Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_pilon, whole genome shotgun sequence
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: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:273032 original size:16 final size:16
Alignment explanation
Indices: 273011--273066 Score: 112
Period size: 16 Copynumber: 3.5 Consensus size: 16
273001 AAGCCGAGTC
273011 GAGCTCGAGTATCGCT
1 GAGCTCGAGTATCGCT
273027 GAGCTCGAGTATCGCT
1 GAGCTCGAGTATCGCT
273043 GAGCTCGAGTATCGCT
1 GAGCTCGAGTATCGCT
273059 GAGCTCGA
1 GAGCTCGA
273067 CTCGACTCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (16 bp):
GAGCTCGAGTATCGCT
Found at i:274905 original size:43 final size:42
Alignment explanation
Indices: 274666--274911 Score: 242
Period size: 42 Copynumber: 5.8 Consensus size: 42
274656 CAATAAATCA
* * * *
274666 AGATCTATAGCGGCGTTTTTGGAACAAGCGCCGTAAAAAGTC
1 AGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * ** * *
274708 AGATTTATAGCGCCGTTTTTTTATACAAACGCCACAAAAGGTT
1 AGATCTATAGTGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTC
* *
274751 AGATCTATTGTAGCGTTTTTGGAACAAACGCCGCAAAAGGTC
1 AGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * *
274793 ATATCTATAGTGGCATTTTTGG-ACAAACGCTGGAAAAGGTC
1 AGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* * * * *
274834 AAAATCTATAGCGGCATTTTTGAAACAAACACCGCAAAAGGTC
1 -AGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
* *
274877 ATATCTATAGTTGCGTTTTTGGATACAAACGCCGC
1 AGATCTATAGTGGCGTTTTTGGA-ACAAACGCCGC
274912 TAATTACCTT
Statistics
Matches: 164, Mismatches: 36, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
41 17 0.10
42 91 0.55
43 56 0.34
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (42 bp):
AGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAAAGGTC
Found at i:278043 original size:41 final size:41
Alignment explanation
Indices: 277998--278351 Score: 313
Period size: 41 Copynumber: 8.6 Consensus size: 41
277988 GTAAATTTGT
* ** * *
277998 GGCGTTTGTACAAAAATACCACTAAAACACGTGTCTATAGC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
* * *
278039 GGCGTTTGTAATTAAAAATGCCACTAAAACAAGAGTCTATAGC
1 GGCGTTTGT-A-TAAAAACGCCACTAAAATACGAGTCTATAGC
* ** * * *
278082 GGCGTTTTTATAAAAAAACCACTAAAGTACTAGTCTTTA--
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * *
278121 -GCATTTATATAAAAACGCCACTAAAGTACGAGTCTTTAGC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * *
278161 GGCGTTTGTACAAAAATGCCACTAAAATACGAATCTATAAC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * *
278202 GGCATTTGTAATTAAAAA-GCTACTAAAACACAAGTCTATAGC
1 GGCGTTTGT-A-TAAAAACGCCACTAAAATACGAGTCTATAGC
* * *
278244 GGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAAC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
* * * *
278285 AGCGTTTGTATAAAAACGCCACTGAAATGC-ATGTCTATAAC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGA-GTCTATAGC
* *
278326 GGCGTTTTTATAAAAACGCCGCTAAA
1 GGCGTTTGTATAAAAACGCCACTAAA
278352 GTACTACTCT
Statistics
Matches: 259, Mismatches: 45, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
38 33 0.13
40 7 0.03
41 149 0.58
42 30 0.12
43 40 0.15
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (41 bp):
GGCGTTTGTATAAAAACGCCACTAAAATACGAGTCTATAGC
Found at i:278246 original size:83 final size:82
Alignment explanation
Indices: 277998--278351 Score: 306
Period size: 83 Copynumber: 4.3 Consensus size: 82
277988 GTAAATTTGT
* ** * ** * * *
277998 GGCGTTTGTACAAAAATACCACTAAAACACGTGTCTATAGCGGCGTTTGTAATTAAAAATGCCAC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAATCTATAACGGCATTTGT-A-TAAAAACGCCAC
278063 TAAAACA-AGAGTCTATAGC
64 TAAAACACA-AGTCTATAGC
* ** * * * * *
278082 GGCGTTTTTATAAAAAAACCACTAAAGTACTAGTCT-TTA--GCATTTATATAAAAACGCCACTA
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAATCTATAACGGCATTTGTATAAAAACGCCACTA
** * *
278144 AAGTACGAGTCTTTAGC
66 AAACACAAGTCTATAGC
* * *
278161 GGCGTTTGTACAAAAATGCCACTAAAATACGAATCTATAACGGCATTTGTAATTAAAAA-GCTAC
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAATCTATAACGGCATTTGT-A-TAAAAACGCCAC
278225 TAAAACACAAGTCTATAGC
64 TAAAACACAAGTCTATAGC
* * *
278244 GGCGTTTGTATAAAAACGCCACTAAAGTAC-AAGTCTATAACAGCGTTTGTATAAAAACGCCACT
1 GGCGTTTGTATAAAAACGCCACTAAAATACGAA-TCTATAACGGCATTTGTATAAAAACGCCACT
* ** * *
278308 GAAATGCATGTCTATAAC
65 AAAACACAAGTCTATAGC
* *
278326 GGCGTTTTTATAAAAACGCCGCTAAA
1 GGCGTTTGTATAAAAACGCCACTAAA
278352 GTACTACTCT
Statistics
Matches: 219, Mismatches: 43, Indels: 18
0.78 0.15 0.06
Matches are distributed among these distances:
79 54 0.25
80 3 0.01
81 12 0.05
82 52 0.24
83 63 0.29
84 35 0.16
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (82 bp):
GGCGTTTGTATAAAAACGCCACTAAAATACGAATCTATAACGGCATTTGTATAAAAACGCCACTA
AAACACAAGTCTATAGC
Found at i:278268 original size:162 final size:165
Alignment explanation
Indices: 277998--278307 Score: 448
Period size: 163 Copynumber: 1.9 Consensus size: 165
277988 GTAAATTTGT
** * *
277998 GGCGTTTGTACAAAAATACCACTAAAACACGTGTCTATAGCGGCGTTTGTAATTAAAAATGCCAC
1 GGCGTTTGTACAAAAATACCACTAAAACACGAATCTATAACGGCATTTGTAATTAAAAATGCCAC
* * *
278063 TAAAACAAGAGTCTATAGCGGCGTTTTTATAAAAAAACCACTAAAGTACTAGTCT-T-TAGCATT
66 TAAAACAAGAGTCTATAGCGGCGTTTGTATAAAAAAACCACTAAAGTACAAGTCTATACAGCATT
278126 TATATAAAAACGCCACTAAAGTACGAGTCTTTAGC
131 TATATAAAAACGCCACTAAAGTACGAGTCTTTAGC
* * *
278161 GGCGTTTGTACAAAAATGCCACTAAAATACGAATCTATAACGGCATTTGTAATTAAAAA-GCTAC
1 GGCGTTTGTACAAAAATACCACTAAAACACGAATCTATAACGGCATTTGTAATTAAAAATGCCAC
** *
278225 TAAAACACA-AGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAACAGCG
66 TAAAACA-AGAGTCTATAGCGGCGTTTGTATAAAAAAACCACTAAAGTACAAGTCTAT-ACAGCA
*
278289 TTTGTATAAAAACGCCACT
129 TTTATATAAAAACGCCACT
278308 GAAATGCATG
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
162 53 0.41
163 55 0.43
165 21 0.16
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (165 bp):
GGCGTTTGTACAAAAATACCACTAAAACACGAATCTATAACGGCATTTGTAATTAAAAATGCCAC
TAAAACAAGAGTCTATAGCGGCGTTTGTATAAAAAAACCACTAAAGTACAAGTCTATACAGCATT
TATATAAAAACGCCACTAAAGTACGAGTCTTTAGC
Found at i:279235 original size:32 final size:32
Alignment explanation
Indices: 279133--279256 Score: 139
Period size: 31 Copynumber: 3.9 Consensus size: 32
279123 CCTCAGCAAT
* *
279133 TGTCCATAGGTCCCG-AAGAACCTAGGTAAA-C
1 TGTCCATATGTCCCGAAAG-ACATAGGTAAATC
* * ** *
279164 TGTCCATATATTTCTTAAA-ACATAGGTATAT-
1 TGTCCATAT-GTCCCGAAAGACATAGGTAAATC
279195 TGTCCATATGTCCCGAAAGACATAGGTAAATC
1 TGTCCATATGTCCCGAAAGACATAGGTAAATC
279227 TGTCCATATGTCCCGAAAGACATAGGTAAA
1 TGTCCATATGTCCCGAAAGACATAGGTAAA
279257 CCCTGACTCT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
30 5 0.07
31 37 0.49
32 32 0.42
33 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAAATC
Found at i:279969 original size:2 final size:2
Alignment explanation
Indices: 279962--279995 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
279952 ACTTATGTTC
279962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279996 CACACAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283567 original size:24 final size:24
Alignment explanation
Indices: 283529--283608 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
283519 CTATTCTTTC
*
283529 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGGGCTCAAATTTTAG
*
283553 GTTTCAATTGGGCTCAAATTTTAG
1 GCTTCAATTGGGCTCAAATTTTAG
283577 GCTTCAATTGGGCTCAAATTTTAG
1 GCTTCAATTGGGCTCAAATTTTAG
283601 GCTTCAAT
1 GCTTCAAT
283609 CGAAATTCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGGGCTCAAATTTTAG
Found at i:285216 original size:23 final size:23
Alignment explanation
Indices: 285203--285262 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
285193 TCCTTAAATT
285203 TCAATCCCTAAAATCCCAAATAC
1 TCAATCCCTAAAATCCCAAATAC
285226 TCAATCCCTAAAATCCCAAATAC
1 TCAATCCCTAAAATCCCAAATAC
* *
285249 CCAATCCCTTAAAT
1 TCAATCCCTAAAAT
285263 TCATTTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (23 bp):
TCAATCCCTAAAATCCCAAATAC
Found at i:285406 original size:14 final size:14
Alignment explanation
Indices: 285387--285446 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 14
285377 ACGAAAGGAG
285387 AGAGGAGGGAGGGC
1 AGAGGAGGGAGGGC
285401 AGAGGACGGGAGGGAGGGC
1 --A-GA-G-GAGGGAGGGC
285420 AGAGGACGGGAGGG-
1 AGAGGA-GGGAGGGC
*
285434 AGAGCAGGGAGGG
1 AGAGGAGGGAGGG
285447 GAAGCATGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 7 0.18
14 7 0.18
15 8 0.21
16 3 0.08
17 3 0.08
18 1 0.03
19 10 0.26
ACGTcount: A:0.28, C:0.08, G:0.63, T:0.00
Consensus pattern (14 bp):
AGAGGAGGGAGGGC
Found at i:285414 original size:19 final size:19
Alignment explanation
Indices: 285390--285440 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
285380 AAAGGAGAGA
285390 GGAGGGAGGGCAGAGGACG
1 GGAGGGAGGGCAGAGGACG
285409 GGAGGGAGGGCAGAGGACG
1 GGAGGGAGGGCAGAGGACG
*
285428 GGAGGGAGAGCAG
1 GGAGGGAGGGCAG
285441 GGAGGGGAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.63, T:0.00
Consensus pattern (19 bp):
GGAGGGAGGGCAGAGGACG
Found at i:285604 original size:31 final size:31
Alignment explanation
Indices: 285563--285640 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
285553 CTGAGGAATA
285563 TAAAGTGGTAACGTTTGTAATGACAATCACC
1 TAAAGTGGTAACGTTTGTAATGACAATCACC
* *
285594 TAAAGCGGTAACGTTTGTAATGACAGTCACC
1 TAAAGTGGTAACGTTTGTAATGACAATCACC
285625 TAAAGTGGTAACGTTT
1 TAAAGTGGTAACGTTT
285641 ATAACTTAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (31 bp):
TAAAGTGGTAACGTTTGTAATGACAATCACC
Found at i:285760 original size:49 final size:49
Alignment explanation
Indices: 285703--285803 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
285693 AAAACGGTAT
285703 TGTTTAGGCACTTATTTTATACTTAAGTCAAATTCAAATCATGGTCACA
1 TGTTTAGGCACTTATTTTATACTTAAGTCAAATTCAAATCATGGTCACA
285752 TGTTTAGGCACTTATTTTATACTTAAGTCAAATTCAAATCATGGTCACA
1 TGTTTAGGCACTTATTTTATACTTAAGTCAAATTCAAATCATGGTCACA
285801 TGT
1 TGT
285804 CAGCAAATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (49 bp):
TGTTTAGGCACTTATTTTATACTTAAGTCAAATTCAAATCATGGTCACA
Found at i:292736 original size:36 final size:37
Alignment explanation
Indices: 292696--292766 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
292686 ATGGAGACAA
*
292696 TTTTC-CTTAAAACAAAATTAATCTCACTTGAGATTG
1 TTTTCTCTAAAAACAAAATTAATCTCACTTGAGATTG
* * **
292732 TTTTCTCTAAAAATAAATTTTGTCTCACTTGAGAT
1 TTTTCTCTAAAAACAAAATTAATCTCACTTGAGAT
292767 AGTTCCCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 5 0.17
37 24 0.83
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (37 bp):
TTTTCTCTAAAAACAAAATTAATCTCACTTGAGATTG
Found at i:292910 original size:194 final size:197
Alignment explanation
Indices: 292576--293162 Score: 857
Period size: 194 Copynumber: 3.0 Consensus size: 197
292566 GAGTTTGCCT
292576 CTCTC-AAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
1 CTCTCAAAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
292640 ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
66 ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
292705 AAACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACTTGAGA-TAG
131 AAACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACTTGAGACT-G
292769 TT-
195 TTC
292771 C-C-CAAAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
1 CTCTCAAAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
292834 ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
66 ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
*
292899 AAACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACTTGAGACGTT
131 AAACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACTTGAGAC-TG
292964 TTC
195 TTC
* * * * * * *
292967 CTCTCAAAA-CAAATTTCGTCTCGCTTGATACATTTT-CC---A-----AAAT-TTT-GAACAAA
1 CTCTCAAAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
* * * * * *
293020 ATTGATCTCACATGATATAGTTTTCCTAAGAACAAATTTTGTCTCGCTGGAGACAATTTTCCTCA
66 ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
* *
293085 AAACAAAATTATTCTCACTTGAGATTGTTTTCTCTAAAAAATAAATTTTATCTCACTTGAGACAT
131 AAACAAAATTAATCTCACTTGAGATTGTTTTCTCT-AAAAATAAATTTTGTCTCACTTGAGAC-T
*
293150 CTTC
194 GTTC
*
293154 CTCCCAAAA
1 CTCTCAAAA
293163 CAAATTTTGT
Statistics
Matches: 366, Mismatches: 19, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
186 99 0.27
187 41 0.11
188 4 0.01
193 2 0.01
194 186 0.51
195 3 0.01
196 4 0.01
197 22 0.06
198 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (197 bp):
CTCTCAAAAGCGAACTTCATCTTGTTTGAGACATTTTCCCAAAAGTGTGAAATATTTAGAACAAG
ATTGTTCTCATATGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGATGGAGACAATTTTCCTTA
AAACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACTTGAGACTGT
TC
Found at i:292930 original size:36 final size:36
Alignment explanation
Indices: 292846--293199 Score: 139
Period size: 36 Copynumber: 9.6 Consensus size: 36
292836 TGTTCTCATA
* * *
292846 TGAGATAGTTTTCCTTAGAACAAATTTTGTCTCGA-T
1 TGAGATAGTTTTCCTTAAAACAAAATTTATCTC-ACT
* * * *
292882 GGAGACAATTTTCCTTAAAACAAAATTAATCTCACT
1 TGAGATAGTTTTCCTTAAAACAAAATTTATCTCACT
* * * * *
292918 TGAGATTGTTTTCTCTAAAAATAAATTTTGTCTCACT
1 TGAGATAGTTTTC-CTTAAAACAAAATTTATCTCACT
* * *
292955 TGAGA-CGTTTTCCTCTCAAAAC-AAATTTCGTCTCGCT
1 TGAGATAGTTTTCCT-T-AAAACAAAATTT-ATCTCACT
* * ** * *
292992 TGATACA-TTTTCCAAAATTTTGAACAAAATTGATCTCACA
1 TGAGATAGTTTTCC-----TTAAAACAAAATTTATCTCACT
* * * *
293032 TGATATAGTTTTCC-TAAGAACAAATTTTGTCTCGCT
1 TGAGATAGTTTTCCTTAA-AACAAAATTTATCTCACT
* * * *
293068 GGAGACAATTTTCCTCAAAACAAAA-TTATTCTCACT
1 TGAGATAGTTTTCCTTAAAACAAAATTTA-TCTCACT
* *
293104 TGAGATTGTTTT-CTCTAAAAAATAAATTTTATCTCACT
1 TGAGATAGTTTTCCT-TAAAACA-AAA-TTTATCTCACT
* * * * * *
293142 TGAGACA-TCTTCCTCCCAAAACAAATTTTGTCTCGCT
1 TGAGATAGTTTTCCT--TAAAACAAAATTTATCTCACT
* *
293179 TGAGACAGTTTTTCTTTAAAA
1 TGAGATAG-TTTTCCTTAAAA
293200 TAGAAATTCT
Statistics
Matches: 232, Mismatches: 62, Indels: 47
0.68 0.18 0.14
Matches are distributed among these distances:
35 8 0.03
36 95 0.41
37 72 0.31
38 16 0.07
39 14 0.06
40 14 0.06
41 12 0.05
42 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (36 bp):
TGAGATAGTTTTCCTTAAAACAAAATTTATCTCACT
Found at i:292981 original size:37 final size:36
Alignment explanation
Indices: 292864--293190 Score: 157
Period size: 37 Copynumber: 8.8 Consensus size: 36
292854 TTTTCCTTAG
* * *
292864 AACAAATTTTGTCTCGA-TGGAGACAATTTTC-CTTAA
1 AACAAATTTTGTCTC-ACTTGAGAC-GTTTTCTCTCAA
* ** * *
292900 AACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAA
1 AACAAATTTTGTCTCACTTGAGA-CGTTTTCTCTCAA
*
292937 AATAAATTTTGTCTCACTTGAGACGTTTTCCTCTCAA
1 AACAAATTTTGTCTCACTTGAGACGTTTT-CTCTCAA
* * * * **
292974 AACAAATTTCGTCTCGCTTGATACATTTTC-CAAAA
1 AACAAATTTTGTCTCACTTGAGACGTTTTCTCTCAA
* * * *
293009 TTTTGAACAAA-ATTGATCTCACATGATATAGTTTTC-CT-AA
1 -----AACAAATTTTG-TCTCACTTGAGA-CGTTTTCTCTCAA
* * *
293049 GAACAAATTTTGTCTCGCTGGAGACAATTTTC-CTCAA
1 -AACAAATTTTGTCTCACTTGAGAC-GTTTTCTCTCAA
* * *
293086 AACAAAATTAT-TCTCACTTGAGATTGTTTTCTCTAAAA
1 AAC-AAATTTTGTCTCACTTGAGA-CGTTTTCTCT-CAA
* * * * *
293124 AATAAATTTTATCTCACTTGAGACATCTTCCTCCCAA
1 AACAAATTTTGTCTCACTTGAGACGT-TTTCTCTCAA
*
293161 AACAAATTTTGTCTCGCTTGAGACAGTTTT
1 AACAAATTTTGTCTCACTTGAGAC-GTTTT
293191 TCTTTAAAAT
Statistics
Matches: 218, Mismatches: 52, Indels: 41
0.70 0.17 0.13
Matches are distributed among these distances:
35 4 0.02
36 68 0.31
37 98 0.45
38 22 0.10
39 2 0.01
40 18 0.08
41 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (36 bp):
AACAAATTTTGTCTCACTTGAGACGTTTTCTCTCAA
Found at i:293369 original size:36 final size:36
Alignment explanation
Indices: 293322--293417 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
293312 TCTTTGAATT
* *
293322 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC
1 TGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGAC
* * *
293358 TGTTTCCCTTGAAATAAGTTTTGTCTCCCTTGATAC
1 TGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGAC
***
293394 AACTTCCCTTGAAAAAAATCTTTG
1 TGTTTCCCTTGAAAAAAAT-TTTG
293418 AGATCTTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 46 0.92
37 4 0.08
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (36 bp):
TGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGAC
Found at i:293434 original size:100 final size:101
Alignment explanation
Indices: 293258--293604 Score: 324
Period size: 109 Copynumber: 3.3 Consensus size: 101
293248 GATTTTTTCC
* * * ** *** *
293258 TCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTTTTTTCGAAACAAAAGTCTTTGAATTT
1 TCCCTAGAAACAAAGTTTTGTCTCCCTTGAGACAACTTCCCTT-GAAA-AAAA-TCTTTGAATCT
* *
293323 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTGTT
63 GTTTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTT
* * *
293362 TCCCTTGAAA-TAAGTTTTGTCTCCCTTGATACAACTTCCCTTGAAAAAAATCTTTGAGATCT-T
1 TCCCTAGAAACAAAGTTTTGTCTCCCTTGAGACAACTTCCCTTGAAAAAAATCTTTGA-ATCTGT
*
293425 TTCCCTTGAAACGAATTTTGTCTCTATTGAGACAGTT
65 TTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTT
* ** *
293462 TCCCTAGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTG
1 TCCCTAGAAACAAAGTTTTGTCTCCCTTGAGACAACTTCCCTTGAAA-AAA----ATCT---TTG
* **
293527 AGA-CAGTTTCCCTTGAAACAAATTTTGTCTCCGTTGAGACAGTT
58 A-ATCTGTTTCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTT
* * *
293571 TCCCTTGAAACAAA-TTTTATCTCCCTTGAAACAA
1 TCCCTAGAAACAAAGTTTTGTCTCCCTTGAGACAA
293605 ATTTTGTCTC
Statistics
Matches: 203, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
100 51 0.25
101 38 0.19
102 7 0.03
103 23 0.11
104 10 0.05
106 3 0.01
108 17 0.08
109 54 0.27
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (101 bp):
TCCCTAGAAACAAAGTTTTGTCTCCCTTGAGACAACTTCCCTTGAAAAAAATCTTTGAATCTGTT
TCCCTTGAAACAAATTTTGTCTCTATTGAGACAGTT
Found at i:293464 original size:36 final size:36
Alignment explanation
Indices: 293424--293765 Score: 407
Period size: 36 Copynumber: 9.3 Consensus size: 36
293414 TTTGAGATCT
* **
293424 TTTCCCTTGAAACGAATTTTGTCTCTATTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* *
293460 TTTCCCTAGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAG
*
293497 TTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
293533 TTTCCCTTGAAACAAATTTTGTCTCCGTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* *
293569 TTTCCCTTGAAACAAATTTTATCTCCCTTGAAACAAATTTTG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC--A----G
* * *
293611 TCTCCCTTGAAACAAATTTTGTC-CCTCTTGAGAAAA
1 TTTCCCTTGAAACAAATTTTGTCTCC-CTTGAGACAG
* * *
293647 TTTTCCTTCAAACAAATTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAA-TTTTGTCTCCCTTGAGACAG
* * *
293684 TTTCCCTTTAAAAAAATTTTATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* *
293720 TCTCCCTTGAAACAAATTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
293756 TCTCCCTTGA
1 TTTCCCTTGA
293766 GAAAGTTTCC
Statistics
Matches: 265, Mismatches: 31, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
36 171 0.65
37 61 0.23
38 2 0.01
40 1 0.00
41 2 0.01
42 28 0.11
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:293465 original size:64 final size:64
Alignment explanation
Indices: 293351--293471 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 64
293341 TTTGTCTCTC
* * * *
293351 TTGAGACTGTTTCCCTTGAAATAAGTTTTGTCTCCCTTGATACAACTTCCCTTGAAAAAAATCT
1 TTGAGACTGTTTCCCTTGAAAGAAGTTTTGTCTCCATTGAGACAACTTCCCTAGAAAAAAATCT
* **
293415 TTGAGATCT-TTTCCCTTGAAACGAA-TTTTGTCTCTATTGAGACAGTTTCCCTAGAAA
1 TTGAGA-CTGTTTCCCTTGAAA-GAAGTTTTGTCTCCATTGAGACAACTTCCCTAGAAA
293472 CAAAGTTTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
64 44 0.92
65 4 0.08
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (64 bp):
TTGAGACTGTTTCCCTTGAAAGAAGTTTTGTCTCCATTGAGACAACTTCCCTAGAAAAAAATCT
Found at i:293649 original size:20 final size:21
Alignment explanation
Indices: 293499--293650 Score: 125
Period size: 21 Copynumber: 7.9 Consensus size: 21
293489 TGAGACAGTT
*
293499 TCCCTTGAAATAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
293520 TCCCTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
293535 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* * *
293556 TCCGTTGAGAC--A----GTT
1 TCCCTTGAAACAAATTTTGTC
*
293571 TCCCTTGAAACAAATTTTATC
1 TCCCTTGAAACAAATTTTGTC
293592 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
293613 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
293634 -CCTCTTGAGA-AAATTTT
1 TCC-CTTGAAACAAATTTT
293651 CCTTCAAACA
Statistics
Matches: 104, Mismatches: 14, Indels: 27
0.72 0.10 0.19
Matches are distributed among these distances:
15 23 0.22
17 2 0.02
19 2 0.02
20 9 0.09
21 68 0.65
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:293662 original size:187 final size:187
Alignment explanation
Indices: 293426--293765 Score: 536
Period size: 187 Copynumber: 1.8 Consensus size: 187
293416 TGAGATCTTT
* * * * *
293426 TCCCTTGAAACGAATTTTGTCTCTATTGAGACAGTTTCCCTAGAAACAAAGTTTTGTCTCTCTTG
1 TCCCTTGAAACAAATTTTGTCCCTATTGAGAAAATTTCCCTACAAACAAAGTTTTGTCTCTCTTG
* * *
293491 AGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
66 AGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTGTC
* *
293556 TCCGTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTTGAAACAAATTTTGTC
131 TCCCTTGAGACAGTCTCCCTTGAAACAAATTTTATCTCCCTTGAAACAAATTTTGTC
* * * *
293613 TCCCTTGAAACAAATTTTGTCCCTCTTGAGAAAATTTTCCTTCAAACAAATTTTTGTCTCTCTTG
1 TCCCTTGAAACAAATTTTGTCCCTATTGAGAAAATTTCCCTACAAACAAAGTTTTGTCTCTCTTG
* *
293678 AGACAGTTTCCCTTTAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTTTC
66 AGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTGTC
293743 TCCCTTGAGACAGTCTCCCTTGA
131 TCCCTTGAGACAGTCTCCCTTGA
293766 GAAAGTTTCC
Statistics
Matches: 137, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
187 137 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (187 bp):
TCCCTTGAAACAAATTTTGTCCCTATTGAGAAAATTTCCCTACAAACAAAGTTTTGTCTCTCTTG
AGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTGTC
TCCCTTGAGACAGTCTCCCTTGAAACAAATTTTATCTCCCTTGAAACAAATTTTGTC
Found at i:293670 original size:151 final size:151
Alignment explanation
Indices: 293462--293750 Score: 436
Period size: 151 Copynumber: 1.9 Consensus size: 151
293452 TGAGACAGTT
* * * * *
293462 TCCCTAGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTG
1 TCCCTAGAAACAAAGTTTTGTCCCTCTTGAGAAAATTTCCCTTCAAACAAATTTTGTCTCCCTTG
* * * *
293527 AGACAGTTTCCCTTGAAACAAATTTTGTCTCCGTTGAGACAGTTTCCCTTGAAACAAATTTTATC
66 AGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTATC
293592 TCCCTTGAAACAAATTTTGTC
131 TCCCTTGAAACAAATTTTGTC
* * *
293613 TCCCTTGAAACAAA-TTTTGTCCCTCTTGAGAAAATTTTCCTTCAAACAAATTTTTGTCTCTCTT
1 TCCCTAGAAACAAAGTTTTGTCCCTCTTGAGAAAATTTCCCTTCAAACAAA-TTTTGTCTCCCTT
* *
293677 GAGACAGTTTCCCTTTAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTTT
65 GAGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTAT
293742 CTCCCTTGA
130 CTCCCTTGA
293751 GACAGTCTCC
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
150 30 0.24
151 93 0.76
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (151 bp):
TCCCTAGAAACAAAGTTTTGTCCCTCTTGAGAAAATTTCCCTTCAAACAAATTTTGTCTCCCTTG
AGACAGTTTCCCTTGAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTATC
TCCCTTGAAACAAATTTTGTC
Found at i:293725 original size:15 final size:15
Alignment explanation
Indices: 293705--293780 Score: 62
Period size: 15 Copynumber: 4.7 Consensus size: 15
293695 AAAAATTTTA
293705 TCTCCCTTGAGACAG
1 TCTCCCTTGAGACAG
* *
293720 TCTCCCTTGAAACAAATTTT
1 TCTCCCTTGAGAC--A---G
293740 TTCTCCCTTGAGACAG
1 T-CTCCCTTGAGACAG
*
293756 TCTCCCTTGAGAAAG
1 TCTCCCTTGAGACAG
*
293771 TTTCCCTTGA
1 TCTCCCTTGA
293781 AATAAATTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 34 0.69
16 1 0.02
17 1 0.02
19 1 0.02
20 1 0.02
21 11 0.22
ACGTcount: A:0.22, C:0.29, G:0.14, T:0.34
Consensus pattern (15 bp):
TCTCCCTTGAGACAG
Found at i:293760 original size:51 final size:51
Alignment explanation
Indices: 293704--293816 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
293694 AAAAAATTTT
* *
293704 ATCTCCCTTGAGACAGTCTCCCTTGAAACAAATTTTTTCTCCCTTGAGACA
1 ATCTCCCTTGAGAAAGTCTCCCTTGAAACAAATTTGTTCTCCCTTGAGACA
* * *
293755 GTCTCCCTTGAGAAAGTTTCCCTTGAAATAAATTTGTTCTCCCTTGAGACA
1 ATCTCCCTTGAGAAAGTCTCCCTTGAAACAAATTTGTTCTCCCTTGAGACA
*
293806 ATTTCCCTTGA
1 ATCTCCCTTGA
293817 AACAAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (51 bp):
ATCTCCCTTGAGAAAGTCTCCCTTGAAACAAATTTGTTCTCCCTTGAGACA
Found at i:293796 original size:36 final size:36
Alignment explanation
Indices: 293755--293841 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 36
293745 CCTTGAGACA
*
293755 GTCTCCCTTGAGA-AAGTTTCCCTTGAAATAAA-TTT
1 GTCTCCCTTGAGACAA-TTTCCCTTGAAACAAATTTT
293790 GTTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTT
1 G-TCTCCCTTGAGACAATTTCCCTTGAAACAAATTTT
293827 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
293842 GTCTCAATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
35 1 0.02
36 41 0.85
37 6 0.12
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (36 bp):
GTCTCCCTTGAGACAATTTCCCTTGAAACAAATTTT
Found at i:293814 original size:87 final size:87
Alignment explanation
Indices: 293481--293907 Score: 419
Period size: 87 Copynumber: 4.8 Consensus size: 87
293471 ACAAAGTTTT
* * *
293481 GTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
*
293546 AAATTTTGTCTCCGTTGAGACA
66 AAATTTTGTCTCCCTTGAGACA
* * * *
293568 GTTTCCCTTGAAACAAATTTTATCTCCCTTGAAACAAATTTTGTCTCCCTTGAAACAAATTTTGT
1 GTCTCCCTTGAGAC--A--GT-T-TCCCTTGAAACAAATTTTGTCTCCCTTGAGAC-AA--TT-T
* * * **** * **
293633 CCCTCTTGAGA-AAATTTT-CCTTCAAACAAATTTTT
56 -CC-CTTGAAACAAATTTTGTCTCCCTTGAGA---CA
* * * * * *
293668 GTCTCTCTTGAGACAGTTTCCCTTTAAAAAAATTTTATCTCCCTTGAGACAGTCTCCCTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
*
293733 AAATTTTTTCTCCCTTGAGACA
66 AAATTTTGTCTCCCTTGAGACA
* *
293755 GTCTCCCTTGAGAAAGTTTCCCTTGAAATAAA-TTTGTTCTCCCTTGAGACAATTTCCCTTGAAA
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTG-TCTCCCTTGAGACAATTTCCCTTGAAA
293819 CAAATTTTGTCTCCCTTGAGACA
65 CAAATTTTGTCTCCCTTGAGACA
** *
293842 GTCTCAATTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCTTTGAAAC
1 GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
293907 A
66 A
293908 GAAGATTTTA
Statistics
Matches: 271, Mismatches: 50, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
86 3 0.01
87 142 0.52
88 10 0.04
89 10 0.04
90 6 0.02
91 2 0.01
92 1 0.00
93 31 0.11
94 29 0.11
95 1 0.00
96 3 0.01
97 6 0.02
98 10 0.04
99 6 0.02
100 11 0.04
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (87 bp):
GTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCCCTTGAAAC
AAATTTTGTCTCCCTTGAGACA
Found at i:293867 original size:15 final size:15
Alignment explanation
Indices: 293827--293867 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
293817 AACAAATTTT
293827 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
**
293842 GTCTCAATTGAGACA
1 GTCTCCCTTGAGACA
*
293857 GTTTCCCTTGA
1 GTCTCCCTTGA
293868 AACAAATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:293927 original size:39 final size:39
Alignment explanation
Indices: 293849--293994 Score: 165
Period size: 39 Copynumber: 3.8 Consensus size: 39
293839 ACAGTCTCAA
* * *
293849 TTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTCCC
1 TTGAGACAGTTTCCTTTGAAACAGAAGATTTTATCTCGC
*
293885 TTGAGACAATTTCCTTTGAAACAGAAGATTTTATCTCGC
1 TTGAGACAGTTTCCTTTGAAACAGAAGATTTTATCTCGC
**
293924 TTGAGATTGTTTCAC-TTGAAACAGAAGATTTTATCTCGC
1 TTGAGACAGTTTC-CTTTGAAACAGAAGATTTTATCTCGC
* * * *
293963 TTGAGATAGTTTCATTCGAAACAAAAGATTTT
1 TTGAGACAGTTTCCTTTGAAACAGAAGATTTT
293995 TAGAAACTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
36 20 0.21
38 2 0.02
39 71 0.76
40 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (39 bp):
TTGAGACAGTTTCCTTTGAAACAGAAGATTTTATCTCGC
Found at i:294066 original size:53 final size:52
Alignment explanation
Indices: 293996--294187 Score: 235
Period size: 52 Copynumber: 3.7 Consensus size: 52
293986 AAAGATTTTT
*
293996 AGAAACTAAGCAC-GATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTAAA
1 AGAAACTAAGC-CTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTT-AA
* * *
294049 AGAATCTAAGCCTGATTTT-AGGGGTTTTTTAATGTTTTCAAATGAATTTCAA
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTT-AA
* * * * * **
294101 AGAAATTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAGTTTTT
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTAA
*
294153 AGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATG
1 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
294188 ATGATTTTCA
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
52 76 0.64
53 42 0.36
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (52 bp):
AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTAA
Found at i:294084 original size:52 final size:52
Alignment explanation
Indices: 293996--294244 Score: 234
Period size: 52 Copynumber: 4.6 Consensus size: 52
293986 AAAGATTTTT
*
293996 AGAAACTAAGCAC-GATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTAAA
1 AGAAACTAAGC-CTGATTTT-AGGGGTTTCTTGATGTTTTCAAATGAATTTAAA
* * * *
294049 AGAATCTAAGCCTGATTTTAGGGGTTTTTTAATGTTTTCAAATGAATTTCAA
1 AGAAACTAAGCCTGATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAA
* * * * **
294101 AGAAATTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAGTTT-TT
1 AGAAACTAAGCCTGA-TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAA
* *
294153 AGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATGATTTTC-AATGAGTTTTTAAA
1 AGAAACTAAGCCTGATTTT-AGGGGTTTC-T--TGATG-TTTTCAAATGA--ATTTAAA
* *
294211 AGGAAACTAAGCCTAATTTTTAGGGGTTCCTTGA
1 A-GAAACTAAGCCTGA-TTTTAGGGGTTTCTTGA
294245 CAATTAAGAA
Statistics
Matches: 160, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
51 4 0.03
52 62 0.39
53 47 0.29
55 10 0.06
56 8 0.05
57 3 0.02
58 2 0.01
59 20 0.12
60 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (52 bp):
AGAAACTAAGCCTGATTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAA
Found at i:294140 original size:105 final size:109
Alignment explanation
Indices: 293997--294244 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 109
293987 AAGATTTTTA
* * * *
293997 GAAACTAAGCAC-GATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTAAAAGAATCTAAGCC
1 GAAACTAAGC-CTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTT-AAAGAAACTAAGCC
* *
294061 TGATTTT-AGGGGTTT-TT-TAATG-TTTTCAAATGA-ATTTCAAA-
64 TGATTTTCAAGGGTTTCTTATAATGATTTTC-AATGAGATTTAAAAG
* * * **
294102 GAAATTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTG
1 GAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAAGAAACTAAGCCTG
* *
294167 ATTTTCAAGGGTTTCTTGATGATGATTTTCAATGAGTTTTTAAAAG
66 ATTTTCAAGGGTTTCTT-ATAATGATTTTCAATGAG-ATTTAAAAG
*
294213 GAAACTAAGCCTAATTTTTAGGGGTTCCTTGA
1 GAAACTAAGCCTAATTTTTAGGGGTTTCTTGA
294245 CAATTAAGAA
Statistics
Matches: 118, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
104 19 0.16
105 48 0.41
106 2 0.02
108 9 0.08
109 5 0.04
110 6 0.05
111 29 0.25
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.40
Consensus pattern (109 bp):
GAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTAAAGAAACTAAGCCTG
ATTTTCAAGGGTTTCTTATAATGATTTTCAATGAGATTTAAAAG
Found at i:294378 original size:41 final size:41
Alignment explanation
Indices: 294288--294378 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
294278 TCTTGTTGAG
* *
294288 TAAGTCCTTTGGCCATCAGTAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTTGGCCATCAGTAAGTCTTTCGAGCAAGATGCA
* * *
294329 TAAATCCTTTGGGCCATTTA-TAAGTCTTTCGAGTAAGATG-A
1 TAAGTCCTTT-GGCCA-TCAGTAAGTCTTTCGAGCAAGATGCA
294370 TAAGTCCTT
1 TAAGTCCTT
294379 CGAGCAATCC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
41 17 0.40
42 23 0.55
43 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (41 bp):
TAAGTCCTTTGGCCATCAGTAAGTCTTTCGAGCAAGATGCA
Found at i:294559 original size:22 final size:22
Alignment explanation
Indices: 294533--294608 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
294523 CGGGCCATCA
*
294533 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCCTTCGAGCATGATGT
*
294555 GTAAGTCCTTCAAGACAT--TG-
1 GTAAGTCCTTCGAG-CATGATGT
*
294575 GTAAGTCTTTCGAGCATGATGT
1 GTAAGTCCTTCGAGCATGATGT
294597 GTAAGTCCTTCG
1 GTAAGTCCTTCG
294609 GGCCATCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
19 3 0.07
20 12 0.27
21 4 0.09
22 23 0.51
23 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (22 bp):
GTAAGTCCTTCGAGCATGATGT
Found at i:294622 original size:42 final size:42
Alignment explanation
Indices: 294514--294662 Score: 160
Period size: 42 Copynumber: 3.6 Consensus size: 42
294504 TGAATAAACT
294514 TAAGTCATTCGGGCCATC-AGTAAGTCTTTCGAGCATGATGTG
1 TAAGTCATTCGGGCCATCTA-TAAGTCTTTCGAGCATGATGTG
* ** * *
294556 TAAGTCCTTCAAGACAT-TGGTAAGTCTTTCGAGCATGATGTG
1 TAAGTCATTCGGGCCATCT-ATAAGTCTTTCGAGCATGATGTG
* * * *
294598 TAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGTAAGATG-A
1 TAAGTCATTCGGGCCATCTATAAGTCTTTCGAGCATGATGTG
* *
294639 TAAGTCATTCGGGTCATCCATAAG
1 TAAGTCATTCGGGCCATCTATAAG
294663 ACCTTCAAGC
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
41 21 0.24
42 67 0.75
43 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (42 bp):
TAAGTCATTCGGGCCATCTATAAGTCTTTCGAGCATGATGTG
Found at i:295634 original size:15 final size:14
Alignment explanation
Indices: 295610--295643 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
295600 AAACTTATTT
*
295610 AAAAATGAAAAATGA
1 AAAAAAGAAAAA-GA
295625 AAAAAAGAAAAAGA
1 AAAAAAGAAAAAGA
295639 AAAAA
1 AAAAA
295644 GGTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:298218 original size:17 final size:17
Alignment explanation
Indices: 298198--298282 Score: 88
Period size: 17 Copynumber: 5.2 Consensus size: 17
298188 CGAGTGACGT
298198 TTATATATATATTATTA
1 TTATATATATATTATTA
*
298215 TTATATTTATATTATTA
1 TTATATATATATTATTA
* *
298232 TTATATACATA--ATAA
1 TTATATATATATTATTA
* *
298247 ATATA-ATA-AATATTA
1 TTATATATATATTATTA
*
298262 TTATATTTATATTATTA
1 TTATATATATATTATTA
298279 TTAT
1 TTAT
298283 TATTTTTAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.02
14 2 0.04
15 14 0.26
16 2 0.04
17 35 0.65
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATATATATTATTA
Found at i:298285 original size:14 final size:14
Alignment explanation
Indices: 298210--298279 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
298200 ATATATATAT
298210 TATTATTATATTTA
1 TATTATTATATTTA
*
298224 TATTATTATTATATACA
1 TATTATTA-TAT-T-TA
* * **
298241 TAATAAATATAATAAA
1 T-ATTATTAT-ATTTA
298257 TATTATTATATTTA
1 TATTATTATATTTA
298271 TATTATTAT
1 TATTATTAT
298280 TATTATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
14 20 0.48
15 9 0.21
16 3 0.07
17 3 0.07
18 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTATATTTA
Found at i:311337 original size:3 final size:3
Alignment explanation
Indices: 311329--311385 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
311319 TTTATATATA
311329 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
311376 TAT TAT TAT T
1 TAT TAT TAT T
311386 CTTAATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:317200 original size:20 final size:20
Alignment explanation
Indices: 317175--317215 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
317165 GGTCCGGTCC
*
317175 GGTTCGAACGGTTCAAAGCG
1 GGTTCGAAAGGTTCAAAGCG
317195 GGTTCGAAAGGTTCAAAGCG
1 GGTTCGAAAGGTTCAAAGCG
317215 G
1 G
317216 TTCACTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.37, T:0.20
Consensus pattern (20 bp):
GGTTCGAAAGGTTCAAAGCG
Found at i:317278 original size:28 final size:28
Alignment explanation
Indices: 317246--317309 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
317236 CGGGATATAA
*
317246 TGAACCGGATTAGACAGCGGTTCCCGAT
1 TGAACCGGATTAGACAGCAGTTCCCGAT
*
317274 TGAACCGGATTAGACAGCAGTTCCCGGT
1 TGAACCGGATTAGACAGCAGTTCCCGAT
317302 TGAACCGG
1 TGAACCGG
317310 CCGATCCGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (28 bp):
TGAACCGGATTAGACAGCAGTTCCCGAT
Found at i:320353 original size:2 final size:2
Alignment explanation
Indices: 320346--320372 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
320336 ATTCTCTTTC
320346 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
320373 CATCATTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:320991 original size:2 final size:2
Alignment explanation
Indices: 320962--321021 Score: 77
Period size: 2 Copynumber: 30.0 Consensus size: 2
320952 TTAAATAATT
* * *
320962 TA TA TA -A TA TG TA TG TA TA AA CTA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
321004 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
321022 AGTAAGTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:321093 original size:7 final size:7
Alignment explanation
Indices: 321083--321126 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
321073 TAGTTTATAG
321083 AAACCCT
1 AAACCCT
*
321090 AAACCAT
1 AAACCCT
*
321097 AAACACT
1 AAACCCT
*
321104 AACCCCT
1 AAACCCT
*
321111 AAACCAT
1 AAACCCT
321118 AAACCCT
1 AAACCCT
321125 AA
1 AA
321127 TATAAATGGA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:321111 original size:21 final size:21
Alignment explanation
Indices: 321086--321126 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
321076 TTTATAGAAA
321086 CCCTAAACCATAAACACTAAC
1 CCCTAAACCATAAACACTAAC
*
321107 CCCTAAACCATAAACCCTAA
1 CCCTAAACCATAAACACTAA
321127 TATAAATGGA
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:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (21 bp):
CCCTAAACCATAAACACTAAC
Found at i:321519 original size:19 final size:20
Alignment explanation
Indices: 321464--321539 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
321454 TAAATAATTT
*
321464 TATATAATATGTATGTATAAAC
1 TATAT-ATA-GTATATATAAAC
* *
321486 CATGTATAGTATATATAAAC
1 TATATATAGTATATATAAAC
*
321506 TATATATA-TATATAAAAAC
1 TATATATAGTATATATAAAC
*
321525 TATATAAAGTATATA
1 TATATATAGTATATA
321540 GTTTATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.37
20 23 0.50
21 3 0.07
22 3 0.07
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
TATATATAGTATATATAAAC
Found at i:321528 original size:28 final size:27
Alignment explanation
Indices: 321497--321558 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
321487 ATGTATAGTA
321497 TATATAAACTATATA-TATATATAAAAAC
1 TATATAAACTATATAGT-T-TATAAAAAC
*
321525 TATATAAAGTATATAGTTTATAAAAAC
1 TATATAAACTATATAGTTTATAAAAAC
321552 -AT-TAAAC
1 TATATAAAC
321559 CTTAAACCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 2 0.06
27 9 0.29
28 15 0.48
29 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (27 bp):
TATATAAACTATATAGTTTATAAAAAC
Found at i:321584 original size:21 final size:21
Alignment explanation
Indices: 321556--321612 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
321546 AAAAACATTA
*
321556 AACCTTAAACCCTAAACCCTG
1 AACCTTAAACCCTAAACACTG
* **
321577 AACTTTAAACTATAAACACTG
1 AACCTTAAACCCTAAACACTG
*
321598 AACCATAAACCCTAA
1 AACCTTAAACCCTAA
321613 TGTAAATAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.21
Consensus pattern (21 bp):
AACCTTAAACCCTAAACACTG
Found at i:321803 original size:23 final size:24
Alignment explanation
Indices: 321776--321825 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
321766 TTATTTTTTC
*
321776 TTTATATAAATTAAATTATA-TAA
1 TTTATATAAATTAAACTATATTAA
321799 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
321823 TTT
1 TTT
321826 TTCTGTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:322163 original size:16 final size:16
Alignment explanation
Indices: 322085--322161 Score: 118
Period size: 16 Copynumber: 4.8 Consensus size: 16
322075 TCATTTATAG
*
322085 GTCAGGTTAAAAACAA
1 GTCAGGTTGAAAACAA
*
322101 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
*
322117 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
*
322133 GTCAGGTTGAAAATAA
1 GTCAGGTTGAAAACAA
322149 GTCAGGTTGAAAA
1 GTCAGGTTGAAAA
322162 TAGGTCGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:323094 original size:3 final size:3
Alignment explanation
Indices: 323086--323115 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
323076 TTATTTTAAT
*
323086 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
323116 CAAATTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:324522 original size:30 final size:29
Alignment explanation
Indices: 324487--324682 Score: 148
Period size: 30 Copynumber: 6.6 Consensus size: 29
324477 AAAATTACTA
324487 TTTAGTCCTTTATA-TTTCTGTTTTGGCTAT
1 TTTAGTCCTTTA-AGTTTCTGTTTT-GCTAT
* * * *
324517 TTTAGTCCCTTAATTTTTTGTAATTGCTAT
1 TTTAGTCCTTTAAGTTTCTGT-TTTGCTAT
*
324547 TTTAGTCCTTTAA-TTTCTGTTTCTTCTAT
1 TTTAGTCCTTTAAGTTTCTGTTT-TGCTAT
* * *
324576 TTTAATCCTTTAAGTTTCTATTTTATCTAT
1 TTTAGTCCTTTAAGTTTCTGTTTT-GCTAT
* * *
324606 TTTAGTCC-CTAAGTTTTTGTTTTAGTTAT
1 TTTAGTCCTTTAAGTTTCTGTTTT-GCTAT
* **
324635 TTTAGTCCTTTAA-ATTCTTGTTTATATTAT
1 TTTAGTCCTTTAAGTTTC-TGTTT-TGCTAT
*
324665 TTTAGGTCCTTTGAGTTT
1 TTTA-GTCCTTTAAGTTT
324683 TTACTTTTTC
Statistics
Matches: 135, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.01
29 51 0.38
30 70 0.52
31 11 0.08
32 2 0.01
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (29 bp):
TTTAGTCCTTTAAGTTTCTGTTTTGCTAT
Found at i:324609 original size:89 final size:88
Alignment explanation
Indices: 324487--324698 Score: 234
Period size: 89 Copynumber: 2.4 Consensus size: 88
324477 AAAATTACTA
* * *
324487 TTTAGTCCTTTATA-TTTCTGTTTTGGCTATTTTAGTCCCTTAATTTTTTGTAATT-GCTATTTT
1 TTTAGTCCTTTA-AGTTTCTATTTT-TCTATTTTAGTCCC-TAAGTTTTTGT-ATTAGCTATTTT
* *
324550 AGTCCTTTAATTTC-TGTTTCT-TCTAT
62 AGTCCTTTAAATTCTTGTTTATAT-TAT
* * *
324576 TTTAATCCTTTAAGTTTCTATTTTATCTATTTTAGTCCCTAAGTTTTTGTTTTAGTTATTTTAGT
1 TTTAGTCCTTTAAGTTTCTATTTT-TCTATTTTAGTCCCTAAGTTTTTGTATTAGCTATTTTAGT
324641 CCTTTAAATTCTTGTTTATATTAT
65 CCTTTAAATTCTTGTTTATATTAT
* *
324665 TTTAGGTCCTTTGAGTTTTTACTTTTTCTATTTT
1 TTTA-GTCCTTTAAGTTTCTA-TTTTTCTATTTT
324699 TGTCTTTGTA
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
87 2 0.02
88 31 0.30
89 46 0.44
90 22 0.21
91 4 0.04
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.60
Consensus pattern (88 bp):
TTTAGTCCTTTAAGTTTCTATTTTTCTATTTTAGTCCCTAAGTTTTTGTATTAGCTATTTTAGTC
CTTTAAATTCTTGTTTATATTAT
Found at i:325545 original size:29 final size:29
Alignment explanation
Indices: 325504--325559 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
325494 CTCCTAATCT
* *
325504 ATTTATTCCAAATCAATTCAAAATCATCA
1 ATTTATTCCAAATAAAGTCAAAATCATCA
*
325533 ATTT-TTCCAAAATAAAGTCATAATCAT
1 ATTTATTCC-AAATAAAGTCAAAATCAT
325560 TTTTTTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.36
Consensus pattern (29 bp):
ATTTATTCCAAATAAAGTCAAAATCATCA
Found at i:326324 original size:16 final size:16
Alignment explanation
Indices: 326303--326334 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
326293 TGAATAACAG
326303 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
326319 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
326335 ATGTACTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
CATGCGAACTAGATAC
Found at i:329033 original size:2 final size:2
Alignment explanation
Indices: 329022--329064 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
329012 TATACCCAAA
329022 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
329063 AT
1 AT
329065 TTATGCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:330528 original size:36 final size:37
Alignment explanation
Indices: 330465--330570 Score: 119
Period size: 36 Copynumber: 2.9 Consensus size: 37
330455 TTTTCTTAAA
* *
330465 AAAAACAAAGTGTCGTCTCGCTAGAGACAATTTTCT-T
1 AAAAACAAA-TGTTGTCTCGCTTGAGACAATTTTCTCT
*
330502 AAAAACAAATGTTGTCTCGCTTGAGACAGTTTTCTCT
1 AAAAACAAATGTTGTCTCGCTTGAGACAATTTTCTCT
* * *
330539 TAAAACAAAT-TTCATTTCGCTTGAGA-AATTTT
1 AAAAACAAATGTT-GTCTCGCTTGAGACAATTTT
330571 TCCTTTGAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
36 30 0.50
37 30 0.50
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (37 bp):
AAAAACAAATGTTGTCTCGCTTGAGACAATTTTCTCT
Found at i:330544 original size:37 final size:36
Alignment explanation
Indices: 330465--330570 Score: 115
Period size: 37 Copynumber: 2.9 Consensus size: 36
330455 TTTTCTTAAA
330465 AAAAACAAAGTGTCGTCTCGCTAGAGACAATTTTCTT
1 AAAAACAAA-TGTCGTCTCGCTAGAGACAATTTTCTT
* * *
330502 AAAAACAAATGTTGTCTCGCTTGAGACAGTTTTCTCT
1 AAAAACAAATGTCGTCTCGCTAGAGACAATTTTCT-T
* * * * *
330539 TAAAACAAATTTCATTTCGCTTGAGA-AATTTT
1 AAAAACAAATGTCGTCTCGCTAGAGACAATTTT
330571 TCCTTTGAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 28 0.47
37 31 0.53
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (36 bp):
AAAAACAAATGTCGTCTCGCTAGAGACAATTTTCTT
Found at i:330822 original size:38 final size:38
Alignment explanation
Indices: 330771--330878 Score: 157
Period size: 38 Copynumber: 2.9 Consensus size: 38
330761 TAGTGTTCTT
* *
330771 AAGAAAACTTTGAGTTTGTTTCACTCGAAACAAATCAA
1 AAGAAAACTTTGAGTCTGTTTCACTTGAAACAAATCAA
*
330809 AAGAAAACTTTGAGTCTGTTTCACTTGAAACAAATTAA
1 AAGAAAACTTTGAGTCTGTTTCACTTGAAACAAATCAA
* *
330847 AA-AAATCTTTGAATCTGTTTC-CTTGAAACAAA
1 AAGAAAACTTTGAGTCTGTTTCACTTGAAACAAA
330879 GTTTTGTCTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 11 0.17
37 17 0.26
38 37 0.57
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (38 bp):
AAGAAAACTTTGAGTCTGTTTCACTTGAAACAAATCAA
Found at i:330949 original size:65 final size:64
Alignment explanation
Indices: 330845--331010 Score: 203
Period size: 65 Copynumber: 2.6 Consensus size: 64
330835 GAAACAAATT
* * *
330845 AAAAAAATCTTTGAATCTGTTTCCTT-GAAACAAAGTTTTG-TCTCTTGAGACAATTTCTTTTGA
1 AAAAAAATCTTTGAATCTATTTCTTTGGAAACAAAATTTTGCTCTCTTGAGACAATTTCTTTT--
330908 AA
64 -A
* * *
330910 AAAAAAACCTTTGACT-TATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTA
1 AAAAAAATCTTTGAATCTATTTCTTTGGAAACAAAATTTTG-CTCTCTTGAGACAATTTCTTTTA
* *
330974 AGAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAAT
1 AAAAAAATCTTTGAATCTATTTCTTTGGAAACAAAAT
331011 CTACCATCTT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
64 21 0.24
65 47 0.53
67 20 0.23
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (64 bp):
AAAAAAATCTTTGAATCTATTTCTTTGGAAACAAAATTTTGCTCTCTTGAGACAATTTCTTTTA
Found at i:331032 original size:64 final size:64
Alignment explanation
Indices: 330885--331024 Score: 158
Period size: 64 Copynumber: 2.1 Consensus size: 64
330875 CAAAGTTTTG
* * * *
330885 TCTCTTGAGACAATTTCTTTTGAAAAAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTTTG
1 TCTCTTGAGACAGTTTCTTTT---AAGAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTA
*
330950 TC
63 CC
* *
330952 TCTCTTGAGACAGTTTCTTTTAAGAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAA-TCTACC
1 TCTCTTGAGACAGTTTCTTTTAAGAAAAACCTTTGACT-TATTTCTTTGGAAACAAAATTCTACC
331016 ATCT-TTGAG
1 -TCTCTTGAG
331025 TCTGTTTCCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
64 22 0.34
65 22 0.34
67 20 0.31
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (64 bp):
TCTCTTGAGACAGTTTCTTTTAAGAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTACC
Found at i:331044 original size:64 final size:63
Alignment explanation
Indices: 330910--331044 Score: 139
Period size: 64 Copynumber: 2.1 Consensus size: 63
330900 TCTTTTGAAA
* ** * *
330910 AAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTT
1 AAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTACCTCTCTTGAGACAGTTTCCTTG
* * * *
330973 AAGAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAA-TCTACCATCT-TTGAGTCTGTTTCCCT
1 AA-AAAAACCTTTGACT-TATTTCTTTGGAAACAAAATTCTACC-TCTCTTGAGACAGTTT-CCT
331036 TG
62 TG
331038 AAAAAAA
1 AAAAAAA
331045 ACAAATATCT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
63 2 0.03
64 30 0.51
65 27 0.46
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (63 bp):
AAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTACCTCTCTTGAGACAGTTTCCTTG
Found at i:331045 original size:65 final size:64
Alignment explanation
Indices: 330885--331046 Score: 148
Period size: 65 Copynumber: 2.5 Consensus size: 64
330875 CAAAGTTTTG
* * * *
330885 TCTCTTGAGACAATTTCTTTTGAAAAAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTTTG
1 TCTCTTGAGACAGTTTC-CTTG--AAAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTA
*
330950 TC
63 CC
* * * * *
330952 TCTCTTGAGACAGTTTCTTTTAAGAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAA-TCTACC
1 TCTCTTGAGACAGTTTCCTTGAAAAAAAACCTTTGACT-TATTTCTTTGGAAACAAAATTCTACC
* *
331016 ATCT-TTGAGTCTGTTTCCCTTGAAAAAAAAC
1 -TCTCTTGAGACAGTTT-CCTTGAAAAAAAAC
331047 AAATATCTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
64 27 0.35
65 32 0.41
66 3 0.04
67 16 0.21
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (64 bp):
TCTCTTGAGACAGTTTCCTTGAAAAAAAACCTTTGACTTATTTCTTTGGAAACAAAATTCTACC
Found at i:331282 original size:28 final size:28
Alignment explanation
Indices: 331235--331316 Score: 112
Period size: 28 Copynumber: 2.8 Consensus size: 28
331225 GAGACAGTTG
331235 CTTTTGAAACATATCATCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTTTGTTT
*
331266 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTTTGTTT
331294 CTTTTGAAACAAATCTTTGAGTT
1 CTTTTGAAACAAATCTTTGAGTT
331317 GATTTCCCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
28 34 0.72
29 2 0.04
30 3 0.06
31 8 0.17
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTTTGTTT
Found at i:331322 original size:28 final size:27
Alignment explanation
Indices: 331235--331331 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 27
331225 GAGACAGTTG
331235 CTTTTGAAACATATCATCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAG-TTGTTT
331266 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGT-TGTTT
331294 CTTTTGAAACAAATCTTTGAGTTGATTT
1 CTTTTGAAACAAATCTTTGAGTTG-TTT
**
331322 CCCTTGAAAC
1 CTTTTGAAAC
331332 CATTATTCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.05
28 44 0.73
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (27 bp):
CTTTTGAAACAAATCTTTGAGTTGTTT
Found at i:331545 original size:40 final size:40
Alignment explanation
Indices: 331482--331620 Score: 149
Period size: 40 Copynumber: 3.4 Consensus size: 40
331472 TGGTCAGTCG
* *
331482 TCCTCTTCACGTAGGAACCGTGTCATCCCCT-GACCAGACC
1 TCCTCATCACGTAGGAACTGTGTCAT-CCCTAGACCAGACC
* *
331522 TCCTCATCACGTA-GAAGCTGTGTCAACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAA-CTGTGTCATCCCTAG---ACCAGACC
* *
331564 ATCCTCATCACATAGGAACTGTGTCATCCCTCGACCAGACC
1 -TCCTCATCACGTAGGAACTGTGTCATCCCTAGACCAGACC
331605 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
331621 GCCATGTCAC
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
39 6 0.07
40 40 0.49
41 2 0.02
42 2 0.02
43 29 0.35
44 3 0.04
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (40 bp):
TCCTCATCACGTAGGAACTGTGTCATCCCTAGACCAGACC
Found at i:331573 original size:43 final size:43
Alignment explanation
Indices: 331514--331644 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 43
331504 TCATCCCCTG
*
331514 ACCAGACCTCCTCATCACGTAGAAGCTGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGAAGCTGTGTCAACCCTAGATA
* * *
331557 ACCAG-CCATCCTCATCACATAGGAA-CTGTGTCATCCCTCG---
1 ACCAGACC-TCCTCATCACGTA-GAAGCTGTGTCAACCCTAGATA
* ** *
331597 ACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCCTAGATA
1 ACCAGACCTCCTCATCACGTAGAAGCTGTGTCAACCCTAGATA
331640 ACCAG
1 ACCAG
331645 TCGTCATCAT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
39 2 0.03
40 28 0.39
41 2 0.03
42 2 0.03
43 34 0.48
44 3 0.04
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGAAGCTGTGTCAACCCTAGATA
Found at i:331655 original size:83 final size:83
Alignment explanation
Indices: 331476--331655 Score: 245
Period size: 83 Copynumber: 2.2 Consensus size: 83
331466 TAAAGATGGT
* * *
331476 CAGTCGTCCTCTTCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGAAGCT
1 CAGTCGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGAAGCC
*
331541 GTGTCAACCATAGATAAC
66 ATGTCAACCATAGATAAC
* * * *
331559 CAGCCATCCTCATCACATAGGAACTGTGTCAT-CCCTCGACCAGACCTCCTCATCACGTAGGAGC
1 CAGTCGTCCTCATCACATAGGAACCGTGTCATCCCCT-GACCAGACCTCCTCATCACGTAGAAGC
* *
331623 CATGTCACCCCTAGATAAC
65 CATGTCAACCATAGATAAC
*
331642 CAGTCGTCATCATC
1 CAGTCGTCCTCATC
331656 GTGTTGGAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 4 0.05
83 79 0.95
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.22
Consensus pattern (83 bp):
CAGTCGTCCTCATCACATAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGTAGAAGCC
ATGTCAACCATAGATAAC
Found at i:331999 original size:14 final size:14
Alignment explanation
Indices: 331971--332008 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
331961 CTATTTAATT
*
331971 TTATT-TTAATTTA
1 TTATTATTATTTTA
331984 TTATTATTATTTTA
1 TTATTATTATTTTA
*
331998 TTAATATTATT
1 TTATTATTATT
332009 ATTACAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTATTTTA
Found at i:333429 original size:29 final size:30
Alignment explanation
Indices: 333397--333501 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 30
333387 TTTGAAATTG
*
333397 CTATTTTAGTCCTTTAA-TTTAT-TTTTCTT
1 CTATTTTAGTCCTTTAAGTTTATATTTT-AT
* *
333426 CTATTTTAATCCTTTAAGTTTCTATTTTAT
1 CTATTTTAGTCCTTTAAGTTTATATTTTAT
* * * *
333456 CTATTTTAGTCC-CTAAGTTTCTGTTTTAG
1 CTATTTTAGTCCTTTAAGTTTATATTTTAT
*
333485 CTATTTCAGTCCTTTAA
1 CTATTTTAGTCCTTTAA
333502 ATTCATGTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 41 0.64
30 19 0.30
31 4 0.06
ACGTcount: A:0.20, C:0.16, G:0.07, T:0.57
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAGTTTATATTTTAT
Found at i:334457 original size:23 final size:22
Alignment explanation
Indices: 334431--334478 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
334421 AAATCAATTC
334431 AAAATCATCAAT-TTTTCTAAAAT
1 AAAATCAT-AATCTTTT-TAAAAT
334454 AAAATCATAATCGTTTTTAAAAT
1 AAAATCATAATC-TTTTTAAAAT
334477 AA
1 AA
334479 TATTTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATCATAATCTTTTTAAAAT
Found at i:336068 original size:31 final size:31
Alignment explanation
Indices: 336030--336093 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
336020 CCTTCCCAAC
336030 CCACGGAGGAAACTCATCGACTAACTGTAAA
1 CCACGGAGGAAACTCATCGACTAACTGTAAA
*
336061 CCACGGAGGAAACTCATCGTCTAACTGTAAA
1 CCACGGAGGAAACTCATCGACTAACTGTAAA
336092 CC
1 CC
336094 TCGAGAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (31 bp):
CCACGGAGGAAACTCATCGACTAACTGTAAA
Found at i:339221 original size:23 final size:22
Alignment explanation
Indices: 339170--339223 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
339160 TAATTTATTA
339170 TTATTA-TTATTATTATATACT
1 TTATTATTTATTATTATATACT
* *
339191 TCTTTTATTTATTATTAGTATAGT
1 T-TATTATTTATTATTA-TATACT
339215 TTATTATTT
1 TTATTATTT
339224 TGTGACAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 4 0.15
23 16 0.59
24 6 0.22
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TTATTATTTATTATTATATACT
Found at i:340012 original size:26 final size:26
Alignment explanation
Indices: 339982--340044 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
339972 AATCACTTTA
339982 AAAATTTCAAACCAATTTTGAATTAT
1 AAAATTTCAAACCAATTTTGAATTAT
*
340008 AAAATTTCAAATCAATTTTGAATTAT
1 AAAATTTCAAACCAATTTTGAATTAT
340034 AAAATTTCAAA
1 AAAATTTCAAA
340045 ATCATTCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (26 bp):
AAAATTTCAAACCAATTTTGAATTAT
Found at i:342255 original size:35 final size:37
Alignment explanation
Indices: 342213--342300 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 37
342203 TGTTTTTTTT
342213 AACTATATATTATATAAATTTT-AAAACGATTTT-AA
1 AACTATATATTATATAAATTTTCAAAACGATTTTAAA
* * * *
342248 AATTATATATTATATAAGTTTTCAAAATGGTTTTAAA
1 AACTATATATTATATAAATTTTCAAAACGATTTTAAA
*
342285 AACTATATAATATATA
1 AACTATATATTATATA
342301 TGGTTTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 20 0.44
36 9 0.20
37 16 0.36
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (37 bp):
AACTATATATTATATAAATTTTCAAAACGATTTTAAA
Found at i:342292 original size:37 final size:36
Alignment explanation
Indices: 342213--342392 Score: 134
Period size: 38 Copynumber: 4.9 Consensus size: 36
342203 TGTTTTTTTT
* *
342213 AACTATATATTATATAAATTTT-AAAACGATTTT-AA
1 AACTATATATTATATAAGTTTTCAAAATG-TTTTAAA
*
342248 AATTATATATTATATAAGTTTTCAAAATGGTTTTAAA
1 AACTATATATTATATAAGTTTTCAAAAT-GTTTTAAA
* * * *** *
342285 AACTATATAATATATATGGTTTCAAAAAACAATTCAAA
1 AACTATATATTATATAAGTTTTC--AAAATGTTTTAAA
* * *
342323 AATTATATAATATATATGTTTTCAAAAAATGTTTTCAAA
1 AACTATATATTATATAAGTTTTC--AAAATGTTTT-AAA
* *
342362 AACCATATATTATAT-A-TTTTCAAGATGTTTT
1 AACTATATATTATATAAGTTTTCAAAATGTTTT
342393 CTTTTTTAGA
Statistics
Matches: 117, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
35 29 0.25
36 8 0.07
37 27 0.23
38 34 0.29
39 19 0.16
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.42
Consensus pattern (36 bp):
AACTATATATTATATAAGTTTTCAAAATGTTTTAAA
Found at i:342356 original size:13 final size:13
Alignment explanation
Indices: 342338--342363 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
342328 TATAATATAT
342338 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
342351 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
342364 CCATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:342383 original size:75 final size:74
Alignment explanation
Indices: 342246--342384 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 74
342236 AAACGATTTT
* *
342246 AAAATTATATATTATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
1 AAAATTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACCATATAATATATAT-GTTTCAAA
342311 AAACAATTCA
65 AAACAATTCA
* *
342321 AAAATTATATAATATATATGTTTTCAAAAAAT-GTTTTCAAAAACCATATATTATATAT-TTTCA
1 AAAATTATATAATATATAAGTTTTC--AAAATGGTTTT-AAAAACCATATAATATATATGTTTCA
342384 A
63 A
342385 GATGTTTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
75 29 0.51
76 5 0.09
77 23 0.40
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (74 bp):
AAAATTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACCATATAATATATATGTTTCAAAA
AACAATTCA
Found at i:343148 original size:84 final size:82
Alignment explanation
Indices: 343028--343734 Score: 712
Period size: 84 Copynumber: 8.6 Consensus size: 82
343018 GCTATGTTGT
*
343028 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
1 AAATGATATGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGATAACCCTTC
* * *
343092 TAGACTTGAGTTATACTGT
64 TAGACTTAAGTTATGCTGC
* * * * ** * *
343111 GAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGATAGCTCTTCT
1 AAATGATATGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
* *
343174 CGACTTAAGCTATGCTGC
65 AGACTTAAGTTATGCTGC
* * * * * * *
343192 AAATGATGTGTCGTTGAGCTGAGCGTATTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-GCAGATAACCCTTC
* *
343257 TAGACTTAAGTTGTGATGC
64 TAGACTTAAGTTATGCTGC
*
343276 AAATGATATG-TCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
1 AAATGATATGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGATAACCCTTC
* * *
343340 TAGACTTGAGTTATGTTGT
64 TAGACTTAAGTTATGCTGC
* * * * ** * *
343359 GAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGATAGCTCTTCT
1 AAATGATATGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
* *
343422 CGACTTAAGCTATGCTGC
65 AGACTTAAGTTATGCTGC
* * * * * *
343440 AAATAATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-GCAGATAACCCTTC
*
343505 TAGACTTAAGTTGTGCTGC
64 TAGACTTAAGTTATGCTGC
*
343524 AAATGATATG-CCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTGTCAGATAACCCTTC
1 AAATGATATGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGATAACCCTTC
* *
343588 TAGACTTGAGTTATGCTGT
64 TAGACTTAAGTTATGCTGC
* * * * ** *
343607 GAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGATAGCCCTTCT
1 AAATGATATGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCT
* *
343670 CGACTTAAGCTATGCTGC
65 AGACTTAAGTTATGCTGC
* *
343688 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
1 AAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
343735 ATTGGCAAAT
Statistics
Matches: 501, Mismatches: 104, Indels: 40
0.78 0.16 0.06
Matches are distributed among these distances:
80 70 0.14
81 117 0.23
82 5 0.01
83 102 0.20
84 207 0.41
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (82 bp):
AAATGATATGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATAACCCTTCTA
GACTTAAGTTATGCTGC
Found at i:343216 original size:164 final size:162
Alignment explanation
Indices: 343018--343734 Score: 724
Period size: 164 Copynumber: 4.3 Consensus size: 162
343008 CTTGCTTTGG
* *
343018 GCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
1 GCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGA
* ** *
343083 TAACCCTTCTAGACTTGAGTTATACTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
64 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
** * * *
343148 GGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAA
129 GAAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
* * * *
343182 GCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTATTCGAACTCAAAGGTCTTTTGTTGGCAG
1 GCTATGCTGCAAATGATGTG-CCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-GCAG
* * * * * *
343247 ACAACCCTTCTAGACTTAAGTTGTGA-TGCAAATGATATG-TCTTGGAGCTGAGCGTAGTCGAAC
63 ATAACCCTTCTAGACTTAAGTTAT-ACTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAAC
*
343310 TCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGA
127 TCGAAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAA
* * ** * * * * **
343349 GTTATGTTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAGA
1 GCTATGCTGCAAATGATGTG-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGA
* * * * * * * * * *
343412 TAGCTCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCGTTG-AGCTGAGCGTAGTCGAACTC
64 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
* *
343476 AAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
129 GAAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAA
* * * *
343514 GTTGTGCTGCAAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTGTCAGA
1 GCTATGCTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAGA
* * ** *
343579 TAACCCTTCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
64 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
** * *
343644 GGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
129 GAAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
343678 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
1 GCTATGCTGCAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTG
343735 ATTGGCAAAT
Statistics
Matches: 450, Mismatches: 83, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
164 233 0.52
165 88 0.20
166 5 0.01
167 78 0.17
168 46 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (162 bp):
GCTATGCTGCAAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGATA
ACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGA
AGGTCTTTGGCAGATAACCCTTCTAGACTTAA
Found at i:343753 original size:248 final size:248
Alignment explanation
Indices: 343028--343741 Score: 1295
Period size: 248 Copynumber: 2.9 Consensus size: 248
343018 GCTATGTTGT
*
343028 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
*
343093 AGACTTGAGTTATACTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
* *
343158 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTATTCG
131 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
343223 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGC
196 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGC
*
343276 AAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
*
343341 AGACTTGAGTTATGTTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
343406 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCGTTGAGCTGAGCGTAGTCG
131 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
*
343471 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGC
196 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGC
* *
343524 AAATGATATGCCTTGGAGCTTAGCGTAGTCGAACTCGAAGGTCTTTGGTGTCAGATAACCCTTCT
1 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
343589 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
* *
343654 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCG
131 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
*
343719 AACTCGAAGGTC-TTTGATTGGCA
196 AACTCAAAGGTCTTTTG-TTGGCA
343742 AATAGCCCTT
Statistics
Matches: 449, Mismatches: 16, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
247 4 0.01
248 445 0.99
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (248 bp):
AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGC
Found at i:350218 original size:19 final size:18
Alignment explanation
Indices: 350191--350230 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
350181 AAAAAACGAT
*
350191 AAAATAAATAATAAAAACA
1 AAAACAAATAATAAAAA-A
350210 AAAACAAATAATAAAAAA
1 AAAACAAATAATAAAAAA
350228 AAA
1 AAA
350231 TACTATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAACAAATAATAAAAAA
Found at i:350352 original size:33 final size:32
Alignment explanation
Indices: 350315--350491 Score: 117
Period size: 31 Copynumber: 5.2 Consensus size: 32
350305 TATAAATTTA
*
350315 AAAAACGTTTTCAAACTATATGTTATA-GTTTTC
1 AAAAACGTTTTAAAACTATAT-TTATATG-TTTC
350348 AAAAACGTTTTAAAACTATA-TTATATGTTTC
1 AAAAACGTTTTAAAACTATATTTATATGTTTC
* ** *
350379 AAAAATGTTTTTTAACTATATATTATATAAATTT-
1 AAAAACGTTTTAAAACTATAT-TTATAT--GTTTC
* *
350413 TAAAACGATTTTAAAATTATATATTATATAAGTTTTC
1 AAAAACG-TTTTAAAACTATAT-TTATAT--G-TTTC
**
350450 AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAACGTTTT-AAAACTATAT--T-TATAT-GTTTC
350487 AAAAA
1 AAAAA
350492 ACAATTCAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
31 26 0.22
32 1 0.01
33 25 0.22
34 5 0.04
35 23 0.20
36 7 0.06
37 21 0.18
38 3 0.03
39 5 0.04
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (32 bp):
AAAAACGTTTTAAAACTATATTTATATGTTTC
Found at i:350471 original size:37 final size:35
Alignment explanation
Indices: 350245--350571 Score: 160
Period size: 35 Copynumber: 9.3 Consensus size: 35
350235 ATATGATAAA
* * *
350245 AAAATGTTTTTAAACTTTATATAATAT-A-TATTTC
1 AAAATGTTTTAAAACTATATATTATATAAGT-TTTC
* * **
350279 AAAGATATTTTCAAAA-TCATATATTATATAAATTTAA
1 AAA-ATGTTTT-AAAACT-ATATATTATATAAGTTTTC
* * *
350316 AAAACGTTTTCAAACTATAT-GT-TAT-AGTTTTC
1 AAAATGTTTTAAAACTATATATTATATAAGTTTTC
*
350348 AAAAACGTTTTAAAAC--TATATTATAT--G-TTTC
1 -AAAATGTTTTAAAACTATATATTATATAAGTTTTC
** *
350379 AAAAATGTTTTTTAACTATATATTATATAAATTTT-
1 -AAAATGTTTTAAAACTATATATTATATAAGTTTTC
* *
350414 AAAACGATTTTAAAATTATATATTATATAAGTTTTC
1 AAAATG-TTTTAAAACTATATATTATATAAGTTTTC
* * *
350450 AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAT-GTTTT-AAAACTATATATTATATAAGTTTTC
** ** * * *
350487 AAAAAACAATTCAAAAATTATATAATATATATGTTTTC
1 --AAAA-TGTTTTAAAACTATATATTATATAAGTTTTC
*
350525 AAAAAATGTTTTCAAAAACCATATATTATAT-A-TTTTC
1 --AAAATGTTTT--AAAACTATATATTATATAAGTTTTC
*
350562 AAGATGTTTT
1 AAAATGTTTT
350572 CTTTTTTAGA
Statistics
Matches: 226, Mismatches: 44, Indels: 45
0.72 0.14 0.14
Matches are distributed among these distances:
31 20 0.09
32 6 0.03
33 30 0.13
34 9 0.04
35 47 0.21
36 29 0.13
37 35 0.15
38 30 0.13
39 20 0.09
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (35 bp):
AAAATGTTTTAAAACTATATATTATATAAGTTTTC
Found at i:350535 original size:13 final size:13
Alignment explanation
Indices: 350517--350542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
350507 TATAATATAT
350517 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
350530 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
350543 CCATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:350562 original size:75 final size:74
Alignment explanation
Indices: 350425--350563 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 74
350415 AAACGATTTT
* *
350425 AAAATTATATATTATATAAGTTTTCAAAATGGTTTTAAAAACTATATAATATATATGGTTTCAAA
1 AAAATTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACCATATAATATATAT-GTTTCAAA
350490 AAACAATTCA
65 AAACAATTCA
* *
350500 AAAATTATATAATATATATGTTTTCAAAAAAT-GTTTTCAAAAACCATATATTATATAT-TTTCA
1 AAAATTATATAATATATAAGTTTTC--AAAATGGTTTT-AAAAACCATATAATATATATGTTTCA
350563 A
63 A
350564 GATGTTTTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
75 29 0.51
76 5 0.09
77 23 0.40
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (74 bp):
AAAATTATATAATATATAAGTTTTCAAAATGGTTTTAAAAACCATATAATATATATGTTTCAAAA
AACAATTCA
Found at i:351034 original size:14 final size:14
Alignment explanation
Indices: 351003--351032 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
350993 TAGTTTATCC
351003 TTTATTTTAAATAA
1 TTTATTTTAAATAA
351017 TTTATTTTAAA-AA
1 TTTATTTTAAATAA
351030 TTT
1 TTT
351033 TAACTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTTTAAATAA
Found at i:351337 original size:21 final size:21
Alignment explanation
Indices: 351311--351350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
351301 GAACCCGGGA
351311 CCTCTAAGAATAACAACAATT
1 CCTCTAAGAATAACAACAATT
* *
351332 CCTCTATGAATAATAACAA
1 CCTCTAAGAATAACAACAA
351351 CAATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (21 bp):
CCTCTAAGAATAACAACAATT
Found at i:355564 original size:19 final size:19
Alignment explanation
Indices: 355540--355584 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
355530 AGGTGGTGGC
*
355540 TCACCGGTTGTTGACGACT
1 TCACCGGTTGTCGACGACT
*
355559 TCACCGATTGTCGACGACT
1 TCACCGGTTGTCGACGACT
355578 TCACCGG
1 TCACCGG
355585 CAGTGGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (19 bp):
TCACCGGTTGTCGACGACT
Found at i:362950 original size:31 final size:31
Alignment explanation
Indices: 362912--363096 Score: 309
Period size: 31 Copynumber: 6.0 Consensus size: 31
362902 GGGTCGAGGG
*
362912 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
362943 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
362974 TTACCTTTGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
363005 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
363036 TTACCTATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
363067 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
363097 GTCCTTCGGG
Statistics
Matches: 146, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 145 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:374691 original size:3 final size:3
Alignment explanation
Indices: 374670--374752 Score: 93
Period size: 3 Copynumber: 28.7 Consensus size: 3
374660 GGCCTGTTTG
* * *
374670 TAA TAA TAT TAA TAG TAA TAA TAA TAC TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
374715 TAA -AA TAA -AA TAA TAT TAA TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
374753 TAAAAAATAA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.12
3 56 0.84
4 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:374735 original size:40 final size:40
Alignment explanation
Indices: 374686--374764 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 40
374676 TATTAATAGT
* *
374686 AATAATAATACTAATAA-ATAAT-ATAATA-ATAAAATAA
1 AATAATAATAATAATAATATAATAATAATATAAAAAATAA
*
374723 AATAATATTAATAATAATATAATAATAATATAAAAAATAA
1 AATAATAATAATAATAATATAATAATAATATAAAAAATAA
374763 AA
1 AA
374765 AAATGGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 15 0.42
38 5 0.14
39 6 0.17
40 10 0.28
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (40 bp):
AATAATAATAATAATAATATAATAATAATATAAAAAATAA
Found at i:374739 original size:33 final size:34
Alignment explanation
Indices: 374689--374761 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
374679 TAATAGTAAT
374689 AATAATACTAATAAATAATATAATAATAAAATAA
1 AATAATACTAATAAATAATATAATAATAAAATAA
* *
374723 AATAATATTAAT-AATAATATAATAATAATATAA
1 AATAATACTAATAAATAATATAATAATAAAATAA
374756 AA-AATA
1 AATAATA
374762 AAAAAATGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 4 0.11
33 22 0.59
34 11 0.30
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (34 bp):
AATAATACTAATAAATAATATAATAATAAAATAA
Found at i:375992 original size:16 final size:15
Alignment explanation
Indices: 375968--376001 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
375958 TAGCTCATAT
375968 ATACATCTCATAGCAC
1 ATACATCTCATAG-AC
*
375984 ATACTTCTCATAGAC
1 ATACATCTCATAGAC
375999 ATA
1 ATA
376002 TAAAAACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (15 bp):
ATACATCTCATAGAC
Found at i:376309 original size:13 final size:13
Alignment explanation
Indices: 376291--376315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
376281 TCTAATTTTC
376291 ATATAATCATATA
1 ATATAATCATATA
376304 ATATAATCATAT
1 ATATAATCATAT
376316 GCACTCACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATCATATA
Found at i:376573 original size:24 final size:24
Alignment explanation
Indices: 376521--376601 Score: 125
Period size: 24 Copynumber: 3.5 Consensus size: 24
376511 TCCCCTTGAA
376521 GTGCATCGATGCATTC--T-ACA-
1 GTGCATCGATGCATTCTTTAACAT
376541 GTGCATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
*
376565 GTGCATCGATACATTCTTTAACAT
1 GTGCATCGATGCATTCTTTAACAT
376589 GTGCATCGATGCA
1 GTGCATCGATGCA
376602 CTACCCATGC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 16 0.29
22 1 0.02
23 3 0.05
24 35 0.64
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (24 bp):
GTGCATCGATGCATTCTTTAACAT
Found at i:376712 original size:64 final size:62
Alignment explanation
Indices: 376589--376725 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 62
376579 TCTTTAACAT
* *
376589 GTGCATCGATGCACTACCCATGCATCGATACACAAAGCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAAGCA-CTTCGATGTTTTCATTTTAAAGA
* * * *
376652 GATGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCA-TTCGATG-TTTCTTCTTTAAA
1 G-TGCATCGATGCACTACC-CATGCATCGATACAC-AA-AGCACTTCGATGTTTTCAT-TTTAAA
376714 GA
61 GA
376716 GTGCATCGAT
1 GTGCATCGAT
376726 ACACATTGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
63 17 0.27
64 41 0.65
65 2 0.03
66 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAAGCACTTCGATGTTTTCATTTTAAAGA
Found at i:378844 original size:30 final size:30
Alignment explanation
Indices: 378808--378879 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
378798 CCCGAAGGAC
*
378808 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
*
378838 CTATCCAGATGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
378868 CTGTCCATAGGT
1 CTATCCAGAGGT
378880 TCCGAAGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:378904 original size:31 final size:31
Alignment explanation
Indices: 378866--378990 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
378856 GATCCTCGGC
* *
378866 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
378897 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
378928 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* **
378959 ATTCTGTCCATATGTTCCTTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
378991 TACCCTCAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.04
31 50 0.64
32 22 0.28
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:383436 original size:30 final size:30
Alignment explanation
Indices: 383400--383471 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
383390 CCCGAATGAC
*
383400 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
383430 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
383460 CTGTCCATAGGT
1 CTATCCAGAGGT
383472 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:383496 original size:31 final size:31
Alignment explanation
Indices: 383458--383645 Score: 186
Period size: 31 Copynumber: 6.0 Consensus size: 31
383448 GATCCTCGGC
* *
383458 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
383489 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
383520 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* **
383551 ATTCTGTCCATATGTTCCTTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
*
383583 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* **
383614 ATTCTGTCCATATGTTCCTTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
383646 TACCCCCAAC
Statistics
Matches: 128, Mismatches: 19, Indels: 19
0.77 0.11 0.11
Matches are distributed among these distances:
30 6 0.05
31 72 0.56
32 44 0.34
33 6 0.05
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:383570 original size:63 final size:63
Alignment explanation
Indices: 383483--383648 Score: 316
Period size: 63 Copynumber: 2.7 Consensus size: 63
383473 CCGAAGAACC
*
383483 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
383545 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
383608 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAC
383649 CCCCAACTCT
Statistics
Matches: 102, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
62 7 0.07
63 95 0.93
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:390394 original size:17 final size:17
Alignment explanation
Indices: 390372--390404 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
390362 TCTATTTATC
390372 TATATAATGATT-TAAAT
1 TATATAA-GATTATAAAT
390389 TATATAAGATTATAAA
1 TATATAAGATTATAAA
390405 AATGATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
TATATAAGATTATAAAT
Found at i:392883 original size:17 final size:18
Alignment explanation
Indices: 392861--392902 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
392851 AAAATATTTA
392861 AATATTAT-ATTTTTCAT
1 AATATTATGATTTTTCAT
*
392878 AATATTTTTGATTTTTCAT
1 AATA-TTATGATTTTTCAT
392897 AATATT
1 AATATT
392903 TTCGGTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 13 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
AATATTATGATTTTTCAT
Found at i:394211 original size:55 final size:55
Alignment explanation
Indices: 394096--394396 Score: 293
Period size: 55 Copynumber: 5.5 Consensus size: 55
394086 CTTAGATATC
* * ** * * **
394096 GATTGTAGCACAGAGGTGCTCAATCGTTTGTAAAAGTACAGAGGTGCTTGATTTTA
1 GATTGAAGCACAGAGGTGCTCAATC-ATCCTAAATGCACAGAGGTGCCAGATTTTA
* *
394152 GATTGCAGCACAGAGGTGCTCAATCATCCTAAATGTACAGAGGTGCCAGATTTTA
1 GATTGAAGCACAGAGGTGCTCAATCATCCTAAATGCACAGAGGTGCCAGATTTTA
* * * **
394207 GATTGCAGCACAGAGGTGCTCAATCAGCCTAAATGCACAGAGGTGCCAAATCCTA
1 GATTGAAGCACAGAGGTGCTCAATCATCCTAAATGCACAGAGGTGCCAGATTTTA
* * * *
394262 GATTGAAGCACAAAGGTGCTCAATCAAT--TAAAAGCACAAAGGTGCCAGATTATA
1 GATTGAAGCACAGAGGTGCTCAATC-ATCCTAAATGCACAGAGGTGCCAGATTTTA
* * * * ** * * *
394316 GACTGAAACGCAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAG-TTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TCCTAAATGCACAGAGGTGCCAGATTT-TA
394372 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
394397 GTTAATTCAA
Statistics
Matches: 205, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.00
54 42 0.20
55 99 0.48
56 63 0.31
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATCCTAAATGCACAGAGGTGCCAGATTTTA
Found at i:394250 original size:27 final size:27
Alignment explanation
Indices: 394159--394252 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
394149 TTAGATTGCA
*
394159 GCACAGAGGTGCTCAATCATCCTAAAT
1 GCACAGAGGTGCTCAATCAGCCTAAAT
* * ** **
394186 GTACAGAGGTGC-CAGATTTTAGATTGCA-
1 GCACAGAGGTGCTCA-A--TCAGCCTAAAT
394214 GCACAGAGGTGCTCAATCAGCCTAAAT
1 GCACAGAGGTGCTCAATCAGCCTAAAT
394241 GCACAGAGGTGC
1 GCACAGAGGTGC
394253 CAAATCCTAG
Statistics
Matches: 49, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
26 7 0.14
27 24 0.49
28 12 0.24
29 6 0.12
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (27 bp):
GCACAGAGGTGCTCAATCAGCCTAAAT
Found at i:394279 original size:28 final size:26
Alignment explanation
Indices: 394236--394308 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 26
394226 TCAATCAGCC
* *
394236 TAAATGCACAGAGGTGCCAAATCCTAGAT
1 TAAAAGCACAAAGGTGCCAAAT-C-A-AT
*
394265 T-GAAGCACAAAGGTGCTC-AATCAAT
1 TAAAAGCACAAAGGTGC-CAAATCAAT
394290 TAAAAGCACAAAGGTGCCA
1 TAAAAGCACAAAGGTGCCA
394309 GATTATAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
25 4 0.11
26 15 0.41
27 1 0.03
28 15 0.41
29 2 0.05
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (26 bp):
TAAAAGCACAAAGGTGCCAAATCAAT
Found at i:399914 original size:16 final size:15
Alignment explanation
Indices: 399857--399915 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
399847 ATATGACTAT
399857 TAAATTTTTAATTTG
1 TAAATTTTTAATTTG
* **
399872 TAAA-TTCTAATTAA
1 TAAATTTTTAATTTG
*
399886 TAATTATTTTAATTTG
1 TAAAT-TTTTAATTTG
399902 TAAATTTTGTAATT
1 TAAATTTT-TAATT
399916 GTAGTAGTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 10 0.30
15 7 0.21
16 16 0.48
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (15 bp):
TAAATTTTTAATTTG
Found at i:404225 original size:15 final size:16
Alignment explanation
Indices: 404205--404240 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
404195 AAGTTACTAC
404205 AAGAATAT-GAAAAAA
1 AAGAATATGGAAAAAA
*
404220 AAGAATATGGAAATAA
1 AAGAATATGGAAAAAA
404236 AAGAA
1 AAGAA
404241 AATTTCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (16 bp):
AAGAATATGGAAAAAA
Found at i:412926 original size:72 final size:69
Alignment explanation
Indices: 412809--412948 Score: 217
Period size: 72 Copynumber: 2.0 Consensus size: 69
412799 GCCGAGGCCG
* * *
412809 GACTTGTGCAAACGTGGTATGAAGCATTCTATCGTCACTTTGGTACTATGATGTTGCGTATATCC
1 GACTTGTGCAAACGTGGTATGAAGCATTCTATCATCACTTCGGTAC---GATGTTGCATATATCC
412874 TGTTTGA
63 TGTTTGA
*
412881 GACTTGTGCAAACGTGGTATGAAGCATTCTATCATCACTTCGGTACGATGTTGCATATATCTTGT
1 GACTTGTGCAAACGTGGTATGAAGCATTCTATCATCACTTCGGTACGATGTTGCATATATCCTGT
412946 TTG
66 TTG
412949 GATATTAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 20 0.31
72 44 0.69
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (69 bp):
GACTTGTGCAAACGTGGTATGAAGCATTCTATCATCACTTCGGTACGATGTTGCATATATCCTGT
TTGA
Found at i:420124 original size:55 final size:55
Alignment explanation
Indices: 420073--420917 Score: 1273
Period size: 55 Copynumber: 15.5 Consensus size: 55
420063 CTCCCTAGTC
* * * *
420073 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
*
420128 CTTCAGAGAGTATAAGAC-C-CACAATCTTCAAT-AATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTC-ATCAATCGCGTCTGCCCCCTATTT
*
420181 CTTCAGAGAGTATAAGACTCGAACAATCTTTATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * * *
420236 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTATGCCCCCTATTG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
*
420291 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* *
420344 CTTCAGAGAGTATAAGACTCAAACAATCTTCATCGATCGCGTCT-CTCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGC-CCCCTATTT
*
420399 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * * *
420452 CTTCAGAGATTATAAGAATCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* *
420507 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
420560 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * * * *
420615 CTTCAGAGAATATAAGACTCGAACAATCTTCAACGATCACTTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * *
420670 CTTCATAGAGTATAAGAC-C-CACAATCTTCATCAATCGCATCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
*
420723 CTTCAGAGAGTATAAGACTCGAACAATCTTTATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * *
420778 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * *
420833 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
420888 CTTCAGAGAGTATAAGACTCGAACAATCTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTT
420918 TTTTTGCTTC
Statistics
Matches: 720, Mismatches: 56, Indels: 28
0.90 0.07 0.03
Matches are distributed among these distances:
53 232 0.32
54 15 0.02
55 473 0.66
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTT
Found at i:420185 original size:108 final size:110
Alignment explanation
Indices: 420035--420917 Score: 1247
Period size: 108 Copynumber: 8.1 Consensus size: 110
420025 GGAGAATAGA
* * * * * * *
420035 ACTCGAAC-ATTTTCAAAAATCACGTCAGCTCCCTAGTCCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * * *
420099 TCTTCAACGATCGTGTCTTCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
420144 AC-C-CACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
420207 TCTTTATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** * * *
420252 ACTCGAACAATCTTCAACGATCGCGTATGCCCCCTATTGCTTCAGAGAGTATAAGAC-C-CACAA
1 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
420315 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* * *
420360 ACTCAAACAATCTTC-ATCGATCGCGTCT-CTCCCCTATTTCTTCAGAGAGTATAAGAC-C-CAC
1 ACTCGAACAATCTTCAAT-AATCGCGTCTGC-CCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
420421 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGATTATAAG
64 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* ** *
420468 AATCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAA
1 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
*
420531 TCTTCATCAATCGCGTCTCCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
*
420576 ACTCGAACAATCTTC-ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAATATAAGACTCGAACA
1 ACTCGAACAATCTTCAAT-AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
* * * * *
420640 ATCTTCAACGATCACTTCTGCCCCCTATTTCTTCATAGAGTATAAG
65 ATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
* *
420686 AC-C-CACAATCTTC-ATCAATCGCATCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
1 ACTCGAACAATCTTCAAT-AATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
*
420748 ATCTTTATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
65 ATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
** *
420794 ACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
1 ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
* * *
420859 TCTTCAACGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
420904 ACTCGAACAATCTT
1 ACTCGAACAATCTT
420918 TTTTTGCTTC
Statistics
Matches: 702, Mismatches: 59, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
107 5 0.01
108 487 0.69
109 9 0.01
110 200 0.28
111 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (110 bp):
ACTCGAACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAA
TCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
Found at i:420257 original size:163 final size:162
Alignment explanation
Indices: 420073--420917 Score: 1277
Period size: 163 Copynumber: 5.2 Consensus size: 162
420063 CTCCCTAGTC
* * * *
420073 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGTGTCTTCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* **
420138 TATAAGACCCACAATCTTCAATAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGA
66 TATAAGACCAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-A
*
420203 ACAATCTTTATCAATCGCGTCTGCCCCCTATTT
130 ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
* * * *
420236 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTATGCCCCCTATTGCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
420301 TATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAA
66 TATAAGACCAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC-A
*
420366 ACAATCTTCATCGATCGCGTCT-CTCCCCTATTT
130 ACAATCTTCATCAATCGCGTCTGC-CCCCTATTT
* *
420399 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
*
420462 TATAAGAATCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C
66 TATAAG-A-CCAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* *
420526 CACAATCTTCATCAATCGCGTCTCCCCCCTATTT
129 AACAATCTTCATCAATCGCGTCTGCCCCCTATTT
*
420560 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAA
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
420625 TATAAGACTCGAACAATCTTCAACGATCACTTCTGCCCCCTATTTCTTCATAGAGTATAAGAC-C
66 TATAAGAC-C-AACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* *
420689 CACAATCTTCATCAATCGCATCTGCCCCCTATTT
129 AACAATCTTCATCAATCGCGTCTGCCCCCTATTT
*
420723 CTTCAGAGAGTATAAGACTCGAACAATCTTTATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
*
420788 TATAAGACTCGAACAATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
66 TATAAGAC-C-AACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* * *
420853 GAACAATCTTCAACGATCACGTCTGCCCCCTATTT
129 -AACAATCTTCATCAATCGCGTCTGCCCCCTATTT
420888 CTTCAGAGAGTATAAGACTCGAACAATCTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTT
420918 TTTTTGCTTC
Statistics
Matches: 632, Mismatches: 40, Indels: 18
0.92 0.06 0.03
Matches are distributed among these distances:
161 93 0.15
162 7 0.01
163 472 0.75
164 1 0.00
165 59 0.09
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (162 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
TATAAGACCAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCAA
CAATCTTCATCAATCGCGTCTGCCCCCTATTT
Found at i:423964 original size:5 final size:5
Alignment explanation
Indices: 423954--423998 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
423944 ATTTTCAATT
423954 TTTTC TTTTC TTTTC TTTATTC TTTTC TTTTCC TTTTC TCTTTC T
1 TTTTC TTTTC TTTTC -TT-TTC TTTTC TTTT-C TTTTC T-TTTC T
423999 ACATTTCTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 19 0.53
6 14 0.39
7 3 0.08
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:423976 original size:12 final size:11
Alignment explanation
Indices: 423954--423998 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
423944 ATTTTCAATT
423954 TTTTC-TTTTC
1 TTTTCTTTTTC
423964 TTTTCTTTATTC
1 TTTTCTTT-TTC
*
423976 TTTTCTTTTCC
1 TTTTCTTTTTC
*
423987 TTTTCTCTTTC
1 TTTTCTTTTTC
423998 T
1 T
423999 ACATTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 5 0.17
11 14 0.47
12 11 0.37
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:423978 original size:17 final size:16
Alignment explanation
Indices: 423954--423998 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
423944 ATTTTCAATT
*
423954 TTTTCTTTTCTTTTCT
1 TTTTCTTTTCTTTTCC
423970 TTATTCTTTTCTTTTCC
1 TT-TTCTTTTCTTTTCC
423987 TTTTCTCTTTCT
1 TTTTCT-TTTCT
423999 ACATTTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCC
Found at i:423998 original size:22 final size:22
Alignment explanation
Indices: 423954--423998 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
423944 ATTTTCAATT
*
423954 TTTTCTTTTCTTTTCTTTATTC
1 TTTTCTTTTCTTTTCTCTATTC
423976 TTTTCTTTTCCTTTTCTCT-TTC
1 TTTTCTTTT-CTTTTCTCTATTC
423998 T
1 T
423999 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCTTTTCTTTTCTCTATTC
Found at i:424233 original size:2 final size:2
Alignment explanation
Indices: 424226--424284 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
424216 ACCACAAGGG
424226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424268 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
424285 GGATAAATGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:426646 original size:21 final size:21
Alignment explanation
Indices: 426621--426759 Score: 183
Period size: 21 Copynumber: 6.6 Consensus size: 21
426611 CCATGCGATG
*
426621 TGGTCTTCTCGTCTTTATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
426642 GGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
426663 TGGTCTTCTCATCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
**
426684 TGACCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
426705 T-GTCATTCTCGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
426726 T-GACATTCTCGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
426747 TGTTCTTCTCGTC
1 TGGTCTTCTCGTC
426760 CTTGGTACGA
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
20 1 0.01
21 102 0.98
22 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTGATGAA
Done.