Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 206 of 213
Found at i:61675997 original size:16 final size:18
Alignment explanation
Indices: 61675971--61676005 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
61675961 AGGGGCATGG
61675971 TAAATTA-TTTTAAAAAA
1 TAAATTATTTTTAAAAAA
61675988 TAAA-TATTTTTAAAAAA
1 TAAATTATTTTTAAAAAA
61676005 T
1 T
61676006 GAGCCACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATTATTTTTAAAAAA
Found at i:61681264 original size:6 final size:6
Alignment explanation
Indices: 61681255--61681288 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
61681245 ACAAAAGAAA
61681255 ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGG
1 ATGGGC ATGGGC ATGGGC ATGGGC ATGGGC ATGG
61681289 TAAATATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.15, G:0.50, T:0.18
Consensus pattern (6 bp):
ATGGGC
Found at i:61681707 original size:18 final size:17
Alignment explanation
Indices: 61681679--61681713 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61681669 ATTATTAAGA
*
61681679 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61681696 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61681714 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61681943 original size:44 final size:45
Alignment explanation
Indices: 61681878--61681968 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
61681868 ACCTCTATTC
* * *
61681878 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
61681922 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
61681967 CA
1 CA
61681969 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:61681970 original size:16 final size:16
Alignment explanation
Indices: 61681949--61682017 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
61681939 GATTAGCTAT
61681949 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
61681965 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
61681982 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
61681998 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
61682014 TACA
1 TACA
61682018 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:61681991 original size:33 final size:32
Alignment explanation
Indices: 61681949--61682017 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
61681939 GATTAGCTAT
61681949 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
61681982 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
61682014 TACA
1 TACA
61682018 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:61695919 original size:30 final size:29
Alignment explanation
Indices: 61695883--61696007 Score: 94
Period size: 30 Copynumber: 4.1 Consensus size: 29
61695873 GACACTTTCG
61695883 AAAATTTTCATTAAACCTTTCAAAATTTTT
1 AAAATTTTCATTAAA-CTTTCAAAATTTTT
* *
61695913 AAAATTTTCTATT-AAGTCTT-AAACTTTTT
1 AAAATTTTC-ATTAAACT-TTCAAAATTTTT
* * * * *
61695942 GAAAGTTTTAATTAAACATACAAAAATTTT
1 -AAAATTTTCATTAAACTTTCAAAATTTTT
61695972 AAAATATTCTCATTAAA-TTCTCCAAAATTTTT
1 AAAAT-TT-TCATTAAACTT-T-CAAAATTTTT
61696004 AAAA
1 AAAA
61696008 AATTTAATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
29 17 0.24
30 32 0.44
31 10 0.14
32 13 0.18
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (29 bp):
AAAATTTTCATTAAACTTTCAAAATTTTT
Found at i:61701501 original size:11 final size:11
Alignment explanation
Indices: 61701485--61701515 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61701475 TATATATATT
61701485 TAAAAATTATA
1 TAAAAATTATA
*
61701496 TAAAAATAATA
1 TAAAAATTATA
61701507 TAAAAATTA
1 TAAAAATTA
61701516 ATACGGGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:61704620 original size:46 final size:46
Alignment explanation
Indices: 61704519--61704762 Score: 316
Period size: 46 Copynumber: 5.6 Consensus size: 46
61704509 TACGTATGAT
*
61704519 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
61704562 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
61704608 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
61704654 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A----A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * * *
61704690 CACTTATCACTTTTTCATTTAATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
61704736 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
61704763 AGTACTCAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 23
0.84 0.05 0.11
Matches are distributed among these distances:
36 27 0.15
37 1 0.01
38 3 0.02
40 1 0.01
41 2 0.01
42 1 0.01
43 10 0.06
44 8 0.05
45 21 0.12
46 103 0.58
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:61704692 original size:36 final size:36
Alignment explanation
Indices: 61704651--61704721 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
61704641 TAGCTAAGGC
*
61704651 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTGTCACTTAATCAGATAAGTA
* *
61704687 TAACACTTATCACTTTTTCATTTAATCAGATAAGT
1 TAACACTTATCACTTTGTCACTTAATCAGATAAGT
61704722 GTAGCTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (36 bp):
TAACACTTATCACTTTGTCACTTAATCAGATAAGTA
Found at i:61704716 original size:82 final size:82
Alignment explanation
Indices: 61704608--61704762 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 82
61704598 CTAAGGCTAC
* * *
61704608 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTAATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
61704673 TGATCAGATAAGTATAA
66 TGATCAGATAAGTATAA
* * * *
61704690 CACTTATCACTTTTTCATTTAATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTCTCACTTAATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
61704755 TGATCAGA
66 TGATCAGA
61704763 AGTACTCAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 66 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTCTCACTTAATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTATCACT
TGATCAGATAAGTATAA
Found at i:61709714 original size:22 final size:21
Alignment explanation
Indices: 61709679--61709812 Score: 77
Period size: 19 Copynumber: 6.7 Consensus size: 21
61709669 AAAGGGTATC
* *
61709679 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
61709700 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
61709723 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
61709742 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
61709761 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* * *
61709780 TATATAT--TATATCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
61709799 TGCATATCATATCT
1 TACAAATCATATCT
61709813 AAGATTGCAT
Statistics
Matches: 94, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
17 2 0.02
19 60 0.64
21 7 0.07
22 15 0.16
23 10 0.11
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:61709722 original size:23 final size:22
Alignment explanation
Indices: 61709679--61709736 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
61709669 AAAGGGTATC
* *
61709679 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
61709700 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
61709723 TGCATATCATATCT
1 TACAAATCATATCT
61709737 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:61709739 original size:19 final size:19
Alignment explanation
Indices: 61709715--61709825 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
61709705 AATCATATCT
61709715 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
61709734 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
61709753 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
** *
61709772 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
61709791 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
61709810 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
61709826 CTTGAAGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:61709762 original size:38 final size:38
Alignment explanation
Indices: 61709715--61709818 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
61709705 AATCATATCT
61709715 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
61709753 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
61709791 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
61709819 GCATATCCTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:61710375 original size:132 final size:132
Alignment explanation
Indices: 61710189--61710517 Score: 480
Period size: 132 Copynumber: 2.5 Consensus size: 132
61710179 GGGAGATATG
* *
61710189 ATTACTGGCTTCAATGTAATCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* * * ** *
61710254 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGTTTAGGTAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCAACTATTATCCAGGGAAGTA
61710319 GA
131 GA
* * *
61710321 ATTACTGGTTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGTCATCTTCGATCTGCT
1 ATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* *
61710386 CCACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCAACTGTTATCCAGGGAAGTG
66 CCACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCAACTATTATCCAGGGAAGTA
61710451 GA
131 GA
* * * **
61710453 ATTGCTGGCTTT-AATGTACTCCACTGTAACCATAGGGAGGTAAAATCTGCCATCTTTTATCTGC
1 ATTACTGG-TTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGC
61710517 T
65 T
61710518 TCGCTGTCAA
Statistics
Matches: 175, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
132 172 0.98
133 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (132 bp):
ATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTAAAATCTTCAATCTATTCAACTATTATCCAGGGAAGTA
GA
Found at i:61711849 original size:20 final size:19
Alignment explanation
Indices: 61711826--61711874 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
61711816 TCACCTTGGC
61711826 TTCTCCTTTTTCTTTTTTT
1 TTCTCCTTTTTCTTTTTTT
*
61711845 TT-TCTTTCTTTCTTTTTTT
1 TTCTCCTT-TTTCTTTTTTT
*
61711864 TTGTCCTTTTT
1 TTCTCCTTTTT
61711875 TTTATTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (19 bp):
TTCTCCTTTTTCTTTTTTT
Found at i:61711854 original size:15 final size:14
Alignment explanation
Indices: 61711832--61711877 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 14
61711822 TGGCTTCTCC
61711832 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
61711846 TTCTTTCTTTCTTTTT
1 TT-TTTCTTT-TTTTT
61711862 TTTTGTCCTTTTTTTT
1 TTTT-T-CTTTTTTTT
61711878 ATTGAACCTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 13 0.46
17 4 0.14
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:61715254 original size:50 final size:51
Alignment explanation
Indices: 61715138--61715318 Score: 161
Period size: 40 Copynumber: 3.8 Consensus size: 51
61715128 GGTAAAAACA
* * ** *
61715138 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACAAGGGACCTACTCATCTCGG
* * *
61715189 TGCCTATGCCATGTCCCAGACATGGTCTTATAAGGGACCT-CTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACAAGGGACCTACTCATCTCGG
* * *
61715239 TGCCAACGCTATGTCCCAGACA------T----GGGACC-CCTCATCTCGG
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACAAGGGACCTACTCATCTCGG
* *
61715279 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACAAGGGACCT
61715319 CTTTACCCAA
Statistics
Matches: 105, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
40 36 0.34
44 1 0.01
46 1 0.01
50 34 0.32
51 33 0.31
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (51 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACAAGGGACCTACTCATCTCGG
Found at i:61719559 original size:19 final size:19
Alignment explanation
Indices: 61719532--61719661 Score: 188
Period size: 19 Copynumber: 6.8 Consensus size: 19
61719522 AAATTAAATC
*
61719532 TCTAAGATTATATATCATA
1 TCTAAGATTGTATATCATA
* *
61719551 TCTACGATTGCATATCATA
1 TCTAAGATTGTATATCATA
*
61719570 TCTAAGATTATATATCATA
1 TCTAAGATTGTATATCATA
*
61719589 TCTAAGATTGCATATCATA
1 TCTAAGATTGTATATCATA
* *
61719608 TCTAAGATTATATATTATA
1 TCTAAGATTGTATATCATA
*
61719627 TCTAAGATTGCATATCATA
1 TCTAAGATTGTATATCATA
61719646 TCTAAGATTGTATATC
1 TCTAAGATTGTATATC
61719662 CCTGAAGATT
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 96 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGTATATCATA
Found at i:61719576 original size:38 final size:38
Alignment explanation
Indices: 61719532--61719661 Score: 233
Period size: 38 Copynumber: 3.4 Consensus size: 38
61719522 AAATTAAATC
*
61719532 TCTAAGATTATATATCATATCTACGATTGCATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
61719570 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
*
61719608 TCTAAGATTATATATTATATCTAAGATTGCATATCATA
1 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
*
61719646 TCTAAGATTGTATATC
1 TCTAAGATTATATATC
61719662 CCTGAAGATT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 88 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (38 bp):
TCTAAGATTATATATCATATCTAAGATTGCATATCATA
Found at i:61720714 original size:19 final size:19
Alignment explanation
Indices: 61720690--61720726 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61720680 ATAAATTTAT
*
61720690 TTTTACATATACCTACAAA
1 TTTTACATATACCAACAAA
61720709 TTTTACATATACCAACAA
1 TTTTACATATACCAACAA
61720727 TTAATTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTTACATATACCAACAAA
Found at i:61720973 original size:33 final size:33
Alignment explanation
Indices: 61720936--61721001 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
61720926 AAATGAAATT
61720936 TTAATTTTAGCTCAATTATACATATACCAACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
*
61720969 TTAATTTTAGCTCAATTATACATATACCTACAA
1 TTAATTTTAGCTCAATTATACATATACCAACAA
61721002 ATTTTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAATTTTAGCTCAATTATACATATACCAACAA
Found at i:61722881 original size:49 final size:49
Alignment explanation
Indices: 61722824--61722927 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
61722814 TCATGTGTTA
* * *
61722824 TAATTTTATATAGTGTTGAGCTTTTGATTCATGATATTTAACTTAATTT
1 TAATTTTATAAAGTGTTCAGCTTTTGATTCATGATATTAAACTTAATTT
*
61722873 TAATTTTATAAAGTGTTCATCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCAGCTTTTGATTCATGATATTAAACTTAATTT
61722922 TAATTT
1 TAATTT
61722928 GTTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.53
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCAGCTTTTGATTCATGATATTAAACTTAATTT
Found at i:61724297 original size:15 final size:16
Alignment explanation
Indices: 61724269--61724298 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61724259 TAAATTCATA
61724269 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
61724285 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
61724299 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:61724318 original size:18 final size:17
Alignment explanation
Indices: 61724290--61724324 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
61724280 ATTATTAAGA
61724290 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
61724307 ATTTTAATTAAATTATAT
1 ATTTT-ATTAAATTATAT
61724325 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:61724332 original size:18 final size:18
Alignment explanation
Indices: 61724295--61724343 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
61724285 TAAGAATTTT
*
61724295 ATTAAATTATATATT-TTA
1 ATTAAATTATAT-TTAATA
61724313 ATTAAATTATATTTAATA
1 ATTAAATTATATTTAATA
61724331 A-T-AATTAT-TTTAA
1 ATTAAATTATATTTAA
61724344 AATATGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.17
16 6 0.21
17 3 0.10
18 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTAAATTATATTTAATA
Found at i:61724694 original size:20 final size:20
Alignment explanation
Indices: 61724671--61724710 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
61724661 ATTACAAATG
61724671 ATGGTTAAAGAAGAATTAAC
1 ATGGTTAAAGAAGAATTAAC
*
61724691 ATGGTTAAAGTAGAATTAAC
1 ATGGTTAAAGAAGAATTAAC
61724711 TAGAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (20 bp):
ATGGTTAAAGAAGAATTAAC
Found at i:61724744 original size:20 final size:20
Alignment explanation
Indices: 61724704--61724744 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61724694 GTTAAAGTAG
**
61724704 AATTAACTAGAAATATGCAA
1 AATTAACTAGAAATAAACAA
*
61724724 AATTAACTAGAATTAAACAA
1 AATTAACTAGAAATAAACAA
61724744 A
1 A
61724745 TAACAGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTAACTAGAAATAAACAA
Found at i:61724885 original size:26 final size:26
Alignment explanation
Indices: 61724856--61724909 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
61724846 TTAAAAAAAG
*
61724856 TTTGAATCGAGTTGAGT-AAATAGAAA
1 TTTGAATCGAGTTGAATCAAAT-GAAA
* *
61724882 TTTGAGTTGAGTTGAATCAAATGAAA
1 TTTGAATCGAGTTGAATCAAATGAAA
61724908 TT
1 TT
61724910 GTTTGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (26 bp):
TTTGAATCGAGTTGAATCAAATGAAA
Found at i:61725152 original size:18 final size:19
Alignment explanation
Indices: 61725120--61725173 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
61725110 TTAAAAAAAA
*
61725120 TTTATATATTCTTTAGAATT-
1 TTTA-ATATT-TTTAAAATTC
61725140 TTTAATATTTTTAAAATTC
1 TTTAATATTTTTAAAATTC
*
61725159 TGTAAT-TTTTTAAAA
1 TTTAATATTTTTAAAA
61725174 AAATATACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 17 0.55
19 10 0.32
20 4 0.13
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTAATATTTTTAAAATTC
Found at i:61726048 original size:69 final size:68
Alignment explanation
Indices: 61725920--61726063 Score: 164
Period size: 69 Copynumber: 2.1 Consensus size: 68
61725910 TAGTTTGAAA
* * * * * *
61725920 TTAAATTCGAATTTTAATAAAAGATTTGATTTCGATTTTAATCCGATCCGATTCAAATATAATTT
1 TTAAATTCGAATTTTAATAAAAGACTTAATTCCGATTTAAATCCGACCCGACTCAAATATAA-TT
61725985 TAAT
65 TAAT
* ** *
61725989 TTAAATTTGAATTTTAATAAAAGACTTAATTCCGATTTAAATTTGACCCGAC-CTGAATATAATT
1 TTAAATTCGAATTTTAATAAAAGACTTAATTCCGATTTAAATCCGACCCGACTC-AAATATAATT
61726053 TAAT
65 TAAT
61726057 TGTAAAT
1 T-TAAAT
61726064 AAGATTACTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
68 8 0.13
69 55 0.87
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (68 bp):
TTAAATTCGAATTTTAATAAAAGACTTAATTCCGATTTAAATCCGACCCGACTCAAATATAATTT
AAT
Found at i:61728947 original size:22 final size:23
Alignment explanation
Indices: 61728897--61728947 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
61728887 TATTCTGCTG
*
61728897 TTATT-TTACTGTCATTTTATTA
1 TTATTATTACTATCATTTTATTA
*
61728919 TTA-TATTACTATTATTTTATT-
1 TTATTATTACTATCATTTTATTA
61728940 TTATTATT
1 TTATTATT
61728948 TAGATATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (23 bp):
TTATTATTACTATCATTTTATTA
Found at i:61729155 original size:35 final size:35
Alignment explanation
Indices: 61729109--61729182 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
61729099 AGAATTAATA
61729109 AGGATGATGTAATTAATGACACCAAATTTTTTCTT
1 AGGATGATGTAATTAATGACACCAAATTTTTTCTT
61729144 AGGATGATGTAATTAATGACACCAAATTTTTTCTT
1 AGGATGATGTAATTAATGACACCAAATTTTTTCTT
61729179 AGGA
1 AGGA
61729183 AACGCTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (35 bp):
AGGATGATGTAATTAATGACACCAAATTTTTTCTT
Found at i:61733768 original size:31 final size:29
Alignment explanation
Indices: 61733730--61733803 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
61733720 ACTACCAAAA
* *
61733730 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
61733761 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
61733790 TAGTCACTTATGTT
1 TAGTCACTTATGTT
61733804 ATCACGTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 23 0.59
31 16 0.41
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:61733825 original size:31 final size:29
Alignment explanation
Indices: 61733755--61733828 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
61733745 GACTCAGGTT
* *
61733755 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
61733784 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
61733815 ACATTTTAGTCACT
1 ACATTTTAGTCACT
61733829 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:61734432 original size:29 final size:29
Alignment explanation
Indices: 61734385--61734454 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
61734375 CACGATAACG
61734385 TAAGTGACTAAAACATAACATT-TCAAACA
1 TAAGTGACTAAAACATAAC-TTGTCAAACA
**
61734414 TAAGTGACTAAAATGTAACTTGAGTCAAACA
1 TAAGTGACTAAAACATAACTT--GTCAAACA
*
61734445 AAAGTGACTA
1 TAAGTGACTA
61734455 TTTTGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
31 16 0.46
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
TAAGTGACTAAAACATAACTTGTCAAACA
Found at i:61736184 original size:3 final size:3
Alignment explanation
Indices: 61736176--61736218 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
61736166 GCCTATAACC
*
61736176 ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
61736219 GAAATTGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:61736272 original size:18 final size:18
Alignment explanation
Indices: 61736237--61736272 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61736227 TAACATTTAA
* *
61736237 AGTGAGATTTTATTATAT
1 AGTGAGATTTCATGATAT
61736255 AGTGAGATTTCATGATAT
1 AGTGAGATTTCATGATAT
61736273 CCTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (18 bp):
AGTGAGATTTCATGATAT
Found at i:61743910 original size:11 final size:11
Alignment explanation
Indices: 61743894--61743924 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61743884 TAGAATATAC
61743894 CCCATACCTTG
1 CCCATACCTTG
*
61743905 CCCATACCTTT
1 CCCATACCTTG
61743916 CCCATACCT
1 CCCATACCT
61743925 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:61744495 original size:18 final size:18
Alignment explanation
Indices: 61744468--61744560 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
61744458 TACGACCGTT
*
61744468 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
61744486 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
61744504 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
*
61744522 TACGGAACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
61744540 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
61744558 TAC
1 TAC
61744561 AGTAGTTGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:61748611 original size:11 final size:11
Alignment explanation
Indices: 61748595--61748625 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61748585 TAGAATATAC
61748595 CCCATACCTTG
1 CCCATACCTTG
*
61748606 CCCATACCTTT
1 CCCATACCTTG
61748617 CCCATACCT
1 CCCATACCT
61748626 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:61749459 original size:11 final size:11
Alignment explanation
Indices: 61749443--61749473 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
61749433 AAGTATGGGT
61749443 AGGTATGGGAA
1 AGGTATGGGAA
*
61749454 AGGTATGGGCA
1 AGGTATGGGAA
61749465 AGGTATGGG
1 AGGTATGGG
61749474 GTATATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:61753540 original size:18 final size:18
Alignment explanation
Indices: 61753517--61753627 Score: 150
Period size: 18 Copynumber: 6.2 Consensus size: 18
61753507 CCTAACTACT
*
61753517 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
61753535 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
*
61753553 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
61753571 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * *
61753589 ATATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
61753607 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
61753625 GTA
1 GTA
61753628 AACGGTCGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:61753602 original size:54 final size:54
Alignment explanation
Indices: 61753517--61753627 Score: 177
Period size: 54 Copynumber: 2.1 Consensus size: 54
61753507 CCTAACTACT
* * *
61753517 GTATACGTGAACAGTACCGTATACGTGAATAGTTCCATATACGTGAATAGTACC
1 GTATACGTGAACAGTACCATATACGTAAATAGTGCCATATACGTGAATAGTACC
* *
61753571 GTATACGTGAATAGTGCCATATACGTAAATAGTGCCATATACGTGAATAGTACC
1 GTATACGTGAACAGTACCATATACGTAAATAGTGCCATATACGTGAATAGTACC
61753625 GTA
1 GTA
61753628 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (54 bp):
GTATACGTGAACAGTACCATATACGTAAATAGTGCCATATACGTGAATAGTACC
Found at i:61758063 original size:29 final size:30
Alignment explanation
Indices: 61758012--61758068 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
61758002 AGAATTGGAG
* *
61758012 CAAATTAAGATTTCATGTTTAAAATTATTC
1 CAAATTAAGAATTCATGTATAAAATTATTC
61758042 CAAATTAA-AATTCATGTATAAAATTAT
1 CAAATTAAGAATTCATGTATAAAATTAT
61758069 GTATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (30 bp):
CAAATTAAGAATTCATGTATAAAATTATTC
Found at i:61758076 original size:13 final size:14
Alignment explanation
Indices: 61758045--61758076 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61758035 ATTATTCCAA
61758045 ATTAAAATTCATGT
1 ATTAAAATTCATGT
61758059 A-TAAAATT-ATGT
1 ATTAAAATTCATGT
61758071 ATTAAA
1 ATTAAA
61758077 CTAAAGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 11 0.65
14 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTAAAATTCATGT
Found at i:61767981 original size:17 final size:18
Alignment explanation
Indices: 61767953--61767992 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
61767943 TTGATTTGAT
61767953 TAAATAAAATAAAATTTA
1 TAAATAAAATAAAATTTA
*
61767971 TAAAT-AAATAAATTTTA
1 TAAATAAAATAAAATTTA
*
61767988 AAAAT
1 TAAAT
61767993 TAGTACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATAAAATAAAATTTA
Found at i:61769371 original size:48 final size:51
Alignment explanation
Indices: 61769301--61769414 Score: 117
Period size: 51 Copynumber: 2.3 Consensus size: 51
61769291 ATAAATATAA
* * * * *
61769301 ATATTTATATTAAATACAAGATCTGAAA-AATA-ATA-TAAACAAAAATTT
1 ATATTTATATAAAACACAAGATCTAAAACAAGACAAATTAAACAAAAATTT
* * * *
61769349 ATATTTATGTAAAACACCAGATCTAAAACAAGACAAATTAAATAAATATTT
1 ATATTTATATAAAACACAAGATCTAAAACAAGACAAATTAAACAAAAATTT
*
61769400 ATATTTATTTAAAAC
1 ATATTTATATAAAAC
61769415 TTCAAATTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
48 23 0.43
49 3 0.06
50 2 0.04
51 25 0.47
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (51 bp):
ATATTTATATAAAACACAAGATCTAAAACAAGACAAATTAAACAAAAATTT
Found at i:61772265 original size:19 final size:19
Alignment explanation
Indices: 61772241--61772277 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
61772231 TAAAATTCTA
61772241 TTTTTTAAAGAAA-TATAAT
1 TTTTTTAAA-AAATTATAAT
61772260 TTTTTTAAAAAATTATAA
1 TTTTTTAAAAAATTATAA
61772278 AAATTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTTTTAAAAAATTATAAT
Found at i:61772523 original size:51 final size:51
Alignment explanation
Indices: 61772455--61772565 Score: 195
Period size: 51 Copynumber: 2.2 Consensus size: 51
61772445 AAATATAAGA
*
61772455 TATATTTATTTAAATAATTTTTAAATAAGAAATAAAAATATATAATACAAT
1 TATATTTATTTAAATAATTTTTAAATAAAAAATAAAAATATATAATACAAT
61772506 TATATTTATTTAAATAATTTTTAAATAAAAAATAAAAATATATAATACAAT
1 TATATTTATTTAAATAATTTTTAAATAAAAAATAAAAATATATAATACAAT
* *
61772557 CATGTTTAT
1 TATATTTAT
61772566 ATTCATTCTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (51 bp):
TATATTTATTTAAATAATTTTTAAATAAAAAATAAAAATATATAATACAAT
Found at i:61772626 original size:16 final size:16
Alignment explanation
Indices: 61772591--61772623 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61772581 ATTTAGATTA
*
61772591 TTAAGTCAAACTAAAT
1 TTAAATCAAACTAAAT
61772607 TTAAATCAAA-TAAAT
1 TTAAATCAAACTAAAT
61772622 TT
1 TT
61772624 TAATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (16 bp):
TTAAATCAAACTAAAT
Found at i:61790461 original size:16 final size:16
Alignment explanation
Indices: 61790437--61790470 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61790427 TTGTTGGTTC
*
61790437 AATTAAAAATTATTAA
1 AATTAAAAAATATTAA
*
61790453 AATTTAAAAATATTAA
1 AATTAAAAAATATTAA
61790469 AA
1 AA
61790471 AATCCTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTAAAAAATATTAA
Found at i:61794036 original size:22 final size:23
Alignment explanation
Indices: 61794005--61794047 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
61793995 CATCTAATTC
61794005 AACCACGTAGAAACT-ACAAAAG
1 AACCACGTAGAAACTGACAAAAG
* *
61794027 AACCATGTAGGAACTGACAAA
1 AACCACGTAGAAACTGACAAA
61794048 CAATCACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (23 bp):
AACCACGTAGAAACTGACAAAAG
Found at i:61799205 original size:154 final size:153
Alignment explanation
Indices: 61798720--61799423 Score: 681
Period size: 154 Copynumber: 4.6 Consensus size: 153
61798710 ATCAGAGTAA
* * *
61798720 CTTGATCATGAATTATATCTAATATTGATGCAAATAGATAACAATGAAGAAGGTAAAATCCTATT
1 CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
* * * *
61798785 TCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGCGGACCCACGATTCAGGTACGTGTTTCTAC
66 TCAAGTCCTCAAACAAGTTTATC-T-TATCTTATGTGGACCCATGATT-AGGTACATGTTTCTAC
* *
61798850 TCAATAAAA-TGATCCAT-TGGATAG
128 TCAATAAAACAGAACCATCTGGATAG
* * * * * * * *
61798874 CTTGATGATGAATTAAATCTAATAGTCAAGCGAACAGATCACAATGAAGAAGGAAAAAGCCTATT
1 CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
* * * ** *
61798939 TCAAGTCCTCAAACAAGTTTATCTTCTTCTATCTTAGGTGGACTCTTGATTAGGATACATAATTG
66 TCAAGTCCTCAAACAAGTTTA---TC-T-TATCTTATGTGGACCCATGATTAGG-TACATGTTTC
* *
61799004 TACTCAATAAAACAAAATCATCT-GACTAG
125 TACTCAATAAAACAGAACCATCTGGA-TAG
* * * * * *
61799033 CTTGATCATTAATGAAATCAAATATTCATGCAAATAGGTGACGATGAAGAAGGTAAAATCCCATT
1 CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
* * * *
61799098 TCAAGCCCTCAAACAAGTTTATCTTATCTTATGTGGACCCATGATTCAAGTCCGTGTTTCTACTC
66 TCAAGTCCTCAAACAAGTTTATCTTATCTTATGTGGACCCATGATT-AGGTACATGTTTCTACTC
61799163 AATAAAACAGAACCATCTGGATAG
130 AATAAAACAGAACCATCTGGATAG
* * * * * *
61799187 CTTGATAATGAATTAAATCTAATAGTCATGCAGAGAGATGACAATGAAGAAGGAAAAAGCCTATT
1 CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
* * **** *
61799252 TCAAGTCCTCAAAC-A----A-C-TACCTTAAGTGGATTTGTGATTAGGGTACATGTTTGTACTC
66 TCAAGTCCTCAAACAAGTTTATCTTATCTTATGTGGACCCATGATTA-GGTACATGTTTCTACTC
* ***
61799310 GATAAAACAGAACCATCCAAATAG
130 AATAAAACAGAACCATCTGGATAG
* * * * ** * *
61799334 CTAGATCATGAATAAAATCAAATATTCATGCAAATAGGTGATGATGAAGAAGGTAAATTCCCATT
1 CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
*
61799399 TCATGTCCTCAAACAAGTTTATCTT
66 TCAAGTCCTCAAACAAGTTTATCTT
61799424 CTTCTATCTT
Statistics
Matches: 441, Mismatches: 92, Indels: 34
0.78 0.16 0.06
Matches are distributed among these distances:
146 1 0.00
147 113 0.26
148 2 0.00
149 1 0.00
152 1 0.00
153 2 0.00
154 190 0.43
155 5 0.01
156 5 0.01
157 40 0.09
158 6 0.01
159 75 0.17
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (153 bp):
CTTGATCATGAATTAAATCTAATATTCATGCAAATAGATGACAATGAAGAAGGTAAAATCCTATT
TCAAGTCCTCAAACAAGTTTATCTTATCTTATGTGGACCCATGATTAGGTACATGTTTCTACTCA
ATAAAACAGAACCATCTGGATAG
Found at i:61799265 original size:313 final size:299
Alignment explanation
Indices: 61798697--61799423 Score: 920
Period size: 313 Copynumber: 2.4 Consensus size: 299
61798687 ATAGTACTTG
* * * * * * * * *
61798697 ATAAAACAGAATGATCAGAGTAACTTGATCATGAATTATATCTAATATTGATGCAAATAGATAAC
1 ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGGTGAC
* *
61798762 AATGAAGAAGGTAAAATCCTATTTCAAGCCCTCAAACAAGTTTATCTTCTATCTTATGCGGACCC
66 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATC-T-TATCTTATGCGGACCC
* * * *
61798827 ACGATTCAGGTACGTGTTTCTACTCAATAAAATGATCCATTGGATAGCTTGATGATGAATTAAAT
129 ACGATTCAAGTACGTGTTTCTACTCAATAAAAAGAACCATTGGATAGCTTGATAATGAATTAAAT
61798892 CTAATAGTCAAGCGAACAGATCACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAAGT
194 CTAATAGTCAAGCGAACAGATCACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAA--
*
61798957 TTATCTTCTTCTATCTTAGGTGGACTCT-TGATTAGGATACATAATTGTACTCA
257 CTA-C--C-T-TA----A-GTGGA-TCTGTGATTAGGATACATAATTGTACTCA
* * * * *
61799010 ATAAAACAAAATCATCTGACTAGCTTGATCATTAATGAAATCAAATATTCATGCAAATAGGTGAC
1 ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGGTGAC
* *
61799075 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGTGGACCCAT
66 GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGCGGACCCAC
*
61799140 GATTCAAGTCCGTGTTTCTACTCAATAAAACAGAACCATCTGGATAGCTTGATAATGAATTAAAT
131 GATTCAAGTACGTGTTTCTACTCAATAAAA-AGAACCAT-TGGATAGCTTGATAATGAATTAAAT
* * *
61799205 CTAATAGTCATGC-AGAGAGATGACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAAC
194 CTAATAGTCAAGCGA-ACAGATCACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAAC
* * ** *
61799269 TACCTTAAGTGGATTTGTGATTAGGGTACATGTTTGTACTCG
258 TACCTTAAGTGGATCTGTGATTAGGATACATAATTGTACTCA
* *
61799311 ATAAAACAGAACCATCCA-AATAGCTAGATCATGAATAAAATCAAATATTCATGCAAATAGGTGA
1 ATAAAACAGAATCAT-CAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGGTGA
* * * *
61799375 TGATGAAGAAGGTAAATTCCCATTTCATGTCCTCAAACAAGTTTATCTT
65 CGATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTT
61799424 CTTCTATCTT
Statistics
Matches: 368, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
300 2 0.01
301 126 0.34
302 2 0.01
306 2 0.01
307 1 0.00
308 1 0.00
310 1 0.00
311 46 0.12
312 8 0.02
313 179 0.49
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (299 bp):
ATAAAACAGAATCATCAGAATAGCTTGATCATGAATAAAATCAAATATTCATGCAAATAGGTGAC
GATGAAGAAGGTAAAATCCCATTTCAAGCCCTCAAACAAGTTTATCTTATCTTATGCGGACCCAC
GATTCAAGTACGTGTTTCTACTCAATAAAAAGAACCATTGGATAGCTTGATAATGAATTAAATCT
AATAGTCAAGCGAACAGATCACAATGAAGAAGGAAAAAGCCTATTTCAAGTCCTCAAACAACTAC
CTTAAGTGGATCTGTGATTAGGATACATAATTGTACTCA
Found at i:61805102 original size:58 final size:57
Alignment explanation
Indices: 61805035--61805179 Score: 191
Period size: 57 Copynumber: 2.5 Consensus size: 57
61805025 TTCCCGGGCT
* * * *
61805035 TGAATTTTTTTTGTCCAAGTTAGTATCTGAACTTGACGATTATTTCCACATTGGGGTC
1 TGAACTTTTTTTGTCCAAGTTAGTCTCTGAACTTCACGACTA-TTCCACATTGGGGTC
* * * *
61805093 TGAACTTTTTTTATCCAAGTTAGCCCCTGAACTTCATGACTATTCCACATTGGGGTC
1 TGAACTTTTTTTGTCCAAGTTAGTCTCTGAACTTCACGACTATTCCACATTGGGGTC
* *
61805150 TAAACTTTTTTGGTCCAAGTTAGTCTCTGA
1 TGAACTTTTTTTGTCCAAGTTAGTCTCTGA
61805180 TATTTCCTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
57 40 0.54
58 34 0.46
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (57 bp):
TGAACTTTTTTTGTCCAAGTTAGTCTCTGAACTTCACGACTATTCCACATTGGGGTC
Found at i:61808834 original size:29 final size:30
Alignment explanation
Indices: 61808799--61808865 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
61808789 CTTAACAAGC
*
61808799 CAATGACTTAAAT-AAACTTTCGAATAGTT
1 CAATGACTTAAATAAAACTTTCGAATAATT
61808828 CAATGACTTAAATGAAAACTTTCGAATAATT
1 CAATGACTTAAAT-AAAACTTTCGAATAATT
*
61808859 CAGTGAC
1 CAATGAC
61808866 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 13 0.38
31 21 0.62
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (30 bp):
CAATGACTTAAATAAAACTTTCGAATAATT
Found at i:61812552 original size:17 final size:17
Alignment explanation
Indices: 61812530--61812563 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61812520 TTTGTTTATT
61812530 ACATATTATATAAATTA
1 ACATATTATATAAATTA
* *
61812547 ACATATTTTATTAATTA
1 ACATATTATATAAATTA
61812564 GACAGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
ACATATTATATAAATTA
Found at i:61812592 original size:18 final size:18
Alignment explanation
Indices: 61812535--61812593 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
61812525 TTATTACATA
61812535 TTATATAAATT-AACATATT
1 TTAT-TAAATTAAACAT-TT
*
61812554 TTATT-AATTAGACAGTTT
1 TTATTAAATTAAACA-TTT
*
61812572 TTATTAAATTAAACATGT
1 TTATTAAATTAAACATTT
61812590 TTAT
1 TTAT
61812594 CCAAACTAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.12
18 17 0.50
19 13 0.38
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TTATTAAATTAAACATTT
Found at i:61816295 original size:3 final size:3
Alignment explanation
Indices: 61816281--61816330 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
61816271 AAATGACATT
* * *
61816281 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61816327 TTA T
1 TTA T
61816331 GACATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:61816316 original size:18 final size:18
Alignment explanation
Indices: 61816284--61816325 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
61816274 TGACATTTTA
*
61816284 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
61816301 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
61816319 TTATTAT
1 TTATTAT
61816326 ATTATGACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:61818243 original size:5 final size:5
Alignment explanation
Indices: 61818233--61818259 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
61818223 AAGTTATAAT
61818233 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
61818260 TTATTATCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:61819155 original size:25 final size:25
Alignment explanation
Indices: 61819075--61819189 Score: 124
Period size: 25 Copynumber: 4.6 Consensus size: 25
61819065 GGCCACCGTT
* * *
61819075 TTCAACTCTTATGAGCTTCCCGTTA
1 TTCAGCTCGTATGAGCTTCCTGTTA
* * *
61819100 TTCAGATCTTATGAGCTTCATGTTA
1 TTCAGCTCGTATGAGCTTCCTGTTA
*
61819125 TTCAGCTCGCATGAGCTTCCTGTTA
1 TTCAGCTCGTATGAGCTTCCTGTTA
* * *
61819150 TTCAGCTCGAAAGAGCTTACTGTT-
1 TTCAGCTCGTATGAGCTTCCTGTTA
*
61819174 TACAGCTCGTATGAGC
1 TTCAGCTCGTATGAGC
61819190 ATACATGTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 13 0.17
25 63 0.83
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (25 bp):
TTCAGCTCGTATGAGCTTCCTGTTA
Found at i:61822003 original size:3 final size:3
Alignment explanation
Indices: 61821995--61822047 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
61821985 GATGCAGTAA
*
61821995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
61822043 AAT AA
1 AAT AA
61822048 AAGATACTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:61825699 original size:7 final size:7
Alignment explanation
Indices: 61825674--61825730 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
61825664 GAGTCGTAAA
61825674 AAAAATG
1 AAAAATG
* *
61825681 AGATATG
1 AAAAATG
61825688 AAAAAATG
1 -AAAAATG
61825696 -AAAATG
1 AAAAATG
61825702 AAAAATG
1 AAAAATG
61825709 AAAAATGG
1 AAAAAT-G
61825717 AAAAA-G
1 AAAAATG
61825723 TAAAAATG
1 -AAAAATG
61825731 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
6 7 0.17
7 22 0.54
8 12 0.29
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:61825705 original size:13 final size:14
Alignment explanation
Indices: 61825673--61825712 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
61825663 TGAGTCGTAA
*
61825673 AAAAAATGAGATATG
1 AAAAAATGA-AAATG
61825688 AAAAAATGAAAATG
1 AAAAAATGAAAATG
61825702 -AAAAATGAAAA
1 AAAAAATGAAAA
61825713 ATGGAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAAATGAAAATG
Found at i:61825719 original size:15 final size:15
Alignment explanation
Indices: 61825674--61825732 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
61825664 GAGTCGTAAA
* * *
61825674 AAAAATGAGATATGA
1 AAAAATGAAAAATGG
61825689 AAAAATG-AAAAT-G
1 AAAAATGAAAAATGG
61825702 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
61825717 AAAAA-GTAAAAATGG
1 AAAAATG-AAAAATGG
61825732 A
1 A
61825733 GAGGCTAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.18
14 9 0.24
15 22 0.58
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:61827139 original size:88 final size:88
Alignment explanation
Indices: 61826973--61827147 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 88
61826963 GTGAAACTTC
* * * *
61826973 AGCCTTATCTCCCTGAGCAGCAGTGGAATAGGCTGAAAATAGTAGATCTTGTCTTCCTGTATTGG
1 AGCCTTATCTCCCTGAGCAGCAGTGGAATAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAG
*
61827038 CAGCGAAGTAGATCGAAGATACT
66 CAGCGAAGCAGATCGAAGATACT
* * * * * *
61827061 AGCCTTGTCTCCCTGGGTAGTAGTGGAGTAGGTTGAAAAT-GACAGATCTTGCCTTCCTGTACTA
1 AGCCTTATCTCCCTGAGCAGCAGTGGAATAGGCTGAAAATAG-CAGATCTTGCCTTCCTGTACTA
* *
61827125 GCGGTGAAGCAGATCGAAGATAC
65 GCAGCGAAGCAGATCGAAGATAC
61827148 CCGTCTTATC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 1 0.01
88 72 0.99
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (88 bp):
AGCCTTATCTCCCTGAGCAGCAGTGGAATAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAG
CAGCGAAGCAGATCGAAGATACT
Found at i:61827550 original size:101 final size:100
Alignment explanation
Indices: 61827347--61827609 Score: 341
Period size: 101 Copynumber: 2.6 Consensus size: 100
61827337 CAGTGGAATG
* *
61827347 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGTAGTGGAACAGATTGAAGTCACGAT
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGAC
* *
61827412 GGCGGATCTGATTTCTCCAACATTGCAATTAAAAA
66 AGCAGATCTGATTTCTCCAACATTGCAATTAAAAA
* *
61827447 GATTGAAGCCACAACAGCGAATCTTACTTCCTTGGCGGTGTAGTAGGAACAGATTGAAG-CTACG
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGT-GGAACAGATTGAAGTC-ACG
* * *
61827511 ACAGCAGATCTGGTTTC-CCTGACATTGTAATTAAAAA
64 ACAGCAGATCTGATTTCTCC-AACATTGCAATTAAAAA
* ** * * **
61827548 GATTGAAGCCACAACGGCGGATCTTACTTTTCTAGCAGTACAGTGGAACAGATTGAAGTCAC
1 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGTCAC
61827610 AACGGCGAAT
Statistics
Matches: 141, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
100 60 0.43
101 81 0.57
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (100 bp):
GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGAC
AGCAGATCTGATTTCTCCAACATTGCAATTAAAAA
Found at i:61827654 original size:100 final size:100
Alignment explanation
Indices: 61827347--61827645 Score: 340
Period size: 100 Copynumber: 3.0 Consensus size: 100
61827337 CAGTGGAATG
* * *
61827347 GATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGGTGTAGTGGAACAGATTGAAGTCACGAT
1 GATTGAAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGAC
* *
61827412 GGCGGATC-TGATTT-CTCCAACATTGCAATTAAAAA
66 GGCGAATCTTG-TTTCCT-CGACATTGCAATTAAAAA
*
61827447 GATTGAAGCCACAACAGCGAATCTTAC-TTCCTTGGCGGTGTAGTAGGAACAGATTGAAG-CTAC
1 GATTGAAGCCACAACGGCGAATCTTACTTTCC-TGGCGGTGTAGT-GGAACAGATTGAAGTC-AC
* * *
61827510 GACAGC-AGATCTGGTTTCC-CTGACATTGTAATTAAAAA
63 GACGGCGA-ATCTTGTTTCCTC-GACATTGCAATTAAAAA
* * * * ** *
61827548 GATTGAAGCCACAACGGCGGATCTTACTTTTCTAGCAGTACAGTGGAACAGATTGAAGTCACAAC
1 GATTGAAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGAC
*
61827613 GGCGAATCTTGTTTCCTCGACATTGCAGTTAAA
66 GGCGAATCTTGTTTCCTCGACATTGCAATTAAA
61827646 CAATTTGAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
99 3 0.02
100 82 0.49
101 77 0.46
102 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (100 bp):
GATTGAAGCCACAACGGCGAATCTTACTTTCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGAC
GGCGAATCTTGTTTCCTCGACATTGCAATTAAAAA
Found at i:61827716 original size:44 final size:44
Alignment explanation
Indices: 61827657--61827852 Score: 158
Period size: 44 Copynumber: 4.5 Consensus size: 44
61827647 AATTTGAAAA
* *
61827657 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCATAG
1 ATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATAG
* * ***
61827701 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT-ATAG
1 ATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATAG
* * ** *
61827742 -TCTTATCT-TCCTGAAATTGCAGTGGAGCAGACAGAAGAAAC-TA-
1 ATCCTATCTCT-CTGAAGTTGCAGTGGAGCAGA-TTAA-AATCATAG
* *
61827785 ATCCTATCTCTCCGAAGTTGCAGTGGAGCAGATTAAAATGAT-G
1 ATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATAG
61827828 AATCCTATAC-CTCTGAAGTTGCAGT
1 -ATCCTAT-CTCTCTGAAGTTGCAGT
61827853 AGGTCGGATT
Statistics
Matches: 118, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
39 1 0.01
40 19 0.16
41 11 0.09
42 5 0.04
43 9 0.08
44 71 0.60
45 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
ATCCTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCATAG
Found at i:61828809 original size:3 final size:3
Alignment explanation
Indices: 61828801--61828854 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
61828791 TGTTAAATTG
* **
61828801 TTA TTA TTA CTGTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA TGG TTA
1 TTA TTA TTA -T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
61828849 TTA TTA
1 TTA TTA
61828855 CCATTTTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 36 0.86
4 4 0.10
5 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:61829022 original size:18 final size:18
Alignment explanation
Indices: 61828985--61829018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61828975 TACATATATT
*
61828985 TACGTTTTATAATATTTA
1 TACGTTTTACAATATTTA
61829003 TACGTTTT-CAATATTT
1 TACGTTTTACAATATTT
61829019 TATAATCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (18 bp):
TACGTTTTACAATATTTA
Found at i:61831659 original size:15 final size:13
Alignment explanation
Indices: 61831621--61831652 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61831611 ATGTTTAAGA
*
61831621 TTTTAAAATTAAT
1 TTTTAAAAATAAT
61831634 TTTTAAAAATAAT
1 TTTTAAAAATAAT
61831647 TTTTAA
1 TTTTAA
61831653 GAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAAAAATAAT
Found at i:61833766 original size:24 final size:24
Alignment explanation
Indices: 61833739--61833795 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
61833729 AAACCTAATT
61833739 CTAATCAAA-GCCAAATATATTATG
1 CTAAT-AAATGCCAAATATATTATG
*
61833763 CTAATAAATGCTAAATATATTATG
1 CTAATAAATGCCAAATATATTATG
*
61833787 CTCATAAAT
1 CTAATAAAT
61833796 ACTAAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (24 bp):
CTAATAAATGCCAAATATATTATG
Found at i:61833800 original size:24 final size:24
Alignment explanation
Indices: 61833751--61833802 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
61833741 AATCAAAGCC
*
61833751 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATACT
*
61833775 AAATATATTATGCTCATAAATACT
1 AAATATATTATGCTAATAAATACT
61833799 AAAT
1 AAAT
61833803 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATACT
Found at i:61835275 original size:42 final size:42
Alignment explanation
Indices: 61835211--61835294 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
61835201 CCACAATACC
* * *
61835211 AAGCAAAGCTCGAATCGGACTATGCTTCACAACTGGGGAGAA
1 AAGCAAAGCTCGAATCGAACTATGCTTCAAAACTGAGGAGAA
61835253 AAGCAAAGCTCGAATCGAACTATGCTTCAAAACTGAGGAGAA
1 AAGCAAAGCTCGAATCGAACTATGCTTCAAAACTGAGGAGAA
61835295 CACATCTGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (42 bp):
AAGCAAAGCTCGAATCGAACTATGCTTCAAAACTGAGGAGAA
Found at i:61838144 original size:24 final size:24
Alignment explanation
Indices: 61838117--61838164 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
61838107 AAAGTCAAAA
* *
61838117 ATATTATGCTAATAAATGCTAAAT
1 ATATTATACTAATAAATACTAAAT
*
61838141 ATATTATACTCATAAATACTAAAT
1 ATATTATACTAATAAATACTAAAT
61838165 CTTCTAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAT
Found at i:61841269 original size:85 final size:85
Alignment explanation
Indices: 61841193--61841359 Score: 244
Period size: 85 Copynumber: 2.0 Consensus size: 85
61841183 AAACGCGTTT
* * * * *
61841193 AATTGGGCATGCTCTCCTTGACATGTTATCAGAAAAGCTTTTCTAGCTGGACGCGCTTTTACACT
1 AATTGGGCATGCTCTCCTTGACATGTCATCAGAAAAGCTCTTCCAGCTGGACACGCTTTCACACT
61841258 ACTGTGAAGAAAACGCATCC
66 ACTGTGAAGAAAACGCATCC
* * * *
61841278 AATTGGGCATGCTCTCCTTGACATGTCATCAGGAAAGCTCTTCCAGTTTGACATGCTTTCACACT
1 AATTGGGCATGCTCTCCTTGACATGTCATCAGAAAAGCTCTTCCAGCTGGACACGCTTTCACACT
*
61841343 ACTGTGAAGAAAGCGCA
66 ACTGTGAAGAAAACGCA
61841360 CCCAGCTAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 72 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (85 bp):
AATTGGGCATGCTCTCCTTGACATGTCATCAGAAAAGCTCTTCCAGCTGGACACGCTTTCACACT
ACTGTGAAGAAAACGCATCC
Found at i:61843029 original size:18 final size:19
Alignment explanation
Indices: 61842991--61843028 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
61842981 TATACACCTA
61842991 TATATATATGTACATATTTT
1 TATATATATG-ACATATTTT
61843011 TATATATATG-CAT-TTTT
1 TATATATATGACATATTTT
61843028 T
1 T
61843029 TTTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
20 10 0.56
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
TATATATATGACATATTTT
Found at i:61855410 original size:15 final size:14
Alignment explanation
Indices: 61855385--61855415 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
61855375 GAAATAATTT
61855385 ATTTTAAAAATAAA
1 ATTTTAAAAATAAA
61855399 ATTTTGAAAAATAAA
1 ATTTT-AAAAATAAA
61855414 AT
1 AT
61855416 CAATTTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATTTTAAAAATAAA
Found at i:61856417 original size:14 final size:14
Alignment explanation
Indices: 61856398--61856427 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61856388 TGTTAAATTG
*
61856398 ATTTTATTTTTCAA
1 ATTTTATTTTTAAA
61856412 ATTTTATTTTTAAA
1 ATTTTATTTTTAAA
61856426 AT
1 AT
61856428 AAATTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTATTTTTAAA
Found at i:61858798 original size:170 final size:170
Alignment explanation
Indices: 61858510--61858896 Score: 573
Period size: 170 Copynumber: 2.3 Consensus size: 170
61858500 ACAAAGCTTG
* * * * *
61858510 TTAATAACTGTTTGATTAAGTTAATTGAGCAATGAATTTATAATTTAGCTTTATGCACTAATCAC
1 TTAATTACTGTTTAATTAACTTAATTTAGCAATGAATTTATAATTTAGCTTCATGCACTAATCAC
* * *
61858575 ATCACTGATTTTAGATTTGATTTAGTTTCGTTAATCTATGAAATAATCACATCATTGAAACTAGA
66 ATCACTGATTTTAGATCTGATTTAGTTTCATTAATCTATGAAATAATCACATCACTGAAACTAGA
* *
61858640 TCAATCTGAGTTGGAGGTTTTTAC-AGACGGGAAACCTTCT
131 TCAATCTGAGTTGAAGGTTTTTACTA-ACGAGAAACCTTCT
* *
61858680 TTAATTACTGTTTAATTAGA-TTAATTTAGTAATGAATTTATAATTTAGCTTCATGGC-CTATTC
1 TTAATTACTGTTTAATTA-ACTTAATTTAGCAATGAATTTATAATTTAGCTTCAT-GCACTAATC
* *
61858743 ACATCACTGATTTTAGATCTGATTTAGTTTCATTAATCTATGCAATGATCACATCACTGAAACTA
64 ACATCACTGATTTTAGATCTGATTTAGTTTCATTAATCTATGAAATAATCACATCACTGAAACTA
61858808 GATCAATCTGAGTTGAAGGTTTTTACTAACGAGAAACCTTCT
129 GATCAATCTGAGTTGAAGGTTTTTACTAACGAGAAACCTTCT
* * *
61858850 TTAATTACTGTTTAATTAACTTAATTTAGGAAAGAATTTAGAATTTA
1 TTAATTACTGTTTAATTAACTTAATTTAGCAATGAATTTATAATTTA
61858897 AATCAATTGA
Statistics
Matches: 197, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
169 1 0.01
170 192 0.97
171 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (170 bp):
TTAATTACTGTTTAATTAACTTAATTTAGCAATGAATTTATAATTTAGCTTCATGCACTAATCAC
ATCACTGATTTTAGATCTGATTTAGTTTCATTAATCTATGAAATAATCACATCACTGAAACTAGA
TCAATCTGAGTTGAAGGTTTTTACTAACGAGAAACCTTCT
Found at i:61862187 original size:26 final size:26
Alignment explanation
Indices: 61862158--61862222 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 26
61862148 AACTTTAAAA
61862158 ATTATATTTAATACAATAAAATATTT
1 ATTATATTTAATACAATAAAATATTT
* *
61862184 ATTATGTTTTTTAATATAATAAAATATTT
1 ATTA---TATTTAATACAATAAAATATTT
*
61862213 ATTTTATTTA
1 ATTATATTTA
61862223 TGATAGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 9 0.28
29 23 0.72
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTATATTTAATACAATAAAATATTT
Found at i:61865654 original size:6 final size:6
Alignment explanation
Indices: 61865649--61865694 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
61865639 GTAGTCATAT
* *
61865649 ATATAT ATATAC ATATAC ATATAC ATATAC ATATAC ATATAT ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
61865695 TGAATGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:61865676 original size:18 final size:18
Alignment explanation
Indices: 61865649--61865694 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
61865639 GTAGTCATAT
61865649 ATATATATATACATATAC
1 ATATATATATACATATAC
*
61865667 ATATACATATACATATAC
1 ATATATATATACATATAC
61865685 ATATATATAT
1 ATATATATAT
61865695 TGAATGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATATATATACATATAC
Found at i:61865861 original size:26 final size:26
Alignment explanation
Indices: 61865832--61865884 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
61865822 TTCTTATAGT
61865832 ATTAATTATATACCAAAATAAAACTC
1 ATTAATTATATACCAAAATAAAACTC
61865858 ATTAATTATATACCAAAATAAAACTC
1 ATTAATTATATACCAAAATAAAACTC
61865884 A
1 A
61865885 ATGGCTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (26 bp):
ATTAATTATATACCAAAATAAAACTC
Found at i:61869922 original size:12 final size:12
Alignment explanation
Indices: 61869905--61869935 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
61869895 CATACCATAT
61869905 TGATGATGCTGA
1 TGATGATGCTGA
*
61869917 TGATGATGGTGA
1 TGATGATGCTGA
61869929 TGATGAT
1 TGATGAT
61869936 TCTCCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.35, T:0.35
Consensus pattern (12 bp):
TGATGATGCTGA
Found at i:61874799 original size:16 final size:17
Alignment explanation
Indices: 61874778--61874820 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
61874768 AGCATTACCG
*
61874778 CAGAACAACTCT-TATT
1 CAGAACAACTCTAAATT
61874794 CAGAACAACTCTAAATT
1 CAGAACAACTCTAAATT
*
61874811 GAGAACAACT
1 CAGAACAACT
61874821 ATGTCGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (17 bp):
CAGAACAACTCTAAATT
Found at i:61887848 original size:3 final size:3
Alignment explanation
Indices: 61887770--61887839 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
61887760 AGTACTTTGC
61887770 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
61887818 CAT CT-T TAC TAT TAT TAG TAT T
1 TAT -TAT TAT TAT TAT TAT TAT T
61887840 GGTATTATTG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 58 0.98
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:61888310 original size:18 final size:19
Alignment explanation
Indices: 61888272--61888309 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
61888262 TATACACCTA
61888272 TATATATATGTACATATTTT
1 TATATATATG-ACATATTTT
61888292 TATATATATG-CAT-TTTT
1 TATATATATGACATATTTT
61888309 T
1 T
61888310 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 3 0.17
20 10 0.56
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (19 bp):
TATATATATGACATATTTT
Found at i:61892290 original size:19 final size:17
Alignment explanation
Indices: 61892245--61892290 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
61892235 CCGTCTCTTA
61892245 TTTTTATATTTTAATAT
1 TTTTTATATTTTAATAT
61892262 TTTCTGTATATGTTTATATAT
1 TTT-T-TATAT-TTTA-ATAT
61892283 TTTTTATA
1 TTTTTATA
61892291 ATTCTACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 9 0.36
20 5 0.20
21 7 0.28
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTTATATTTTAATAT
Found at i:61897254 original size:21 final size:21
Alignment explanation
Indices: 61897230--61897270 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
61897220 CCTTCTCTGG
* *
61897230 TTTTATTCTTATGTAAAATTA
1 TTTTAGTCTGATGTAAAATTA
*
61897251 TTTTAGTCTGATTTAAAATT
1 TTTTAGTCTGATGTAAAATT
61897271 TACAACAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTAGTCTGATGTAAAATTA
Found at i:61904095 original size:16 final size:16
Alignment explanation
Indices: 61904074--61904104 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61904064 CCTTTAGGGT
61904074 TCTTTAGTTTTTTTAA
1 TCTTTAGTTTTTTTAA
*
61904090 TCTTTATTTTTTTTA
1 TCTTTAGTTTTTTTA
61904105 GAAAATGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TCTTTAGTTTTTTTAA
Found at i:61907641 original size:15 final size:15
Alignment explanation
Indices: 61907611--61907650 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
61907601 AGTGTTTGTA
*
61907611 TTTTAAT-TTAATAT
1 TTTTAATATTTATAT
61907625 TTTTAATATTTATAT
1 TTTTAATATTTATAT
*
61907640 TTTTAAAATTT
1 TTTTAATATTT
61907651 TAGTTATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTAATATTTATAT
Found at i:61909062 original size:21 final size:21
Alignment explanation
Indices: 61909032--61909076 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
61909022 TTGCCCCTAG
*
61909032 CATGTCACACCTTGAAACCAA
1 CATGTAACACCTTGAAACCAA
61909053 CATGTAACACCTTGAAACCAA
1 CATGTAACACCTTGAAACCAA
61909074 CAT
1 CAT
61909077 ATCACATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (21 bp):
CATGTAACACCTTGAAACCAA
Found at i:61909972 original size:31 final size:32
Alignment explanation
Indices: 61909913--61909977 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
61909903 GGCAAATTAC
61909913 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
61909945 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
61909976 AA
1 AA
61909978 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:61915347 original size:13 final size:13
Alignment explanation
Indices: 61915329--61915358 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
61915319 GGTAGGCAAC
61915329 TTTTTTTACGCTT
1 TTTTTTTACGCTT
*
61915342 TTTTTTTGCGCTT
1 TTTTTTTACGCTT
61915355 TTTT
1 TTTT
61915359 GCGCTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.10, T:0.73
Consensus pattern (13 bp):
TTTTTTTACGCTT
Found at i:61915369 original size:9 final size:10
Alignment explanation
Indices: 61915343--61915367 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
61915333 TTTACGCTTT
61915343 TTTTTTGCGC
1 TTTTTTGCGC
61915353 TTTTTTGCGC
1 TTTTTTGCGC
61915363 TTTTT
1 TTTTT
61915368 GCTTCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (10 bp):
TTTTTTGCGC
Found at i:61916008 original size:31 final size:32
Alignment explanation
Indices: 61915949--61916013 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
61915939 GGCAAATTAC
61915949 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
61915981 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
61916012 AA
1 AA
61916014 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:61924366 original size:13 final size:14
Alignment explanation
Indices: 61924345--61924377 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61924335 CTCTGAACCC
61924345 CGAACCTTGAA-CT
1 CGAACCTTGAATCT
*
61924358 CGAATCTTGAATCT
1 CGAACCTTGAATCT
61924372 CGAACC
1 CGAACC
61924378 CCAAAGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (14 bp):
CGAACCTTGAATCT
Found at i:61924487 original size:14 final size:15
Alignment explanation
Indices: 61924456--61924509 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
61924446 CAAGGTTTAA
* *
61924456 GTTTAGGGTTCAAGG
1 GTTTGGGGTTTAAGG
61924471 GTTTGGGGTTT-AGG
1 GTTTGGGGTTTAAGG
** *
61924485 GTTTAAGATTTAAGG
1 GTTTGGGGTTTAAGG
61924500 GTTTGGGGTT
1 GTTTGGGGTT
61924510 CGGAGTTCAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.17, C:0.02, G:0.41, T:0.41
Consensus pattern (15 bp):
GTTTGGGGTTTAAGG
Found at i:61924528 original size:29 final size:29
Alignment explanation
Indices: 61924462--61924530 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
61924452 TTAAGTTTAG
*
61924462 GGTTCAAGGGTTTGGGGTTTAGGGTTTAA
1 GGTTCAAGGGTTTGGGGTTTAGGGTTCAA
* * *
61924491 GATTTAAGGGTTTGGGG-TTCGGAGTTCAA
1 GGTTCAAGGGTTTGGGGTTTAGG-GTTCAA
61924520 GGTTCAAGGGT
1 GGTTCAAGGGT
61924531 ATAAGATTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.19, C:0.06, G:0.41, T:0.35
Consensus pattern (29 bp):
GGTTCAAGGGTTTGGGGTTTAGGGTTCAA
Found at i:61927981 original size:22 final size:22
Alignment explanation
Indices: 61927939--61927982 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
61927929 ATAAAAAAAT
*
61927939 AAAATTACATTTTTATTATTATA
1 AAAATTACAATTTTA-TATTATA
61927962 AAAATATACAATTTTA-ATTAT
1 AAAAT-TACAATTTTATATTAT
61927983 TGTAGTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 5 0.26
24 9 0.47
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATTACAATTTTATATTATA
Found at i:61929203 original size:14 final size:14
Alignment explanation
Indices: 61929186--61929214 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61929176 AATATCAAAT
61929186 TAATAAGAGATAAA
1 TAATAAGAGATAAA
61929200 TAATAAGAGATAAA
1 TAATAAGAGATAAA
61929214 T
1 T
61929215 TATATCAAAT
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:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (14 bp):
TAATAAGAGATAAA
Found at i:61930050 original size:271 final size:271
Alignment explanation
Indices: 61929552--61930094 Score: 955
Period size: 271 Copynumber: 2.0 Consensus size: 271
61929542 TGAAGAAAAG
*
61929552 AGATCCGAAACCGTTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
1 AGATCCGAAACCATTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
61929617 TGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
66 TGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
61929682 GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGACGTCGAATTTCCAAGTCAATATTTTAC
131 GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGACGTCGAATTTCCAAGTCAATATTTTAC
* * * * *
61929747 TCGAAATTTGTGTGTACAAATTTCTGGCACACCTAGTAAGACAATCTTTGTCTTTTATCTTTTCT
196 TCGAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTTCT
61929812 CTTGAAAGTCA
261 CTTGAAAGTCA
*
61929823 AGATCC-AAACCCATTTTAAGAGCAAGTTGTCATGACACTTGAAGCAATCCAAGTCAGATGACCC
1 AGATCCGAAA-CCATTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCC
61929887 TTGGATCAAAGTTAAATC-GAAGAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTT
65 TTGGATCAAAGTTAAATCGGAA-AGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTT
* * *
61929951 AAGAGATTGTAACTTTCTTTCAAGTTATCAATAAATTTGACTTTGAATTTCCAAGTCAATATTTT
129 AAGAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGACGTCGAATTTCCAAGTCAATATTTT
*
61930016 ACTCGAAATTTGTGTGTACAAATTTCTCGCACACCCAATAGGACAATCTTTATCTTTCATCTTTT
194 ACTCGAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTT
61930081 CTCTTGAAAGTCA
259 CTCTTGAAAGTCA
61930094 A
1 A
61930095 AATTCAAAGT
Statistics
Matches: 259, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
270 6 0.02
271 253 0.98
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (271 bp):
AGATCCGAAACCATTTTAAGAGCAAGTTGTCACGACACTTGAAGCAATCCAAGTCAGATGACCCT
TGGATCAAAGTTAAATCGGAAAGAAGAATCAATTGATATTTTTCTTTGTATTCAAGAAATTTTAA
GAGATTGTAACTCTCTTTCAAGTTATCAATAAATTTGACGTCGAATTTCCAAGTCAATATTTTAC
TCGAAATTTGTGTGTACAAATTTCTCGCACACCCAATAAGACAATCTTTATCTTTCATCTTTTCT
CTTGAAAGTCA
Found at i:61944084 original size:16 final size:15
Alignment explanation
Indices: 61944058--61944092 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
61944048 TTACATGTTT
61944058 TGTTCAATTAACTTC
1 TGTTCAATTAACTTC
*
61944073 TGTTCTAATTAACTTT
1 TGTTC-AATTAACTTC
61944089 TGTT
1 TGTT
61944093 TTGTTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (15 bp):
TGTTCAATTAACTTC
Found at i:61944560 original size:23 final size:24
Alignment explanation
Indices: 61944530--61944592 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
61944520 TTGTGTTTCT
* *
61944530 TAATATTTATATTATTT-TTAATC
1 TAATATTTATATTATTTAATAATA
* *
61944553 TAATATTTA-ATAATTTAATATTA
1 TAATATTTATATTATTTAATAATA
61944576 TAATATTATATATTATT
1 TAATATT-TATATTATT
61944593 ATAGATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 6 0.19
23 19 0.59
24 2 0.06
25 5 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATATTTATATTATTTAATAATA
Found at i:61944571 original size:15 final size:16
Alignment explanation
Indices: 61944548--61944580 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61944538 ATATTATTTT
61944548 TAATCTAATATT-TAA
1 TAATCTAATATTATAA
*
61944563 TAATTTAATATTATAA
1 TAATCTAATATTATAA
61944579 TA
1 TA
61944581 TTATATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATCTAATATTATAA
Found at i:61949779 original size:19 final size:20
Alignment explanation
Indices: 61949737--61949780 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
61949727 ATAATAAGTA
* *
61949737 ATATATAATGTATTACTATT
1 ATATATAATCTATTACTATG
*
61949757 ATATATAA-CTATTATTATG
1 ATATATAATCTATTACTATG
61949776 ATATA
1 ATATA
61949781 GATTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
ATATATAATCTATTACTATG
Found at i:61950671 original size:19 final size:19
Alignment explanation
Indices: 61950644--61950683 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61950634 TGTGATATAG
61950644 TATTATATAATGAATAATA
1 TATTATATAATGAATAATA
* * *
61950663 TATTTTATAATTATTAATA
1 TATTATATAATGAATAATA
61950682 TA
1 TA
61950684 ATAACTACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATTATATAATGAATAATA
Found at i:61951946 original size:24 final size:24
Alignment explanation
Indices: 61951890--61951936 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
61951880 TTCACGAGGG
61951890 TTGCTCATTCTAAGAGAGAAACAA
1 TTGCTCATTCTAAGAGAGAAACAA
61951914 TTGCTCATTCTAAGAGAGAAACA
1 TTGCTCATTCTAAGAGAGAAACA
61951937 CTCTTCCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (24 bp):
TTGCTCATTCTAAGAGAGAAACAA
Found at i:61957105 original size:39 final size:39
Alignment explanation
Indices: 61957062--61957139 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
61957052 TGTGATGATG
61957062 AAGAAAGGGATTATGTTTGTGATGCCTTCGGTAGGGCAA
1 AAGAAAGGGATTATGTTTGTGATGCCTTCGGTAGGGCAA
61957101 AAGAAAGGGATTATGTTTGTGATGCCTTCGGTAGGGCAA
1 AAGAAAGGGATTATGTTTGTGATGCCTTCGGTAGGGCAA
61957140 CTATATTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.28
Consensus pattern (39 bp):
AAGAAAGGGATTATGTTTGTGATGCCTTCGGTAGGGCAA
Found at i:61962061 original size:85 final size:88
Alignment explanation
Indices: 61961894--61962061 Score: 261
Period size: 85 Copynumber: 1.9 Consensus size: 88
61961884 AGGGTGTAAA
* * * * *
61961894 AAGCCTTCAAACTTTTTCAAAAAAAAGTAATTAAGCCCCTACTTTTTTTTTTGCATTCATTTGGG
1 AAGCCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTAC-TTTTTTTTTGCACTCAATTGGG
61961959 TACTTGAACTTTCAAAATATTTTG
65 TACTTGAACTTTCAAAATATTTTG
61961983 AAGCCCTCAAACCTTTTC-AAAAAAAGCAATTAAGCCCCTAC-TTTTTTTT-CACTCAATTGGGT
1 AAGCCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACTCAATTGGGT
61962045 ACTTGAACTTTCAAAAT
66 ACTTGAACTTTCAAAAT
61962062 GCATCAAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
85 28 0.38
86 8 0.11
88 22 0.30
89 16 0.22
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (88 bp):
AAGCCCTCAAACCTTTTCAAAAAAAAGCAATTAAGCCCCTACTTTTTTTTTGCACTCAATTGGGT
ACTTGAACTTTCAAAATATTTTG
Found at i:61962096 original size:88 final size:87
Alignment explanation
Indices: 61961891--61962106 Score: 249
Period size: 88 Copynumber: 2.4 Consensus size: 87
61961881 TTAAGGGTGT
* * * *
61961891 AAAAAGCCTTCAAACTTTTTCAAAAAAAAGTAATTAAGCCCCTACTTTTTTTTTTGCATTCATTT
1 AAAAAACCCTCAAACTTTTTC-AAAAAAAGTAATTAAGCCCCTAC-TTTTTTTTTGCACTCAATT
*
61961956 GGGTACTTGAACTTTCAAAATATT
64 GGGTACTTGAACTTTCAAAATATC
*** * * *
61961980 TTGAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTAC-TTTTTTTT-CACTCAATTGG
1 AAAAAACCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCTACTTTTTTTTTGCACTCAATTGG
61962043 GTACTTGAACTTTCAAAATGCATC
66 GTACTTGAACTTTCAAAAT--ATC
*
61962067 AAAAATACCCTCAAACTTTTTTC-AAAAAAGTAGTTAAGCC
1 AAAAA-ACCCTCAAAC-TTTTTCAAAAAAAGTAATTAAGCC
61962107 ATGCTTTTAT
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
85 28 0.26
86 8 0.07
87 4 0.04
88 46 0.43
89 21 0.20
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (87 bp):
AAAAAACCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCCTACTTTTTTTTTGCACTCAATTGG
GTACTTGAACTTTCAAAATATC
Found at i:61962211 original size:9 final size:9
Alignment explanation
Indices: 61962169--61962265 Score: 64
Period size: 8 Copynumber: 11.0 Consensus size: 9
61962159 TTATTAAATT
61962169 ATAAT-AAA
1 ATAATAAAA
*
61962177 A-AATTAAA
1 ATAATAAAA
*
61962185 ATATTAAAA
1 ATAATAAAA
61962194 AT--TAGAAA
1 ATAATA-AAA
61962202 ATAATAAAA
1 ATAATAAAA
61962211 ATAATAAAA
1 ATAATAAAA
61962220 A-AATATATAA
1 ATAATA-A-AA
*
61962230 AAAATATAAA
1 ATAATA-AAA
*
61962240 ATAGATAGAA
1 ATA-ATAAAA
61962250 AT-ATAAAA
1 ATAATAAAA
61962258 AT-ATAAAA
1 ATAATAAAA
61962266 TTTTATAAAG
Statistics
Matches: 75, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
7 5 0.07
8 27 0.36
9 21 0.28
10 13 0.17
11 9 0.12
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
ATAATAAAA
Found at i:61962214 original size:39 final size:41
Alignment explanation
Indices: 61962171--61962266 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 41
61962161 ATTAAATTAT
*
61962171 AATAAAAAATTAAAATAT-TAAAAATTAGAAAATA-ATAAA
1 AATAAAAAATTAAAATATATAAAAAATAGAAAATAGATAAA
* * *
61962210 AATAATAAA--AAAATATATAAAAAATATAAAATAGATAGA
1 AATAAAAAATTAAAATATATAAAAAATAGAAAATAGATAAA
61962249 AATATAAAAATATAAAAT
1 AATA-AAAAAT-TAAAAT
61962267 TTTATAAAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
37 7 0.15
38 14 0.30
39 16 0.35
40 4 0.09
43 5 0.11
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (41 bp):
AATAAAAAATTAAAATATATAAAAAATAGAAAATAGATAAA
Found at i:61962216 original size:29 final size:29
Alignment explanation
Indices: 61962174--61962242 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
61962164 AAATTATAAT
*
61962174 AAAAAAT-TAAAAT-AT-TAAAAAT-TAG
1 AAAAAATATAAAATAATAAAAAAATATAG
*
61962199 AAAATAATA-AAAATAATAAAAAAATATAT
1 AAAA-AATATAAAATAATAAAAAAATATAG
61962228 AAAAAATATAAAATA
1 AAAAAATATAAAATA
61962243 GATAGAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 4 0.11
26 8 0.22
27 2 0.06
28 10 0.28
29 12 0.33
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (29 bp):
AAAAAATATAAAATAATAAAAAAATATAG
Found at i:61962231 original size:21 final size:20
Alignment explanation
Indices: 61962199--61962240 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
61962189 TAAAAATTAG
61962199 AAAATAAT-AAAAATAATAAA
1 AAAATAATAAAAAAT-ATAAA
61962219 AAAATATATAAAAAATATAAA
1 AAAATA-ATAAAAAATATAAA
61962240 A
1 A
61962241 TAGATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 8 0.40
22 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATAAAAAATATAAA
Done.