 143
58115965 TCTTCCTAAA
* * * * * *
58115975 GTTGCAGTTGAGCAGATTAAAGCTACAAGTTATTGCGAATCTTATCTTCCTGAAGTTGCAGTGGA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
*
58116040 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTACAGCGGAGCAGACTGAAGACAGCGAATC
66 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
58116105 TTATTTCCCTGGC
131 TTATTTCCCTGGC
* *
58116118 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATC-TTCTTGAAGTTACGGTGG
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTC-TGAAGTTGCAGTGG
* *
58116182 AGCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAAACATCGAAT
65 AGCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAAT
**
58116247 CTTATTTCCCTAAC
130 CTTATTTCCCTGGC
* * *
58116261 GTTGCAGTGGAACAAATTAAAGCTACAAATTATGGCGGATTTTATCTTTCTGAAGTTGCAGTAGA
1 GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
58116326 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
66 GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
58116391 TTATTTCCCTGGC
131 TTATTTCCCTGGC
* *
58116404 GTTGCAATGGAGCAGA
1 GTTGCAGTGGAACAGA
58116420 CTAGAACCAC
Statistics
Matches: 275, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
142 2 0.01
143 270 0.98
144 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (143 bp):
GTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGGATCTTATCTTTCTGAAGTTGCAGTGGA
GCAGATTAAAGCCACCAGCATTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATC
TTATTTCCCTGGC
Found at i:58116630 original size:133 final size:133
Alignment explanation
Indices: 58116354--58116636 Score: 413
Period size: 133 Copynumber: 2.1 Consensus size: 133
58116344 CATTATCTCC
* *
58116354 CTGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
1 CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
* * * * *
58116419 ACTAGAACCACAAATCTCGTCCCCCTGAAGTTGCGGCAGAGTAGATTGAGGGTACAAATCGTATT
66 ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
*
58116484 TCT
131 TAT
* * * * * *
58116487 TTGAAATTGTAGCGGAGCAGACTGAATACAGCAAATCTTATTTCCTTGGCGTTGTAGTGGAGCAG
1 CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
* *
58116552 ATTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGGTTGAGGGTACAAATCGTATC
66 ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
58116617 TAT
131 TAT
*
58116620 CTGAAGTTGTAGTGGAG
1 CTGAAGTTGTAGCGGAG
58116637 TGGATCGAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
133 131 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.25
Consensus pattern (133 bp):
CTGAAGTTGTAGCGGAGCAGACTGAAGACAGCAAATCTTATTTCCCTGGCGTTGCAATGGAGCAG
ACTAAAACAAAAAATCTCGTCCCCCTGAAGTTGCGGCAGAATAGATTGAGGGTACAAATCGTATC
TAT
Found at i:58116668 original size:28 final size:28
Alignment explanation
Indices: 58116628--58116684 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
58116618 ATCTGAAGTT
*
58116628 GTAGTGGAGTGGATCGAAACAACAAGAC
1 GTAGTGGACTGGATCGAAACAACAAGAC
*
58116656 GTAGTGGACTGGATCGAAGCAACAAGAC
1 GTAGTGGACTGGATCGAAACAACAAGAC
58116684 G
1 G
58116685 CATAGACTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.33, T:0.14
Consensus pattern (28 bp):
GTAGTGGACTGGATCGAAACAACAAGAC
Found at i:58118274 original size:5 final size:6
Alignment explanation
Indices: 58118226--58118281 Score: 51
Period size: 6 Copynumber: 8.7 Consensus size: 6
58118216 AATTAGTTTG
*
58118226 TTTTAT TTTTATT TCTTTCAT TATTTA- TCTTAT TATTTAT TTTTAT TTTTAT
1 TTTTAT TTTTA-T T-TTT-AT T-TTTAT TTTTAT T-TTTAT TTTTAT TTTTAT
58118278 TTTT
1 TTTT
58118282 CTCTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
5 3 0.07
6 22 0.52
7 8 0.19
8 8 0.19
9 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:58118287 original size:30 final size:34
Alignment explanation
Indices: 58118227--58118292 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 34
58118217 ATTAGTTTGT
58118227 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
1 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
*
58118261 TTTATTTTTA-TT-TTT-ATT-TTTCTCTTATTA
1 TTTATTTTTATTTCTTTCATTATTTATCTTATTA
58118291 TT
1 TT
58118293 GTCGTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 13 0.42
31 3 0.10
32 3 0.10
33 2 0.06
34 10 0.32
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (34 bp):
TTTATTTTTATTTCTTTCATTATTTATCTTATTA
Found at i:58121283 original size:4 final size:4
Alignment explanation
Indices: 58121282--58121328 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
58121272 TTTATATATA
* *
58121282 TATG TATG TATG TATG TATG TATG TATG TATG TATA TATA TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
58121329 TGCTTATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:58125618 original size:27 final size:27
Alignment explanation
Indices: 58125580--58125631 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
58125570 ATCCATGATG
*
58125580 CTTTTACTTATTAAAAATTTCAAATTT
1 CTTTTACCTATTAAAAATTTCAAATTT
58125607 CTTTTACCTATTAAAAATTTCAAAT
1 CTTTTACCTATTAAAAATTTCAAAT
58125632 ATATTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.48
Consensus pattern (27 bp):
CTTTTACCTATTAAAAATTTCAAATTT
Found at i:58126469 original size:16 final size:16
Alignment explanation
Indices: 58126448--58126502 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
58126438 AGAATGGAAA
58126448 GAAAATTGAAAGGATG
1 GAAAATTGAAAGGATG
**
58126464 GAAAATTGGAGGGGATG
1 GAAAATT-GAAAGGATG
*
58126481 GAAAACT-AGAAGGATG
1 GAAAATTGA-AAGGATG
58126497 GAAAAT
1 GAAAAT
58126503 ATAATTTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 1 0.03
16 17 0.55
17 13 0.42
ACGTcount: A:0.47, C:0.02, G:0.35, T:0.16
Consensus pattern (16 bp):
GAAAATTGAAAGGATG
Found at i:58127286 original size:18 final size:17
Alignment explanation
Indices: 58127247--58127288 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
58127237 TATTTCTTTT
*
58127247 TTTTTC-TTTTTCTAAA
1 TTTTTCTTTTTTCAAAA
58127263 TCTTTTCTTTTTTCAATAA
1 T-TTTTCTTTTTTCAA-AA
58127282 TTTTTCT
1 TTTTTCT
58127289 CATCTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 5 0.23
18 13 0.59
19 3 0.14
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTCTTTTTTCAAAA
Found at i:58127569 original size:11 final size:11
Alignment explanation
Indices: 58127553--58127578 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58127543 TATTTTTTAA
58127553 TTTTAAAATAT
1 TTTTAAAATAT
58127564 TTTTAAAATAT
1 TTTTAAAATAT
58127575 TTTT
1 TTTT
58127579 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:58129624 original size:297 final size:293
Alignment explanation
Indices: 58129073--58129892 Score: 821
Period size: 298 Copynumber: 2.8 Consensus size: 293
58129063 GCATATGATG
* * * * *
58129073 TTTAT-CTATACTATTATTTAAGCTCCTAACTGAGTTGGTGTCACCCTTAATTAGGTCACCAACT
1 TTTATACT-TACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACTAGATCACCAAAT
* * **
58129137 CGATTAG-GAAAATTAT-GAAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGA-ACACA
65 TGATTAGAAAAAATTATAG-AAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGA-GTA
* * * * * *
58129199 CTTTAGTTTTTT-TTATTAAAAAGATCAATAAAAATATGCAAATGATGATATTTGAGA-TTGAAC
128 CTTTAGTTTTTTATTTTTTAAAA-AT--A-AAAAATATGCATATG-TGA-ATTT-AAACCTAAAC
* * * *
58129262 TAATTGCATTAATAAAATCTTTAATTTACCACTCAACTAAAATTTTATTTTAATATTTTATACAT
186 -AATTGCATTAGTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTTATACAT
58129327 TTTAA-TTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
250 TTTAATTTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
58129370 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACCTA-ATCACCAAAT
1 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAA-CTAGATCACCAAAT
* *
58129434 TGATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTTGAGGGTACT
65 TGATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGAGTACT
58129499 TTAGTATTTTTATTTTTTAAAAATAAAAAATATGCATATAGTGAGATTTAAACCTAAATCAATTG
130 TTAGT-TTTTTATTTTTTAAAAATAAAAAATATGCATAT-GTGA-ATTTAAACCTAAA-CAATTG
* *
58129564 CATTAGTAAATTTTTTAATTTGCCACTCAACTAAAATTTTATTTTGACATTTTCATACATTTTAA
191 CATTAGTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTT-ATACATTTTAA
* * * * *
58129629 TTTTATTATGCATACTTTATTACTTCCATCAATTTTATT
255 TTTTATTATGCAAACTTAATCACTTCCATCAATTGTATA
*** * * * *
58129668 TTTATACTTACTATTA-TT--GCTCTTGTTTGAGTTGATGTTACCCTCAA-TCAGATTACC-AAC
1 TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACT-AGATCACCAAAT
* * * * * *
58129728 TCATTA-AAGAATTTACGAAATACCATTACCCTTTTGTAATTAAAATAAATTATATTATTCGAGA
65 TGATTAGAAAAAATTA-TAGA-A--A-TACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGA
* * * *
58129792 GTACTTTAGTCTTTTTATTTTTTTTAAAAAT-AAAATTAAGCATATGGTGTAATTTGAACCCAAA
125 GTACTTTAGT-TTTTTA--TTTTTTAAAAATAAAAAATATGCATAT-GTG-AATTTAAACCTAAA
**
58129856 CCAATTATATTAGTAAAATTTTTT-A-TTACCAC-CAACT
185 -CAATTGCATTAGT-AAATTTTTTAATTTACCACTCAACT
58129893 CGGTTAGAAA
Statistics
Matches: 446, Mismatches: 54, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
293 8 0.02
294 10 0.02
295 32 0.07
296 75 0.17
297 81 0.18
298 164 0.37
299 46 0.10
300 30 0.07
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (293 bp):
TTTATACTTACTATTATTTAAGCTCTTAACTGAGTTGGTGTCACCCTCAACTAGATCACCAAATT
GATTAGAAAAAATTATAGAAATACCCTTTTGTAATTAAAATAAGTTATATTATTCGAGAGTACTT
TAGTTTTTTATTTTTTAAAAATAAAAAATATGCATATGTGAATTTAAACCTAAACAATTGCATTA
GTAAATTTTTTAATTTACCACTCAACTAAAATTTTATTTTAACATTTTATACATTTTAATTTTAT
TATGCAAACTTAATCACTTCCATCAATTGTATA
Found at i:58134490 original size:29 final size:29
Alignment explanation
Indices: 58134445--58134518 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
58134435 ACGACGCAGA
58134445 CCCATCAACAGCACCCAGACAATCACCGG
1 CCCATCAACAGCACCCAGACAATCACCGG
* * * *
58134474 CCCATCATCAGCGCCCATACAATCACCAAG
1 CCCATCAACAGCACCCAGACAATCACC-GG
*
58134504 CCCAACAACAGCACC
1 CCCATCAACAGCACC
58134519 GACACAGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 24 0.65
30 13 0.35
ACGTcount: A:0.35, C:0.46, G:0.11, T:0.08
Consensus pattern (29 bp):
CCCATCAACAGCACCCAGACAATCACCGG
Found at i:58138555 original size:125 final size:126
Alignment explanation
Indices: 58138330--58138871 Score: 696
Period size: 125 Copynumber: 4.3 Consensus size: 126
58138320 TCAGGCCAAA
* * * *
58138330 CAGGAGCTACTGTAGCAAAAGCGTGTCCATGTAGGAGCTTCTTTCAGTACTTTTGCTGTCAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
*
58138395 ATCCTGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTACTCGAAATTA-TTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * * * *
58138455 CAGGAGTTACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTTAGTATTTTTGTTGGCAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
* ** *
58138520 ATCCTACTTAAAATGTTTTTGACACTATTTGCTCAGAAATGTCTACTCGAAATTA-TTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* * * * * * *
58138580 CAAGAGCTACTATAGCAAAAGTGCGTCAATGGGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
* * * ** *
58138645 ATCTTGCTTAAAGCATTTTTGACACTATTTGCTTAGAAATATCTACTTGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
* ** * *
58138706 CAGGAGCTACTGTAGCAAAAGCGCGTCCACATGAAAGCTTCTTTCAGTACTTTTACT-GAAAATG
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAA-G
** *
58138770 CATCCTGCTTAAAGCGTTTTT-ACACTATTTGCTCAGAAACGTCTTTTCAAAATTATTTTTTT
65 CATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTA-TTTTTT
* * *
58138832 CAGAAGCTACTGTAACAAAAGAGCGTCCACGTGGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
58138872 TTTTAAATTA
Statistics
Matches: 355, Mismatches: 59, Indels: 5
0.85 0.14 0.01
Matches are distributed among these distances:
125 243 0.68
126 112 0.32
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGGCAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTT
Found at i:58139108 original size:95 final size:95
Alignment explanation
Indices: 58138908--58139206 Score: 397
Period size: 95 Copynumber: 3.1 Consensus size: 95
58138898 AGTAACCATA
* * *
58138908 AACCCCAAACCCTAATTTATTTGAGTTTTTCCTTTAAAACCCTAAACACTAAACCCTAATCTAAT
1 AACCCTAAACCCTAATTTATTTGA-TTTTTTC-TTAAAAACCTAAACACTAAACCCTAATCTAAT
*
58138973 TTTTTAAAAATTTATAATTAATTTACTCAAGT
64 TTTTTAAAAATTTATAATTAATTTACTTAAGT
*
58139005 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACTCTTAACACTAAACCCTAATCTAATT
1 AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAAC-CTAAACACTAAACCCTAATCTAATT
*
58139070 TTTTAAAAATTT-TAATTAAATTACTTAAGT
65 TTTTAAAAATTTATAATTAATTTACTTAAGT
* * *
58139100 AACCCTAAACCCTAATTTAATTGATTTTTTCTTTAAAAACCATAAACAC-AAAACCTAATCCAA-
1 AACCCTAAACCCTAATTTATTTGATTTTTTC-TTAAAAACC-TAAACACTAAACCCTAATCTAAT
* * * * *
58139163 TTTTGAAAATTTTATAATTAATTTAATTGAGA
64 TTTTTAAAAATTTATAATTAATTTACTTAAGT
*
58139195 AATCCTAAACCC
1 AACCCTAAACCC
58139207 CAATCCCTTA
Statistics
Matches: 181, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
94 11 0.06
95 91 0.50
96 56 0.31
97 23 0.13
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (95 bp):
AACCCTAAACCCTAATTTATTTGATTTTTTCTTAAAAACCTAAACACTAAACCCTAATCTAATTT
TTTAAAAATTTATAATTAATTTACTTAAGT
Found at i:58145543 original size:24 final size:24
Alignment explanation
Indices: 58145509--58145559 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
58145499 TTTCTAGAAG
* *
58145509 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
58145533 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
58145557 ATT
1 ATT
58145560 CGACTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:58149275 original size:22 final size:22
Alignment explanation
Indices: 58149229--58149304 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 22
58149219 TGTCAATGAA
58149229 TTTCCAGAGAAAAAGA-AAAGG-T
1 TTTCCAG-GAAAAA-ACAAAGGAT
*
58149251 TTTCCAGGAAAAAACATAGGAT
1 TTTCCAGGAAAAAACAAAGGAT
* **
58149273 TTTCCGAGAAAGAAAACCGAGGAT
1 TTTCC-AGGAA-AAAACAAAGGAT
58149297 TTTCCAGG
1 TTTCCAGG
58149305 GTCTAAAAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 10 0.22
22 13 0.29
23 6 0.13
24 15 0.33
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.21
Consensus pattern (22 bp):
TTTCCAGGAAAAAACAAAGGAT
Found at i:58152739 original size:17 final size:16
Alignment explanation
Indices: 58152712--58152746 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
58152702 ATTTTCTCAA
58152712 AAATAAATAAAAAAAG
1 AAATAAATAAAAAAAG
*
58152728 AAATACAATAAAAATAG
1 AAATA-AATAAAAAAAG
58152745 AA
1 AA
58152747 TTTTGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAATAAAAAAAG
Found at i:58153934 original size:4 final size:4
Alignment explanation
Indices: 58153919--58153959 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
58153909 TATTTTATCT
58153919 TTTA TCTTA TTTA TTTA TTTA TTT- TTTCA TTTA TTTA TTTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA
58153960 CCTATCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 3 0.09
4 24 0.71
5 7 0.21
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:58161047 original size:13 final size:13
Alignment explanation
Indices: 58161022--58161059 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
58161012 ATTAAAAATC
58161022 TAAATTATT-ATT
1 TAAATTATTAATT
58161034 T-AATATATTAATT
1 TAAAT-TATTAATT
58161047 TAAATTATTAATT
1 TAAATTATTAATT
58161060 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.13
12 5 0.22
13 12 0.52
14 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAAATTATTAATT
Found at i:58161191 original size:105 final size:103
Alignment explanation
Indices: 58161040--58161337 Score: 304
Period size: 105 Copynumber: 2.9 Consensus size: 103
58161030 TATTTAATAT
* * *** **
58161040 ATTAATTTAAATTATTAATTATTTTAAATAAATTAGGTTTAGAATTATCCTAATTTAATTTAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
58161105 TCATAATTATCTTAATTGAAATCCAAATTAATATCTAAACA
66 TCATAATTATCTTAATT-AAAT--AAATTAATATCTAAACA
* ** *
58161146 ATTAA-TTAAATTCCTAATTATCTTATCTAAATTAGAACTCTAATTATCCTAATTTAATTCAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
* * * * * *
58161210 TCTTAA-T-TC--AA--ATATAAAATATTATCTAACCT
66 TCATAATTATCTTAATTAAATAAATTAATATCTAAACA
* * *
58161242 ATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCTAGTTATCCTTATTTAATTTAAAC
1 ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
* *
58161307 TCCTAATTATCTTATTTAAATTAAAATTAAT
66 TCATAATTATCTTAATTAAA-T-AAATTAAT
58161338 TTAATTTAAA
Statistics
Matches: 154, Mismatches: 29, Indels: 19
0.76 0.14 0.09
Matches are distributed among these distances:
96 18 0.12
97 57 0.37
98 4 0.03
99 2 0.01
101 3 0.02
103 4 0.03
104 2 0.01
105 59 0.38
106 5 0.03
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.44
Consensus pattern (103 bp):
ATTAATTTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTTAATTTAAAC
TCATAATTATCTTAATTAAATAAATTAATATCTAAACA
Found at i:58161279 original size:97 final size:96
Alignment explanation
Indices: 58161136--58161314 Score: 259
Period size: 97 Copynumber: 1.9 Consensus size: 96
58161126 TCCAAATTAA
* **
58161136 TATCTAAACAATTAATTAAATTCCTAATTATCTTATCTAAATTAGAACTCTAATTATCCTAATTT
1 TATCTAAACAATTAATTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTT
*
58161201 AATTCAAACTCTTAATTCAAATATAAAATAT
66 AATTCAAACTCCTAATTCAAATATAAAATAT
* * * * *
58161232 TATCTAACCTATTAATTTAAATTATTAATTATCTTAAATAAATTAGAACTCTAGTTATCCTTATT
1 TATCTAAACAATTAA-TTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATT
*
58161297 TAATTTAAACTCCTAATT
65 TAATTCAAACTCCTAATT
58161315 ATCTTATTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 13 0.18
97 59 0.82
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (96 bp):
TATCTAAACAATTAATTAAATTACTAATTATCTTAAATAAATTAGAACTCTAATTATCCTAATTT
AATTCAAACTCCTAATTCAAATATAAAATAT
Found at i:58161301 original size:26 final size:26
Alignment explanation
Indices: 58161243--58161331 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
58161233 ATCTAACCTA
* ** *
58161243 TTAATTTAAATTATTAATTATCTTAA
1 TTAATTTAAACTCCTAATTATCTTAT
* * *
58161269 ATAAATTAGAACT-CTAGTTATCCTTAT
1 TTAATTTA-AACTCCTAATTAT-CTTAT
58161296 TTAATTTAAACTCCTAATTATCTTAT
1 TTAATTTAAACTCCTAATTATCTTAT
*
58161322 TTAAATTAAA
1 TTAATTTAAA
58161332 ATTAATTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 30 0.60
27 20 0.40
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TTAATTTAAACTCCTAATTATCTTAT
Found at i:58161316 original size:21 final size:21
Alignment explanation
Indices: 58161292--58161350 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
58161282 CTAGTTATCC
**
58161292 TTATTTAATTTAAACTCCTAA
1 TTATTTAATTTAAACTCAAAA
*
58161313 TTATCTT-ATTTAAA-TTAAAA
1 TTAT-TTAATTTAAACTCAAAA
58161333 TTAATTTAATTTAAACTC
1 TT-ATTTAATTTAAACTC
58161351 TTAGTTGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 7 0.23
21 20 0.67
22 3 0.10
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATTTAATTTAAACTCAAAA
Found at i:58161316 original size:27 final size:25
Alignment explanation
Indices: 58161257--58161331 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
58161247 TTTAAATTAT
**
58161257 TAATTATCTTAAATAAATTAGAACTC
1 TAATTATCTTATTTAAATTA-AACTC
* *
58161283 TAGTTATCCTTATTTAATTTAAACTCC
1 TAATTAT-CTTATTTAAATTAAACT-C
58161310 TAATTATCTTATTTAAATTAAA
1 TAATTATCTTATTTAAATTAAA
58161332 ATTAATTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 24 0.59
27 17 0.41
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (25 bp):
TAATTATCTTATTTAAATTAAACTC
Found at i:58165438 original size:14 final size:14
Alignment explanation
Indices: 58165419--58165447 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58165409 CCATACTTCC
58165419 GTGAAACCCATATG
1 GTGAAACCCATATG
58165433 GTGAAACCCATATG
1 GTGAAACCCATATG
58165447 G
1 G
58165448 ACAAGATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (14 bp):
GTGAAACCCATATG
Found at i:58170359 original size:6 final size:6
Alignment explanation
Indices: 58170342--58170388 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
58170332 AAAATGAGAC
*
58170342 TATAAA TGTAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAA
58170389 TTTGACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:58174266 original size:14 final size:14
Alignment explanation
Indices: 58174243--58174273 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
58174233 TGTCGTGTTT
*
58174243 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
58174257 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
58174271 TTA
1 TTA
58174274 AAACAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:58174829 original size:103 final size:103
Alignment explanation
Indices: 58174650--58174854 Score: 365
Period size: 103 Copynumber: 2.0 Consensus size: 103
58174640 GTACAGCTCG
* *
58174650 CAGAAACCGTAGAGAAGCAAGGCATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
1 CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
58174715 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
66 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
* * *
58174753 CAGAAACCGTAAAGAAGCACGACATAGTTGACAGTATATAGTGGAAGAGTAATAGGACGTTATTA
1 CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
58174818 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCA
66 TTATCACTGAAGAGATGGGTGATAATCAGAATAATCA
58174855 GCTACCTCTT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (103 bp):
CAGAAACCGTAAAGAAGCAAGACATAGTCGACAGTATATAGTGGAAGAGCAATAGGACGTTATTA
TTATCACTGAAGAGATGGGTGATAATCAGAATAATCAC
Found at i:58191544 original size:12 final size:12
Alignment explanation
Indices: 58191527--58191552 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58191517 ACCGTCCACC
58191527 CATTACTAAGCA
1 CATTACTAAGCA
58191539 CATTACTAAGCA
1 CATTACTAAGCA
58191551 CA
1 CA
58191553 ATGCTGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.23
Consensus pattern (12 bp):
CATTACTAAGCA
Found at i:58195274 original size:19 final size:19
Alignment explanation
Indices: 58195252--58195288 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
58195242 TTTTTATTTT
58195252 TTTA-TTTAATTATAAAGTA
1 TTTAGTTTAATT-TAAAGTA
58195271 TTTAGTTTAATTTAAAGT
1 TTTAGTTTAATTTAAAGT
58195289 TTTTCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTAGTTTAATTTAAAGTA
Found at i:58196415 original size:106 final size:109
Alignment explanation
Indices: 58196294--58196501 Score: 343
Period size: 106 Copynumber: 1.9 Consensus size: 109
58196284 TTAAACAAAA
*
58196294 TTATTAGTAAAAAAACTATATAGTTT-ATCTATATAATACCTAATTGAAAATATATGATTTGTAT
1 TTATTAGTAAAAAAACTATATA-TTTGATCTATATAATACCCAATTGAAAATATATGATTTGTAT
*
58196358 TAAAATTATAATTCT-AAAA-AAA-TTGTAATTAAAATACAAGTG
65 TAAAATTATAATTCTAAAAATAAATTTATAATTAAAATACAAGTG
* *
58196400 TTATTAGTAAAAAAACTATATATTTGATCTTTATAATACCCAATTGAAAATATATTATTTGTATT
1 TTATTAGTAAAAAAACTATATATTTGATCTATATAATACCCAATTGAAAATATATGATTTGTATT
58196465 AAAATTATAATTCTAAAAATAAATTTATAATTAAAAT
66 AAAATTATAATTCTAAAAATAAATTTATAATTAAAAT
58196502 GAAAGTTTTA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
105 3 0.03
106 72 0.77
107 4 0.04
108 3 0.03
109 12 0.13
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (109 bp):
TTATTAGTAAAAAAACTATATATTTGATCTATATAATACCCAATTGAAAATATATGATTTGTATT
AAAATTATAATTCTAAAAATAAATTTATAATTAAAATACAAGTG
Found at i:58211470 original size:18 final size:19
Alignment explanation
Indices: 58211447--58211484 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58211437 GGAAGCAAGC
*
58211447 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
58211465 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
58211484 A
1 A
58211485 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:58213644 original size:20 final size:19
Alignment explanation
Indices: 58213619--58213662 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
58213609 TAGTGAAATT
58213619 GGAGAAATAAAGAATAAAG-A
1 GGAGAAA-AAAGAA-AAAGAA
58213639 GGAG-AAAAAGAAAAAGAA
1 GGAGAAAAAAGAAAAAGAA
58213657 GGAGAA
1 GGAGAA
58213663 GATACATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 3 0.14
20 4 0.18
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.05
Consensus pattern (19 bp):
GGAGAAAAAAGAAAAAGAA
Found at i:58213828 original size:66 final size:68
Alignment explanation
Indices: 58213728--58213864 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 68
58213718 CAAGGAGGCA
* * * * *
58213728 AAGATGAAGAAAGAAGGAAAACACGAGGATAAAGAGG-T-GGTAAAAGAAGATGAAGAGAAAGAA
1 AAGAAGAAGAAAGAAGAAAAACACAAGGAAAAAGAGGTTAGGGAAAAGAAGATGAAGAGAAAGAA
58213791 GAG
66 GAG
*
58213794 AAGAAGAAGAAAGAA-AAAAAGCACAAGGAAAAAGAGGTTGAGGGAGAAGAAGATGAAGAGAAAG
1 AAGAAGAAGAAAGAAGAAAAA-CACAAGGAAAAAGAGGTT-AGGGAAAAGAAGATGAAGAGAAAG
*
58213858 ATGAG
64 AAGAG
58213863 AA
1 AA
58213865 AAAATAGAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
65 4 0.07
66 28 0.47
67 1 0.02
69 27 0.45
ACGTcount: A:0.58, C:0.03, G:0.33, T:0.07
Consensus pattern (68 bp):
AAGAAGAAGAAAGAAGAAAAACACAAGGAAAAAGAGGTTAGGGAAAAGAAGATGAAGAGAAAGAA
GAG
Found at i:58220675 original size:18 final size:16
Alignment explanation
Indices: 58220641--58220676 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
58220631 CAATGTATAA
58220641 TATTTTTAATAACTTT
1 TATTTTTAATAACTTT
58220657 TATTTTATAATATACTTT
1 TATTTT-TAATA-ACTTT
58220675 TA
1 TA
58220677 AAAACCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 5 0.28
18 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTTTAATAACTTT
Found at i:58225500 original size:22 final size:21
Alignment explanation
Indices: 58225470--58225520 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
58225460 CAAAAAAAGT
*
58225470 AGCAACAAAATAGTAAGAAAAC
1 AGCAACAAAATAATAA-AAAAC
* *
58225492 AGCAGCAAAATAATAAAAAAT
1 AGCAACAAAATAATAAAAAAC
*
58225513 AACAACAA
1 AGCAACAA
58225521 TAAAACAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.67, C:0.14, G:0.10, T:0.10
Consensus pattern (21 bp):
AGCAACAAAATAATAAAAAAC
Found at i:58229629 original size:17 final size:17
Alignment explanation
Indices: 58229607--58229641 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58229597 ATGATAGTTC
58229607 AAAAAT-AAATAGATTTT
1 AAAAATAAAATA-ATTTT
58229624 AAAAATAAAATAATTTT
1 AAAAATAAAATAATTTT
58229641 A
1 A
58229642 CATCATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATAAAATAATTTT
Found at i:58231530 original size:35 final size:37
Alignment explanation
Indices: 58231475--58231547 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
58231465 GGCCCGGGAA
* *
58231475 TAAATATATTTTTTTATTTTTTA-TTTTAAAATACTTT
1 TAAATATA-TTTTTAATTTTTTATTTTTAAAATAATTT
58231512 TAAA-ATATTTTT-ATTTTTTATTTTTAAAATAATTT
1 TAAATATATTTTTAATTTTTTATTTTTAAAATAATTT
58231547 T
1 T
58231548 TTAATGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 8 0.24
35 19 0.56
36 3 0.09
37 4 0.12
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (37 bp):
TAAATATATTTTTAATTTTTTATTTTTAAAATAATTT
Found at i:58231557 original size:26 final size:24
Alignment explanation
Indices: 58231509--58231559 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
58231499 TTTAAAATAC
* *
58231509 TTTTAAAATATTTTTATTTTTTAT
1 TTTTAAAATATTTTTAATGTTTAT
58231533 TTTTAAAATAATTTTTTAATGTTTAT
1 TTTTAAAAT-A-TTTTTAATGTTTAT
58231559 T
1 T
58231560 AAAAAATGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 13 0.57
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTAAAATATTTTTAATGTTTAT
Found at i:58231848 original size:17 final size:18
Alignment explanation
Indices: 58231826--58231860 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
58231816 TTTTATTAAT
58231826 TAAAAAAATT-CAAAAAG
1 TAAAAAAATTACAAAAAG
58231843 TAAAAAAATTACAAAAAG
1 TAAAAAAATTACAAAAAG
58231861 ACCCCTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (18 bp):
TAAAAAAATTACAAAAAG
Found at i:58233260 original size:12 final size:13
Alignment explanation
Indices: 58233243--58233271 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
58233233 AGGTTTCCAA
58233243 AAATGGAAA-TGG
1 AAATGGAAATTGG
58233255 AAATGGAAATTGG
1 AAATGGAAATTGG
58233268 AAAT
1 AAAT
58233272 TTGTAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (13 bp):
AAATGGAAATTGG
Found at i:58233493 original size:26 final size:27
Alignment explanation
Indices: 58233423--58233512 Score: 112
Period size: 26 Copynumber: 3.3 Consensus size: 27
58233413 AATTTATCAG
58233423 GGGTAAAATCGTCAAAATTTTGACATCCAT
1 GGGTAAAATCGTCAAAATTTTGACA---AT
*
58233453 GAGTAAAATCGTCAAAATTTT-ACAAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
* *
58233479 GGGTAAAATCATCAAAATTTTGA-TAT
1 GGGTAAAATCGTCAAAATTTTGACAAT
58233505 GGGTAAAA
1 GGGTAAAA
58233513 CATGGATAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
26 31 0.56
27 1 0.02
29 3 0.05
30 20 0.36
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (27 bp):
GGGTAAAATCGTCAAAATTTTGACAAT
Found at i:58241552 original size:346 final size:346
Alignment explanation
Indices: 58240919--58241612 Score: 1253
Period size: 346 Copynumber: 2.0 Consensus size: 346
58240909 TAGATAAATT
*
58240919 GTGAAAATGTTAATATGAGATCATATGCATCAAGTTAAATGTTATAAGGCAATTAGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
* * *
58240984 TTGAAATAAATTCATGTATAAATCAAAAACTGATAGATAATAGTGGAAAAAGGAAATTTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
* * *
58241049 TAGTCTCTGATACTTCTATCCTTGTTGTTTGTTCTTGGTAAGTTCGTACAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
*
58241114 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATATAATGCTTTT
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
58241179 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
261 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
58241244 GTAATTGATTAATGGTATAAA
326 GTAATTGATTAATGGTATAAA
* *
58241265 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATTTTATAAGGCAATTGGGACTGATAA
1 GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
*
58241330 TTGAAATAAATTCATGTATAAATCAAGAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
66 TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
*
58241395 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATGCAAGACTTACTTTATTA
131 TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
* * *
58241460 ATTGATGATATATTTGTGCTATGTTGTTTTGTTTTATGGTTGAATTGTTATTATACAATGTTTTT
196 ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
58241525 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
261 GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
58241590 GTAATTGATTAATGGTATAAA
326 GTAATTGATTAATGGTATAAA
58241611 GT
1 GT
58241613 AAATACTATA
Statistics
Matches: 333, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
346 333 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (346 bp):
GTGAAAATGTTAATATGAGATCATATGCATCAAATTAAATGTTATAAGGCAATTAGGACTGATAA
TTGAAATAAATTCATGTATAAATCAAAAACCGATAGATAATAGTGGAAAAAAGAAAATTTCAAAT
TAGTCCCTGATACTTCTATCCTTGTTGTTTGTTCCTGGTAAGTTCATACAAGACTTACTTTATTA
ATTGATGATATATTTGTGCTATGTTATTTTGTTTTATAGTTGAATTGTTATTATACAATGCTTTT
GGCATCAAAAGGATTAAATCGAAAAATATTAAATATCTATATGTGAAATTGATATTAACTAAGTA
GTAATTGATTAATGGTATAAA
Found at i:58244175 original size:17 final size:17
Alignment explanation
Indices: 58244153--58244188 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
58244143 TTTATATAAA
58244153 AGTAAAATTATCCTTTG
1 AGTAAAATTATCCTTTG
*
58244170 AGTAAAATTATCTTTTG
1 AGTAAAATTATCCTTTG
58244187 AG
1 AG
58244189 AAACTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (17 bp):
AGTAAAATTATCCTTTG
Found at i:58249691 original size:9 final size:9
Alignment explanation
Indices: 58249677--58249707 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58249667 TTTGGTTAAA
58249677 AATTAACCG
1 AATTAACCG
58249686 AATTAACCG
1 AATTAACCG
*
58249695 AATTACCCG
1 AATTAACCG
58249704 AATT
1 AATT
58249708 GAATCACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:58249753 original size:37 final size:37
Alignment explanation
Indices: 58249706--58249780 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
58249696 ATTACCCGAA
*
58249706 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
* *
58249743 TTGAATCACTACATAATTAAAAACATTATATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
58249780 T
1 T
58249781 GAAATTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:58249794 original size:37 final size:37
Alignment explanation
Indices: 58249706--58249797 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
58249696 ATTACCCGAA
* *
58249706 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* * *
58249743 TTGAATCACTACATAATTAAAAACATTATATAATTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
58249779 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
58249798 GAAATGTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.06
37 43 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:58249966 original size:38 final size:39
Alignment explanation
Indices: 58249915--58249990 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
58249905 CTTAAGAGTT
*
58249915 AGACTTTAGTTTTATTTTTA-TGGAGTT-GGTAATTGGGG
1 AGACTTTAGTTTTAGTTTTATTGG-GTTGGGTAATTGGGG
58249953 AGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 AGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
58249991 TTGGGTTGGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 22 0.63
39 13 0.37
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (39 bp):
AGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGG
Found at i:58249990 original size:13 final size:13
Alignment explanation
Indices: 58249972--58249996 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58249962 TTTTAGTTTT
58249972 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
58249985 ATTGGGTTGGGT
1 ATTGGGTTGGGT
58249997 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:58251330 original size:20 final size:22
Alignment explanation
Indices: 58251278--58251332 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
58251268 AACTATAACA
*
58251278 AAATAAAAATATATTAAATTATT
1 AAATATAAATATATTAAA-TATT
58251301 AAATAT---TATATTAAA-A-T
1 AAATATAAATATATTAAATATT
58251318 AAATATAAATATATT
1 AAATATAAATATATT
58251333 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
20 15 0.54
23 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAATATATTAAATATT
Found at i:58251782 original size:26 final size:25
Alignment explanation
Indices: 58251716--58251782 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
58251706 CACGACCATA
* *
58251716 TTAT-TTTTTTATTTTTTTAAATAT
1 TTATATTTTATATATTTTTAAATAT
*
58251740 TTATATTATAT-TA-TTTT-AATAT
1 TTATATTTTATATATTTTTAAATAT
58251762 TTAATAATTTTATATATTTTT
1 TT-AT-ATTTTATATATTTTT
58251783 TATTTATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 7 0.21
23 6 0.18
24 11 0.32
25 6 0.18
26 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATATTTTATATATTTTTAAATAT
Found at i:58251803 original size:26 final size:27
Alignment explanation
Indices: 58251745--58251805 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
58251735 AATATTTATA
*
58251745 TTATATTATTTTAATATTTAATAATTT
1 TTATATTATTTTAATATTGAATAATTT
*
58251772 TATATATT-TTTTATTTATTGAA-AATTT
1 T-TATATTATTTTA-ATATTGAATAATTT
58251799 TTATATT
1 TTATATT
58251806 CATCTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 6 0.20
27 12 0.40
28 12 0.40
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:58252765 original size:12 final size:12
Alignment explanation
Indices: 58252748--58252773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58252738 CAAAACAGGC
58252748 TTTTAGCGGCGT
1 TTTTAGCGGCGT
58252760 TTTTAGCGGCGT
1 TTTTAGCGGCGT
58252772 TT
1 TT
58252774 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:58252961 original size:73 final size:72
Alignment explanation
Indices: 58252842--58253010 Score: 232
Period size: 73 Copynumber: 2.3 Consensus size: 72
58252832 AAAAAAAGCA
* * * *
58252842 TTAGCGGCGTTTTTGAGCAAAGCGCCGCAAATAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGA-TAAAGCGCCGCAAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTT
* *
58252907 TCGGGGAT
65 TCAGAGAT
* *
58252915 TTAGCGACGTTTTTGATAAAGCGCCGCAAAAAAACCCAAGCCCAACGATGCCGTTTTCTGAACTT
1 TTAGCGGCGTTTTTGATAAAGCGCCGC-AAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTT
58252980 TCAGAGAT
65 TCAGAGAT
58252988 TTAGCGGCGTTTTTCG-TAAAGCG
1 TTAGCGGCGTTTTT-GATAAAGCG
58253011 TCGCTAAAGG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
72 10 0.12
73 74 0.87
74 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (72 bp):
TTAGCGGCGTTTTTGATAAAGCGCCGCAAAAAACCCAAGCCCAACGACGCCGTTTTCTGAACTTT
CAGAGAT
Found at i:58253299 original size:147 final size:147
Alignment explanation
Indices: 58253006--58254071 Score: 2050
Period size: 147 Copynumber: 7.3 Consensus size: 147
58252996 GTTTTTCGTA
* *
58253006 AAGCGTCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253071 TAT-AAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253135 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
58253152 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253217 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253282 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
*
58253299 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253364 TAT-AAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
*
58253428 TTGCGGCGCTTTATATG
131 TTGCGGCGCTTTATAAG
58253445 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253510 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253575 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
*
58253592 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253657 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253722 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
58253739 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253804 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253869 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
58253886 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
*
58253951 TAT-AAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58254015 TTGCGGCGCTTTATAAG
131 TTGCGGCGCTTTATAAG
58254032 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT-TATAAA
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAA
58254072 TAAATCAACT
Statistics
Matches: 909, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
145 6 0.01
146 321 0.35
147 582 0.64
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (147 bp):
AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
TTGCGGCGCTTTATAAG
Found at i:58253539 original size:293 final size:293
Alignment explanation
Indices: 58253006--58254375 Score: 2491
Period size: 293 Copynumber: 4.8 Consensus size: 293
58252996 GTTTTTCGTA
*
58253006 AAGCGTCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
58253071 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
58253136 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
58253201 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
196 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
58253266 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
261 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
58253299 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
58253364 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
*
58253429 TGCGGCGCTTTATATGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
58253494 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
196 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
58253559 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
261 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
58253592 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
58253657 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TAT-AAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253722 TTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCG
130 TTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCG
58253787 CAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTG
195 CAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTG
58253852 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
260 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
*
58253886 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
*
58253951 TATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
58254016 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT-TAT-----------
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
* *
58254069 ---AAATAAATCAACTTAT-AAAAAAAT-AAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTT
196 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATT-TTAGAATAGCAAAACGGCGTCGTTTTG
58254129 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
260 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
*
58254163 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATATAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
58254228 TAT-----AA-AAAAAAA-TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
58254286 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
58254351 AAAAAATAAATCAATTTATAAAAAA
196 AAAAAATAAATCAATTTATAAAAAA
58254376 TTTCCTAAAT
Statistics
Matches: 1049, Mismatches: 10, Indels: 43
0.95 0.01 0.04
Matches are distributed among these distances:
270 96 0.09
271 10 0.01
272 2 0.00
276 8 0.01
277 134 0.13
278 15 0.01
285 15 0.01
286 5 0.00
292 3 0.00
293 470 0.45
294 291 0.28
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (293 bp):
AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
TCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
Found at i:58253960 original size:440 final size:438
Alignment explanation
Indices: 58253006--58254375 Score: 2453
Period size: 440 Copynumber: 3.2 Consensus size: 438
58252996 GTTTTTCGTA
* *
58253006 AAGCGTCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253071 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
58253136 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGC
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCG-TTTCTATAAAAACGCCGC
58253201 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
195 AAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGT
58253266 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
260 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
58253331 TCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTAGAATAGCAA
325 TCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTAGAATAGCAA
*
58253396 AACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATATG
390 AACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
58253445 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58253510 TATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
66 TAT-AAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATT
58253575 TTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCG
130 TTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTT-CTATAAAAACGCCG
58253640 CAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTG
194 CAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTG
58253705 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGT
259 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGT
*
58253770 TTTCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGC
324 TTCCTATAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAAATAAAAAAATTTTAGAATAGC
58253835 AAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
388 AAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
58253886 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
*
58253951 TATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
66 TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
58254016 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTT-T-T------------
131 TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCTATAAAAACGCCGCA
* * *
58254067 ATAAATAAATCAACTTAT-AAAAAAAT-AAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTT
196 AAAAATAAATCAATTTATAAAAAAAATAAAAAAATT-TTAGAATAGCAAAACGGCGTCGTTTTGT
58254130 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
260 TCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTT
*
58254195 TCCTATATAAACGCCGCAAAAAATAAATCAATTTAT-----AA-AAAAAAA-TTTAGAATAGCAA
325 TCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTAGAATAGCAA
58254253 AACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
390 AACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
58254302 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
1 AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
58254367 TATAAAAAA
66 TATAAAAAA
58254376 TTTCCTAAAT
Statistics
Matches: 917, Mismatches: 10, Indels: 31
0.96 0.01 0.03
Matches are distributed among these distances:
416 136 0.15
417 7 0.01
418 2 0.00
423 8 0.01
424 134 0.15
425 16 0.02
437 1 0.00
438 1 0.00
439 69 0.08
440 398 0.43
441 145 0.16
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (438 bp):
AAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAATCAATT
TATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTT
TGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCTATAAAAACGCCGCA
AAAAATAAATCAATTTATAAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTT
CAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTT
CCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAATTTTAGAATAGCAAA
ACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAG
Found at i:58254090 original size:131 final size:132
Alignment explanation
Indices: 58253938--58254342 Score: 607
Period size: 131 Copynumber: 3.0 Consensus size: 132
58253928 ACGCCGCAAA
*
58253938 AAATAAATCAATTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAA
1 AAATAAATCAAATTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAA
58254003 AATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTT-T
66 AATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTAT
58254067 AT
131 AT
* * *
58254069 AAATAAATCAACTTATAAAAAAAT-AAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTTTCA
1 AAATAAATCAAATTATAAAAAAATAAAAAAAAT-TTAGAATAGCAAAACGGCGTCGTTTTGTTCA
58254133 AAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCC
65 AAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTT--
58254198 TATAT
128 TATAT
***** ** *
58254203 AAACGCCGCAAAAAATAAATCAATTTATAAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTG
1 AAATAAATCAAATTATAAA--AA--AAT-AAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTG
58254268 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGT
61 TTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGT
*
58254333 TTTCTAT
126 TTTATAT
58254340 AAA
1 AAA
58254343 AACGCCGCAA
Statistics
Matches: 249, Mismatches: 15, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
130 7 0.03
131 116 0.47
133 1 0.00
134 14 0.06
136 2 0.01
137 7 0.03
138 2 0.01
139 93 0.37
140 7 0.03
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.27
Consensus pattern (132 bp):
AAATAAATCAAATTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAA
AATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTAT
AT
Found at i:58254307 original size:139 final size:140
Alignment explanation
Indices: 58254093--58254375 Score: 523
Period size: 139 Copynumber: 2.0 Consensus size: 140
58254083 ATAAAAAAAT
* *
58254093 AAAAAATTGTTAGAATAGCAAAACGGCGTCGTTTTTTTCAAAATGAAAAAATTTTGCGGCGCTTT
1 AAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTT
*
58254158 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATATAAACGCCGCAAAAAATAAAT
66 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAAT
58254223 CAATTTATAA
131 CAATTTATAA
58254233 AAAAAAAT-TTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTT
1 AAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTT
*
58254297 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTTCTATAAAAACGCCGCAAAAAATAAAT
66 ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAAT
58254362 CAATTTATAA
131 CAATTTATAA
58254372 AAAA
1 AAAA
58254376 TTTCCTAAAT
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
139 132 0.95
140 7 0.05
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (140 bp):
AAAAAAATGTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTT
ATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAAT
CAATTTATAA
Found at i:58254970 original size:14 final size:15
Alignment explanation
Indices: 58254942--58254974 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
58254932 AAGTTTTATA
58254942 GATTATGGAATTAGG
1 GATTATGGAATTAGG
58254957 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
58254971 GATT
1 GATT
58254975 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:58255016 original size:14 final size:14
Alignment explanation
Indices: 58254997--58255063 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
58254987 TTAATGTGAT
* *
58254997 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
58255011 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
58255025 TTAAGGGTTA--GG
1 TTAAGGGTTAGGGG
* **
58255037 TTAGGGGTTAGATG
1 TTAAGGGTTAGGGG
*
58255051 TTAAGAGTTAGGG
1 TTAAGGGTTAGGG
58255064 ATTTAGGGCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 11 0.26
14 32 0.74
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:58255044 original size:26 final size:26
Alignment explanation
Indices: 58255009--58255062 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
58254999 AAGGTTTATG
* *
58255009 GGTTAAGGGTTAGGGGTTAAGGGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
* *
58255035 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
58255061 GG
1 GG
58255063 GATTTAGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.31
Consensus pattern (26 bp):
GGTTAAGGGTTAGAGGTTAAGAGTTA
Found at i:58255053 original size:19 final size:20
Alignment explanation
Indices: 58255008--58255046 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
58254998 TAAGGTTTAT
58255008 GGGTTAAGGGTTAGGGGTTAA
1 GGGTTAA-GGTTAGGGGTTAA
58255029 GGGTT-AGGTTAGGGGTTA
1 GGGTTAAGGTTAGGGGTTA
58255047 GATGTTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 1 0.06
21 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.49, T:0.31
Consensus pattern (20 bp):
GGGTTAAGGTTAGGGGTTAA
Found at i:58255349 original size:21 final size:21
Alignment explanation
Indices: 58255325--58255403 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
58255315 TGGGTTTAAA
*
58255325 GGTTAGGATTTAAGGTTTAGG
1 GGTTAGGAGTTAAGGTTTAGG
* *
58255346 GGTTAGTG-GTTAGGGGTTAGG
1 GGTTAG-GAGTTAAGGTTTAGG
* *
58255367 GGTTAAGAGTTAGGGATTTAGG
1 GGTTAGGAGTTAAGG-TTTAGG
*
58255389 GGTTAGGACTTAAGG
1 GGTTAGGAGTTAAGG
58255404 ATTCAAGGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 28 0.60
22 18 0.38
ACGTcount: A:0.23, C:0.01, G:0.43, T:0.33
Consensus pattern (21 bp):
GGTTAGGAGTTAAGGTTTAGG
Found at i:58255351 original size:7 final size:7
Alignment explanation
Indices: 58255341--58255395 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
58255331 GATTTAAGGT
58255341 TTAGGGG
1 TTAGGGG
*
58255348 TTAGTGG
1 TTAGGGG
58255355 TTAGGGG
1 TTAGGGG
58255362 TTAGGGG
1 TTAGGGG
* *
58255369 TTAAGAG
1 TTAGGGG
*
58255376 TTAGGGAT
1 TTAGGG-G
58255384 TTAGGGG
1 TTAGGGG
58255391 TTAGG
1 TTAGG
58255396 ACTTAAGGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
7 33 0.85
8 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:58255742 original size:19 final size:18
Alignment explanation
Indices: 58255713--58255766 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
58255703 GGACCAAATT
*
58255713 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAATTAAA
* *
58255731 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAATTAAA
58255750 ATAAAAACACTAAAATT
1 ATAAAAA-A-TAAAATT
58255767 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:58255820 original size:47 final size:48
Alignment explanation
Indices: 58255751--58255849 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
58255741 AAAAATGAAA
*
58255751 TAAAAACACTAAAATTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
58255799 TAAAAA-ACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
58255846 TAAA
1 TAAA
58255850 CAAAACTATG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.88
48 6 0.12
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (48 bp):
TAAAAACACTAAAATTTATAATTTTATCTAATTTTTATAAATATTACT
Found at i:58256190 original size:16 final size:15
Alignment explanation
Indices: 58256169--58256208 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
58256159 TGGTTGAAAT
58256169 ATTTATTCCCCTCCAA
1 ATTTATTCCCCTCC-A
*
58256185 ATTTATTCCCCTTCA
1 ATTTATTCCCCTCCA
58256200 ATTT-TTCCC
1 ATTTATTCCC
58256209 ATACCCGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 13 0.57
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTATTCCCCTCCA
Found at i:58260786 original size:43 final size:42
Alignment explanation
Indices: 58260585--58260793 Score: 292
Period size: 43 Copynumber: 4.9 Consensus size: 42
58260575 GCTTTTATCA
* *
58260585 AAAGCGTCGCTAAAGATCATGTTTTTTAGCGGCGTTTGTGGTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGG-T
* * *
58260628 AAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTG-GT
* *
58260671 AAAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGCGGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTG-TGGT
*
58260714 AAGGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAGGT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GGT
* *
58260757 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
58260794 TGCCTCATAA
Statistics
Matches: 149, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
43 148 0.99
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGT
Found at i:58261274 original size:24 final size:25
Alignment explanation
Indices: 58261224--58261275 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
58261214 AATCCTAAGA
* ** *
58261224 AAATTTTATTAAATTATTTTTATTT
1 AAATTTAATTAAATTATCATTACTT
58261249 AAATTTAATT-AATTATCATTACTT
1 AAATTTAATTAAATTATCATTACTT
58261273 AAA
1 AAA
58261276 AAGTTTTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTTAATTAAATTATCATTACTT
Found at i:58265724 original size:15 final size:15
Alignment explanation
Indices: 58265704--58265735 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58265694 CTTGACAGCC
58265704 ATCTCCATTCCGGAT
1 ATCTCCATTCCGGAT
58265719 ATCTCCATTCCGGAT
1 ATCTCCATTCCGGAT
58265734 AT
1 AT
58265736 AGCTATCTCT
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:0.22, C:0.31, G:0.12, T:0.34
Consensus pattern (15 bp):
ATCTCCATTCCGGAT
Found at i:58265908 original size:14 final size:13
Alignment explanation
Indices: 58265878--58265934 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
58265868 ATATGTTTCG
58265878 TAATTTTATAATA
1 TAATTTTATAATA
* *
58265891 TAATTTTTTCAATT
1 TAATTTTAT-AATA
*
58265905 TAA-TTCATAATA
1 TAATTTTATAATA
* *
58265917 TAATTGTATAATT
1 TAATTTTATAATA
58265930 TAATT
1 TAATT
58265935 GGTCATTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
12 6 0.18
13 22 0.65
14 6 0.18
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (13 bp):
TAATTTTATAATA
Found at i:58265915 original size:26 final size:25
Alignment explanation
Indices: 58265885--58265934 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
58265875 TCGTAATTTT
* *
58265885 ATAATATAATTTTTTCAATTTAATTC
1 ATAATATAATTGTAT-AATTTAATTC
58265911 ATAATATAATTGTATAATTTAATT
1 ATAATATAATTGTATAATTTAATT
58265935 GGTCATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
ATAATATAATTGTATAATTTAATTC
Found at i:58266381 original size:29 final size:33
Alignment explanation
Indices: 58266334--58266393 Score: 92
Period size: 30 Copynumber: 1.9 Consensus size: 33
58266324 ATCTTAATCA
58266334 ATAAATAATATTTCATTTA-ATTTAAAATAAAT
1 ATAAATAATATTTCATTTATATTTAAAATAAAT
58266366 ATAAAT-AT-TTTC-TTTATATTTAAAATAA
1 ATAAATAATATTTCATTTATATTTAAAATAA
58266394 CTTTCTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 15 0.56
31 2 0.07
32 6 0.22
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
ATAAATAATATTTCATTTATATTTAAAATAAAT
Found at i:58267147 original size:25 final size:25
Alignment explanation
Indices: 58267118--58267178 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
58267108 AAAAATATAT
58267118 TAAATTATTAAATAT-TATATTAAAA
1 TAAATTA-TAAATATATATATTAAAA
* *
58267143 TAAA-TATAAATATATTTTTTAAAA
1 TAAATTATAAATATATATATTAAAA
*
58267167 -AAATTAAAAATA
1 TAAATTATAAATA
58267179 ATAATATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 10 0.32
24 17 0.55
25 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAAATTATAAATATATATATTAAAA
Found at i:58267156 original size:20 final size:22
Alignment explanation
Indices: 58267104--58267158 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 22
58267094 AACTATAACA
*
58267104 AAATAAAAATATATTAAATTATT
1 AAATATAAATATATTAAA-TATT
58267127 AAATAT---TATATTAAA-A-T
1 AAATATAAATATATTAAATATT
58267144 AAATATAAATATATT
1 AAATATAAATATATT
58267159 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 7 0.25
18 1 0.04
20 15 0.54
23 5 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATAAATATATTAAATATT
Found at i:58277023 original size:12 final size:12
Alignment explanation
Indices: 58277006--58277046 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
58276996 TTTGTCTTCC
58277006 ATTTGAGTTTTT
1 ATTTGAGTTTTT
58277018 ATTTGAGTTTTT
1 ATTTGAGTTTTT
**
58277030 ATTTGCTTTTTT
1 ATTTGAGTTTTT
58277042 ATTTG
1 ATTTG
58277047 CTTTATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.15, C:0.02, G:0.15, T:0.68
Consensus pattern (12 bp):
ATTTGAGTTTTT
Found at i:58277047 original size:12 final size:12
Alignment explanation
Indices: 58277013--58277050 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
58277003 TCCATTTGAG
**
58277013 TTTTTATTTGAG
1 TTTTTATTTGCT
58277025 TTTTTATTTGCT
1 TTTTTATTTGCT
58277037 TTTTTATTTGCT
1 TTTTTATTTGCT
58277049 TT
1 TT
58277051 ATTAGTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (12 bp):
TTTTTATTTGCT
Found at i:58279988 original size:22 final size:22
Alignment explanation
Indices: 58279963--58280076 Score: 90
Period size: 22 Copynumber: 5.2 Consensus size: 22
58279953 TTCTTATTCC
*
58279963 TAATTTAAAACACGTTAAATTA
1 TAATTTAAAACACATTAAATTA
* * * * *
58279985 TAATATAATATACATGCATATT-
1 TAATTTAAAACACAT-TAAATTA
58280007 TAATTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
** * *
58280029 TAATACAATATACA-TACATATT-
1 TAATTTAAAACACATTA-A-ATTA
58280051 TAATTTAAAACACATTAAATTA
1 TAATTTAAAACACATTAAATTA
58280073 TAAT
1 TAAT
58280077 ACAATATACA
Statistics
Matches: 67, Mismatches: 19, Indels: 12
0.68 0.19 0.12
Matches are distributed among these distances:
21 9 0.13
22 49 0.73
23 9 0.13
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATTTAAAACACATTAAATTA
Found at i:58280011 original size:44 final size:44
Alignment explanation
Indices: 58279963--58280114 Score: 259
Period size: 44 Copynumber: 3.5 Consensus size: 44
58279953 TTCTTATTCC
* * *
58279963 TAATTTAAAACACGTTAAATTATAATATAATATACATGCATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
58280007 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
*
58280051 TAATTTAAAACACATTAAATTATAATACAATATACATACATGTT
1 TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
*
58280095 TATTTTAAAACACATTAAAT
1 TAATTTAAAACACATTAAAT
58280115 ATATTAATTC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 103 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.38
Consensus pattern (44 bp):
TAATTTAAAACACATTAAATTATAATACAATATACATACATATT
Found at i:58280437 original size:18 final size:18
Alignment explanation
Indices: 58280414--58280480 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
58280404 AAGTGAAATG
58280414 AATATGAAATGAAAATAA
1 AATATGAAATGAAAATAA
*
58280432 AATATGAAATG-AAATGA
1 AATATGAAATGAAAATAA
58280449 AATATGAAATGAAAATAA
1 AATATGAAATGAAAATAA
*
58280467 AGTAT-AAATTGAAA
1 AATATGAAA-TGAAA
58280481 TGAAATAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 19 0.43
18 25 0.57
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (18 bp):
AATATGAAATGAAAATAA
Found at i:58280457 original size:35 final size:35
Alignment explanation
Indices: 58280401--58280487 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 35
58280391 TAAAATGTGA
*
58280401 ATAAAGTGAAATG-AATATGAAATGAAAATAAAAT
1 ATAAATTGAAATGAAATATGAAATGAAAATAAAAT
*
58280435 ATGAAA-TGAAATGAAATATGAAATGAAAATAAAGT
1 AT-AAATTGAAATGAAATATGAAATGAAAATAAAAT
58280470 ATAAATTGAAATGAAATA
1 ATAAATTGAAATGAAATA
58280488 AATTACAATC
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
34 12 0.24
35 37 0.76
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (35 bp):
ATAAATTGAAATGAAATATGAAATGAAAATAAAAT
Found at i:58280602 original size:23 final size:24
Alignment explanation
Indices: 58280576--58280627 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
58280566 CAAATTTAGA
58280576 TGAAATGAAATGAGAAATGAAAG-
1 TGAAATGAAATGAGAAATGAAAGT
* *
58280599 TGAAATGAATTTAGAAATGAAAGT
1 TGAAATGAAATGAGAAATGAAAGT
58280623 TGAAA
1 TGAAA
58280628 ATTGAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (24 bp):
TGAAATGAAATGAGAAATGAAAGT
Found at i:58280627 original size:12 final size:11
Alignment explanation
Indices: 58280576--58280651 Score: 64
Period size: 12 Copynumber: 6.5 Consensus size: 11
58280566 CAAATTTAGA
58280576 TGAAATGAAAT
1 TGAAATGAAAT
* *
58280587 GAGAAATGAAAG
1 -TGAAATGAAAT
*
58280599 TGAAATGAATT
1 TGAAATGAAAT
58280610 TAGAAATGAAAGT
1 T-GAAATGAAA-T
58280623 TGAAAATTGAAAT
1 TG-AAA-TGAAAT
58280636 TGAAATTGAAA-
1 TGAAA-TGAAAT
58280647 TGAAA
1 TGAAA
58280652 AAAGAAAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
11 14 0.26
12 27 0.50
13 8 0.15
14 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (11 bp):
TGAAATGAAAT
Found at i:58282244 original size:58 final size:58
Alignment explanation
Indices: 58282164--58282291 Score: 186
Period size: 58 Copynumber: 2.2 Consensus size: 58
58282154 ACGGACTAAA
*
58282164 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATGCA-AAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATAT-AAGAAAATT
* * * *
58282222 TTAAATTTAAACACTCATCAAACTACAAATAGATGGGTAAAATTAATGTAAGAAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATAAGAAAATT
*
58282280 TTAAATTCAAAC
1 TTAAATTTAAAC
58282292 TATATATAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 62 0.98
ACGTcount: A:0.51, C:0.13, G:0.09, T:0.27
Consensus pattern (58 bp):
TTAAATTTAAACACCCAACAAACTACAAACAGATGGGTAAAATTAATATAAGAAAATT
Found at i:58282324 original size:90 final size:90
Alignment explanation
Indices: 58282222--58282410 Score: 272
Period size: 90 Copynumber: 2.1 Consensus size: 90
58282212 TGCAAAAATT
* * * * **
58282222 TTAAATTTAAACACTCATCAAACTACAAATAGATGGGTAAAATTAATGTA-AGAAAATTTTAAAT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACA-AAAATTTTAAAT
*
58282286 TCAAACTATATATAATACAAAATAAA
65 TCAAACTACATATAATACAAAATAAA
58282312 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
1 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
** *
58282377 CAAACTACATATAATACGGACTAAA
66 CAAACTACATATAATACAAAATAAA
58282402 TTAAATTTA
1 TTAAATTTA
58282411 TAGATACAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 87 0.99
91 1 0.01
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.29
Consensus pattern (90 bp):
TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACAAAAATTTTAAATT
CAAACTACATATAATACAAAATAAA
Found at i:58282429 original size:90 final size:90
Alignment explanation
Indices: 58282222--58282432 Score: 244
Period size: 90 Copynumber: 2.3 Consensus size: 90
58282212 TGCAAAAATT
* ** * * * **
58282222 TTAAATTTAAACACTCATCAAACTACAAATAGATGGGTAAAATTAATGTAAGAAAATTTTAAATT
1 TTAAATTTAAACACACAAAAAAATACAAACAGATAGGTAAAATTAATACAAGAAAATTTTAAATT
*
58282287 CAAACTATATATAATACAAAATAAA
66 CAAACTACATATAATACAAAATAAA
* * *
58282312 TTAAATTTAAACACCCAACAAACTACAAACAGATAGGTAAAATTAATACACA-AAAATTTTAAAT
1 TTAAATTTAAACACACAAAAAAATACAAACAGATAGGTAAAATTAATACA-AGAAAATTTTAAAT
** *
58282376 TCAAACTACATATAATACGGACTAAA
65 TCAAACTACATATAATACAAAATAAA
* * *
58282402 TTAAATTTATAGATACAAAAAAATACAAACA
1 TTAAATTTAAACACACAAAAAAATACAAACA
58282433 TTCTCAGAAA
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 103 0.99
91 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.27
Consensus pattern (90 bp):
TTAAATTTAAACACACAAAAAAATACAAACAGATAGGTAAAATTAATACAAGAAAATTTTAAATT
CAAACTACATATAATACAAAATAAA
Done.