Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 88 of 311
Found at i:28079146 original size:27 final size:28
Alignment explanation
Indices: 28079088--28079177 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
28079078 AGGAAGCGTC
*
28079088 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
28079116 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
28079143 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
28079172 CTGGTG
1 CTGGTG
28079178 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:28079188 original size:29 final size:28
Alignment explanation
Indices: 28079098--28079188 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
28079088 CTGGTGGCTA
* * *
28079098 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
28079126 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
28079153 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
28079182 TGTCACA
1 TGCCACA
28079189 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:28079196 original size:55 final size:56
Alignment explanation
Indices: 28079088--28079202 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
28079078 AGGAAGCGTC
* * *
28079088 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
28079143 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28079199 CTGG
1 CTGG
28079203 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28086791 original size:28 final size:28
Alignment explanation
Indices: 28086759--28086819 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
28086749 ATTTACTAGA
*
28086759 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* *
28086787 ATACCCCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
28086815 ATACC
1 ATACC
28086820 TCTAGGGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:28086970 original size:28 final size:27
Alignment explanation
Indices: 28086929--28087018 Score: 101
Period size: 28 Copynumber: 3.2 Consensus size: 27
28086919 AGGAAGCGTC
28086929 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
28086957 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
28086984 CTGGTGGCACTGCCATAAAATATCTGTAT
1 CTGGTGGCACTGCCA-CAAATATCTGT-T
28087013 CTGGTG
1 CTGGTG
28087019 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:28087037 original size:55 final size:56
Alignment explanation
Indices: 28086929--28087043 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
28086919 AGGAAGCGTC
* * *
28086929 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
28086984 CTGGTGGC-ACTGCCATAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
28087040 CTGG
1 CTGG
28087044 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.58
56 20 0.40
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:28087506 original size:19 final size:19
Alignment explanation
Indices: 28087482--28087520 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28087472 TTTTAATTAT
* *
28087482 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
28087501 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
28087520 T
1 T
28087521 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:28088646 original size:40 final size:40
Alignment explanation
Indices: 28088602--28089100 Score: 827
Period size: 40 Copynumber: 12.5 Consensus size: 40
28088592 GAGAATTGAG
*
28088602 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
28088642 AGTGATGTATCCGGGCTAAGTTCTGAAGAGCATTCGTACT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
** *
28088682 AGTGATGTATCCGAACTAAGTTCCGAAGAGCATTTGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
28088722 AGTGATGTATCCGGGCTAAGTTCCAAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
28088762 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* * *
28088802 AGTGATATATTCGGGCTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
28088842 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* **
28088882 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCCCGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
28088922 AGTGATGTATCCGGGCTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
28088962 AGTGATGTATCCGGTCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
28089002 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* * *
28089042 AGTGATATATCTGGGCTAAGTTCTGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
28089082 AGTGATATATCCGGGCTAA
1 AGTGATGTATCCGGGCTAA
28089101 ACCTCGAAGG
Statistics
Matches: 426, Mismatches: 33, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 426 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
Found at i:28089194 original size:29 final size:28
Alignment explanation
Indices: 28089160--28089288 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
28089150 CTTCAACCGA
* *
28089160 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
28089189 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
28089217 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
28089246 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
28089274 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
28089289 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:28089218 original size:57 final size:57
Alignment explanation
Indices: 28089128--28089295 Score: 239
Period size: 57 Copynumber: 2.9 Consensus size: 57
28089118 GCTGGAATTA
* * * *
28089128 TGAGGCACTGTGTGTG-GAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCG-AGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
**
28089185 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
* * *
28089242 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT
28089296 CAGTGGCACT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 98 0.99
58 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAAT
Found at i:28089229 original size:28 final size:27
Alignment explanation
Indices: 28089132--28089288 Score: 136
Period size: 28 Copynumber: 5.6 Consensus size: 27
28089122 GAATTATGAG
* *
28089132 GCACTGTGTGTG-GAAGTTCTTCAACCGA
1 GCACTATGTGTGCG-AGTTCTT-AATCGA
* * * * *
28089160 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
28089188 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
28089217 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
28089245 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
28089274 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
28089289 AATCAGTCAG
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
28 56 0.54
29 47 0.46
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:28092689 original size:47 final size:47
Alignment explanation
Indices: 28092635--28092966 Score: 522
Period size: 47 Copynumber: 7.1 Consensus size: 47
28092625 TTAGGATTTT
** *
28092635 ATGTGATGAATGTGAATGTGCATATATGTGATAAGGCCGAATAGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28092682 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28092729 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28092776 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
28092823 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
** **
28092870 ATGTGATGAATAAGAACATGCATATATGTGATAAGGCAAAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
28092917 ATGTGACGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
28092964 ATG
1 ATG
28092967 CGAAATGTGT
Statistics
Matches: 266, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
47 263 0.99
48 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:28093083 original size:46 final size:46
Alignment explanation
Indices: 28092940--28093058 Score: 186
Period size: 46 Copynumber: 2.6 Consensus size: 46
28092930 GGAAGTGTAT
* *
28092940 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATATGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
28092986 GTATGA-GGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATAT-ATGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
*
28093032 ATATATGGTAAAGCCAAATGGCTAATG
1 ATATATGGTAAAGCCGAATGGCTAATG
28093059 TGAGAGATGT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
45 1 0.02
46 65 0.98
ACGTcount: A:0.34, C:0.10, G:0.31, T:0.24
Consensus pattern (46 bp):
ATATATGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
Found at i:28095819 original size:32 final size:32
Alignment explanation
Indices: 28095775--28095841 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
28095765 TACTCAATTG
* *
28095775 AATTTCCATACATACCTGTACCATCTTGTACC
1 AATTTCCATACATACCTATACCATCTCGTACC
*
28095807 AATTTCCGTACATACCTATACCATCTCGTACC
1 AATTTCCATACATACCTATACCATCTCGTACC
28095839 AAT
1 AAT
28095842 CTCATACTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.31, G:0.06, T:0.33
Consensus pattern (32 bp):
AATTTCCATACATACCTATACCATCTCGTACC
Found at i:28096067 original size:84 final size:84
Alignment explanation
Indices: 28095906--28096071 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 84
28095896 GTTACTCAGA
* * *
28095906 ATCTCGCACACTAAGTGTCAATACGTAGCCGAAGCTAACTCAATCACGCACACAAAGTGCCAATG
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAACCCAATCACGCACACAAAGTGCCAATG
* *
28095971 CATAGCCGAAGCTATCTTG
66 CATAACCAAAGCTATCTTG
* * * * * * *
28095990 ATCTCGTACACTGAGTGCCAATGCATAGCCGAAGCTATCCCTATCTCGCACACTAAGTGCCAATG
1 ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAACCCAATCACGCACACAAAGTGCCAATG
*
28096055 CATAACTAAAGCTATCT
66 CATAACCAAAGCTATCT
28096072 CAAATATTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (84 bp):
ATCTCGCACACTAAGTGCCAATACATAGCCGAAGCTAACCCAATCACGCACACAAAGTGCCAATG
CATAACCAAAGCTATCTTG
Found at i:28096070 original size:42 final size:42
Alignment explanation
Indices: 28095906--28096058 Score: 191
Period size: 42 Copynumber: 3.6 Consensus size: 42
28095896 GTTACTCAGA
* * * * * *
28095906 ATCTCGCACACTAAGTGTCAATACGTAGCCGAAGCTAACTCA
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCCCT
* * *
28095948 ATCACGCACACAAAGTGCCAATGCATAGCCGAAGCTAT-CTT
1 ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCCCT
* *
28095989 GATCTCGTACACTGAGTGCCAATGCATAGCCGAAGCTATCCCT
1 -ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCCCT
28096032 ATCTCGCACACTAAGTGCCAATGCATA
1 ATCTCGCACACTAAGTGCCAATGCATA
28096059 ACTAAAGCTA
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 91 0.98
43 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (42 bp):
ATCTCGCACACTAAGTGCCAATGCATAGCCGAAGCTATCCCT
Found at i:28101830 original size:25 final size:25
Alignment explanation
Indices: 28101802--28101861 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
28101792 GGACGCTTAT
28101802 AAGAGCCATAATTAGGAAGCTCACA
1 AAGAGCCATAATTAGGAAGCTCACA
* *
28101827 AAGAACCAT-ATTGGGAAGCTCACA
1 AAGAGCCATAATTAGGAAGCTCACA
28101851 AAGAGCCATAA
1 AAGAGCCATAA
28101862 AACGGGACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (25 bp):
AAGAGCCATAATTAGGAAGCTCACA
Found at i:28101977 original size:26 final size:26
Alignment explanation
Indices: 28101908--28101980 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
28101898 AGTGAGCACT
* *
28101908 ATCGGGAAGCTCACAAAGAGCCTTAA
1 ATCGGGAAGCTCACGAAGAGCCATAA
** *
28101934 ATCTAGAAGCTCATGAAGAGCCATATA
1 ATCGGGAAGCTCACGAAGAGCCATA-A
28101961 ATCGGGAAGCTCA-GAAGAGC
1 ATCGGGAAGCTCACGAAGAGC
28101981 TAAGGTGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 27 0.69
27 12 0.31
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (26 bp):
ATCGGGAAGCTCACGAAGAGCCATAA
Found at i:28107560 original size:17 final size:18
Alignment explanation
Indices: 28107538--28107578 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
28107528 TTCTATCAAA
28107538 TTCCTTTTTTC-CCTATT
1 TTCCTTTTTTCTCCTATT
28107555 TTCC-TTTTTCTCCTATT
1 TTCCTTTTTTCTCCTATT
*
28107572 TCCCTTT
1 TTCCTTT
28107579 CGATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (18 bp):
TTCCTTTTTTCTCCTATT
Found at i:28111569 original size:21 final size:21
Alignment explanation
Indices: 28111513--28111570 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
28111503 ATATTGATAT
* *
28111513 ACATGATATGAC-CTGATATGC
1 ACATGATATG-CTATGACATGC
*
28111534 ACATGATATGTTATGACATGC
1 ACATGATATGCTATGACATGC
28111555 ACATGATATGCTATGA
1 ACATGATATGCTATGA
28111571 TATACTCATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGACATGC
Found at i:28111655 original size:25 final size:25
Alignment explanation
Indices: 28111619--28111687 Score: 120
Period size: 25 Copynumber: 2.8 Consensus size: 25
28111609 GGAGGAAGTG
28111619 CAAAAAGGGCTTTGCCCCAGTTTAC
1 CAAAAAGGGCTTTGCCCCAGTTTAC
* *
28111644 CGAAAAGGGCTTTGCCCCAGTTTAT
1 CAAAAAGGGCTTTGCCCCAGTTTAC
28111669 CAAAAAGGGCTTTGCCCCA
1 CAAAAAGGGCTTTGCCCCA
28111688 ATTATTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (25 bp):
CAAAAAGGGCTTTGCCCCAGTTTAC
Found at i:28111703 original size:24 final size:25
Alignment explanation
Indices: 28111621--28111703 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
28111611 AGGAAGTGCA
* *
28111621 AAAAG-GGCTTTGCCCCAGTTTACC
1 AAAAGAGGCTTTGCCCCAGATTATC
*
28111645 GAAAAG-GGCTTTGCCCCAGTTTATC
1 -AAAAGAGGCTTTGCCCCAGATTATC
*
28111670 AAAA-AGGGCTTTGCCCCA-ATTATT
1 AAAAGA-GGCTTTGCCCCAGATTATC
28111694 AAAAGAGGCT
1 AAAAGAGGCT
28111704 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 16 0.31
25 36 0.69
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGATTATC
Found at i:28111714 original size:50 final size:50
Alignment explanation
Indices: 28111619--28111715 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 50
28111609 GGAGGAAGTG
* **
28111619 CAAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTAT
1 CAAAAAGGGCTTTGCCCCAGATTACCGAAAAGGGCTAGGCCCCAGTTTAT
**
28111669 CAAAAAGGGCTTTGCCCCA-ATTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 CAAAAAGGGCTTTGCCCCAGATTACCGAAAAG-GGCTAGGCC-CCAGTT
28111716 ACATGATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 5 0.12
49 10 0.25
50 25 0.62
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (50 bp):
CAAAAAGGGCTTTGCCCCAGATTACCGAAAAGGGCTAGGCCCCAGTTTAT
Found at i:28117063 original size:21 final size:21
Alignment explanation
Indices: 28117039--28117079 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
28117029 ATGACCTAAT
*
28117039 ATGCACATGATATGTTATGAC
1 ATGCACATGATATGCTATGAC
28117060 ATGCACATGATATGCTATGA
1 ATGCACATGATATGCTATGA
28117080 TATACTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (21 bp):
ATGCACATGATATGCTATGAC
Found at i:28117188 original size:24 final size:25
Alignment explanation
Indices: 28117130--28117188 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
28117120 AGGAAGTGCA
*
28117130 AAAAGGGGCTTTGCCCCAGTTTATC
1 AAAAGAGGCTTTGCCCCAGTTTATC
*
28117155 AAAA-AGGGCTTTGCCCCAG-TTATT
1 AAAAGA-GGCTTTGCCCCAGTTTATC
28117179 AAAAGAGGCT
1 AAAAGAGGCT
28117189 AGGCCTCCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGTTTATC
Found at i:28122063 original size:18 final size:18
Alignment explanation
Indices: 28122040--28122075 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28122030 TTTGAGGGAC
28122040 TAAAATGTGAAATTAATG
1 TAAAATGTGAAATTAATG
28122058 TAAAATGTGAAATTAATG
1 TAAAATGTGAAATTAATG
28122076 AAATATATGG
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:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (18 bp):
TAAAATGTGAAATTAATG
Found at i:28132444 original size:13 final size:13
Alignment explanation
Indices: 28132423--28132455 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28132413 TTAATTAACC
*
28132423 TTTGAGACTTATG
1 TTTGTGACTTATG
28132436 TTTGTGACTTATG
1 TTTGTGACTTATG
28132449 TTTGTGA
1 TTTGTGA
28132456 TTAATTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.24, T:0.52
Consensus pattern (13 bp):
TTTGTGACTTATG
Found at i:28138563 original size:8 final size:7
Alignment explanation
Indices: 28138526--28138560 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
28138516 GAATTGTATG
28138526 ATAAAAA
1 ATAAAAA
*
28138533 A-ATAAA
1 ATAAAAA
28138539 ATAAAAA
1 ATAAAAA
28138546 ATAAAAA
1 ATAAAAA
28138553 ATAAAAA
1 ATAAAAA
28138560 A
1 A
28138561 ATACAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:28148410 original size:7 final size:7
Alignment explanation
Indices: 28148345--28148406 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
28148335 ATTAAAAATA
28148345 ATTGAGG
1 ATTGAGG
28148352 ATTGAGG
1 ATTGAGG
28148359 ATTGAGG
1 ATTGAGG
28148366 ATTGAGG
1 ATTGAGG
* *
28148373 ATTAAGA
1 ATTGAGG
*
28148380 ATTGATG
1 ATTGAGG
**
28148387 ATTGAAA
1 ATTGAGG
*
28148394 ATTGAGT
1 ATTGAGG
28148401 ATTGAG
1 ATTGAG
28148407 TATTAAATTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (7 bp):
ATTGAGG
Found at i:28148644 original size:38 final size:38
Alignment explanation
Indices: 28148593--28148670 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
28148583 TGTTGGTTCT
*
28148593 GAGTTTTATTTTGTAAAACAACTATATATTTTTTTAAG
1 GAGTTTTATTTTGTAAAACAACTATATATATTTTTAAG
*
28148631 GAGTTTTATTTTGTGAAACAACTATATATATTTTTAAG
1 GAGTTTTATTTTGTAAAACAACTATATATATTTTTAAG
28148669 GA
1 GA
28148671 ATGAAGGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (38 bp):
GAGTTTTATTTTGTAAAACAACTATATATATTTTTAAG
Found at i:28150263 original size:27 final size:28
Alignment explanation
Indices: 28150200--28150263 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
28150190 AATAATCAAT
*
28150200 TACAGTCTGGGGCCTGAGCCCATTACAGA
1 TACAGT-TTGGGCCTGAGCCCATTACAGA
*
28150229 TTCAGTTTGGGCCTTG-GCCCATT-CAGA
1 TACAGTTTGGGCC-TGAGCCCATTACAGA
28150256 TACAGTTT
1 TACAGTTT
28150264 CAAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 11 0.35
28 13 0.42
29 7 0.23
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (28 bp):
TACAGTTTGGGCCTGAGCCCATTACAGA
Found at i:28158514 original size:14 final size:15
Alignment explanation
Indices: 28158495--28158523 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28158485 AGATATCTCA
28158495 TATTCAAT-GCATAT
1 TATTCAATAGCATAT
28158509 TATTCAATAGCATAT
1 TATTCAATAGCATAT
28158524 AAGCACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
TATTCAATAGCATAT
Found at i:28162079 original size:19 final size:19
Alignment explanation
Indices: 28162032--28162071 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
28162022 AGAGAATTTT
28162032 GATGAAATTGTGATTTAGG
1 GATGAAATTGTGATTTAGG
28162051 GATGAAATTGTGATTTAGG
1 GATGAAATTGTGATTTAGG
28162070 GA
1 GA
28162072 CTAAATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (19 bp):
GATGAAATTGTGATTTAGG
Found at i:28176065 original size:12 final size:12
Alignment explanation
Indices: 28176048--28176072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28176038 CTACAACAAC
28176048 AGTTTGAAGATG
1 AGTTTGAAGATG
28176060 AGTTTGAAGATG
1 AGTTTGAAGATG
28176072 A
1 A
28176073 CACCTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AGTTTGAAGATG
Found at i:28202204 original size:80 final size:80
Alignment explanation
Indices: 28202105--28202259 Score: 240
Period size: 80 Copynumber: 1.9 Consensus size: 80
28202095 GTACCCCCGG
* * * * *
28202105 TTTGTAAAATTACCGAAATACCCTCTATTTGTAAAATTACTGAAATACCCCTA-ATTTGTTAAAT
1 TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACAGAAATACCCCTATA-GTGTAAAAT
28202169 TACCGAAATACTCCAA
65 TACCGAAATACTCCAA
*
28202185 TTTGTAAAATTACCAAAATACTCTCAATTTGTAAAATTACAGAAATACCCCTATAGTGTAAAATT
1 TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACAGAAATACCCCTATAGTGTAAAATT
28202250 ACCGAAATAC
66 ACCGAAATAC
28202260 CCTTGTAGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 67 0.99
81 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (80 bp):
TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACAGAAATACCCCTATAGTGTAAAATT
ACCGAAATACTCCAA
Found at i:28202214 original size:53 final size:53
Alignment explanation
Indices: 28202079--28202290 Score: 221
Period size: 54 Copynumber: 4.0 Consensus size: 53
28202069 AGACCCCGGA
* * ***
28202079 TTGTAAAATTATCGAAGTACCCCCGGTTTGTAAAATTACCGAAATACCCTCTAT
1 TTGTAAAATTACCGAAATACCCCTAATTTGTAAAATTACCGAAATACCC-CTAT
* * * *
28202133 TTGTAAAATTACTGAAATACCCCTAATTTGTTAAATTACCGAAATACTCCAAT
1 TTGTAAAATTACCGAAATACCCCTAATTTGTAAAATTACCGAAATACCCCTAT
* * *
28202186 TTGTAAAATTACCAAAATA-CTCTCAATTTGTAAAATTACAGAAATACCCCTAT
1 TTGTAAAATTACCGAAATACCCCT-AATTTGTAAAATTACCGAAATACCCCTAT
* ** * *
28202239 AGTGTAAAATTACCGAAATA-CCCTTGTAGTGTAAAATTATCGAAATACCCCT
1 -TTGTAAAATTACCGAAATACCCCTAAT-TTGTAAAATTACCGAAATACCCCT
28202291 GTAAGGCAAA
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
52 3 0.02
53 46 0.35
54 82 0.63
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (53 bp):
TTGTAAAATTACCGAAATACCCCTAATTTGTAAAATTACCGAAATACCCCTAT
Found at i:28202293 original size:27 final size:27
Alignment explanation
Indices: 28202078--28202293 Score: 181
Period size: 27 Copynumber: 8.0 Consensus size: 27
28202068 AAGACCCCGG
* * *
28202078 ATTGTAAAATTATCGAAGTACCCCCGGT
1 ATTGTAAAATTACCGAAATA-CCCCTGT
*
28202106 -TTGTAAAATTACCGAAATA-CCCTCT
1 ATTGTAAAATTACCGAAATACCCCTGT
* *
28202131 ATTTGTAAAATTACTGAAATACCCCT-A
1 A-TTGTAAAATTACCGAAATACCCCTGT
* * **
28202158 ATTTGTTAAATTACCGAAATACTCCAAT
1 A-TTGTAAAATTACCGAAATACCCCTGT
* * **
28202186 -TTGTAAAATTACCAAAATA-CTCTCA
1 ATTGTAAAATTACCGAAATACCCCTGT
* *
28202211 ATTTGTAAAATTACAGAAATACCCCTAT
1 A-TTGTAAAATTACCGAAATACCCCTGT
* *
28202239 AGTGTAAAATTACCGAAATACCCTTGT
1 ATTGTAAAATTACCGAAATACCCCTGT
* *
28202266 AGTGTAAAATTATCGAAATACCCCTGT
1 ATTGTAAAATTACCGAAATACCCCTGT
28202293 A
1 A
28202294 AGGCAAAATG
Statistics
Matches: 152, Mismatches: 29, Indels: 15
0.78 0.15 0.08
Matches are distributed among these distances:
25 5 0.03
26 17 0.11
27 122 0.80
28 8 0.05
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.31
Consensus pattern (27 bp):
ATTGTAAAATTACCGAAATACCCCTGT
Found at i:28208799 original size:38 final size:38
Alignment explanation
Indices: 28208749--28208824 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
28208739 GAGGCTGATA
* * *
28208749 TGTGTAATCGTTTTGAAGAGGGTTTAAATGAAGATATC
1 TGTGTAAACGTTTGGAAGAGGGCTTAAATGAAGATATC
28208787 TGTGTAAACGTTTGGAAGAGGGCTTAAATGAAGATATC
1 TGTGTAAACGTTTGGAAGAGGGCTTAAATGAAGATATC
28208825 AAGCTATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (38 bp):
TGTGTAAACGTTTGGAAGAGGGCTTAAATGAAGATATC
Found at i:28242663 original size:19 final size:19
Alignment explanation
Indices: 28242639--28242686 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
28242629 TCATCCCTAT
28242639 ATCCCTCATCCTTTACTCA
1 ATCCCTCATCCTTTACTCA
28242658 ATCCCTCATCCTTTACTCA
1 ATCCCTCATCCTTTACTCA
28242677 ATCCCTCATC
1 ATCCCTCATC
28242687 TCTCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (19 bp):
ATCCCTCATCCTTTACTCA
Found at i:28243045 original size:35 final size:35
Alignment explanation
Indices: 28242999--28243066 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
28242989 TTGAAGTTTG
28242999 TTTAAATCATGTCTATGGTGTTTGTGCCTCAGTTA
1 TTTAAATCATGTCTATGGTGTTTGTGCCTCAGTTA
28243034 TTTAAATCATGTCTATGGTGTTTGTGCCTCAGT
1 TTTAAATCATGTCTATGGTGTTTGTGCCTCAGT
28243067 CGATCATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.46
Consensus pattern (35 bp):
TTTAAATCATGTCTATGGTGTTTGTGCCTCAGTTA
Found at i:28246357 original size:93 final size:93
Alignment explanation
Indices: 28246245--28246416 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
28246235 CGCCCATAAG
*
28246245 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
28246309 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
28246338 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28246403 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28246417 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28246411 original size:46 final size:46
Alignment explanation
Indices: 28246238--28246413 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
28246228 TGTAACCCGC
* *
28246238 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
28246284 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28246334 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28246377 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28246414 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28253927 original size:93 final size:93
Alignment explanation
Indices: 28253815--28253986 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28253805 CGCCCATAAG
* *
28253815 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28253880 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28253908 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28253973 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28253987 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28253983 original size:46 final size:46
Alignment explanation
Indices: 28253808--28253983 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28253798 TGTAACCCGC
* * *
28253808 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
28253854 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28253904 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28253947 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28253984 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28257174 original size:18 final size:18
Alignment explanation
Indices: 28257151--28257208 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
28257141 TTCCCTACAG
28257151 AGTCCAATCTGGATTACC
1 AGTCCAATCTGGATTACC
* * *
28257169 AGTCCAAGCT-AAAT-CC
1 AGTCCAATCTGGATTACC
28257185 AGT-CAAT-TAGGATTACC
1 AGTCCAATCT-GGATTACC
28257202 AGTCCAA
1 AGTCCAA
28257209 GCTTAATCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 1 0.03
15 3 0.10
16 7 0.23
17 7 0.23
18 12 0.40
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (18 bp):
AGTCCAATCTGGATTACC
Found at i:28259405 original size:37 final size:37
Alignment explanation
Indices: 28259355--28259433 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
28259345 TTATTACGAA
* * *
28259355 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
28259392 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
28259429 GTCTT
1 GTCTT
28259434 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:28259824 original size:49 final size:47
Alignment explanation
Indices: 28259552--28260243 Score: 1096
Period size: 47 Copynumber: 14.5 Consensus size: 47
28259542 CCCTTCGGGA
* * * * * * * *
28259552 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28259599 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28259646 CTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28259693 CTTATTACAGATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28259740 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28259787 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28259836 CTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
28259885 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
28259934 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28259983 CTTATCACATATATACACTTTCACATTCATCACATCTGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28260030 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28260077 CTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
28260126 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28260175 CTTATCACATATATACACTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28260222 CTTATCACATATATACACTTTC
1 CTTATCACATATATACACTTTC
28260244 TTGGCTGAAT
Statistics
Matches: 613, Mismatches: 28, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
47 328 0.54
49 285 0.46
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28260048 original size:192 final size:192
Alignment explanation
Indices: 28259567--28260243 Score: 1137
Period size: 192 Copynumber: 3.5 Consensus size: 192
28259557 CACATTTATG
* * * * * * * *
28259567 CACTTTCACATCCATTACGTTGGCCACTCGGCCCTGTCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
*
28259632 ATCGGCCATTAGGCCTTATCACATATATACACTTTCCCATTCATCACATCGGCCATTAGGCCTTA
66 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
* * *
28259697 TTACAGAT--ATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACAT--ATA
131 TCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACATA
*
28259755 CACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACATACACTTTCACATTCATC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT--ATACACTTTCACATTCATC
*
28259820 ACATCGGCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGC
64 ACATCGGCCATTAGGCCTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28259885 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATACAT
127 CTTATCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACAT
28259950 A
192 A
28259951 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
*
28260016 ATCTGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
66 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
28260081 TCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACATA
131 TCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACATA
28260143 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
*
28260208 ATCGGTCATTAGGCCTTATCACATATATACACTTTC
66 ATCGGCCATTAGGCCTTATCACATATATACACTTTC
28260244 TTGGCTGAAT
Statistics
Matches: 460, Mismatches: 21, Indels: 12
0.93 0.04 0.02
Matches are distributed among these distances:
188 35 0.08
190 47 0.10
192 241 0.52
194 91 0.20
196 46 0.10
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (192 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
ATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
TCACATATACATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACATA
Found at i:28266195 original size:2 final size:2
Alignment explanation
Indices: 28266188--28266215 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28266178 TGAGTGCTTA
28266188 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28266216 AAGTCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:28267493 original size:10 final size:10
Alignment explanation
Indices: 28267480--28267511 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
28267470 TGATACCATT
28267480 CAATACAACA
1 CAATACAACA
28267490 CAATACAACA
1 CAATACAACA
28267500 CAATACAACA
1 CAATACAACA
28267510 CA
1 CA
28267512 TATCATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.09
Consensus pattern (10 bp):
CAATACAACA
Found at i:28267713 original size:23 final size:24
Alignment explanation
Indices: 28267676--28267725 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
28267666 CGATAACAAT
28267676 ATGCAAAAAATTCTGCCAGTAAAA
1 ATGCAAAAAATTCTGCCAGTAAAA
28267700 ATGCAAAAAA-TCTGCCAGTAAAA
1 ATGCAAAAAATTCTGCCAGTAAAA
28267723 ATG
1 ATG
28267726 TGATAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
ATGCAAAAAATTCTGCCAGTAAAA
Found at i:28269277 original size:18 final size:17
Alignment explanation
Indices: 28269251--28269284 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28269241 CCATAATGCG
28269251 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
28269269 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
28269285 AAGCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:28269384 original size:17 final size:18
Alignment explanation
Indices: 28269362--28269396 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28269352 GTTTACCCAT
*
28269362 GTGGGGCCTACA-AGCCC
1 GTGGGGCCCACACAGCCC
28269379 GTGGGGCCCACACAGCCC
1 GTGGGGCCCACACAGCCC
28269397 ATTTCAGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.17, C:0.40, G:0.34, T:0.09
Consensus pattern (18 bp):
GTGGGGCCCACACAGCCC
Found at i:28277835 original size:216 final size:216
Alignment explanation
Indices: 28277461--28277892 Score: 819
Period size: 216 Copynumber: 2.0 Consensus size: 216
28277451 AGTACTAGTA
28277461 TTAACCTTCTTGTTATTATCTAGCCTAAAAATAAGGGGATTTGCTTTATCTAAACTAATTAACTA
1 TTAACCTTCTTGTTATTATCTAGCCTAAAAATAAGGGGATTTGCTTTATCTAAACTAATTAACTA
28277526 AATTAAGAATGCACAAGAAGTAAATTGGGGAAATACTTTTGGGAAAACTGATTGATTTAAACAAT
66 AATTAAGAATGCACAAGAAGTAAATTGGGGAAATACTTTTGGGAAAACTGATTGATTTAAACAAT
*
28277591 ACCCAAGGAAGAATCCACCTAGACTTCACTTGATATTTGACTCTGAAATAGACAATTTATTCACT
131 ACCCAAGGAAGAACCCACCTAGACTTCACTTGATATTTGACTCTGAAATAGACAATTTATTCACT
28277656 TGACTCGATCCATAGAAATCC
196 TGACTCGATCCATAGAAATCC
*
28277677 TTAACCTTCTTTTTATTATCTAGCCTAAAAATAAGGGGATTTGCTTTATCTAAACTAATTAACTA
1 TTAACCTTCTTGTTATTATCTAGCCTAAAAATAAGGGGATTTGCTTTATCTAAACTAATTAACTA
*
28277742 AATTAAGAATGCACAGGAAGTAAATTGGGGAAATACTTTTGGGAAAACTGATTGATTTAAACAAT
66 AATTAAGAATGCACAAGAAGTAAATTGGGGAAATACTTTTGGGAAAACTGATTGATTTAAACAAT
* *
28277807 ACCCAAGGAAGAACCCACCTAGACTTCACTTGATATTTGACTCTGAACTAGACGATTTATTCACT
131 ACCCAAGGAAGAACCCACCTAGACTTCACTTGATATTTGACTCTGAAATAGACAATTTATTCACT
28277872 TGACTCGATCCATAGAAATCC
196 TGACTCGATCCATAGAAATCC
28277893 CTAATTTATA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
216 211 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (216 bp):
TTAACCTTCTTGTTATTATCTAGCCTAAAAATAAGGGGATTTGCTTTATCTAAACTAATTAACTA
AATTAAGAATGCACAAGAAGTAAATTGGGGAAATACTTTTGGGAAAACTGATTGATTTAAACAAT
ACCCAAGGAAGAACCCACCTAGACTTCACTTGATATTTGACTCTGAAATAGACAATTTATTCACT
TGACTCGATCCATAGAAATCC
Found at i:28278646 original size:48 final size:48
Alignment explanation
Indices: 28278574--28278677 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
28278564 GTGCCATGCC
* * * *
28278574 CGTGTGGGGTGGTTTAGGCTATGTTA-AAGTCTGCTAAATAGACACGGG
1 CGTGTGGTGTGGCTTAGGCCATGTTACAA-TCTGCTAAATAGACACGAG
**
28278622 CGTGTGGTGTGGCTTAGGCCATGTTACAATCTTTTAAATAGACACGAG
1 CGTGTGGTGTGGCTTAGGCCATGTTACAATCTGCTAAATAGACACGAG
28278670 CGTGTGGT
1 CGTGTGGT
28278678 CTACCCGTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (48 bp):
CGTGTGGTGTGGCTTAGGCCATGTTACAATCTGCTAAATAGACACGAG
Found at i:28282995 original size:55 final size:55
Alignment explanation
Indices: 28282892--28283020 Score: 143
Period size: 55 Copynumber: 2.3 Consensus size: 55
28282882 TGCACAAATG
* * * * * *
28282892 CGCACGCCCATGTTATTTTCACAGTTTCAACCACGGTTGGTAGGCACGGGCATGT
1 CGCACGCCCATGTTAATTTCACAGTTTCAACCAAGGTTGATAGACACGGACAGGT
* * * *
28282947 CGCACGCCCGTGTTAATTTCTCAGTTTCTACCAAGGATT-ATAGACACGGACGGGT
1 CGCACGCCCATGTTAATTTCACAGTTTCAACCAAGG-TTGATAGACACGGACAGGT
*
28283002 CGCACGCCCATGTTGATTT
1 CGCACGCCCATGTTAATTT
28283021 GGTAGGATTG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 59 0.97
56 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (55 bp):
CGCACGCCCATGTTAATTTCACAGTTTCAACCAAGGTTGATAGACACGGACAGGT
Found at i:28287457 original size:46 final size:45
Alignment explanation
Indices: 28287407--28287582 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 45
28287397 TGTTTGGGCA
*
28287407 TCCGAACTCGTTGAGTGGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
*
28287453 TCCGAACTCGTTGAGTTGAGTCCGA-TT---TTGA-GAGATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTT-ATG-GATGGAA-T--G
* * *
28287498 CATCCGAGCTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGAGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
28287546 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCATTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28287583 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
42 5 0.05
43 6 0.06
45 3 0.03
46 58 0.54
47 23 0.21
48 3 0.03
50 5 0.05
51 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:28289998 original size:48 final size:48
Alignment explanation
Indices: 28289912--28290015 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
28289902 GTGCCACGCC
* * *
28289912 CGTGTGGGGTGGTTTAGGCCGGGTTAAAGTCTGCTAAATAGAAACGGG
1 CGTGTGGTGTGGCTTAGGCCGGGTTAAAGTCTACTAAATAGAAACGGG
* * * *
28289960 CGTGTGGTGTGGCTTAGGCCGTGTTACAA-TCTATTAAATAGACATGGG
1 CGTGTGGTGTGGCTTAGGCCGGGTTA-AAGTCTACTAAATAGAAACGGG
*
28290008 CATGTGGT
1 CGTGTGGT
28290016 CTACCCGTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 45 0.96
49 2 0.04
ACGTcount: A:0.22, C:0.13, G:0.36, T:0.29
Consensus pattern (48 bp):
CGTGTGGTGTGGCTTAGGCCGGGTTAAAGTCTACTAAATAGAAACGGG
Found at i:28293555 original size:125 final size:125
Alignment explanation
Indices: 28293333--28293584 Score: 495
Period size: 125 Copynumber: 2.0 Consensus size: 125
28293323 TAACCCTTGT
28293333 CTGATGTCGAAACAAGTTACGAAGCATTACCGGACTTATAAATCAAACAATCATACGTTTCATGA
1 CTGATGTCGAAACAAGTTACGAAGCATTACCGGACTTATAAATCAAACAATCATACGTTTCATGA
28293398 CCAATTCTCTAACAAATTAAAATCCATTCATAAACATTCATATAGTCCCTAATACGAGCC
66 CCAATTCTCTAACAAATTAAAATCCATTCATAAACATTCATATAGTCCCTAATACGAGCC
28293458 CTGATGTCGAAACAAGTTACGAAGCATTACCGGACTTATAAATCAAACAATCATACGTTTCATGA
1 CTGATGTCGAAACAAGTTACGAAGCATTACCGGACTTATAAATCAAACAATCATACGTTTCATGA
*
28293523 CCAATTCTCTAACAAATTAAAATCCATTCATAAACATTCATATAGTCCTTAATACGAGCC
66 CCAATTCTCTAACAAATTAAAATCCATTCATAAACATTCATATAGTCCCTAATACGAGCC
28293583 CT
1 CT
28293585 CGAGGCCCCA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (125 bp):
CTGATGTCGAAACAAGTTACGAAGCATTACCGGACTTATAAATCAAACAATCATACGTTTCATGA
CCAATTCTCTAACAAATTAAAATCCATTCATAAACATTCATATAGTCCCTAATACGAGCC
Found at i:28298663 original size:19 final size:18
Alignment explanation
Indices: 28298641--28298689 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
28298631 TTTTCTTATA
*
28298641 ATATTTTAAAAAATTATTT
1 ATATTTTAAAAAATT-TCT
*
28298660 ATATTTCTAATAAATTTCT
1 ATATTT-TAAAAAATTTCT
28298679 ATATTTTAAAA
1 ATATTTTAAAA
28298690 CAAATCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 8 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTTAAAAAATTTCT
Found at i:28298814 original size:17 final size:17
Alignment explanation
Indices: 28298710--28298820 Score: 68
Period size: 17 Copynumber: 6.2 Consensus size: 17
28298700 TTTTTACAAT
*
28298710 TTTTCTATATTTTCATAA
1 TTTTATATATTTT-ATAA
*
28298728 -TTTATATTTTTTATAA
1 TTTTATATATTTTATAA
28298744 -TTTATAT-TTTTAATATA
1 TTTTATATATTTT-ATA-A
* *
28298761 TTTAAATTTAAATTTTATAA
1 TTT---TATATATTTTATAA
28298781 -TTTATAATAATTTTTATAA
1 TTTTAT-AT-A-TTTTATAA
*
28298800 TTTTCTATATTTTATAA
1 TTTTATATATTTTATAA
28298817 TTTT
1 TTTT
28298821 TTTAATTTGT
Statistics
Matches: 75, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
15 4 0.05
16 16 0.21
17 24 0.32
18 4 0.05
19 12 0.16
20 5 0.07
21 6 0.08
22 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATATATTTTATAA
Found at i:28298826 original size:9 final size:9
Alignment explanation
Indices: 28298696--28298828 Score: 76
Period size: 9 Copynumber: 15.8 Consensus size: 9
28298686 AAAACAAATC
28298696 ATAATTTTT
1 ATAATTTTT
*
28298705 ACAATTTTT
1 ATAATTTTT
* *
28298714 CTATATTTTC
1 ATA-ATTTTT
28298724 ATAA--TTT
1 ATAATTTTT
*
28298731 ATATTTTTT
1 ATAATTTTT
28298740 ATAA--TTT
1 ATAATTTTT
28298747 AT-ATTTTT
1 ATAATTTTT
*
28298755 A-ATATATTT
1 ATA-ATTTTT
28298764 A-AA--TTT
1 ATAATTTTT
28298770 A-AA-TTTT
1 ATAATTTTT
*
28298777 ATAATTTATA
1 ATAATTT-TT
28298787 ATAATTTTT
1 ATAATTTTT
28298796 ATAATTTTCT
1 ATAATTTT-T
28298806 AT-A-TTTT
1 ATAATTTTT
28298813 ATAATTTTT
1 ATAATTTTT
*
28298822 TTAATTT
1 ATAATTT
28298829 GTAGAGTCCT
Statistics
Matches: 98, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
6 7 0.07
7 17 0.17
8 11 0.11
9 45 0.46
10 18 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:28302242 original size:19 final size:21
Alignment explanation
Indices: 28302211--28302266 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
28302201 AAAAATATAA
*
28302211 ATTTGGAAT-TTTTATAA-AT
1 ATTTTGAATATTTTATAATAT
*
28302230 ATTTTGAA-ATTTTA-AATTT
1 ATTTTGAATATTTTATAATAT
28302249 ATTTTGAATTATTTTATA
1 ATTTTGAA-TATTTTATA
28302267 TTTTTTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.07
19 21 0.70
21 6 0.20
22 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTTGAATATTTTATAATAT
Found at i:28302269 original size:21 final size:19
Alignment explanation
Indices: 28302229--28302269 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
28302219 TTTTTATAAA
*
28302229 TATTTTGAAATTTTAAATT
1 TATTTTGAAATTTTATATT
28302248 TATTTTGAATTATTTTATATT
1 TATTTTGAA--ATTTTATATT
28302269 T
1 T
28302270 TTTATTGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTTTGAAATTTTATATT
Found at i:28305941 original size:104 final size:104
Alignment explanation
Indices: 28305817--28306053 Score: 366
Period size: 104 Copynumber: 2.3 Consensus size: 104
28305807 TCTAACATGT
* ** * *
28305817 AAACAGAGAGTTACATGGCTTGGACACATAGCCGTGTCCTTGTCTGTGTGATTCACACGGCATGG
1 AAACAGTGAGTTACATGGCTTGGACACATAGCCGTGTCCTTACCCGTGTGACTCACACGGCATGG
28305882 GCACACGCCCGTGTGCTTACCCACGTAGTCCTAAGTCAC
66 GCACACGCCCGTGTGCTTACCCACGTAGTCCTAAGTCAC
* * *
28305921 AAACAGTGAGTTACACGGCTTGGACACACAGCCGTGTCCTTACCCGTGTGACTCACACGGCCTGG
1 AAACAGTGAGTTACATGGCTTGGACACATAGCCGTGTCCTTACCCGTGTGACTCACACGGCATGG
* *
28305986 GCACACGCCTGTGTGCTTACCCATGTAGTCCTAAGTCAC
66 GCACACGCCCGTGTGCTTACCCACGTAGTCCTAAGTCAC
* *
28306025 AAAGAGTGAGTTACATGGCCTGGACACAT
1 AAACAGTGAGTTACATGGCTTGGACACAT
28306054 GCCCATGTCT
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
104 119 1.00
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (104 bp):
AAACAGTGAGTTACATGGCTTGGACACATAGCCGTGTCCTTACCCGTGTGACTCACACGGCATGG
GCACACGCCCGTGTGCTTACCCACGTAGTCCTAAGTCAC
Found at i:28307750 original size:30 final size:29
Alignment explanation
Indices: 28307702--28307762 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
28307692 CAAGTAGCCG
*
28307702 AAGCTAGTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTAAATAGCACACTTAGTGCCA
*
28307731 AAGCTAGTTTAAATAGCACACTTAGTTCCA
1 AAGCTAG-TTAAATAGCACACTTAGTGCCA
28307761 AA
1 AA
28307763 ACTTCCGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (29 bp):
AAGCTAGTTAAATAGCACACTTAGTGCCA
Found at i:28309731 original size:19 final size:20
Alignment explanation
Indices: 28309709--28309753 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
28309699 GGGTTTATTT
*
28309709 ATGAAATTTAATG-TATATG-
1 ATGAAATGTAATGCTA-ATGA
28309728 ATGAAATGTAATGCTAATGA
1 ATGAAATGTAATGCTAATGA
28309748 ATGAAA
1 ATGAAA
28309754 AATGAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (20 bp):
ATGAAATGTAATGCTAATGA
Found at i:28313315 original size:16 final size:15
Alignment explanation
Indices: 28313291--28313320 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28313281 AACTATTTTA
28313291 TTACAAATTTCACTC
1 TTACAAATTTCACTC
28313306 TTACATAATTTCACT
1 TTACA-AATTTCACT
28313321 TACTTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTACAAATTTCACTC
Found at i:28313664 original size:100 final size:101
Alignment explanation
Indices: 28313525--28313712 Score: 279
Period size: 101 Copynumber: 1.9 Consensus size: 101
28313515 AAGCTATCTA
* * * * * *
28313525 GTACTCATAGTAGCTTGCACTTAGTACTACACATGCGACC-AAAAATCTGGTCCACGTTGTAGCC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAAAATCTAGTACACATAGTAGCC
28313589 TGCACTTAGTACTACACACGTGATTGAAGTTGCCGG
66 TGCACTTAGTACTACACACGTGATTGAAGTTGCCGG
* ** *
28313625 GTACGCATAGTAGCCTGCACTTAGTACTACACATTCGACCTAATTATCTAGTACACATAGTAGTC
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAAAATCTAGTACACATAGTAGCC
28313690 TGCACTTAGTACTACACACGTGA
66 TGCACTTAGTACTACACACGTGA
28313713 CCTAAAACCA
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
100 37 0.48
101 40 0.52
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (101 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAAAATCTAGTACACATAGTAGCC
TGCACTTAGTACTACACACGTGATTGAAGTTGCCGG
Found at i:28313704 original size:50 final size:50
Alignment explanation
Indices: 28313519--28313760 Score: 188
Period size: 50 Copynumber: 4.8 Consensus size: 50
28313509 TAACCGAAGC
* * *
28313519 TATCTAGTACTCATAGTAGCTTGCACTTAGTACTACACATGCGACC-AAA-
1 TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACAT-TGACCTAAAT
* * * * * * * *
28313568 AATCTGGTCCACGTTGTAGCCTGCACTTAGTACTACACACGTGA-TTGAAGT
1 TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACA-TTGACCT-AAAT
** ** *
28313619 TGCCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATTCGACCT-AAT
1 TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACATT-GACCTAAAT
* * *
28313669 TATCTAGTACACATAGTAGTCTGCACTTAGTACTACACACGTGACCTAAAAC
1 TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACA-TTGACCT-AAAT
* * *
28313721 CATCTTA-AACACATAGTAGCCTGCACATAGTACTACACAT
1 TATC-TAGTACACATAGTAGCCTGCACTTAGTACTACACAT
28313761 GTGTTCTCAC
Statistics
Matches: 148, Mismatches: 35, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
49 34 0.23
50 43 0.29
51 34 0.23
52 35 0.24
53 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (50 bp):
TATCTAGTACACATAGTAGCCTGCACTTAGTACTACACATTGACCTAAAT
Found at i:28313755 original size:52 final size:50
Alignment explanation
Indices: 28313630--28313759 Score: 156
Period size: 52 Copynumber: 2.6 Consensus size: 50
28313620 GCCGGGTACG
* ** *
28313630 CATAGTAGCCTGCACTTAGTACTACACATTCGACCTAATTATCTAGTACA
1 CATAGTAGCCTGCACTTAGTACTACACAGTCGACCTAACCATCTAGAACA
*
28313680 CATAGTAGTCTGCACTTAGTACTACACACGT-GACCTAAAACCATCTTA-AACA
1 CATAGTAGCCTGCACTTAGTACTACACA-GTCGACCT--AACCATC-TAGAACA
*
28313732 CATAGTAGCCTGCACATAGTACTACACA
1 CATAGTAGCCTGCACTTAGTACTACACA
28313760 TGTGTTCTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 32 0.46
51 1 0.01
52 34 0.49
53 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.26
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACAGTCGACCTAACCATCTAGAACA
Found at i:28316945 original size:3 final size:3
Alignment explanation
Indices: 28316937--28316975 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
28316927 GACCATTATC
*
28316937 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28316976 AAAAGTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28319988 original size:22 final size:21
Alignment explanation
Indices: 28319963--28320010 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
28319953 TGAGCTGGAC
28319963 AAAATTGAGCTATTACA-ATATT
1 AAAATTG-GCTA-TACACATATT
* *
28319985 AAAAATGGTTATACACATATT
1 AAAATTGGCTATACACATATT
28320006 AAAAT
1 AAAAT
28320011 CTTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 12 0.55
22 6 0.27
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATTGGCTATACACATATT
Found at i:28323611 original size:18 final size:16
Alignment explanation
Indices: 28323590--28323623 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
28323580 TAACTAGGCT
28323590 TTTTTAAATACTTTTTTA
1 TTTTTAAA-A-TTTTTTA
28323608 TTTTTAAAATTTTTTA
1 TTTTTAAAATTTTTTA
28323624 ATGATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAAAATTTTTTA
Found at i:28324156 original size:10 final size:9
Alignment explanation
Indices: 28324134--28324263 Score: 58
Period size: 9 Copynumber: 14.0 Consensus size: 9
28324124 TTATAATCTC
*
28324134 TAATTTTTC
1 TAATTTTTA
28324143 TAATTTTTAA
1 TAATTTTT-A
*
28324153 TAA-TATTA
1 TAATTTTTA
28324161 TAATTTATTA
1 TAATTT-TTA
**
28324171 -GCTTTTT-
1 TAATTTTTA
28324178 T-ATTATTTA
1 TAATT-TTTA
28324187 TAAGTTTTTA
1 TAA-TTTTTA
*
28324197 TAATATTT-
1 TAATTTTTA
*
28324205 CAATATTTTA
1 TAAT-TTTTA
28324215 -AATATGCTTTA
1 TAAT-T--TTTA
28324226 TTAA-TTTTA
1 -TAATTTTTA
28324235 TAATTTTTTA
1 TAA-TTTTTA
28324245 TAATTTTTA
1 TAATTTTTA
28324254 TAAATTTTTA
1 T-AATTTTTA
28324264 GGTAAACTAT
Statistics
Matches: 95, Mismatches: 9, Indels: 33
0.69 0.07 0.24
Matches are distributed among these distances:
7 2 0.02
8 15 0.16
9 39 0.41
10 30 0.32
11 7 0.07
13 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:28324195 original size:19 final size:19
Alignment explanation
Indices: 28324158--28324200 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
28324148 TTTAATAATA
*
28324158 TTATAATTTATTAGCTTTT
1 TTATAATTTATAAGCTTTT
*
28324177 TTATTATTTATAAG--TTT
1 TTATAATTTATAAGCTTTT
28324194 TTATAAT
1 TTATAAT
28324201 ATTTCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATAATTTATAAGCTTTT
Found at i:28324313 original size:30 final size:30
Alignment explanation
Indices: 28324279--28324353 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
28324269 ACTATCAAAA
*
28324279 TAGTCACTTTTGTTTACCTCATGTTATATT
1 TAGTCACTTTTGTTTACCTCAGGTTATATT
* *
28324309 TAGTCACTTTTGTTTACTTTAGGTTATATT
1 TAGTCACTTTTGTTTACCTCAGGTTATATT
*
28324339 TAGTCACTTATGTTT
1 TAGTCACTTTTGTTT
28324354 GAAATGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.20, C:0.13, G:0.12, T:0.55
Consensus pattern (30 bp):
TAGTCACTTTTGTTTACCTCAGGTTATATT
Found at i:28325095 original size:19 final size:19
Alignment explanation
Indices: 28325063--28325100 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28325053 TTACTCTAAT
*
28325063 TTTTTTATAATTTTTATGA
1 TTTTTAATAATTTTTATGA
*
28325082 TTTTTAATATTTTTTATGA
1 TTTTTAATAATTTTTATGA
28325101 ACAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTAATAATTTTTATGA
Found at i:28338729 original size:33 final size:33
Alignment explanation
Indices: 28338669--28338738 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
28338659 TAGAATTTTT
*
28338669 TTTGAAATTTTTATAATTTTTAAAAAATATAAA
1 TTTGAAATTTTTATAATTTTTAAAAATTATAAA
* *
28338702 TTTGGAATTTTTATAAATATTTT-AAAATTTTAAA
1 TTTGAAATTTTTAT-AAT-TTTTAAAAATTATAAA
28338736 TTT
1 TTT
28338739 ATTTTGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.41
34 15 0.47
35 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (33 bp):
TTTGAAATTTTTATAATTTTTAAAAATTATAAA
Found at i:28357083 original size:42 final size:42
Alignment explanation
Indices: 28357036--28357118 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
28357026 TCTCTTCGGG
* *
28357036 TGGGGGTTGAGTATCGTCCTTTTGTTCATTCTCTGTGTATCA
1 TGGGGGTTGAGTATCGTCCTCTTATTCATTCTCTGTGTATCA
28357078 TGGGGGTTGAGTATCGTCCTCTTATTCATTCTCTGTGTATC
1 TGGGGGTTGAGTATCGTCCTCTTATTCATTCTCTGTGTATC
28357119 TTAAGGTTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.12, C:0.18, G:0.25, T:0.45
Consensus pattern (42 bp):
TGGGGGTTGAGTATCGTCCTCTTATTCATTCTCTGTGTATCA
Found at i:28363334 original size:19 final size:19
Alignment explanation
Indices: 28363306--28363347 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
28363296 ATACAGACTC
*
28363306 AATT-TATGTCCTAGGCAA
1 AATTATATGTCCTAAGCAA
*
28363324 AATTATATGTCTTAAGCAA
1 AATTATATGTCCTAAGCAA
28363343 AATTA
1 AATTA
28363348 CCATTTTGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (19 bp):
AATTATATGTCCTAAGCAA
Found at i:28364829 original size:26 final size:27
Alignment explanation
Indices: 28364781--28364833 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
28364771 GTGTCTTAAT
*
28364781 TTATTATTTGTGTTTAATATGTCCTAG
1 TTATTACTTGTGTTTAATATGTCCTAG
*
28364808 TTATTACTTGT-TTTAATGTGTCCTAG
1 TTATTACTTGTGTTTAATATGTCCTAG
28364834 CTGAATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (27 bp):
TTATTACTTGTGTTTAATATGTCCTAG
Found at i:28367820 original size:54 final size:54
Alignment explanation
Indices: 28367632--28367827 Score: 261
Period size: 54 Copynumber: 3.6 Consensus size: 54
28367622 AACTTACCAT
* * *
28367632 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
** *
28367685 TGCCATGTCTTGACATGGTCTTACATGGGA-CCTTTGCCTTATATAACTCATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCCTTATAGAACTCATCAA
* * *
28367739 TGCCATGTCTTGACACGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
* * *
28367793 TTCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 TGCCATGTCTTGACATGGTCTTACATGATATCCTT
28367828 ATCTTACCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
52 2 0.02
53 37 0.30
54 84 0.67
55 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
TGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATAGAACTCATCAA
Found at i:28368601 original size:30 final size:31
Alignment explanation
Indices: 28368558--28368616 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
28368548 CTAACTCAAA
*
28368558 CTTTGGAAAAATTATAATTTTGCACCTAGAC
1 CTTTGGAAAAATTACAATTTTGCACCTAGAC
* * *
28368589 CTTT-GAAGAATTACGATTTTGCCCCTAG
1 CTTTGGAAAAATTACAATTTTGCACCTAG
28368617 GCTCGAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (31 bp):
CTTTGGAAAAATTACAATTTTGCACCTAGAC
Found at i:28370466 original size:44 final size:44
Alignment explanation
Indices: 28370416--28370504 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
28370406 AACCAAGCTA
28370416 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
1 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
*
28370460 AATCATAATGGATACTTCAATTGTCAATATCTTCAGCTGTTTAT
1 AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
28370504 A
1 A
28370505 CTTTATTAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (44 bp):
AATCATAATGGATACTTCAATTGTCAATATCTTCAACTGTTTAT
Found at i:28374380 original size:55 final size:54
Alignment explanation
Indices: 28374255--28374442 Score: 233
Period size: 55 Copynumber: 3.5 Consensus size: 54
28374245 AACTTACCAT
* * *
28374255 TGCCATGTCTTGACATGGTCTTAC-GTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATTGG-ATCCTTGCCTTATAGAACTCATCAA
*
28374308 TGCCATGCCTTGGCATGGTCTTACATTGGA-CCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATTGGATCC-TTGCCTTATAG-AACTCATCAA
* *
28374363 TGCCATGTCTTGACATGGTCTTACA-T-GATTTCCTTGCCTTATAGAACTTATCAA
1 TGCCATGCCTTGACATGGTCTTACATTGGA--TCCTTGCCTTATAGAACTCATCAA
*
28374417 TGCCATGCCTTGGCATGGTCTTACAT
1 TGCCATGCCTTGACATGGTCTTACAT
28374443 GATATCCTTA
Statistics
Matches: 118, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
52 2 0.02
53 34 0.29
54 37 0.31
55 43 0.36
56 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGACATGGTCTTACATTGGATCCTTGCCTTATAGAACTCATCAA
Found at i:28376838 original size:44 final size:44
Alignment explanation
Indices: 28376770--28376855 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
28376760 GGTCGAGGTC
*
28376770 GAAGGCAAGTTCAAGATGACGAGTTATCCGAACCAAGTGAGGCT
1 GAAGGCAAGTTCAAGATGAAGAGTTATCCGAACCAAGTGAGGCT
28376814 GAAGGCAAGTTCAAGATGAAGAGTTATCCGAACCAAGTGAGG
1 GAAGGCAAGTTCAAGATGAAGAGTTATCCGAACCAAGTGAGG
28376856 GCAAAAGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.17
Consensus pattern (44 bp):
GAAGGCAAGTTCAAGATGAAGAGTTATCCGAACCAAGTGAGGCT
Found at i:28379763 original size:27 final size:26
Alignment explanation
Indices: 28379732--28379784 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
28379722 GTGTCTTAAT
*
28379732 TTATTAATTGTATTTAATATGTCCTAG
1 TTATTAATTAT-TTTAATATGTCCTAG
* *
28379759 TTATTACTTATTTTAATGTGTCCTAG
1 TTATTAATTATTTTAATATGTCCTAG
28379785 CTGAATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (26 bp):
TTATTAATTATTTTAATATGTCCTAG
Found at i:28384251 original size:27 final size:27
Alignment explanation
Indices: 28384218--28384390 Score: 238
Period size: 27 Copynumber: 6.4 Consensus size: 27
28384208 TGGATAAGTT
* *
28384218 GTAGAATTACCGAAATACCCCTATAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
28384245 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
28384272 GTAAAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
28384299 ATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
28384326 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
28384353 GTAGAATTACTGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
28384380 GTAAAATTACC
1 GTAGAATTACC
28384391 ATTTTTCCCC
Statistics
Matches: 128, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 128 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:28386768 original size:56 final size:58
Alignment explanation
Indices: 28386673--28386796 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 58
28386663 TGTTGTATGA
** * * *
28386673 TAGGATTACCAGTCCAGGATAAATCTTTTATCTAGCGTATGCTCAAAAAGC-TTG-AT
1 TAGGATTACCAGTCCAGGATAAATCCCTAATCTAACGTATACTCAAAAAGCATTGTAT
* * * *
28386729 TAGGATTACCAGTCCAGGCTAAA-CCCTAATCTTAACGTATACTCGAGAGGCATTGTAT
1 TAGGATTACCAGTCCAGGATAAATCCCTAATC-TAACGTATACTCAAAAAGCATTGTAT
28386787 TAGGATTACC
1 TAGGATTACC
28386797 CGTCTGAGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 5 0.09
56 36 0.64
57 3 0.05
58 12 0.21
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (58 bp):
TAGGATTACCAGTCCAGGATAAATCCCTAATCTAACGTATACTCAAAAAGCATTGTAT
Found at i:28395728 original size:15 final size:14
Alignment explanation
Indices: 28395693--28395738 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
28395683 ATATAAAGTA
*
28395693 AAAGAAATAAAAA-
1 AAAGAAAAAAAAAG
28395706 AAAGAAAAAAAAAG
1 AAAGAAAAAAAAAG
*
28395720 AATAGAAAAAGAAAG
1 AA-AGAAAAAAAAAG
28395735 AAAG
1 AAAG
28395739 GATGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.41
14 4 0.14
15 13 0.45
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:28395736 original size:10 final size:10
Alignment explanation
Indices: 28395704--28395737 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28395694 AAGAAATAAA
*
28395704 AAAAAGAAAA
1 AAAAAGAAAG
28395714 AAAAAGAATAG
1 AAAAAGAA-AG
28395725 AAAAAGAAAG
1 AAAAAGAAAG
28395735 AAA
1 AAA
28395738 GGATGAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:28395799 original size:21 final size:22
Alignment explanation
Indices: 28395764--28395805 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28395754 AGAGCAGGGG
*
28395764 AAAGAAAGAAGGAAGGAAAAAA
1 AAAGAAAGAAAGAAGGAAAAAA
28395786 AAAG-AAGAAAGAAGGAAAAA
1 AAAGAAAGAAAGAAGGAAAAA
28395806 GGGAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAGAAGGAAAAAA
Found at i:28397883 original size:46 final size:46
Alignment explanation
Indices: 28397832--28398159 Score: 363
Period size: 46 Copynumber: 7.0 Consensus size: 46
28397822 GCTCTCTGAT
* **
28397832 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGGT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
28397878 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGTCAACGTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
28397924 ATGAAATATGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* **
28397970 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
28398016 A-GAAAATGAATGAACAAGACCATAGTTGAAAGACACTATGGCAACATGAC
1 ATG-AAATG--TG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* **
28398066 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
28398112 A-GAAAATGAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATG--T--GTAAGACCATGGTTGAAAGATACCATGGCAACATG
28398160 TCAAAGATAA
Statistics
Matches: 239, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
45 2 0.01
46 169 0.71
50 67 0.28
51 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:28398067 original size:96 final size:95
Alignment explanation
Indices: 28397842--28398159 Score: 428
Period size: 96 Copynumber: 3.4 Consensus size: 95
28397832 ATGAAATGTG
* * * ** * **
28397842 TAAGACCATGGTTGAAAGATACCATGGCAACCTGGTATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
* * *
28397907 TACCATGTCAACGTGATATG-AAAT--ATG-
66 TACCATGGCAACATGACA-GAAAATGAATGA
* *
28397934 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
28397999 TACCATGGCAACATGACAGAAAATGAATGAA
66 TACCATGGCAACATGACAGAAAATGAATG-A
* *
28398030 CAAGACCATAGTTGAAAGACACTATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGACACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
28398095 TACCATGGCAACATGACAGAAAATGAATGA
66 TACCATGGCAACATGACAGAAAATGAATGA
* *
28398125 GTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 -TAAGACCATAGTTGAAAGACACCATGGCAACATG
28398160 TCAAAGATAA
Statistics
Matches: 205, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
91 1 0.00
92 78 0.38
94 3 0.01
95 1 0.00
96 122 0.60
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (95 bp):
TAAGACCATAGTTGAAAGACACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACAGAAAATGAATGA
Found at i:28400164 original size:22 final size:22
Alignment explanation
Indices: 28400122--28400164 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28400112 CACTAAGTCA
* *
28400122 ACAGAACGGCTCAACGTCGTAG
1 ACAGAACGGCTAAACGCCGTAG
*
28400144 ACAGAACGGCTAAAGGCCGTA
1 ACAGAACGGCTAAACGCCGTA
28400165 AATATCGCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.28, T:0.12
Consensus pattern (22 bp):
ACAGAACGGCTAAACGCCGTAG
Found at i:28400434 original size:26 final size:26
Alignment explanation
Indices: 28400400--28400474 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
28400390 GCATAATCGC
*
28400400 CATTCTACCATACAGGGTATTACGGT
1 CATTTTACCATACAGGGTATTACGGT
** * *
28400426 TGTTTTACCCTACAGGGGCATTACGGT
1 CATTTTACCATACA-GGGTATTACGGT
28400453 CATTTTACACTATA-AGGGTATT
1 CATTTTAC-C-ATACAGGGTATT
28400475 TCAATAATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
26 10 0.27
27 23 0.62
28 2 0.05
29 2 0.05
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (26 bp):
CATTTTACCATACAGGGTATTACGGT
Found at i:28400521 original size:26 final size:27
Alignment explanation
Indices: 28400468--28400524 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
28400458 TACACTATAA
28400468 GGGTATTTCAATAATTTTACAAACCAG
1 GGGTATTTCAATAATTTTACAAACCAG
*
28400495 GGGTATTTCGATAATTTTACAAA-CAG
1 GGGTATTTCAATAATTTTACAAACCAG
28400521 GGGT
1 GGGT
28400525 CTTAACAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTACAAACCAG
Found at i:28410215 original size:20 final size:19
Alignment explanation
Indices: 28410166--28410215 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
28410156 ATTGGGTCTT
28410166 GCCCATATTAACACATTGG
1 GCCCATATTAACACATTGG
* *
28410185 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACA-TTGG
28410204 GCCCATAATTAA
1 GCCCAT-ATTAA
28410216 ATAGTCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (19 bp):
GCCCATATTAACACATTGG
Found at i:28412471 original size:20 final size:22
Alignment explanation
Indices: 28412433--28412472 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
28412423 TTCAAATACG
*
28412433 ATAATATATATATATTTTCCTA
1 ATAATATATATATAATTTCCTA
28412455 ATAATA-AT-TATAATTTCC
1 ATAATATATATATAATTTCC
28412473 ATAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATATATATATAATTTCCTA
Found at i:28418096 original size:27 final size:26
Alignment explanation
Indices: 28418042--28418144 Score: 75
Period size: 27 Copynumber: 3.8 Consensus size: 26
28418032 ATCATCTTTC
*
28418042 TACCATACAGGGGTATTATGGTCGTTT
1 TACC-TACAGGGGTATTATGGTCATTT
*
28418069 TACCTTACAGGGGTATTACT-GTTATTT
1 TACC-TACAGGGGTATTA-TGGTCATTT
* *
28418096 TACACTACAAGGGTATT-TCGGTAATTT
1 TAC-CTACAGGGGTATTAT-GGTCATTT
** *
28418123 TACAAACCAGGGGTATTTTGGT
1 TACCTA-CAGGGGTATTATGGT
28418145 AATTGTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
25 1 0.02
26 1 0.02
27 57 0.92
28 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (26 bp):
TACCTACAGGGGTATTATGGTCATTT
Found at i:28418145 original size:27 final size:27
Alignment explanation
Indices: 28418106--28418158 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28418096 TACACTACAA
* *
28418106 GGGTATTTCGGTAATTTTACAAACCAG
1 GGGTATTTCGGTAATTGTAAAAACCAG
*
28418133 GGGTATTTTGGTAATTGTAAAAACCA
1 GGGTATTTCGGTAATTGTAAAAACCA
28418159 AGATCTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (27 bp):
GGGTATTTCGGTAATTGTAAAAACCAG
Found at i:28418408 original size:19 final size:19
Alignment explanation
Indices: 28418375--28418422 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
28418365 GTGTGGGGCC
28418375 CACGAGCCCATTAGGCCC-A
1 CACG-GCCCATTAGGCCCAA
28418394 CACGGCCCATCTAGGCCCAA
1 CACGGCCCAT-TAGGCCCAA
*
28418414 CATGGCCCA
1 CACGGCCCA
28418423 GAACTACCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 11 0.42
20 9 0.35
ACGTcount: A:0.25, C:0.44, G:0.21, T:0.10
Consensus pattern (19 bp):
CACGGCCCATTAGGCCCAA
Found at i:28419319 original size:19 final size:19
Alignment explanation
Indices: 28419295--28419332 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28419285 TCCTCTCAGG
28419295 ACCCTTAACCACTTGAGCA
1 ACCCTTAACCACTTGAGCA
28419314 ACCCTTAACCACTTGAGCA
1 ACCCTTAACCACTTGAGCA
28419333 GACATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (19 bp):
ACCCTTAACCACTTGAGCA
Found at i:28419714 original size:31 final size:31
Alignment explanation
Indices: 28419625--28419715 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 31
28419615 TTGGATTAGA
28419625 TCTTATGAGCGA-TTGGCATGTTTCGATTGGATTAGC
1 TCTTATGAGC-ATTTGGCATG-TT--ATTGG--TAGC
**
28419661 TCTTATGAGCATTTGGTGTGTTATTGGTAGC
1 TCTTATGAGCATTTGGCATGTTATTGGTAGC
*
28419692 TTTTATGAGCATTTGGCATGTTAT
1 TCTTATGAGCATTTGGCATGTTAT
28419716 CAGTTGGATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
31 25 0.51
33 5 0.10
35 3 0.06
36 16 0.33
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.44
Consensus pattern (31 bp):
TCTTATGAGCATTTGGCATGTTATTGGTAGC
Found at i:28419744 original size:37 final size:37
Alignment explanation
Indices: 28419606--28419813 Score: 173
Period size: 37 Copynumber: 5.8 Consensus size: 37
28419596 TGTTATAGGT
* * *
28419606 TGTTATCGGTTGGATTAGATCTTATGAGCGATTGGCA
1 TGTTATCAGTTGGATTAGCTCTTATGAGCGTTTGGCA
*
28419643 TGTT-TC-GATTGGATTAGCTCTTATGAGCATTTGG--
1 TGTTATCAG-TTGGATTAGCTCTTATGAGCGTTTGGCA
* *
28419677 TGTGT-T-A-TTGG--TAGCTTTTATGAGCATTTGGCA
1 TGT-TATCAGTTGGATTAGCTCTTATGAGCGTTTGGCA
* *
28419710 TGTTATCAGTTGGATTAACTCTTATGAACGTTTGGCA
1 TGTTATCAGTTGGATTAGCTCTTATGAGCGTTTGGCA
** * ****
28419747 TGTTATTGGGTGGATTAGCTCTTATGAGCGTTTAATG
1 TGTTATCAGTTGGATTAGCTCTTATGAGCGTTTGGCA
** *
28419784 TGTTATTGGGTGGATTAGCTCTTATGAGCG
1 TGTTATCAGTTGGATTAGCTCTTATGAGCG
28419814 ATTTTCATGT
Statistics
Matches: 144, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
31 19 0.13
32 1 0.01
33 8 0.06
34 4 0.03
35 7 0.05
36 25 0.17
37 80 0.56
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.42
Consensus pattern (37 bp):
TGTTATCAGTTGGATTAGCTCTTATGAGCGTTTGGCA
Found at i:28419744 original size:68 final size:67
Alignment explanation
Indices: 28419627--28419755 Score: 172
Period size: 68 Copynumber: 1.9 Consensus size: 67
28419617 GGATTAGATC
* * **
28419627 TTATGAGCGATTGGCATGTTTCGATTGGATTAGCTCTTATGAGCATTTGGTGTGTTATTGGTAGC
1 TTATGAGCGATTGGCATGTTTCGATTGGATTAACTCTTATGAACATTTGGCATGTTATTGGTAGC
28419692 TT
66 TT
*
28419694 TTATGAGC-ATTTGGCATGTTATC-AGTTGGATTAACTCTTATGAACGTTTGGCATGTTATTGG
1 TTATGAGCGA-TTGGCATGTT-TCGA-TTGGATTAACTCTTATGAACATTTGGCATGTTATTGG
28419756 GTGGATTAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
66 1 0.02
67 19 0.35
68 34 0.63
ACGTcount: A:0.20, C:0.11, G:0.26, T:0.43
Consensus pattern (67 bp):
TTATGAGCGATTGGCATGTTTCGATTGGATTAACTCTTATGAACATTTGGCATGTTATTGGTAGC
TT
Found at i:28421395 original size:42 final size:42
Alignment explanation
Indices: 28421336--28421419 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
28421326 TTGGACCAAC
28421336 CCTTGTGGTAGGCATTATCATATGATAAGTCAAGAAATTCTA
1 CCTTGTGGTAGGCATTATCATATGATAAGTCAAGAAATTCTA
28421378 CCTTGTGGTAGGCATTATCATATGATAAGTCAAGAAATTCTA
1 CCTTGTGGTAGGCATTATCATATGATAAGTCAAGAAATTCTA
28421420 TCTTCAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (42 bp):
CCTTGTGGTAGGCATTATCATATGATAAGTCAAGAAATTCTA
Found at i:28424842 original size:28 final size:28
Alignment explanation
Indices: 28424802--28424954 Score: 272
Period size: 28 Copynumber: 5.5 Consensus size: 28
28424792 TAAATTGTAC
28424802 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
28424830 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
28424858 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28424886 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28424914 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
28424941 AGCACTGAGTGTGC
1 AGCACTAAGTGTGC
28424955 AGACTTAATA
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 23 0.19
28 100 0.81
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:28424868 original size:56 final size:56
Alignment explanation
Indices: 28424777--28424954 Score: 277
Period size: 56 Copynumber: 3.2 Consensus size: 56
28424767 GAGATTGGCG
* * * *
28424777 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
28424834 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
28424890 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
28424945 CTGAGTGTGC
1 CTAAGTGTGC
28424955 AGACTTAATA
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
55 22 0.19
56 76 0.67
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:28427812 original size:13 final size:13
Alignment explanation
Indices: 28427787--28427820 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
28427777 AAGATATAGT
28427787 ACACAGAATCAGAA
1 ACACAG-ATCAGAA
*
28427801 ATACAGATCAGAA
1 ACACAGATCAGAA
28427814 ACACAGA
1 ACACAGA
28427821 ATTCCTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.56, C:0.21, G:0.15, T:0.09
Consensus pattern (13 bp):
ACACAGATCAGAA
Found at i:28436554 original size:5 final size:5
Alignment explanation
Indices: 28436544--28436576 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
28436534 TTGAACTTAG
28436544 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
28436577 TTATAAACCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:28447575 original size:26 final size:27
Alignment explanation
Indices: 28447505--28447578 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
28447495 TATTTTCTCG
* *
28447505 AAATTTTAC-CAGGGCTAAAATTGTCAA
1 AAATTTTACTC-GGGGTAAAATCGTCAA
**
28447532 AAATTTTA-TCCGAAGTAAAATCGTC-A
1 AAATTTTACT-CGGGGTAAAATCGTCAA
28447558 AAATTTTACTCGGGGTAAAAT
1 AAATTTTACTCGGGGTAAAAT
28447579 GGGAACAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
26 18 0.47
27 19 0.50
28 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (27 bp):
AAATTTTACTCGGGGTAAAATCGTCAA
Found at i:28453883 original size:398 final size:398
Alignment explanation
Indices: 28453147--28453938 Score: 1548
Period size: 398 Copynumber: 2.0 Consensus size: 398
28453137 TTGAGTATGA
28453147 GATTGATACGAGATGGTACAGGTATGTACATAAATCATATAAGCTTTAAATCGAAGAAATAGTGA
1 GATTGATACGAGATGGTACAGGTATGTACATAAATCATATAAGCTTTAAATCGAAGAAATAGTGA
28453212 AGAATACATAAAGTTTTGTGAATGAGTATGATAAACCATAAATTATACATATTTTTACCCCATGT
66 AGAATACATAAAGTTTTGTGAATGAGTATGATAAACCATAAATTATACATATTTTTACCCCATGT
*
28453277 TTAATGCATTTTATTGATGATTTCTCATTAGAATTAGTGAATTCGATGCTCCTAATGCTTTAATT
131 TTAATGCATTTTATGGATGATTTCTCATTAGAATTAGTGAATTCGATGCTCCTAATGCTTTAATT
28453342 TCATATTTTGTACTTAGGAGAGCATAGGAGAGTGAAAGGAACGAGAAACAAGCCAAAAACGGAGA
196 TCATATTTTGTACTTAGGAGAGCATAGGAGAGTGAAAGGAACGAGAAACAAGCCAAAAACGGAGA
*
28453407 AAATGGGCCAAAGTACGAAATCAACATGGCCTGGACCTCCTCACACAGGCAGACCACACGGTCGT
261 AAATGGGCCAAAGTACGAAATCAACATGACCTGGACCTCCTCACACAGGCAGACCACACGGTCGT
28453472 GTCAATTTGGCAGGCTCAAACACGGCCTGAAGTAATTGAACACGAGTGTGTCCCTGCCAAGCCCA
326 GTCAATTTGGCAGGCTCAAACACGGCCTGAAGTAATTGAACACGAGTGTGTCCCTGCCAAGCCCA
28453537 AGTTTTGT
391 AGTTTTGT
28453545 GATTGATACGAGATGGTACAGGTATGTACATAAATCATATAAGCTTTAAATCGAAGAAATAGTGA
1 GATTGATACGAGATGGTACAGGTATGTACATAAATCATATAAGCTTTAAATCGAAGAAATAGTGA
28453610 AGAATACATAAAGTTTTGTGAATGAGTATGATAAACCATAAATTATACATATTTTTACCCCATGT
66 AGAATACATAAAGTTTTGTGAATGAGTATGATAAACCATAAATTATACATATTTTTACCCCATGT
28453675 TTAATGCATTTTATGGATGATTTCTCATTAGAATTAGTGAATTCGATGCTCCTAATGCTTTAATT
131 TTAATGCATTTTATGGATGATTTCTCATTAGAATTAGTGAATTCGATGCTCCTAATGCTTTAATT
*
28453740 TCATATTTTGTACTTAGGAGAGCATAGGAGAGTGAAAGGAACGAGAAACAGGCCAAAAACGGAGA
196 TCATATTTTGTACTTAGGAGAGCATAGGAGAGTGAAAGGAACGAGAAACAAGCCAAAAACGGAGA
28453805 AAATGGGCCAAAGTACGAAATCAACATGACCTGGACCTCCTCACACAGGCAGACCACACGGTCGT
261 AAATGGGCCAAAGTACGAAATCAACATGACCTGGACCTCCTCACACAGGCAGACCACACGGTCGT
*
28453870 GTCAATTTGGCAGGCTCAAACATGGCCTGAAGTAATTGAACACGAGTGTGTCCCTGCCAAGCCCA
326 GTCAATTTGGCAGGCTCAAACACGGCCTGAAGTAATTGAACACGAGTGTGTCCCTGCCAAGCCCA
28453935 AGTT
391 AGTT
28453939 GAGTCCAATT
Statistics
Matches: 390, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
398 390 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (398 bp):
GATTGATACGAGATGGTACAGGTATGTACATAAATCATATAAGCTTTAAATCGAAGAAATAGTGA
AGAATACATAAAGTTTTGTGAATGAGTATGATAAACCATAAATTATACATATTTTTACCCCATGT
TTAATGCATTTTATGGATGATTTCTCATTAGAATTAGTGAATTCGATGCTCCTAATGCTTTAATT
TCATATTTTGTACTTAGGAGAGCATAGGAGAGTGAAAGGAACGAGAAACAAGCCAAAAACGGAGA
AAATGGGCCAAAGTACGAAATCAACATGACCTGGACCTCCTCACACAGGCAGACCACACGGTCGT
GTCAATTTGGCAGGCTCAAACACGGCCTGAAGTAATTGAACACGAGTGTGTCCCTGCCAAGCCCA
AGTTTTGT
Found at i:28457216 original size:30 final size:30
Alignment explanation
Indices: 28457181--28457241 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
28457171 TCCTTAACTC
28457181 AAACTTTTGCAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
28457211 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
28457241 A
1 A
28457242 GGCTCGGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:28468772 original size:17 final size:16
Alignment explanation
Indices: 28468750--28468811 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
28468740 TTGAATGTTA
28468750 TGTGATTATATGAGTAT
1 TGTGA-TATATGAGTAT
** *
28468767 TGTGATATATGCTTAAA
1 TGTGATATATGAGT-AT
*
28468784 TGTGATTATATAAGTAT
1 TGTGA-TATATGAGTAT
28468801 TGTGATATATG
1 TGTGATATATG
28468812 TTTTAAAGTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 12 0.34
17 17 0.49
18 6 0.17
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (16 bp):
TGTGATATATGAGTAT
Found at i:28468792 original size:34 final size:36
Alignment explanation
Indices: 28468721--28468811 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 36
28468711 AACATGTTTT
28468721 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAA---TATGTGATTATA
28468760 TGAGTATTGTGATATATGCTT-AA-ATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATATGTGATTATA
*
28468794 TAAGTATTGTGATATATG
1 TGAGTATTGTGATATATG
28468812 TTTTAAAGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
34 28 0.55
38 2 0.04
39 21 0.41
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (36 bp):
TGAGTATTGTGATATATGCTTGAATATGTGATTATA
Found at i:28473247 original size:8 final size:8
Alignment explanation
Indices: 28473234--28473260 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
28473224 AGTTGAAACG
28473234 TGATTGTA
1 TGATTGTA
28473242 TGATTGTA
1 TGATTGTA
28473250 TGATTGTA
1 TGATTGTA
28473258 TGA
1 TGA
28473261 ACAAATCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (8 bp):
TGATTGTA
Found at i:28473678 original size:28 final size:28
Alignment explanation
Indices: 28473638--28473724 Score: 111
Period size: 28 Copynumber: 3.1 Consensus size: 28
28473628 AAGGACTACC
*
28473638 TTCATAGAGAACTCTTAAAGAAATTATG
1 TTCATAGAGAACTCTTAAAGAAATGATG
* * *
28473666 TTCATGGAGAACTCTGAAGGAAATGATG
1 TTCATAGAGAACTCTTAAAGAAATGATG
* * *
28473694 TTTATAGTGAACTCTAAAAGAAATGATG
1 TTCATAGAGAACTCTTAAAGAAATGATG
28473722 TTC
1 TTC
28473725 TTGGTGAACT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (28 bp):
TTCATAGAGAACTCTTAAAGAAATGATG
Found at i:28473714 original size:56 final size:55
Alignment explanation
Indices: 28473641--28473745 Score: 147
Period size: 56 Copynumber: 1.9 Consensus size: 55
28473631 GACTACCTTC
* *
28473641 ATAGAGAACTCTTAAAGAAATTATGTTCATGGAGAACTCTGAAGGAAATGATGTTT
1 ATAGAGAACTCTAAAAGAAATGATGTTCATGGAGAACTCTGAA-GAAATGATGTTT
* * * *
28473697 ATAGTGAACTCTAAAAGAAATGATGTTCTTGGTGAACTTTGAAGAAATG
1 ATAGAGAACTCTAAAAGAAATGATGTTCATGGAGAACTCTGAAGAAATG
28473746 GAATTCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 6 0.14
56 37 0.86
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (55 bp):
ATAGAGAACTCTAAAAGAAATGATGTTCATGGAGAACTCTGAAGAAATGATGTTT
Done.