Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 80 of 182
Found at i:25294455 original size:37 final size:38
Alignment explanation
Indices: 25294371--25294465 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
25294361 TTGCACCTAA
* *
25294371 AACTATCGCTGCATAAATATTCTTCAAATTGCATCTTG
1 AACTATCGCTGCATAAACATTCTTCAAATTGCATCTGG
* *
25294409 AACTATCGCTGCATAAGCATTCTT-AAATTGTATCTAGG
1 AACTATCGCTGCATAAACATTCTTCAAATTGCATCT-GG
* *
25294447 AA-TGTCGCTGCATGAACAT
1 AACTATCGCTGCATAAACAT
25294466 GTACAGAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 24 0.49
38 25 0.51
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (38 bp):
AACTATCGCTGCATAAACATTCTTCAAATTGCATCTGG
Found at i:25294501 original size:26 final size:26
Alignment explanation
Indices: 25294449--25294501 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
25294439 TATCTAGGAA
*
25294449 TGTCGCTGCATGAACATGTACAGAAT
1 TGTCGCTGCATGAACATGTACAAAAT
*
25294475 TGTCGCTGCATGAACATGTCCAAAAT
1 TGTCGCTGCATGAACATGTACAAAAT
25294501 T
1 T
25294502 ACGCCTAGAA
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:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAAAAT
Found at i:25295500 original size:40 final size:40
Alignment explanation
Indices: 25295445--25295523 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
25295435 GTCGGTAGAC
25295445 TGGAATTGTACTCTCGTGGTCAAGTAGTTAAATCCAAGAT
1 TGGAATTGTACTCTCGTGGTCAAGTAGTTAAATCCAAGAT
25295485 TGGAATTGTACTCTCGTGGTCAAGTAGTTAAATCCAAGA
1 TGGAATTGTACTCTCGTGGTCAAGTAGTTAAATCCAAGA
25295524 ATAAACAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (40 bp):
TGGAATTGTACTCTCGTGGTCAAGTAGTTAAATCCAAGAT
Found at i:25296695 original size:25 final size:26
Alignment explanation
Indices: 25296642--25296696 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
25296632 TGGCAATATA
**
25296642 TTTC-TTTTCTTCTCTTTTGTTCTTC
1 TTTCTTTTTCTTCTCTTTTGTGATTC
25296667 TTTCTTTTTCTT-TCTTTTTGTGATT-
1 TTTCTTTTTCTTCTC-TTTTGTGATTC
25296692 TTTCT
1 TTTCT
25296697 GTAAGTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (26 bp):
TTTCTTTTTCTTCTCTTTTGTGATTC
Found at i:25298334 original size:16 final size:17
Alignment explanation
Indices: 25298310--25298352 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
25298300 GGGCGCATTT
*
25298310 TCCTGCTTTTCCTTTT-
1 TCCTTCTTTTCCTTTTG
* *
25298326 TCTTTCTTTCCCTTTTG
1 TCCTTCTTTTCCTTTTG
25298343 TCCTTCTTTT
1 TCCTTCTTTT
25298353 TTATGCCTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.65
Consensus pattern (17 bp):
TCCTTCTTTTCCTTTTG
Found at i:25299533 original size:13 final size:15
Alignment explanation
Indices: 25299515--25299552 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
25299505 GCATAAGATT
25299515 TAAAAG-AAATAAG-
1 TAAAAGTAAATAAGA
25299528 TAAAAGTAAA-AAGA
1 TAAAAGTAAATAAGA
25299542 TAAAAGTAAAT
1 TAAAAGTAAAT
25299553 GTAAAAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (15 bp):
TAAAAGTAAATAAGA
Found at i:25299541 original size:20 final size:20
Alignment explanation
Indices: 25299516--25299559 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25299506 CATAAGATTT
25299516 AAAAGA-AATAAGTAAAAGTA
1 AAAAGATAA-AAGTAAAAGTA
*
25299536 AAAAGATAAAAGTAAATGTA
1 AAAAGATAAAAGTAAAAGTA
25299556 AAAA
1 AAAA
25299560 TGCGTTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAAGATAAAAGTAAAAGTA
Found at i:25307820 original size:14 final size:15
Alignment explanation
Indices: 25307796--25307829 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25307786 TTTTGGAATA
*
25307796 ATTTTTCAAAAAATC
1 ATTTTTAAAAAAATC
25307811 ATTTTTAAAAAAATC
1 ATTTTTAAAAAAATC
25307826 ATTT
1 ATTT
25307830 GAATCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTTAAAAAAATC
Found at i:25310636 original size:10 final size:10
Alignment explanation
Indices: 25310623--25310653 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
25310613 ATTTCTCTAA
*
25310623 ATTTTGATAT
1 ATTTTGAAAT
25310633 ATTTTGAAAT
1 ATTTTGAAAT
25310643 ATTTTGAAAT
1 ATTTTGAAAT
25310653 A
1 A
25310654 ATATTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (10 bp):
ATTTTGAAAT
Found at i:25315270 original size:16 final size:16
Alignment explanation
Indices: 25315249--25315279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25315239 ATAATGTGAA
25315249 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
25315265 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
25315280 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:25318008 original size:21 final size:21
Alignment explanation
Indices: 25317948--25318009 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
25317938 CTATGTGGCA
* *
25317948 AGTTAACTGGCCACATCAGCT
1 AGTTAACTTGCCACATCATCT
*
25317969 AATTAACTTGCCACATCATCT
1 AGTTAACTTGCCACATCATCT
25317990 AGTTAACTTGCCACATCATC
1 AGTTAACTTGCCACATCATC
25318010 ATGCCCATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (21 bp):
AGTTAACTTGCCACATCATCT
Found at i:25325336 original size:49 final size:49
Alignment explanation
Indices: 25325264--25325528 Score: 208
Period size: 49 Copynumber: 5.4 Consensus size: 49
25325254 GACTACGATG
* * ** *
25325264 AATCTTATACCTTAAAATCGAAGAGTTAGAGATTAAAGCCGCAATGATA
1 AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
*
25325313 AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATG
1 AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
* * * * * * * * *
25325362 AATTTTACACCGTAAAACTGAAGATGGAAAGATTAAAGTCACAA-AAAA
1 AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
* *** * * * * * *
25325410 GAATCTTACACCCTAAAATTAAAGAGGAAAAGATTAAATCCACAACGGTG
1 -AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
* * * * * * *
25325460 AATCTTACACCTTAGAACCGAAGAGGGAAAGATTAAAGCCGTAACGGTG
1 AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
* *
25325509 AATCTTACACCTTAAAACCG
1 AATCTTATACCCTAAAACCG
25325529 GCACGGTCAA
Statistics
Matches: 176, Mismatches: 38, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
48 1 0.01
49 175 0.99
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (49 bp):
AATCTTATACCCTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATGATA
Found at i:25325512 original size:98 final size:98
Alignment explanation
Indices: 25325258--25325527 Score: 279
Period size: 98 Copynumber: 2.8 Consensus size: 98
25325248 TTGGTGGACT
* * ** * * * *
25325258 ACGATGAATCTTATACCTTAAAATCGAAGAGTTAGAGATTAAAGCCGCAATGATAAATCTTATAC
1 ACGATGAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAAAGATGAATCTTACAC
* * *
25325323 CCTAAAACCGAAGAGGGAAAGATTAAAGCCGCA
66 CCTAAAACCAAAGAGGAAAAGATTAAAGCCACA
* * * * * * * * *
25325356 ATGATGAATTTTACACCGTAAAACTGAAGATGGAAAGATTAAAGTCACAAAAAAGAATCTTACAC
1 ACGATGAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAAAGATGAATCTTACAC
** *
25325421 CCTAAAATTAAAGAGGAAAAGATTAAATCCACA
66 CCTAAAACCAAAGAGGAAAAGATTAAAGCCACA
* * * * *
25325454 ACGGTGAATCTTACACCTTAGAACCGAAGAGGGAAAGATTAAAGCCGTAACGGTGAATCTTACAC
1 ACGATGAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAAAGATGAATCTTACAC
*
25325519 CTTAAAACC
66 CCTAAAACC
25325528 GGCACGGTCA
Statistics
Matches: 132, Mismatches: 40, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
98 132 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (98 bp):
ACGATGAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAAAGATGAATCTTACAC
CCTAAAACCAAAGAGGAAAAGATTAAAGCCACA
Found at i:25327219 original size:49 final size:49
Alignment explanation
Indices: 25326892--25327237 Score: 311
Period size: 49 Copynumber: 7.0 Consensus size: 49
25326882 ATCCTAAAGT
* * * ** *
25326892 CGAAGAGAGAAAGATTAAAGCCGCAATGACT-AATCTTATACTTTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCACAATGA-TGAATCTTACACCCTAAAAC
* * * *
25326941 CAAAGAGGGAAAAGATTAAAGCTACAATGATGAATCTTATACCCTAAAAT
1 CGAAGAGGG-AAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
** * * * *
25326991 CGAAGAGTTAAAAATTAAAGCCGCAATGATAAATCTTATACCCTAAAAC
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
* * * *
25327040 CG-AGAAGGCAAAGACTAAAGCCACAATGATGAATTTTACACCCTAAACC
1 CGAAG-AGGGAAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
* * ** * *
25327089 CGAAGATGGAAAGATTAAAGTCACAAAAAAGAATCTTACACCCTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
* * * * * *
25327138 TGAAGAGGAAAATATTAAAGCCACAA-CAGTGAATCGTACACCCTAGAAC
1 CGAAGAGGGAAAGATTAAAGCCACAATGA-TGAATCTTACACCCTAAAAC
* * * *
25327187 CGAAGAGGGAAAGATTAAAGCCGCAACGGTGAATCTTACACCTTAAAAC
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
25327236 CG
1 CG
25327238 GCATGGTCAG
Statistics
Matches: 239, Mismatches: 52, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.01
49 194 0.81
50 42 0.18
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.19
Consensus pattern (49 bp):
CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCCTAAAAC
Found at i:25328801 original size:49 final size:49
Alignment explanation
Indices: 25328619--25328951 Score: 289
Period size: 49 Copynumber: 6.8 Consensus size: 49
25328609 CGAAGAAAGG
* **
25328619 AAGATTAAAGCCGCAATGACT-AATCTTATACTTTAAAATCAAAGAGGGAA
1 AAGATTAAAGCCGCAATGA-TGAATCTTACACCCTAAAATCAAAGAGGG-A
** * * **
25328669 AAGATTAAAGCTACAAAGATGAATCTTATACCCTAAAATCAAAGAGTTA
1 AAGATTAAAGCCGCAATGATGAATCTTACACCCTAAAATCAAAGAGGGA
* * **
25328718 AAGATTAAAGCCGTAATGATAAATCCTT-TTCCCTAAAATCAAAGAGGGA
1 AAGATTAAAGCCGCAATGATGAAT-CTTACACCCTAAAATCAAAGAGGGA
* * *
25328767 AAGATTAAAGCCGCAATGATGAATTTTACACCCTAAAATCGAAGATGGA
1 AAGATTAAAGCCGCAATGATGAATCTTACACCCTAAAATCAAAGAGGGA
* * * * * * *
25328816 AAGATTAAAGTCACAAAGAAGAATCTTACACCCCAAAATTGAAA-AGGAA
1 AAGATTAAAGCCGCAATGATGAATCTTACACCCTAAAA-TCAAAGAGGGA
* * * * * *
25328865 AATATTAAAGCCACAACTG-TGAATCTTACACCTTAGAACCGAAA-AAGGA
1 AAGATTAAAGCCGCAA-TGATGAATCTTACACCCTAAAATC-AAAGAGGGA
* * *
25328914 AAGATTAAAGCCGCAATGGTGAATCTTGCACCTTAAAA
1 AAGATTAAAGCCGCAATGATGAATCTTACACCCTAAAA
25328952 CCGACACGGT
Statistics
Matches: 229, Mismatches: 47, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
48 4 0.02
49 179 0.78
50 46 0.20
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.22
Consensus pattern (49 bp):
AAGATTAAAGCCGCAATGATGAATCTTACACCCTAAAATCAAAGAGGGA
Found at i:25330654 original size:49 final size:49
Alignment explanation
Indices: 25330328--25330670 Score: 258
Period size: 49 Copynumber: 7.0 Consensus size: 49
25330318 ATCCTAAAGT
* * * * * *
25330328 CGAAGAGAGAAAGATTAAAGCCGCAATGA-GTTATCTTATACTTTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCACAATGATG-AATCTTACACCTTAAAAC
* ** * * *
25330377 C-ATAGAGGGAAAAGATTAAAGCTACAACCATGAATCTTATACCCTAAAAT
1 CGA-AGAGGG-AAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
* ** * *** * * *
25330427 TGAAGAGTTAAAGATTAAGGCCGTGATGATAAATCTTATACCTTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
** * * *
25330476 CGAAGAGGGAAAGATTAAAGCCGTAATAATGAATTTTACACCCTAAAAC
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
* * ** * * *
25330525 CGAAGATGGAAAGATTAAAGTCACAAACAAGAATCTTACACCCTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
* * * * *
25330574 TGAAGAGGGAAAGGTTAAAGCCACAACGGTGAATCTTACACCTTAGAAC
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
* * * *
25330623 CGAAGAGGGAAAGATTAAAGTCGCAATGGTGAATCTAACACCTTAAAA
1 CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAA
25330671 TCGGCACGAT
Statistics
Matches: 232, Mismatches: 58, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
48 1 0.00
49 194 0.84
50 35 0.15
51 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (49 bp):
CGAAGAGGGAAAGATTAAAGCCACAATGATGAATCTTACACCTTAAAAC
Found at i:25330656 original size:147 final size:147
Alignment explanation
Indices: 25330387--25330670 Score: 345
Period size: 147 Copynumber: 1.9 Consensus size: 147
25330377 CATAGAGGGA
* * * ** * ***
25330387 AAAGATTAAAGCTACAACCATGAATCTTATACCCTAAAATTGAAGAGTTAAAGATTAAGGCCGTG
1 AAAGATTAAAGCTACAAACAAGAATCTTACACCCTAAAATTGAAGAGGGAAAGATTAAAGCCACA
* * * * * *
25330452 ATGATAAATCTTATACCTTAAAATCGAAGAGGGAAAGATTAAAGCCGTAATAATGAATTTTACAC
66 ACGATAAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATAATGAATCTAACAC
25330517 CCTAAAACCGAAGATGG
131 CCTAAAACCGAAGATGG
*
25330534 AAAGATTAAAG-TCACAAACAAGAATCTTACACCCTAAAATTGAAGAGGGAAAGGTTAAAGCCAC
1 AAAGATTAAAGCT-ACAAACAAGAATCTTACACCCTAAAATTGAAGAGGGAAAGATTAAAGCCAC
* * * * **
25330598 AACGGTGAATCTTACACCTTAGAACCGAAGAGGGAAAGATTAAAGTCGCAATGGTGAATCTAACA
65 AACGATAAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATAATGAATCTAACA
*
25330663 CCTTAAAA
130 CCCTAAAA
25330671 TCGGCACGAT
Statistics
Matches: 113, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
146 1 0.01
147 112 0.99
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (147 bp):
AAAGATTAAAGCTACAAACAAGAATCTTACACCCTAAAATTGAAGAGGGAAAGATTAAAGCCACA
ACGATAAATCTTACACCTTAAAACCGAAGAGGGAAAGATTAAAGCCGCAATAATGAATCTAACAC
CCTAAAACCGAAGATGG
Found at i:25330657 original size:98 final size:98
Alignment explanation
Indices: 25330328--25330671 Score: 314
Period size: 98 Copynumber: 3.5 Consensus size: 98
25330318 ATCCTAAAGT
* * * * *
25330328 CGAAGAGAGAAAGATTAAAGCCGCAATGA-GTTATCTTATACTTTAAAA-TCATAGAGGGAAAAG
1 CGAAGAGGGAAAGATTAAAGCCGCAATGATG-AATCTTACACCTTAAAATTGA-AGAGGG-AAAG
* * * *
25330391 ATTAAAGCTACAACCATGAATCTTATACCCTAAAAT
63 ATTAAAGCCACAACAATGAATCTTACACCCTAAAAC
* ** * ** * * *
25330427 TGAAGAGTTAAAGATTAAGGCCGTGATGATAAATCTTATACCTTAAAATCGAAGAGGGAAAGATT
1 CGAAGAGGGAAAGATTAAAGCCGCAATGATGAATCTTACACCTTAAAATTGAAGAGGGAAAGATT
** * *
25330492 AAAGCCGTAATAATGAATTTTACACCCTAAAAC
66 AAAGCCACAACAATGAATCTTACACCCTAAAAC
* * * ** * * *
25330525 CGAAGATGGAAAGATTAAAGTCACAAACAAGAATCTTACACCCTAAAATTGAAGAGGGAAAGGTT
1 CGAAGAGGGAAAGATTAAAGCCGCAATGATGAATCTTACACCTTAAAATTGAAGAGGGAAAGATT
** * *
25330590 AAAGCCACAACGGTGAATCTTACACCTTAGAAC
66 AAAGCCACAACAATGAATCTTACACCCTAAAAC
* * *
25330623 CGAAGAGGGAAAGATTAAAGTCGCAATGGTGAATCTAACACCTTAAAAT
1 CGAAGAGGGAAAGATTAAAGCCGCAATGATGAATCTTACACCTTAAAAT
25330672 CGGCACGATC
Statistics
Matches: 191, Mismatches: 52, Indels: 5
0.77 0.21 0.02
Matches are distributed among these distances:
98 146 0.76
99 44 0.23
100 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (98 bp):
CGAAGAGGGAAAGATTAAAGCCGCAATGATGAATCTTACACCTTAAAATTGAAGAGGGAAAGATT
AAAGCCACAACAATGAATCTTACACCCTAAAAC
Found at i:25332275 original size:49 final size:49
Alignment explanation
Indices: 25332044--25332311 Score: 254
Period size: 49 Copynumber: 5.4 Consensus size: 49
25332034 TCCTAAAGTC
* *
25332044 GAAGAGGGAAAGATTAAAGGCGCAACGACT-AATCTTATACCTTAAAATT
1 GAAGAGGGAAAGATTAAAGCCGCAACGA-TGAATCTTATACCTTAAAACT
** * *
25332093 GAAGAGGGAAAAGATTAAAGCTACAATGATGAATCTTATACCCTAAAACT
1 GAAGAGGG-AAAGATTAAAGCCGCAACGATGAATCTTATACCTTAAAACT
** ** * *
25332143 GAAGAGCAAAAGATTAAAGTTGTAACGATGAATCTTATACCCTAAAA-T
1 GAAGAGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAAAACT
** * ** * * *
25332191 CGAAGAGGGAAAGATTAAAGTTGCAACAACAAATCTTACACCTTTAAACC
1 -GAAGAGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAAAACT
* * *
25332241 AAAGAGGGAAAGATTAAAGCCACAACGGTGAATCTT-TCACCTTAAAACT
1 GAAGAGGGAAAGATTAAAGCCGCAACGATGAATCTTAT-ACCTTAAAACT
**
25332290 GAAGAAAGAAAGATTAAAGCCG
1 GAAGAGGGAAAGATTAAAGCCG
25332312 TAATAGTGGA
Statistics
Matches: 177, Mismatches: 37, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
48 1 0.01
49 137 0.77
50 39 0.22
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (49 bp):
GAAGAGGGAAAGATTAAAGCCGCAACGATGAATCTTATACCTTAAAACT
Found at i:25332332 original size:147 final size:148
Alignment explanation
Indices: 25332035--25332339 Score: 375
Period size: 147 Copynumber: 2.1 Consensus size: 148
25332025 CACACCAAAT
* * * * ***
25332035 CCTAAAGTCGAAGAGGGAAAGATTAAAGGCGCAACGACTAATCTTATACCTTAAAATTGAAGAGG
1 CCTAAAATCGAAGAGGGAAAGATTAAAGGCGCAACAACAAATCTTACACCTTAAAACCAAAGAGG
* * * **
25332100 GAAAAGATTAAAGCTACAATGATGAATCTTATACCCTAAAACTGAAGAGCAAAAGATTAAAGTTG
66 GAAAAGATTAAAGCCACAACGATGAATCTTATACCCTAAAACTGAAGAGAAAAAGATTAAAGCCG
* *
25332165 TAACGATGAATCTTATAC
131 TAAAGATGAATCTTACAC
** *
25332183 CCTAAAATCGAAGAGGGAAAGATTAAAGTTGCAACAACAAATCTTACACCTTTAAACCAAAGAGG
1 CCTAAAATCGAAGAGGGAAAGATTAAAGGCGCAACAACAAATCTTACACCTTAAAACCAAAGAGG
* *
25332248 G-AAAGATTAAAGCCACAACGGTGAATCTT-TCACCTTAAAACTGAAGA-AAGAAAGATTAAAGC
66 GAAAAGATTAAAGCCACAACGATGAATCTTAT-ACCCTAAAACTGAAGAGAA-AAAGATTAAAGC
*
25332310 CGTAATAG-TGGATCTTACAC
129 CGTAA-AGATGAATCTTACAC
25332330 CCTAAAATCG
1 CCTAAAATCG
25332340 GCATGATCAA
Statistics
Matches: 134, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
146 2 0.01
147 75 0.56
148 57 0.43
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (148 bp):
CCTAAAATCGAAGAGGGAAAGATTAAAGGCGCAACAACAAATCTTACACCTTAAAACCAAAGAGG
GAAAAGATTAAAGCCACAACGATGAATCTTATACCCTAAAACTGAAGAGAAAAAGATTAAAGCCG
TAAAGATGAATCTTACAC
Found at i:25333814 original size:49 final size:49
Alignment explanation
Indices: 25333758--25334173 Score: 345
Period size: 49 Copynumber: 8.5 Consensus size: 49
25333748 TCTTACACCT
* * *
25333758 CAATGGTGAATCTTATACCTTAAAATTGAAGAGGGAAAAATTAAAGCCG
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * *
25333807 CAATGGTGAATCTTATACCTTAAAATTGAAGAGGGAAAAATTAAAGCCG
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * * * * * * *
25333856 AAACGATGAATCTTAAACCCTAAAATCAAAAAAGG-AAAGTTAAAGCCG
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * * * *
25333904 CAATGGTAAATATTACACCCTAAAATCGAAGAGGGGAAGATTAAAGCCA
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * * * *
25333953 TAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAGATTAAAGTCA
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * * * * * **
25334002 TAACGATAAATCTTACACCTTAAAACCGAAGAGGGAAGGATTAAAGCCG
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
* * ** *
25334051 CAACGATGAATCTTA-AGCCCTAAAATCGAA-A-AAAAGAAGATTAAAGCCA
1 CAATGGTGAATCTTACA-CCCTAAAATCGAAGAGGGAA-AA-ATTAAAGCCG
* * * * * * *
25334100 TAACGGTGAATCATACACCCTAAAATCGTAGAGGGACATATTAATGCCG
1 CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
*** *
25334149 CAATGACAAATCTTACACTCTAAAA
1 CAATGGTGAATCTTACACCCTAAAA
25334174 ATTGAAAAAG
Statistics
Matches: 297, Mismatches: 63, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
47 2 0.01
48 40 0.13
49 251 0.85
50 3 0.01
51 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (49 bp):
CAATGGTGAATCTTACACCCTAAAATCGAAGAGGGAAAAATTAAAGCCG
Found at i:25334117 original size:147 final size:146
Alignment explanation
Indices: 25333797--25334173 Score: 407
Period size: 147 Copynumber: 2.6 Consensus size: 146
25333787 AGAGGGAAAA
** * *
25333797 ATTAAAGCCGCAATGGTGAATCTTATACCTTAAAATTGAAGAGGGAAAAATTAAAGCCGAAACGA
1 ATTAAAGCCATAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAAATTAAAGCCGAAACGA
* * * *
25333862 TGAATCTTAAACCCTAAAATCAAAAAAGGAAAGTTAAAGCCGCAATGGTAAATATTACACCCTAA
66 TAAATCTTAAACCCTAAAACCAAAAAAGGAAAGTTAAAGCCGCAACGATAAATATTACACCCTAA
* ***
25333927 AATCGAAGAGGGGAAG
131 AATCGAAAAAAAGAAG
* *
25333943 ATTAAAGCCATAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAGATTAAAGTC-ATAACG
1 ATTAAAGCCATAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAAATTAAAGCCGA-AACG
* * * * * * * *
25334007 ATAAATCTTACACCTTAAAACCGAAGAGGGAAGGATTAAAGCCGCAACGATGAATCTTA-AGCCC
65 ATAAATCTTAAACCCTAAAACCAAAAAAGGAAAG-TTAAAGCCGCAACGATAAATATTACA-CCC
25334071 TAAAATCGAAAAAAAGAAG
128 TAAAATCGAAAAAAAGAAG
* * * * * * * * *
25334090 ATTAAAGCCATAACGGTGAATCATACACCCTAAAATCGTAGAGGGACATATTAATGCCGCAATGA
1 ATTAAAGCCATAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAAATTAAAGCCGAAACGA
* * *
25334155 CAAATCTTACACTCTAAAA
66 TAAATCTTAAACCCTAAAA
25334174 ATTGAAAAAG
Statistics
Matches: 192, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
145 1 0.01
146 83 0.43
147 108 0.56
ACGTcount: A:0.45, C:0.17, G:0.18, T:0.20
Consensus pattern (146 bp):
ATTAAAGCCATAATGGTGAATCTTACACCCTAAAATTGAAGAGGGAAAAATTAAAGCCGAAACGA
TAAATCTTAAACCCTAAAACCAAAAAAGGAAAGTTAAAGCCGCAACGATAAATATTACACCCTAA
AATCGAAAAAAAGAAG
Found at i:25334439 original size:45 final size:45
Alignment explanation
Indices: 25334278--25334615 Score: 311
Period size: 45 Copynumber: 7.4 Consensus size: 45
25334268 CTTAAAACTG
* *
25334278 TAGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACTCCTAAT-
1 TAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
* ** * *
25334322 TCAAAAAGGTAGATTGAAGACACCAAATCCAATCTTTTACCCCTAAT-
1 T-AGAGGGGCAGATTGAAGCCACC--ATCCAATCTTTTACCCCTAATC
* * * * * ** * *
25334369 TCGGAGGGCCATATTGATGCTACCATTGAATCTTGTACCCTTAATC
1 T-AGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
* * **
25334415 CAGAGGGGCAGATTAAAGCCACCATCCTGTCTTTTACCCCTAATC
1 TAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
* * **
25334460 TAGAGGGGCAGATTGAAGTCATCAAATCCAATCTTTTATACCTAATC
1 TAGAGGGGCAGATTGAAGCCA-C-CATCCAATCTTTTACCCCTAATC
* * * * *
25334507 TAGAGGAGTAGATTGAAGTCATCATCCAATCTTTTACCCTTAATC
1 TAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
* * *
25334552 TAGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACCCCTAATC
1 TAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
*
25334597 TAGAAGGGCAGATTGAAGC
1 TAGAGGGGCAGATTGAAGC
25334616 TACAACAGCA
Statistics
Matches: 229, Mismatches: 59, Indels: 11
0.77 0.20 0.04
Matches are distributed among these distances:
44 1 0.00
45 156 0.68
46 1 0.00
47 71 0.31
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (45 bp):
TAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATC
Found at i:25334512 original size:92 final size:90
Alignment explanation
Indices: 25334278--25334615 Score: 306
Period size: 92 Copynumber: 3.7 Consensus size: 90
25334268 CTTAAAACTG
* * * * ** * *
25334278 TAGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACTCCTAAT-TCAAAAAGGTAGATTGAAGA
1 TAGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACACCTAATCT-AGAGGGGCAGATTGAAGC
25334342 CACCAAATCCAATCTTTTACCCCTAAT-
65 CACC--ATCCAATCTTTTACCCCTAATC
* * * * * * ** * * *
25334369 TCGGAGGGCCATATTGATGCTACCATTGAATCTTGTAC-CCTTAATCCAGAGGGGCAGATTAAAG
1 T-AGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACACC-TAATCTAGAGGGGCAGATTGAAG
**
25334433 CCACCATCCTGTCTTTTACCCCTAATC
64 CCACCATCCAATCTTTTACCCCTAATC
* * * *
25334460 TAGAGGGGCAGATTGAAG-TCATCAAATCCAATCTTTTATACCTAATCTAGAGGAGTAGATTGAA
1 TAGAGGGGCAGATTAAAGCT-A-C-AATCCAATCTTTTACACCTAATCTAGAGGGGCAGATTGAA
* * *
25334524 GTCATCATCCAATCTTTTACCCTTAATC
63 GCCACCATCCAATCTTTTACCCCTAATC
* *
25334552 TAGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACCCCTAATCTAGAAGGGCAGATTGAAGC
1 TAGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACACCTAATCTAGAGGGGCAGATTGAAGC
25334616 TACAACAGCA
Statistics
Matches: 195, Mismatches: 43, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
89 1 0.01
90 69 0.35
91 6 0.03
92 116 0.59
93 3 0.02
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (90 bp):
TAGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACACCTAATCTAGAGGGGCAGATTGAAGCC
ACCATCCAATCTTTTACCCCTAATC
Found at i:25334538 original size:137 final size:137
Alignment explanation
Indices: 25334279--25334614 Score: 410
Period size: 137 Copynumber: 2.5 Consensus size: 137
25334269 TTAAAACTGT
* * * *
25334279 AGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACTCCTAAT-TCAAAAAGGTAGATTGAAGAC
1 AGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCT-AGAAGGGCAGATTGAAGAC
* * * * **
25334343 ACCAAATCCAATCTTTTACCCCTAATTCGGAGGGCCATATTGATGCTACCATTGAATCTTGTACC
65 ACCAAATCCAATCTTTTACACCTAATTCAGAGGGCCAGATTGAAGCTACCATCCAATCTTGTACC
25334408 CTTAATCC
130 CTTAATCC
** * *
25334416 AGAGGGGCAGATTAAAGCCACCATCCTGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGTCA
1 AGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCTAGAAGGGCAGATTGAAGACA
* * * * *
25334481 TCAAATCCAATCTTTTATACCTAA-TCTAGAGGAG-TAGATTGAAG-TCATCATCCAATCTTTTA
66 CCAAATCCAATCTTTTACACCTAATTC-AGAGG-GCCAGATTGAAGCT-ACCATCCAATCTTGTA
*
25334543 CCCTTAATCT
128 CCCTTAATCC
* *
25334553 AGAGGGGCAGATTAAAGCTACAATCCAATCTTTTACCCCTAATCTAGAAGGGCAGATTGAAG
1 AGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCTAGAAGGGCAGATTGAAG
25334615 CTACAACAGC
Statistics
Matches: 170, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
136 3 0.02
137 165 0.97
138 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (137 bp):
AGAGGGGCAGATTAAAGCCACCATCCAATCTTTTACCCCTAATCTAGAAGGGCAGATTGAAGACA
CCAAATCCAATCTTTTACACCTAATTCAGAGGGCCAGATTGAAGCTACCATCCAATCTTGTACCC
TTAATCC
Found at i:25335505 original size:16 final size:16
Alignment explanation
Indices: 25335486--25335528 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
25335476 TTTTAGCATT
* *
25335486 TTTACTTATTTTTTTG
1 TTTATTTATTTTGTTG
*
25335502 TTTATTTATCTTGTTG
1 TTTATTTATTTTGTTG
25335518 -TTATTTATTTT
1 TTTATTTATTTT
25335529 CATGTCATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTATTTATTTTGTTG
Found at i:25335556 original size:100 final size:99
Alignment explanation
Indices: 25335347--25335535 Score: 235
Period size: 98 Copynumber: 1.9 Consensus size: 99
25335337 TTCGTCTTTT
25335347 TATTATTATTATTTATATTTAGTTGTTTATTTTGACATTTAATTTACTGATTTTTTGTTTATTTA
1 TATT-TTATTATTTATATTTAGTTGTTTATTTTGACATTT-ATTTACTGATTTTTTGTTTATTTA
25335412 TTTATTCTCCATTTATTTTCATGTCTAATCCCAATTA
64 TTTATTCTCCATTTATTTTCATGTC-AATCCCAATTA
* * *
25335449 T-TTTTATTGTTTATATTTATTTGTTTATTTT-AGCA-TT-TTTACTTATTTTTTTGTTTATTTA
1 TATTTTATTATTTATATTTAGTTGTTTATTTTGA-CATTTATTTACTGA-TTTTTTGTTTATTTA
* * *
25335510 TCTTGTTGT-TATTTATTTTCATGTCA
64 T-TTATTCTCCATTTATTTTCATGTCA
25335536 TCTCTTTTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
97 8 0.10
98 31 0.40
99 8 0.10
100 28 0.36
101 2 0.03
102 1 0.01
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.64
Consensus pattern (99 bp):
TATTTTATTATTTATATTTAGTTGTTTATTTTGACATTTATTTACTGATTTTTTGTTTATTTATT
TATTCTCCATTTATTTTCATGTCAATCCCAATTA
Found at i:25335731 original size:16 final size:16
Alignment explanation
Indices: 25335684--25335731 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
25335674 GATATTTTTA
25335684 TTATTGCATTTCATATAT
1 TTATT-CATTT-ATATAT
* *
25335702 TTATTCATTGATATTT
1 TTATTCATTTATATAT
*
25335718 TTATTTATTTATAT
1 TTATTCATTTATAT
25335732 GTCATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 17 0.65
17 4 0.15
18 5 0.19
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (16 bp):
TTATTCATTTATATAT
Found at i:25335845 original size:4 final size:4
Alignment explanation
Indices: 25335836--25335861 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25335826 TGCTTATACT
25335836 ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA AT
25335862 ATTTATTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:25335965 original size:18 final size:18
Alignment explanation
Indices: 25335928--25335979 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
25335918 TTTTATTGTG
*
25335928 TTATTAATTGTATTTAATT
1 TTATTAATT-TATTTTATT
25335947 TTATTAATTTATTTTATT
1 TTATTAATTTATTTTATT
* *
25335965 TTATTCATGTATTTT
1 TTATTAATTTATTTT
25335980 TTATTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 21 0.70
19 9 0.30
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TTATTAATTTATTTTATT
Found at i:25351240 original size:30 final size:30
Alignment explanation
Indices: 25351204--25351262 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
25351194 ATTATTGATA
* *
25351204 AAAAAATCAACACAT-TAATATTTTATACAT
1 AAAAAATCAACAAATCAAATA-TTTATACAT
*
25351234 AAAAAATTAACAAATCAAATATTTATACA
1 AAAAAATCAACAAATCAAATATTTATACA
25351263 CCATAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (30 bp):
AAAAAATCAACAAATCAAATATTTATACAT
Found at i:25351255 original size:31 final size:30
Alignment explanation
Indices: 25351220--25351277 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
25351210 TCAACACATT
*
25351220 AATATTTTATACATAAAAAATTAACAAATCA
1 AATA-TTTATACACAAAAAATTAACAAATCA
* *
25351251 AATATTTATACACCATAAATTAACAAA
1 AATATTTATACACAAAAAATTAACAAA
25351278 AATTAGCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (30 bp):
AATATTTATACACAAAAAATTAACAAATCA
Found at i:25355213 original size:15 final size:15
Alignment explanation
Indices: 25355193--25355226 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25355183 AGTAGAAATA
25355193 AAAACAAAAAAAGAC
1 AAAACAAAAAAAGAC
* *
25355208 AAAACAAATAATGAC
1 AAAACAAAAAAAGAC
25355223 AAAA
1 AAAA
25355227 AATTCCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.12, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAACAAAAAAAGAC
Found at i:25373581 original size:23 final size:23
Alignment explanation
Indices: 25373556--25373605 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 23
25373546 TGATTGTGCA
25373556 TTTAGGAATAGAATTTGGTTTTAT
1 TTTA-GAATAGAATTTGGTTTTAT
*
25373580 TTTAGAATAGAATTTGGTTTTCT
1 TTTAGAATAGAATTTGGTTTTAT
25373603 TTT
1 TTT
25373606 TATTTTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (23 bp):
TTTAGAATAGAATTTGGTTTTAT
Found at i:25374407 original size:30 final size:31
Alignment explanation
Indices: 25374371--25374432 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
25374361 TGTCTCTCCC
25374371 ATTGGTTACTTCCTTATAGCTTGAGT-AAAA
1 ATTGGTTACTTCCTTATAGCTTGAGTCAAAA
* *
25374401 ATTGGTTACTTCTTTATGGCTTGAGTCAAAA
1 ATTGGTTACTTCCTTATAGCTTGAGTCAAAA
25374432 A
1 A
25374433 GATCAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (31 bp):
ATTGGTTACTTCCTTATAGCTTGAGTCAAAA
Found at i:25378600 original size:52 final size:52
Alignment explanation
Indices: 25378536--25378827 Score: 397
Period size: 52 Copynumber: 5.6 Consensus size: 52
25378526 TTGTAATTTA
* * *
25378536 ATACTCATGATGACACATAGTCATCGGACCTCATAATCTGTAAAAGATTCAA
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* *
25378588 ATACTCACGATGACACATAATCATCGGACCTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* *
25378640 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAAAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
** * * * * *
25378692 ATACTCATAATGACACATAATAATCGAACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* * *
25378744 ATACTCACGATGACATATAGTCATCGAAACTCGA-AATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTC-ATAATCCGTAAAAGATTCAT
*
25378796 ATAACTCACGATGACACAGAGTCATCGGACCT
1 AT-ACTCACGATGACACATAGTCATCGGACCT
25378828 TTTGCATTTA
Statistics
Matches: 208, Mismatches: 30, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
52 182 0.88
53 26 0.12
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
Found at i:25380140 original size:16 final size:16
Alignment explanation
Indices: 25380119--25380159 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
25380109 TGTTTCGGCT
25380119 AAGAAAGAAGAAGATG
1 AAGAAAGAAGAAGATG
25380135 AAGAAAGAAGAAGATG
1 AAGAAAGAAGAAGATG
25380151 AAGAAAGAA
1 AAGAAAGAA
25380160 ATAAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (16 bp):
AAGAAAGAAGAAGATG
Found at i:25387445 original size:28 final size:28
Alignment explanation
Indices: 25387380--25387477 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
25387370 ATGCTAGAAG
* * * *
25387380 TGAAATGAAAGTCTTTGTGACGAACCTC
1 TGAAAAGAAAGCCTTTGTGGCAAACCTC
*
25387408 T-AAAAGGAAAGCCTTTGTGGCAAACCTT
1 TGAAAA-GAAAGCCTTTGTGGCAAACCTC
* * * *
25387436 TGAAAAGAAAACCCTTGTGGTGAATCC-C
1 TGAAAAGAAAGCCTTTGTGG-CAAACCTC
*
25387464 TGAAAAGAAGGCCT
1 TGAAAAGAAAGCCT
25387478 ATATGGTGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
27 3 0.06
28 43 0.80
29 8 0.15
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23
Consensus pattern (28 bp):
TGAAAAGAAAGCCTTTGTGGCAAACCTC
Found at i:25389699 original size:15 final size:15
Alignment explanation
Indices: 25389672--25389704 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
25389662 TTTGAGATAT
25389672 ATAATTATTTTTTTA
1 ATAATTATTTTTTTA
25389687 ATAA-TATTATTTTTA
1 ATAATTATT-TTTTTA
25389702 ATA
1 ATA
25389705 TTTAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAATTATTTTTTTA
Found at i:25412863 original size:17 final size:16
Alignment explanation
Indices: 25412833--25412883 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
25412823 ATAGCAAACA
25412833 TTTTTTTTCTTCTTTTC
1 TTTTTTTTC-TCTTTTC
25412850 TTTTCTTTTCTCTTTTC
1 TTTT-TTTTCTCTTTTC
25412867 TTTTTCTTTCT-TTTTC
1 TTTTT-TTTCTCTTTTC
25412883 T
1 T
25412884 CATTTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.22
17 20 0.62
18 5 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTCTTTTC
Found at i:25412875 original size:23 final size:25
Alignment explanation
Indices: 25412845--25412897 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
25412835 TTTTTTCTTC
25412845 TTTTCTTT-TCTTTTCTC-TTTT-CT
1 TTTTCTTTCT-TTTTCTCATTTTGCT
25412868 TTTTCTTTCTTTTTCTCATTTTGCT
1 TTTTCTTTCTTTTTCTCATTTTGCT
25412893 TTTTC
1 TTTTC
25412898 AAGTGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 15 0.56
24 5 0.19
25 7 0.26
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTCTTTCTTTTTCTCATTTTGCT
Found at i:25412881 original size:10 final size:10
Alignment explanation
Indices: 25412836--25412883 Score: 55
Period size: 10 Copynumber: 4.7 Consensus size: 10
25412826 GCAAACATTT
25412836 TTTTTC-TTC
1 TTTTTCTTTC
25412845 -TTTTCTTTTC
1 TTTTTC-TTTC
25412855 TTTTCTCTTTTC
1 TTTT-TC-TTTC
25412867 TTTTTCTTTC
1 TTTTTCTTTC
25412877 TTTTTCT
1 TTTTTCT
25412884 CATTTTGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 5 0.14
10 14 0.40
11 5 0.14
12 11 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:25415032 original size:14 final size:12
Alignment explanation
Indices: 25415013--25415046 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
25415003 AAAAGATAAC
25415013 AAGTAAAAGCGAA
1 AAGTAAAAG-GAA
25415026 AAGGTAAAAGGAA
1 AA-GTAAAAGGAA
25415039 AAGTAAAA
1 AAGTAAAA
25415047 TGCGTTGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 7 0.35
14 7 0.35
ACGTcount: A:0.65, C:0.03, G:0.24, T:0.09
Consensus pattern (12 bp):
AAGTAAAAGGAA
Found at i:25420935 original size:15 final size:15
Alignment explanation
Indices: 25420901--25420939 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
25420891 CCTCGACAGG
25420901 TTCTTT-TTCTT-CT
1 TTCTTTCTTCTTCCT
25420914 TTC--TCTTCTTCCT
1 TTCTTTCTTCTTCCT
25420927 TTCTTTCTTCTTC
1 TTCTTTCTTCTTC
25420940 TTCTTCTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.05
12 5 0.23
13 8 0.36
15 8 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTCTTCTTCCT
Found at i:25420953 original size:27 final size:26
Alignment explanation
Indices: 25420901--25420954 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
25420891 CCTCGACAGG
*
25420901 TTCTTTTTCTTCTTTCTCTTCTTCCT
1 TTCTTTTTCTTCTTTCTCTTCATCCT
*
25420927 TTCTTTCTTCTTC-TTCTTCTTGATCCT
1 TTCTTT-TTCTTCTTTC-TCTTCATCCT
25420954 T
1 T
25420955 CCCCTTCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.67
Consensus pattern (26 bp):
TTCTTTTTCTTCTTTCTCTTCATCCT
Found at i:25433986 original size:37 final size:37
Alignment explanation
Indices: 25433936--25434019 Score: 150
Period size: 37 Copynumber: 2.3 Consensus size: 37
25433926 TGTTCAATGT
*
25433936 TGTCACCGCAATTTTAATCCAAAATTGCGCCCAAACA
1 TGTCACCGCAATTTTAATCCAAAATTGCACCCAAACA
*
25433973 TGTCACCGCAATTTTAATCCAAAGTTGCACCCAAACA
1 TGTCACCGCAATTTTAATCCAAAATTGCACCCAAACA
25434010 TGTCACCGCA
1 TGTCACCGCA
25434020 TGAGAACTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (37 bp):
TGTCACCGCAATTTTAATCCAAAATTGCACCCAAACA
Found at i:25434194 original size:26 final size:26
Alignment explanation
Indices: 25434159--25434213 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
25434149 CACCTAGGAA
*
25434159 TGTCGTTGCATGAACATGTACAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
* *
25434185 TGTCGCTGCATGAACGTGTTCAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
25434211 TGT
1 TGT
25434214 GCCCAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAGAAT
Found at i:25437174 original size:23 final size:23
Alignment explanation
Indices: 25437148--25437288 Score: 118
Period size: 23 Copynumber: 6.4 Consensus size: 23
25437138 AGTGTTGGCC
25437148 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
25437171 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
25437190 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * * *
25437210 ATCAGAGTGCATACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
25437233 ATCAGAGAGCAC-CGAAGTGCAAA
1 AACAGAGAGCACACAAAGTGC-TA
*
25437256 TAACAGAGAGCACACACAGTGCTA
1 -AACAGAGAGCACACAAAGTGCTA
25437280 AACAGAGAG
1 AACAGAGAG
25437289 TGCGCTAGTG
Statistics
Matches: 93, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
16 10 0.11
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 8 0.09
23 50 0.54
24 12 0.13
25 6 0.06
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:25443162 original size:26 final size:26
Alignment explanation
Indices: 25443114--25443206 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
25443104 CGAAGTACTG
* * *
25443114 AACAAAGAGCACA-TAAGTTCTAGCC
1 AACAGAGAGCACACAAAGTGCTAGCC
*
25443139 AGCAGAGAGCACACAAAGTGCTAGCC
1 AACAGAGAGCACACAAAGTGCTAGCC
25443165 AACAGAGAGCACACAAAGTGCTA---
1 AACAGAGAGCACACAAAGTGCTAGCC
*
25443188 AACAGAGAGTACACAAAGT
1 AACAGAGAGCACACAAAGT
25443207 ACTGAGCACA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 18 0.30
25 11 0.18
26 32 0.52
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (26 bp):
AACAGAGAGCACACAAAGTGCTAGCC
Found at i:25443195 original size:23 final size:23
Alignment explanation
Indices: 25443141--25443306 Score: 150
Period size: 23 Copynumber: 7.3 Consensus size: 23
25443131 TTCTAGCCAG
25443141 CAGAGAGCACACAAAGTGCTAGCCAA
1 CAGAGAGCACACAAAGTGCTA---AA
25443167 CAGAGAGCACACAAAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
*
25443190 CAGAGAGTACACAAA--G-T--A
1 CAGAGAGCACACAAAGTGCTAAA
* *
25443208 C--TGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* * *
25443229 TAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
25443252 CAAAGAGCAC-CGAAGTGCTAATAA
1 CAGAGAGCACACAAAGTGCT-A-AA
*
25443276 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
25443299 CAGAGAGC
1 CAGAGAGC
25443307 GCGCTAGTGT
Statistics
Matches: 117, Mismatches: 13, Indels: 23
0.76 0.08 0.15
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 1 0.01
22 9 0.08
23 53 0.45
24 11 0.09
25 7 0.06
26 21 0.18
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:25443225 original size:39 final size:39
Alignment explanation
Indices: 25443171--25443245 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
25443161 AGCCAACAGA
*
25443171 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
** *
25443210 GAGCACACAAAGTGCTAATTAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
25443246 GCTAATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:25448216 original size:30 final size:30
Alignment explanation
Indices: 25448167--25448296 Score: 101
Period size: 29 Copynumber: 4.4 Consensus size: 30
25448157 AAGGTTAAAC
*
25448167 GTAATTTT-GGAAACTTTTAGGGGTAAAAAT
1 GTAATTTTAGGAAA-ATTTAGGGGTAAAAAT
*
25448197 GTTATTTTAGGAAAATTTA-GGGTAAAAAT
1 GTAATTTTAGGAAAATTTAGGGGTAAAAAT
* *
25448226 GTGATTTTTA--AAAA-TTAGGGGGCAAAAAT
1 GT-AATTTTAGGAAAATTTA-GGGGTAAAAAT
* * * * *
25448255 GTAATTTTTGG-AAGTTCAAGGGCAAAAAT
1 GTAATTTTAGGAAAATTTAGGGGTAAAAAT
*
25448284 GTAATTTTTGGAA
1 GTAATTTTAGGAA
25448297 GTTTGAGGAC
Statistics
Matches: 82, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
27 3 0.04
28 9 0.11
29 46 0.56
30 19 0.23
31 5 0.06
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
GTAATTTTAGGAAAATTTAGGGGTAAAAAT
Found at i:25448277 original size:29 final size:28
Alignment explanation
Indices: 25448245--25448349 Score: 129
Period size: 29 Copynumber: 3.6 Consensus size: 28
25448235 AAAAATTAGG
*
25448245 GGGCAAAAATGTAATTTTTGGAAGTTCAA
1 GGGC-AAAATGTAATTTTTGGAAGTTCGA
*
25448274 GGGCAAAAATGTAATTTTTGGAAGTTTGA
1 GGGC-AAAATGTAATTTTTGGAAGTTCGA
* *
25448303 GGACAAAATGTAATTTTTAAGAAGTTCGA
1 GGGCAAAATGTAATTTTT-GGAAGTTCGA
*
25448332 GGGTCAAAATGTGATTTT
1 GGG-CAAAATGTAATTTT
25448350 GAGAAAGTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 14 0.21
29 40 0.60
30 13 0.19
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (28 bp):
GGGCAAAATGTAATTTTTGGAAGTTCGA
Found at i:25448282 original size:58 final size:58
Alignment explanation
Indices: 25448215--25448349 Score: 148
Period size: 58 Copynumber: 2.3 Consensus size: 58
25448205 AGGAAAATTT
* * * *
25448215 AGGGTAAAAATGTGATTTTTAAAAATTAGGGGGCAAAAATGTAATTTTT-GGAAGTTCA
1 AGGGCAAAAATGTGATTTTTAAAAATTAGAGGAC-AAAATGTAATTTTTAAGAAGTTCA
* ** * * *
25448273 AGGGCAAAAATGTAATTTTTGGAAGTTTGAGGACAAAATGTAATTTTTAAGAAGTTCG
1 AGGGCAAAAATGTGATTTTTAAAAATTAGAGGACAAAATGTAATTTTTAAGAAGTTCA
25448331 AGGGTC-AAAATGTGATTTT
1 AGGG-CAAAAATGTGATTTT
25448350 GAGAAAGTGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 14 0.22
58 49 0.77
59 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.33
Consensus pattern (58 bp):
AGGGCAAAAATGTGATTTTTAAAAATTAGAGGACAAAATGTAATTTTTAAGAAGTTCA
Found at i:25449550 original size:20 final size:21
Alignment explanation
Indices: 25449525--25449566 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25449515 GTACATAAAT
25449525 ATATAATA-GATAAATATTAA
1 ATATAATACGATAAATATTAA
* *
25449545 ATATAATACTATATATATTAA
1 ATATAATACGATAAATATTAA
25449566 A
1 A
25449567 ACATTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAATACGATAAATATTAA
Found at i:25450168 original size:6 final size:6
Alignment explanation
Indices: 25450157--25450233 Score: 65
Period size: 6 Copynumber: 13.7 Consensus size: 6
25450147 TAGATTTGAA
* * * *
25450157 TAAATT TAAATT TAAA-- TAATTT TAAATT TAAA-A TAAATA TAAACT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
25450202 TAAAAT T-AATT TAAATT TAAAAT T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
25450234 CCTAAAACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 42 0.74
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:25450169 original size:16 final size:16
Alignment explanation
Indices: 25450145--25450233 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 16
25450135 CATTATTTAT
* *
25450145 TTTAGATTTGAATAAA
1 TTTAAATTTAAATAAA
*
25450161 TTTAAATTTAAATAAT
1 TTTAAATTTAAATAAA
25450177 TTTAAATTTAAAATAAA
1 TTTAAATTT-AAATAAA
* * *
25450194 TATAAACTTAAAATTAA
1 TTTAAA-TTTAAATAAA
*
25450211 TTTAAATTTAAAATTAA
1 TTTAAATTT-AAATAAA
25450228 TTTAAA
1 TTTAAA
25450234 CCTAAAACAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 24 0.39
17 35 0.57
18 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:25450192 original size:17 final size:17
Alignment explanation
Indices: 25450155--25450233 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
25450145 TTTAGATTTG
25450155 AATAAATTTAAATTT-A
1 AATAAATTTAAATTTAA
*
25450171 AATAATTTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
25450188 AATAAATATAAACTTAA
1 AATAAATTTAAATTTAA
*
25450205 AATTAATTTAAATTTAA
1 AATAAATTTAAATTTAA
*
25450222 AATTAATTTAAA
1 AATAAATTTAAA
25450234 CCTAAAACAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
16 14 0.25
17 41 0.75
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:25450757 original size:39 final size:39
Alignment explanation
Indices: 25450706--25451581 Score: 261
Period size: 39 Copynumber: 22.5 Consensus size: 39
25450696 TGATCTGTCT
**
25450706 CAGGCTCAAGGTAAGAGATCGAATGGCTACAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* * * * ** * *** *
25450745 CAAGCTTGAGGTAAGAGATTGGTTGACTGTGATTTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* * * *
25450784 TAAGCTCGGGGTAAGAGATCGACTGATGG-T--GATCTACCC
1 CAGGCTCGGGGTAAGAGATCGA---ATGGCTACAATCTGCCC
* * * * *
25450823 TAGGCTCGGGGTAAAAGATCGAATGGATGCAATCTACCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* *
25450862 CAAGCTCGGGGT-AGAAGATCGAATGGCTGCAATCTG-CC
1 CAGGCTCGGGGTAAG-AGATCGAATGGCTACAATCTGCCC
* * * * **
25450900 TAGGCTCGGGATAAGAGATCAAATGACTGTAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* ** * * ** **
25450939 CATGAACGAGGTAAGAGATTGGTTGG-TGATGATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCT-ACAATCTGCCC
* * * * *
25450978 CAGGCTTGGGGTAAGAGATGGAACGGCTGCAATATGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* ** ** * *
25451017 CAGGCTCGGGGTAAGAGATTGGCTGG-TGATGATTTGTCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCT-ACAATCTGCCC
* * * *
25451056 CAGGCTCTGGGTAACAGATCAAACGGCTACAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* * ** *
25451095 CAGGCTCGGGGTAAAAGATTGGCTGG-TA-ATGATCTGTCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACA--ATCTGCCC
* * * *
25451134 CAAGCTCGGGGTAAGAGATCGAATGGCCACAATCTACCT
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* * * * * * **
25451173 TATGCTTGGGGTAAGAGATTTG--TTGATGATGATC-GACCC
1 CAGGCTCGGGGTAAGAGA-TCGAATGGCT-ACAATCTG-CCC
* * * * * * *
25451212 TAGGCTTGGGGTAAGAGATCGGATAGCTGCAATTTACCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
* * * * **
25451251 CATGATTGGGGTAAGAGATTTACTAAT-G--ATGATCTGCCC
1 CAGGCTCGGGGTAAGAGA--T-CGAATGGCTACAATCTGCCC
* * * *
25451290 TAGGCTCGGGGTACA-AGATCTAATGGTTGCAATCTGCCC
1 CAGGCTCGGGGTA-AGAGATCGAATGGCTACAATCTGCCC
* * ** * * **
25451329 TAGGCTTGGGGTAAGAGATTTACT-GATGATGATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCT-ACAATCTGCCC
* * * *
25451368 CAGGCTCGAGGTAAGAGATTGGATGGC-AGCAATCTGCCT
1 CAGGCTCGGGGTAAGAGATCGAATGGCTA-CAATCTGCCC
* ** * * **
25451407 TAGGCTCGGGGTAAGAGATTTACT-GATGATGATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGAATGGCT-ACAATCTGCCC
* * *
25451446 CAAGCTCGAGGTAAGAGATC-AGATAGCTACAATCTGCCC
1 CAGGCTCGGGGTAAGAGATCGA-ATGGCTACAATCTGCCC
* * * * * * * *
25451485 CATGATCGAGGTAAAAGATTTG--CGGATAATAATCTGCCC
1 CAGGCTCGGGGTAAGAGA-TCGAATGGCT-ACAATCTGCCC
* * * *
25451524 TAAGCTTGGGGTACA-AGATCTGAA-GGCTGCAATCTGCCC
1 CAGGCTCGGGGTA-AGAGATC-GAATGGCTACAATCTGCCC
*
25451563 CACGCTCGGGGTAAGAGAT
1 CAGGCTCGGGGTAAGAGAT
25451582 TTGCTGATGA
Statistics
Matches: 602, Mismatches: 189, Indels: 92
0.68 0.21 0.10
Matches are distributed among these distances:
36 9 0.01
37 4 0.01
38 48 0.08
39 514 0.85
40 18 0.03
41 4 0.01
42 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (39 bp):
CAGGCTCGGGGTAAGAGATCGAATGGCTACAATCTGCCC
Found at i:25450872 original size:78 final size:78
Alignment explanation
Indices: 25450787--25451859 Score: 794
Period size: 78 Copynumber: 13.8 Consensus size: 78
25450777 TTTGCCCTAA
* * * * *
25450787 GCTCGGGGTAAGAGATCGACTGATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGAATGGATG
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
* *
25450852 CAATCTACCCCAA
66 CAATCTGCCCCAT
* * * * * * * *
25450865 GCTCGGGGT-AGAAGATCGAATG--GCTGCAATCT-GCCTAGGCTCGGGATAAGAGATCAAATGA
1 GCTCGGGGTAAG-AGATTGACTGATGATG--ATCTACCCCAGGCTCGGGGTAAGAGATCGAATGG
*
25450926 CTGTAATCTGCCCCAT
63 CTGCAATCTGCCCCAT
** * ** * * * * *
25450942 GAACGAGGTAAGAGATTGGTTGGTGATGATCTGCCCCAGGCTTGGGGTAAGAGATGGAACGGCTG
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
* *
25451007 CAATATGCCCCAG
66 CAATCTGCCCCAT
* * * ** * * * * *
25451020 GCTCGGGGTAAGAGATTGGCTGGTGATGATTTGTCCCAGGCTCTGGGTAACAGATCAAACGGCTA
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
*
25451085 CAATCTGCCCCAG
66 CAATCTGCCCCAT
* * * * ** * **
25451098 GCTCGGGGTAAAAGATTGGCTGGTAATGATCTGTCCCAAGCTCGGGGTAAGAGATCGAATGGCCA
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
* **
25451163 CAATCTACCTTAT
66 CAATCTGCCCCAT
* * * * * * *
25451176 GCTTGGGGTAAGAGATTTG-TTGATGATGATCGACCCTAGGCTTGGGGTAAGAGATCGGATAGCT
1 GCTCGGGGTAAGAGA-TTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCT
* *
25451240 GCAATTTACCCCAT
65 GCAATCTGCCCCAT
* * * * * * * *
25451254 GATTGGGGTAAGAGATTTACTAATGATGATCTGCCCTAGGCTCGGGGTACA-AGATCTAATGGTT
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTA-AGAGATCGAATGGCT
* *
25451318 GCAATCTGCCCTAG
65 GCAATCTGCCCCAT
* * * * * * *
25451332 GCTTGGGGTAAGAGATTTACTGATGATGATCTGCCCCAGGCTCGAGGTAAGAGATTGGATGGCAG
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
** *
25451397 CAATCTGCCTTAG
66 CAATCTGCCCCAT
* * * * *
25451410 GCTCGGGGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATC-AGATAGCT
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGA-ATGGCT
*
25451474 ACAATCTGCCCCAT
65 GCAATCTGCCCCAT
* * * * * * * * * *
25451488 GATCGAGGTAAAAGATTTG-CGGATAATAATCTGCCCTAAGCTTGGGGTACA-AGATCTGAA-GG
1 GCTCGGGGTAAGAGA-TTGACTGATGATGATCTACCCCAGGCTCGGGGTA-AGAGATC-GAATGG
*
25451550 CTGCAATCTGCCCCAC
63 CTGCAATCTGCCCCAT
* * * **
25451566 GCTCGGGGTAAGAGATTTG-CTGATGATGATCTACCCGAGGCTCGGGGTAAGGGATCGGATAACT
1 GCTCGGGGTAAGAGA-TTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCT
* *
25451630 GTAATCTGCCTCAT
65 GCAATCTGCCCCAT
* * *
25451644 GATCAGGGTAAGAGATTTG-CTGATTATGATCTACCCCAGGCTCGGGGTACA-AGATCTG-ATGG
1 GCTCGGGGTAAGAGA-TTGACTGATGATGATCTACCCCAGGCTCGGGGTA-AGAGATC-GAATGG
* *
25451706 CTGTAATCTGCCCTGA-
63 CTGCAATCTGCCC-CAT
* * * * * * * **
25451722 GCTCGGGGTAAAAGATTTACTGATGATGATCTTCCCCAAGCTCGAGGTAAAAGATCGGATAACTG
1 GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
*
25451787 CGATCTGCCCCAT
66 CAATCTGCCCCAT
* *
25451800 -CATCGGGGTAAGAGATTTG-CTGATGATGATCTACCCCAAGCTCGGGATAAGAGATCGAAT
1 GC-TCGGGGTAAGAGA-TTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAAT
25451860 CTTTAATCTG
Statistics
Matches: 801, Mismatches: 167, Indels: 54
0.78 0.16 0.05
Matches are distributed among these distances:
76 3 0.00
77 67 0.08
78 714 0.89
79 16 0.02
80 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
GCTCGGGGTAAGAGATTGACTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG
CAATCTGCCCCAT
Found at i:25451159 original size:272 final size:271
Alignment explanation
Indices: 25450667--25451160 Score: 602
Period size: 272 Copynumber: 1.8 Consensus size: 271
25450657 CCATCTGTGT
* * * *
25450667 CATGATCGAGGTAAGAGATTGGTTGATGATGATCTGTCTCAGGCTCAAGGTAAGAGATCGAATGG
1 CATGAACGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAAGGTAAGAGATCGAACGG
* * *
25450732 CTACAATCTGCCCCAAGCTTGAGGTAAGAGATTGGTTGACTGTGATTTGCCCTAAGCTCGGGGTA
66 CTACAATATGCCCCAAGCTCGAGGTAAGAGATTGGCTGACTGTGATTTGCCCTAAGCTCGGGGTA
* * * *** *
25450797 AGAGATCGACTGATGGTGATCTACCCTAGGCTCGGGGTAAAAGATCGAATGGATGCAATCTACCC
131 ACAGATCAACGGATGACAATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATG-AATCTACCC
25450862 CAAGCTCGGGGTAGAAGATCGAATGGCTGCAATCTGCCTAGGCTCGGGATAAGAGATCAAATGAC
195 CAAGCTCGGGGTAGAAGATCGAATGGCTGCAATCTGCCTAGGCTCGGGATAAGAGATCAAATGAC
25450927 TGTAATCTGCCC
260 TGTAATCTGCCC
* *** *
25450939 CATGAACGAGGTAAGAGATTGGTTGGTGATGATCTGCCCCAGGCTTGGGGTAAGAGATGGAACGG
1 CATGAACGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAAGGTAAGAGATCGAACGG
* * * * * *
25451004 CTGCAATATGCCCCAGGCTCGGGGTAAGAGATTGGCTG-GTGATGATTTGTCCC-AGGCTCTGGG
66 CTACAATATGCCCCAAGCTCGAGGTAAGAGATTGGCTGACTG-TGATTTG-CCCTAAGCTCGGGG
* * * **
25451067 TAACAGATCAAACGGCT-ACAATCTGCCCCAGGCTCGGGGTAAAAGATTGGCTGGTAATG-ATCT
129 TAACAGATC-AACGGATGACAATCTACCCCAGGCTCGGGGTAAAAGATCGAATGG--ATGAATCT
**
25451130 GTCCCAAGCTCGGGGTA-AGAGATCGAATGGC
191 ACCCCAAGCTCGGGGTAGA-AGATCGAATGGC
25451161 CACAATCTAC
Statistics
Matches: 184, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
271 3 0.02
272 171 0.93
273 7 0.04
274 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (271 bp):
CATGAACGAGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAAGGTAAGAGATCGAACGG
CTACAATATGCCCCAAGCTCGAGGTAAGAGATTGGCTGACTGTGATTTGCCCTAAGCTCGGGGTA
ACAGATCAACGGATGACAATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGATGAATCTACCCC
AAGCTCGGGGTAGAAGATCGAATGGCTGCAATCTGCCTAGGCTCGGGATAAGAGATCAAATGACT
GTAATCTGCCC
Found at i:25451461 original size:234 final size:234
Alignment explanation
Indices: 25450948--25451856 Score: 904
Period size: 234 Copynumber: 3.9 Consensus size: 234
25450938 CCATGAACGA
* * * *
25450948 GGTAAGAGATTGGTTGGTGATGATCTGCCCCAGGCTTGGGGTAAGAGAT-GGA-ACGGCTGCAAT
1 GGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGGATA--GCTGCAAT
* * * * ** * * * *
25451011 ATGCCCCAGGCTCGGGGTAAGAGATTGGCTGGTGATGATTTGTCCC-AGGCTCTGGGTA-ACAGA
64 CTGCCCCATGATCGGGGTAAAAGATTTACTGATGATGATCTG-CCCTAAGCTCGGGGTACA-AGA
* * * * * * * **
25451074 TCAAACGGCTACAATCTGCCCCAGGCTCGGGGTAAAAGATTGGCTGGTAATGATCTGTCCCAAGC
127 TCTAATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGC
* * *
25451139 TCGGGGTAAGAGATCGAATGGCCA-CAATCTACCTTATGCTTGG
192 TCGGGGTAAGAGATCGGATGG-CAGCAATCTGCCTTATGCTCGG
* * * *
25451182 GGTAAGAGATTTGTTGATGATGATC-GACCCTAGGCTTGGGGTAAGAGATCGGATAGCTGCAATT
1 GGTAAGAGATTTGCTGATGATGATCTG-CCCCAGGCTCGGGGTAAGAGATCGGATAGCTGCAATC
* * * * *
25451246 TACCCCATGATTGGGGTAAGAGATTTACTAATGATGATCTGCCCTAGGCTCGGGGTACAAGATCT
65 TGCCCCATGATCGGGGTAAAAGATTTACTGATGATGATCTGCCCTAAGCTCGGGGTACAAGATCT
* * * * * *
25451311 AATGGTTGCAATCTGCCCTAGGCTTGGGGTAAGAGATTTACTGATGATGATCTGCCCCAGGCTCG
130 AATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCG
* * *
25451376 AGGTAAGAGATTGGATGGCAGCAATCTGCCTTAGGCTCGG
195 GGGTAAGAGATCGGATGGCAGCAATCTGCCTTATGCTCGG
* * * * *
25451416 GGTAAGAGATTTACTGATGATGATCTGCCCCAAGCTCGAGGTAAGAGATCAGATAGCTACAATCT
1 GGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGGATAGCTGCAATCT
* * * * * *
25451481 GCCCCATGATCGAGGTAAAAGATTTGCGGATAATAATCTGCCCTAAGCTTGGGGTACAAGATCTG
66 GCCCCATGATCGGGGTAAAAGATTTACTGATGATGATCTGCCCTAAGCTCGGGGTACAAGATCT-
* * *
25451546 AA-GGCTGCAATCTGCCCCACGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCGAGGCTCG
130 AATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCG
* ** * * * * *
25451610 GGGTAAGGGATCGGATAACTGTAATCTGCCTCATGATCAG
195 GGGTAAGAGATCGGATGGCAGCAATCTGCCTTATGCTCGG
* * * * *
25451650 GGTAAGAGATTTGCTGATTATGATCTACCCCAGGCTCGGGGTACA-AGATCTGATGGCTGTAATC
1 GGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTA-AGAGATCGGATAGCTGCAATC
* * * *
25451714 TG-CCC-TGAGCTCGGGGTAAAAGATTTACTGATGATGATCTTCCCCAAGCTCGAGGTAAAAGAT
65 TGCCCCATGA--TCGGGGTAAAAGATTTACTGATGATGATCTGCCCTAAGCTCGGGGTACAAGAT
** ** * *
25451777 CGGATAACTGCGATCTGCCCCA-TCATCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGC
128 CTAATGGCTGCAATCTGCCCCAGGC-TCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGC
*
25451841 TCGGGATAAGAGATCG
192 TCGGGGTAAGAGATCG
25451857 AATCTTTAAT
Statistics
Matches: 562, Mismatches: 100, Indels: 26
0.82 0.15 0.04
Matches are distributed among these distances:
232 3 0.01
233 11 0.02
234 539 0.96
235 8 0.01
236 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (234 bp):
GGTAAGAGATTTGCTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGGATAGCTGCAATCT
GCCCCATGATCGGGGTAAAAGATTTACTGATGATGATCTGCCCTAAGCTCGGGGTACAAGATCTA
ATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCGG
GGTAAGAGATCGGATGGCAGCAATCTGCCTTATGCTCGG
Found at i:25451609 original size:39 final size:38
Alignment explanation
Indices: 25451555--25451854 Score: 176
Period size: 39 Copynumber: 7.7 Consensus size: 38
25451545 GAAGGCTGCA
*
25451555 ATCTGCCCCACGCTCGGGGTAAGAGATTTGCTGATGATG
1 ATCTACCCCA-GCTCGGGGTAAGAGATTTGCTGATGATG
* * ** * * *
25451594 ATCTACCCGAGGCTCGGGGTAAGGGATCGGATAACTG-TA
1 ATCTACCCCA-GCTCGGGGTAAGAGATTTGCTGA-TGATG
* * * * *
25451633 ATCTGCCTCATGATCAGGGTAAGAGATTTGCTGATTATG
1 ATCTACCCCA-GCTCGGGGTAAGAGATTTGCTGATGATG
* * * *
25451672 ATCTACCCCAGGCTCGGGGTACA-AGATCTGATGGCTG-TA
1 ATCTACCCCA-GCTCGGGGTA-AGAGATTTGCT-GATGATG
* * * *
25451711 ATCTGCCCTGAGCTCGGGGTAAAAGATTTACTGATGATG
1 ATCTACCC-CAGCTCGGGGTAAGAGATTTGCTGATGATG
* * * ** * * *
25451750 ATCTTCCCCAAGCTCGAGGTAAAAGATCGGATAACTG-CG
1 ATCTACCCC-AGCTCGGGGTAAGAGATTTGCTGA-TGATG
* *
25451789 ATCTGCCCCATCATCGGGGTAAGAGATTTGCTGATGATG
1 ATCTACCCCAGC-TCGGGGTAAGAGATTTGCTGATGATG
*
25451828 ATCTACCCCAAGCTCGGGATAAGAGAT
1 ATCTACCCC-AGCTCGGGGTAAGAGAT
25451855 CGAATCTTTA
Statistics
Matches: 189, Mismatches: 60, Indels: 24
0.69 0.22 0.09
Matches are distributed among these distances:
38 9 0.05
39 170 0.90
40 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
ATCTACCCCAGCTCGGGGTAAGAGATTTGCTGATGATG
Found at i:25463567 original size:97 final size:97
Alignment explanation
Indices: 25463394--25463587 Score: 284
Period size: 97 Copynumber: 2.0 Consensus size: 97
25463384 AACCTTGAAG
* **
25463394 AAGGGTATTTAATTATCCTGGTTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCAATTATCCTGGTTTGAAGAAAAACCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
*
25463459 AATCCCAAAATAAAGGAATATTGCCTCGATTT
66 AAACCCAAAATAAAGGAATATTGCCTCGATTT
* *
25463491 AAGGGTATTCGATTAT-CTCGGTTTGAAGAAAAACCGC-CCTTAGTAAGTTAAGGCACGAATTTT
1 AAGGGTATTCAATTATCCT-GGTTTGAAGAAAAACCGCGCC-TAGTAAGTTAAGGCACAAATTTT
* *
25463554 CAAAACTCGAAATAAAGGAATATTGCCTCGATTT
64 CAAAACCCAAAATAAAGGAATATTGCCTCGATTT
25463588 TAAATATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 4 0.05
97 83 0.95
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (97 bp):
AAGGGTATTCAATTATCCTGGTTTGAAGAAAAACCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCAAAATAAAGGAATATTGCCTCGATTT
Found at i:25463719 original size:14 final size:15
Alignment explanation
Indices: 25463700--25463747 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
25463690 AAGAATGAAC
25463700 AAATATACG-AAAAT
1 AAATATACGAAAAAT
25463714 AAATATGA-GAAAAAT
1 AAATAT-ACGAAAAAT
25463729 AAA-ATACGATAAAAT
1 AAATATACGA-AAAAT
25463744 AAAT
1 AAAT
25463748 GAGAAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.03
14 11 0.38
15 17 0.59
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (15 bp):
AAATATACGAAAAAT
Found at i:25463945 original size:30 final size:28
Alignment explanation
Indices: 25463842--25464070 Score: 153
Period size: 30 Copynumber: 7.9 Consensus size: 28
25463832 AGTTTCGAAG
* *
25463842 AGTTT-GGGGTTAAAATATAATTTTGGAA
1 AGTTTAGGGGTAAAAATGTAATTTTGG-A
* *
25463870 ACTTTTTA-GGGTAAAAATGTTATTTTGGGAA
1 A--GTTTAGGGGTAAAAATGTAATTTT-GG-A
* * *
25463901 AATTCA-AGGTAAAAATGTGAATTTTGGA
1 AGTTTAGGGGTAAAAATGT-AATTTTGGA
* * *
25463929 AGTTTAGGGGCAAAAAAGTGAGTTTTGGAA
1 AGTTTAGGGGTAAAAATGT-AATTTTGG-A
* * *
25463959 AGTTTGGGGGCAAAAATATAATTTTTGAGA
1 AGTTTAGGGGTAAAAATGTAA-TTTTG-GA
**
25463989 AGTTT-GAGGGTAAAAATGTAATTTTTTTA
1 AGTTTAG-GGGTAAAAATGTAA-TTTTGGA
* *
25464018 AGTTTAGGGGTAAAAATGTGATTTTTTGA
1 AGTTTAGGGGTAAAAATGT-AATTTTGGA
25464047 AGTTTA-GGGTAAAAATGTAATTTT
1 AGTTTAGGGGTAAAAATGTAATTTT
25464071 CAAGAAGTTC
Statistics
Matches: 164, Mismatches: 25, Indels: 25
0.77 0.12 0.12
Matches are distributed among these distances:
27 5 0.03
28 18 0.11
29 65 0.40
30 70 0.43
31 6 0.04
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.38
Consensus pattern (28 bp):
AGTTTAGGGGTAAAAATGTAATTTTGGA
Found at i:25464001 original size:89 final size:87
Alignment explanation
Indices: 25463908--25464079 Score: 211
Period size: 89 Copynumber: 2.0 Consensus size: 87
25463898 GAAAATTCAA
*
25463908 GGTAAAAATGTGAA-TTTTGGAAGTTTAGGGGCAAAAAAGTGAGTTTTGGAAAGTTTGGGGGCAA
1 GGTAAAAATGT-AATTTTTGGAAGTTTAGGGGCAAAAAAGTGAGTTTTGG-AAGTTT-AGGGCAA
**
25463972 AAATATAATTTTTGAGAAGTTTGAG
63 AAATATAATTTTCAAGAAGTTTGAG
** * * * * *
25463997 GGTAAAAATGTAATTTTTTTAAGTTTAGGGGTAAAAATGTGATTTTTTGAAGTTTAGGGTAAAAA
1 GGTAAAAATGTAATTTTTGGAAGTTTAGGGGCAAAAAAGTGAGTTTTGGAAGTTTAGGGCAAAAA
*
25464062 TGTAATTTTCAAGAAGTT
66 TATAATTTTCAAGAAGTT
25464080 CAATTGTAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
87 23 0.32
88 8 0.11
89 40 0.56
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (87 bp):
GGTAAAAATGTAATTTTTGGAAGTTTAGGGGCAAAAAAGTGAGTTTTGGAAGTTTAGGGCAAAAA
TATAATTTTCAAGAAGTTTGAG
Found at i:25464077 original size:29 final size:28
Alignment explanation
Indices: 25463874--25464108 Score: 148
Period size: 29 Copynumber: 8.1 Consensus size: 28
25463864 TTGGAAACTT
* ** *
25463874 TTTAGGGTAAAAATGTTATTTTGGGAAAA
1 TTTAGGGTAAAAATGTAATTTTTAG-AAG
* * *
25463903 TTCAAGGTAAAAATGTGAA-TTTTGGAAG
1 TTTAGGGTAAAAATGT-AATTTTTAGAAG
* * * * *
25463931 TTTAGGGGCAAAAAAGTGAGTTTTGGAAAG
1 TTTA-GGGTAAAAATGTAATTTTTAG-AAG
* * *
25463961 TTTGGGGGCAAAAATATAATTTTTGAGAAG
1 TTT-AGGGTAAAAATGTAATTTTT-AGAAG
**
25463991 TTTGAGGGTAAAAATGTAATTTTTTTAAG
1 TTT-AGGGTAAAAATGTAATTTTTAGAAG
* *
25464020 TTTAGGGGTAAAAATGTGATTTTTTGAAG
1 TTTA-GGGTAAAAATGTAATTTTTAGAAG
*
25464049 TTTAGGGTAAAAATGTAATTTTCAAGAAG
1 TTTAGGGTAAAAATGTAATTTT-TAGAAG
* ** **
25464078 TTCAATTGTAAAAACATAATTTTTAGAAG
1 TT-TAGGGTAAAAATGTAATTTTTAGAAG
25464107 TT
1 TT
25464109 CGAGGGTACC
Statistics
Matches: 165, Mismatches: 32, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
28 24 0.15
29 79 0.48
30 61 0.37
31 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (28 bp):
TTTAGGGTAAAAATGTAATTTTTAGAAG
Found at i:25477155 original size:18 final size:20
Alignment explanation
Indices: 25477127--25477163 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
25477117 CTTATTATAA
25477127 TTTTAGAGTTTT-ATGAATT
1 TTTTAGAGTTTTAATGAATT
25477146 TTTTAG-GTTTTAATGAAT
1 TTTTAGAGTTTTAATGAAT
25477164 CCACAAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTTAGAGTTTTAATGAATT
Found at i:25477386 original size:18 final size:18
Alignment explanation
Indices: 25477363--25477398 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25477353 GGAAGTTTAG
25477363 ATTTGTGAGGTTTACTAA
1 ATTTGTGAGGTTTACTAA
25477381 ATTTGTGAGGTTTACTAA
1 ATTTGTGAGGTTTACTAA
25477399 CATATTGGAT
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:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (18 bp):
ATTTGTGAGGTTTACTAA
Found at i:25484076 original size:23 final size:23
Alignment explanation
Indices: 25484050--25484095 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25484040 AAGGTTTCGG
25484050 TTTGTACTTAAATATTAATGTGA
1 TTTGTACTTAAATATTAATGTGA
* *
25484073 TTTGTGCTTAAATATTCATGTGA
1 TTTGTACTTAAATATTAATGTGA
25484096 AAAGATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (23 bp):
TTTGTACTTAAATATTAATGTGA
Found at i:25484232 original size:23 final size:23
Alignment explanation
Indices: 25484169--25484549 Score: 561
Period size: 23 Copynumber: 16.7 Consensus size: 23
25484159 TGCGGATGAA
*
25484169 TGATTTATGCTT-AATATTAATG
1 TGATTTGTGCTTAAATATTAATG
25484191 TGATTTGTGC-TAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484213 TGATTTGTG-TTCAAATATTAATA
1 TGATTTGTGCTT-AAATATTAATG
*
25484236 TGATTTGTGCTCAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
* *
25484259 TGATTTATGATTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484282 TGATTTGTGCTTAAGTATTAATG
1 TGATTTGTGCTTAAATATTAATG
* *
25484305 TGATTTATGCTTAAATATTAATT
1 TGATTTGTGCTTAAATATTAATG
* *
25484328 TGATTTGTCCTCAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484351 TGATTTATGCTTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484374 TGATTTGTGCTCAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
25484397 TGATTTGTGCTTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484420 TGATTTGTGCTTAAATATTAATA
1 TGATTTGTGCTTAAATATTAATG
*
25484443 TGATTTGTGCTCAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484466 TGATTTATGCTTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
*
25484489 TGATTTGTGCTTAAATATTAATA
1 TGATTTGTGCTTAAATATTAATG
* * *
25484512 TGACTTATGATTAAATATTAATG
1 TGATTTGTGCTTAAATATTAATG
25484535 TGATTTGTGCTTAAA
1 TGATTTGTGCTTAAA
25484550 GAATTAAAAT
Statistics
Matches: 318, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
21 1 0.00
22 29 0.09
23 287 0.90
24 1 0.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.47
Consensus pattern (23 bp):
TGATTTGTGCTTAAATATTAATG
Found at i:25486736 original size:52 final size:50
Alignment explanation
Indices: 25486662--25486951 Score: 251
Period size: 52 Copynumber: 5.6 Consensus size: 50
25486652 TGCATTTTTC
* * * * * *
25486662 ATACTCACAATGACATAGAGTCAACAGACCCTTAATCTGTAATGGAAATCAT
1 ATACTCACAATGACATATAGTCATCGGACCCATAATCCGTAA-GG-ATTCAT
*
25486714 ATACTCACGATGACATATAGTCATCGGACCCCATAATCCGTAAAGCG-TTCAT
1 ATACTCACAATGACATATAGTCATCGGA-CCCATAATCCGT-AAG-GATTCAT
*
25486766 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAGAGGATTCAT
1 ATACTCACAATGACATATAGTCATCGGACC-CATAATCCGTA-AGGATTCAT
* * * * * * *
25486818 ATATTCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGATTTAC
1 ATACTCACAATGACATATAGTCATCGGACC-CATAATCCGT-AAGGATTCAT
* * * *
25486870 ATACTCACGATGAAACT-TAGTCATCGGACCTTATAATCCGTAAATGATTCAT
1 ATACTCACAATGACA-TATAGTCATCGGACC-CATAATCCGT-AAGGATTCAT
* * * *
25486922 ATACTCACGATGATACATAGTCATCAGACC
1 ATACTCACAATGACATATAGTCATCGGACC
25486952 TATTTCATTC
Statistics
Matches: 202, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
51 4 0.02
52 183 0.91
53 12 0.06
54 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (50 bp):
ATACTCACAATGACATATAGTCATCGGACCCATAATCCGTAAGGATTCAT
Found at i:25486780 original size:104 final size:104
Alignment explanation
Indices: 25486662--25486946 Score: 288
Period size: 104 Copynumber: 2.7 Consensus size: 104
25486652 TGCATTTTTC
* * *
25486662 ATACTCACAATGACATAGAGTCAACAGACC-CTTAATCTGTA-ATGGAAATCATATACTCACGAT
1 ATACTCACAATGACACAGAGTCAACAGACCTCATAATCCGTAGA-GG-AATCATATACTCACGAT
* * *
25486725 GACATATAGTCATCGGACCCCATAATCCGTAAAGCGTTCAT
64 GACACATAATCATCGAACCCCATAATCCGTAAAGCGTTCAT
* * * * *
25486766 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAGAGGATTCATATATTCACGATGA
1 ATACTCACAATGACACAGAGTCAACAGACCTCATAATCCGTAGAGGAATCATATACTCACGATGA
* * *
25486831 CACATAATCATCGAACCTCATAATCCGTAAAG-GATTTAC
66 CACATAATCATCGAACCCCATAATCCGTAAAGCG-TTCAT
* * ** * * * * * *
25486870 ATACTCACGATGAAACTTAGTCATCGGACCTTATAATCCGTAAATGATTCATATACTCACGATGA
1 ATACTCACAATGACACAGAGTCAACAGACCTCATAATCCGTAGAGGAATCATATACTCACGATGA
* *
25486935 TACATAGTCATC
66 CACATAATCATC
25486947 AGACCTATTT
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
103 1 0.01
104 142 0.92
105 11 0.07
106 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (104 bp):
ATACTCACAATGACACAGAGTCAACAGACCTCATAATCCGTAGAGGAATCATATACTCACGATGA
CACATAATCATCGAACCCCATAATCCGTAAAGCGTTCAT
Found at i:25486952 original size:52 final size:52
Alignment explanation
Indices: 25486710--25486952 Score: 335
Period size: 52 Copynumber: 4.7 Consensus size: 52
25486700 GTAATGGAAA
* *
25486710 TCATATACTCACGATGACATATAGTCATCGGACCCCATAATCCGTAAAGCG-T
1 TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAG-GAT
* *
25486762 TCATATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAGAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAT
* * *
25486814 TCATATATTCACGATGACACATAATCATCGAACCTCATAATCCGTAAAGGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAT
* * * * * *
25486866 TTACATACTCACGATGAAACTTAGTCATCGGACCTTATAATCCGTAAATGAT
1 TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAT
* *
25486918 TCATATACTCACGATGATACATAGTCATCAGACCT
1 TCATATACTCACGATGACACATAGTCATCGGACCT
25486953 ATTTCATTCA
Statistics
Matches: 167, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
51 1 0.01
52 166 0.99
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
TCATATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAT
Found at i:25492649 original size:9 final size:9
Alignment explanation
Indices: 25492635--25492667 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
25492625 CTTTCCATAC
25492635 TTATTTTAT
1 TTATTTTAT
*
25492644 TTATTTTGT
1 TTATTTTAT
25492653 TTA-TTTAT
1 TTATTTTAT
25492661 TTATTTT
1 TTATTTT
25492668 TAGAACTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:25492907 original size:6 final size:6
Alignment explanation
Indices: 25492896--25492921 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25492886 TAATTAATTA
25492896 TTATTC TTATTC TTATTC TTATTC TT
1 TTATTC TTATTC TTATTC TTATTC TT
25492922 CTTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATTC
Found at i:25496502 original size:23 final size:22
Alignment explanation
Indices: 25496470--25496513 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
25496460 AAAGAAATAA
*
25496470 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
25496492 AATTAAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
25496514 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:25497013 original size:23 final size:23
Alignment explanation
Indices: 25496987--25497031 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
25496977 TATTACATTT
* *
25496987 TAATTATTGTGTTTAAAATGTCC
1 TAATGATTGTGTTCAAAATGTCC
25497010 TAATGATTGTGTTCAAAATGTC
1 TAATGATTGTGTTCAAAATGTC
25497032 TTAGGTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (23 bp):
TAATGATTGTGTTCAAAATGTCC
Found at i:25508814 original size:23 final size:22
Alignment explanation
Indices: 25508767--25508815 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
25508757 TATATATTTC
*
25508767 TTTTCTTTTCTCTTTTCTTCTT
1 TTTTCTTTTCTCTTTTCTTCAT
25508789 TTTTCTTTT-TCTTATTCATTCAT
1 TTTTCTTTTCTCTT-TTC-TTCAT
25508812 TTTT
1 TTTT
25508816 TTATATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 12 0.50
23 8 0.33
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTCTTTTCTTCAT
Found at i:25509431 original size:18 final size:18
Alignment explanation
Indices: 25509405--25509441 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25509395 CTAACAAATG
25509405 AAATACAATGACAAATAA
1 AAATACAATGACAAATAA
* *
25509423 AAATGCAATGACAACTAA
1 AAATACAATGACAAATAA
25509441 A
1 A
25509442 TAAGATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.14, G:0.08, T:0.16
Consensus pattern (18 bp):
AAATACAATGACAAATAA
Found at i:25509580 original size:21 final size:21
Alignment explanation
Indices: 25509554--25509594 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25509544 CTCGCCTTCT
*
25509554 TCTTTGCGCTTTTTCTTCTTA
1 TCTTTGCGCTTTCTCTTCTTA
*
25509575 TCTTTGCTCTTTCTCTTCTT
1 TCTTTGCGCTTTCTCTTCTT
25509595 GTCCTTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.27, G:0.07, T:0.63
Consensus pattern (21 bp):
TCTTTGCGCTTTCTCTTCTTA
Found at i:25527474 original size:75 final size:75
Alignment explanation
Indices: 25527384--25527545 Score: 243
Period size: 75 Copynumber: 2.1 Consensus size: 75
25527374 ATTTTTGAAC
*
25527384 TTTGGCTCGTAAGAGAGATATTCTGTCTGGCTAGTAAGAGCGATATTCTGTCTGGCTCGTAAGAG
1 TTTGGCTCGTAAGAGAGATATTATGTCTGGCTAGTAAGAGCGATATTCTGTCTGGCTCGTAAGAG
25527449 CGATATTCTG
66 CGATATTCTG
* * * * *
25527459 TTTGGCTGGTAAGAGAGATATTATGTCTGGCTCGTAAGAGTGATATTCTGTTTGGCTTGTAAGAG
1 TTTGGCTCGTAAGAGAGATATTATGTCTGGCTAGTAAGAGCGATATTCTGTCTGGCTCGTAAGAG
* *
25527524 CGATGTTTTG
66 CGATATTCTG
25527534 TTTGGGCTCGTA
1 TTT-GGCTCGTA
25527546 TTGTAACACC
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 70 0.91
76 7 0.09
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (75 bp):
TTTGGCTCGTAAGAGAGATATTATGTCTGGCTAGTAAGAGCGATATTCTGTCTGGCTCGTAAGAG
CGATATTCTG
Found at i:25527535 original size:25 final size:25
Alignment explanation
Indices: 25527384--25527545 Score: 207
Period size: 25 Copynumber: 6.4 Consensus size: 25
25527374 ATTTTTGAAC
*
25527384 TTTGGCTCGTAAGAGAGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTG
* *
25527409 TCTGGCTAGTAAGAGCGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTG
*
25527434 TCTGGCTCGTAAGAGCGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTG
* * *
25527459 TTTGGCTGGTAAGAGAGATATTATG
1 TTTGGCTCGTAAGAGCGATATTCTG
* *
25527484 TCTGGCTCGTAAGAGTGATATTCTG
1 TTTGGCTCGTAAGAGCGATATTCTG
* * *
25527509 TTTGGCTTGTAAGAGCGATGTTTTG
1 TTTGGCTCGTAAGAGCGATATTCTG
25527534 TTTGGGCTCGTA
1 TTT-GGCTCGTA
25527546 TTGTAACACC
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
25 111 0.94
26 7 0.06
ACGTcount: A:0.21, C:0.13, G:0.30, T:0.36
Consensus pattern (25 bp):
TTTGGCTCGTAAGAGCGATATTCTG
Found at i:25528757 original size:52 final size:52
Alignment explanation
Indices: 25528689--25529028 Score: 542
Period size: 52 Copynumber: 6.6 Consensus size: 52
25528679 TTCTTATTTA
*
25528689 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
25528741 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
25528793 ATACTCATGATGACACAAAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
25528845 ATACTCACGATGACAC--AGTCATCGGACCTCAAAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
25528895 ATACTCACGATGACACATAGTCATCGAACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
25528947 ATACTCACGATG-CAACATAGTCATTGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGAC-ACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
25528999 ATACTAACGATGATACATAGTCATCGGACC
1 ATACTCACGATGACACATAGTCATCGGACC
25529029 ATTTGCATTT
Statistics
Matches: 267, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
50 48 0.18
51 1 0.00
52 218 0.82
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:25528799 original size:26 final size:26
Alignment explanation
Indices: 25528770--25528851 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
25528760 GTCATCGGAC
25528770 CTCATAATCCGTAAAGGATTCATATA
1 CTCATAATCCGTAAAGGATTCATATA
* * ** **
25528796 CTCATGATGACACAAA-G--TCATCGGA
1 CTCATAAT-CCGTAAAGGATTCAT-ATA
25528821 CCTCATAATCCGTAAAGGATTCATATA
1 -CTCATAATCCGTAAAGGATTCATATA
25528848 CTCA
1 CTCA
25528852 CGATGACACA
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
24 4 0.11
25 5 0.13
26 20 0.53
27 5 0.13
28 4 0.11
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (26 bp):
CTCATAATCCGTAAAGGATTCATATA
Found at i:25528987 original size:154 final size:154
Alignment explanation
Indices: 25528689--25529028 Score: 520
Period size: 154 Copynumber: 2.2 Consensus size: 154
25528679 TTCTTATTTA
* * * *
25528689 ATACTCACGATAACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCATGATGA
1 ATACTCACGATGACAC--AGTCATCGGACCTCAAAATCCGTAAAAGATTCATATACTCACGATGA
* *
25528754 CACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACAAAGTCATCG
64 CACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACAAAGTCATCG
25528819 GACCTCATAATCCGTAAAGGATTCAT
129 GACCTCATAATCCGTAAAGGATTCAT
25528845 ATACTCACGATGACACAGTCATCGGACCTCAAAATCCGTAAAAGATTCATATACTCACGATGACA
1 ATACTCACGATGACACAGTCATCGGACCTCAAAATCCGTAAAAGATTCATATACTCACGATGACA
* * *
25528910 CATAGTCATCGAACCTCATAATCTGTAAAGGATTCATATACTCACGATG-CAACATAGTCATTGG
66 CATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCACGATGAC-ACAAAGTCATCGG
*
25528974 ACCTTATAATCCGTAAAGGATTCAT
130 ACCTCATAATCCGTAAAGGATTCAT
* *
25528999 ATACTAACGATGATACATAGTCATCGGACC
1 ATACTCACGATG--ACACAGTCATCGGACC
25529029 ATTTGCATTT
Statistics
Matches: 169, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
153 1 0.01
154 138 0.82
156 30 0.18
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (154 bp):
ATACTCACGATGACACAGTCATCGGACCTCAAAATCCGTAAAAGATTCATATACTCACGATGACA
CATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACAAAGTCATCGGA
CCTCATAATCCGTAAAGGATTCAT
Found at i:25530043 original size:16 final size:16
Alignment explanation
Indices: 25530019--25530051 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25530009 TCCTTACAAA
*
25530019 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
25530035 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
25530051 T
1 T
25530052 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:25532813 original size:8 final size:8
Alignment explanation
Indices: 25532800--25532824 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
25532790 AAATAGCGGA
25532800 AGAAATTG
1 AGAAATTG
25532808 AGAAATTG
1 AGAAATTG
25532816 AGAAATTG
1 AGAAATTG
25532824 A
1 A
25532825 TTACACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:25541561 original size:15 final size:17
Alignment explanation
Indices: 25541531--25541563 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
25541521 TGATTTTTAT
25541531 TAATTCATATTTAATAA
1 TAATTCATATTTAATAA
25541548 TAATT-ATA-TTAATAA
1 TAATTCATATTTAATAA
25541563 T
1 T
25541564 GTTATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTCATATTTAATAA
Found at i:25541660 original size:56 final size:57
Alignment explanation
Indices: 25541524--25541676 Score: 202
Period size: 56 Copynumber: 2.7 Consensus size: 57
25541514 TATATTATGA
* * *
25541524 TTTTTATT-AATTCATATTTAATAATAATTATATTAATAATGTTATTAAATTATATACT
1 TTTTTATTAAATT-ATATTTAATAATAATCATATTAA-AATATGATTAAATTATATACT
* * *
25541582 ATTTTATTAAATTGTATTTAATAATAATCATATTAAAATATGATTAAATTATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATTATATACT
* *
25541638 TTTTTATTAAATTATATTTAATAATAATCTTAATAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAAT
25541677 TTAACAACAA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
56 36 0.43
57 16 0.19
58 28 0.33
59 4 0.05
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (57 bp):
TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATTATATACT
Found at i:25545154 original size:23 final size:23
Alignment explanation
Indices: 25545124--25545197 Score: 67
Period size: 30 Copynumber: 2.9 Consensus size: 23
25545114 GACGTGGCAT
25545124 CCAGTTAGCAGCTTCTAGAAGAC
1 CCAGTTAGCAGCTTCTAGAAGAC
25545147 CCAGTTAGCAATCAGCAGCTTCTAGAAGAC
1 CCAG-T-----T-AGCAGCTTCTAGAAGAC
* *
25545177 CCAGTCAGCAGCTTCCAGAAG
1 CCAGTTAGCAGCTTCTAGAAG
25545198 GTCTAATCAG
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
23 18 0.43
24 1 0.02
29 2 0.05
30 21 0.50
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (23 bp):
CCAGTTAGCAGCTTCTAGAAGAC
Found at i:25545165 original size:30 final size:30
Alignment explanation
Indices: 25545130--25545186 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
25545120 GCATCCAGTT
*
25545130 AGCAGCTTCTAGAAGACCCAGTTAGCAATC
1 AGCAGCTTCTAGAAGACCCAGTCAGCAATC
25545160 AGCAGCTTCTAGAAGACCCAGTCAGCA
1 AGCAGCTTCTAGAAGACCCAGTCAGCA
25545187 GCTTCCAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (30 bp):
AGCAGCTTCTAGAAGACCCAGTCAGCAATC
Found at i:25549686 original size:18 final size:17
Alignment explanation
Indices: 25549665--25549709 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
25549655 CAACAGGTTC
25549665 GAAAAGAAAAGAAAAAAA
1 GAAAA-AAAAGAAAAAAA
* *
25549683 GAAAAAAAGGGAGAAAAA
1 GAAAAAAA-AGAAAAAAA
25549701 GAAAAAAAA
1 GAAAAAAAA
25549710 ACATGGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAGAAAAAAA
Found at i:25556533 original size:37 final size:37
Alignment explanation
Indices: 25556483--25556556 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
25556473 ATCAGTTGGT
25556483 GGTGTCTCAATATACATGGCCCACTTAAAAAGTGACA
1 GGTGTCTCAATATACATGGCCCACTTAAAAAGTGACA
*
25556520 GGTGTGTCAATATACATGGCCCACTTAAAAAGTGACA
1 GGTGTCTCAATATACATGGCCCACTTAAAAAGTGACA
25556557 TGTGGCATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (37 bp):
GGTGTCTCAATATACATGGCCCACTTAAAAAGTGACA
Found at i:25562576 original size:76 final size:76
Alignment explanation
Indices: 25562450--25562603 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
25562440 ATTAAATATT
*
25562450 ATCATGCCTAAGTTATTATTGCATTACCCTTGTGATATAACTATTGAATTAATCATTTAAGAGTG
1 ATCATGCCTAAGTTATTATTGCATTACCCTTGTGATATAACTATTGAATTAATCATTTAAGAGCG
25562515 TTGAAATTGTG
66 TTGAAATTGTG
* *
25562526 ATCATGCCTAAGTTATTATTGCATTACTCTTGTGATATAACTATTGAATTAATCATTTAAGCGCG
1 ATCATGCCTAAGTTATTATTGCATTACCCTTGTGATATAACTATTGAATTAATCATTTAAGAGCG
25562591 TTGAAATTGTG
66 TTGAAATTGTG
25562602 AT
1 AT
25562604 TAACGGATAC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (76 bp):
ATCATGCCTAAGTTATTATTGCATTACCCTTGTGATATAACTATTGAATTAATCATTTAAGAGCG
TTGAAATTGTG
Found at i:25569060 original size:14 final size:11
Alignment explanation
Indices: 25569028--25569052 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25569018 TTTTTTGTTT
25569028 TTTAATATTTG
1 TTTAATATTTG
25569039 TTTAATATTTG
1 TTTAATATTTG
25569050 TTT
1 TTT
25569053 GAAAATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTAATATTTG
Found at i:25569085 original size:9 final size:9
Alignment explanation
Indices: 25569057--25569106 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
25569047 TTGTTTGAAA
*
25569057 ATATAATAT
1 ATATAAAAT
*
25569066 ATAT-ATAT
1 ATATAAAAT
*
25569074 ATATAAAGT
1 ATATAAAAT
25569083 ATA-AAAAT
1 ATATAAAAT
25569091 ATATAAAAT
1 ATATAAAAT
*
25569100 AAATAAA
1 ATATAAA
25569107 TAAGTACAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
8 15 0.43
9 20 0.57
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (9 bp):
ATATAAAAT
Found at i:25569107 original size:17 final size:17
Alignment explanation
Indices: 25569057--25569108 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
25569047 TTGTTTGAAA
* * *
25569057 ATATAATATATATATAT
1 ATATAAAATAAATAAAT
*
25569074 ATATAAAGTATAA-AAAT
1 ATATAAAATA-AATAAAT
25569091 ATATAAAATAAATAAAT
1 ATATAAAATAAATAAAT
25569108 A
1 A
25569109 AGTACAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 2 0.07
17 25 0.89
18 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
ATATAAAATAAATAAAT
Found at i:25569655 original size:15 final size:15
Alignment explanation
Indices: 25569635--25569667 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25569625 TTTATAAAAT
*
25569635 AATAAATAAAAATAA
1 AATAAATAAAAACAA
25569650 AATAAATAAAAACAA
1 AATAAATAAAAACAA
25569665 AAT
1 AAT
25569668 TGGATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAATAAAAACAA
Found at i:25570316 original size:40 final size:39
Alignment explanation
Indices: 25570272--25570481 Score: 106
Period size: 40 Copynumber: 5.3 Consensus size: 39
25570262 CCCATGATCG
* *
25570272 GGGTAAGAGATCTGATGGTCTTCAATCTACCCTCTGGTTA
1 GGGTAAAAGATCGGATGGTCTTCAATCTACCCTCT-GTTA
** * * * *
25570312 GGGTAAAAGATTAGAT-TTCTTCAATC-AGCACC-ATGATC
1 GGGTAAAAGATCGGATGGTCTTCAATCTA-C-CCTCTGTTA
* * *
25570350 GGAGTAAAAGATCGGATGGTCTTCTATTTGCCCTCTAGTTA
1 GG-GTAAAAGATCGGATGGTCTTCAATCTACCCTCT-GTTA
* * * **
25570391 GGGTAAGAGATCGGATGGT-TCTCAATTTGCCC-CATGATCG
1 GGGTAAAAGATCGGATGGTCT-TCAATCTACCCTC-TG-TTA
* * * * *
25570431 GGGCAAGAGATCGGACGGTATTCAATCTACCCTCTTATTA
1 GGGTAAAAGATCGGATGGTCTTCAATCTACCCTC-TGTTA
*
25570471 AGGTAAAAGAT
1 GGGTAAAAGAT
25570482 TGGAAGTTGT
Statistics
Matches: 127, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
38 5 0.04
39 28 0.22
40 87 0.69
41 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (39 bp):
GGGTAAAAGATCGGATGGTCTTCAATCTACCCTCTGTTA
Found at i:25570346 original size:79 final size:79
Alignment explanation
Indices: 25570263--25570482 Score: 246
Period size: 79 Copynumber: 2.8 Consensus size: 79
25570253 TTAATCTGCC
* *
25570263 CCATGATCGGGGTAAGAGATCTGATGGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTAGAT
1 CCATGATCGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGAT
25570328 -TTCTTCAATCAGCA
66 GTTC-TCAATCAGCA
* * * * * * **
25570342 CCATGATCGGAGTAAAAGATCGGATGGTCTTCTATTTGCCCTCTAGTTAGGGTAAGAGATCGGAT
1 CCATGATCGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGAT
** *
25570407 GGTTCTCAATTTGCC
66 -GTTCTCAATCAGCA
* * * *
25570422 CCATGATCGGGGCAAGAGATCGGACGGTATTCAATCTACCCTCTTA-TTAAGGTAAAAGATT
1 CCATGATCGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTC-TAGTTAGGGTAAAAGATT
25570483 GGAAGTTGTA
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
79 55 0.48
80 54 0.47
81 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (79 bp):
CCATGATCGGGGTAAGAGATCGGATGGTCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTAGAT
GTTCTCAATCAGCA
Found at i:25570598 original size:50 final size:50
Alignment explanation
Indices: 25570531--25570648 Score: 139
Period size: 50 Copynumber: 2.3 Consensus size: 50
25570521 TAAGATTCAT
* * * *
25570531 CCCCTTCTATAGCTTTAGGTGAATGAGATTTGGCATTTCGGCTTCATTCTG
1 CCCC-TCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCAATCTG
* * *
25570582 CCCCTCTACAGCTTTAGGTGTATGAGATTTTCCATTGCGGTTTCAATCTG
1 CCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCAATCTG
*
25570632 CACCT-TCACAGCTTTAG
1 CCCCTCT-ACAGCTTTAG
25570649 AGGTAAAAGA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 53 0.91
51 4 0.07
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (50 bp):
CCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCAATCTG
Found at i:25583213 original size:13 final size:14
Alignment explanation
Indices: 25583194--25583263 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
25583184 ATTTGTTTGA
25583194 AAATATAAATATAT
1 AAATATAAATATAT
*
25583208 -AATATATATATAT
1 AAATATAAATATAT
25583221 AAAGTATAGAAATATAT
1 AAA-TAT--AAATATAT
* *
25583238 GAA-ATAAATAAAT
1 AAATATAAATATAT
* *
25583251 AAGTACAAATATA
1 AAATATAAATATA
25583264 GTTAACAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
13 20 0.47
14 9 0.21
15 5 0.12
17 9 0.21
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:25583228 original size:9 final size:8
Alignment explanation
Indices: 25583196--25583251 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
25583186 TTGTTTGAAA
25583196 ATATAAAT
1 ATATAAAT
25583204 ATAT-AAT
1 ATATAAAT
25583211 ATAT--AT
1 ATATAAAT
25583217 ATATAAAGT
1 ATATAAA-T
*
25583226 ATAGAAAT
1 ATATAAAT
25583234 ATATGAAAT
1 ATAT-AAAT
*
25583243 AAATAAAT
1 ATATAAAT
25583251 A
1 A
25583252 AGTACAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 6 0.15
7 7 0.17
8 14 0.34
9 14 0.34
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (8 bp):
ATATAAAT
Found at i:25583228 original size:15 final size:15
Alignment explanation
Indices: 25583196--25583251 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
25583186 TTGTTTGAAA
25583196 ATATAAATATATAAT
1 ATATAAATATATAAT
*
25583211 ATATATATATA-AAGT
1 ATATAAATATATAA-T
*
25583226 ATAGAAATATATGAAAT
1 ATATAAATATAT--AAT
*
25583243 AAATAAATA
1 ATATAAATA
25583252 AGTACAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 2 0.06
15 20 0.62
17 8 0.25
18 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (15 bp):
ATATAAATATATAAT
Found at i:25587093 original size:37 final size:37
Alignment explanation
Indices: 25587043--25587119 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
25587033 ATGACTATGT
*
25587043 GTCATCATGAGTATATGATTCCTTTACGGATTATGAG
1 GTCATCATGAGTATATGAATCCTTTACGGATTATGAG
*
25587080 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCATCATGAGTATATGAATCCTTTACGGATTATGAG
25587117 GTC
1 GTC
25587120 CGATGGCTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (37 bp):
GTCATCATGAGTATATGAATCCTTTACGGATTATGAG
Found at i:25587142 original size:52 final size:52
Alignment explanation
Indices: 25587080--25587300 Score: 320
Period size: 52 Copynumber: 4.3 Consensus size: 52
25587070 GGATTATGAG
*
25587080 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGT
** *
25587132 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCTAATGGCTATGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGT
*
25587184 GTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATGACTATGT
1 GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGT
* * * * *
25587236 GCCATCGTGAGCATAT-AGATCTTTTACGGATT-TAAGGTCCGATGACTTTGT
1 GTCATCGTGAGTATATGA-ATCCTTTACGGATTATGAGGTCCGATGACTATGT
*
25587287 GTTATCGTGAGTAT
1 GTCATCGTGAGTAT
25587301 TAAATGGGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
51 28 0.18
52 125 0.82
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (52 bp):
GTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGT
Found at i:25589253 original size:16 final size:16
Alignment explanation
Indices: 25589232--25589265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25589222 GCGAGCCCAA
*
25589232 GTTGCTGCGCGTTGCT
1 GTTGCTGCGCGTTACT
*
25589248 GTTGCTGTGCGTTACT
1 GTTGCTGCGCGTTACT
25589264 GT
1 GT
25589266 CGAGCCAGGT
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:0.03, C:0.21, G:0.35, T:0.41
Consensus pattern (16 bp):
GTTGCTGCGCGTTACT
Found at i:25589504 original size:9 final size:9
Alignment explanation
Indices: 25589492--25589548 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
25589482 TTTTCTAATT
25589492 TTTAATTTA
1 TTTAATTTA
25589501 TTTAATTTA
1 TTTAATTTA
*
25589510 TTTAACTTA
1 TTTAATTTA
25589519 -TTAATTTA
1 TTTAATTTA
*
25589527 TTTAACTTA
1 TTTAATTTA
25589536 -TTAATTTA
1 TTTAATTTA
25589544 TTTAA
1 TTTAA
25589549 ATTGTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 14 0.33
9 28 0.67
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTAATTTA
Found at i:25589548 original size:26 final size:27
Alignment explanation
Indices: 25589492--25589548 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
25589482 TTTTCTAATT
*
25589492 TTTAATTTATTTAATTTATTTAACTTA
1 TTTAATTTATTTAACTTATTTAACTTA
*
25589519 -TTAATTTATTTAACTTA-TTAATTTA
1 TTTAATTTATTTAACTTATTTAACTTA
25589544 TTTAA
1 TTTAA
25589549 ATTGTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTAATTTATTTAACTTATTTAACTTA
Found at i:25589557 original size:17 final size:17
Alignment explanation
Indices: 25589492--25589548 Score: 96
Period size: 17 Copynumber: 3.3 Consensus size: 17
25589482 TTTTCTAATT
*
25589492 TTTAATTTATTTAATTTA
1 TTTAACTTA-TTAATTTA
25589510 TTTAACTTATTAATTTA
1 TTTAACTTATTAATTTA
25589527 TTTAACTTATTAATTTA
1 TTTAACTTATTAATTTA
25589544 TTTAA
1 TTTAA
25589549 ATTGTTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
17 30 0.79
18 8 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAACTTATTAATTTA
Found at i:25591167 original size:41 final size:41
Alignment explanation
Indices: 25591098--25591355 Score: 331
Period size: 41 Copynumber: 6.3 Consensus size: 41
25591088 TTTACATAAA
* **
25591098 CGCCGCAAAAGGT-AGAGCAATAATGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
*
25591138 TC-CCGCTAAAGGTAAGAGCAATAGCGGCGCTTATGGGAAAG
1 -CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * * * *
25591179 CGTCGCTACAGGTCAGAACAATAGCGGTGCTTATTGGCAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* *
25591220 TGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGAGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* *
25591261 CGCCGCTAAAGGTTAGATCAATAGCGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
* * * *
25591302 CGCCGCTAAAGGTCAGATCAATAGTGACGCTTTTGGGAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
25591343 CGCCGCTAAAGGT
1 CGCCGCTAAAGGT
25591356 TAGAACATAA
Statistics
Matches: 189, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 11 0.06
41 178 0.94
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.19
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAG
Found at i:25591682 original size:40 final size:40
Alignment explanation
Indices: 25591625--25591723 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
25591615 AAAAACCGCC
* * * *
25591625 GCAAAAGGTAAATCAATAGCGGCGTTTTTACATTAACGCCA
1 GCAAAAGGTAGAGCAATAGCGACGTTTTTACATAAACG-CA
*
25591666 -TAAAAGGTAGAGCAATAGCGACGTTTTTACATAAACGCA
1 GCAAAAGGTAGAGCAATAGCGACGTTTTTACATAAACGCA
25591705 GCAAAAGGTAGAGCAATAG
1 GCAAAAGGTAGAGCAATAG
25591724 TAACGCTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.04
40 49 0.96
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (40 bp):
GCAAAAGGTAGAGCAATAGCGACGTTTTTACATAAACGCA
Found at i:25591772 original size:41 final size:41
Alignment explanation
Indices: 25591727--25592226 Score: 529
Period size: 41 Copynumber: 12.2 Consensus size: 41
25591717 GCAATAGTAA
* * * *
25591727 CGCTTATGGGAAAGCGCCACTAAAGATAAGAGCAATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
*
25591768 CGCTTATGGGAAAGCGCTGCTAAAGGTCAGAAT-AATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAG-ATCAATAGCGG
* * * * * * *
25591809 CGCTTATTGGCAAGTGCTGCTAAACGTGAGATCAGTAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
*** * **
25591850 CGCTTATGATCAAGCGCCACTAAAGGTCAGAGAAATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
* * * *
25591891 TGCTTATGAGAAAGCACCGTTAAAGGTCAGATCAATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
* * * *
25591932 CGCTTATGGGCAAGCGGCGCTAAGGGTCAGATCAATAGTGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
*
25591973 CGCTTATGGGAAAGCGCCGCTAAAGATCAGATCAATAG-GG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
25592013 ACGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
1 -CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
* *
25592055 CGCTTATGGGCAAGCACCGCTAAAGGTCAGATCAATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
* * * **
25592096 CACTTATGGGAAAACGCTGCTAAAGGTCAGAGAAATAGCGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
** * * * * *
25592137 TTCTTATGGGCAAGCGCTGCTAAAGGTCAGAGCAAAAGTGG
1 CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
* ** * *
25592178 CGCTTATGGGTAAA-TGCCATTAAAGGTCAGAGCATTAGCGG
1 CGCTTATGGG-AAAGCGCCGCTAAAGGTCAGATCAATAGCGG
*
25592219 TGCTTATG
1 CGCTTATG
25592227 TAAAAAACGC
Statistics
Matches: 384, Mismatches: 70, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
40 4 0.01
41 375 0.98
42 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (41 bp):
CGCTTATGGGAAAGCGCCGCTAAAGGTCAGATCAATAGCGG
Found at i:25594126 original size:15 final size:15
Alignment explanation
Indices: 25594106--25594136 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
25594096 CTGTCACCGA
25594106 CGCCTATCACCATTG
1 CGCCTATCACCATTG
25594121 CGCCTATCACCATTG
1 CGCCTATCACCATTG
25594136 C
1 C
25594137 TGTTTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.13, T:0.26
Consensus pattern (15 bp):
CGCCTATCACCATTG
Found at i:25596975 original size:34 final size:33
Alignment explanation
Indices: 25596937--25597072 Score: 191
Period size: 34 Copynumber: 4.0 Consensus size: 33
25596927 TTATAAATAA
*
25596937 TATTTAATTGTTAAAAACAACCTAAATATTTAAT
1 TATTTAATTATTAAAAACAACC-AAATATTTAAT
* * *
25596971 TATTTAATTATTTAAAACAACCCAATTAATTAAT
1 TATTTAATTATTAAAAACAA-CCAAATATTTAAT
* *
25597005 TAATTAATTATTAAAAATAATCCAAATATTTAAT
1 TATTTAATTATTAAAAACAA-CCAAATATTTAAT
25597039 TATTTAATTATTAAAAACAACCAAATATTTAAT
1 TATTTAATTATTAAAAACAACCAAATATTTAAT
25597072 T
1 T
25597073 CAAAATATTT
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
33 14 0.16
34 73 0.82
35 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (33 bp):
TATTTAATTATTAAAAACAACCAAATATTTAAT
Found at i:25597089 original size:22 final size:20
Alignment explanation
Indices: 25597064--25597127 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 20
25597054 AACAACCAAA
25597064 TATTTAATTCAAAATATTTAAT
1 TATTTAATT--AAATATTTAAT
25597086 TATTTAATT--ATATTTAAT
1 TATTTAATTAAATATTTAAT
25597104 TATTTAATTAAATATTTAAT
1 TATTTAATTAAATATTTAAT
25597124 TATT
1 TATT
25597128 AAAAATAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
18 18 0.45
20 13 0.32
22 9 0.22
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTAATTAAATATTTAAT
Found at i:25597127 original size:8 final size:8
Alignment explanation
Indices: 25597078--25597113 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
25597068 TAATTCAAAA
25597078 TATTTAAT
1 TATTTAAT
25597086 TATTTAATT
1 TATTTAA-T
25597095 ATATTTAAT
1 -TATTTAAT
25597104 TATTTAAT
1 TATTTAAT
25597112 TA
1 TA
25597114 AATATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 17 0.65
9 2 0.08
10 7 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTTAAT
Found at i:25603177 original size:43 final size:43
Alignment explanation
Indices: 25603121--25603434 Score: 398
Period size: 43 Copynumber: 7.3 Consensus size: 43
25603111 AATCTGTTAA
* * * *
25603121 TTTAACGGTGTTTGTGGGAAAAGCGCCGCTAAAAATCATGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
* *
25603164 TTTAGTGGCGTTTGTGGGAAAAGCGCCTCTAAAGATCGTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
* * * *
25603207 TTTAGTGGCGTTTTTGGGAAAAGTGCCTCTAAAGATCGTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
* * *
25603250 TTTAGTGGCGTTTTTGGGGAAAA-CGCCGCTAAAGATTGTGTTC
1 TTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGATCGTGTTC
*
25603293 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCGTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
* *
25603336 TTTAGCGGCGTTTGTGAGGAAAA-CGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTG-GGAAAAGCGCCGCTAAAGATCGTGTTC
** * * *
25603379 TTTAGCGATGTTTGTGGGGAAAGCGTCGCTAAAGACCGTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
*
25603422 TATAGCGGCGTTT
1 TTTAGCGGCGTTT
25603435 TTCCACAAAA
Statistics
Matches: 243, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 12 0.05
43 218 0.90
44 13 0.05
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCGTGTTC
Done.