Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 87 of 284
Found at i:28780889 original size:50 final size:50
Alignment explanation
Indices: 28780809--28780953 Score: 161
Period size: 48 Copynumber: 2.9 Consensus size: 50
28780799 AAAAGGGTAA
* * * * *
28780809 AATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCTCAT-TCATC
1 AATGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAT-AAC
* * * *
28780859 AGTGTCGATGCCATGTCCCAGACATGGTCTTACA-TTG-ACACATATAAC
1 AATGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATAAC
* *
28780907 AATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCGCATAT
1 AATGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAT
28780954 TGAGGCTATA
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
48 37 0.48
49 5 0.06
50 35 0.45
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (50 bp):
AATGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATAAC
Found at i:28781095 original size:175 final size:175
Alignment explanation
Indices: 28780786--28781127 Score: 542
Period size: 175 Copynumber: 2.0 Consensus size: 175
28780776 AGGATATCCG
28780786 ATAAGCCTCATACAAAAGGGTAAAATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCT
1 ATAAGCCTCATACAAAAGGGTAAAATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCT
* * * *
28780851 CATTCATCAGTGTCGATGCCATGTCCCAGACATGGTCTTACATTGACACATATAACAATGTCGAT
66 CATTCATCAGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGACACACATAACAATGCCAAT
**
28780916 GCCATGTTCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCT
131 GCCATGCCCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCT
28780961 ATAAGCCTCATACAAAAGGGTAAAATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCT
1 ATAAGCCTCATACAAAAGGGTAAAATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCT
* * **
28781026 CATTCATCAGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATGTCGAA-GCCAA
66 CATTCATCAGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGACACACATAAC-AATGCCAA
** * *
28781090 TGCCATGCCCCAAATTTGGTCTTACTCTGGCTCTCATA
130 TGCCATGCCCCAAACATGGTCTTACACTGGCTCGCATA
28781128 GCATTGCTGA
Statistics
Matches: 152, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
175 150 0.99
176 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (175 bp):
ATAAGCCTCATACAAAAGGGTAAAATGCCGATGCCATGTCTCAAACAAGGTCTTACACTGGCTCT
CATTCATCAGTGTCGATGCCATGTCCCAGACATGGTCTTACACTGACACACATAACAATGCCAAT
GCCATGCCCCAAACATGGTCTTACACTGGCTCGCATATTGAGGCT
Found at i:28787669 original size:17 final size:17
Alignment explanation
Indices: 28787649--28787682 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28787639 CTCCAAAAGG
28787649 AAGATGAATA-ATACATT
1 AAGAT-AATATATACATT
28787666 AAGATAATATATACATT
1 AAGATAATATATACATT
28787683 TAGTAGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (17 bp):
AAGATAATATATACATT
Found at i:28794072 original size:18 final size:18
Alignment explanation
Indices: 28794049--28794087 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28794039 GTATCGGAGA
28794049 AGGACTAATCGGGGGTGG
1 AGGACTAATCGGGGGTGG
28794067 AGGACTAATCGGGGGTGG
1 AGGACTAATCGGGGGTGG
28794085 AGG
1 AGG
28794088 TTGTTGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.51, T:0.15
Consensus pattern (18 bp):
AGGACTAATCGGGGGTGG
Found at i:28796273 original size:45 final size:43
Alignment explanation
Indices: 28796066--28796270 Score: 188
Period size: 43 Copynumber: 4.8 Consensus size: 43
28796056 ATATCGAACA
* * * *
28796066 ATGCCAACGTCCCAGATGTGGTCTTACATGCG-ATCT-CATACCG
1 ATGCCAACGTCCCAGACGTGGTCTTACA--CGAAACTAAATATCG
* *
28796109 ATGCC-ACTGTCCCAGACAG-GGTATTACACGAATC-AAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAACTAAATATCG
* * * * * * * *
28796150 ATGCCGATGTCCCAGACATGGTCTTACTCGTAACCACATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAACTAAATATCG
28796193 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACATAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAAC-TAAATATCG
28796238 ATGCCAACGTCCCAGACGTGGTCTTACACGAAA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAA
28796271 ACACATAGCA
Statistics
Matches: 133, Mismatches: 19, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
41 29 0.22
42 13 0.10
43 48 0.36
44 7 0.05
45 36 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAACTAAATATCG
Found at i:28801019 original size:21 final size:21
Alignment explanation
Indices: 28800989--28801032 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
28800979 CCCTCTTTCA
28800989 ACTCCAACACGAACAAAAATG
1 ACTCCAACACGAACAAAAATG
* *
28801010 ACTCCGACACTAACAAAAATG
1 ACTCCAACACGAACAAAAATG
28801031 AC
1 AC
28801033 AATAGCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.30, G:0.09, T:0.11
Consensus pattern (21 bp):
ACTCCAACACGAACAAAAATG
Found at i:28801954 original size:24 final size:24
Alignment explanation
Indices: 28801927--28801973 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28801917 TTCTATAGTC
*
28801927 ATGAATTTGAATTTAATTTATTAT
1 ATGAATTTCAATTTAATTTATTAT
*
28801951 ATGAATTTCAATTTTATTTATTA
1 ATGAATTTCAATTTAATTTATTA
28801974 GATAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
ATGAATTTCAATTTAATTTATTAT
Found at i:28802466 original size:13 final size:13
Alignment explanation
Indices: 28802450--28802476 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28802440 ATGTCTTATA
28802450 TTAGCATTTCTCT
1 TTAGCATTTCTCT
28802463 TTAGCATTTCTCT
1 TTAGCATTTCTCT
28802476 T
1 T
28802477 GAGTCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TTAGCATTTCTCT
Found at i:28803032 original size:53 final size:53
Alignment explanation
Indices: 28802970--28803075 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
28802960 ACTATATTTT
*
28802970 TCCCACATTGATACCTAAATTTGACAACTAAATTTATTATAATCTTTGAATTC
1 TCCCACATTGATACCTAAATTTGACAACTAAATTCATTATAATCTTTGAATTC
28803023 TCCCACATTGATACCTAAATTTGACAACTAAATTCATTATAATCTTTGAATTC
1 TCCCACATTGATACCTAAATTTGACAACTAAATTCATTATAATCTTTGAATTC
28803076 AAAAAGAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.39
Consensus pattern (53 bp):
TCCCACATTGATACCTAAATTTGACAACTAAATTCATTATAATCTTTGAATTC
Found at i:28809061 original size:18 final size:20
Alignment explanation
Indices: 28809030--28809066 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28809020 AAATTCTTTT
28809030 AAATTTTTTCTAAA-AAAAG
1 AAATTTTTTCTAAATAAAAG
28809049 AAATTTTTT-TAAATAAAA
1 AAATTTTTTCTAAATAAAA
28809067 AGCAGAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
AAATTTTTTCTAAATAAAAG
Found at i:28815027 original size:12 final size:12
Alignment explanation
Indices: 28815012--28815041 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28815002 AAGAGAAAAG
28815012 AAAATATAAACT
1 AAAATATAAACT
*
28815024 AAAATATAAATT
1 AAAATATAAACT
28815036 AAAATA
1 AAAATA
28815042 AATAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATATAAACT
Found at i:28818179 original size:25 final size:26
Alignment explanation
Indices: 28818151--28818202 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28818141 CTTAAAATGA
*
28818151 TCAAG-GACAAAGCTAGAAATT-TATT
1 TCAAGAGACAAAGATA-AAATTATATT
*
28818176 TCAAGAGACCAAGATAAAATTATATT
1 TCAAGAGACAAAGATAAAATTATATT
28818202 T
1 T
28818203 TTTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (26 bp):
TCAAGAGACAAAGATAAAATTATATT
Found at i:28820549 original size:24 final size:24
Alignment explanation
Indices: 28820517--28820851 Score: 245
Period size: 24 Copynumber: 14.1 Consensus size: 24
28820507 GTGTTCTCCT
* * * *
28820517 TAGGGGTTCGTAGATATTTTGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* *
28820541 TAGGGGTTCGCATATGTTTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* * *
28820565 TAGGGATT--CATATGTCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
*
28820587 TAGAGGTTCGCA-AGTGTCTGGTGA
1 TAGGGGTTCGCAGA-TGTCTGGTGA
* * *
28820611 TAGAGGTTCACAGATGTTTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* * ** *
28820635 TAGGGGTTCGTAGGTACCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* * *
28820659 TAGGGGTTCACAGGTGTTTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* * *
28820683 TAGGAGTTCGTAAATGTCTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* * * * *
28820707 TAGGGGTTAGTAGGTATCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
*
28820731 TA-GGGTTCGCATG-TTTCTGGTGA
1 TAGGGGTTCGCA-GATGTCTGGTGA
* *
28820754 TAGGGGTTCGTAAATGTCTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
* *
28820778 TAGGGGTTCGCATATGTCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGA
28820802 TAGGGGTTCGCAGGAATG--TGGTGA
1 TAGGGGTTCGCA-G-ATGTCTGGTGA
* *
28820826 TAGGTGTTCGCATG-TGTCTAGTGA
1 TAGGGGTTCGCA-GATGTCTGGTGA
28820850 TA
1 TA
28820852 AGAGTTCACA
Statistics
Matches: 247, Mismatches: 53, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
22 20 0.08
23 18 0.07
24 205 0.83
25 1 0.00
26 3 0.01
ACGTcount: A:0.21, C:0.09, G:0.36, T:0.34
Consensus pattern (24 bp):
TAGGGGTTCGCAGATGTCTGGTGA
Found at i:28820569 original size:48 final size:48
Alignment explanation
Indices: 28820517--28820851 Score: 272
Period size: 48 Copynumber: 7.0 Consensus size: 48
28820507 GTGTTCTCCT
* * * * *
28820517 TAGGGGTTCGTAGATATTTTGTGATAGGGGTTCGCATATGTTTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
* * * *
28820565 TAGGGATT--CATATGTCTAGTGATAGAGGTTCGCA-AGTGTCTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATA-TGTCTGGTGA
* * * * *
28820611 TAGAGGTTCACAGATGTTTGGTGATAGGGGTTCG--TAGGTACCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGT--CTGGTGA
* * * * * *
28820659 TAGGGGTTCACAGGTGTTTGGTGATAGGAGTTCGTAAATGTCTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
* * * * * * *
28820707 TAGGGGTTAGTAGGTATCTAGTGATA-GGGTTCGCATGTTTCTGGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
* * *
28820754 TAGGGGTTCGTAAATGTCTGGTGATAGGGGTTCGCATATGTCTAGTGA
1 TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
* * *
28820802 TAGGGGTTCGCAGGAATG--TGGTGATAGGTGTTCGCATGTGTCTAGTGA
1 TAGGGGTTCGCA-G-ATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
28820850 TA
1 TA
28820852 AGAGTTCACA
Statistics
Matches: 231, Mismatches: 45, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.00
46 37 0.16
47 38 0.16
48 149 0.65
50 6 0.03
ACGTcount: A:0.21, C:0.09, G:0.36, T:0.34
Consensus pattern (48 bp):
TAGGGGTTCGCAGATGTCTGGTGATAGGGGTTCGCATATGTCTGGTGA
Found at i:28820576 original size:22 final size:22
Alignment explanation
Indices: 28820530--28820589 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
28820520 GGGTTCGTAG
*
28820530 ATAT-TTTGTGATAGGGGTTCGC
1 ATATGTTTGTGATAGGGATTC-C
28820552 ATATGTTTGGTGATAGGGATT-C
1 ATATGTTT-GTGATAGGGATTCC
*
28820574 ATATGTCTAGTGATAG
1 ATATGT-TTGTGATAG
28820590 AGGTTCGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 18 0.55
23 4 0.12
24 11 0.33
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (22 bp):
ATATGTTTGTGATAGGGATTCC
Found at i:28820683 original size:72 final size:70
Alignment explanation
Indices: 28820517--28820851 Score: 323
Period size: 72 Copynumber: 4.7 Consensus size: 70
28820507 GTGTTCTCCT
* * * * * * * * *
28820517 TAGGGGTTCGTAGATATTTTGTGATAGGGGTTCGCATATGTTTGGTGATAGGGATTCATATGTCT
1 TAGGGGTTCGCAGGTGTTTGGTGATAGGGGTTCGCAAATGTCTGGTGATAGGGGTTCGTAGGTCT
28820582 AGTGA
66 AGTGA
* * * * * * *
28820587 TAGAGGTTCGCAAGTGTCTGGTGATAGAGGTTCACAGATGTTTGGTGATAGGGGTTCGTAGGTAC
1 TAGGGGTTCGCAGGTGTTTGGTGATAGGGGTTCGCAAATGTCTGGTGATAGGGGTTCGTAGGT--
28820652 CTAGTGA
64 CTAGTGA
* * * *
28820659 TAGGGGTTCACAGGTGTTTGGTGATAGGAGTTCGTAAATGTCTGGTGATAGGGGTTAGTAGGTAT
1 TAGGGGTTCGCAGGTGTTTGGTGATAGGGGTTCGCAAATGTCTGGTGATAGGGGTTCGTAGG--T
28820724 CTAGTGA
64 CTAGTGA
* * *
28820731 TA-GGGTTCGCATGT-TTCTGGTGATAGGGGTTCGTAAATGTCTGGTGATAGGGGTTCGCATATG
1 TAGGGGTTCGCAGGTGTT-TGGTGATAGGGGTTCGCAAATGTCTGGTGATAGGGGTTCG--TAGG
28820794 TCTAGTGA
63 TCTAGTGA
** * * ** *
28820802 TAGGGGTTCGCAGGAATGTGGTGATAGGTGTTCGCATGTGTCTAGTGATA
1 TAGGGGTTCGCAGGTGTTTGGTGATAGGGGTTCGCAAATGTCTGGTGATA
28820852 AGAGTTCACA
Statistics
Matches: 219, Mismatches: 37, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
70 52 0.24
71 58 0.26
72 104 0.47
73 4 0.02
74 1 0.00
ACGTcount: A:0.21, C:0.09, G:0.36, T:0.34
Consensus pattern (70 bp):
TAGGGGTTCGCAGGTGTTTGGTGATAGGGGTTCGCAAATGTCTGGTGATAGGGGTTCGTAGGTCT
AGTGA
Found at i:28821177 original size:15 final size:15
Alignment explanation
Indices: 28821153--28821182 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28821143 GTTGGTCCAA
*
28821153 ATTTATTATTTACGT
1 ATTTAATATTTACGT
28821168 ATTTAATATTTACGT
1 ATTTAATATTTACGT
28821183 TGTGTAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTTAATATTTACGT
Found at i:28821627 original size:23 final size:23
Alignment explanation
Indices: 28821601--28821645 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28821591 ATCTACAGGC
28821601 AATTCA-TCTGTAAATCTACTGAT
1 AATTCATTC-GTAAATCTACTGAT
* *
28821624 AATTTATTCGTATATCTACTGA
1 AATTCATTCGTAAATCTACTGA
28821646 CGGTATATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (23 bp):
AATTCATTCGTAAATCTACTGAT
Found at i:28821630 original size:46 final size:46
Alignment explanation
Indices: 28821543--28821642 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 46
28821533 GTTTATTTGC
* * * * **
28821543 ATATCTACTGGCAGTTCATCTACAAATCTATTGGTGGTTTATCCAT
1 ATATCTACAGGCAATTCATCTACAAATCTACTGATAATTTATCCAT
** * *
28821589 ATATCTACAGGCAATTCATCTGTAAATCTACTGATAATTTATTCGT
1 ATATCTACAGGCAATTCATCTACAAATCTACTGATAATTTATCCAT
28821635 ATATCTAC
1 ATATCTAC
28821643 TGACGGTATA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (46 bp):
ATATCTACAGGCAATTCATCTACAAATCTACTGATAATTTATCCAT
Found at i:28832739 original size:41 final size:41
Alignment explanation
Indices: 28832676--28832776 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
28832666 AAAATTAATT
28832676 ATACCC-TGAATTGCACATATGTGCCCCTGTTTGTACTTCA
1 ATACCCTTGAATTGCACATATGTGCCCCTGTTTGTACTTCA
* *
28832716 GTACTCTTGAATTGCACATATGTGCCCCTGTTTGTACTTCA
1 ATACCCTTGAATTGCACATATGTGCCCCTGTTTGTACTTCA
*
28832757 ATACCCTTGAATTTCACATA
1 ATACCCTTGAATTGCACATA
28832777 CGTACCCTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 4 0.07
41 51 0.93
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.37
Consensus pattern (41 bp):
ATACCCTTGAATTGCACATATGTGCCCCTGTTTGTACTTCA
Found at i:28834349 original size:17 final size:17
Alignment explanation
Indices: 28834329--28834371 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
28834319 AATTTGTTTG
28834329 TTTATTTTTCTTATTTA
1 TTTATTTTTCTTATTTA
* *
28834346 TTTATTTTTGTTCTTTA
1 TTTATTTTTCTTATTTA
28834363 TTTATTTTT
1 TTTATTTTT
28834372 ATCCTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTATTTTTCTTATTTA
Found at i:28836265 original size:11 final size:10
Alignment explanation
Indices: 28836236--28836305 Score: 62
Period size: 9 Copynumber: 7.5 Consensus size: 10
28836226 AAAATTGTTA
28836236 TTTTA-AATT
1 TTTTATAATT
28836245 TTTT-TAATT
1 TTTTATAATT
28836254 TTTTATATATT
1 TTTTATA-ATT
* *
28836265 TTTTAGAACT
1 TTTTATAATT
28836275 TTTTATAA--
1 TTTTATAATT
28836283 -TTTATAA-T
1 TTTTATAATT
*
28836291 TTATATAATT
1 TTTTATAATT
28836301 TTTTA
1 TTTTA
28836306 AAATATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
7 7 0.14
9 18 0.36
10 16 0.32
11 9 0.18
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:28836268 original size:19 final size:17
Alignment explanation
Indices: 28836244--28836306 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
28836234 TATTTTAAAT
28836244 TTTTTTAATTTTTTATATA
1 TTTTTTAA-TTTTTATA-A
28836263 TTTTTTAGAACTTTTTATAA
1 TTTTTT--AA-TTTTTATAA
* *
28836283 -TTTATAATTTATATAA
1 TTTTTTAATTTTTATAA
28836299 TTTTTTAA
1 TTTTTTAA
28836307 AATATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.22
17 8 0.22
19 10 0.27
20 1 0.03
21 10 0.27
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTTAATTTTTATAA
Found at i:28840679 original size:12 final size:12
Alignment explanation
Indices: 28840662--28840686 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28840652 TGTGCATGTC
28840662 TGTCTGTGTGTG
1 TGTCTGTGTGTG
28840674 TGTCTGTGTGTG
1 TGTCTGTGTGTG
28840686 T
1 T
28840687 ATGTATTGTT
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:0.00, C:0.08, G:0.40, T:0.52
Consensus pattern (12 bp):
TGTCTGTGTGTG
Found at i:28844513 original size:44 final size:44
Alignment explanation
Indices: 28844450--28844535 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
28844440 TTGAAATGAG
28844450 TATGTTTAATTTTTGTATGTTTGAGGATCCTTGGAGGGTCCTCT
1 TATGTTTAATTTTTGTATGTTTGAGGATCCTTGGAGGGTCCTCT
28844494 TATGTTTAATTTTTGTATGTTTGAGGATCCTTGGAGGGTCCT
1 TATGTTTAATTTTTGTATGTTTGAGGATCCTTGGAGGGTCCT
28844536 ATCCTGGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.16, C:0.10, G:0.26, T:0.48
Consensus pattern (44 bp):
TATGTTTAATTTTTGTATGTTTGAGGATCCTTGGAGGGTCCTCT
Found at i:28848120 original size:27 final size:30
Alignment explanation
Indices: 28848086--28848155 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
28848076 GACTTTGCAC
28848086 ATTT-AAAATTTAG-T-CTCTACTTTTAAT
1 ATTTAAAAATTTAGTTACTCTACTTTTAAT
* *
28848113 -TTTAAAAATTTAGTTACTTTACTTTTCAT
1 ATTTAAAAATTTAGTTACTCTACTTTTAAT
*
28848142 ATTTAATAATTTAG
1 ATTTAAAAATTTAG
28848156 GTCTAGTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 3 0.08
27 9 0.25
28 1 0.03
29 11 0.31
30 12 0.33
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (30 bp):
ATTTAAAAATTTAGTTACTCTACTTTTAAT
Found at i:28853608 original size:21 final size:21
Alignment explanation
Indices: 28853578--28853622 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
28853568 GAAGGATCAA
28853578 ATGCTAGAGTC-CTAGAAAAAC
1 ATGCTAGAGTCAC-AGAAAAAC
* *
28853599 ATGCTGGAGTCACAGAACAAC
1 ATGCTAGAGTCACAGAAAAAC
28853620 ATG
1 ATG
28853623 ATGAGCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (21 bp):
ATGCTAGAGTCACAGAAAAAC
Found at i:28861489 original size:90 final size:90
Alignment explanation
Indices: 28861381--28861679 Score: 272
Period size: 90 Copynumber: 3.3 Consensus size: 90
28861371 ACATACCCGA
28861381 TCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAGTCTTATCTTCACTGAGTAG
1 TCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAGTCTTATCTTCACTGAGTAG
* *
28861446 GAGTGGAGCAGATTTCAGCCACCAG
66 GAGTGGAGCAGAATTCAACCACCAG
* ** * * *
28861471 TCTTATCTTCACTGAGCAGGAGTGGAGCAGAT----TTCAGCCACCAGCCTTATCTTCACTGAGT
1 TCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTG--GCGAGTCTTATCTTCACTGAGT
** * * *
28861532 AGGAGTGGAGCAG-GCTAAACATACCCG
64 AGGAGTGGAGCAGAATTCAAC-CACCAG
* * * *
28861559 ATCTTTTCTTCACTGAGCAGGACTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCA-TGTA-T
1 -TCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAGTCTTATCTTCACTG-AGT
* * * *
28861622 CGGCAATGGAGCA-AATTCTAATCATCAG
64 AGG-AGTGGAGCAGAATTC-AACCACCAG
* *
28861650 CCTTATCTTCACTGAGTAGGAGTGAAGCAG
1 TCTTATCTTCACTGAGCAGGAGTGAAGCAG
28861680 GCTAAGTATA
Statistics
Matches: 161, Mismatches: 36, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
86 3 0.02
87 3 0.02
88 36 0.22
89 28 0.17
90 61 0.38
91 25 0.16
92 2 0.01
93 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (90 bp):
TCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCGAGTCTTATCTTCACTGAGTAG
GAGTGGAGCAGAATTCAACCACCAG
Found at i:28861492 original size:44 final size:44
Alignment explanation
Indices: 28861425--28861544 Score: 222
Period size: 44 Copynumber: 2.7 Consensus size: 44
28861415 AATTTTGGCG
28861425 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
*
28861469 AGTCTTATCTTCACTGAGCAGGAGTGGAGCAGATTTCAGCCACC
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
*
28861513 AGCCTTATCTTCACTGAGTAGGAGTGGAGCAG
1 AGTCTTATCTTCACTGAGTAGGAGTGGAGCAG
28861545 GCTAAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 73 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (44 bp):
AGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATTTCAGCCACC
Found at i:28861634 original size:179 final size:179
Alignment explanation
Indices: 28861333--28861679 Score: 493
Period size: 179 Copynumber: 1.9 Consensus size: 179
28861323 CAGATATCAT
* *
28861333 CAGCCTTATCTTCACTTAGCAGGAGTGAAGCGGGCTAAACATACCCGATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATACCCGATCTTATCTTCACTGAGC
* * * * *
28861398 AGGAGTGAAGCAGATCAAATTTTGGCGAGTCTTATCTTCACTGAGTAGGAGTGGAGCAGATT-TC
66 AGGACTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCACTGAGTAGGAATGGAGCAAATTCT-
* * *
28861462 AGCCACCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGATTTCAGCCAC
130 AACCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGATTTCAGCCAC
* * *
28861512 CAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAACATACCCGATCTTTTCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATACCCGATCTTATCTTCACTGAGC
*
28861577 AGGACTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCA-TGTA-TCGGCAATGGAGCAAATTC
66 AGGACTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCACTG-AGTAGG-AATGGAGCAAATTC
* * *
28861640 TAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAG
129 TAACCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAG
28861680 GCTAAGTATA
Statistics
Matches: 148, Mismatches: 17, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
178 5 0.03
179 142 0.96
180 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (179 bp):
CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATACCCGATCTTATCTTCACTGAGC
AGGACTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCACTGAGTAGGAATGGAGCAAATTCTA
ACCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGATTTCAGCCAC
Found at i:28861843 original size:135 final size:135
Alignment explanation
Indices: 28861493--28861859 Score: 425
Period size: 135 Copynumber: 2.7 Consensus size: 135
28861483 TGAGCAGGAG
* ** * * * * *
28861493 TGGAGCAGATTTCAGCCACCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAACATACCC
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAATATATCA
* * * * *
28861558 GATCTTTTCTTCACTGAGCAGGA-CTGAAGCAAATCAAATTTTGGCGAGTCTTATCTCCATGTAT
66 GATCTTATCTTCGCTGAGCAGGAGC-GGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
*
28861622 CGGCAA
130 CAGCAA
* * *
28861628 TGGAGCAAATTCTAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAGTATAGT-
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAATATA-TC
* * * *
28861692 AGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCGAATTTTGGTGAATCTTATGTCCCTGTA-
65 AGATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTAT
*
28861756 CTAGCGA
130 C-AGCAA
* * *
28861763 TGGAGCAGATTCCAATCATCAGACTTATCTTCAATGAGCAGGAGTGAAGCAGGCTAAATATATCA
1 TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAATATATCA
* * * *
28861828 GATCTTATCTCCGCTGAACAAGAGTGGAGCAG
66 GATCTTATCTTCGCTGAGCAGGAGCGGAGCAG
28861860 GTCAGATACA
Statistics
Matches: 196, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
134 2 0.01
135 193 0.98
136 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (135 bp):
TGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGTAGGAGTGAAGCAGGCTAAATATATCA
GATCTTATCTTCGCTGAGCAGGAGCGGAGCAGATCAAATTTTGGCGAATCTTATCTCCATGTATC
AGCAA
Found at i:28870186 original size:20 final size:20
Alignment explanation
Indices: 28870161--28870199 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28870151 ACAAATTCTA
28870161 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
28870181 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
28870200 AATAGCCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:28873329 original size:28 final size:28
Alignment explanation
Indices: 28873289--28873344 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28873279 CTTGGTAAGT
*
28873289 TTACTTTCGATTATTCGAGCTTACTACG
1 TTACTTTCGATTATTCAAGCTTACTACG
28873317 TTACTTTCGATTATTCAAGCTTACTACG
1 TTACTTTCGATTATTCAAGCTTACTACG
28873345 CATATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.43
Consensus pattern (28 bp):
TTACTTTCGATTATTCAAGCTTACTACG
Found at i:28887957 original size:17 final size:19
Alignment explanation
Indices: 28887927--28887973 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
28887917 TCATATTTAG
*
28887927 ATTTGATATATTCT-A-TT
1 ATTTGATTTATTCTGATTT
*
28887944 ATTTGATTTCTTCTGATTT
1 ATTTGATTTATTCTGATTT
28887963 ATTT-ATTTATT
1 ATTTGATTTATT
28887974 TTCATTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.48
18 7 0.28
19 6 0.24
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (19 bp):
ATTTGATTTATTCTGATTT
Found at i:28889559 original size:31 final size:31
Alignment explanation
Indices: 28889521--28889579 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28889511 TCATACTTCA
28889521 TATTTCATAACACTGGGCCGAAGCCTTTTTG
1 TATTTCATAACACTGGGCCGAAGCCTTTTTG
**
28889552 TATTTCATATTACTGGGCCGAAGCCTTT
1 TATTTCATAACACTGGGCCGAAGCCTTT
28889580 ACTGCAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (31 bp):
TATTTCATAACACTGGGCCGAAGCCTTTTTG
Found at i:28889937 original size:24 final size:24
Alignment explanation
Indices: 28889785--28889936 Score: 218
Period size: 24 Copynumber: 6.4 Consensus size: 24
28889775 CTAGAGGCCT
* *
28889785 AGCCTCTTTTAATAATTGGGACA-A
1 AGCC-CTTTTAATAACTGGGGCATA
28889809 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
28889833 AGTCC-TTTAATAACCGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
28889856 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
28889880 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
28889904 AGCCCTTTTGATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
28889928 AGCCCTTTT
1 AGCCCTTTT
28889937 GCACTTCCTC
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 37 0.31
24 81 0.69
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:28890011 original size:20 final size:20
Alignment explanation
Indices: 28889986--28890052 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
28889976 TTATGAATAC
28889986 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
28890006 ATCATGTGCATAGT-ATACAT
1 ATCATGTGCATA-TCATACAT
*
28890026 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28890046 ACCATGT
1 ATCATGT
28890053 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28893680 original size:25 final size:26
Alignment explanation
Indices: 28893652--28893700 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
28893642 ATACTTCACA
* *
28893652 TATATTATTCAAATCAA-TCTATTAG
1 TATACTATTCAAACCAATTCTATTAG
*
28893677 TATACTATTTAAACCAATTCTATT
1 TATACTATTCAAACCAATTCTATT
28893701 TTTCACACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (26 bp):
TATACTATTCAAACCAATTCTATTAG
Found at i:28899696 original size:17 final size:18
Alignment explanation
Indices: 28899664--28899700 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
28899654 AAATCCATGC
28899664 TCTAAACCTCCTTAAAAT
1 TCTAAACCTCCTTAAAAT
28899682 TCTAAACCT-CTTAAAAT
1 TCTAAACCTCCTTAAAAT
28899699 TC
1 TC
28899701 CTTCAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.35
Consensus pattern (18 bp):
TCTAAACCTCCTTAAAAT
Found at i:28901965 original size:13 final size:13
Alignment explanation
Indices: 28901947--28901971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28901937 ATAGACATTT
28901947 TAAACTTTTACCC
1 TAAACTTTTACCC
28901960 TAAACTTTTACC
1 TAAACTTTTACC
28901972 TTTTATTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAACTTTTACCC
Found at i:28904860 original size:13 final size:14
Alignment explanation
Indices: 28904844--28904879 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28904834 CAATCTCATA
28904844 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
28904857 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
28904870 TCTC-ATTTCA
1 TCTCAATTTCA
28904880 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:28904869 original size:18 final size:19
Alignment explanation
Indices: 28904831--28904871 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
28904821 TGGTTCATGT
28904831 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
28904850 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
28904868 TTTC
1 TTTC
28904872 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:28905006 original size:23 final size:23
Alignment explanation
Indices: 28904976--28905041 Score: 123
Period size: 23 Copynumber: 2.8 Consensus size: 23
28904966 GCGGATTCCT
28904976 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
28904999 CCCAAACACACCAGAATATCCAA
1 CCCAAACACACCAGAATATCCAA
28905022 CCCAAACACACCCAGAATAT
1 CCCAAACACA-CCAGAATAT
28905042 TATAAACCCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 33 0.79
24 9 0.21
ACGTcount: A:0.47, C:0.39, G:0.05, T:0.09
Consensus pattern (23 bp):
CCCAAACACACCAGAATATCCAA
Found at i:28905535 original size:15 final size:15
Alignment explanation
Indices: 28905515--28905561 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
28905505 TAATATATAT
28905515 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
28905530 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
28905545 TTCAATCAATATAAA
1 TTCAATCAATATAAA
28905560 TT
1 TT
28905562 TGAGAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:28906431 original size:19 final size:19
Alignment explanation
Indices: 28906407--28906445 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28906397 AATACTTATT
*
28906407 TATTATTTATACATGTGTA
1 TATTATTAATACATGTGTA
28906426 TATTATTAATACATGTGTA
1 TATTATTAATACATGTGTA
28906445 T
1 T
28906446 CTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAATACATGTGTA
Found at i:28906453 original size:19 final size:19
Alignment explanation
Indices: 28906410--28906453 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28906400 ACTTATTTAT
28906410 TATTT-ATACATGTGTATA
1 TATTTAATACATGTGTATA
*
28906428 T-TATTAATACATGTGTATC
1 TAT-TTAATACATGTGTATA
28906447 TATTTAA
1 TATTTAA
28906454 AACCATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 17 0.77
20 1 0.05
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TATTTAATACATGTGTATA
Found at i:28922611 original size:29 final size:29
Alignment explanation
Indices: 28922569--28922628 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28922559 AATTTAAGAG
28922569 TAAAAAGTTGAATCTCATTAAAAGGACTC
1 TAAAAAGTTGAATCTCATTAAAAGGACTC
28922598 TAAAAAGTTGAATCTCATTAAAAGGACTC
1 TAAAAAGTTGAATCTCATTAAAAGGACTC
28922627 TA
1 TA
28922629 TTAAAGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (29 bp):
TAAAAAGTTGAATCTCATTAAAAGGACTC
Found at i:28933254 original size:40 final size:40
Alignment explanation
Indices: 28933196--28933333 Score: 110
Period size: 40 Copynumber: 3.6 Consensus size: 40
28933186 TAGAAGTTGC
*
28933196 GCCCAG-TGCTAGTCGGATAAACTGACAAAATAATTATTGA
1 GCCCAGCT-CTAGTTGGATAAACTGACAAAATAATTATTGA
* * *
28933236 GCCCAGCTTTAGTTGGATAAAC---CAACGAT-A-T-TTGC
1 GCCCAGCTCTAGTTGGATAAACTGACAA-AATAATTATTGA
* * * * ** *
28933271 GTCCAACGCTAGTTGGATAAACCGATGAAATAATTAGTGA
1 GCCCAGCTCTAGTTGGATAAACTGACAAAATAATTATTGA
28933311 GCCCAGCTCTAGTTGGATAAACT
1 GCCCAGCTCTAGTTGGATAAACT
28933334 AACGATATTT
Statistics
Matches: 73, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
35 21 0.29
36 1 0.01
37 6 0.08
38 4 0.05
39 1 0.01
40 39 0.53
41 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (40 bp):
GCCCAGCTCTAGTTGGATAAACTGACAAAATAATTATTGA
Found at i:28933374 original size:75 final size:75
Alignment explanation
Indices: 28933203--28933374 Score: 238
Period size: 75 Copynumber: 2.3 Consensus size: 75
28933193 TGCGCCCAGT
** * *
28933203 GCTAGTCGGATAAACTGACAAAATAATTATTGAGCCCAGCTTTAGTTGGATAAACCAACGATATT
1 GCTAGTCGGATAAACTGATGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
*
28933268 TGCGTCCAAC
66 TGCGACCAAC
* * *
28933278 GCTAGTTGGATAAACCGATGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACTAACGATATT
1 GCTAGTCGGATAAACTGATGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
*
28933343 TGC-ACCTAGC
66 TGCGACC-AAC
*
28933353 GCTAGTCGGATAAACTAATGAA
1 GCTAGTCGGATAAACTGATGAA
28933375 TGTGTGCCCA
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 2 0.02
75 82 0.98
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (75 bp):
GCTAGTCGGATAAACTGATGAAATAATTAGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATT
TGCGACCAAC
Found at i:28933399 original size:34 final size:33
Alignment explanation
Indices: 28933311--28933407 Score: 97
Period size: 35 Copynumber: 2.8 Consensus size: 33
28933301 TAATTAGTGA
*
28933311 GCCCAGCTCTAGTTGGATAAACTAACGATATTT
1 GCCCAGCACTAGTTGGATAAACTAACGATATTT
* * *
28933344 GCACCTAGCGCTAGTCGGATAAACTAATGA-ATGTGT
1 GC-CC-AGCACTAGTTGGATAAACTAACGATAT-T-T
* *
28933380 GCCCAGCACTAGTTAGATAAACTGACGA
1 GCCCAGCACTAGTTGGATAAACTAACGA
28933408 AGTTGCATCC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
33 2 0.04
34 23 0.44
35 24 0.46
36 3 0.06
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (33 bp):
GCCCAGCACTAGTTGGATAAACTAACGATATTT
Found at i:28933420 original size:34 final size:33
Alignment explanation
Indices: 28933313--28933426 Score: 113
Period size: 34 Copynumber: 3.3 Consensus size: 33
28933303 ATTAGTGAGC
* *
28933313 CCAGCTCTAGTTGGATAAACTAACGATATTTGCA
1 CCAGCGCTAGTTGGATAAACTAACGA-AGTTGCA
* *
28933347 CCTAGCGCTAGTCGGATAAACTAATGAATGTGTGC-
1 CC-AGCGCTAGTTGGATAAACTAACGAA-GT-TGCA
* * *
28933382 CCAGCACTAGTTAGATAAACTGACGAAGTTGCA
1 CCAGCGCTAGTTGGATAAACTAACGAAGTTGCA
28933415 TCCAGCGCTAGT
1 -CCAGCGCTAGT
28933427 CGAACAAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
32 3 0.05
33 2 0.03
34 33 0.51
35 24 0.37
36 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (33 bp):
CCAGCGCTAGTTGGATAAACTAACGAAGTTGCA
Found at i:28934395 original size:3 final size:3
Alignment explanation
Indices: 28934389--28934428 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
28934379 CATCATCATC
28934389 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28934429 AACATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:28935921 original size:25 final size:25
Alignment explanation
Indices: 28935900--28935972 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
28935890 CATAGCTCTT
** *
28935900 ATGAGCTTCCCGGTACTCAGCTCGC
1 ATGAGCTTCCCAATACTCAGCTCAC
*
28935925 ATGAGCTTCCCAATACTCAACTCAC
1 ATGAGCTTCCCAATACTCAGCTCAC
* *
28935950 ATGAGCTTCCCATTACTTAGCTC
1 ATGAGCTTCCCAATACTCAGCTC
28935973 GGAAGATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.27
Consensus pattern (25 bp):
ATGAGCTTCCCAATACTCAGCTCAC
Found at i:28940835 original size:37 final size:36
Alignment explanation
Indices: 28940784--28940853 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
28940774 ATTTCAAAAA
* *
28940784 TAATATTATTTTAATAGT-TTAATATTAAATTAAATT
1 TAATATTATCTTAATAATATT-ATATTAAATTAAATT
*
28940820 TAATACTTATCTTAATAATATTATATTAATTTAA
1 TAATA-TTATCTTAATAATATTATATTAAATTAA
28940854 TGTTAAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 22 0.76
38 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (36 bp):
TAATATTATCTTAATAATATTATATTAAATTAAATT
Found at i:28942748 original size:14 final size:14
Alignment explanation
Indices: 28942729--28942756 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28942719 TAGATTAGAG
28942729 TTTGCCTATAAATA
1 TTTGCCTATAAATA
28942743 TTTGCCTATAAATA
1 TTTGCCTATAAATA
28942757 AGACAACCCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTGCCTATAAATA
Found at i:28952747 original size:29 final size:29
Alignment explanation
Indices: 28952715--28952773 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28952705 GTTTCTAATG
28952715 ATGCCATAGCTTCTTTCAGCCATGGTCTT
1 ATGCCATAGCTTCTTTCAGCCATGGTCTT
28952744 ATGCCATAGCTTCTTTCAGCCATGGTCTT
1 ATGCCATAGCTTCTTTCAGCCATGGTCTT
28952773 A
1 A
28952774 CTCATTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (29 bp):
ATGCCATAGCTTCTTTCAGCCATGGTCTT
Found at i:28958734 original size:39 final size:38
Alignment explanation
Indices: 28958678--28958777 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 38
28958668 TGAATATAAT
* * * *
28958678 AATTATAATTACCATAATTATAATAATGTTTGATCAAAA
1 AATTACAATTACAATAATTATAATAATATTCGATC-AAA
* *
28958717 AATTACAGTTACAATAATTATAATAATATTCGATCATA
1 AATTACAATTACAATAATTATAATAATATTCGATCAAA
*
28958755 AATTATAATTACAATAATTATAA
1 AATTACAATTACAATAATTATAA
28958778 CAAGTATTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 23 0.43
39 30 0.57
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (38 bp):
AATTACAATTACAATAATTATAATAATATTCGATCAAA
Found at i:28960293 original size:30 final size:30
Alignment explanation
Indices: 28960259--28960318 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28960249 AGAAGGATTA
*
28960259 ATTGAACGACACAAGCATAAGATGTGGGTT
1 ATTGAACGACAAAAGCATAAGATGTGGGTT
28960289 ATTGAACGACAAAAGCATAAGATGTGGGTT
1 ATTGAACGACAAAAGCATAAGATGTGGGTT
28960319 GAATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (30 bp):
ATTGAACGACAAAAGCATAAGATGTGGGTT
Found at i:28965403 original size:33 final size:33
Alignment explanation
Indices: 28965366--28965433 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
28965356 AATCTCATAT
*
28965366 TTATCATAGCCTCTTTTCAAGCAGAATAATTGA
1 TTATCATAGCCTCTTTCCAAGCAGAATAATTGA
*
28965399 TTATCATAGCCTCTTTCCAAGTAGAATAATTGA
1 TTATCATAGCCTCTTTCCAAGCAGAATAATTGA
28965432 TT
1 TT
28965434 CCAGCAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (33 bp):
TTATCATAGCCTCTTTCCAAGCAGAATAATTGA
Found at i:28968673 original size:25 final size:22
Alignment explanation
Indices: 28968629--28968676 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
28968619 GGTTTCAATT
*
28968629 AAATAATATTAAAAGTTTATAA
1 AAATAATATTAAAAATTTATAA
28968651 AAATAAATATATAAAAATCTTATAA
1 AAAT-AATAT-TAAAAAT-TTATAA
28968676 A
1 A
28968677 CCATAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 5 0.23
24 6 0.27
25 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAATATTAAAAATTTATAA
Found at i:28971718 original size:27 final size:27
Alignment explanation
Indices: 28971680--28971733 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
28971670 TCATACAACC
*
28971680 CATGTAATATTAATTTAACATTCAATT
1 CATGTAACATTAATTTAACATTCAATT
**
28971707 CATGTAACATTAATTTGCCATTCAATT
1 CATGTAACATTAATTTAACATTCAATT
28971734 TCACATGACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.43
Consensus pattern (27 bp):
CATGTAACATTAATTTAACATTCAATT
Found at i:28976642 original size:40 final size:40
Alignment explanation
Indices: 28976593--28976670 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
28976583 CACAAGAAAG
*
28976593 AAGCCCATAAGAGCTAATCCAACCGAAACACGCCAAACAA
1 AAGCCCATAAGAGCTAATCCAACCAAAACACGCCAAACAA
* *
28976633 AAGCTCATAAGAGCTGATCCAACCAAAACACGCCAAAC
1 AAGCCCATAAGAGCTAATCCAACCAAAACACGCCAAAC
28976671 GGACAGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.46, C:0.32, G:0.13, T:0.09
Consensus pattern (40 bp):
AAGCCCATAAGAGCTAATCCAACCAAAACACGCCAAACAA
Found at i:28978629 original size:33 final size:33
Alignment explanation
Indices: 28978585--28978671 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
28978575 AGACTTTATT
* * *
28978585 TGTTCTATGTTTAGTGTCCCAATCCACTATCTC
1 TGTTTTATGTTTACTGTCCCAATCAACTATCTC
* * * *
28978618 TGTTTTGTGTTTACTATCCCAATGAACTATCTT
1 TGTTTTATGTTTACTGTCCCAATCAACTATCTC
28978651 TGTTTTATGTTTACTGTCCCA
1 TGTTTTATGTTTACTGTCCCA
28978672 GCAAACTTTC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (33 bp):
TGTTTTATGTTTACTGTCCCAATCAACTATCTC
Found at i:28978831 original size:7 final size:7
Alignment explanation
Indices: 28978821--28978856 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
28978811 CATCTATAGT
*
28978821 CTTACAC
1 CTTATAC
28978828 CTTATAC
1 CTTATAC
28978835 CTTATAC
1 CTTATAC
28978842 CTTATAC
1 CTTATAC
*
28978849 CTTGTAC
1 CTTATAC
28978856 C
1 C
28978857 ATGCTTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.25, C:0.33, G:0.03, T:0.39
Consensus pattern (7 bp):
CTTATAC
Found at i:28979845 original size:35 final size:35
Alignment explanation
Indices: 28979797--28979864 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
28979787 TTCTTTCAAC
* *
28979797 TGAGGTCGTTAACAGGCGATCTCTTTTAATTTAAT
1 TGAGGTCGCTAACAGACGATCTCTTTTAATTTAAT
*
28979832 TGAGGTCGCTAACAGACTATCTCTTTTAATTTA
1 TGAGGTCGCTAACAGACGATCTCTTTTAATTTA
28979865 GTCCTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (35 bp):
TGAGGTCGCTAACAGACGATCTCTTTTAATTTAAT
Found at i:28983760 original size:61 final size:63
Alignment explanation
Indices: 28983688--28983806 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 63
28983678 ATCATTTTGG
*
28983688 ATTTTAAAAAAAATTATA-ATTTAGAATTTTT-AGA-ATTTTTAATTTTTTG-AATATATATAAA
1 ATTTTAAAAAAAA--ATAGATTTAGAATTTTTAAGATATTTTGAATTTTTTGTAATATATATAAA
* *
28983749 ATTTTAGAAAAAAATAGATTTTGAATTTTTGAAGATTATTTTGAATTTTTTGTAATAT
1 ATTTTAAAAAAAAATAGATTTAGAATTTTT-AAGA-TATTTTGAATTTTTTGTAATAT
28983807 TTTTATGGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
59 3 0.06
60 12 0.24
61 12 0.24
62 3 0.06
64 14 0.29
65 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (63 bp):
ATTTTAAAAAAAAATAGATTTAGAATTTTTAAGATATTTTGAATTTTTTGTAATATATATAAA
Found at i:28988362 original size:35 final size:34
Alignment explanation
Indices: 28988323--28988450 Score: 89
Period size: 35 Copynumber: 3.7 Consensus size: 34
28988313 GTTGGACTAT
28988323 CTCTTAAGAACACTAGTGTGTTTCGGAAGGATTAG
1 CTCTTAAGAACACTAGTGTGTTT-GGAAGGATTAG
* * * *
28988358 CTCTTATGAGA-ATTGGTGTGTTTTGGAGGGATTAG
1 CTCTTAAGA-ACACTAGTGTG-TTTGGAAGGATTAG
* * * * * *
28988393 CTCTTACGAGCATTGGTGTGTTTGGATGGATTGG
1 CTCTTAAGAACACTAGTGTGTTTGGAAGGATTAG
* *
28988427 CTTTTATA-AGCATCTAGTGTGTTT
1 CTCTTA-AGAACA-CTAGTGTGTTT
28988451 TGGTTGGATT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
34 21 0.28
35 51 0.67
36 4 0.05
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (34 bp):
CTCTTAAGAACACTAGTGTGTTTGGAAGGATTAG
Found at i:28988424 original size:34 final size:35
Alignment explanation
Indices: 28988338--28988460 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 35
28988328 AAGAACACTA
* * *
28988338 GTGTGTTTCGGAAGGATTAGCTCTTATGAGAATTG
1 GTGTGTTTTGGATGGATTAGCTCTTATGAGCATTG
* *
28988373 GTGTGTTTTGGAGGGATTAGCTCTTACGAGCATTG
1 GTGTGTTTTGGATGGATTAGCTCTTATGAGCATTG
* * * *
28988408 GTGTG-TTTGGATGGATTGGCTTTTATAAGCATCTA
1 GTGTGTTTTGGATGGATTAGCTCTTATGAGCAT-TG
*
28988443 GTGTGTTTTGGTTGGATT
1 GTGTGTTTTGGATGGATT
28988461 GTCGATGTAC
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
34 22 0.29
35 42 0.56
36 11 0.15
ACGTcount: A:0.18, C:0.08, G:0.33, T:0.41
Consensus pattern (35 bp):
GTGTGTTTTGGATGGATTAGCTCTTATGAGCATTG
Found at i:28993638 original size:64 final size:64
Alignment explanation
Indices: 28993562--28993741 Score: 168
Period size: 67 Copynumber: 2.8 Consensus size: 64
28993552 AGACATTATG
* * *
28993562 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTGCGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTACGAGATAA
* * * * * * *
28993626 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAAAGCTACGAGAT
28993691 AA
63 AA
* * * *
28993693 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGA
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGA
28993742 GAGCCGAACT
Statistics
Matches: 92, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
62 1 0.01
63 15 0.16
64 21 0.23
65 8 0.09
66 16 0.17
67 29 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAAAGCTACGAGATAA
Found at i:28995857 original size:49 final size:49
Alignment explanation
Indices: 28995752--28995883 Score: 176
Period size: 49 Copynumber: 2.7 Consensus size: 49
28995742 GGGTTAAGAT
* *
28995752 GCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAG
1 GCCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGTGAG
* * **
28995802 GCCGATGCCATGTCCAAGACAGGTCTTACACTGGCTCTCATCTA-TCGTT
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGT-GAG
*
28995851 GTCGATGCCATGTCCCAGACAGGTCTTACACTG
1 GCCGATGCCATGTCCCAGACAGGTCTTACACTG
28995884 ACACACCACA
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
48 1 0.01
49 53 0.73
50 19 0.26
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (49 bp):
GCCGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGTGAG
Found at i:28996105 original size:46 final size:48
Alignment explanation
Indices: 28995990--28996112 Score: 153
Period size: 48 Copynumber: 2.6 Consensus size: 48
28995980 GTCTCAATGT
* * *
28995990 CGATACATGTCCCATACATGTCTTACACTGGCTTAAATATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTTAAATAGCTCGAGGC
* * *
28996038 CGATGCATGTCCCAGAGATGTCTTACACTGGCTCT-CAT-GCT-GTGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCT-TAAATAGCTCGAGGC
*
28996084 TGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
28996113 AGCACACATA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 31 0.47
47 2 0.03
48 32 0.48
49 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTTAAATAGCTCGAGGC
Found at i:28996486 original size:30 final size:30
Alignment explanation
Indices: 28996450--28996507 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
28996440 TTAAAATTGG
28996450 GTAAAATGACCATTTTACCCCTAGACTCTT
1 GTAAAATGACCATTTTACCCCTAGACTCTT
*
28996480 GTAAAATGACCATTTTACCCTTAGACTC
1 GTAAAATGACCATTTTACCCCTAGACTC
28996508 GAAAATTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (30 bp):
GTAAAATGACCATTTTACCCCTAGACTCTT
Found at i:29007380 original size:5 final size:5
Alignment explanation
Indices: 29007370--29007417 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
29007360 AAGAAATAAG
* *
29007370 TAAAA TAAAA TAGAA TAAAA TAAAAA GAAAA TAAAA CTTAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAAAA --TAAAA TAAAA
29007418 AAATAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
5 27 0.75
6 4 0.11
7 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:29007388 original size:27 final size:26
Alignment explanation
Indices: 29007340--29007419 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
29007330 TAATAATCAG
* *
29007340 AAGTAAGAATTAAA-AGACTAAAGAAAT
1 AAGTAA-AATAAAATAGAATAAA-AAAT
*
29007367 AAGTAAAATAAAATAGAATAAAATAAA
1 AAGTAAAATAAAATAGAATAAAA-AAT
*
29007394 AAG-AAAATAAAACTTAAAATAAAAAA
1 AAGTAAAATAAAA--TAGAATAAAAAA
29007420 ATAATAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 16 0.36
27 20 0.44
28 9 0.20
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (26 bp):
AAGTAAAATAAAATAGAATAAAAAAT
Found at i:29011261 original size:22 final size:23
Alignment explanation
Indices: 29011227--29011271 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
29011217 TAAAGAAAGG
29011227 AAAATTAGGAATTAAAATAAAAAC
1 AAAATTA-GAATTAAAATAAAAAC
*
29011251 AAAATTA-AATTGAAATAAAAA
1 AAAATTAGAATTAAAATAAAAA
29011272 AATGGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (23 bp):
AAAATTAGAATTAAAATAAAAAC
Found at i:29012397 original size:30 final size:30
Alignment explanation
Indices: 29012345--29012402 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29012335 CACGGCCATG
* *
29012345 ACACACGGGCGTGTGTCCTACCCGTGTGTC
1 ACACACGGGCATGTGGCCTACCCGTGTGTC
**
29012375 ACACACGGGCATGTGGGTTACCCGTGTG
1 ACACACGGGCATGTGGCCTACCCGTGTG
29012403 GAAGTGCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (30 bp):
ACACACGGGCATGTGGCCTACCCGTGTGTC
Found at i:29017817 original size:14 final size:14
Alignment explanation
Indices: 29017800--29017832 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29017790 TAGCCATTTT
*
29017800 TATTTTTATTTTAA
1 TATTTTTAATTTAA
29017814 TATTTTTAATTTAA
1 TATTTTTAATTTAA
29017828 T-TTTT
1 TATTTT
29017833 ACATTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTAATTTAA
Found at i:29017871 original size:19 final size:19
Alignment explanation
Indices: 29017820--29017863 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
29017810 TTAATATTTT
29017820 TAATTTAATTTTTACATTC
1 TAATTTAATTTTTACATTC
29017839 TAATTTAATTTTTACATTC
1 TAATTTAATTTTTACATTC
29017858 TAATTT
1 TAATTT
29017864 TTTGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTTAATTTTTACATTC
Found at i:29026574 original size:27 final size:27
Alignment explanation
Indices: 29026543--29026720 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29026533 TAAATTGTAC
29026543 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29026570 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29026596 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
29026624 GGCACTAAGTGTGCGAGTTTAACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
29026652 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29026679 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29026706 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29026721 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.83
28 22 0.17
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29026660 original size:82 final size:81
Alignment explanation
Indices: 29026544--29026699 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29026534 AAATTGTACA
* *
29026544 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
29026608 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29026625 GCACTAAGTGTGCGAGTTTAACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
29026690 TGCGAGTTGA
65 TGCGAATTGA
29026700 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29026711 original size:82 final size:81
Alignment explanation
Indices: 29026540--29026720 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
29026530 GATTAAATTG
* *
29026540 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
29026605 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29026621 TGCGGCACTAAGTGTGCGAGTTTAACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
29026685 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29026703 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29026721 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29037665 original size:42 final size:42
Alignment explanation
Indices: 29037617--29037870 Score: 355
Period size: 42 Copynumber: 6.0 Consensus size: 42
29037607 GCGTTTATTA
29037617 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
* *
29037659 AAAAAAAGCGCCGCTAAAAGTCCTGGCATTTAGCGGCGTTTG
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
* * * *
29037701 AAAAAAAGCGCTGTTAAAAGTCGTGGCCTTTAGCGGCGTTTA
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
*
29037743 AAAAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGG
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTT-G
* * *
29037786 AAAAAAAAGCGCCGTTAAAAGTCATGGCCTTTAACGCCGTTTGG
1 -AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTT-G
* * **
29037830 GAAAAAAGCGCCGCTAAAAGTCACGATCTTTAGCGGCGTTT
1 AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTT
29037871 TTCCCTCAAA
Statistics
Matches: 189, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
42 116 0.61
43 34 0.18
44 39 0.21
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.22
Consensus pattern (42 bp):
AAAAAAAGCGCCGCTAAAAGTCATGGCCTTTAGCGGCGTTTG
Found at i:29037978 original size:31 final size:30
Alignment explanation
Indices: 29037943--29038008 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
29037933 CTTCCTACAT
29037943 TAAAATCCAACCAAAAACAACAAATATAGCA
1 TAAAATCCAACC-AAAACAACAAATATAGCA
* * * * *
29037974 TAAAATGCAGCCAAAATAGCAAATTTAGCA
1 TAAAATCCAACCAAAACAACAAATATAGCA
29038004 TAAAA
1 TAAAA
29038009 AAATACAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.17
Consensus pattern (30 bp):
TAAAATCCAACCAAAACAACAAATATAGCA
Found at i:29038721 original size:13 final size:14
Alignment explanation
Indices: 29038696--29038724 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29038686 TGATGAATTG
29038696 AATTAAACAATTAT
1 AATTAAACAATTAT
29038710 AATTAAAC-ATTAT
1 AATTAAACAATTAT
29038723 AA
1 AA
29038725 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:29038899 original size:17 final size:18
Alignment explanation
Indices: 29038872--29038906 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29038862 AGTAAAAATA
29038872 TTATCTAATATTAGAAAG
1 TTATCTAATATTAGAAAG
*
29038890 TTAT-TAATATTTGAAAG
1 TTATCTAATATTAGAAAG
29038907 AATTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
TTATCTAATATTAGAAAG
Found at i:29038913 original size:16 final size:17
Alignment explanation
Indices: 29038877--29038914 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29038867 AAATATTATC
*
29038877 TAATATTAGAAAGTTAT
1 TAATATTAGAAAGTAAT
*
29038894 TAATATTTGAAAG-AAT
1 TAATATTAGAAAGTAAT
29038910 TAATA
1 TAATA
29038915 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (17 bp):
TAATATTAGAAAGTAAT
Found at i:29043917 original size:9 final size:9
Alignment explanation
Indices: 29043903--29044022 Score: 79
Period size: 9 Copynumber: 13.6 Consensus size: 9
29043893 TATCTAAGTA
29043903 TTATGTAAG
1 TTATGTAAG
29043912 TTATGT-A-
1 TTATGTAAG
*
29043919 -TATCTAAG
1 TTATGTAAG
29043927 TATTATGTAAG
1 --TTATGTAAG
29043938 TTATGTAAG
1 TTATGTAAG
*
29043947 TTATGATATG
1 TTATG-TAAG
* * *
29043957 ATATAT-AT
1 TTATGTAAG
*
29043965 TTATGTAAA
1 TTATGTAAG
* *
29043974 TTATAT-AT
1 TTATGTAAG
*
29043982 TTATCTAAG
1 TTATGTAAG
*
29043991 TTATATAAG
1 TTATGTAAG
29044000 TTATGTAAG
1 TTATGTAAG
*
29044009 TTATGTAAA
1 TTATGTAAG
29044018 TTATG
1 TTATG
29044023 ATATAAAATA
Statistics
Matches: 86, Mismatches: 17, Indels: 16
0.72 0.14 0.13
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 11 0.13
9 57 0.66
10 6 0.07
11 7 0.08
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:29043920 original size:26 final size:26
Alignment explanation
Indices: 29043891--29043944 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
29043881 TGATATGATA
29043891 TATATCTAAGTATTATGTAAGTTATG
1 TATATCTAAGTATTATGTAAGTTATG
29043917 TATATCTAAGTATTATGTAAGTTATG
1 TATATCTAAGTATTATGTAAGTTATG
29043943 TA
1 TA
29043945 AGTTATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TATATCTAAGTATTATGTAAGTTATG
Found at i:29043991 original size:44 final size:45
Alignment explanation
Indices: 29043938--29044026 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
29043928 ATTATGTAAG
* * *
29043938 TTATGTAAGTTATGATATGATATAT-ATTTATGTAAATTAT-ATAT
1 TTATCTAAGTTAT-ATAAGATATATAAGTTATGTAAATTATGATAT
* *
29043982 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATAT
1 TTATCTAAGTTATATAAGATATATAAGTTATGTAAATTATGATAT
29044027 AAAATATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
43 8 0.21
44 26 0.68
45 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.48
Consensus pattern (45 bp):
TTATCTAAGTTATATAAGATATATAAGTTATGTAAATTATGATAT
Found at i:29043994 original size:26 final size:25
Alignment explanation
Indices: 29043901--29044022 Score: 84
Period size: 26 Copynumber: 4.6 Consensus size: 25
29043891 TATATCTAAG
*
29043901 TATTATGTAAGTTATGTATATCTA-A
1 TATTATGTAAGTTATGTAAAT-TATA
*
29043926 GTATTATGTAAGTTATGTAAGTTATGA
1 -TATTATGTAAGTTATGTAAATTAT-A
* * *
29043953 TATGATATATATTTATGTAAATTATA
1 TATTATGTA-AGTTATGTAAATTATA
* * * *
29043979 TATTTATCTAAGTTATATAAGTTATG
1 TA-TTATGTAAGTTATGTAAATTATA
*
29044005 TAAGTTATGTAAATTATG
1 T-A-TTATGTAAGTTATG
29044023 ATATAAAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
25 2 0.03
26 42 0.56
27 31 0.41
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.48
Consensus pattern (25 bp):
TATTATGTAAGTTATGTAAATTATA
Found at i:29049864 original size:40 final size:40
Alignment explanation
Indices: 29049819--29049916 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 40
29049809 TTGTAGAAAC
*
29049819 CGCCGCTAATGCGTCACA-TATTGCGGCGTTTTTGGTAAAA
1 CGCCGCTAATGCGTCA-AGTATAGCGGCGTTTTTGGTAAAA
* * *
29049859 TGCCGCTAATGCTTGAAGTTATAGCGGCGTTTTTGGTAAAA
1 CGCCGCTAATGCGTCAAG-TATAGCGGCGTTTTTGGTAAAA
*
29049900 CGCCGCTAATGCCTCAA
1 CGCCGCTAATGCGTCAA
29049917 AAGAGCTCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.02
40 13 0.27
41 35 0.71
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (40 bp):
CGCCGCTAATGCGTCAAGTATAGCGGCGTTTTTGGTAAAA
Found at i:29049890 original size:155 final size:156
Alignment explanation
Indices: 29049664--29050030 Score: 391
Period size: 155 Copynumber: 2.3 Consensus size: 156
29049654 CTGCTAAAAA
* * * * * *
29049664 CGCCGCTAATACTTCACCCATTGCGGCGCTTTTACAAAAACGCCGCTAATGCTTGAACTTTTTGT
1 CGCCGCTAATGCGTCA-CCATTGCGGCGTTTTTACAAAAACGCCGCTAATGCTTGAACTTATAGC
* * **
29049729 GGCGTTTTACG-AGAAACGCCACTAATGCCTC-AATAGCTCACCTACACACGGTGCCGTTTTGCT
65 GGCGTTTTACGTA-AAACGCCACTAATGCCTCAAAGAGCTCACCAACACACGGCACCGTTTTGCT
* *
29049792 CAATACTTTTGCGACATTTGTAGA-AAC
129 CAACACTTTTACGACATTTGTAGACAAC
* *** * *
29049819 CGCCGCTAATGCGTCACATATTGCGGCGTTTTTGGTAAAATGCCGCTAATGCTTGAAGTTATAGC
1 CGCCGCTAATGCGTCAC-CATTGCGGCGTTTTTACAAAAACGCCGCTAATGCTTGAACTTATAGC
** * *
29049884 GGCGTTTTTGGTAAAACGCCGCTAATGCCTCAAAAGAGCTCACCAACATACGGCACCGTTTTGCT
65 GGCGTTTTACGTAAAACGCCACTAATGCCTC-AAAGAGCTCACCAACACACGGCACCGTTTTGCT
* * *
29049949 CAACACTTTTACGGCATTTTTTGACAAC
129 CAACACTTTTACGACATTTGTAGACAAC
* * * *
29049977 CGCCGCTAATGTGTCAGCCATTGCGGCGTTCTTT-TATAAACGCCGTTAATGCTT
1 CGCCGCTAATGCGTCA-CCATTGCGGCGTT-TTTACAAAAACGCCGCTAATGCTT
29050031 TATTTTTTAT
Statistics
Matches: 173, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
154 1 0.01
155 77 0.45
156 1 0.01
157 46 0.27
158 44 0.25
159 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (156 bp):
CGCCGCTAATGCGTCACCATTGCGGCGTTTTTACAAAAACGCCGCTAATGCTTGAACTTATAGCG
GCGTTTTACGTAAAACGCCACTAATGCCTCAAAGAGCTCACCAACACACGGCACCGTTTTGCTCA
ACACTTTTACGACATTTGTAGACAAC
Found at i:29052922 original size:40 final size:40
Alignment explanation
Indices: 29052860--29053076 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
29052850 AAGCCAAGTA
* * *
29052860 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACGAATG
* *
29052899 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* *
29052939 CCTTCGGGACTTAGCCCGGACATAATAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
* * *
29052979 CCTTCGGGAATTAGCCCGGGTATAATAACTCGCAC-AATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAA-TG
* * *
29053019 CCTTC-GGACTTAGCCCGGA-ACTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACGAATG
29053058 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29053077 TTATCATCCA
Statistics
Matches: 155, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
38 1 0.01
39 43 0.28
40 111 0.72
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACGAATG
Found at i:29053072 original size:79 final size:80
Alignment explanation
Indices: 29052895--29053076 Score: 253
Period size: 79 Copynumber: 2.3 Consensus size: 80
29052885 TACTCGCTCG
* *
29052895 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAC
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAC
* *
29052960 ATAATAACTCGCACG
66 ATAATAACTAGCACA
* *
29052975 AATGCCTTCGGGAATTAGCCCGGGTATAATAACTCGCA-CAATTGCCTTC-GGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACCAA-TGCCTTCGGGACTTAGCCCGGA
* *
29053038 -ACTAGTCACTAGCACA
65 CA-TAATAACTAGCACA
29053054 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
29053077 TTATCATCCA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
78 1 0.01
79 49 0.54
80 41 0.45
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.21
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACCAATGCCTTCGGGACTTAGCCCGGAC
ATAATAACTAGCACA
Found at i:29056262 original size:142 final size:142
Alignment explanation
Indices: 29056090--29056382 Score: 505
Period size: 142 Copynumber: 2.1 Consensus size: 142
29056080 ATCAATGAAA
* * * *
29056090 AGTTTGATTCCAAGGAAAGTAAATAAAATTTGACATACCAAACGTTAGAATTACTTTCCAATTGA
1 AGTTAGATTCCAAGGAAAGCAAATAAAATTTGACATACCAAACGTTAGAATCACTCTCCAATTGA
29056155 TTAAATTTCTAAGAAAATGATTACTTTCCATCATACCAAATGCTACCCAAAAATATCATGAAGAC
66 TTAAATTTCTAAGAAAATGATTACTTTCCATCATACCAAATGCTACCCAAAAATATCATGAAGAC
29056220 CTTTATACTAAG
131 CTTTATACTAAG
*
29056232 AGTTAGATTCCAAGGAAAGCAAATAAAATTTGACATACCAAACGTTAGAATCACTCTCCAGTTGA
1 AGTTAGATTCCAAGGAAAGCAAATAAAATTTGACATACCAAACGTTAGAATCACTCTCCAATTGA
* * *
29056297 TTAAATTTCTAAGAAAGTGATTACTTTCCATCATACCAAATGCTACCCAAAAATATCATGGAGGC
66 TTAAATTTCTAAGAAAATGATTACTTTCCATCATACCAAATGCTACCCAAAAATATCATGAAGAC
29056362 CTTTATACTAAG
131 CTTTATACTAAG
*
29056374 AGTCAGATT
1 AGTTAGATT
29056383 GCATTTTGTC
Statistics
Matches: 142, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (142 bp):
AGTTAGATTCCAAGGAAAGCAAATAAAATTTGACATACCAAACGTTAGAATCACTCTCCAATTGA
TTAAATTTCTAAGAAAATGATTACTTTCCATCATACCAAATGCTACCCAAAAATATCATGAAGAC
CTTTATACTAAG
Found at i:29059791 original size:14 final size:15
Alignment explanation
Indices: 29059772--29059801 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29059762 ATATCATGTT
29059772 GCATGTTTTG-AATG
1 GCATGTTTTGTAATG
29059786 GCATGTTTTGTAATG
1 GCATGTTTTGTAATG
29059801 G
1 G
29059802 AATAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.07, G:0.30, T:0.43
Consensus pattern (15 bp):
GCATGTTTTGTAATG
Found at i:29061459 original size:35 final size:37
Alignment explanation
Indices: 29061388--29061485 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
29061378 ATAATCTTCA
29061388 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
29061426 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
29061461 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
29061486 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:29061485 original size:17 final size:19
Alignment explanation
Indices: 29061388--29061478 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
29061378 ATAATCTTCA
29061388 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29061407 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29061426 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29061443 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29061461 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29061479 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:29061504 original size:22 final size:22
Alignment explanation
Indices: 29061388--29061501 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
29061378 ATAATCTTCA
29061388 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29061407 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29061426 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29061443 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29061461 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
29061483 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
29061502 GATTTAATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 34 0.40
22 8 0.09
23 12 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:29071539 original size:78 final size:78
Alignment explanation
Indices: 29071410--29071756 Score: 536
Period size: 78 Copynumber: 4.4 Consensus size: 78
29071400 TCGAAGAAAT
** * ** * *
29071410 TGATTTGGCATCTCCATATTTGACGGAAAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTG
1 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTG
*
29071474 AAGCAGATCTAAGA
65 AAGCAGATCCAAGA
* * *
29071488 TGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAGACACAGCAGATCT-GACCTTCATTG
1 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTG
*
29071552 AAGCAGATCAAAGA
65 AAGCAGATCCAAGA
29071566 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGA
1 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGA
*
29071631 AGCAGGTCCAAGA
66 AGCAGATCCAAGA
29071644 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGA
1 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGA
*
29071709 AGCAGGTCCAAGA
66 AGCAGATCCAAGA
29071722 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
1 TGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
29071757 TGAAGAAGTA
Statistics
Matches: 254, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
77 1 0.00
78 253 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (78 bp):
TGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGA
AGCAGATCCAAGA
Found at i:29072211 original size:19 final size:19
Alignment explanation
Indices: 29072163--29072217 Score: 103
Period size: 18 Copynumber: 2.9 Consensus size: 19
29072153 ATAATCTTCA
29072163 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29072182 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
29072200 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
29072218 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 18 0.51
19 17 0.49
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:29072243 original size:22 final size:22
Alignment explanation
Indices: 29072163--29072240 Score: 80
Period size: 18 Copynumber: 3.8 Consensus size: 22
29072153 ATAATCTTCA
29072163 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29072182 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
29072200 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
29072222 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
29072241 GATTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 18 0.35
19 14 0.27
22 8 0.15
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:29072532 original size:18 final size:17
Alignment explanation
Indices: 29072509--29072542 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29072499 TTTCCCAGAT
*
29072509 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
29072527 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
29072543 GTATCATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:29073524 original size:17 final size:18
Alignment explanation
Indices: 29073502--29073536 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29073492 GATATGATAC
*
29073502 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
29073519 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
29073537 AAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:29073825 original size:22 final size:21
Alignment explanation
Indices: 29073790--29073863 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
29073780 ATAAGATATC
* *
29073790 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
29073811 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
29073834 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
29073853 TGC-AATCATAT
1 TACAAATCATAT
29073864 ATAAGATTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:29073850 original size:19 final size:19
Alignment explanation
Indices: 29073826--29073916 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
29073816 AATCATATCT
29073826 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
29073845 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
29073863 TATAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
29073880 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
* *
29073899 TCTACGATTTCATATCAT
1 TCTAAGATTGCATATCAT
29073917 TGAAGATTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 15 0.23
18 15 0.23
19 34 0.53
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29073880 original size:35 final size:37
Alignment explanation
Indices: 29073828--29073899 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 37
29073818 TCATATCTTC
29073828 TAAGATTGCATATCATATCTAAGATTGCA-ATCATATA
1 TAAGATTG-ATATCATATCTAAGATTGCATATCATATA
*
29073865 TAAGATTG-TATCATATCTAAGATTGTATATCATAT
1 TAAGATTGATATCATATCTAAGATTGCATATCATAT
29073900 CTACGATTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 18 0.55
36 7 0.21
37 8 0.24
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (37 bp):
TAAGATTGATATCATATCTAAGATTGCATATCATATA
Found at i:29074064 original size:20 final size:20
Alignment explanation
Indices: 29074036--29074074 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29074026 TGGACTTCGT
* *
29074036 TTTTTTTTTGGGATTTATTA
1 TTTTATTTTGGGACTTATTA
*
29074056 TTTTATTTTTGGACTTATT
1 TTTTATTTTGGGACTTATT
29074075 TCTGGGCCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.13, T:0.69
Consensus pattern (20 bp):
TTTTATTTTGGGACTTATTA
Found at i:29074515 original size:21 final size:21
Alignment explanation
Indices: 29074491--29074587 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
29074481 TTTTGTTTAA
*
29074491 CTCTTACGAGTTTCTATTCAG
1 CTCTTACGAGCTTCTATTCAG
* * *
29074512 CTCTTATGAGCTTCTGTTCAA
1 CTCTTACGAGCTTCTATTCAG
* * * * *
29074533 CTTTTATGAGTTTCTGTTTAG
1 CTCTTACGAGCTTCTATTCAG
*
29074554 CTCTTACGAGCTTCTATTTAG
1 CTCTTACGAGCTTCTATTCAG
*
29074575 -T-TTTCGAGCTTCT
1 CTCTTACGAGCTTCT
29074588 GTTGCAGCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
19 11 0.17
20 1 0.02
21 51 0.81
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.47
Consensus pattern (21 bp):
CTCTTACGAGCTTCTATTCAG
Found at i:29074524 original size:42 final size:42
Alignment explanation
Indices: 29074471--29074568 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
29074461 TTTTTTCAAT
* * *
29074471 TCTTACAAGCTTTTGTTTAACTCTTACGAGTTTCTATTCAGC
1 TCTTACGAGCTTCTGTTCAACTCTTACGAGTTTCTATTCAGC
* * * * *
29074513 TCTTATGAGCTTCTGTTCAACTTTTATGAGTTTCTGTTTAGC
1 TCTTACGAGCTTCTGTTCAACTCTTACGAGTTTCTATTCAGC
29074555 TCTTACGAGCTTCT
1 TCTTACGAGCTTCT
29074569 ATTTAGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.47
Consensus pattern (42 bp):
TCTTACGAGCTTCTGTTCAACTCTTACGAGTTTCTATTCAGC
Found at i:29076924 original size:31 final size:30
Alignment explanation
Indices: 29076885--29076943 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
29076875 TTTCACAATA
*
29076885 GAGGTTTTGGCAACCAATTTTTCCAAAACT
1 GAGGTTTTGGCAACCAATTTTGCCAAAACT
*
29076915 GAGGCTTTTGGTAACCAATTTTGCCAAAA
1 GAGG-TTTTGGCAACCAATTTTGCCAAAA
29076944 ATATTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (30 bp):
GAGGTTTTGGCAACCAATTTTGCCAAAACT
Found at i:29078120 original size:30 final size:30
Alignment explanation
Indices: 29078084--29078142 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
29078074 ATTACCGAAT
*
29078084 TAAACCTAAAAAAAGGCTTAGGAACCAAAC
1 TAAACCTAAAAAAAAGCTTAGGAACCAAAC
*
29078114 TAAACCTAAAAAAAAGCTTAGGTACCAAA
1 TAAACCTAAAAAAAAGCTTAGGAACCAAA
29078143 TTAGCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (30 bp):
TAAACCTAAAAAAAAGCTTAGGAACCAAAC
Found at i:29080188 original size:30 final size:30
Alignment explanation
Indices: 29080152--29080210 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
29080142 ATTACCGAAT
*
29080152 TAAACCTAAAAAAAGGCTTAGGAACCAAAC
1 TAAACCTAAAAAAAAGCTTAGGAACCAAAC
*
29080182 TAAACCTAAAAAAAAGCTTAGGTACCAAA
1 TAAACCTAAAAAAAAGCTTAGGAACCAAA
29080211 TTAGCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (30 bp):
TAAACCTAAAAAAAAGCTTAGGAACCAAAC
Found at i:29082593 original size:20 final size:19
Alignment explanation
Indices: 29082568--29082609 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
29082558 CTTTTCTATC
29082568 CTTCTCTCATCTCTTCCCCT
1 CTTCTCTCATCT-TTCCCCT
* *
29082588 CTTCTCTCTTCTTTCTCCT
1 CTTCTCTCATCTTTCCCCT
29082607 CTT
1 CTT
29082610 GTCGATTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (19 bp):
CTTCTCTCATCTTTCCCCT
Found at i:29089512 original size:3 final size:3
Alignment explanation
Indices: 29089504--29089532 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29089494 ATTCGATCTT
29089504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29089533 TAAAAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29091215 original size:149 final size:148
Alignment explanation
Indices: 29090849--29091220 Score: 516
Period size: 149 Copynumber: 2.5 Consensus size: 148
29090839 AAGTCAAAAC
*
29090849 TTTATTTTGAAATAGTT-AAAAAAATCAAAACTTTGTTTTAAAAATTTAAAGTTTCCTTTAAAAT
1 TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
* * * * *
29090913 GACTTTTATAAATAGATTTTATTTCTCAAAATCTAAACTTTCTCTTTTTTTTAGAAAAAACATTA
66 AAC--TAAAAAATAGATTTTATTTCTCAAAATCAAAACTTTCTCTTTTTTTAAGAAAAAACA-TA
29090978 TTTTTCTTAAAGATTAAAGCT
128 TTTTTCTTAAAGATTAAAGCT
* * * * *
29090999 TTTATTTTGAAGTAGTTGAAAAAAATTAAAATTTTGTTTTAAAAATTTAAGCTTTCCTTTAGAAT
1 TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
* * **
29091064 AACTAAAAAATAGATTTTTATTTTTCAAAATCAAAACTTTTTCATTTTTTTAAG-AAGTAC-TAT
66 AACTAAAAAATAGA-TTTTATTTCTCAAAATCAAAACTTTCTC-TTTTTTTAAGAAAAAACATAT
29091127 TTTTCTTAAAGATTAAAGCT
129 TTTTCTTAAAGATTAAAGCT
* *
29091147 TTTACTTTGAAATAGTTGAAAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAA
1 TTTATTTTGAAATAGTTG-AAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAA
29091212 TAACTAAAA
65 TAACTAAAA
29091221 GAAAAAAATT
Statistics
Matches: 196, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
148 39 0.20
149 59 0.30
150 45 0.23
151 53 0.27
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.44
Consensus pattern (148 bp):
TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
AACTAAAAAATAGATTTTATTTCTCAAAATCAAAACTTTCTCTTTTTTTAAGAAAAAACATATTT
TTCTTAAAGATTAAAGCT
Found at i:29092589 original size:149 final size:148
Alignment explanation
Indices: 29092223--29092594 Score: 516
Period size: 149 Copynumber: 2.5 Consensus size: 148
29092213 AAGTCAAAAC
*
29092223 TTTATTTTGAAATAGTT-AAAAAAATCAAAACTTTGTTTTAAAAATTTAAAGTTTCCTTTAAAAT
1 TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
* * * * *
29092287 GACTTTTATAAATAGATTTTATTTCTCAAAATCTAAACTTTCTCTTTTTTTTAGAAAAAACATTA
66 AAC--TAAAAAATAGATTTTATTTCTCAAAATCAAAACTTTCTCTTTTTTTAAGAAAAAACA-TA
29092352 TTTTTCTTAAAGATTAAAGCT
128 TTTTTCTTAAAGATTAAAGCT
* * * * *
29092373 TTTATTTTGAAGTAGTTGAAAAAAATTAAAATTTTGTTTTAAAAATTTAAGCTTTCCTTTAGAAT
1 TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
* * **
29092438 AACTAAAAAATAGATTTTTATTTTTCAAAATCAAAACTTTTTCATTTTTTTAAG-AAGTAC-TAT
66 AACTAAAAAATAGA-TTTTATTTCTCAAAATCAAAACTTTCTC-TTTTTTTAAGAAAAAACATAT
29092501 TTTTCTTAAAGATTAAAGCT
129 TTTTCTTAAAGATTAAAGCT
* *
29092521 TTTACTTTGAAATAGTTGAAAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAA
1 TTTATTTTGAAATAGTTG-AAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAA
29092586 TAACTAAAA
65 TAACTAAAA
29092595 GAAAAAAATT
Statistics
Matches: 196, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
148 39 0.20
149 59 0.30
150 45 0.23
151 53 0.27
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.44
Consensus pattern (148 bp):
TTTATTTTGAAATAGTTGAAAAAAATCAAAACTTTGTTTTAAAAATTTAAACTTTCCTTTAAAAT
AACTAAAAAATAGATTTTATTTCTCAAAATCAAAACTTTCTCTTTTTTTAAGAAAAAACATATTT
TTCTTAAAGATTAAAGCT
Found at i:29093461 original size:42 final size:42
Alignment explanation
Indices: 29093372--29093595 Score: 245
Period size: 42 Copynumber: 5.4 Consensus size: 42
29093362 AAGTAAACTA
** ** *
29093372 GAAAAGTAAACAGACCTCC-CACCTAAGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * *
29093413 GAAAAGTCAAAT-GACCTCCACACTTGGGCCCCCAAATGCAAT
1 GAAAAGT-AAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * * *
29093455 GTAAAGTCAATGGACCTCCATACCTGGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * * *
29093497 GGAAAGTGAATGGACCTCAACACCCGGGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
29093539 GAAAAGTAAATGGACCTCCACACCTGTGCCTCTAAATGCATT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
29093581 AAAAAGTGAATGGAC
1 GAAAAGTAAATGGAC
29093596 TTTCATTTCA
Statistics
Matches: 152, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 17 0.11
42 135 0.89
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
Found at i:29107005 original size:44 final size:44
Alignment explanation
Indices: 29106942--29107094 Score: 270
Period size: 44 Copynumber: 3.5 Consensus size: 44
29106932 ATAGGATTCC
29106942 GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
1 GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
29106986 GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
1 GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
* * *
29107030 GATATATGTGTGCGAGTAAGACCATGGCATCGATATGTGCTTCT
1 GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
*
29107074 AATATATGTGTGCGAGTAAGA
1 GATATATGTGTGCGAGTAAGA
29107095 TCATATCTGG
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.34
Consensus pattern (44 bp):
GATATATGTGTGCGAGTAAGACCATGGCATTGATATGTGATTTT
Found at i:29115158 original size:44 final size:44
Alignment explanation
Indices: 29115095--29115211 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 44
29115085 CATGACATAG
*
29115095 GATTCCAATATATGTGTGCGAGTAAGACCATGGCATCGATATGT
1 GATTCTAATATATGTGTGCGAGTAAGACCATGGCATCGATATGT
* *
29115139 GATTCTAATATATATGTGCGAGTACGACCATGGCATCGATATGT
1 GATTCTAATATATGTGTGCGAGTAAGACCATGGCATCGATATGT
*
29115183 GCTTCTAATATATGTGTGCGAGTAAGACC
1 GATTCTAATATATGTGTGCGAGTAAGACC
29115212 CTGTCTGGGA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 67 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (44 bp):
GATTCTAATATATGTGTGCGAGTAAGACCATGGCATCGATATGT
Done.