Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 286 of 362
Found at i:96188969 original size:46 final size:46
Alignment explanation
Indices: 96188853--96189067 Score: 156
Period size: 46 Copynumber: 4.7 Consensus size: 46
96188843 AGTTATAGTG
* * * * *
96188853 AGCCAGTGTAAGACATGTCTAGGACATGCATCGGCCA-C-ATTATGAA
1 AGCCAGTGTAAGACTTGTCTGGGACATGCATCGG-CATCGA-GACGTA
*
96188899 ATGCCAGTGTAAGACATT-TCTGGGACATGCATCGGCATTGAGACG-A
1 A-GCCAGTGTAAGAC-TTGTCTGGGACATGCATCGGCATCGAGACGTA
* * * * *
96188945 GAGCTAGTGTAAGACTTGTTTGGGACATGTATCGGCCTCGAGATGTA
1 -AGCCAGTGTAAGACTTGTCTGGGACATGCATCGGCATCGAGACGTA
* * * *
96188992 AGCCAGTTTAAGACATGTCTGGGACATGCATCGG-TTACGAGATGT-
1 AGCCAGTGTAAGACTTGTCTGGGACATGCATCGGCAT-CGAGACGTA
* * * *
96189037 -GCTAGTGTAAGACATGTCTAGGATATGCATC
1 AGCCAGTGTAAGACTTGTCTGGGACATGCATC
96189068 AGCACGGATA
Statistics
Matches: 140, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
44 27 0.19
45 3 0.02
46 75 0.54
47 33 0.24
48 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (46 bp):
AGCCAGTGTAAGACTTGTCTGGGACATGCATCGGCATCGAGACGTA
Found at i:96191855 original size:16 final size:16
Alignment explanation
Indices: 96191830--96191863 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96191820 ATTAATTATT
*
96191830 AATTAGTAAATGAAAG
1 AATTAGTAAAAGAAAG
*
96191846 AATTATTAAAAGAAAG
1 AATTAGTAAAAGAAAG
96191862 AA
1 AA
96191864 AGAAAGAAGG
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:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (16 bp):
AATTAGTAAAAGAAAG
Found at i:96192579 original size:17 final size:17
Alignment explanation
Indices: 96192539--96192582 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
96192529 AATGATTTGT
*
96192539 GATTGAATTGTTATTGC
1 GATTGATTTGTTATTGC
96192556 GATTGATTTGTTATTGC
1 GATTGATTTGTTATTGC
96192573 GATTGATTTG
1 GATTGATTTG
96192583 AATTCAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (17 bp):
GATTGATTTGTTATTGC
Found at i:96193135 original size:18 final size:18
Alignment explanation
Indices: 96193112--96193147 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
96193102 AAATGAACCA
96193112 AAGGTTCATGAATAGTTG
1 AAGGTTCATGAATAGTTG
96193130 AAGGTTCATGAATAGTTG
1 AAGGTTCATGAATAGTTG
96193148 GTAATCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
AAGGTTCATGAATAGTTG
Found at i:96193268 original size:22 final size:22
Alignment explanation
Indices: 96193220--96193269 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
96193210 TTGGTACGAA
*
96193220 TTATATGTATGATTTATCAATT
1 TTATATGCATGATTTATCAATT
* *
96193242 ATATATGCATG-TTTATGATATT
1 TTATATGCATGATTTATCA-ATT
96193264 TTATAT
1 TTATAT
96193270 TTGCTATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (22 bp):
TTATATGCATGATTTATCAATT
Found at i:96200284 original size:26 final size:26
Alignment explanation
Indices: 96200244--96200308 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
96200234 GAAAAATCAA
* *
96200244 ATGAAATTGATAAATTGA-ATTAT-AG
1 ATGAAA-TGAGAAAATGATATTATAAG
*
96200269 AATGAAATGAGAAAATGATATTGTAAG
1 -ATGAAATGAGAAAATGATATTATAAG
96200296 ATGAAATGAGAAA
1 ATGAAATGAGAAA
96200309 TGCAATTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.26
26 23 0.68
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.28
Consensus pattern (26 bp):
ATGAAATGAGAAAATGATATTATAAG
Found at i:96200434 original size:18 final size:18
Alignment explanation
Indices: 96200411--96200446 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
96200401 AGATGAACCA
96200411 AAGGTTCATGAATAGTTG
1 AAGGTTCATGAATAGTTG
96200429 AAGGTTCATGAATAGTTG
1 AAGGTTCATGAATAGTTG
96200447 GTAATCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (18 bp):
AAGGTTCATGAATAGTTG
Found at i:96201043 original size:42 final size:42
Alignment explanation
Indices: 96200955--96201044 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
96200945 TGGGTGTGTG
* * *
96200955 CCCAC-GCCGTGTGGCAAAGTCAGAATTGCCCACAAGTTAGT
1 CCCACGGCCATGTGGCAAAGTCAGAATTGCCCACAAGCTAGC
* *
96200996 TCCACGGCCATGTGAGC-AAGTCAG-ATCTGCCCACAAGCTGGC
1 CCCACGGCCATGTG-GCAAAGTCAGAAT-TGCCCACAAGCTAGC
96201038 CCCACGG
1 CCCACGG
96201045 GCAGGCCACA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
41 6 0.15
42 32 0.80
43 2 0.05
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (42 bp):
CCCACGGCCATGTGGCAAAGTCAGAATTGCCCACAAGCTAGC
Found at i:96210300 original size:29 final size:29
Alignment explanation
Indices: 96210258--96210313 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
96210248 ACTGCAAGCC
96210258 GTCGTAACGGATTAAAATAGTTTCATGCA
1 GTCGTAACGGATTAAAATAGTTTCATGCA
96210287 GTCGTAACGGATTAAAATAGTTTCATG
1 GTCGTAACGGATTAAAATAGTTTCATG
96210314 TTCTTTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.32
Consensus pattern (29 bp):
GTCGTAACGGATTAAAATAGTTTCATGCA
Found at i:96214235 original size:7 final size:7
Alignment explanation
Indices: 96214215--96214278 Score: 101
Period size: 7 Copynumber: 9.0 Consensus size: 7
96214205 ATACTTAACA
96214215 TAGTCATT
1 TAGT-ATT
*
96214223 TTGTATT
1 TAGTATT
96214230 TAGTATT
1 TAGTATT
*
96214237 TTGTATT
1 TAGTATT
96214244 TAGTATT
1 TAGTATT
96214251 TAGTATT
1 TAGTATT
96214258 TAGTATT
1 TAGTATT
96214265 TAGTATT
1 TAGTATT
96214272 TAGTATT
1 TAGTATT
96214279 ATGTATATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
7 49 0.94
8 3 0.06
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (7 bp):
TAGTATT
Found at i:96221021 original size:46 final size:45
Alignment explanation
Indices: 96220969--96221144 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 45
96220959 TATTTGGGCA
*
96220969 TCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
96221015 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
96221060 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGGAACG
1 --TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT-GGAATG
* *
96221108 TCCGAGCTCGTTGAGTTGAGTCCAAGTTCCCTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
96221145 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:96221124 original size:93 final size:93
Alignment explanation
Indices: 96220965--96221136 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
96220955 AGGATATTTG
*
96220965 GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAG
*
96221030 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCAAGTTCGTGAGATGTAACTA
* *
96221058 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGGAACGTCCGAGCTCGTTGAG
1 GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAG
96221123 TTGAGTCCAAGTTC
66 TTGAGTCCAAGTTC
96221137 CCTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAGCTCGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAG
TTGAGTCCAAGTTCGTGAGATGTAACTA
Found at i:96224711 original size:126 final size:125
Alignment explanation
Indices: 96224464--96224857 Score: 560
Period size: 126 Copynumber: 3.1 Consensus size: 125
96224454 GGCCAAGCAG
*
96224464 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTACATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATC
* *
96224529 CTGCTTGAAGCTTTTTTTACACTATTTTTTCAGAA-CTGTCTTTTCAAAATTATTTTTTCAA
66 CTGCTTGAAGC-GTTTTTACACTATTTTTTCAGAACCT-TCTTCTCAAAATTATTTTTTCAA
* * * * *
96224590 GAACTACTGTAGAAAAAGAGCATCCACATGGGAGTTTTTTTCAGTAATTTTACTGACAGCGCATC
1 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATC
* * *
96224655 CTGCTTGAAGCGGTTTTTACACTA-TTTTTCAAAACCTTCTTCTCAAAATTATTTTTTTAG
66 CTGCTTGAAGC-GTTTTTACACTATTTTTTCAGAACCTTCTTCTCAAAATTATTTTTTCAA
* * * *
96224715 GAACTACTGTAAAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATACTTTTGCTGACAATGCATA
1 GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATC
* *
96224780 CTGCTTGAAGCGTTTTTGACATTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTC-A
66 CTGCTTGAAGCGTTTTT-ACACTATTTTTTCAGAACCTTCTTCTCAAAATTATTTTTTCAA
*
96224840 GAAACTACTATAGAAAAA
1 G-AACTACTGTAGAAAAA
96224858 AAACAAAATC
Statistics
Matches: 236, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
124 6 0.03
125 102 0.43
126 128 0.54
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (125 bp):
GAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTACACTATTTTTTCAGAACCTTCTTCTCAAAATTATTTTTTCAA
Found at i:96224993 original size:34 final size:34
Alignment explanation
Indices: 96224955--96225078 Score: 112
Period size: 34 Copynumber: 3.7 Consensus size: 34
96224945 AAAATTATTT
**
96224955 TTAAAAATTTTAAACCCTAATTTAATTAATTTTC
1 TTAAAAATCCTAAACCCTAATTTAATTAATTTTC
* * *
96224989 TTAAAAATCCTAAACCCCAGTTTAATTAATTTAC
1 TTAAAAATCCTAAACCCTAATTTAATTAATTTTC
* *
96225023 TT-CAAA-CCTTAAA-ACTAATTTAATTAATTTT-
1 TTAAAAATCC-TAAACCCTAATTTAATTAATTTTC
* * *
96225054 TAAAAAAATTCTAAACCCTGATTTA
1 T-TAAAAATCCTAAACCCTAATTTA
96225079 TTTTTTAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
31 1 0.01
32 16 0.23
33 14 0.20
34 39 0.56
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.40
Consensus pattern (34 bp):
TTAAAAATCCTAAACCCTAATTTAATTAATTTTC
Found at i:96225639 original size:13 final size:13
Alignment explanation
Indices: 96225613--96225653 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
96225603 GACATGTGAC
96225613 AAAAAAATTATTA
1 AAAAAAATTATTA
96225626 AAAATAAATT-TTA
1 AAAA-AAATTATTA
*
96225639 ATAAAAATTATTA
1 AAAAAAATTATTA
96225652 AA
1 AA
96225654 TTTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAAAAATTATTA
Found at i:96226412 original size:30 final size:31
Alignment explanation
Indices: 96226377--96226450 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
96226367 AAAAATTACA
*
96226377 AATTTTTTATA-AATTCTTTACAATTTTTTAT
1 AATTTTTTATATAATT-TTTACAATTTTTAAT
* * *
96226408 -ATTTTTTTTATAATTTTTTCTATTTTTAAT
1 AATTTTTTATATAATTTTTACAATTTTTAAT
96226438 AATTCTTTTATAT
1 AATT-TTTTATAT
96226451 TTTTCTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 21 0.60
31 7 0.20
32 7 0.20
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.66
Consensus pattern (31 bp):
AATTTTTTATATAATTTTTACAATTTTTAAT
Found at i:96226414 original size:11 final size:11
Alignment explanation
Indices: 96226379--96226507 Score: 58
Period size: 11 Copynumber: 12.4 Consensus size: 11
96226369 AAATTACAAA
*
96226379 TTTTTTATAAA
1 TTTTTTATAAT
* *
96226390 TTCTTTACAA-
1 TTTTTTATAAT
*
96226400 TTTTTTATATT
1 TTTTTTATAAT
96226411 TTTTTTATAA-
1 TTTTTTATAAT
*
96226421 TTTTTTCT-A-
1 TTTTTTATAAT
*
96226430 TTTTTAATAAT
1 TTTTTTATAAT
*
96226441 TCTTTTAT-AT
1 TTTTTTATAAT
*
96226451 TTTTCTAT-AT
1 TTTTTTATAAT
* *
96226461 ACTTTTTATAAA
1 -TTTTTTATAAT
* *
96226473 ATTTTAAT-AT
1 TTTTTTATAAT
* *
96226483 TTTTCTATAAC
1 TTTTTTATAAT
*
96226494 TTTTAT-TAAT
1 TTTTTTATAAT
96226504 TTTT
1 TTTT
96226508 ATTTTTTTAT
Statistics
Matches: 87, Mismatches: 25, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
9 7 0.08
10 38 0.44
11 41 0.47
12 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:96226431 original size:21 final size:21
Alignment explanation
Indices: 96226372--96226434 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
96226362 TATAAAAAAA
** *
96226372 TTACAAATTTTTTATAAATTCT
1 TTAC-AATTTTTTATATTTTTT
96226394 TTACAATTTTTTATATTTTTT
1 TTACAATTTTTTATATTTTTT
* *
96226415 TTATAATTTTTTCTATTTTT
1 TTACAATTTTTTATATTTTT
96226435 AATAATTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (21 bp):
TTACAATTTTTTATATTTTTT
Found at i:96226433 original size:19 final size:20
Alignment explanation
Indices: 96226393--96226459 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
96226383 TTATAAATTC
*
96226393 TTTACAATT-TTTTATATTTTT
1 TTTATAATTCTTTTATA--TTT
*
96226414 TTTATAATT-TTTTCTATTT
1 TTTATAATTCTTTTATATTT
*
96226433 TTAATAATTCTTTTATATTT
1 TTTATAATTCTTTTATATTT
96226453 TTCTATA
1 TT-TATA
96226460 TACTTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 11 0.28
20 11 0.28
21 17 0.44
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATAATTCTTTTATATTT
Found at i:96226467 original size:21 final size:20
Alignment explanation
Indices: 96226399--96226524 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 20
96226389 ATTCTTTACA
*
96226399 ATTTTTTATATTTTTTTTAT
1 ATTTTTTATATTTTTTATAT
* *
96226419 AATTTTTTCTATTTTTAATA-
1 -ATTTTTTATATTTTTTATAT
96226439 ATTCTTTTATATTTTTCTATAT
1 ATT-TTTTATATTTTT-TATAT
* **
96226461 ACTTTTTATAAAATTTTA-AT
1 ATTTTTTAT-ATTTTTTATAT
**
96226481 ATTTTTCTATAACTTTTAT-T
1 ATTTTT-TATATTTTTTATAT
*
96226501 AATTTTTAT-TTTTTTAT-T
1 ATTTTTTATATTTTTTATAT
96226519 ATTTTT
1 ATTTTT
96226525 GTCACATGTC
Statistics
Matches: 85, Mismatches: 14, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
18 12 0.14
19 6 0.07
20 31 0.36
21 30 0.35
22 6 0.07
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTTTTTATATTTTTTATAT
Found at i:96229780 original size:32 final size:32
Alignment explanation
Indices: 96229744--96229838 Score: 136
Period size: 32 Copynumber: 3.0 Consensus size: 32
96229734 CAATTGAATC
*
96229744 TCCGTACATACATGTACCATATTGTACCAATT
1 TCCGTACATACCTGTACCATATTGTACCAATT
*
96229776 TCCGTACATACCTGTACTATATTGTACCAATT
1 TCCGTACATACCTGTACCATATTGTACCAATT
* * * *
96229808 TCCGTAGATACCTGTATCATCTCGTACCAAT
1 TCCGTACATACCTGTACCATATTGTACCAAT
96229839 CACATACTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (32 bp):
TCCGTACATACCTGTACCATATTGTACCAATT
Found at i:96229950 original size:28 final size:28
Alignment explanation
Indices: 96229917--96230015 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
96229907 CGATACCTTT
* *
96229917 CACACTAAGTGTCGTTCTGGATGTTTCG
1 CACACTAAGTGCCATTCTGGATGTTTCG
* * * **
96229945 CACACTAAGTGCCATCCTCGTTACTTCG
1 CACACTAAGTGCCATTCTGGATGTTTCG
*
96229973 CACACTAAGTGCCATTCTGGATGTATCG
1 CACACTAAGTGCCATTCTGGATGTTTCG
96230001 CACACTAAGTGCCAT
1 CACACTAAGTGCCAT
96230016 CCCCGATACT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (28 bp):
CACACTAAGTGCCATTCTGGATGTTTCG
Found at i:96229978 original size:56 final size:56
Alignment explanation
Indices: 96229917--96230042 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
96229907 CGATACCTTT
* * * * *
96229917 CACACTAAGTGTCGTTCTGGATGTTTCGCACACTAAGTGCCATCCTCGTTACTTCG
1 CACACTAAGTGCCATTCTGGATGTATCGCACACTAAGTGCCATCCCCGATACTTCG
96229973 CACACTAAGTGCCATTCTGGATGTATCGCACACTAAGTGCCATCCCCGATACTTCG
1 CACACTAAGTGCCATTCTGGATGTATCGCACACTAAGTGCCATCCCCGATACTTCG
**
96230029 CACGTTAAGTGCCA
1 CACACTAAGTGCCA
96230043 CATATAATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (56 bp):
CACACTAAGTGCCATTCTGGATGTATCGCACACTAAGTGCCATCCCCGATACTTCG
Found at i:96230029 original size:28 final size:28
Alignment explanation
Indices: 96229941--96230042 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
96229931 TTCTGGATGT
*
96229941 TTCGCACACTAAGTGCCATCCTCGTTAC
1 TTCGCACACTAAGTGCCATCCTCGATAC
* * *
96229969 TTCGCACACTAAGTGCCATTCTGGAT-G
1 TTCGCACACTAAGTGCCATCCTCGATAC
*
96229996 TATCGCACACTAAGTGCCATCCCCGATAC
1 T-TCGCACACTAAGTGCCATCCTCGATAC
**
96230025 TTCGCACGTTAAGTGCCA
1 TTCGCACACTAAGTGCCA
96230043 CATATAATTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 1 0.02
28 60 0.97
29 1 0.02
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (28 bp):
TTCGCACACTAAGTGCCATCCTCGATAC
Found at i:96236332 original size:39 final size:39
Alignment explanation
Indices: 96236208--96236308 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
96236198 GAGATTGGAA
*
96236208 ATATCCGGACATGAGATCCGCGGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
96236247 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
1 ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
* *
96236286 ATATCCGGACTTGAGGTCCGCAG
1 ATATCCGGACATGAGATCCGCAG
96236309 ACTACGTGCT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (39 bp):
ATATCCGGACATGAGATCCGCAGGCTATATGCTAGAAAT
Found at i:96236802 original size:58 final size:58
Alignment explanation
Indices: 96236712--96236827 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
96236702 CTGATGCCGT
96236712 TTGTTTCTATAGAAACTAGACTCAGAGAGGAATCTATACATATATGGCATGACTCCTA
1 TTGTTTCTATAGAAACTAGACTCAGAGAGGAATCTATACATATATGGCATGACTCCTA
96236770 TTGTTTCTATAGAAACTAGACTCAGAGAGGAATCTATACATATATGGCATGACTCCTA
1 TTGTTTCTATAGAAACTAGACTCAGAGAGGAATCTATACATATATGGCATGACTCCTA
96236828 ATTATCTCTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (58 bp):
TTGTTTCTATAGAAACTAGACTCAGAGAGGAATCTATACATATATGGCATGACTCCTA
Found at i:96238330 original size:47 final size:47
Alignment explanation
Indices: 96238267--96238910 Score: 929
Period size: 47 Copynumber: 13.6 Consensus size: 47
96238257 CCCTTCGGGA
* * *
96238267 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
96238314 CTTATCATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
96238361 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
96238408 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
96238455 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGCC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
96238502 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
96238549 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
96238596 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
96238645 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
96238692 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
96238741 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
96238788 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
96238835 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
96238884 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
96238911 TATTCAAATA
Statistics
Matches: 561, Mismatches: 28, Indels: 16
0.93 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 423 0.75
49 136 0.24
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:96238753 original size:143 final size:143
Alignment explanation
Indices: 96238267--96238910 Score: 932
Period size: 143 Copynumber: 4.5 Consensus size: 143
96238257 CCCTTCGGGA
* * *
96238267 CTTATCACAT-T-TATACACTTCCACATCCATCACATTGGCCATTCGGCCTTATCATATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
96238330 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACA
* *
96238395 TTGGCCATTCGGC
131 TCGGCCATTAGGC
* * * *
96238408 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATG
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
* * *
96238470 CA-TGTTCACATTCATCACATTGGCCATTCGCCCTTATCACACATACACATGTTCACATTCATCA
65 CACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCA
* *
96238534 CATTGGCCATTCGGC
129 CATCGGCCATTAGGC
* *
96238549 CTTATCAC--ACATACACA-TGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
1 CTTATCACATATATATACACT-TTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATA
96238611 TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT-TTCACATTCAT
63 TACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCAT
96238675 CACATCGGCCATTAGGC
127 CACATCGGCCATTAGGC
* *
96238692 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* * *
96238757 ACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACT-TTCACATTCATCAC
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA-TGTTCACATTCATCAC
96238821 ATCGGCCATTAGGC
130 ATCGGCCATTAGGC
*
96238835 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
96238900 ACTTTCACATT
66 ACTTTCACATT
96238911 TATTCAAATA
Statistics
Matches: 465, Mismatches: 27, Indels: 20
0.91 0.05 0.04
Matches are distributed among these distances:
140 2 0.00
141 177 0.38
143 242 0.52
144 2 0.00
145 41 0.09
146 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:96240305 original size:85 final size:85
Alignment explanation
Indices: 96240176--96240354 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
96240166 TATTTTATTG
*
96240176 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
96240241 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
96240261 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
96240326 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
96240346 CCCATGCTC
1 CCCATGCTC
96240355 ATGGCCAGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:96246309 original size:3 final size:3
Alignment explanation
Indices: 96246303--96246331 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
96246293 GCTCTGTTGT
96246303 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
96246332 TCATTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:96264674 original size:17 final size:17
Alignment explanation
Indices: 96264652--96264685 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
96264642 CACCACCATT
96264652 TATACTTGAATAAGCAA
1 TATACTTGAATAAGCAA
96264669 TATACTTGAATAAGCAA
1 TATACTTGAATAAGCAA
96264686 CAAACATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
TATACTTGAATAAGCAA
Found at i:96276470 original size:27 final size:27
Alignment explanation
Indices: 96276397--96276486 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
96276387 GTCTTCCCGA
* *
96276397 GTTTACCGTCTCAGCAA-ACTACC-CTGT
1 GTTTACTGTCCCAG-AAGACTACCTC-GT
* *
96276424 GTTTATTGTCCTAGAAGACTACCTCGT
1 GTTTACTGTCCCAGAAGACTACCTCGT
** *
96276451 GTTTACTGTCCCAGTGGACTA-GTCCGT
1 GTTTACTGTCCCAGAAGACTACCT-CGT
96276478 GTTTACTGT
1 GTTTACTGT
96276487 TTCGACGGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.06
27 47 0.92
28 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (27 bp):
GTTTACTGTCCCAGAAGACTACCTCGT
Found at i:96278536 original size:5 final size:5
Alignment explanation
Indices: 96278526--96278578 Score: 54
Period size: 5 Copynumber: 9.8 Consensus size: 5
96278516 ATCCTAAAAT
96278526 AATAA AATAAA AATAAA AATAAA TAATAA AACT-A AATAA AATAA AATAA
1 AATAA AAT-AA AAT-AA AAT-AA -AATAA AA-TAA AATAA AATAA AATAA
96278575 AATA
1 AATA
96278579 TTCTATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.02
5 23 0.52
6 17 0.39
7 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:96278540 original size:6 final size:6
Alignment explanation
Indices: 96278529--96278576 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
96278519 CTAAAATAAT
* *
96278529 AAAATA AAAATA AAAATA AATAATA AAACTA AATAAAA TAAAATA AAA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AA-AATA -AAAATA AAA
96278577 TATTCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 22 0.63
7 11 0.31
8 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:96287511 original size:528 final size:528
Alignment explanation
Indices: 96286515--96287574 Score: 2093
Period size: 528 Copynumber: 2.0 Consensus size: 528
96286505 CTTCCCACTC
96286515 CTTAGCGTCATAGCGCTTGCATTGTGTCGTGGATTTGGCTCAGTTTGGGATTGCAGCTTACCCTG
1 CTTAGCGTCATAGCGCTTGCATTGTGTCGTGGATTTGGCTCAGTTTGGGATTGCAGCTTACCCTG
96286580 GGACTCCAAACGGCTAACTGTGAGCGCAAGTTTGCTCACTTGCTTGTCCAACTCCTACAAATGAA
66 GGACTCCAAACGGCTAACTGTGAGCGCAAGTTTGCTCACTTGCTTGTCCAACTCCTACAAATGAA
96286645 TGTCAGTTTTTTGTTGGAATTTCTCAGTACTGTTGGCTAACCTTTCCACTATGGCTTCCAAGGAT
131 TGTCAGTTTTTTGTTGGAATTTCTCAGTACTGTTGGCTAACCTTTCCACTATGGCTTCCAAGGAT
96286710 GACTTCGGGGGTGGCATCTGTTGATTCTGCGGTGGCCTCTGTTGAAACGGTTGATTGAACCGCGG
196 GACTTCGGGGGTGGCATCTGTTGATTCTGCGGTGGCCTCTGTTGAAACGGTTGATTGAACCGCGG
96286775 ATTCGTCCCATAACTAAGATTCGGGTGATCTTTCCACCCCACATTATACGAGTTCAAGTAGGGGT
261 ATTCGTCCCATAACTAAGATTCGGGTGATCTTTCCACCCCACATTATACGAGTTCAAGTAGGGGT
96286840 CATTTCGTCCTTGGGGCGGTCCTGGAAAGTTCCCGACAGCATTCGCTTGTTCCGCTGAATCCTCC
326 CATTTCGTCCTTGGGGCGGTCCTGGAAAGTTCCCGACAGCATTCGCTTGTTCCGCTGAATCCTCC
*
96286905 TGTAAAATCGGACATGAGTCTGTCGGGTGGTCTGGCTTGGCGCAAATTTTGCATAATCGTGCTGG
391 TGTAAAATCGGACATGAGTCTGTCGGGTGGTCTGGCTTGGCACAAATTTTGCATAATCGTGCTGG
96286970 GGCTGTTTTATCTAAAAGCAAAGTTTGAACAACATTAGTCAGCTTATCAATCTTATCTTCCAGAG
456 GGCTGTTTTATCTAAAAGCAAAGTTTGAACAACATTAGTCAGCTTATCAATCTTATCTTCCAGAG
96287035 ACAAAGAA
521 ACAAAGAA
96287043 CTTAGCGTCATAGCGCTTGCATTGTGTCGTGGATTTGGCTCAGTTTGGGATTGCAGCTTACCCTG
1 CTTAGCGTCATAGCGCTTGCATTGTGTCGTGGATTTGGCTCAGTTTGGGATTGCAGCTTACCCTG
*
96287108 GGACTCCAAACGGCTAACTGTGAGCGTAAGTTTGCTCACTTGCTTGTCCAACTCCTACAAATGAA
66 GGACTCCAAACGGCTAACTGTGAGCGCAAGTTTGCTCACTTGCTTGTCCAACTCCTACAAATGAA
96287173 TGTCAGTTTTTTGTTGGAATTTCTCAGTACTGTTGGCTAACCTTTCCACTATGGCTTCCAAGGAT
131 TGTCAGTTTTTTGTTGGAATTTCTCAGTACTGTTGGCTAACCTTTCCACTATGGCTTCCAAGGAT
96287238 GACTTCGGGGGTGGCATCTGTTGATTCTGCGGTGGCCTCTGTTGAAACGGTTGATTGAACCGCGG
196 GACTTCGGGGGTGGCATCTGTTGATTCTGCGGTGGCCTCTGTTGAAACGGTTGATTGAACCGCGG
96287303 ATTCGTCCCATAACTAAGATTCGGGTGATCTTTCCACCCCACATTATACGAGTTCAAGTAGGGGT
261 ATTCGTCCCATAACTAAGATTCGGGTGATCTTTCCACCCCACATTATACGAGTTCAAGTAGGGGT
96287368 CATTTCGTCCTTGGGGCGGTCCTGGAAAGTTCCCGACAGCATTCGCTTGTTCCGCTGAATCCTCC
326 CATTTCGTCCTTGGGGCGGTCCTGGAAAGTTCCCGACAGCATTCGCTTGTTCCGCTGAATCCTCC
96287433 TGTAAAATCGGACATGAGTCTGTCGGGTGGTCTGGCTTGGCACAAATTTTGCATAATCGTGCTGG
391 TGTAAAATCGGACATGAGTCTGTCGGGTGGTCTGGCTTGGCACAAATTTTGCATAATCGTGCTGG
96287498 GGCTGTTTTATCTAAAAGCAAAGTTTGAACAACATTAGTCAGCTTATCAATCTTATCTTCCAGAG
456 GGCTGTTTTATCTAAAAGCAAAGTTTGAACAACATTAGTCAGCTTATCAATCTTATCTTCCAGAG
*
96287563 ATAAAGAA
521 ACAAAGAA
96287571 CTTA
1 CTTA
96287575 ATCCATGAAC
Statistics
Matches: 529, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
528 529 1.00
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (528 bp):
CTTAGCGTCATAGCGCTTGCATTGTGTCGTGGATTTGGCTCAGTTTGGGATTGCAGCTTACCCTG
GGACTCCAAACGGCTAACTGTGAGCGCAAGTTTGCTCACTTGCTTGTCCAACTCCTACAAATGAA
TGTCAGTTTTTTGTTGGAATTTCTCAGTACTGTTGGCTAACCTTTCCACTATGGCTTCCAAGGAT
GACTTCGGGGGTGGCATCTGTTGATTCTGCGGTGGCCTCTGTTGAAACGGTTGATTGAACCGCGG
ATTCGTCCCATAACTAAGATTCGGGTGATCTTTCCACCCCACATTATACGAGTTCAAGTAGGGGT
CATTTCGTCCTTGGGGCGGTCCTGGAAAGTTCCCGACAGCATTCGCTTGTTCCGCTGAATCCTCC
TGTAAAATCGGACATGAGTCTGTCGGGTGGTCTGGCTTGGCACAAATTTTGCATAATCGTGCTGG
GGCTGTTTTATCTAAAAGCAAAGTTTGAACAACATTAGTCAGCTTATCAATCTTATCTTCCAGAG
ACAAAGAA
Found at i:96289558 original size:5 final size:5
Alignment explanation
Indices: 96289548--96289594 Score: 60
Period size: 5 Copynumber: 9.0 Consensus size: 5
96289538 ATCCTAAAAT
96289548 AATAA AATAA AATAA AATAAA TAATAA AACT-A AATAA AATAA AATAA
1 AATAA AATAA AATAA AAT-AA -AATAA AA-TAA AATAA AATAA AATAA
96289595 TATCTTCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 1 0.03
5 29 0.76
6 5 0.13
7 3 0.08
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:96289571 original size:22 final size:23
Alignment explanation
Indices: 96289542--96289596 Score: 87
Period size: 22 Copynumber: 2.4 Consensus size: 23
96289532 AGCTTAATCC
96289542 TAAAATAATAAAA-TAAAATAAAA
1 TAAAATAATAAAACT-AAATAAAA
96289565 T-AAATAATAAAACTAAATAAAA
1 TAAAATAATAAAACTAAATAAAA
96289587 TAAAATAATA
1 TAAAATAATA
96289597 TCTTCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (23 bp):
TAAAATAATAAAACTAAATAAAA
Found at i:96300443 original size:18 final size:18
Alignment explanation
Indices: 96300420--96300457 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
96300410 AAATGTATGG
96300420 GAAAAATTTACAAAAAGT
1 GAAAAATTTACAAAAAGT
96300438 GAAAAATTTACAAAAAGT
1 GAAAAATTTACAAAAAGT
96300456 GA
1 GA
96300458 TTCTCAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (18 bp):
GAAAAATTTACAAAAAGT
Found at i:96300669 original size:29 final size:29
Alignment explanation
Indices: 96300636--96300693 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
96300626 ATGTAAAAAA
* *
96300636 ATTAAATATTAAAATGGTATGTTAATAGG
1 ATTAAATACTAAAATGGTATGTCAATAGG
96300665 ATTAAATACTAAAATGGTATGTCAATAGG
1 ATTAAATACTAAAATGGTATGTCAATAGG
96300694 GGTGGTGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.34
Consensus pattern (29 bp):
ATTAAATACTAAAATGGTATGTCAATAGG
Found at i:96301275 original size:101 final size:95
Alignment explanation
Indices: 96301164--96301461 Score: 294
Period size: 89 Copynumber: 3.1 Consensus size: 95
96301154 GTTTAGTGTT
* * *
96301164 TTGTGATTTTTTATGAATGTAAATTTTTTTATTCTTTTTAAAATTATTTTAAAGTCATTTTGTTA
1 TTGTAATTTTTTATGAATTTAAA----TTTATT-TTTTT--AATTATTTTAAAGTTATTTTGTTA
*
96301229 GTAATTTATGGTTAGGTTATAAATTGTTTGTGTTTA-
59 GTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAG
*
96301265 TTGTAA-TTTTTATGAATTTAAA---A-TTTTTTAATTATTTGAAAGTTATTTTGTTAGTAATTT
1 TTGTAATTTTTTATGAATTTAAATTTATTTTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTT
96301325 ATGATTAGGTTATAAATTGTTTGTGTTTAG
66 ATGATTAGGTTATAAATTGTTTGTGTTTAG
* * * *
96301355 TT-TAGTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTTAATT-TTTTAAAGTTATTTTGTT
1 TTGTAAT-TTT-TTATGA--ATTTA--AAT-TTA-TTTTTTTAATTATTTTAAAGTTATTTTGTT
*
96301418 AGTAATTTATGATTAGGTTATAAATT-ATT-TGTTTAG
58 AGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAG
96301454 TT-TAATTT
1 TTGTAATTT
96301462 GTATTGTGAT
Statistics
Matches: 172, Mismatches: 11, Indels: 31
0.80 0.05 0.14
Matches are distributed among these distances:
89 59 0.34
90 2 0.01
91 8 0.05
92 6 0.03
93 1 0.01
94 4 0.02
96 2 0.01
98 2 0.01
99 12 0.07
100 18 0.10
101 48 0.28
102 10 0.06
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.58
Consensus pattern (95 bp):
TTGTAATTTTTTATGAATTTAAATTTATTTTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTT
ATGATTAGGTTATAAATTGTTTGTGTTTAG
Found at i:96301366 original size:89 final size:95
Alignment explanation
Indices: 96301205--96301467 Score: 305
Period size: 89 Copynumber: 2.8 Consensus size: 95
96301195 TTCTTTTTAA
* *
96301205 AATTATTTTAAAGTCATTTTGTTAGTAATTTATGGTTAGGTTATAAATTGTTTGTGTTTA-TTGT
1 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTT-T
*
96301269 AATTTTTA-TGA-ATT-T-AA-AA-TTTTTT
65 AATGTTTATTGATATTATGAATAATTTTTTT
*
96301294 AATTATTTGAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTA
1 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTA
* *
96301359 GTGTTTATTGTGATTTTTTATGAATGTAATTTTTTTT
66 ATGTTTA-T-TGA--TATTATGAA--TAA-TTTTTTT
*
96301396 AATT-TTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTTTAGTTTA
1 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTA
96301458 AT-TTGTATTG
66 ATGTT-TATTG
96301468 TGATTTGTTA
Statistics
Matches: 150, Mismatches: 9, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
89 64 0.43
90 2 0.01
92 3 0.02
95 2 0.01
96 1 0.01
97 4 0.03
98 3 0.02
99 14 0.09
100 4 0.03
101 43 0.29
102 10 0.07
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (95 bp):
AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTA
ATGTTTATTGATATTATGAATAATTTTTTT
Found at i:96301520 original size:22 final size:21
Alignment explanation
Indices: 96301495--96301535 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
96301485 ATTTTATTTG
96301495 TTTTT-TTTATTTATTTGAAAA
1 TTTTTATTTATTTA-TTGAAAA
96301516 TTTTTATTTATTTATTGAAA
1 TTTTTATTTATTTATTGAAA
96301536 TGTTGATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTTTATTTATTTATTGAAAA
Found at i:96301848 original size:13 final size:13
Alignment explanation
Indices: 96301830--96301854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
96301820 GACCCTCTAG
96301830 AAATTAATTATCA
1 AAATTAATTATCA
96301843 AAATTAATTATC
1 AAATTAATTATC
96301855 TCAGTTTAGT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAATTATCA
Found at i:96303701 original size:43 final size:42
Alignment explanation
Indices: 96303653--96303806 Score: 125
Period size: 43 Copynumber: 3.6 Consensus size: 42
96303643 TGATTACATG
* *
96303653 TAAGACCATGTCTGGGAAATTGGCATTGTATTATGT-TTACGTA
1 TAAGACCATGTCTGGGAAATCGGCATCG--TTATGTATTACGTA
* * *
96303696 TAAGACCATGTCTAGGACATCGGCATCGTTATGTGATTTCGTA
1 TAAGACCATGTCTGGGAAATCGGCATCGTTATGT-ATTACGTA
* * * * * *
96303739 TAAGACCCTGTCTGGTACAAT-GGCATCGATATGTGATAACATG
1 TAAGACCATGTCTGGGA-AATCGGCATCGTTATGT-ATTACGTA
* *
96303782 TAAGACCATATCTGGGATAT-GGCAT
1 TAAGACCATGTCTGGGAAATCGGCAT
96303807 TGTACGAGTT
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
41 6 0.07
42 7 0.08
43 75 0.83
44 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (42 bp):
TAAGACCATGTCTGGGAAATCGGCATCGTTATGTATTACGTA
Found at i:96306422 original size:45 final size:45
Alignment explanation
Indices: 96306371--96306540 Score: 188
Period size: 45 Copynumber: 3.7 Consensus size: 45
96306361 TAACCCGCCC
*
96306371 TAAGTGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCA
*
96306416 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCA
* * * *
96306464 TCA-CGAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCA
96306508 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
96306541 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 6 0.06
43 2 0.02
44 2 0.02
45 37 0.35
46 22 0.21
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
Found at i:96306533 original size:92 final size:92
Alignment explanation
Indices: 96306376--96306544 Score: 286
Period size: 92 Copynumber: 1.8 Consensus size: 92
96306366 CGCCCTAAGT
* *
96306376 GAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
96306441 GAGTTCGGATGCCTAGTTACATCTCAC
66 GAGTTCGGATGCCTAGTTACATCTCAC
* *
96306468 GAACTCGGACTCAACTCAACGAGTTC-GACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
96306532 CGAGTTCGGATGC
65 CGAGTTCGGATGC
96306545 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 54 0.75
93 18 0.25
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:96311791 original size:46 final size:48
Alignment explanation
Indices: 96311671--96311800 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 48
96311661 TGTAACCCGC
96311671 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * * * *
96311721 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTTGGA-C-ATTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
*
96311764 CCATAAGTGAACTCGGACTCAACTCAACAAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
96311801 TGCTCAACCA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 2 0.03
46 26 0.39
47 27 0.41
48 2 0.03
49 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:96312661 original size:26 final size:26
Alignment explanation
Indices: 96312625--96312677 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
96312615 AGGATATTAC
* *
96312625 ACACGGCCGGGGCACACGGGCGTGTG
1 ACACGGCCGGGCCACACGGGCATGTG
96312651 ACACGGCCGGGCCACACGGGCATGTG
1 ACACGGCCGGGCCACACGGGCATGTG
96312677 A
1 A
96312678 TCCTTGCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.19, C:0.32, G:0.42, T:0.08
Consensus pattern (26 bp):
ACACGGCCGGGCCACACGGGCATGTG
Found at i:96314004 original size:25 final size:25
Alignment explanation
Indices: 96313976--96314028 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
96313966 TGAATAAGTG
* *
96313976 ATTGAATGAGTTGATTTTTATTGTA
1 ATTGAATGAGTTAATTTTGATTGTA
96314001 ATTGAATGAGTTAATTTTGATTGTA
1 ATTGAATGAGTTAATTTTGATTGTA
96314026 ATT
1 ATT
96314029 AGATCAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (25 bp):
ATTGAATGAGTTAATTTTGATTGTA
Found at i:96314367 original size:43 final size:42
Alignment explanation
Indices: 96314302--96314425 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 42
96314292 TACCGAGATG
* *
96314302 TGATTACATGTAAGACCCTGTGTGGGACAGTGGCATTGTATTA
1 TGATTACATATAAGACCCTGTGTGGGACAGTGGCATTGT-TAA
* * *
96314345 TGATTACATATAATACCATGTGTGGGACA-TCGGCATCGTTAA
1 TGATTACATATAAGACCCTGTGTGGGACAGT-GGCATTGTTAA
* * *
96314387 TCGATTTCGTATAAGACCCTGTGTGGAACAGTGGCATTG
1 T-GATTACATATAAGACCCTGTGTGGGACAGTGGCATTG
96314426 ATATGTGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
42 4 0.06
43 62 0.93
44 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (42 bp):
TGATTACATATAAGACCCTGTGTGGGACAGTGGCATTGTTAA
Found at i:96318259 original size:17 final size:17
Alignment explanation
Indices: 96318237--96318271 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
96318227 AGTTGAGAGT
*
96318237 CAAAAACTCCGATGTGC
1 CAAAAACTCCGATATGC
96318254 CAAAAACTCCGATATGC
1 CAAAAACTCCGATATGC
96318271 C
1 C
96318272 TTTCGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.31, G:0.14, T:0.17
Consensus pattern (17 bp):
CAAAAACTCCGATATGC
Found at i:96321969 original size:43 final size:46
Alignment explanation
Indices: 96321904--96322024 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 46
96321894 TACCGATATG
* * *
96321904 TGATTACATGTAAGACCCTGTGTGGGACAGTGGC-GT-T-G-TATT
1 TGATTACGTATAAGACCCTGTGTGGGACAGTGGCAGTATCGTTAAT
*
96321946 ATGATTACGTATAAGACCATGTGTGGGACA-T--CAGTATCGTTAAT
1 -TGATTACGTATAAGACCCTGTGTGGGACAGTGGCAGTATCGTTAAT
*
96321990 TGATTTCGTATAAGACCCTGTGTGGGACAGTGGCA
1 TGATTACGTATAAGACCCTGTGTGGGACAGTGGCA
96322025 TCGATATGTG
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
40 1 0.02
41 2 0.03
42 2 0.03
43 54 0.83
44 4 0.06
46 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (46 bp):
TGATTACGTATAAGACCCTGTGTGGGACAGTGGCAGTATCGTTAAT
Found at i:96328149 original size:105 final size:106
Alignment explanation
Indices: 96327912--96328178 Score: 320
Period size: 115 Copynumber: 2.4 Consensus size: 106
96327902 AACTAATAAT
* * *
96327912 TAATTTATAATAGTTACTAACAAAATAACTTTCAAATAAATTAAAAAATATTAAAAGATTACATT
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAAAATTACATT
* *
96327977 AATAACTTAACAAATCACAATAAACCCTAAACTCTAAACAAA
66 AATAACCTAACAAATCACAATAAACACTAAAC-CTAAACAAA
* * * *
96328019 CAATTAACCTAATCACAAAACTTACTAACAAAATAACTTTAAAATAAATTAAAAATTAATAAAAA
1 TAATT----T-AT---AATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAAA
* * * *
96328084 ATTACATTCATAACCTAACAAATCACGATAAACATTAAA-CTAAACAGA
58 ATTACATTAATAACCTAACAAATCACAATAAACACTAAACCTAAACAAA
*
96328132 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAGATTAAAAA
1 TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAA
96328179 CAGCATAAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
105 36 0.27
107 4 0.03
108 2 0.01
109 1 0.01
111 1 0.01
112 2 0.01
113 12 0.09
115 77 0.57
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (106 bp):
TAATTTATAATAGTTACTAACAAAATAACTTTAAAATAAATTAAAAAATAATAAAAAATTACATT
AATAACCTAACAAATCACAATAAACACTAAACCTAAACAAA
Found at i:96328684 original size:29 final size:29
Alignment explanation
Indices: 96328642--96328699 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
96328632 AGACACCATC
96328642 CCTACTGACATACCATTTTGATATTTAAT
1 CCTACTGACATACCATTTTGATATTTAAT
*
96328671 CCTACTGACATACCATTTTGGTATTTAAT
1 CCTACTGACATACCATTTTGATATTTAAT
96328700 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (29 bp):
CCTACTGACATACCATTTTGATATTTAAT
Found at i:96330034 original size:2 final size:2
Alignment explanation
Indices: 96330027--96330052 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
96330017 AAACCCTCTC
96330027 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
96330053 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96330502 original size:24 final size:24
Alignment explanation
Indices: 96330475--96330520 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
96330465 TCATCATTTT
* *
96330475 CAACAACAGCAACATCACCATCTG
1 CAACAACAACAACATCAACATCTG
*
96330499 CAACAGCAACAACATCAACATC
1 CAACAACAACAACATCAACATC
96330521 AACAGCAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.37, G:0.07, T:0.11
Consensus pattern (24 bp):
CAACAACAACAACATCAACATCTG
Found at i:96330777 original size:13 final size:15
Alignment explanation
Indices: 96330759--96330790 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
96330749 ATGTTTACAG
96330759 TTATTG-ATTTT-TT
1 TTATTGAATTTTCTT
96330772 TTATTGAATTTTCTT
1 TTATTGAATTTTCTT
96330787 TTAT
1 TTAT
96330791 GTATTGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (15 bp):
TTATTGAATTTTCTT
Found at i:96335469 original size:29 final size:30
Alignment explanation
Indices: 96335361--96335489 Score: 85
Period size: 29 Copynumber: 4.4 Consensus size: 30
96335351 TATGATAATA
* *
96335361 TTTATAATTCTTTTATGAATTT-TATAT-T
1 TTTATAATTTTTTTATCAATTTCTATATAT
* *
96335389 TCTT-TACATTTTTTTATCATTTTC-ATATGAC
1 T-TTATA-ATTTTTTTATCAATTTCTATAT-AT
**
96335420 TTTATAA-AGTTTTAT-ATATTTCTATATAT
1 TTTATAATTTTTTTATCA-ATTTCTATATAT
* *
96335449 TTTATAATTTTTTTA-CAATTTGTATATGT
1 TTTATAATTTTTTTATCAATTTCTATATAT
96335478 ATTT-TAATTTTT
1 -TTTATAATTTTT
96335490 AATAAAAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
28 4 0.05
29 55 0.71
30 16 0.21
31 3 0.04
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTATAATTTTTTTATCAATTTCTATATAT
Found at i:96341253 original size:21 final size:22
Alignment explanation
Indices: 96341227--96341273 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
96341217 CTCTGCTCAA
*
96341227 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
96341248 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
96341270 ACTC
1 ACTC
96341274 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:96367463 original size:17 final size:17
Alignment explanation
Indices: 96367441--96367474 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
96367431 AAGTAAAAGA
96367441 TATTT-ATTGATTATTAT
1 TATTTAATTGA-TATTAT
96367458 TATTTAATTGATATTAT
1 TATTTAATTGATATTAT
96367475 ATTAGTGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATTTAATTGATATTAT
Found at i:96368781 original size:11 final size:12
Alignment explanation
Indices: 96368767--96368809 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 12
96368757 TTGATTGTAT
96368767 ATTGAAA-TGAA
1 ATTGAAATTGAA
*
96368778 ATTGAAATTGAT
1 ATTGAAATTGAA
96368790 A-TGAAATTGAA
1 ATTGAAATTGAA
96368801 ATTGAAATT
1 ATTGAAATT
96368810 AAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (12 bp):
ATTGAAATTGAA
Found at i:96368785 original size:6 final size:6
Alignment explanation
Indices: 96368767--96368809 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
96368757 TTGATTGTAT
*
96368767 ATTGAA A-TGAA ATTGAA ATTGAT A-TGAA ATTGAA ATTGAA ATT
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATT
96368810 AAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
ATTGAA
Found at i:96368793 original size:17 final size:17
Alignment explanation
Indices: 96368767--96368808 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
96368757 TTGATTGTAT
96368767 ATTGAAATGAAATTGAA
1 ATTGAAATGAAATTGAA
*
96368784 ATTGATATGAAATTGAA
1 ATTGAAATGAAATTGAA
96368801 ATTGAAAT
1 ATTGAAAT
96368809 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
ATTGAAATGAAATTGAA
Found at i:96368800 original size:23 final size:24
Alignment explanation
Indices: 96368760--96368809 Score: 77
Period size: 23 Copynumber: 2.1 Consensus size: 24
96368750 TATTGAATTG
96368760 ATTGTATATTGAAATGAAATTGAA
1 ATTGTATATTGAAATGAAATTGAA
96368784 ATTG-ATA-TGAAATTGAAATTGAA
1 ATTGTATATTGAAA-TGAAATTGAA
96368807 ATT
1 ATT
96368810 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.20
23 16 0.64
24 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (24 bp):
ATTGTATATTGAAATGAAATTGAA
Found at i:96368911 original size:13 final size:14
Alignment explanation
Indices: 96368893--96368922 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
96368883 TTTGGAAAGG
96368893 GATTTGGAGATG-T
1 GATTTGGAGATGCT
96368906 GATTTGGAGATGCT
1 GATTTGGAGATGCT
96368920 GAT
1 GAT
96368923 GTTTATATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.37, T:0.37
Consensus pattern (14 bp):
GATTTGGAGATGCT
Found at i:96369016 original size:28 final size:28
Alignment explanation
Indices: 96368976--96369046 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
96368966 TCTGGTGTAT
* **
96368976 TTTGGATGGATTATATTATTTTGATGTG-
1 TTTGGA-GGATTATATGATACTGATGTGC
*
96369004 TTTGGGAGGATTATATGATACTGGTGTGC
1 TTT-GGAGGATTATATGATACTGATGTGC
96369033 TTTGGAGGATTATA
1 TTTGGAGGATTATA
96369047 CTAGCGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.23, C:0.03, G:0.30, T:0.45
Consensus pattern (28 bp):
TTTGGAGGATTATATGATACTGATGTGC
Found at i:96370691 original size:10 final size:11
Alignment explanation
Indices: 96370660--96370692 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
96370650 CTGCCCGCCC
96370660 ATATTAATTTT
1 ATATTAATTTT
*
96370671 ATATTATTTTT
1 ATATTAATTTT
96370682 ATA-TAATTTT
1 ATATTAATTTT
96370692 A
1 A
96370693 AAATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:96370851 original size:30 final size:30
Alignment explanation
Indices: 96370815--96370877 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
96370805 ACTTAACAAG
96370815 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
96370845 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
96370875 CAA
1 CAA
96370878 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:96373933 original size:17 final size:17
Alignment explanation
Indices: 96373913--96374028 Score: 169
Period size: 17 Copynumber: 6.6 Consensus size: 17
96373903 CAATGATATG
96373913 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
* *
96373930 CAATCTTAAATATGATTG
1 CAATCTTAGATATGA-TA
96373948 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
96373965 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
96373983 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
96374000 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
96374019 CAATCTTAGA
1 CAATCTTAGA
96374029 AGATATAATT
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
17 45 0.51
18 31 0.35
19 13 0.15
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:96373951 original size:35 final size:36
Alignment explanation
Indices: 96373905--96374028 Score: 216
Period size: 35 Copynumber: 3.5 Consensus size: 36
96373895 ATAATCTTCA
*
96373905 ATGATATGCAATCTTAGATATGATACAATCTTAAAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
96373941 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
96373976 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
*
96374011 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
96374029 AGATATAATT
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 69 0.81
36 16 0.19
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (36 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGAT
Found at i:96373954 original size:52 final size:52
Alignment explanation
Indices: 96373897--96374028 Score: 162
Period size: 52 Copynumber: 2.5 Consensus size: 52
96373887 ATGGAAATAT
* *
96373897 AATCTTCA-ATGATATGCAATCTTAGATATGA-TACAATCTTAAATATGATTGC
1 AATCTT-AGATGATATACAATCTTAGATATGATTACAATCTTAAATATGA-TAC
* *
96373949 AATCTTAGAT-ATGATACAATCTTAGATATGATTGCAATCTTAGATATGATAC
1 AATCTTAGATGAT-ATACAATCTTAGATATGATTACAATCTTAAATATGATAC
96374001 AATCTTAGATATGATATACAATCTTAGA
1 AATCTTAG--ATGATATACAATCTTAGA
96374029 AGATATAATT
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
51 3 0.04
52 35 0.50
53 15 0.21
54 15 0.21
55 2 0.03
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (52 bp):
AATCTTAGATGATATACAATCTTAGATATGATTACAATCTTAAATATGATAC
Found at i:96374351 original size:12 final size:11
Alignment explanation
Indices: 96374336--96374369 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
96374326 TATTTTTAAT
96374336 TTATTATATATA
1 TTATT-TATATA
96374348 TTATTTATTATA
1 TTATTTA-TATA
96374360 TTATTTATAT
1 TTATTTATAT
96374370 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTATATA
Found at i:96374361 original size:21 final size:21
Alignment explanation
Indices: 96374337--96374442 Score: 59
Period size: 21 Copynumber: 5.3 Consensus size: 21
96374327 ATTTTTAATT
96374337 TATTATATATATTATTTATTA
1 TATTATATATATTATTTATTA
* *
96374358 TATTATTTATATT-TTCA--A
1 TATTATATATATTATTTATTA
* * *
96374376 AATT-TGTAAATTA-TTA-TA
1 TATTATATATATTATTTATTA
*
96374394 TATTATAT-T-TTAACTTATATA
1 TATTATATATATT-ATTTAT-TA
*
96374415 TCTTATATAT-TTATTTATTTA
1 TATTATATATATTATTTA-TTA
96374436 TATTATA
1 TATTATA
96374443 CATTATTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
17 10 0.16
18 9 0.14
19 5 0.08
20 3 0.05
21 33 0.52
22 4 0.06
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (21 bp):
TATTATATATATTATTTATTA
Found at i:96374367 original size:16 final size:16
Alignment explanation
Indices: 96374334--96374364 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96374324 CTTATTTTTA
96374334 ATTTATTATATATATT
1 ATTTATTATATATATT
96374350 ATTTATTATAT-TATT
1 ATTTATTATATATATT
96374365 TATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATATATATT
Found at i:96374829 original size:3 final size:3
Alignment explanation
Indices: 96374821--96374858 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
96374811 TATGTTACTA
*
96374821 TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
96374859 CTATTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:96380340 original size:13 final size:13
Alignment explanation
Indices: 96380313--96380373 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
96380303 CTTCTATTTC
96380313 AAAAA-AAAAGAAA
1 AAAAAGAAAAG-AA
96380326 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
96380339 AAAGAGAAAA-AA
1 AAAAAGAAAAGAA
*
96380351 AATAAAGAGAAAAAA
1 AA-AAAGA-AAAGAA
96380366 GAAAAAGA
1 -AAAAAGA
96380374 TTGAGAGGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 4 0.10
13 20 0.49
14 8 0.20
15 7 0.17
16 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:96380346 original size:22 final size:22
Alignment explanation
Indices: 96380316--96380371 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
96380306 CTATTTCAAA
96380316 AAAAAAGAAAAAAAAGAAA-AG
1 AAAAAAGAAAAAAAAGAAAGAG
*
96380337 AAAAAGAGAAAAAAAATAAAGAG
1 AAAAA-AGAAAAAAAAGAAAGAG
96380360 AAAAAAGAAAAA
1 AAAAAAGAAAAA
96380372 GATTGAGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 5 0.16
22 20 0.62
23 7 0.22
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAGAAAGAG
Found at i:96380351 original size:30 final size:30
Alignment explanation
Indices: 96380314--96380373 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
96380304 TTCTATTTCA
* *
96380314 AAAAAAAAGAAAAAAAAGAAAAGAAAAAGAG
1 AAAAAAAATAAAGAAAA-AAAAGAAAAAGAG
*
96380345 AAAAAAAATAAAGAGAAAAAAGAAAAAGA
1 AAAAAAAATAAAGAAAAAAAAGAAAAAGA
96380374 TTGAGAGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (30 bp):
AAAAAAAATAAAGAAAAAAAAGAAAAAGAG
Found at i:96381469 original size:17 final size:17
Alignment explanation
Indices: 96381449--96381529 Score: 126
Period size: 17 Copynumber: 4.6 Consensus size: 17
96381439 CAATGATATG
96381449 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
96381466 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
96381484 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
96381501 CAATCTTAGATATGATATA
1 CAATCTTAGATATG--ATA
96381520 CAATCTTAGA
1 CAATCTTAGA
96381530 AGATATGATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
17 30 0.51
18 16 0.27
19 13 0.22
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:96381487 original size:35 final size:36
Alignment explanation
Indices: 96381441--96381529 Score: 162
Period size: 35 Copynumber: 2.5 Consensus size: 36
96381431 ATAATCTTCA
96381441 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
96381477 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
*
96381512 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
96381530 AGATATGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
35 35 0.69
36 16 0.31
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (36 bp):
ATGATATGCAATCTTAGATATGATACAATCTTAGAT
Found at i:96381517 original size:22 final size:20
Alignment explanation
Indices: 96381456--96381538 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
96381446 ATGCAATCTT
96381456 AGATATGATACAATCTT---
1 AGATATGATACAATCTTAGA
*
96381473 AGATATGATTGCAATCTT---
1 AGATATGA-TACAATCTTAGA
96381491 AGATATGATACAATCTTAG-
1 AGATATGATACAATCTTAGA
*
96381510 ATATGAT-ATACAATCTTAGA
1 AGAT-ATGATACAATCTTAGA
96381530 AGATATGAT
1 AGATATGAT
96381539 TTTGTAATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
17 16 0.29
18 16 0.29
19 17 0.30
20 7 0.12
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (20 bp):
AGATATGATACAATCTTAGA
Found at i:96381534 original size:17 final size:17
Alignment explanation
Indices: 96381443--96381535 Score: 75
Period size: 17 Copynumber: 5.3 Consensus size: 17
96381433 AATCTTCAAT
*
96381443 GATATGCAATCTTAG-A
1 GATATACAATCTTAGAA
*
96381459 TATGATACAATCTTAGATA
1 GAT-ATACAATCTTAGA-A
*
96381478 TGAT-TGCAATCTTAG-A
1 -GATATACAATCTTAGAA
*
96381494 TATGATACAATCTTAGATA
1 GAT-ATACAATCTTAGA-A
96381513 TGATATACAATCTTAGAA
1 -GATATACAATCTTAGAA
96381531 GATAT
1 GATAT
96381536 GATTTTGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
15 2 0.03
16 3 0.05
17 26 0.43
18 11 0.18
19 15 0.25
20 4 0.07
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (17 bp):
GATATACAATCTTAGAA
Found at i:96381852 original size:12 final size:11
Alignment explanation
Indices: 96381837--96381870 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
96381827 TATTTTTAAT
96381837 TTATTATATATA
1 TTATT-TATATA
96381849 TTATTTATTATA
1 TTATTTA-TATA
96381861 TTATTTATAT
1 TTATTTATAT
96381871 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTATATA
Found at i:96381862 original size:21 final size:21
Alignment explanation
Indices: 96381838--96381946 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
96381828 ATTTTTAATT
96381838 TATTATATATATTATTTATTA
1 TATTATATATATTATTTATTA
* *
96381859 TATTATTTATATT-TTCA--A
1 TATTATATATATTATTTATTA
* * *
96381877 AATT-TGTAAATTA-TTATTA
1 TATTATATATATTATTTATTA
* *
96381896 TA-TATTATATTTTAACTTATATA
1 TATTA-TATATATT-ATTTAT-TA
*
96381919 TCTTATATAT-TTATTTATTTA
1 TATTATATATATTATTTA-TTA
96381940 TATTATA
1 TATTATA
96381947 CATTATTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
17 8 0.12
18 5 0.08
19 2 0.03
20 8 0.12
21 25 0.38
22 7 0.11
23 8 0.12
24 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTATATATATTATTTATTA
Found at i:96381868 original size:16 final size:16
Alignment explanation
Indices: 96381835--96381865 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96381825 CTTATTTTTA
96381835 ATTTATTATATATATT
1 ATTTATTATATATATT
96381851 ATTTATTATAT-TATT
1 ATTTATTATATATATT
96381866 TATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATATATATT
Found at i:96381903 original size:7 final size:7
Alignment explanation
Indices: 96381886--96381992 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
96381876 AAATTTGTAA
96381886 ATTAT-T
1 ATTATAT
96381892 ATTATAT
1 ATTATAT
96381899 ATTATAT
1 ATTATAT
96381906 -TT-TA-
1 ATTATAT
96381910 ACTTATAT
1 A-TTATAT
96381918 ATCTTATAT
1 A--TTATAT
*
96381927 ATTTATTT
1 A-TTATAT
96381935 ATT-TAT
1 ATTATAT
*
96381941 ATTATAC
1 ATTATAT
96381948 ATTAT-T
1 ATTATAT
* *
96381954 -TTAAAA
1 ATTATAT
*
96381960 ACTTACAT
1 A-TTATAT
*
96381968 -TTTTAT
1 ATTATAT
96381974 ATTATAT
1 ATTATAT
*
96381981 ATTATAA
1 ATTATAT
96381988 ATTAT
1 ATTAT
96381993 TTCATTTATT
Statistics
Matches: 77, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 35 0.45
8 11 0.14
9 8 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (7 bp):
ATTATAT
Found at i:96388004 original size:78 final size:78
Alignment explanation
Indices: 96387894--96388186 Score: 457
Period size: 78 Copynumber: 3.8 Consensus size: 78
96387884 CGAAGAAACA
** * *
96387894 GATTTGGCATCTCCATATTCGACAGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
96387959 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
96387972 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
96388037 GC--ATCCAAGAT
66 GCAGATCCAAGAT
* *
96388048 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
96388112 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* *
96388126 GATTTGGCATCTCTGTATTAGACAGCGAGCAAATCGAAGACATAGCAGATCTGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
96388187 GTGTTTACAT
Statistics
Matches: 197, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
75 1 0.01
76 71 0.36
78 124 0.63
79 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:96388174 original size:154 final size:154
Alignment explanation
Indices: 96387894--96388186 Score: 471
Period size: 154 Copynumber: 1.9 Consensus size: 154
96387884 CGAAGAAACA
* *
96387894 GATTTGGCATCTCCATATTCGACAGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCCATATTAGACAGAGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAA
* * *
96387959 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACACAGCAGATCT
66 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGCGAGCAAATCAAAGACACAGCAGATCT
96388024 GACCTTCATTGAAGCATCCAAGAT
131 GACCTTCATTGAAGCATCCAAGAT
** * *
96388048 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCCATATTAGACAGAGAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGA
* *
96388112 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGCGAGCAAATCGAAGACATAGCAGATC
65 AGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGCGAGCAAATCAAAGACACAGCAGATC
96388177 TGACCTTCAT
130 TGACCTTCAT
96388187 GTGTTTACAT
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
153 1 0.01
154 126 0.99
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (154 bp):
GATTTGGCATCTCCATATTAGACAGAGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAA
GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGCGAGCAAATCAAAGACACAGCAGATCT
GACCTTCATTGAAGCATCCAAGAT
Found at i:96388280 original size:45 final size:45
Alignment explanation
Indices: 96388126--96388349 Score: 209
Period size: 45 Copynumber: 4.9 Consensus size: 45
96388116 GATCCAAGAT
* *
96388126 GATTTGGCATCTCTGTATTAGACAGCGAGCAAATCGAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAG--ATAACA
* * * * * * * * * *
96388173 GATCTGACCT-TCATGTGTT-TACATCGAAGCAGATCCAAGATGACA
1 GATTTGGCATCTC-TGTATTAGACA-GGGAGCAAATCGAAGATAACA
* * *
96388218 GATTTGGTATCTTTGTATTAGACAGGGAGCAAATCGGAGATAACA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACA
* *
96388263 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACA
* * * *
96388308 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATA
96388350 GAAGATATCG
Statistics
Matches: 141, Mismatches: 32, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
45 110 0.78
46 9 0.06
47 22 0.16
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACA
Found at i:96388734 original size:17 final size:17
Alignment explanation
Indices: 96388714--96388777 Score: 92
Period size: 17 Copynumber: 3.6 Consensus size: 17
96388704 CAATGATATC
96388714 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
*
96388731 CAATCTTAGATATGATTG
1 CAATCTTAGATATGA-TA
96388749 CAATCTTAGATATGATA
1 CAATCTTAGATATGATA
96388766 TGCAATCTTAGA
1 --CAATCTTAGA
96388778 AGATATGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.38
18 16 0.38
19 10 0.24
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (17 bp):
CAATCTTAGATATGATA
Found at i:96388754 original size:18 final size:18
Alignment explanation
Indices: 96388714--96388777 Score: 103
Period size: 18 Copynumber: 3.6 Consensus size: 18
96388704 CAATGATATC
*
96388714 CAATCTTAGATATGA-TA
1 CAATCTTAGATATGATTG
96388731 CAATCTTAGATATGATTG
1 CAATCTTAGATATGATTG
96388749 CAATCTTAGATATGATATG
1 CAATCTTAGATATGAT-TG
96388768 CAATCTTAGA
1 CAATCTTAGA
96388778 AGATATGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
17 15 0.34
18 17 0.39
19 12 0.27
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (18 bp):
CAATCTTAGATATGATTG
Found at i:96388784 original size:17 final size:19
Alignment explanation
Indices: 96388706--96388777 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
96388696 ATAATCTTCA
*
96388706 ATGATATCCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
96388725 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
96388742 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
96388760 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
96388778 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:96388803 original size:22 final size:22
Alignment explanation
Indices: 96388738--96388800 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
96388728 ATACAATCTT
96388738 AGATATGAT-TGCAATCTT---
1 AGATATGATATGCAATCTTAGA
96388756 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCTTAGA
* *
96388778 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGCAATCTTAGA
96388801 GATTTAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
18 9 0.24
19 9 0.24
22 8 0.21
23 12 0.32
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATCTTAGA
Found at i:96389092 original size:18 final size:18
Alignment explanation
Indices: 96389067--96389103 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
96389057 TGTTTCCCGG
*
96389067 ATTTTTTTTATATATTTTA
1 ATTTTTTTAATA-ATTTTA
96389086 ATTTTTTTAATAATTTTA
1 ATTTTTTTAATAATTTTA
96389104 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTTAATAATTTTA
Found at i:96391622 original size:25 final size:27
Alignment explanation
Indices: 96391585--96391637 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
96391575 TCAAACATGC
96391585 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
96391611 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
96391637 A
1 A
96391638 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:96393159 original size:26 final size:26
Alignment explanation
Indices: 96393123--96393205 Score: 148
Period size: 26 Copynumber: 3.2 Consensus size: 26
96393113 CATGAAATTC
96393123 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
96393149 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
96393175 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
96393201 TTATC
1 TTATC
96393206 TATTTGTATC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:96393707 original size:24 final size:24
Alignment explanation
Indices: 96393680--96393730 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
96393670 AAACAATTTG
96393680 ATTATCATAATTTTTATTTTAAAA
1 ATTATCATAATTTTTATTTTAAAA
* * *
96393704 ATTATTATGATTTTTATTTTAAGA
1 ATTATCATAATTTTTATTTTAAAA
96393728 ATT
1 ATT
96393731 TTCGAAGTAT
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:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTATCATAATTTTTATTTTAAAA
Found at i:96397094 original size:16 final size:16
Alignment explanation
Indices: 96397075--96397106 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
96397065 TTCGTATAAC
96397075 TTTATGTAAATATTTT
1 TTTATGTAAATATTTT
*
96397091 TTTATGTATATATTTT
1 TTTATGTAAATATTTT
96397107 CTTTTCAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTATGTAAATATTTT
Found at i:96403845 original size:17 final size:18
Alignment explanation
Indices: 96403812--96403845 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
96403802 AAATTTTTTA
96403812 ATGATTTCTTGTATTATC
1 ATGATTTCTTGTATTATC
*
96403830 ATGATTT-TTTTATTAT
1 ATGATTTCTTGTATTAT
96403846 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (18 bp):
ATGATTTCTTGTATTATC
Found at i:96405599 original size:17 final size:16
Alignment explanation
Indices: 96405571--96405605 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
96405561 CATTAAAGAG
96405571 ATACCTAAAAATATAT
1 ATACCTAAAAATATAT
96405587 ATACCTAAAAA-ATAT
1 ATACCTAAAAATATAT
96405602 ATAC
1 ATAC
96405606 TTAGGAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (16 bp):
ATACCTAAAAATATAT
Found at i:96408223 original size:21 final size:21
Alignment explanation
Indices: 96408197--96408239 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
96408187 GCAGAGACGT
96408197 GAAGATAGAATTTTTATTAGG
1 GAAGATAGAATTTTTATTAGG
96408218 GAAGATAGAATTTTTATTAGG
1 GAAGATAGAATTTTTATTAGG
96408239 G
1 G
96408240 TTGAGTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (21 bp):
GAAGATAGAATTTTTATTAGG
Found at i:96412810 original size:13 final size:14
Alignment explanation
Indices: 96412792--96412820 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
96412782 TAATAATATA
96412792 ATAAATTATT-AAT
1 ATAAATTATTCAAT
96412805 ATAAATTATTCAAT
1 ATAAATTATTCAAT
96412819 AT
1 AT
96412821 TACAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAAATTATTCAAT
Found at i:96413340 original size:23 final size:26
Alignment explanation
Indices: 96413281--96413341 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 26
96413271 TATAAGGACT
96413281 TATGACATATTTTAACTTAGTATAAAA
1 TATGA-ATATTTTAACTTAGTATAAAA
*
96413308 TATTAATATTTTAA-TTA-TAT-AAA
1 TATGAATATTTTAACTTAGTATAAAA
*
96413331 TATGAGTATTT
1 TATGAATATTT
96413342 ATTTAAATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 12 0.39
24 3 0.10
25 3 0.10
26 9 0.29
27 4 0.13
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (26 bp):
TATGAATATTTTAACTTAGTATAAAA
Found at i:96413938 original size:18 final size:18
Alignment explanation
Indices: 96413915--96413951 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
96413905 CATCAGGTTA
96413915 AATATATGTTATAAGTCC
1 AATATATGTTATAAGTCC
96413933 AATATATGTTATAAGTCC
1 AATATATGTTATAAGTCC
96413951 A
1 A
96413952 TGTACTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
AATATATGTTATAAGTCC
Found at i:96416681 original size:29 final size:29
Alignment explanation
Indices: 96416606--96416682 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
96416596 TAAAATTCAA
*
96416606 AAAGTATAAGGACTAAAATTGATCAATTT
1 AAAGTATAAGGACTAAATTTGATCAATTT
* *
96416635 AAAGTATACAGAACTAAATTTGAT-TATATT
1 AAAGTATA-AGGACTAAATTTGATCAAT-TT
*
96416665 AAAGTATAAGGATTAAAT
1 AAAGTATAAGGACTAAAT
96416683 CCATAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 18 0.44
30 23 0.56
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.32
Consensus pattern (29 bp):
AAAGTATAAGGACTAAATTTGATCAATTT
Found at i:96418400 original size:54 final size:54
Alignment explanation
Indices: 96418318--96418429 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
96418308 GTCAAAAAGG
*
96418318 TAAACACATTTAAAATATAAAAATTAAAATATAATACAAAAATTCACCCGATTA
1 TAAACACATTTAAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTA
96418372 TAAACACATTTAAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTA
1 TAAACACATTTAAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTA
96418426 TAAA
1 TAAA
96418430 ATAAAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (54 bp):
TAAACACATTTAAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTA
Found at i:96418441 original size:54 final size:54
Alignment explanation
Indices: 96418329--96418441 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
96418319 AAACACATTT
* * ***
96418329 AAAATATAAAAATTAAAATATAATACAAAAATTCACCCGATTATAAACACATTT
1 AAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTATAAACAAAAAA
96418383 AAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTATAAA-ATAAAAA
1 AAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTATAAACA-AAAAA
96418437 AAAAT
1 AAAAT
96418442 CCTTACTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.25
Consensus pattern (54 bp):
AAAATATAAAAATTAAAAAATAATACAAAAATTCACCCGATTATAAACAAAAAA
Found at i:96425610 original size:24 final size:23
Alignment explanation
Indices: 96425581--96425627 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
96425571 ACGCAACTCT
96425581 TTATGAGCGTT-CTGATATAGGCTC
1 TTATGAGC-TTCCTGATAT-GGCTC
96425605 TTATGAGCTTCCTGATATGGCTC
1 TTATGAGCTTCCTGATATGGCTC
96425628 GCTTGAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (23 bp):
TTATGAGCTTCCTGATATGGCTC
Found at i:96428265 original size:20 final size:20
Alignment explanation
Indices: 96428249--96428285 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
96428239 ACGGATGGTT
*
96428249 TACTGTTTATATAGATGAAA
1 TACTGTTTATACAGATGAAA
96428269 TACTGTTTATAC-GATGA
1 TACTGTTTATACAGATGA
96428286 GTCACTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (20 bp):
TACTGTTTATACAGATGAAA
Found at i:96439897 original size:73 final size:72
Alignment explanation
Indices: 96439820--96439983 Score: 163
Period size: 72 Copynumber: 2.3 Consensus size: 72
96439810 AGTAACTCGC
* * * * *
96439820 TGAGCGAGCATTTCATGTTAAAGCCATATGGGTCAGAGTATTGACTTTGTGTACA-GTCCCGTAA
1 TGAGCGAGCATTACATGATAAAGCCATA-GGGTCAGAGTACTGACTTGGTGAACATGTCCC-TAA
96439884 GTAGCTCAA
64 GTAGCTCAA
* * * * * * *
96439893 TGAGCGGGCGTTACATGATAATGCTATAGGGTCCGGGTACTGACTTGGTGAACATGTCCCTGAGT
1 TGAGCGAGCATTACATGATAAAGCCATAGGGTCAGAGTACTGACTTGGTGAACATGTCCCTAAGT
96439958 AGCTCAA
66 AGCTCAA
*
96439965 --ATGCGAGTATTACATGATA
1 TGA-GCGAGCATTACATGATA
96439984 TGTGGTAGCT
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
70 1 0.01
71 14 0.19
72 32 0.43
73 27 0.36
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (72 bp):
TGAGCGAGCATTACATGATAAAGCCATAGGGTCAGAGTACTGACTTGGTGAACATGTCCCTAAGT
AGCTCAA
Found at i:96448523 original size:17 final size:19
Alignment explanation
Indices: 96448483--96448523 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
96448473 TCTAATAGAA
*
96448483 AAATTAATTCATTTTTATG
1 AAATTAAGTCATTTTTATG
*
96448502 CAATTAAGT-ATTTTT-TG
1 AAATTAAGTCATTTTTATG
96448519 AAATT
1 AAATT
96448524 TTACAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (19 bp):
AAATTAAGTCATTTTTATG
Found at i:96449916 original size:286 final size:286
Alignment explanation
Indices: 96449404--96449977 Score: 1031
Period size: 286 Copynumber: 2.0 Consensus size: 286
96449394 ACTTGAACCT
* * *
96449404 AATTATTAATTTAAATAACATAATTTGCCAATTCAAAATTTATTTTAATGCTATAATTGACTCGT
1 AATTATTAATTCAAATAAAATAATTTGCCAATTCAAAATTTATTTTAATGCTATAATTGACTCAT
* *
96449469 AAATATTTAATAATAATATTTACGAACTCACTTGTTGGATTTGTGGCCCCGAAACCACTGTTTCT
66 AAATATTTAATAATAATATTTACGAACTCACTTGTCGGATTTGTGGCCCCGAAACCACTATTTCT
* *
96449534 AGCACTACTAAAAAATAGTTGTTACACCACCATACTTGATGGTAATGCATTCAACCATGATCTAG
131 AGCACCACAAAAAAATAGTTGTTACACCACCATACTTGATGGTAATGCATTCAACCATGATCTAG
*
96449599 CACGATCAAGCAATGAATAAGGGAATGATTTTAATCTAAGCGCATCTTCAGGAACGCCCTACTGC
196 CACAATCAAGCAATGAATAAGGGAATGATTTTAATCTAAGCGCATCTTCAGGAACGCCCTACTGC
96449664 TTGAATGAGTCACAGACTTCAAGAAA
261 TTGAATGAGTCACAGACTTCAAGAAA
96449690 AATTATTAATTCAAATAAAATAATTTGCCAATTCAAAATTTATTTTAATGCTATAATTGACTCAT
1 AATTATTAATTCAAATAAAATAATTTGCCAATTCAAAATTTATTTTAATGCTATAATTGACTCAT
* *
96449755 AAATATTTAATAATAATATTTACGGACTCTCTTGTCGGATTTGTGGCCCCGAAACCACTATTTCT
66 AAATATTTAATAATAATATTTACGAACTCACTTGTCGGATTTGTGGCCCCGAAACCACTATTTCT
* *
96449820 AGCACCACAAAAAAATAGTTGTTACATCACCATACTTGATGGTAATGCATTCAACCATGATCTGG
131 AGCACCACAAAAAAATAGTTGTTACACCACCATACTTGATGGTAATGCATTCAACCATGATCTAG
*
96449885 CACAATCAAGCAATGAATAAGGGAATGATTTTAATCTAAGGGCATCTTCAGGAACGCCCTACTGC
196 CACAATCAAGCAATGAATAAGGGAATGATTTTAATCTAAGCGCATCTTCAGGAACGCCCTACTGC
96449950 TTGAATGAGTCACAGACTTCAAGAAA
261 TTGAATGAGTCACAGACTTCAAGAAA
96449976 AA
1 AA
96449978 GTCTCAAGTG
Statistics
Matches: 275, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
286 275 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (286 bp):
AATTATTAATTCAAATAAAATAATTTGCCAATTCAAAATTTATTTTAATGCTATAATTGACTCAT
AAATATTTAATAATAATATTTACGAACTCACTTGTCGGATTTGTGGCCCCGAAACCACTATTTCT
AGCACCACAAAAAAATAGTTGTTACACCACCATACTTGATGGTAATGCATTCAACCATGATCTAG
CACAATCAAGCAATGAATAAGGGAATGATTTTAATCTAAGCGCATCTTCAGGAACGCCCTACTGC
TTGAATGAGTCACAGACTTCAAGAAA
Found at i:96451146 original size:19 final size:21
Alignment explanation
Indices: 96451118--96451161 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
96451108 AGAGCGAAAT
96451118 GAAC-GAG-AAACGGGCCAAA
1 GAACGGAGAAAACGGGCCAAA
*
96451137 -AACGGAGAAAATGGGCCAAA
1 GAACGGAGAAAACGGGCCAAA
96451157 GAACG
1 GAACG
96451162 AAATCAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 11 0.52
21 4 0.19
ACGTcount: A:0.48, C:0.18, G:0.32, T:0.02
Consensus pattern (21 bp):
GAACGGAGAAAACGGGCCAAA
Found at i:96469753 original size:14 final size:14
Alignment explanation
Indices: 96469734--96469763 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
96469724 TTATATCGAG
96469734 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
96469748 ACCAATCCAATTCA
1 ACCAATCCAAATCA
96469762 AC
1 AC
96469764 ATATTTTCAA
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:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:96475518 original size:32 final size:32
Alignment explanation
Indices: 96475474--96475536 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
96475464 GTCATAAGAG
*
96475474 GATGAAATGCATTGATTGAAAACATCACTTGT
1 GATGAAACGCATTGATTGAAAACATCACTTGT
*
96475506 GATGAAACGCATTGATTGAAAGCATCACTTG
1 GATGAAACGCATTGATTGAAAACATCACTTG
96475537 ATACGAGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (32 bp):
GATGAAACGCATTGATTGAAAACATCACTTGT
Found at i:96477423 original size:12 final size:12
Alignment explanation
Indices: 96477406--96477496 Score: 62
Period size: 12 Copynumber: 7.1 Consensus size: 12
96477396 ATTTTAATAG
96477406 ATTTAATATTAA
1 ATTTAATATTAA
96477418 ATTTAATATTAA
1 ATTTAATATTAA
*
96477430 ATTTATCTATAATAA
1 ATTTA---ATATTAA
*
96477445 ATATT-CTATT-A
1 AT-TTAATATTAA
96477456 ATTTAATATATAATA
1 ATTTAATAT-T-A-A
96477471 ATATTAATA-TATA
1 AT-TTAATATTA-A
96477484 ATTTAATATTAA
1 ATTTAATATTAA
96477496 A
1 A
96477497 GAGTTAAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
10 2 0.03
11 6 0.09
12 29 0.45
13 7 0.11
14 1 0.02
15 11 0.17
16 8 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:96477445 original size:27 final size:28
Alignment explanation
Indices: 96477415--96477492 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 28
96477405 GATTTAATAT
*
96477415 TAAAT-TTAATATTAAATTTATCTATAA
1 TAAATATTAATATTAAATTTATATATAA
*
96477442 TAAATATT-CTATT-AATTTAATATATAA
1 TAAATATTAATATTAAATTT-ATATATAA
96477469 T-AATATTAATA-TATAATTTA-ATAT
1 TAAATATTAATATTA-AATTTATATAT
96477493 TAAAGAGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
26 16 0.37
27 20 0.47
28 7 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
TAAATATTAATATTAAATTTATATATAA
Found at i:96477490 original size:18 final size:17
Alignment explanation
Indices: 96477452--96477495 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
96477442 TAAATATTCT
96477452 ATTAAT-TTAATATATA
1 ATTAATATTAATATATA
96477468 A-TAATATTAATATATA
1 ATTAATATTAATATATA
96477484 ATTTAATATTAA
1 A-TTAATATTAA
96477496 AGAGTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 12 0.48
18 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAATATTAATATATA
Found at i:96480885 original size:31 final size:31
Alignment explanation
Indices: 96480852--96480916 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
96480842 TTGAAGAAAT
96480852 AAAAATAAATAATTTACTAAAATAAATAAATAAAG
1 AAAAATAAATAA--T-C-AAAATAAATAAATAAAG
*
96480887 AAAAATAAATAATCAAAATAAATCAATAAA
1 AAAAATAAATAATCAAAATAAATAAATAAA
96480917 CCAATCAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 15 0.52
32 1 0.03
33 1 0.03
35 12 0.41
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (31 bp):
AAAAATAAATAATCAAAATAAATAAATAAAG
Found at i:96493695 original size:27 final size:26
Alignment explanation
Indices: 96493651--96493702 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
96493641 CTCGCTGTAA
*
96493651 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
96493678 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
96493703 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Done.