Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 172 of 187
Found at i:51303814 original size:12 final size:12
Alignment explanation
Indices: 51303799--51303859 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
51303789 TCAAACTCTC
*
51303799 TTTCATTTTGTT
1 TTTCATTTTCTT
*
51303811 TTTCAATTTCTT
1 TTTCATTTTCTT
*
51303823 TTTCTTTTTCTT
1 TTTCATTTTCTT
*
51303835 TTTCGTTTTC-T
1 TTTCATTTTCTT
*
51303846 TTTCTTTTTCTT
1 TTTCATTTTCTT
51303858 TT
1 TT
51303860 GATTGATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 10 0.24
12 32 0.76
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:51303826 original size:6 final size:6
Alignment explanation
Indices: 51303817--51303859 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
51303807 TGTTTTTCAA
*
51303817 TTTCTT TTTCTT TTTCTT TTTCGT TTTC-T TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
51303860 GATTGATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:51308475 original size:20 final size:20
Alignment explanation
Indices: 51308439--51308477 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
51308429 TGTTTTATTC
*
51308439 TACAAAAATTAAATCCTAAT
1 TACAAAAATAAAATCCTAAT
51308459 TACAAAAA-AAAATTCCTAA
1 TACAAAAATAAAA-TCCTAA
51308478 AGACCTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (20 bp):
TACAAAAATAAAATCCTAAT
Found at i:51311277 original size:26 final size:26
Alignment explanation
Indices: 51311248--51311299 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
51311238 TTGGATACAT
51311248 AGTCCACAGCAACTAAGACGTATTTG
1 AGTCCACAGCAACTAAGACGTATTTG
*
51311274 AGTCCACAGCAACTAAGATGTATTTG
1 AGTCCACAGCAACTAAGACGTATTTG
51311300 TTCCCATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (26 bp):
AGTCCACAGCAACTAAGACGTATTTG
Found at i:51316278 original size:32 final size:32
Alignment explanation
Indices: 51316241--51316308 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
51316231 AATTATCCTA
51316241 AGTATGCAAACTAGATGAATGAAATAGATTTT
1 AGTATGCAAACTAGATGAATGAAATAGATTTT
51316273 AGTATGCAAACTAGATGAATGAAATAGATTTT
1 AGTATGCAAACTAGATGAATGAAATAGATTTT
51316305 AGTA
1 AGTA
51316309 AAATTAAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (32 bp):
AGTATGCAAACTAGATGAATGAAATAGATTTT
Found at i:51334924 original size:96 final size:95
Alignment explanation
Indices: 51334803--51334987 Score: 255
Period size: 96 Copynumber: 1.9 Consensus size: 95
51334793 ATGAAAAGGG
* * * *
51334803 GAATATGATTGAGCTATCACCTTTTGTCCAATGTTATTGGTCTAGTTCA-AAAGATCATAAGGGT
1 GAATACGATTGAGATATCAACTTTTGGCCAATGTTATTGGTCTAGTT-AGAAA-ATCATAAGGGT
* *
51334867 TTCCAATGTCCAATTAAATATCCAAATAGAAA
64 TCCCAATGTCAAATTAAATATCCAAATAGAAA
* * *
51334899 GAATACGATTGAGATATCAAGTTTTGGGCAATGTTATTGGTGTAGTTAGGAAAATCATAAGGGTT
1 GAATACGATTGAGATATCAACTTTTGGCCAATGTTATTGGTCTAGTTA-GAAAATCATAAGGGTT
51334964 CCCAATGTCAAATTAAATATCCAA
65 CCCAATGTCAAATTAAATATCCAA
51334988 CTAAAGAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
95 1 0.01
96 74 0.95
97 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (95 bp):
GAATACGATTGAGATATCAACTTTTGGCCAATGTTATTGGTCTAGTTAGAAAATCATAAGGGTTC
CCAATGTCAAATTAAATATCCAAATAGAAA
Found at i:51336984 original size:45 final size:45
Alignment explanation
Indices: 51336919--51337004 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
51336909 CTCGGGGGAT
*
51336919 TCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGGTGGAA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
* *
51336964 TCAGCACATAGC-ACCAACCTTGCTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACC-ACCTTACTAATCAATGATGTCCGGT
51337005 TCCATTAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 3 0.08
45 34 0.92
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGAA
Found at i:51340092 original size:12 final size:12
Alignment explanation
Indices: 51340075--51340114 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
51340065 TGCATTGTTC
51340075 TTGAGTTTTTCT
1 TTGAGTTTTTCT
51340087 TTGAGTTTTTCTCT
1 TTGAG-TTTT-TCT
51340101 TTGAGTTTTTCT
1 TTGAGTTTTTCT
51340113 TT
1 TT
51340115 TCAAGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.38
13 8 0.31
14 8 0.31
ACGTcount: A:0.07, C:0.10, G:0.15, T:0.68
Consensus pattern (12 bp):
TTGAGTTTTTCT
Found at i:51340103 original size:14 final size:14
Alignment explanation
Indices: 51340075--51340112 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
51340065 TGCATTGTTC
51340075 TTGAG-TTTT-TCT
1 TTGAGTTTTTCTCT
51340087 TTGAGTTTTTCTCT
1 TTGAGTTTTTCTCT
51340101 TTGAGTTTTTCT
1 TTGAGTTTTTCT
51340113 TTTCAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 4 0.17
14 15 0.62
ACGTcount: A:0.08, C:0.11, G:0.16, T:0.66
Consensus pattern (14 bp):
TTGAGTTTTTCTCT
Found at i:51346635 original size:14 final size:14
Alignment explanation
Indices: 51346616--51346645 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51346606 TGTGAGAGAG
*
51346616 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
51346630 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
51346644 GA
1 GA
51346646 ATAAGGGATG
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:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:51349250 original size:27 final size:28
Alignment explanation
Indices: 51349196--51349251 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
51349186 AAATATACCC
51349196 TAAATCATTTATTCAAAAAAATGAAAAAT
1 TAAATCATTTATT-AAAAAAATGAAAAAT
*
51349225 TAAATCATTTATT-TAAAAATGAAAAAT
1 TAAATCATTTATTAAAAAAATGAAAAAT
51349252 GAAAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 13 0.50
29 13 0.50
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (28 bp):
TAAATCATTTATTAAAAAAATGAAAAAT
Found at i:51368184 original size:16 final size:15
Alignment explanation
Indices: 51368161--51368201 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
51368151 GTAGTTAATG
51368161 TGATAAATGTGAA-A
1 TGATAAATGTGAAGA
51368175 TAGTATAAATG-GAAGA
1 T-G-ATAAATGTGAAGA
51368191 TGATAAATGTG
1 TGATAAATGTG
51368202 TGAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.35
15 6 0.26
16 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (15 bp):
TGATAAATGTGAAGA
Found at i:51369427 original size:12 final size:12
Alignment explanation
Indices: 51369396--51369429 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
51369386 AGTAGTGACA
*
51369396 CATGGCCGTGTC
1 CATGCCCGTGTC
51369408 CA-GCCCGTGTC
1 CATGCCCGTGTC
51369419 CATGCCCGTGT
1 CATGCCCGTGT
51369430 AACTCTCTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.09, C:0.38, G:0.29, T:0.24
Consensus pattern (12 bp):
CATGCCCGTGTC
Found at i:51372540 original size:25 final size:25
Alignment explanation
Indices: 51372472--51372550 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 25
51372462 TACAAGCTCT
* * *
51372472 GAATTGGTATGCTCTTACGAGCTG-
1 GAATCGGTAAGCTCTAACGAGCTGA
*
51372496 TAATCGGTAAGCT-TAAACGAGCTGA
1 GAATCGGTAAGCTCT-AACGAGCTGA
* *
51372521 GAATCGGTAAGCTCTCACGACCTGA
1 GAATCGGTAAGCTCTAACGAGCTGA
51372546 -AATCG
1 GAATCG
51372551 ATAACCCGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.02
24 23 0.51
25 20 0.44
26 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (25 bp):
GAATCGGTAAGCTCTAACGAGCTGA
Found at i:51382574 original size:22 final size:23
Alignment explanation
Indices: 51382549--51382593 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
51382539 AAACTTATTT
51382549 TAACCCATT-TTT-AACACTAAAA
1 TAACCC-TTATTTCAACACTAAAA
*
51382571 TAACCCTTATTTCAACCCTAAAA
1 TAACCCTTATTTCAACACTAAAA
51382594 CATACTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 9 0.45
23 9 0.45
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (23 bp):
TAACCCTTATTTCAACACTAAAA
Found at i:51389817 original size:15 final size:15
Alignment explanation
Indices: 51389797--51389827 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51389787 GGCACCAAAG
*
51389797 GCCGAGAAGAAGCCT
1 GCCGAGAAAAAGCCT
51389812 GCCGAGAAAAAGCCT
1 GCCGAGAAAAAGCCT
51389827 G
1 G
51389828 TAGCAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.26, G:0.32, T:0.06
Consensus pattern (15 bp):
GCCGAGAAAAAGCCT
Found at i:51392464 original size:58 final size:58
Alignment explanation
Indices: 51392372--51392494 Score: 156
Period size: 58 Copynumber: 2.1 Consensus size: 58
51392362 ACCTCATATA
* * *
51392372 ATGAAAAGGGATAGCTTCGGCTACCGAATATGAAAAGGGATAACTTCAGCTATTGAAT
1 ATGAAAAAGGATAGCTTCGGCTACCAAATATGAAAAGAGATAACTTCAGCTATTGAAT
** * * ** *
51392430 ATGAAAAAGGATAGCTTCGGCTTTCAAATGTGAAAAGAGATAGCTTTGGCTATTGATT
1 ATGAAAAAGGATAGCTTCGGCTACCAAATATGAAAAGAGATAACTTCAGCTATTGAAT
51392488 ATGAAAA
1 ATGAAAA
51392495 GAGATGGTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (58 bp):
ATGAAAAAGGATAGCTTCGGCTACCAAATATGAAAAGAGATAACTTCAGCTATTGAAT
Found at i:51392496 original size:29 final size:29
Alignment explanation
Indices: 51392372--51392499 Score: 134
Period size: 29 Copynumber: 4.4 Consensus size: 29
51392362 ACCTCATATA
* **
51392372 ATGAAAAGGGATAGCTTCGGCTACCGAAT
1 ATGAAAAGAGATAGCTTCGGCTATTGAAT
* * *
51392401 ATGAAAAGGGATAACTTCAGCTATTGAAT
1 ATGAAAAGAGATAGCTTCGGCTATTGAAT
*
51392430 ATGAAAA-AGGATAGCTTCGGCT-TTCAAAT
1 ATGAAAAGA-GATAGCTTCGGCTATT-GAAT
* * *
51392459 GTGAAAAGAGATAGCTTTGGCTATTGATT
1 ATGAAAAGAGATAGCTTCGGCTATTGAAT
51392488 ATGAAAAGAGAT
1 ATGAAAAGAGAT
51392500 GGTGATAACC
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
28 2 0.02
29 77 0.94
30 3 0.04
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (29 bp):
ATGAAAAGAGATAGCTTCGGCTATTGAAT
Found at i:51392570 original size:30 final size:29
Alignment explanation
Indices: 51392487--51392601 Score: 106
Period size: 29 Copynumber: 3.9 Consensus size: 29
51392477 GGCTATTGAT
* * *
51392487 TATGAAAAGAGATGGTGATAACCATC-AA
1 TATGAAAAGGGATGGTTACAACCATCGAA
* * * * *
51392515 CTATAAAAAGAGATGGTGACGACCATCGAT
1 -TATGAAAAGGGATGGTTACAACCATCGAA
* *
51392545 TAATGAAAATGGATGGTTTCAACCATCGAA
1 T-ATGAAAAGGGATGGTTACAACCATCGAA
*
51392575 TATTAAAAGGGATGGTTACAACCATCG
1 TATGAAAAGGGATGGTTACAACCATCG
51392602 TTTAGCACAC
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
29 47 0.67
30 23 0.33
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (29 bp):
TATGAAAAGGGATGGTTACAACCATCGAA
Found at i:51398100 original size:25 final size:25
Alignment explanation
Indices: 51398072--51398128 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
51398062 TGATCTGAAG
*
51398072 ATCGGTATGCTCTCACGAGTTATAA
1 ATCGGTATGCTCTCACGAGCTATAA
51398097 ATCGGTATGCTCTCACGAGCTATAA
1 ATCGGTATGCTCTCACGAGCTATAA
*
51398122 ATTGGTA
1 ATCGGTA
51398129 ACCCTAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (25 bp):
ATCGGTATGCTCTCACGAGCTATAA
Found at i:51402637 original size:40 final size:40
Alignment explanation
Indices: 51402593--51402836 Score: 280
Period size: 40 Copynumber: 6.1 Consensus size: 40
51402583 AACTTTTGTA
** *
51402593 TGAATGCACATATGTGCCCTTGTTTGTACTTTGGTACCCT
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCT
* *
51402633 TGAATGCACATACCTGCCCCTATTTGTACTTTGGTACCCT
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCT
* *
51402673 TGAATGCACATACATGCCCCTTTTTGTACTTCT-ATACCCT
1 TGAATGCACATACATGCCCCTGTTTGTACTT-TGGTACCCT
* * * * * *
51402713 TAAATGCACCTACGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCT
* *
51402753 TAAATGCACATACATGCCCCTGTTTGTACTTCGGTACACC-
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTAC-CCT
* *
51402793 TGAACGCTCATACATG-CCCTGTTTGTACTTTGGTAACCC-
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGT-ACCCT
51402832 TGAAT
1 TGAAT
51402837 CAAATAGTAT
Statistics
Matches: 179, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
39 23 0.13
40 153 0.85
41 3 0.02
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (40 bp):
TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCT
Found at i:51402832 original size:120 final size:120
Alignment explanation
Indices: 51402595--51402822 Score: 316
Period size: 120 Copynumber: 1.9 Consensus size: 120
51402585 CTTTTGTATG
* * * * * * *
51402595 AATGCACATATGTGCCCTTGTTTGTACTTTGGTACCCTTGAATGCACATACCTGCCCCTATTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTAAATGCACATACATGCCCCTATTTGT
* * *
51402660 ACTTTGGTACCCTTGAATGCACATACATGCCCCTTTTTGTACTTCTATACCCTTA
66 ACTTCGGTACCCTTGAACGCACATACATGCCCCTGTTTGTACTTCTATACCCTTA
* *
51402715 AATGCACCTACGTGCCCCTGTTTGTACTTCGATACCCCTAAATGCACATACATGCCCCTGTTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTAAATGCACATACATGCCCCTATTTGT
*
51402780 ACTTCGGTACACC-TGAACGCTCATACATG-CCCTGTTTGTACTT
66 ACTTCGGTAC-CCTTGAACGCACATACATGCCCCTGTTTGTACTT
51402823 TGGTAACCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
119 13 0.14
120 79 0.84
121 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (120 bp):
AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTAAATGCACATACATGCCCCTATTTGT
ACTTCGGTACCCTTGAACGCACATACATGCCCCTGTTTGTACTTCTATACCCTTA
Found at i:51405767 original size:19 final size:19
Alignment explanation
Indices: 51405743--51405780 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
51405733 CTAAAAAAGT
51405743 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
51405762 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
51405781 GGATGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:51406239 original size:21 final size:23
Alignment explanation
Indices: 51406215--51406262 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
51406205 TTAATTAATG
*
51406215 AAATAT-A-CAATTATATAAGAA
1 AAATATGATCAATTATATAAAAA
* *
51406236 AAATGTGATGAATTATATAAAAA
1 AAATATGATCAATTATATAAAAA
51406259 AAAT
1 AAAT
51406263 CCTATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 1 0.05
23 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.29
Consensus pattern (23 bp):
AAATATGATCAATTATATAAAAA
Found at i:51417179 original size:12 final size:13
Alignment explanation
Indices: 51417155--51417183 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
51417145 GGGTTATAAC
51417155 TATTGCATTTATT
1 TATTGCATTTATT
51417168 TATTGC-TTTATT
1 TATTGCATTTATT
51417180 TATT
1 TATT
51417184 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:51421966 original size:13 final size:13
Alignment explanation
Indices: 51421950--51421983 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
51421940 ATTTAACCAC
51421950 TTTAATTAATCAA
1 TTTAATTAATCAA
*
51421963 TTTAATTAATTAA
1 TTTAATTAATCAA
51421976 -TTAATTAA
1 TTTAATTAA
51421984 AACTCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAATTAATCAA
Found at i:51423502 original size:21 final size:21
Alignment explanation
Indices: 51423478--51423523 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
51423468 AAATCTAAGC
51423478 ACAAGAATAAAAAATAA-AATA
1 ACAAGAATAAAAAATAATAA-A
*
51423499 ACAAGAATAATAAATAATAAA
1 ACAAGAATAAAAAATAATAAA
51423520 ACAA
1 ACAA
51423524 CGAAGTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (21 bp):
ACAAGAATAAAAAATAATAAA
Found at i:51423539 original size:25 final size:24
Alignment explanation
Indices: 51423483--51423544 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
51423473 TAAGCACAAG
* *
51423483 AATAAAAAATAAAATAACAAGAAT
1 AATAAATAATAAAACAACAAGAAT
*
51423507 AATAAATAATAAAACAACGAAGTAT
1 AATAAATAATAAAACAAC-AAGAAT
*
51423532 AATAAATAGTAAA
1 AATAAATAATAAA
51423545 GATAATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.69, C:0.05, G:0.06, T:0.19
Consensus pattern (24 bp):
AATAAATAATAAAACAACAAGAAT
Found at i:51424439 original size:14 final size:14
Alignment explanation
Indices: 51424422--51424465 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
51424412 AAAAAAATCA
51424422 AAGTAAATAAAAAT
1 AAGTAAATAAAAAT
*
51424436 AAGT-ATTAAAAGAT
1 AAGTAAATAAAA-AT
*
51424450 AAGTAAATAATAAT
1 AAGTAAATAAAAAT
51424464 AA
1 AA
51424466 AAACACTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 6 0.24
14 14 0.56
15 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (14 bp):
AAGTAAATAAAAAT
Found at i:51435046 original size:41 final size:40
Alignment explanation
Indices: 51434982--51435389 Score: 379
Period size: 41 Copynumber: 9.7 Consensus size: 40
51434972 TTTTTGAATG
* * *
51434982 TAAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAA
1 TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGAT-TA
* *
51435023 TAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTA
1 TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * * *
51435063 TAAGATGGTTGCTAAGTGCTGATTCCACCATATCGTTGATTG
1 TAAG-GGGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTA
* *
51435105 TGAAAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTA
1 T--AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * * *
51435147 TAAGGTGGTTGCTAAGTGTTGATTCAACCGTATCCTTGATTG
1 TAAGG-GGTTGCTAAGTGCTGATTC-CCCGTATCATTGATTA
* * * *
51435189 TGAAAGGGGTTGCTATGTGTTGATTTCCCATATCATTGATTA
1 T--AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
*
51435231 TAAGGTGGTTGCTCAA-TGCTGATTCCACCGTAT-ACTTGATTG
1 TAAGG-GGTTGCT-AAGTGCTGATTCC-CCGTATCA-TTGATTA
* *
51435273 TGAAAGGGGTTGCTATGTGCTAATTCCCCGTATCATTGATTA
1 T--AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * **
51435315 TAAGGTGGTTGCTAAGTGCTGATTCCACCAGGATCCTTTGAACA
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CC-GTAT-CATTGATTA
51435359 TAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 TAAGG-GGTTGCTAAGTGCTGATTCC-CCGT
51435390 GTAGCAGTTA
Statistics
Matches: 303, Mismatches: 44, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
40 17 0.06
41 103 0.34
42 81 0.27
43 56 0.18
44 46 0.15
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (40 bp):
TAAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
Found at i:51435126 original size:84 final size:83
Alignment explanation
Indices: 51435024--51435344 Score: 502
Period size: 84 Copynumber: 3.8 Consensus size: 83
51435014 ATTGATCAAT
*
51435024 AAGGGGTTGCTATGTGCTGA-TTCCCTGTATCATTGATTATAAGATGGTTGCTAAGTGCTGATTC
1 AAGGGGTTGCTATGTGCTGATTTCCC-GTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
51435088 CACCATATCGTTGATTGTGA
65 CACCATATC-TTGATTGTGA
* *
51435108 AAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTCA
1 AAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
*
51435173 ACCGTATCCTTGATTGTGA
66 ACCATAT-CTTGATTGTGA
* *
51435192 AAGGGGTTGCTATGTGTTGATTTCCCATATCATTGATTATAAGGTGGTTGCTCAA-TGCTGATTC
1 AAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTATAAGGTGGTTGCT-AAGTGCTGATTC
*
51435256 CACCGTATACTTGATTGTGA
65 CACCATAT-CTTGATTGTGA
* *
51435276 AAGGGGTTGCTATGTGCTAATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
51435341 ACCA
66 ACCA
51435345 GGATCCTTTG
Statistics
Matches: 219, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
83 2 0.01
84 209 0.95
85 8 0.04
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (83 bp):
AAGGGGTTGCTATGTGCTGATTTCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCC
ACCATATCTTGATTGTGA
Found at i:51442528 original size:22 final size:21
Alignment explanation
Indices: 51442503--51442556 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
51442493 ATTTATTTAA
**
51442503 TTATTTTTTGGTCTTTAGGAAT
1 TTATTTTTTGGTAATTAGG-AT
*
51442525 TTATTTATTTAGTAATTAGGAT
1 TTATTT-TTTGGTAATTAGGAT
*
51442547 TTAATTTTTG
1 TTATTTTTTG
51442557 CAAAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 13 0.50
23 10 0.38
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (21 bp):
TTATTTTTTGGTAATTAGGAT
Found at i:51444742 original size:19 final size:19
Alignment explanation
Indices: 51444706--51444743 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
51444696 TCAATCATCG
*
51444706 CTCATTCCATCATCTCTCA
1 CTCATTCCATCATATCTCA
51444725 CTCATT-CATCATTATCTCA
1 CTCATTCCATCA-TATCTCA
51444744 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATTCCATCATATCTCA
Found at i:51446219 original size:21 final size:22
Alignment explanation
Indices: 51446179--51446219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
51446169 ATAGGCTAGG
* *
51446179 ATTCACTAAGTTATAAAATGAA
1 ATTCACTAAATTAGAAAATGAA
51446201 ATTCACTAAATT-GAAAATG
1 ATTCACTAAATTAGAAAATG
51446220 CTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (22 bp):
ATTCACTAAATTAGAAAATGAA
Found at i:51447142 original size:17 final size:17
Alignment explanation
Indices: 51447120--51447153 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51447110 CACTAACATG
*
51447120 AAAATGTAATGACAATA
1 AAAATGCAATGACAATA
51447137 AAAATGCAATGACAATA
1 AAAATGCAATGACAATA
51447154 TATACTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:51455348 original size:16 final size:15
Alignment explanation
Indices: 51455309--51455350 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
51455299 AGATGATAAT
51455309 TATTAATATATAATTA
1 TATTAAT-TATAATTA
*
51455325 TATCAATTATAATATA
1 TATTAATTATAAT-TA
51455341 TATTAATTAT
1 TATTAATTAT
51455351 TATCAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:51455963 original size:24 final size:25
Alignment explanation
Indices: 51455908--51455967 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
51455898 CTCCTAAATT
* *
51455908 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATATTTCAA
*
51455933 TTTATTAAATTAT-TAATATTT-ATA
1 TTAATTAAATTATCTAATATTTCA-A
51455957 TTAATTAAATT
1 TTAATTAAATT
51455968 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 1 0.03
24 18 0.60
25 11 0.37
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATATTTCAA
Found at i:51460111 original size:101 final size:101
Alignment explanation
Indices: 51459990--51460174 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
51459980 AAAGTGATGG
* * *
51459990 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGAAT-G-ATGGGTCGCATGTGTAGT
1 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCAG-ATGGAAT-GGTCACATGTGCAGT
51460053 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
64 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
* *
51460091 TCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAGATGGAAATGGTCACATGTGCAGTA
1 TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGG-AATGGTCACATGTGCAGTA
51460156 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
51460175 TGAACCGGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 2 0.03
101 39 0.51
102 33 0.43
103 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (101 bp):
TCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGAATGGTCACATGTGCAGTAC
TATGTGCAGGCTACTATGCGTACCGAATAGCTTCGA
Found at i:51460156 original size:51 final size:50
Alignment explanation
Indices: 51459984--51460172 Score: 188
Period size: 51 Copynumber: 3.8 Consensus size: 50
51459974 AAAGTGAAAG
* * *
51459984 TGAT-GGTCACGTATGTAGTACTATGTGCAGGCTACTACGTGTATCGGAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAA
* * * * *
51460033 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTA-CCGAA
1 TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAA
* * * *
51460082 TAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTATTACGTGTATCAG-A
1 T-G-ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAA
*
51460133 TGGAAAT-GGTCACATGTGCAGTACTATGTGCAGGCTACTA
1 T-G--ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTA
51460173 TGTGAACCGG
Statistics
Matches: 113, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 9 0.08
50 35 0.31
51 66 0.58
52 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (50 bp):
TGATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGAA
Found at i:51463086 original size:50 final size:50
Alignment explanation
Indices: 51463011--51463303 Score: 320
Period size: 50 Copynumber: 5.7 Consensus size: 50
51463001 TTTTTTATAC
* * * * **
51463011 TGCCAATGCCATATCCCATATATGGTCTTACATGGGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * ** * * *
51463061 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * *
51463111 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
*
51463161 TGCCAACGCCATGTCCCAGACATGGTCTTACACT-GGACCTCTCATCTTA-G
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCAT-ATAGG
*
51463211 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
*
51463267 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
51463304 TCTCATCCTC
Statistics
Matches: 207, Mismatches: 27, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.00
50 166 0.80
51 2 0.01
52 1 0.00
54 1 0.00
56 36 0.17
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:51463136 original size:100 final size:100
Alignment explanation
Indices: 51463032--51463310 Score: 364
Period size: 100 Copynumber: 2.8 Consensus size: 100
51463022 TATCCCATAT
** * * **
51463032 ATGGTCTTACATGGGAGTTCTCATATAGGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGG
1 ATGGTCTTACATGGGACCTCTCATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACACGGG
* *
51463097 ACCTCTTATCTTGGTGCCAACACCATGTCCCAGAC
66 ACCTCTCATCTTAGTGCCAACACCATGTCCCAGAC
* * * *
51463132 ATGGTCTTACATGGGACCTCTCATCTCGATGCCAACGCCATGTCCCAGACATGGTCTTACACTGG
1 ATGGTCTTACATGGGACCTCTCATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACACGGG
*
51463197 ACCTCTCATCTTAGTGCCAACGCCATGTCCCAGAC
66 ACCTCTCATCTTAGTGCCAACACCATGTCCCAGAC
51463232 ATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGACATGGTCTTA
1 ATGGTCTTACATGGGACCTCTCAT-A--T--A-GATGCCAATGCCATGTCCCAGACATGGTCTTA
*
51463297 CATGGGA--TCTCATC
60 CACGGGACCTCTCATC
51463311 CTCTTAATGT
Statistics
Matches: 155, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
100 111 0.72
103 1 0.01
104 7 0.05
106 36 0.23
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (100 bp):
ATGGTCTTACATGGGACCTCTCATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACACGGG
ACCTCTCATCTTAGTGCCAACACCATGTCCCAGAC
Found at i:51463205 original size:150 final size:151
Alignment explanation
Indices: 51463011--51463310 Score: 376
Period size: 150 Copynumber: 2.0 Consensus size: 151
51463001 TTTTTTATAC
* * * ** * *
51463011 TGCCAATGCCATATCCCATATATGGTCTTACATGGGAGTTCTCAT-ATAGGTGCCCATGCCATGT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCATA-GTGCCAACGCCATGT
* *
51463075 CCCAGACATGGTCTTACGGGGGACCTCT-T-ATCT-TGGTGCCAACACCATGTCCCAGACATGGT
65 CCCAGACATGGTCTTACAGGGGACCTCTATAATCTATGATGCCAACACCATGTCCCAGACATGGT
51463137 CTTACATGGGACCTCTCATCTCGA
130 CTTACATGGGA--TCTCATCTCGA
* *
51463161 TGCCAACGCCATGTCCCAGACATGGTCTTACACT-GGACCTCTCATCTTAGTGCCAACGCCATGT
1 TGCCAACGCCATATCCCAGACATGGTCTTACA-TGGGACCTCTCATCATAGTGCCAACGCCATGT
* **
51463225 CCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGACAT
65 CCCAGACATGGTCTTACAGGGGACCTCT-ATAATCT--ATGATGCCAACACCATGTCCCAGACAT
51463290 GGTCTTACATGGGATCTCATC
127 GGTCTTACATGGGATCTCATC
51463311 CTCTTAATGT
Statistics
Matches: 128, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
150 76 0.59
151 3 0.02
152 1 0.01
153 4 0.03
154 7 0.05
156 37 0.29
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (151 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATCATAGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTATAATCTATGATGCCAACACCATGTCCCAGACATGGTC
TTACATGGGATCTCATCTCGA
Found at i:51470857 original size:21 final size:20
Alignment explanation
Indices: 51470833--51470888 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 20
51470823 TTCTCATTTT
51470833 CAACAACTTCTTCTTCTTTAG
1 CAACAACTTC-TCTTCTTTAG
*
51470854 CAACCACTTC-C-TCTTTAG
1 CAACAACTTCTCTTCTTTAG
51470872 CAACAACTTCATCTTCT
1 CAACAACTTC-TCTTCT
51470889 ACAGTAGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 16 0.53
19 1 0.03
20 1 0.03
21 12 0.40
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.38
Consensus pattern (20 bp):
CAACAACTTCTCTTCTTTAG
Found at i:51473448 original size:18 final size:18
Alignment explanation
Indices: 51473425--51473462 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
51473415 TATAATTGAG
51473425 TTGAGCTTCTATAAGAGT
1 TTGAGCTTCTATAAGAGT
*
51473443 TTGAGCTTCTGTAAGAGT
1 TTGAGCTTCTATAAGAGT
51473461 TT
1 TT
51473463 TGCTAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (18 bp):
TTGAGCTTCTATAAGAGT
Found at i:51483973 original size:21 final size:21
Alignment explanation
Indices: 51483947--51483986 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
51483937 ATTTTAATTC
* *
51483947 ATATACTTTTAGTGAGTTACA
1 ATATACTTCTAATGAGTTACA
51483968 ATATACTTCTAATGAGTTA
1 ATATACTTCTAATGAGTTA
51483987 TCTTTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
ATATACTTCTAATGAGTTACA
Found at i:51485161 original size:21 final size:23
Alignment explanation
Indices: 51485119--51485162 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
51485109 TTTTTATAAT
*
51485119 TAATACATGTTTATATATTTTTA
1 TAATACATGTTTAGATATTTTTA
51485142 TAATACAT-TTTAGA-ATTTTTA
1 TAATACATGTTTAGATATTTTTA
51485163 GGATTGCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (23 bp):
TAATACATGTTTAGATATTTTTA
Found at i:51485194 original size:21 final size:22
Alignment explanation
Indices: 51485155--51485196 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
51485145 TACATTTTAG
*
51485155 AATTTTTAGGATTGCTTTTATA
1 AATTTTTAGGATCGCTTTTATA
51485177 AATTTTTAGGATCG-TTTTAT
1 AATTTTTAGGATCGCTTTTAT
51485197 GTACATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (22 bp):
AATTTTTAGGATCGCTTTTATA
Found at i:51489067 original size:23 final size:24
Alignment explanation
Indices: 51489000--51489055 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
51488990 GCCTTGTGCA
*
51489000 TATTCTATAAATTCCTTTATGGCG
1 TATTCTGTAAATTCCTTTATGGCG
*
51489024 TATTCTGTAAATGCCTTTATGGCG
1 TATTCTGTAAATTCCTTTATGGCG
51489048 TATTCTGT
1 TATTCTGT
51489056 GTTTCCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (24 bp):
TATTCTGTAAATTCCTTTATGGCG
Found at i:51490778 original size:20 final size:20
Alignment explanation
Indices: 51490753--51490799 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
51490743 CTTACCATTC
*
51490753 TTACTTACTTTCCAATTCAT
1 TTACTTAATTTCCAATTCAT
*
51490773 TTACTTAATTTCCATTTCAT
1 TTACTTAATTTCCAATTCAT
51490793 TTACTTA
1 TTACTTA
51490800 GCATAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (20 bp):
TTACTTAATTTCCAATTCAT
Found at i:51497525 original size:41 final size:41
Alignment explanation
Indices: 51497419--51497525 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 41
51497409 ATTTTTGAAT
* * * *
51497419 TACACATATA-TGCCCCTGTTTGTACTTTGATACCCCTGAAT
1 TACACATA-AGTGCCCCTGTTTATACGTTGATACCCCTAAAC
* * * *
51497460 TACACATAAGTTCCCCTATCTATACGTTGGTACCCCTAAAC
1 TACACATAAGTGCCCCTGTTTATACGTTGATACCCCTAAAC
* **
51497501 TGCACATGCGTGCCCCTGTTTATAC
1 TACACATAAGTGCCCCTGTTTATAC
51497526 TTCAGTGCTC
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
40 1 0.02
41 50 0.98
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (41 bp):
TACACATAAGTGCCCCTGTTTATACGTTGATACCCCTAAAC
Found at i:51504699 original size:41 final size:41
Alignment explanation
Indices: 51504615--51504730 Score: 130
Period size: 41 Copynumber: 2.8 Consensus size: 41
51504605 TGTTGAATTT
* * *
51504615 CACATACGTGCCCCTGTTTGTACTTTGGTAACAC-TAAACTG
1 CACATACGTGCCCCTGTTTGTACTTCGATATC-CTTAAACTG
*
51504656 CAC-TAACGTGCCCCTGTTTGTACTTCGATATCCTTAAATTG
1 CACAT-ACGTGCCCCTGTTTGTACTTCGATATCCTTAAACTG
**
51504697 CACATACGTGCCTTTG-TTGTACTTCGATACTCCT
1 CACATACGTGCCCCTGTTTGTACTTCGATA-TCCT
51504731 CAATGCACTT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 15 0.23
41 49 0.75
42 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.35
Consensus pattern (41 bp):
CACATACGTGCCCCTGTTTGTACTTCGATATCCTTAAACTG
Found at i:51521026 original size:54 final size:54
Alignment explanation
Indices: 51520944--51521050 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
51520934 ACTTATTGGT
51520944 TAAATTGTTCCCATTGAGTTATCCTTAGCATATATTATAACATTTTCAGTTTAG
1 TAAATTGTTCCCATTGAGTTATCCTTAGCATATATTATAACATTTTCAGTTTAG
*
51520998 TAAATTGTTCCCATTGAGTTATCCTTAGCATATATTTTAACATTTTCAGTTTA
1 TAAATTGTTCCCATTGAGTTATCCTTAGCATATATTATAACATTTTCAGTTTA
51521051 CTTTATCCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (54 bp):
TAAATTGTTCCCATTGAGTTATCCTTAGCATATATTATAACATTTTCAGTTTAG
Found at i:51523318 original size:50 final size:50
Alignment explanation
Indices: 51523198--51523432 Score: 197
Period size: 50 Copynumber: 4.6 Consensus size: 50
51523188 ACATGCTAAA
*
51523198 GCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCATGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-CGGTGCCAAT
* * * * *
51523247 ACCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAAT
* ** ** * *
51523297 GCCATGTCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAAT
* * * * * *
51523347 GCCATGTCTCAGACATGGTCTTATATGGGACCTATCGTCCTCTCAAGGATACCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GT-TC-TCATATC--GG-TGCCAAT
*
51523403 GCCATGTCCCAGACAAGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
51523433 TCTCTTTACG
Statistics
Matches: 149, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.03
49 31 0.21
50 71 0.48
51 1 0.01
52 2 0.01
53 6 0.04
55 2 0.01
56 32 0.21
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCGGTGCCAAT
Found at i:51530385 original size:50 final size:50
Alignment explanation
Indices: 51530318--51530508 Score: 211
Period size: 50 Copynumber: 3.7 Consensus size: 50
51530308 TTTCTTGTAA
* * * * *
51530318 TGCCAATGCCATATCCCAGATATGATCTTACATGGGAATTTTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* ** * *
51530368 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
* *
51530418 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATTCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATA---TC--GG
*
51530473 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
51530509 CATCTCTTTA
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 79 0.69
53 2 0.02
55 2 0.02
56 32 0.28
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTCATATCGG
Found at i:51530463 original size:100 final size:103
Alignment explanation
Indices: 51530318--51530504 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 103
51530308 TTTCTTGTAA
* * * * *
51530318 TGCCAATGCCATATCCCAGATATGATCTTACATGGGAATTTTCATA-TC-GG-TGCCCATGCCAT
1 TGCCAACGCCATATCCCAAACATGATCTTACATGGGAATTCTCATATTCAGGATGCCAATGCCAT
51530380 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
66 GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
* * * *
51530418 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACTTCTCATATTCTCAAGGATGCCAATGT
1 TGCCAACGCCATATCCCAAACATGATCTTACATGGGAATTCTCATA-T-TC-AGGATGCCAATGC
51530483 CATGTCCCAGACATGGTCTTAC
63 CATGTCCCAGACATGGTCTTAC
51530505 ATGGCATCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 39 0.54
103 2 0.03
105 2 0.03
106 29 0.40
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (103 bp):
TGCCAACGCCATATCCCAAACATGATCTTACATGGGAATTCTCATATTCAGGATGCCAATGCCAT
GTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
Found at i:51533435 original size:21 final size:20
Alignment explanation
Indices: 51533406--51533447 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
51533396 CGAAATGAAA
51533406 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
51533427 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
51533447 T
1 T
51533448 ATCCATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:51537867 original size:30 final size:30
Alignment explanation
Indices: 51537810--51537871 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
51537800 GCTTTTTGAA
* *
51537810 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
*
51537840 AATATTTACAGAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
51537870 AA
1 AA
51537872 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:51556675 original size:17 final size:18
Alignment explanation
Indices: 51556653--51556689 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
51556643 TATTTCATGT
*
51556653 GAACC-ATGTTGTTATGC
1 GAACCAATGTTATTATGC
51556670 GAACCAATGTTATTATGC
1 GAACCAATGTTATTATGC
51556688 GA
1 GA
51556690 CACAAACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (18 bp):
GAACCAATGTTATTATGC
Found at i:51561662 original size:22 final size:22
Alignment explanation
Indices: 51561628--51561680 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
51561618 CATCAGTGTT
* * *
51561628 ATCAGTGGAAGTTTATCTGCAA
1 ATCAATGGTAGTTTATCTACAA
51561650 ATCAATGGTAGTTTATCTACAA
1 ATCAATGGTAGTTTATCTACAA
*
51561672 ATTAATGGT
1 ATCAATGGT
51561681 GGCATGTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (22 bp):
ATCAATGGTAGTTTATCTACAA
Found at i:51562781 original size:7 final size:7
Alignment explanation
Indices: 51562769--51562803 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
51562759 AAGACTGTAG
51562769 GAAACTA
1 GAAACTA
51562776 GAAACTA
1 GAAACTA
*
51562783 GAAACTG
1 GAAACTA
*
51562790 GAAACTG
1 GAAACTA
51562797 GAAACTA
1 GAAACTA
51562804 TAGGGAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.20, T:0.14
Consensus pattern (7 bp):
GAAACTA
Found at i:51563590 original size:24 final size:24
Alignment explanation
Indices: 51563542--51563588 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
51563532 ACTGATCATA
*
51563542 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGAGATATTTG
*
51563566 GAGAGATTTGAGGAGAGACTATT
1 GAGAGAATTGAGGAGAGA-TATT
51563589 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGAGATATTTG
Found at i:51564067 original size:27 final size:27
Alignment explanation
Indices: 51564037--51564192 Score: 161
Period size: 27 Copynumber: 5.8 Consensus size: 27
51564027 TAAATGACTG
* * *
51564037 AAATACCTCTATAGGTTAAAATAACCA
1 AAATACCCCCATAGGGTAAAATAACCA
* ***
51564064 AAATACCCCCATAGGATAAAATAAATG
1 AAATACCCCCATAGGGTAAAATAACCA
* *
51564091 AAATACCTCCATAGGGTAAAATAACTA
1 AAATACCCCCATAGGGTAAAATAACCA
* * * *
51564118 AAGT-CCCCAATACGGTAAAATAATCA
1 AAATACCCCCATAGGGTAAAATAACCA
* *
51564144 AAATACCCCCATAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATAACCA
*
51564171 AAATACCCTCATAGGGTAAAAT
1 AAATACCCCCATAGGGTAAAAT
51564193 GACTATTATA
Statistics
Matches: 105, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
26 20 0.19
27 85 0.81
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATAACCA
Found at i:51564156 original size:53 final size:54
Alignment explanation
Indices: 51564037--51564192 Score: 167
Period size: 53 Copynumber: 2.9 Consensus size: 54
51564027 TAAATGACTG
* * * *
51564037 AAATACCTCTATAGGTTAAAATAACCAAAATACCCCCATAGGATAAAATAAATG
1 AAATACCTCCATAGGGTAAAATAACCAAAATACCCCAATAGGATAAAATAAATA
* *
51564091 AAATACCTCCATAGGGTAAAATAACTAAAGT-CCCCAATACGG-TAAAAT-AATCA
1 AAATACCTCCATAGGGTAAAATAACCAAAATACCCCAATA-GGATAAAATAAAT-A
* * * *
51564144 AAATACCCCCATAGGGTAAAATGACCGAAATACCCTC-ATAGGGTAAAAT
1 AAATACCTCCATAGGGTAAAATAACCAAAATACCC-CAATAGGATAAAAT
51564193 GACTATTATA
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
52 3 0.03
53 41 0.48
54 41 0.48
55 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (54 bp):
AAATACCTCCATAGGGTAAAATAACCAAAATACCCCAATAGGATAAAATAAATA
Found at i:51564603 original size:28 final size:28
Alignment explanation
Indices: 51564560--51564676 Score: 173
Period size: 28 Copynumber: 4.2 Consensus size: 28
51564550 ACTGTATCGA
* *
51564560 TACTGTATTGGGCTAAGGCTCACATTAT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
51564588 TATTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
*
51564616 TACTGTATTGGGATAAGGCCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACATTGT
* *
51564644 TGCTGTATTGGGCTAAGGCCCACACTG-
1 TACTGTATTGGGCTAAGGCCCACATTGT
51564671 TACTGT
1 TACTGT
51564677 TACTTGCATA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 5 0.06
28 75 0.94
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACATTGT
Found at i:51569741 original size:25 final size:25
Alignment explanation
Indices: 51569713--51569805 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
51569703 TCCAACCCAC
* * *
51569713 AGCTCGTGTGAGCATACTGATTTAT
1 AGCTCATGTGAGCATACAGATTTAA
* * *
51569738 AGCTCATGAGAGCATACCGATCTAA
1 AGCTCATGTGAGCATACAGATTTAA
* * *
51569763 AGCTCAAGTGAGCATACAGATTCAG
1 AGCTCATGTGAGCATACAGATTTAA
* *
51569788 AGCTCGTATGAGCATACA
1 AGCTCATGTGAGCATACA
51569806 TGTACATGAA
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (25 bp):
AGCTCATGTGAGCATACAGATTTAA
Found at i:51573340 original size:5 final size:5
Alignment explanation
Indices: 51573330--51573354 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
51573320 CGGGAATGAA
51573330 AAAGG AAAGG AAAGG AAAGG AAAGG
1 AAAGG AAAGG AAAGG AAAGG AAAGG
51573355 TCTGTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:51578285 original size:12 final size:12
Alignment explanation
Indices: 51578268--51578295 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
51578258 TCAAGCTGTT
51578268 ACACGGCCTAGC
1 ACACGGCCTAGC
51578280 ACACGGCCTAGC
1 ACACGGCCTAGC
51578292 ACAC
1 ACAC
51578296 AGCCGTGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.43, G:0.21, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:51579616 original size:25 final size:25
Alignment explanation
Indices: 51579526--51579617 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 25
51579516 TCATTTACAT
** * *
51579526 GTATGCTCACACGAGCTGTTAATCG
1 GTATGCTTTCACGAGCTATAAATCG
** *
51579551 GTATGCTTTCTTGAGCTATAGATCG
1 GTATGCTTTCACGAGCTATAAATCG
* *
51579576 GTATGCTTTCATGAGCTATAAATTG
1 GTATGCTTTCACGAGCTATAAATCG
51579601 GTATGCTTAT-ACGAGCT
1 GTATGCTT-TCACGAGCT
51579618 GTGGGTGGAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
25 54 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (25 bp):
GTATGCTTTCACGAGCTATAAATCG
Found at i:51594776 original size:13 final size:13
Alignment explanation
Indices: 51594760--51594804 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
51594750 GGGTGATTAA
51594760 AAACTAAGATTTT
1 AAACTAAGATTTT
**
51594773 AAACTAAG--TAA
1 AAACTAAGATTTT
51594784 AAACTAAGATTTT
1 AAACTAAGATTTT
51594797 AAACTAAG
1 AAACTAAG
51594805 TGAACTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (13 bp):
AAACTAAGATTTT
Found at i:51594784 original size:24 final size:24
Alignment explanation
Indices: 51594757--51594805 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
51594747 AGAGGGTGAT
51594757 TAAAAACTAAGATTTTAAACTAAG
1 TAAAAACTAAGATTTTAAACTAAG
51594781 TAAAAACTAAGATTTTAAACTAAG
1 TAAAAACTAAGATTTTAAACTAAG
51594805 T
1 T
51594806 GAACTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
TAAAAACTAAGATTTTAAACTAAG
Found at i:51595490 original size:21 final size:20
Alignment explanation
Indices: 51595466--51595511 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
51595456 CAAAATGCAA
51595466 TCAACCTAACA-TGAATTAAAT
1 TCAACCTAA-ATTG-ATTAAAT
*
51595487 TCAAGCTAAATTGATTAAAT
1 TCAACCTAAATTGATTAAAT
51595507 T-AACC
1 TCAACC
51595512 ATTCCAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
TCAACCTAAATTGATTAAAT
Found at i:51607856 original size:50 final size:48
Alignment explanation
Indices: 51607786--51607962 Score: 167
Period size: 51 Copynumber: 3.5 Consensus size: 48
51607776 AACAACTTCC
**
51607786 TTCCCATTTCATATCCAACCTTCCTTCCCAAGACCATTTCAAATCATTATA
1 TTCCCATAACATA-CCAACCTTCCTTCCCAA-ACC-TTTCAAATCATTATA
* * *
51607837 TTCCCATAACATACCAACCTTCATCTGCAAAACCTTTTTCAAATCATTATA
1 TTCCCATAACATACCAACCTTCCT-TCCCAAACC--TTTCAAATCATTATA
* **
51607888 GTCCTGTAACATACCAACCTTCC-TCCGCAAAGCCTTCCTCAAATCATTATA
1 TTCCCATAACATACCAACCTTCCTTCC-CAAA-CCTT--TCAAATCATTATA
* *
51607939 TTCTCGTAACATACCAACCTTCCT
1 TTCCCATAACATACCAACCTTCCT
51607963 CCGTAAAGTT
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
49 4 0.04
50 16 0.15
51 84 0.81
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.32
Consensus pattern (48 bp):
TTCCCATAACATACCAACCTTCCTTCCCAAACCTTTCAAATCATTATA
Found at i:51607877 original size:51 final size:51
Alignment explanation
Indices: 51607822--51607965 Score: 198
Period size: 51 Copynumber: 2.8 Consensus size: 51
51607812 CCCAAGACCA
* *
51607822 TTTCAAATCATTATATTCCCATAACATACCAACCTTCATCTGCAAAACCTT
1 TTTCAAATCATTATATTCCCGTAACATACCAACCTTCATCCGCAAAACCTT
* * * *
51607873 TTTCAAATCATTATAGTCCTGTAACATACCAACCTTCCTCCGCAAAGCCTT
1 TTTCAAATCATTATATTCCCGTAACATACCAACCTTCATCCGCAAAACCTT
** * *
51607924 CCTCAAATCATTATATTCTCGTAACATACCAACCTTCCTCCG
1 TTTCAAATCATTATATTCCCGTAACATACCAACCTTCATCCG
51607966 TAAAGTTATT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.31, C:0.32, G:0.05, T:0.32
Consensus pattern (51 bp):
TTTCAAATCATTATATTCCCGTAACATACCAACCTTCATCCGCAAAACCTT
Found at i:51611653 original size:30 final size:30
Alignment explanation
Indices: 51611597--51611653 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
51611587 ACAGGCAAAG
* * **
51611597 ACACGGGCATGTGACACGGCTTTGTGTGAC
1 ACACGGCCAGGTGACACGGCCGTGTGTGAC
51611627 ACACGGCCAGGTGACACGGCCGTGTGT
1 ACACGGCCAGGTGACACGGCCGTGTGT
51611654 CCCCTGTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.35, T:0.19
Consensus pattern (30 bp):
ACACGGCCAGGTGACACGGCCGTGTGTGAC
Found at i:51618420 original size:13 final size:13
Alignment explanation
Indices: 51618402--51618426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51618392 TAGGTTATAT
51618402 GTGTGAAAATTTC
1 GTGTGAAAATTTC
51618415 GTGTGAAAATTT
1 GTGTGAAAATTT
51618427 AGTCGTTTGA
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:51639072 original size:20 final size:20
Alignment explanation
Indices: 51639028--51639083 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
51639018 TCCCACTACG
*
51639028 GTGCCCCTGTTTGCACATTT
1 GTGCCCCTGTTTGCACATTC
*
51639048 GTGCCTCTGTTTGCAC-TTC
1 GTGCCCCTGTTTGCACATTC
51639067 GATGCCCCTGTTATGCA
1 G-TGCCCCTGTT-TGCA
51639084 TCTATGATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.11, C:0.30, G:0.21, T:0.38
Consensus pattern (20 bp):
GTGCCCCTGTTTGCACATTC
Found at i:51642537 original size:17 final size:18
Alignment explanation
Indices: 51642502--51642537 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
51642492 TCGTTCTTAT
51642502 TGTTTAATCTATCAAACA
1 TGTTTAATCTATCAAACA
*
51642520 TGTTTCATCTAT-AAACA
1 TGTTTAATCTATCAAACA
51642537 T
1 T
51642538 TGGCTGGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.42
Consensus pattern (18 bp):
TGTTTAATCTATCAAACA
Found at i:51649437 original size:23 final size:23
Alignment explanation
Indices: 51649405--51649448 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
51649395 ACTACCATTT
51649405 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
51649428 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
51649449 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:51649441 original size:13 final size:11
Alignment explanation
Indices: 51649409--51649451 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
51649399 CCATTTTCTA
*
51649409 AATAAAATAAT
1 AATAAAATATT
51649420 AAT-AAATATCT
1 AATAAAATAT-T
51649431 AAGTAAAATATT
1 AA-TAAAATATT
51649443 AATAAAATA
1 AATAAAATA
51649452 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:51667865 original size:22 final size:24
Alignment explanation
Indices: 51667831--51667874 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
51667821 CTTGGACCAA
51667831 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
**
51667853 GATTTCCTTGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
51667875 GCTCAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:51667933 original size:69 final size:69
Alignment explanation
Indices: 51667822--51667972 Score: 293
Period size: 69 Copynumber: 2.2 Consensus size: 69
51667812 ATTAGGTTTC
51667822 TTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTCCTTGATTCTTGAAATCGCTCAAAACAGC
1 TTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTCCTTGATTCTTGAAATCGCTCAAAACAGC
51667887 AAAA
66 AAAA
*
51667891 TTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAGC
1 TTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTCCTTGATTCTTGAAATCGCTCAAAACAGC
51667956 AAAA
66 AAAA
51667960 TTGGACCAAGATT
1 TTGGACCAAGATT
51667973 CAGTTTCTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (69 bp):
TTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTCCTTGATTCTTGAAATCGCTCAAAACAGC
AAAA
Found at i:51673950 original size:26 final size:25
Alignment explanation
Indices: 51673896--51673972 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
51673886 ACAAATTTTC
*
51673896 TCAAAATTTTACCGGGGTAAAATCA
1 TCAAAATTTTACCGGGGTAAAATTA
* *
51673921 TCAAAATTTTATCGGGGGTAAAATTG
1 TCAAAATTTTA-CCGGGGTAAAATTA
* *
51673947 TCAAAAAATTTACTGGGGTAAAATTA
1 TC-AAAATTTTACCGGGGTAAAATTA
51673973 GAATGAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 11 0.25
26 25 0.57
27 8 0.18
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACCGGGGTAAAATTA
Found at i:51675182 original size:13 final size:13
Alignment explanation
Indices: 51675147--51675190 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
51675137 TCTAATAATC
*
51675147 TAATTAAA-ATTA
1 TAATTAAATATAA
*
51675159 TAATAAAATATAA
1 TAATTAAATATAA
*
51675172 TTATTAAATATAA
1 TAATTAAATATAA
51675185 TAATTA
1 TAATTA
51675191 TCCAAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATTAAATATAA
Found at i:51676478 original size:5 final size:5
Alignment explanation
Indices: 51676463--51676506 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
51676453 ATTATATTAA
* *
51676463 ATAT- ATATG ATGTG ATATG ATCTG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
51676507 GAATACATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:51676919 original size:16 final size:16
Alignment explanation
Indices: 51676914--51676959 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
51676904 AATTTTGGTA
51676914 AATTTTGGTAAATTTT
1 AATTTTGGTAAATTTT
51676930 AATTTTGGTAAATTTT
1 AATTTTGGTAAATTTT
51676946 AATTTTGGTAAATT
1 AATTTTGGTAAATT
51676960 AATATAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (16 bp):
AATTTTGGTAAATTTT
Found at i:51676959 original size:10 final size:10
Alignment explanation
Indices: 51676904--51676945 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
51676894 TTTTAATTTT
51676904 AATTTTGGTA
1 AATTTTGGTA
51676914 AATTTTGGTA
1 AATTTTGGTA
51676924 AA-TTT--T-
1 AATTTTGGTA
51676930 AATTTTGGTA
1 AATTTTGGTA
51676940 AATTTT
1 AATTTT
51676946 AATTTTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.07
7 4 0.14
9 4 0.14
10 18 0.64
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (10 bp):
AATTTTGGTA
Found at i:51695398 original size:16 final size:16
Alignment explanation
Indices: 51695379--51695426 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
51695369 TAACTGTTCT
51695379 AATCAATAACCTTTTC
1 AATCAATAACCTTTTC
*
51695395 AATCGATAACCTTTTC
1 AATCAATAACCTTTTC
* *
51695411 ATTGAA-AACCTTTTC
1 AATCAATAACCTTTTC
51695426 A
1 A
51695427 TCCTTTTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (16 bp):
AATCAATAACCTTTTC
Found at i:51695422 original size:15 final size:15
Alignment explanation
Indices: 51695386--51695428 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
51695376 TCTAATCAAT
*
51695386 AACCTTTTCAATCGAT
1 AACCTTTTC-ATCGAA
*
51695402 AACCTTTTCATTGAA
1 AACCTTTTCATCGAA
51695417 AACCTTTTCATC
1 AACCTTTTCATC
51695429 CTTTTCATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (15 bp):
AACCTTTTCATCGAA
Found at i:51708219 original size:51 final size:51
Alignment explanation
Indices: 51708135--51708327 Score: 192
Period size: 51 Copynumber: 3.8 Consensus size: 51
51708125 GATCAATGCT
* * *
51708135 ATCCGGTACACATAGTAGCCTACACTTAGTACTAAACATGTGACCACTA-CC
1 ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AAGCC
** * * * * *
51708186 ATCCGGTACATGTAGTAGCCTGCACATAATACTACACACGTGACGAAAGCT
1 ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAAGCC
* *
51708237 ATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAA-CT
1 ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-AAGCC
*** * * *
51708288 ATCTTATACTCATAGTAGCCTACACATAGTACTACACATG
1 ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATG
51708328 AGTTCTCATG
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.01
51 115 0.97
52 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (51 bp):
ATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAAGCC
Found at i:51708304 original size:102 final size:102
Alignment explanation
Indices: 51708132--51708325 Score: 266
Period size: 102 Copynumber: 1.9 Consensus size: 102
51708122 TATGATCAAT
*
51708132 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTAAACATGTGACCACTACCATCCGGTACAT
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTAAACATGTGACCACTACCATCCGATACAT
* *
51708197 GTAGTAGCCTGCACATAATACTACACACGTGACGAAA
66 ATAGTAGCCTACACATAATACTACACACGTGACGAAA
* * * * **
51708234 GCTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-TAACTATCTTATAC-
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTAAACATGTGACCACT-ACCATCCGATACA
*
51708297 TCATAGTAGCCTACACATAGTACTACACA
65 T-ATAGTAGCCTACACATAATACTACACA
51708326 TGAGTTCTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
101 2 0.03
102 78 0.98
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAGCCTACACTTAGTACTAAACATGTGACCACTACCATCCGATACAT
ATAGTAGCCTACACATAATACTACACACGTGACGAAA
Found at i:51711966 original size:25 final size:25
Alignment explanation
Indices: 51711909--51711955 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
51711899 TAGCTCTCAC
* *
51711909 GAGCTTCCCGTTATATGGTTCTTGT
1 GAGCTTCCCGTTATATAGCTCTTGT
51711934 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
51711956 CGGAGCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGT
Found at i:51712159 original size:25 final size:25
Alignment explanation
Indices: 51712139--51712187 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
51712129 ATTGGCTCGT
51712139 ATGAGCTTCCCGTTACATGGCTCAA
1 ATGAGCTTCCCGTTACATGGCTCAA
*
51712164 ATGAGCTTCCCGTTATATGGCTCA
1 ATGAGCTTCCCGTTACATGGCTCA
51712188 CAAGAGTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAA
Found at i:51716650 original size:22 final size:22
Alignment explanation
Indices: 51716606--51716655 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
51716596 TTTTTTTATA
*
51716606 TTTT-TTGTTTATTTCATTCAT
1 TTTTATTGTTTATGTCATTCAT
51716627 TTTTATTGATTTATGTC-TTCAT
1 TTTTATTG-TTTATGTCATTCAT
*
51716649 TTATATT
1 TTTTATT
51716656 TTAAAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.18, C:0.08, G:0.06, T:0.68
Consensus pattern (22 bp):
TTTTATTGTTTATGTCATTCAT
Found at i:51722701 original size:6 final size:6
Alignment explanation
Indices: 51722634--51722690 Score: 71
Period size: 6 Copynumber: 9.3 Consensus size: 6
51722624 TGATGATGGA
* *
51722634 AAAAAG GAAAAG AAAAAG -AAAAG AAAAAAG AAAAAG AAAACG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG
51722682 AAAGAAG AA
1 AAA-AAG AA
51722691 GAGGAAAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
5 5 0.11
6 29 0.66
7 10 0.23
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:51724004 original size:44 final size:44
Alignment explanation
Indices: 51723954--51724089 Score: 141
Period size: 44 Copynumber: 3.1 Consensus size: 44
51723944 AAACTCCAAC
51723954 CTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGAT
* ** * * * * * * *
51723998 CTTGTCTTCCT-ATATTGGCGGTGAAGTAGATCGAAGATACCAG-C
1 CTTGTCTCCCTGA-A-CAGCAGTGGAGTAGGTTGAAAATAGCAGAT
*
51724042 CTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGAT
51724086 CTTG
1 CTTG
51724090 CCTTCCTGTA
Statistics
Matches: 67, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
43 21 0.31
44 25 0.37
45 21 0.31
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (44 bp):
CTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGAT
Found at i:51724063 original size:88 final size:88
Alignment explanation
Indices: 51723953--51724124 Score: 308
Period size: 88 Copynumber: 2.0 Consensus size: 88
51723943 GAAACTCCAA
* *
51723953 CCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCG
1 CCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTATATTGGCA
51724018 GTGAAGTAGATCGAAGATACCAG
66 GTGAAGTAGATCGAAGATACCAG
* *
51724041 CCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTATTGGCA
1 CCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTATATTGGCA
51724106 GTGAAGTAGATCGAAGATA
66 GTGAAGTAGATCGAAGATA
51724125 TCAGTCTTAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (88 bp):
CCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTATATTGGCA
GTGAAGTAGATCGAAGATACCAG
Found at i:51724114 original size:45 final size:45
Alignment explanation
Indices: 51723970--51724114 Score: 150
Period size: 45 Copynumber: 3.3 Consensus size: 45
51723960 TCCCTGAACA
* *
51723970 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTG
1 GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* * * * * * * ***
51724015 GCGGTGAAGTAGATCGAAGATACCAG-CCTTGTCTCCCTG-AGCA
1 GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
* *
51724058 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTATTG
1 GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
51724103 GCAGTGAAGTAG
1 GCAGTGAAGTAG
51724115 ATCGAAGATA
Statistics
Matches: 73, Mismatches: 25, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
43 21 0.29
44 20 0.27
45 32 0.44
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (45 bp):
GCAGTGAAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATTG
Found at i:51724635 original size:267 final size:267
Alignment explanation
Indices: 51724154--51724693 Score: 778
Period size: 267 Copynumber: 2.0 Consensus size: 267
51724144 GTAGCAATGG
* * *
51724154 AAAAGATTGAAGCCACAACGGCGAATCTTATTTCCCTGGCGTTATAGCAGAGCAGATTGAAGCCA
1 AAAAGATTCAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTATAACAGAGCAGATTGAAGCCA
*
51724219 CGACGGCGAATCTTATCTCCCTGGAATTAAGGCTTGGATTAGCTGAAGTGGAGTGGATTGAAGCT
66 CGACGGCGAATCTTATCTCCCTGGAATTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCT
* * ** *
51724284 GTGGGCAGCGAATCCTATCTCTTTGGCATTACAGTGGAGCATATTAAGGCCGCAACGACGAATCT
131 GTGGGCAGCGAATCCTATCTCTTTGGCATTACAATGAAAAAGATTAAGGCCGCAACGACGAATCT
* * * * * *
51724349 TACTCCCCTGGCAGTGTAGTGGAATAGATTGAAGCTACGATGGTGGATCTTGTTTCCTCAACATT
196 TACTCCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTATTTCCCCAACATT
51724414 AT-AATTA
261 -TCAATTA
* * * *
51724421 AAAAGATTCAAGCCGCAACGGCGAATCTTACTTCCCTGGCGTTGTAACGGAGCAGATTTAAGCCA
1 AAAAGATTCAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTATAACAGAGCAGATTGAAGCCA
* * **
51724486 CGGCGGCGAATCTTATCTCCTTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCT
66 CGACGGCGAATCTTATCTCCCTGGAATTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCT
* * *
51724551 GTGGGCAGCGAATCCTATCTTTTTGGCATTACAATGAAAAAGATTGAA-GCCGGAACGGCGAATC
131 GTGGGCAGCGAATCCTATCTCTTTGGCATTACAATGAAAAAGATT-AAGGCCGCAACGACGAATC
* ** *
51724615 TTACTTCTTTGGCGGTGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTATTTCCCCAACAT
195 TTACTCCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTATTTCCCCAACAT
51724680 TTCAATTA
260 TTCAATTA
51724688 AAAAGA
1 AAAAGA
51724694 CTGAAGATGG
Statistics
Matches: 241, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
266 1 0.00
267 238 0.99
268 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (267 bp):
AAAAGATTCAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTATAACAGAGCAGATTGAAGCCA
CGACGGCGAATCTTATCTCCCTGGAATTAAGGCTTGGATTAGCTGAAGTGGAGCGGATTGAAGCT
GTGGGCAGCGAATCCTATCTCTTTGGCATTACAATGAAAAAGATTAAGGCCGCAACGACGAATCT
TACTCCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACAACGGTGAATCTTATTTCCCCAACATT
TCAATTA
Found at i:51724803 original size:44 final size:44
Alignment explanation
Indices: 51724707--51725169 Score: 217
Period size: 44 Copynumber: 10.6 Consensus size: 44
51724697 AAGATGGCGA
* * * ** *
51724707 ATCTTATCTCCCTAAAGTTGTAGTGAAGCAGATTAAAGCCA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA-G
* * *
51724751 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * * * *** *
51724795 ATCTTATCTCTCTAAAGTTGTAG-AGAGTAGA-TCGCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * *
51724836 -TCTTATCTCCCTGAAGTTGCAGTGGAGAAGACTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAG
* * **
51724880 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGATAATGGC-G
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAATCACAG
* ** *
51724923 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACA-G
* *
51724968 ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAATCCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAT-CACAG
* * * * * * *
51725012 ATCTTATCTCTCTGAAGTTGCTGTAGAGTAGA-TCACAT--CGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
* * * *
51725053 GTCTTATCTCCCTGAAGTTGCAGTGCAGCAGACTCAAGAAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TA-AAATCACAG
* * * * *
51725099 -TCTTATC-CCCTTGAAATTGCAGTGGGGCAGACT-AAATAAACAA
1 ATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTAAAAT-CACAG
* * *
51725142 ATCCTATCTCCCTAAAGTTGTAGTGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
51725170 TGGATTAGAA
Statistics
Matches: 306, Mismatches: 83, Indels: 60
0.68 0.18 0.13
Matches are distributed among these distances:
40 19 0.06
41 39 0.13
42 6 0.02
43 15 0.05
44 166 0.54
45 57 0.19
46 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAG
Found at i:51725160 original size:130 final size:129
Alignment explanation
Indices: 51724925--51725161 Score: 282
Period size: 130 Copynumber: 1.8 Consensus size: 129
51724915 TAATGGCGAA
* * * * *
51724925 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGCAGCAGACTAAAGCAAACAATCCTATCTCCCTAAAGTTGCA
* ** * * * *
51724990 GTGGAGCAGATTAAATCCACAGATCTTATCTCTCTGAAGTTGCTGTAGAGTAGATCACATCGGG
66 GTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTGCTGTAGAGTAGATCACATCGGG
* *
51725054 TCTTATCTCCCTGAAGTTGCAGTGCAGCAGACTCAAG-AAAGCAAGTCTTATC-CCCTTGAAA-T
1 TCTTATCTCCCTGAAGTTGCAGTGCAGCAGACTAAAGCAAA-CAA-TCCTATCTCCC-T-AAAGT
*
51725116 TGCAGTGGGGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTG
62 TGCAGTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTG
51725162 TAGTGGAGTG
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
128 2 0.02
129 38 0.43
130 46 0.52
131 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
TCTTATCTCCCTGAAGTTGCAGTGCAGCAGACTAAAGCAAACAATCCTATCTCCCTAAAGTTGCA
GTGGAGCAGACTAAATAAACAAATCCTATCTCCCTAAAGTTGCTGTAGAGTAGATCACATCGGG
Found at i:51725191 original size:174 final size:174
Alignment explanation
Indices: 51724879--51725200 Score: 395
Period size: 174 Copynumber: 1.9 Consensus size: 174
51724869 AAGTAAGCAA
* ** * *
51724879 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGATAATGGCGAATCTTATCTCCTTGAAGTTG
1 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTCATAAAAGCGAATCTTATCCCCTTGAAATTG
* * *
51724944 CAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATCCA
66 CAGTGGAGCAGACTAAAGCAAAAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATCCA
*
51725009 CAGATCTTATCTCTCTGAAGTTGCTGTAGAGTAGATCACATCGG
131 CAGATCTTATCTCGCTGAAGTTGCTGTAGAGTAGATCACATCGG
51725053 GTCTTAT-CTCCCTGAAGTTGCAGTGCA-GCAGACTCA-AGAAAGC-AAGTCTTATCCCCTTGAA
1 GTCTTATCCT-CCTGAAGTTGCAGTG-AGGCAGACTCATA-AAAGCGAA-TCTTATCCCCTTGAA
* * * **
51725114 ATTGCAGTGGGGCAGACTAAA-TAAACAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTAG
62 ATTGCAGTGGAGCAGACTAAAGCAAA-AAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTA-
* **
51725178 AAT-GATGGATCTTATCTCGCTGA
125 AATCCACAGATCTTATCTCGCTGA
51725201 GATTGTGGCA
Statistics
Matches: 125, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
173 7 0.06
174 114 0.91
175 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (174 bp):
GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTCATAAAAGCGAATCTTATCCCCTTGAAATTG
CAGTGGAGCAGACTAAAGCAAAAAATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAATCCA
CAGATCTTATCTCGCTGAAGTTGCTGTAGAGTAGATCACATCGG
Found at i:51726825 original size:28 final size:28
Alignment explanation
Indices: 51726763--51726823 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
51726753 CATATTTTTT
51726763 TTATTTAATAATTTTGATAATATAGATA
1 TTATTTAATAATTTTGATAATATAGATA
* *
51726791 TTATTTAATTATTTT-A-AATATATATA
1 TTATTTAATAATTTTGATAATATAGATA
51726817 TATATTT
1 T-TATTT
51726824 TATATGTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (28 bp):
TTATTTAATAATTTTGATAATATAGATA
Found at i:51727274 original size:10 final size:10
Alignment explanation
Indices: 51727251--51727317 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
51727241 ATTGTCATTG
51727251 TTTA-TTTT-
1 TTTATTTTTA
51727259 TTTATTTTTA
1 TTTATTTTTA
51727269 TTTATTTTTGA
1 TTTATTTTT-A
51727280 --TA--TTT-
1 TTTATTTTTA
51727285 TTTATTTTTA
1 TTTATTTTTA
51727295 TTTATTTTTGA
1 TTTATTTTT-A
*
51727306 TAT-TTTTTA
1 TTTATTTTTA
51727315 TTT
1 TTT
51727318 GATATTTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
7 5 0.10
8 4 0.08
9 12 0.25
10 23 0.48
11 4 0.08
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:51727288 original size:16 final size:15
Alignment explanation
Indices: 51727269--51727326 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
51727259 TTTATTTTTA
51727269 TTTATTTTTGATATTT
1 TTTA-TTTTGATATTT
51727285 TTTATTTT--TA-TT
1 TTTATTTTGATATTT
*
51727297 TAT-TTTTGATATTT
1 TTTATTTTGATATTT
51727311 TTTA-TTTGATATTT
1 TTTATTTTGATATTT
51727325 TT
1 TT
51727327 GCATTGTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 4 0.11
12 4 0.11
13 4 0.11
14 16 0.44
15 4 0.11
16 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTATTTTGATATTT
Found at i:51727292 original size:26 final size:26
Alignment explanation
Indices: 51727256--51727317 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
51727246 CATTGTTTAT
51727256 TTTTTTATTTTTATTTATTTTTGATA
1 TTTTTTATTTTTATTTATTTTTGATA
51727282 TTTTTTATTTTTATTTATTTTTGATA
1 TTTTTTATTTTTATTTATTTTTGATA
51727308 TTTTTTATTT
1 TTTTTTATTT
51727318 GATATTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (26 bp):
TTTTTTATTTTTATTTATTTTTGATA
Found at i:51727738 original size:19 final size:19
Alignment explanation
Indices: 51727716--51727752 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51727706 AAATTATATA
*
51727716 AAATTTTAAAATATAAAAG
1 AAATTATAAAATATAAAAG
*
51727735 AAATTATAAACTATAAAA
1 AAATTATAAAATATAAAA
51727753 ATATATCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATTATAAAATATAAAAG
Found at i:51732087 original size:30 final size:31
Alignment explanation
Indices: 51732022--51732088 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
51732012 AGTATCAAAT
* * **
51732022 TTTTTTATTTCTCCCATATTGGTACTTATGG
1 TTTTTTATTTATCCCAGATTGGTACTTATAC
51732053 TTTTTT-TTTATCCCAGATTGGTACTCTA-AC
1 TTTTTTATTTATCCCAGATTGGTACT-TATAC
51732083 TTTTTT
1 TTTTTT
51732089 CCCGTCAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.57
Consensus pattern (31 bp):
TTTTTTATTTATCCCAGATTGGTACTTATAC
Found at i:51735575 original size:27 final size:26
Alignment explanation
Indices: 51735545--51735614 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 26
51735535 GATTTTCCAG
*
51735545 AAAGGCGTTCCTTAAGATGTTCGCCAC
1 AAAGGCG-TCCTTAAGAGGTTCGCCAC
51735572 AAAGGCGTCCTTAAACAGAGGTTCGCCAC
1 AAAGGCGTCCTT--A-AGAGGTTCGCCAC
*
51735601 AAAGGTGTCCTTAA
1 AAAGGCGTCCTTAA
51735615 ACAAAGGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 6 0.16
27 8 0.21
28 1 0.03
29 23 0.61
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (26 bp):
AAAGGCGTCCTTAAGAGGTTCGCCAC
Found at i:51735633 original size:29 final size:29
Alignment explanation
Indices: 51735563--51735631 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
51735553 TCCTTAAGAT
*
51735563 GTTCGCCACAAAGGCGTCCTTAAACAGAG
1 GTTCGCCACAAAGGCGTCCTTAAACAAAG
*
51735592 GTTCGCCACAAAGGTGTCCTTAAACAAAG
1 GTTCGCCACAAAGGCGTCCTTAAACAAAG
51735621 GTT-GCCACAAA
1 GTTCGCCACAAA
51735632 AGCTTACCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 8 0.21
29 30 0.79
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (29 bp):
GTTCGCCACAAAGGCGTCCTTAAACAAAG
Found at i:51735641 original size:29 final size:29
Alignment explanation
Indices: 51735563--51735641 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
51735553 TCCTTAAGAT
* * *
51735563 GTTCGCCACAAAGGCGTCCTTAAACAGAG
1 GTTCGCCACAAAAGCTTCCTTAAACAAAG
*
51735592 GTTCGCCAC-AAAGGTGTCCTTAAACAAAG
1 GTTCGCCACAAAAGCT-TCCTTAAACAAAG
51735621 GTT-GCCACAAAAGCTTACCTT
1 GTTCGCCACAAAAGCTT-CCTT
51735642 TCCAGAGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 9 0.21
29 33 0.79
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (29 bp):
GTTCGCCACAAAAGCTTCCTTAAACAAAG
Found at i:51742374 original size:50 final size:50
Alignment explanation
Indices: 51742245--51742538 Score: 338
Period size: 50 Copynumber: 5.9 Consensus size: 50
51742235 GATAATAACA
* * ** * * * *
51742245 TGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*** * * * ** * *
51742294 TGCCAATTTCATATCCCAGATATGGCCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * **
51742344 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
* * *
51742394 TGCCAACGCCATGTCCTAGACATGGTTTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
51742444 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
*
51742494 TGCCAACGCCATGTCTCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
51742539 AATCTCAATG
Statistics
Matches: 209, Mismatches: 35, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
49 37 0.18
50 172 0.82
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:51753535 original size:57 final size:58
Alignment explanation
Indices: 51753455--51753565 Score: 145
Period size: 57 Copynumber: 1.9 Consensus size: 58
51753445 ATGTTCCTTA
* * * *
51753455 AGAGGTTCGCCATAAAGGCTTACCTTTCCAA-AGTTTTTCCGCAAAGGCATCCTTAAAT
1 AGAGGTTCGCCAAAAAAGCTTACCTTT-CAAGAGTTTTGCCACAAAGGCATCCTTAAAT
* *
51753513 AGAGGTT-GCCAAAAAAGCTTACCTTTTAAGAGTTTTGCCACAATGGCATCCTT
1 AGAGGTTCGCCAAAAAAGCTTACCTTTCAAGAGTTTTGCCACAAAGGCATCCTT
51753566 TACACTTAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 2 0.04
57 37 0.80
58 7 0.15
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (58 bp):
AGAGGTTCGCCAAAAAAGCTTACCTTTCAAGAGTTTTGCCACAAAGGCATCCTTAAAT
Found at i:51753836 original size:53 final size:52
Alignment explanation
Indices: 51753738--51753988 Score: 234
Period size: 53 Copynumber: 4.7 Consensus size: 52
51753728 CTTCCTTAAA
* * * ** *
51753738 CTTTCCCATATGATGCCACAACCCTCCAGTTACGACCTTACACGATATGGTCTT
1 CTTT-CCATATGATGCCATAACCC-ACAATTACGGTCTTACACGATATGGTATT
* * * ** *
51753792 CTTTCCATATGATGTCATAATCCACCATTAATAGTCTTAGACGATATGGTATT
1 CTTTCCATATGATGCCATAACCCACAATT-ACGGTCTTACACGATATGGTATT
* * * *
51753845 TTTTCCATATGATGCCACAACCCACTAGTTACGGTCTTACATGATATGGT-TT
1 CTTTCCATATGATGCCATAACCCAC-AATTACGGTCTTACACGATATGGTATT
* *
51753897 ACTTTCTATATGATGCCATAACCCATCAATTACGGTCTTACACGATATGATATT
1 -CTTTCCATATGATGCCATAACCCA-CAATTACGGTCTTACACGATATGGTATT
* * * *
51753951 TTTTCCATATGATGTCATAACCCATCAGTTACGATCTT
1 CTTTCCATATGATGCCATAACCCA-CAATTACGGTCTT
51753989 TGTAACACCT
Statistics
Matches: 159, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
52 5 0.03
53 145 0.91
54 9 0.06
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.35
Consensus pattern (52 bp):
CTTTCCATATGATGCCATAACCCACAATTACGGTCTTACACGATATGGTATT
Found at i:51753935 original size:106 final size:106
Alignment explanation
Indices: 51753743--51753988 Score: 309
Period size: 106 Copynumber: 2.3 Consensus size: 106
51753733 TTAAACTTTC
* * * *
51753743 CCATATGATGCCACAACCCTCCAGTTACGACCTTACACGATATGGTCTTCTTTCCATATGATGTC
1 CCATATGATGCCACAACCCACTAGTTACGATCTTACACGATATGGTCTTCTTTCCATATGATGCC
* * * * *
51753808 ATAATCCACCATTAATAGTCTTAGACGATATGGTATTTTTT
66 ATAACCCACAATTAACAGTCTTACACGATATGATATTTTTT
* * *
51753849 CCATATGATGCCACAACCCACTAGTTACGGTCTTACATGATATGGT-TTACTTTCTATATGATGC
1 CCATATGATGCCACAACCCACTAGTTACGATCTTACACGATATGGTCTT-CTTTCCATATGATGC
*
51753913 CATAACCCATCAATT-ACGGTCTTACACGATATGATATTTTTT
65 CATAACCCA-CAATTAACAGTCTTACACGATATGATATTTTTT
* *
51753955 CCATATGATGTCATAACCCA-TCAGTTACGATCTT
1 CCATATGATGCCACAACCCACT-AGTTACGATCTT
51753989 TGTAACACCT
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
105 3 0.02
106 114 0.94
107 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (106 bp):
CCATATGATGCCACAACCCACTAGTTACGATCTTACACGATATGGTCTTCTTTCCATATGATGCC
ATAACCCACAATTAACAGTCTTACACGATATGATATTTTTT
Found at i:51759967 original size:25 final size:25
Alignment explanation
Indices: 51759945--51760051 Score: 94
Period size: 25 Copynumber: 4.3 Consensus size: 25
51759935 GTATGCTCTC
51759945 ATGAGCTGTA-AATCGGTAAGCTCAT
1 ATGAGCTG-AGAATCGGTAAGCTCAT
* * *
51759970 ACGAGCTGAGGATCGGCAAGCTCAT
1 ATGAGCTGAGAATCGGTAAGCTCAT
*
51759995 ATGAGTTGAGAATCGGTAAGCTC-T
1 ATGAGCTGAGAATCGGTAAGCTCAT
* * *
51760019 CAAGAGCT-ACAAATCGATAAGCTCAT
1 -ATGAGCTGA-GAATCGGTAAGCTCAT
*
51760045 ACGAGCT
1 ATGAGCT
51760052 TTTTTAGAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.05
25 62 0.94
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (25 bp):
ATGAGCTGAGAATCGGTAAGCTCAT
Found at i:51761720 original size:24 final size:24
Alignment explanation
Indices: 51761671--51761724 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
51761661 CGAGACACTC
* *
51761671 ACTCAAGCTGCTACTAAAGCAACT
1 ACTCAACCTGCTACCAAAGCAACT
*
51761695 ACTCAACCTGCTACCACAA-CACCT
1 ACTCAACCTGCTACCA-AAGCAACT
51761719 ACTCAA
1 ACTCAA
51761725 AATGTTGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (24 bp):
ACTCAACCTGCTACCAAAGCAACT
Found at i:51766650 original size:3 final size:3
Alignment explanation
Indices: 51766644--51766674 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
51766634 ATCATCTTCT
*
51766644 GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
51766675 TAGTAGTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:51771250 original size:29 final size:28
Alignment explanation
Indices: 51771199--51771369 Score: 162
Period size: 29 Copynumber: 5.9 Consensus size: 28
51771189 AGTGTGCTAA
* *
51771199 TGATGGTTGAAACCATCTCTTTTCATAGT
1 TGATGG-TCAAACCATCCCTTTTCATAGT
* * * **
51771228 TTATAGTCTAAACTATCCCTTTTCATAAC
1 TGATGGTC-AAACCATCCCTTTTCATAGT
* *
51771257 CGATGGTCATCACCATCCCTTTTCATAGT
1 TGATGGTCA-AACCATCCCTTTTCATAGT
*
51771286 TGATGGTCATCACCATCCCTTTTCATAGT
1 TGATGGTCA-AACCATCCCTTTTCATAGT
* * *
51771315 TGATAGTCGAAACTATCCCTTTTCATAAT
1 TGATGGTC-AAACCATCCCTTTTCATAGT
*
51771344 TGATGGGCAAAACCATCCCTTTTCAT
1 TGATGGTC-AAACCATCCCTTTTCAT
51771370 TGATCAATGA
Statistics
Matches: 116, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
28 2 0.02
29 113 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.37
Consensus pattern (28 bp):
TGATGGTCAAACCATCCCTTTTCATAGT
Found at i:51771349 original size:87 final size:87
Alignment explanation
Indices: 51771210--51771369 Score: 248
Period size: 87 Copynumber: 1.8 Consensus size: 87
51771200 GATGGTTGAA
* * * * **
51771210 ACCATCTCTTTTCATAGTTTATAGTCTAAACTATCCCTTTTCATAACCGATGGTCATCACCATCC
1 ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAACCGATGGGCAAAACCATCC
51771275 CTTTTCATAGTTGATGGTCATC
66 CTTTTCATAGTTGATGGTCATC
**
51771297 ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAATTGATGGGCAAAACCATCC
1 ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAACCGATGGGCAAAACCATCC
51771362 CTTTTCAT
66 CTTTTCAT
51771370 TGATCAATGA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (87 bp):
ACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAACCGATGGGCAAAACCATCC
CTTTTCATAGTTGATGGTCATC
Found at i:51775222 original size:30 final size:30
Alignment explanation
Indices: 51775097--51775347 Score: 186
Period size: 30 Copynumber: 8.4 Consensus size: 30
51775087 TCATTGACCA
* ** ***
51775097 ATGAAAAGGGTTAGCTTCAACTATCGACCA
1 ATGAAAAGGGATAGCTTTGACTATCGAATT
* * ***
51775127 ATGAAAAGGGATAGCTTCGACTATTGACCA
1 ATGAAAAGGGATAGCTTTGACTATCGAATT
** *
51775157 ATGAAAAGGGATAGCTTCAATTATCGAATT
1 ATGAAAAGGGATAGCTTTGACTATCGAATT
* *
51775187 ATGAAAAGGGATAGCTTTGGCTATCAAATT
1 ATGAAAAGGGATAGCTTTGACTATCGAATT
* ** * *
51775217 GTGAAAAGGGATAG-TGACGACCATC-AATA
1 ATGAAAAGGGATAGCT-TTGACTATCGAATT
* ** * *
51775246 ATGAAAAGGGAT-GGTGAAGACCATCGAACT
1 ATGAAAAGGGATAGCT-TTGACTATCGAATT
51775276 ATGAAAAGGGATAGCTTTGACTATCGAATT
1 ATGAAAAGGGATAGCTTTGACTATCGAATT
* *
51775306 ATGAAAAGAGATAGCTTTTG-CTATCAAATT
1 ATGAAAAGGGATAGC-TTTGACTATCGAATT
*
51775336 ATGAGAAGGGAT
1 ATGAAAAGGGAT
51775348 GGTGAAAGGG
Statistics
Matches: 183, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.01
29 25 0.14
30 151 0.83
31 6 0.03
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTTGACTATCGAATT
Done.