Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 98 of 410
Found at i:28791619 original size:40 final size:39
Alignment explanation
Indices: 28791574--28791703 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
28791564 CGGAATACAA
28791574 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* **
28791614 CCGGATAGAATGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
28791654 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGCTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
28791694 CCGGATATAA
1 CCGGATATAA
28791704 TTTCCAGCAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.04
40 72 0.96
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:28802693 original size:42 final size:43
Alignment explanation
Indices: 28802634--28802758 Score: 126
Period size: 43 Copynumber: 2.9 Consensus size: 43
28802624 AATTAAGAAG
* * * * *
28802634 TCTGAACTTGTTGAGTGGTCCGGGTTCGTGATATATGTG-GCA
1 TCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATAGATGCGAGCA
* * *
28802676 TCTGAGCTCGTTGAGTGGTCCGAGTTCATTATGGATGCGAGCA
1 TCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATAGATGCGAGCA
* * * * *
28802719 TCCGAGCTCGTTCAGTGGTCAGAGTTCGTAATGGATGCGA
1 TCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATAGATGCGA
28802759 TACATGTGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 31 0.45
43 38 0.55
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (43 bp):
TCTGAGCTCGTTGAGTGGTCCGAGTTCGTGATAGATGCGAGCA
Found at i:28802729 original size:43 final size:43
Alignment explanation
Indices: 28802673--28802758 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
28802663 GATATATGTG
* * * *
28802673 GCATCTGAGCTCGTTGAGTGGTCCGAGTTCATTATGGATGCGA
1 GCATCCGAGCTCGTTCAGTGGTCAGAGTTCATAATGGATGCGA
*
28802716 GCATCCGAGCTCGTTCAGTGGTCAGAGTTCGTAATGGATGCGA
1 GCATCCGAGCTCGTTCAGTGGTCAGAGTTCATAATGGATGCGA
28802759 TACATGTGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (43 bp):
GCATCCGAGCTCGTTCAGTGGTCAGAGTTCATAATGGATGCGA
Found at i:28806069 original size:46 final size:45
Alignment explanation
Indices: 28805939--28806150 Score: 207
Period size: 46 Copynumber: 4.6 Consensus size: 45
28805929 TGTGAGCTAG
* * * *
28805939 TGTAAGACATGTCTGGGACATGCATCGGCCACATT-ATAAG-AGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGG-C-C-TTGAGACGAAGTCAA
** * * *
28805985 TGTAAGACCATGTCAAGGACATGGCATCGTCATTGAGACG-AGTGCTAC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGAGACGAAGT-C-AA
*
28806033 TAG-AAGACATGTCTGGGACATGCATCGGGCTTGAGACGTAAGTCAA
1 T-GTAAGACATGTCTGGGACATGCATCGGCCTTGAGACG-AAGTCAA
*
28806079 TGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGTCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCTTGAGACG-AAGTCAA
28806125 TGTAAGACATGTCTGGGACATGCATC
1 TGTAAGACATGTCTGGGACATGCATC
28806151 CACTACGAGA
Statistics
Matches: 141, Mismatches: 16, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
45 3 0.02
46 95 0.67
47 27 0.19
48 15 0.11
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTTGAGACGAAGTCAA
Found at i:28806160 original size:46 final size:45
Alignment explanation
Indices: 28806036--28806191 Score: 201
Period size: 46 Copynumber: 3.4 Consensus size: 45
28806026 GTGCTACTAG
* *
28806036 AAGACATGTCTGGGACATGCATCGGGCTTGAGACGTAAGTCAATGT
1 AAGACATGTCTGGGACATGCATC-GCCTCGAGACGTAAGTCAATGT
28806082 AAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGTCAATGT
1 AAGACATGTCTGGGACATGCATC-GCCTCGAGACGTAAGTCAATGT
* **
28806128 AAGACATGTCTGGGACATGCATC-CACTACGAGATGT--GTCTGTGT
1 AAGACATGTCTGGGACATGCATCGC-CT-CGAGACGTAAGTCAATGT
28806172 AAGACCATGTCTGGGACATG
1 AAGA-CATGTCTGGGACATG
28806192 ACATTAGCAC
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
44 11 0.11
45 17 0.17
46 74 0.73
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
AAGACATGTCTGGGACATGCATCGCCTCGAGACGTAAGTCAATGT
Found at i:28807267 original size:21 final size:20
Alignment explanation
Indices: 28807243--28807297 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
28807233 TAATTACACA
28807243 CGGGCGTGTTGCCCTTCCACG
1 CGGGCGTG-TGCCCTTCCACG
*
28807264 CGGGTGTGTGCCCTTCCACG
1 CGGGCGTGTGCCCTTCCACG
28807284 CGGGCGTGTGCCCT
1 CGGGCGTGTGCCCT
28807298 ATAACTAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.04, C:0.36, G:0.36, T:0.24
Consensus pattern (20 bp):
CGGGCGTGTGCCCTTCCACG
Found at i:28814692 original size:45 final size:48
Alignment explanation
Indices: 28814534--28814744 Score: 134
Period size: 46 Copynumber: 4.5 Consensus size: 48
28814524 TGTGTGCCAA
* * ** * *
28814534 TGTAAGA-CATGTCTGGGACATGCATCGGC-CATATTATG-AGAGCCAG
1 TGTAAGACCATGTTTGGGACATGCATCGACACGGA-GATGTAGAGCTAG
* * * * * ** *
28814580 TGTAAGATCATGTCTAGGACATGGCATTGATATTGAGACG-AGAGCTAG
1 TGTAAGACCATGTTTGGGACAT-GCATCGACACGGAGATGTAGAGCTAG
* * * * *
28814628 CGTAAGA-TATGTCTGGGACATGCATCGGCTACGG-GATGT-G-TC-AG
1 TGTAAGACCATGTTTGGGACATGCATCGAC-ACGGAGATGTAGAGCTAG
*
28814672 TGTAAGACCATGTTTGGGACATGGCATCGACACGGATATGTGAGAGCTAG
1 TGTAAGACCATGTTTGGGACAT-GCATCGACACGGAGATGT-AGAGCTAG
28814722 TGTAAGACCATGTTTGGGACATG
1 TGTAAGACCATGTTTGGGACATG
28814745 GTGTCGGCCT
Statistics
Matches: 127, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
44 8 0.06
45 17 0.13
46 27 0.21
47 27 0.21
48 21 0.17
49 3 0.02
50 24 0.19
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTTTGGGACATGCATCGACACGGAGATGTAGAGCTAG
Found at i:28814730 original size:50 final size:48
Alignment explanation
Indices: 28814534--28814845 Score: 172
Period size: 47 Copynumber: 6.6 Consensus size: 48
28814524 TGTGTGCCAA
* * *
28814534 TGTAAGA-CATGTCTGGGACAT-GCATCGGC-CATATTATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACACATA-TGTGAGAGCTAG
* * * * * *
28814580 TGTAAGATCATGTCTAGGACATGGCATTGATA-TTGA-GACGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACACAT-ATG-TGAGAGCTAG
* * * * * *
28814628 CGTAAGA-TATGTCTGGGACAT-GCATCG--GC-TACGGGATGTG-TCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACACATATGTGA-GAGCT-AG
*
28814672 TGTAAGACCATGTTTGGGACATGGCATCGACACGGATATGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACAC--ATATGTGAGAGCTAG
* ** * * * *
28814722 TGTAAGACCATGTTTGGGACATGGTGTCGGCCTCA-ATTTCGATAG-TCAG
1 TGTAAGACCATGTCTGGGACATGGCATC-GACACATATGT-GAGAGCT-AG
* *
28814771 TGTAAG-CCATGTCTGGGACATGGCATC-A-ACTTGATG-GATGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGACACAT-ATGTGA-GAGCTAG
28814817 TGTAAGACCATGTCTGGGACATGGCATCG
1 TGTAAGACCATGTCTGGGACATGGCATCG
28814846 GTATTATACC
Statistics
Matches: 203, Mismatches: 37, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
43 4 0.02
44 12 0.06
45 15 0.07
46 28 0.14
47 48 0.24
48 43 0.21
49 14 0.07
50 30 0.15
51 9 0.04
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGACACATATGTGAGAGCTAG
Found at i:28817416 original size:40 final size:40
Alignment explanation
Indices: 28817356--28817521 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
28817346 TGAATGATAC
* *
28817356 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
28817395 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
28817435 CCGGGCTAAGA-CCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
28817474 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
28817514 CC-GGCTAA
1 CCGGGCTAA
28817522 ATTCGAAGAG
Statistics
Matches: 103, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.01
39 45 0.44
40 55 0.53
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:28817487 original size:79 final size:79
Alignment explanation
Indices: 28817356--28817521 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28817346 TGAATGATAC
* * ** *
28817356 CCGGGCTAAGTCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTCG
1 CCGGGCTAAGACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATT-G
*
28817420 TGCGAGTTGTTATAT
65 TGCGAGTGGTTATAT
* * *
28817435 CCGGGCTAAGACCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATTGT
1 CCGGGCTAAGACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATTGT
**
28817500 GCTTGTGGTTATAT
66 GCGAGTGGTTATAT
28817514 CC-GGCTAA
1 CCGGGCTAA
28817522 ATTCGAAGAG
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
78 6 0.08
79 66 0.88
80 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATTGT
GCGAGTGGTTATAT
Found at i:28825621 original size:40 final size:40
Alignment explanation
Indices: 28825566--28825732 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
28825556 TGAATGATAC
* *
28825566 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
28825606 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
28825646 CCGGGCTAAGA-CCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
28825685 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
28825725 CC-GGCTAA
1 CCGGGCTAA
28825733 ATTCCGAAGA
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 35 0.34
40 66 0.63
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:28825698 original size:79 final size:80
Alignment explanation
Indices: 28825566--28825741 Score: 205
Period size: 79 Copynumber: 2.2 Consensus size: 80
28825556 TGAATGATAC
* * ** *
28825566 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGCTAAGTACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATT-
*
28825630 GTGCGAGTTGTTATAT
65 GTGCGAGTGGTTATAT
* * *
28825646 CCGGGCTAAG-ACCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATTG
1 CCGGGCTAAGTACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATTG
**
28825710 TGCTTGTGGTTATAT
66 TGCGAGTGGTTATAT
* *
28825725 CC-GGCTAAATTCCGAAG
1 CCGGGCTAAGTACCGAAG
28825742 AGACTCGGTT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 6 0.07
79 62 0.77
80 13 0.16
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTACCGAAGGCATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCAATTG
TGCGAGTGGTTATAT
Found at i:28829201 original size:38 final size:41
Alignment explanation
Indices: 28829153--28829399 Score: 184
Period size: 47 Copynumber: 5.7 Consensus size: 41
28829143 ATGTACAACT
*
28829153 GTGGCATATCCACTTAGCACCACGTTAC-AT-T-TTTAATC
1 GTGGTATATCCACTTAGCACCACGTTACAATATATTTAATC
* *
28829191 GTGGTATATCCACTTAGCACCACGTTAGTGAATCAATATATGTAACC
1 GTGGTATATCCACTTAGCACCACG-T--T--A-CAATATATTTAATC
** *
28829238 GTGACATATCCACTTAGCACCACGTTAC---ATGTTTAA-C
1 GTGGTATATCCACTTAGCACCACGTTACAATATATTTAATC
* *
28829275 AGTGCTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAATC
1 -GTGGTATATCCACTTAGCACCACG-T--T--A-CAATATATTTAATC
*
28829323 GTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATC
1 GTGGTATATCCACTTAGCACCACGTTACA---AT--ATAT-T-TAATC
28829371 GTGGTATATCCACTTAGCACCACGTTACA
1 GTGGTATATCCACTTAGCACCACGTTACA
28829400 CGTATAACCA
Statistics
Matches: 167, Mismatches: 15, Indels: 44
0.74 0.07 0.19
Matches are distributed among these distances:
37 1 0.01
38 51 0.31
39 2 0.01
41 5 0.03
42 2 0.01
43 2 0.01
44 6 0.04
45 2 0.01
46 7 0.04
47 55 0.33
48 34 0.20
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (41 bp):
GTGGTATATCCACTTAGCACCACGTTACAATATATTTAATC
Found at i:28829259 original size:85 final size:85
Alignment explanation
Indices: 28829157--28829397 Score: 331
Period size: 85 Copynumber: 2.7 Consensus size: 85
28829147 ACAACTGTGG
*
28829157 CATATCCACTTAGCACCACGTTACATTTTTAATCGTGGTATATCCACTTAGCACCACGTTAGTGA
1 CATATCCACTTAGCACCACGTTACATTTTTAATCGTGGTATATCCACTTAGCACCACGTTAATGA
28829222 ATCAATATATGTAACCGTGA
66 ATCAATATATGTAACCGTGA
* *
28829242 CATATCCACTTAGCACCACGTTACATGTTTAA-CAGTGCTATATCCACTTAGCACCACGTTAATG
1 CATATCCACTTAGCACCACGTTACATTTTTAATC-GTGGTATATCCACTTAGCACCACGTTAATG
* *
28829306 AATCAATATATGTAATCGTGG
65 AATCAATATATGTAACCGTGA
28829327 CATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTATATCCACTTAGCACC
1 CATATCCACTTAGCACCACGTTAC----AT---T-T-T-TAATCGTGGTATATCCACTTAGCACC
28829392 ACGTTA
56 ACGTTA
28829398 CACGTATAAC
Statistics
Matches: 137, Mismatches: 7, Indels: 14
0.87 0.04 0.09
Matches are distributed among these distances:
84 1 0.01
85 102 0.74
89 2 0.01
93 1 0.01
94 1 0.01
95 29 0.21
96 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (85 bp):
CATATCCACTTAGCACCACGTTACATTTTTAATCGTGGTATATCCACTTAGCACCACGTTAATGA
ATCAATATATGTAACCGTGA
Found at i:28829380 original size:48 final size:48
Alignment explanation
Indices: 28829280--28829404 Score: 207
Period size: 48 Copynumber: 2.6 Consensus size: 48
28829270 TTAACAGTGC
*
28829280 TATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAATCGTGG
1 TATATCCACTTAGCACCACGTTACATGTATCAATATATGTAATCGTGG
* *
28829327 CATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGG
1 TATATCCACTTAGCACCACGTTACATGTATCAATATATGTAATCGTGG
*
28829375 TATATCCACTTAGCACCACGTTACACGTAT
1 TATATCCACTTAGCACCACGTTACATGTAT
28829405 AACCATGGTA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
47 22 0.31
48 50 0.69
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (48 bp):
TATATCCACTTAGCACCACGTTACATGTATCAATATATGTAATCGTGG
Found at i:28829399 original size:133 final size:132
Alignment explanation
Indices: 28829186--28829430 Score: 366
Period size: 133 Copynumber: 1.8 Consensus size: 132
28829176 GTTACATTTT
* *
28829186 TAATCGTGGTATATCCACTTAGCACCACGTTAGTGAATCAATATATGTAACCGTGACATATCCAC
1 TAATCGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGACATATCCAC
* * *
28829251 TTAGCACCACGTTACATGTTTAA-CAGTGCTATATCCACTTAGCACCACGTTAATGAATCAATAT
66 TTAGCACCACGTTACACGTATAACCA-TGCTATATCCACTTAACACCACGTTAATGAATCAATAT
28829315 ATG
130 ATG
* * * **
28829318 TAATCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTATATCCA
1 TAATCGTGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGACATATCCA
*
28829383 CTTAGCACCACGTTACACGTATAACCATGGTATATCCACTTAACACCA
65 CTTAGCACCACGTTACACGTATAACCATGCTATATCCACTTAACACCA
28829431 TGTTTTTCCA
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
132 31 0.31
133 67 0.67
134 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (132 bp):
TAATCGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGACATATCCAC
TTAGCACCACGTTACACGTATAACCATGCTATATCCACTTAACACCACGTTAATGAATCAATATA
TG
Found at i:28831720 original size:15 final size:15
Alignment explanation
Indices: 28831682--28831722 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28831672 GAAGCCCAGA
28831682 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* * *
28831697 GTAAAGAAATCCATG
1 ATAAGGAAATCCAAG
28831712 ATAAGGAAATC
1 ATAAGGAAATC
28831723 TCATTTGTAG
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:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:28835022 original size:38 final size:38
Alignment explanation
Indices: 28834970--28835256 Score: 178
Period size: 38 Copynumber: 6.8 Consensus size: 38
28834960 TTAACATGTA
*
28834970 TAACCGTGGCATATCCACTTAGCACCATGTTACATTTT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATTTT
* * * *
28835008 TAAGCGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATG
1 TAACCGTGGCATATCCACTTAGCACCACG-T--T--A-C-AT-T-TT
**
28835055 TAACCGTGGCATATCCACTTAGCACCACGTTACATGGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATTTT
* *
28835093 TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATG
1 TAACCGTGGCATATCCACTTAGCACCACG-T--T--A-C-AT-T-TT
28835140 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTAC----AT---T-T-T
* * ** *
28835187 GTAATCGTGGTATATCCACTTAGCACCACGTTACACGTA
1 -TAACCGTGGCATATCCACTTAGCACCACGTTACATTTT
* *
28835226 TAACCATGGTATATCCACTTAGCACCACGTT
1 TAACCGTGGCATATCCACTTAGCACCACGTT
28835257 TTTCCATTCT
Statistics
Matches: 199, Mismatches: 25, Indels: 50
0.73 0.09 0.18
Matches are distributed among these distances:
38 82 0.41
39 2 0.01
40 3 0.02
41 4 0.02
42 2 0.01
43 2 0.01
44 7 0.04
45 4 0.02
46 7 0.04
47 55 0.28
48 31 0.16
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (38 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATTTT
Found at i:28835085 original size:47 final size:47
Alignment explanation
Indices: 28835012--28835219 Score: 272
Period size: 47 Copynumber: 4.6 Consensus size: 47
28835002 CATTTTTAAG
*
28835012 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* **
28835059 CGTGGCATATCCACTTAGCACCACG-T--T--A-C-AT-GGT-TAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
28835097 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* * * *
28835144 CGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAAT
1 CGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAAC
28835192 CGTGGTATATCCACTTAGCACCACGTTA
1 CGTGGTATATCCACTTAGCACCACGTTA
28835220 CACGTATAAC
Statistics
Matches: 139, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
38 28 0.20
39 2 0.01
40 2 0.01
41 2 0.01
42 1 0.01
43 1 0.01
44 2 0.01
45 2 0.01
46 2 0.01
47 54 0.39
48 43 0.31
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (47 bp):
CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
Found at i:28835113 original size:85 final size:85
Alignment explanation
Indices: 28834970--28835175 Score: 367
Period size: 85 Copynumber: 2.4 Consensus size: 85
28834960 TTAACATGTA
* ** * *
28834970 TAACCGTGGCATATCCACTTAGCACCATGTTACATTTTTAAGCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGGTTAACCGTGGTATATCCACTTAGCACCA
28835035 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
28835055 TAACCGTGGCATATCCACTTAGCACCACGTTACATGGTTAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGGTTAACCGTGGTATATCCACTTAGCACCA
28835120 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
28835140 TAACCGTGGCATATCCACTTAGCACCACGTTACATG
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATG
28835176 TATCAATATG
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 116 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGGTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATATG
Found at i:28835202 original size:48 final size:48
Alignment explanation
Indices: 28835093--28835226 Score: 216
Period size: 48 Copynumber: 2.8 Consensus size: 48
28835083 GTTACATGGT
*
28835093 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
28835140 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
* *
28835188 TAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
28835227 AACCATGGTA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 31 0.39
48 49 0.61
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATATG
Found at i:28835210 original size:133 final size:132
Alignment explanation
Indices: 28835012--28835256 Score: 393
Period size: 133 Copynumber: 1.8 Consensus size: 132
28835002 CATTTTTAAG
* *
28835012 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
* *
28835077 CACCACGTTACATGGT-TAACCGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGT
66 CACCACGTTACA-CGTATAACCATGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGT
28835141 AAC
130 AAC
* * * *
28835144 CGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTATATCCACTTA
1 CGTGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCACTTA
28835209 GCACCACGTTACACGTATAACCATGGTATATCCACTTAGCACCACGTT
65 GCACCACGTTACACGTATAACCATGGTATATCCACTTAGCACCACGTT
28835257 TTTCCATTCT
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
132 28 0.27
133 75 0.73
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (132 bp):
CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
CACCACGTTACACGTATAACCATGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTA
AC
Found at i:28841293 original size:40 final size:40
Alignment explanation
Indices: 28841248--28841435 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
28841238 ATAACCACAA
* *
28841248 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
28841288 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
28841328 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
28841368 GCACAAATGCCTTCGGGTCTTAACCCAGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
28841408 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
28841436 GTATCATTCA
Statistics
Matches: 134, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 132 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:28841333 original size:80 final size:79
Alignment explanation
Indices: 28841228--28841439 Score: 309
Period size: 80 Copynumber: 2.7 Consensus size: 79
28841218 TCTTCGGAAT
* *
28841228 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
28841292 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
28841307 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
28841372 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * * *
28841387 TTAACCCAGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
28841440 CATTCAATTG
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 5 0.04
80 113 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:28845034 original size:40 final size:40
Alignment explanation
Indices: 28844907--28845036 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
28844897 ATGCTGGAAA
* *
28844907 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
28844947 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28844987 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28845027 TTATATCCGG
1 TTATATCCGG
28845037 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28847958 original size:40 final size:40
Alignment explanation
Indices: 28847913--28848042 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28847903 CGGAATACAA
28847913 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
28847953 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
28847993 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
28848033 CCGGATATAA
1 CCGGATATAA
28848043 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:28848057 original size:40 final size:40
Alignment explanation
Indices: 28847913--28848076 Score: 145
Period size: 40 Copynumber: 4.1 Consensus size: 40
28847903 CGGAATACAA
* **
28847913 CCGGATATAACCACGTGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCAC-AATTGCCTTCGGGTCTTAGC
* *
28847953 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
28847993 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * * *
28848033 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
28848073 CCGG
1 CCGG
28848077 GTATCATTCA
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
39 2 0.02
40 98 0.98
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:28852716 original size:39 final size:40
Alignment explanation
Indices: 28852575--28852781 Score: 213
Period size: 40 Copynumber: 5.2 Consensus size: 40
28852565 CAATTGAATG
* * ** * **
28852575 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * *
28852615 ATATCCGGGTTAAGACCCGAAGGCCATT-GTGCTAGT-GACT
1 ATATCCGGGCTAAGACCCGAAGG-CATTCGTGCAAGTCG-TT
* *
28852655 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * *
28852695 AAATCC-GGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
* * *
28852734 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
28852774 ATATCCGG
1 ATATCCGG
28852782 TTGTATTCCG
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.27
40 98 0.70
41 5 0.04
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTT
Found at i:28859235 original size:40 final size:40
Alignment explanation
Indices: 28859184--28859371 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
28859174 ATAACCACAA
* * *
28859184 GCACAATTGCCTTCGGGTTTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* * *
28859224 CCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
*
28859264 GCACAAATGCCTTCGGGTCTTAACCTGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
28859304 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
28859344 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
28859372 GTATCATTCA
Statistics
Matches: 131, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 129 0.98
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:28859268 original size:80 final size:79
Alignment explanation
Indices: 28859164--28859375 Score: 291
Period size: 80 Copynumber: 2.7 Consensus size: 79
28859154 TCTTCGGAAT
* * *
28859164 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTTTTAACCCGGGTATAGCAACTCCCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCCCAC
28859228 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
28859243 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCTGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCCCAC
28859308 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
28859323 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
28859376 CATTCAATTG
Statistics
Matches: 116, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 5 0.04
80 110 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCCCACA
AATGCCTTCGGGTC
Found at i:28861956 original size:40 final size:40
Alignment explanation
Indices: 28861901--28862052 Score: 227
Period size: 40 Copynumber: 3.8 Consensus size: 40
28861891 ATTGAGAGTT
*
28861901 ATATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
28861941 ATATATCTGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* *
28861981 TTATATCCAGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
28862021 ATATATCCGGGCTAA-ACCTCGAAG-GCATTCGT
1 ATATATCCGGGCTAAGTCC-CGAAGAGCATTCGT
28862053 ACTGGAATTA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 10 0.10
40 93 0.90
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Found at i:28862107 original size:28 final size:28
Alignment explanation
Indices: 28862067--28862223 Score: 113
Period size: 28 Copynumber: 5.5 Consensus size: 28
28862057 GAATTATAAG
* * *
28862067 GCACTGTGTGTGCAAGCTCTTCAACCGA
1 GCACTATGTGTGCAAGATCTTCAATCGA
* * * *
28862095 GCACTATGTGTGCCAGATCAGT-AGTTGA
1 GCACTATGTGTGCAAGATC-TTCAATCGA
* *
28862123 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCAAGATCTTCAATCGA
* *
28862152 GCACTATGTGTGCGAGAT-TGGT-AATTGA
1 GCACTATGTGTGCAAGATCT--TCAATCGA
* * * *
28862180 GGCACTATGTGTGCGAGTTCTTTAATCAA
1 -GCACTATGTGTGCAAGATCTTCAATCGA
28862209 GCACTATGTGTGCAA
1 GCACTATGTGTGCAA
28862224 AATCAGTCAG
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
27 1 0.01
28 57 0.55
29 44 0.43
30 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTATGTGTGCAAGATCTTCAATCGA
Found at i:28862153 original size:57 final size:57
Alignment explanation
Indices: 28862065--28862230 Score: 224
Period size: 57 Copynumber: 2.9 Consensus size: 57
28862055 TGGAATTATA
* * * * * *
28862065 AGGCACTGTGTGTGCAAGCTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGTTG
1 AGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCAAGATCAGTAATTG
* **
28862122 AGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAATTG
1 AGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCAAGATCAGTAATTG
* * *
28862179 AGGCACTATGTGTGCGAGTTCTTTAATCAAGCACTATGTGTGCAAAATCAGT
1 AGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCAAGATCAGT
28862231 CAGTGGGCAC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 95 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (57 bp):
AGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCAAGATCAGTAATTG
Found at i:28862205 original size:29 final size:29
Alignment explanation
Indices: 28862095--28862221 Score: 127
Period size: 29 Copynumber: 4.4 Consensus size: 29
28862085 CTTCAACCGA
* * * *
28862095 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGTTCTGTAATTGAG
*
28862124 GCACTATGTGTGCGAGTTCT-TCAATCGA-
1 GCACTATGTGTGCGAGTTCTGT-AATTGAG
*
28862152 GCACTATGTGTGCGAGATT-GGTAATTGAG
1 GCACTATGTGTGCGAG-TTCTGTAATTGAG
* * *
28862181 GCACTATGTGTGCGAGTTCTTTAA-TCAA
1 GCACTATGTGTGCGAGTTCTGTAATTGAG
28862209 GCACTATGTGTGC
1 GCACTATGTGTGC
28862222 AAAATCAGTC
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
28 39 0.48
29 43 0.52
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (29 bp):
GCACTATGTGTGCGAGTTCTGTAATTGAG
Found at i:28868315 original size:29 final size:27
Alignment explanation
Indices: 28868281--28868383 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
28868271 TACTCAATCA
*
28868281 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
28868310 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
28868339 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
28868368 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
28868384 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:28880291 original size:7 final size:7
Alignment explanation
Indices: 28880279--28880304 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28880269 AGACCTCATA
28880279 TCATCCC
1 TCATCCC
28880286 TCATCCC
1 TCATCCC
28880293 TCATCCC
1 TCATCCC
28880300 TCATC
1 TCATC
28880305 ATTCTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:28882769 original size:7 final size:7
Alignment explanation
Indices: 28882754--28882794 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
28882744 CTTCAACATT
*
28882754 ACATCTC
1 ACATATC
*
28882761 ACATGTC
1 ACATATC
*
28882768 ACATCTC
1 ACATATC
28882775 ACATATC
1 ACATATC
28882782 ACATATC
1 ACATATC
28882789 ACATAT
1 ACATAT
28882795 ATGGTGGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (7 bp):
ACATATC
Found at i:28882773 original size:14 final size:14
Alignment explanation
Indices: 28882754--28882794 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
28882744 CTTCAACATT
*
28882754 ACATCTCACATGTC
1 ACATCTCACATATC
28882768 ACATCTCACATATC
1 ACATCTCACATATC
*
28882782 ACATATCACATAT
1 ACATCTCACATAT
28882795 ATGGTGGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (14 bp):
ACATCTCACATATC
Found at i:28886314 original size:13 final size:13
Alignment explanation
Indices: 28886296--28886327 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
28886286 AAATAATTCA
28886296 ACACGGGCGAGGG
1 ACACGGGCGAGGG
28886309 ACACGGGCGAGGG
1 ACACGGGCGAGGG
28886322 ACACGG
1 ACACGG
28886328 ACGTGTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (13 bp):
ACACGGGCGAGGG
Found at i:28886775 original size:17 final size:17
Alignment explanation
Indices: 28886753--28886792 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28886743 CCTAAAGTTT
28886753 GCCAAAACTTGAAATTC
1 GCCAAAACTTGAAATTC
* *
28886770 GTCAAAACTTGGAATTC
1 GCCAAAACTTGAAATTC
28886787 GCCAAA
1 GCCAAA
28886793 TGACGAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (17 bp):
GCCAAAACTTGAAATTC
Found at i:28888109 original size:24 final size:22
Alignment explanation
Indices: 28888073--28888120 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
28888063 TAACATTCTC
28888073 AATATTTTGAAAATATTTTAAATT
1 AATATTTTG-AAA-ATTTTAAATT
28888097 AATATGTTT-AAAATTTTAAATT
1 AATAT-TTTGAAAATTTTAAATT
28888119 AA
1 AA
28888121 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 5 0.22
25 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AATATTTTGAAAATTTTAAATT
Found at i:28888481 original size:21 final size:22
Alignment explanation
Indices: 28888433--28888483 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
28888423 TATAAACATT
*
28888433 ATAATTATTTAAAAAATAATAAA
1 ATAATTA-TTAAAAAATAACAAA
* *
28888456 CTAATTA-TAAAAAATTACAAA
1 ATAATTATTAAAAAATAACAAA
28888477 ATAATTA
1 ATAATTA
28888484 AATATGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
23 6 0.25
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATTATTAAAAAATAACAAA
Found at i:28892575 original size:29 final size:29
Alignment explanation
Indices: 28892515--28892579 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
28892505 TACTAAATAA
* *
28892515 TTTTTATTTTATTTTTAATCATATTTACT
1 TTTTTATTTTAATTTTAATCATAATTACT
*
28892544 TTTTTATTTTCAATTTTAAT-ATAATT-GT
1 TTTTTATTTT-AATTTTAATCATAATTACT
28892572 TTTTTATT
1 TTTTTATT
28892580 ATATTTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.28
29 15 0.47
30 8 0.25
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTTTATTTTAATTTTAATCATAATTACT
Found at i:28900621 original size:15 final size:14
Alignment explanation
Indices: 28900565--28900681 Score: 62
Period size: 15 Copynumber: 8.1 Consensus size: 14
28900555 TTATTATGTT
*
28900565 TCTATTTATATTTA
1 TCTATTTTTATTTA
*
28900579 T-T-TTGTTATTCTAA
1 TCTATTTTTATT-T-A
*
28900593 TACTATTATTATTTA
1 T-CTATTTTTATTTA
28900608 TCTAATTTTTATTTA
1 TCT-ATTTTTATTTA
* *
28900623 TCTATTTATATTTC
1 TCTATTTTTATTTA
*
28900637 TACTATTATTATATT-
1 T-CTATTTTTAT-TTA
28900652 TCTATTTATTATATT-
1 TCTATTT-TTAT-TTA
* *
28900667 TTTATTTCTATTTA
1 TCTATTTTTATTTA
28900681 T
1 T
28900682 ATACTAATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
12 6 0.07
13 4 0.05
14 24 0.29
15 37 0.45
16 4 0.05
17 7 0.09
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (14 bp):
TCTATTTTTATTTA
Found at i:28900634 original size:29 final size:28
Alignment explanation
Indices: 28900553--28900660 Score: 82
Period size: 29 Copynumber: 3.8 Consensus size: 28
28900543 TTATTGCTAT
28900553 TATTATTATGTT-TCTATTTATATTTAT-
1 TATTATTAT-TTATCTATTTATATTTATC
*
28900580 T-TTGTTATTCTAATACTA-TTATTATTTATC
1 TATTATTATT-T-AT-CTATTTA-TATTTATC
* *
28900610 TAATTTTTATTTATCTATTTATATTTCTAC
1 T-ATTATTATTTATCTATTTATATTTAT-C
28900640 TATTATTATATT-TCTATTTAT
1 TATTATTAT-TTATCTATTTAT
28900661 TATATTTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
25 1 0.02
26 7 0.11
27 1 0.02
28 4 0.06
29 35 0.53
30 10 0.15
31 1 0.02
32 7 0.11
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTATTATTTATCTATTTATATTTATC
Found at i:28900650 original size:17 final size:15
Alignment explanation
Indices: 28900628--28900673 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
28900618 ATTTATCTAT
28900628 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
28900645 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
28900660 TTATATTTTTATTT
1 TTATATTTCTATTT
28900674 CTATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:28900865 original size:49 final size:48
Alignment explanation
Indices: 28900812--28900934 Score: 117
Period size: 51 Copynumber: 2.5 Consensus size: 48
28900802 TATAACGCTC
28900812 ATTTCAAATTTTTATACATTATTTACTTT-AATAT-TTTCATATATTATGT
1 ATTTCAAATTTTTATACATTATTTACTTTGAAT-TGTTT-ATATATTAT-T
* * *
28900861 ATTTCAAACTTTTTTACACATTATATATTTTGAATTGTTTATATATTATT
1 ATTTCAAA--TTTTTATACATTATTTACTTTGAATTGTTTATATATTATT
* * *
28900911 -TTTAAAGAGTTTTATATATTATTT
1 ATTTCAA-ATTTTTATACATTATTT
28900935 TATCTTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
48 12 0.20
49 13 0.21
50 2 0.03
51 28 0.46
52 6 0.10
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (48 bp):
ATTTCAAATTTTTATACATTATTTACTTTGAATTGTTTATATATTATT
Found at i:28900873 original size:25 final size:24
Alignment explanation
Indices: 28900812--28900873 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
28900802 TATAACGCTC
* *
28900812 ATTTCAAATTTTTATACATTATTT
1 ATTTCAAATTTTCATACATTATGT
*
28900836 ACTTT-AATATTTTCATATATTATGT
1 A-TTTCAA-ATTTTCATACATTATGT
28900861 ATTTCAAACTTTT
1 ATTTCAAA-TTTT
28900874 TTACACATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTCAAATTTTCATACATTATGT
Found at i:28900875 original size:51 final size:49
Alignment explanation
Indices: 28900812--28900909 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 49
28900802 TATAACGCTC
* *
28900812 ATTTCAAATTTTTATACATTATTTACTTT-AATAT-TTTCATATATTATGT
1 ATTTCAAATTTTTACACATTATATACTTTGAAT-TGTTT-ATATATTATGT
*
28900861 ATTTCAAACTTTTTTACACATTATATATTTTGAATTGTTTATATATTAT
1 ATTTCAAA--TTTTTACACATTATATACTTTGAATTGTTTATATATTAT
28900910 TTTTAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 8 0.19
51 28 0.67
52 6 0.14
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (49 bp):
ATTTCAAATTTTTACACATTATATACTTTGAATTGTTTATATATTATGT
Found at i:28906399 original size:18 final size:18
Alignment explanation
Indices: 28906376--28906411 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28906366 CCAATAAAGG
28906376 CATGTAAAAATATGTTTA
1 CATGTAAAAATATGTTTA
28906394 CATGTAAAAATATGTTTA
1 CATGTAAAAATATGTTTA
28906412 TCTCTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
CATGTAAAAATATGTTTA
Found at i:28913826 original size:44 final size:44
Alignment explanation
Indices: 28913770--28914179 Score: 203
Period size: 44 Copynumber: 9.3 Consensus size: 44
28913760 CTCGGCTAGC
28913770 CTTATC-CTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
1 CTTATCTC-CCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
** * * * *
28913814 CTTATCTCCCTAAGCAGTAGTGG-AGTA-GATCAAAGACTGT-GAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAAACAGGCTGAAA-A-T-TACAGAT
*
28913858 CTTATC-CTCCTAAGCAGTAGGGAAACAGGCTGATAATTACAGAT
1 CTTATCTC-CCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
* * ** * *
28913902 CTTATCTCCCTAAGCAGTAGAGG-AGCA-GATCGAAGACGGT-GAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAAACAGGCT-GAA-A-ATTACAGAT
* *
28913946 CTTATC-CTCCTAAACAGTAGGAAAACAGGCTGAAAATTACAGAT
1 CTTATCTC-CCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
* * * *
28913990 CTTATCTCCCTAAGCAGTAGTGG-AGCA-GATCGAAGATGGT-GAG-T
1 CTTATCTCCCTAAGCAGTAG-GGAAACAGGCT-GAAAAT--TACAGAT
***
28914034 CTTATC-CCACTAAGCAGTAGGGAAACAAATTGAAAATTACAGAT
1 CTTATCTCC-CTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
* * * ** * *
28914078 CTTATCTCCCTAAGAAGTAGTGG-AGCAGAAC-GAAGACGGT-GAG-C
1 CTTATCTCCCTAAGCAGTAG-GGAAACAG-GCTGAA-A-ATTACAGAT
* * *
28914122 CTTATCCCCCTAAGCAGTAGGTAAACAGGCTGAAAATTACAAAT
1 CTTATCTCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
*
28914166 TTTATCTCCCTAAG
1 CTTATCTCCCTAAG
28914180 TAATAGTGGA
Statistics
Matches: 268, Mismatches: 59, Indels: 78
0.66 0.15 0.19
Matches are distributed among these distances:
42 4 0.01
43 30 0.11
44 199 0.74
45 31 0.12
46 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGAT
Found at i:28913916 original size:88 final size:88
Alignment explanation
Indices: 28913767--28914253 Score: 724
Period size: 88 Copynumber: 5.5 Consensus size: 88
28913757 AAACTCGGCT
28913767 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
* * *
28913832 AGTGGAGTAGATCAAAGACTGTG
66 AGTGGAGCAGATCGAAGACGGTG
*
28913855 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGATAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
28913920 AGAGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *
28913943 AGCCTTATCCTCCTAAACAGTAGGAAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
*
28914008 AGTGGAGCAGATCGAAGATGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* *** *
28914031 AGTCTTATCC-CACTAAGCAGTAGGGAAACAAATTGAAAATTACAGATCTTATCTCCCTAAGAAG
1 AGCCTTATCCTC-CTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAG
*
28914095 TAGTGGAGCAGAACGAAGACGGTG
65 TAGTGGAGCAGATCGAAGACGGTG
* * * * * *
28914119 AGCCTTATCCCCCTAAGCAGTAGGTAAACAGGCTGAAAATTACAAATTTTATCTCCCTAAGTAAT
1 AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
28914184 AGTGGAGCAGATCGAAGACGGTG
66 AGTGGAGCAGATCGAAGACGGTG
* * * * *
28914207 AGCCCTATCCCCCTAAGCAGTAAGGAAAACGGGCTGAAAATGACAGA
1 AGCCTTATCCTCCTAAGCAGT-AGGGAAACAGGCTGAAAATTACAGA
28914254 CCACCGTAGT
Statistics
Matches: 362, Mismatches: 34, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 339 0.94
89 22 0.06
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (88 bp):
AGCCTTATCCTCCTAAGCAGTAGGGAAACAGGCTGAAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGTG
Found at i:28915764 original size:3 final size:3
Alignment explanation
Indices: 28915756--28915990 Score: 131
Period size: 3 Copynumber: 78.3 Consensus size: 3
28915746 TTAATTAATT
28915756 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * * *
28915804 TTA TT- TTC CTC TTC TAAA TTT TTA TTA TTA GTG TTA TT- TCA TAA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
28915848 TTA TTA GATA TTA CTA TATA TTCA TTA TT- TTT TTA -TA CTC TTT TTA
1 TTA TTA -TTA TTA TTA T-TA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
28915894 TTA ATA TTA TTA CTA CTA TTA TTT TTT TTA -TA CTA TGA TTA -TA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * **
28915941 CTTT TTC TGG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28915987 TTA T
1 TTA T
28915991 ATTTTCTCTT
Statistics
Matches: 182, Mismatches: 39, Indels: 22
0.75 0.16 0.09
Matches are distributed among these distances:
2 11 0.06
3 158 0.87
4 13 0.07
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28920182 original size:24 final size:25
Alignment explanation
Indices: 28920155--28920203 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28920145 TATTTTTTAT
*
28920155 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
28920179 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
28920204 AACAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:28921088 original size:17 final size:17
Alignment explanation
Indices: 28921068--28921100 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28921058 ATTATTTTAA
28921068 TATT-TATATTATAGTAG
1 TATTATATATT-TAGTAG
28921085 TATTATATATTTAGTA
1 TATTATATATTTAGTA
28921101 TAGGTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTATATATTTAGTAG
Found at i:28922492 original size:39 final size:39
Alignment explanation
Indices: 28922438--28922512 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
28922428 GATGCATAAC
* *
28922438 AAGACTATTCTAATTATTAGCATTATAGTATCAGATTAT
1 AAGACCATTCTAATTATTAGCATTAGAGTATCAGATTAT
28922477 AAGACCATTCTAATTATTAGCATTAGAGTATCAGAT
1 AAGACCATTCTAATTATTAGCATTAGAGTATCAGAT
28922513 CATACTCTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (39 bp):
AAGACCATTCTAATTATTAGCATTAGAGTATCAGATTAT
Found at i:28933305 original size:53 final size:53
Alignment explanation
Indices: 28933125--28933331 Score: 218
Period size: 53 Copynumber: 3.8 Consensus size: 53
28933115 ATTAGGGTTT
* * * * * *
28933125 AAGGATAACAAGTAAGACCATGCCAAGGCATGGCAGTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * *
28933179 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACAATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* *
28933234 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* *
28933287 AAGGATACCATGTAAGACCATGTCAAGACATTGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
28933332 TAAAAAGGAA
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
52 4 0.03
53 43 0.34
54 38 0.30
55 36 0.29
56 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:28937641 original size:29 final size:28
Alignment explanation
Indices: 28937608--28937700 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
28937598 GTGACGAGAT
*
28937608 TGGCACTAAGTGTGCCTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAA-ATA
28937637 TGGCACTAAGTGTGCATGCTGGAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAATA
* * *
28937665 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGG-AAAATA
*
28937694 CGGCACT
1 TGGCACT
28937701 GGGTGTGCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 22 0.39
29 35 0.61
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (28 bp):
TGGCACTAAGTGTGCATGCTGGAAAATA
Found at i:28937677 original size:28 final size:28
Alignment explanation
Indices: 28937611--28937690 Score: 115
Period size: 28 Copynumber: 2.8 Consensus size: 28
28937601 ACGAGATTGG
* *
28937611 CACTAAGTGTGCCTGCTGGAAATATATGG
1 CACTAAGTGTGCATGCTGGAAA-ATATGA
28937640 CACTAAGTGTGCATGCTGGAAAATATGA
1 CACTAAGTGTGCATGCTGGAAAATATGA
* *
28937668 CACTATGTGTGCAAGCTGGAAAA
1 CACTAAGTGTGCATGCTGGAAAA
28937691 ATACGGCACT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 26 0.55
29 21 0.45
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (28 bp):
CACTAAGTGTGCATGCTGGAAAATATGA
Found at i:28939468 original size:141 final size:139
Alignment explanation
Indices: 28939273--28939534 Score: 332
Period size: 141 Copynumber: 1.9 Consensus size: 139
28939263 ATATTTAAGC
* * * *
28939273 CAGTGTAAGACATGTCTGGGGCATGCATCGCATTGAGACGAGAGCTAGCGTAAGACATGTCTGGG
1 CAGTGTAAGACATATCTGGGACATGCATCGCACTGAGACGAGAGCCAGCGTAAGACATGTCTGGG
*
28939338 ACATG-CATCGGCCTCACGATATACAAGCTAGTGTAAGACCTAT-T-TGGGACATGGCGTCAGCT
66 ACATGACATCGGCCTCACGATATACAAGCCAGTGTAAGA-CTATGTCTGGGACATGGCGTCAGCT
28939400 TGTGGTGTGT
130 TGTGGTGTGT
* * * *
28939410 CAGTGTAAGACCTATCTGGGACATGGCATCGACACTGATAGACGAGAGCCAGTGTAAGACCTGTT
1 CAGTGTAAGACATATCTGGGACAT-GCATCG-CACTG--AGACGAGAGCCAGCGTAAGACATGTC
* * * **
28939475 TGGGACATGACATTGGCCTCGCTATATGGAAGCCAGTGTAAGACTATGTCTGGGACATGG
62 TGGGACATGACATCGGCCTCACGATATACAAGCCAGTGTAAGACTATGTCTGGGACATGG
28939535 TGTCGGCATC
Statistics
Matches: 104, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
137 21 0.20
138 6 0.06
139 4 0.04
141 35 0.34
142 28 0.27
143 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (139 bp):
CAGTGTAAGACATATCTGGGACATGCATCGCACTGAGACGAGAGCCAGCGTAAGACATGTCTGGG
ACATGACATCGGCCTCACGATATACAAGCCAGTGTAAGACTATGTCTGGGACATGGCGTCAGCTT
GTGGTGTGT
Found at i:28946358 original size:13 final size:13
Alignment explanation
Indices: 28946340--28946369 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28946330 TACACGCCCG
28946340 TGTCTCCAGGCCA
1 TGTCTCCAGGCCA
*
28946353 TGTCTCCAGGCCG
1 TGTCTCCAGGCCA
28946366 TGTC
1 TGTC
28946370 CCTCACACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (13 bp):
TGTCTCCAGGCCA
Found at i:28949231 original size:40 final size:40
Alignment explanation
Indices: 28949172--28949313 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
28949162 GAAATGAATG
* * *
28949172 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
28949212 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
28949252 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
28949292 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
28949314 GCATTTGTGC
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 3 0.04
40 82 0.96
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:28949271 original size:80 final size:80
Alignment explanation
Indices: 28949172--28949323 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
28949162 GAAATGAATG
* *
28949172 ATATCCGGGCTAAGCCCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGTTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGAC-ATTCATGC-GAGAAATTATATCCGGGCTAAGACCCGAAGG
28949235 CAATTGTGCTAGCGGCT
64 CAATTGTGCTAGCGGCT
* * ** *
28949252 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCA
*
28949317 TTTGTGC
66 ATTGTGC
28949324 ACATGCTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 4 0.06
80 58 0.94
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.22
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACATTCATGCGAGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGCGGCT
Found at i:28949337 original size:40 final size:39
Alignment explanation
Indices: 28949210--28949339 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
28949200 ATGCTGGAAA
* * *
28949210 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-A-CAGC
* *
28949251 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAG-C
*
28949289 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACA-GC
28949330 TTATATCCGG
1 TTATATCCGG
28949340 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAGC
Found at i:28951436 original size:86 final size:84
Alignment explanation
Indices: 28951289--28951457 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 84
28951279 CAGAAAGCAT
* * *
28951289 ATACAATGCCAACGTCCTAGACGTGTCTTACATGTAATCAAACATCGATGCCACTGTCCCAGACA
1 ATACAATGCCAACGTCCTAGACATGTCTTACACGTAAACAAACATCGATGCCACTGTCCCAGAC-
28951354 G-GGTCTTACACGAAATCAG
65 GTGGTCTTACACGAAATCAG
* *
28951373 ATACGATGCCAATGTCCTAGACATGGTCTTACACGTAAAACAAA-AGTCGATGCCAAC-GTCCCA
1 ATACAATGCCAACGTCCTAGACAT-GTCTTACACGT-AAACAAACA-TCGATGCC-ACTGTCCCA
*
28951436 GACGTGGTCTTACACGATATCA
62 GACGTGGTCTTACACGAAATCA
28951458 CATATAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
84 21 0.28
85 12 0.16
86 39 0.53
87 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (84 bp):
ATACAATGCCAACGTCCTAGACATGTCTTACACGTAAACAAACATCGATGCCACTGTCCCAGACG
TGGTCTTACACGAAATCAG
Found at i:28951444 original size:44 final size:43
Alignment explanation
Indices: 28951294--28951451 Score: 166
Period size: 42 Copynumber: 3.7 Consensus size: 43
28951284 AGCATATACA
* *
28951294 ATGCCAACGTCCTAGACGT-GTCTTACATGT-AATCAAACATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAA-ATCG
*
28951336 ATGCC-ACTGTCCCAGACAG-GGTCTTACACG-AAATC-AGATACG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCAAAAT-CG
* * * *
28951378 ATGCCAATGTCCTAGACATGGTCTTACACGTAAAACAAAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAAA-TCG
28951422 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
28951452 ATATCACATA
Statistics
Matches: 95, Mismatches: 11, Indels: 18
0.77 0.09 0.15
Matches are distributed among these distances:
41 4 0.04
42 40 0.42
43 19 0.20
44 31 0.33
45 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCAAAATCG
Found at i:28955162 original size:37 final size:36
Alignment explanation
Indices: 28955112--28955198 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
28955102 TACGAAGTCT
28955112 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
28955148 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
28955185 TCACCCGGAACATA
1 T-ACCCGG-ACATA
28955199 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:28955337 original size:49 final size:49
Alignment explanation
Indices: 28955267--28955569 Score: 417
Period size: 49 Copynumber: 6.4 Consensus size: 49
28955257 TTTACCACAT
* *
28955267 ATATATATACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
28955316 ATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
28955365 ATATACATATACTTTCACATTCATCCCATCGGCCATTAGGCCTTATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* * * *
28955414 ATATACATACATTTTCGCATTCATCGCATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
28955463 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCC-T-T-AC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
28955509 --ATACAT----TTTCACATTCATCACATCGGCCATTAGGCCTCATCAC
1 ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
28955552 ATATATATACATTTTCAC
1 ATATACATACACTTTCAC
28955570 GAATCTTGAT
Statistics
Matches: 227, Mismatches: 18, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
40 30 0.13
42 1 0.00
43 2 0.01
44 5 0.02
45 5 0.02
46 2 0.01
47 1 0.00
49 181 0.80
ACGTcount: A:0.30, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
ATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:28955521 original size:40 final size:40
Alignment explanation
Indices: 28955469--28955545 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
28955459 TCACATATAT
28955469 ATACATTTTCACATTCATCACATCGGCCATTAGGCCTTAC
1 ATACATTTTCACATTCATCACATCGGCCATTAGGCCTTAC
28955509 ATACATTTTCACATTCATCACATCGGCCATTAGGCCT
1 ATACATTTTCACATTCATCACATCGGCCATTAGGCCT
28955546 CATCACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.32
Consensus pattern (40 bp):
ATACATTTTCACATTCATCACATCGGCCATTAGGCCTTAC
Found at i:28958348 original size:93 final size:93
Alignment explanation
Indices: 28958236--28958406 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
28958226 GCCCATAAGT
* *
28958236 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28958301 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
28958329 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28958394 CGAGTTCGGATGC
66 CGAGTTCGGATGC
28958407 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28958422 original size:46 final size:46
Alignment explanation
Indices: 28958228--28958408 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
28958218 TGTAACCCGC
* * *
28958228 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
28958274 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
28958324 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
28958367 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
28958409 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:28960826 original size:30 final size:30
Alignment explanation
Indices: 28960782--28960870 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
28960772 CAAAGATAAC
28960782 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
28960811 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
28960841 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
28960871 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:28960830 original size:15 final size:15
Alignment explanation
Indices: 28960782--28960861 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
28960772 CAAAGATAAC
*
28960782 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28960796 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28960811 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
28960826 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28960841 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28960856 AAGAAA
1 AAGAAA
28960862 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28960870 original size:15 final size:15
Alignment explanation
Indices: 28960793--28960870 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
28960783 AGAAAACCGA
28960793 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
28960808 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
28960822 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
28960837 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28960853 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28960868 ATA
1 ATA
28960871 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28963924 original size:93 final size:93
Alignment explanation
Indices: 28963812--28963983 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28963802 GCCCATAAGT
* *
28963812 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28963877 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
28963905 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28963970 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
28963984 CATCCTAGTG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:28963979 original size:46 final size:46
Alignment explanation
Indices: 28963804--28963979 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
28963794 TGTAACCCGC
* * *
28963804 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
28963850 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
28963900 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
28963943 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28963980 TGCCCATCCT
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:28966910 original size:46 final size:46
Alignment explanation
Indices: 28966855--28967000 Score: 115
Period size: 46 Copynumber: 3.2 Consensus size: 46
28966845 GTTTGTATTT
*
28966855 TTTTATATATATAAATTTAATATAGTTGTTTAGGATTTAAGGTATCA
1 TTTT-TATATATAAATTTAATATAGTTGTTTAGGATTTAATGTATCA
* *** * * * *
28966902 TTTTTATATTTTCGTGT-AT-TAATT-TCTTAGAATATT--TGTAT-T
1 TTTTTATATATAAATTTAATATAGTTGT-TTAGGAT-TTAATGTATCA
*
28966944 TTTTTATATATGTAAATTTAATATAGTTGTTTAGGATTTAATGTTTCA
1 TTTTTATATA--TAAATTTAATATAGTTGTTTAGGATTTAATGTATCA
28966992 TTTTTATAT
1 TTTTTATAT
28967001 TTTCATGTAT
Statistics
Matches: 71, Mismatches: 18, Indels: 19
0.66 0.17 0.18
Matches are distributed among these distances:
42 9 0.13
43 5 0.07
44 13 0.18
45 8 0.11
46 18 0.25
47 9 0.13
48 9 0.13
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (46 bp):
TTTTTATATATAAATTTAATATAGTTGTTTAGGATTTAATGTATCA
Found at i:28966965 original size:41 final size:40
Alignment explanation
Indices: 28966920--28967057 Score: 91
Period size: 48 Copynumber: 3.2 Consensus size: 40
28966910 TTTTCGTGTA
28966920 TTAATTTCTTAGAATATTTGTATTTTTTTATATATGTAAAT
1 TTAATTTCTTAGAATATTTGTATTTTTTTATAT-TGTAAAT
* * * **
28966961 TTAATATAGTTGTTTAGGAT-TTAATGT-TTCATTTTTATATTTTCATGT
1 TT-A-AT--TT-CTTAGAATATT--TGTATT--TTTTTATATTGT-AAAT
*
28967009 ATTAATTTCTTAGAATATTTGTATTTTTTTGTATCTGTAAAT
1 -TTAATTTCTTAGAATATTTGTATTTTTTTATAT-TGTAAAT
28967051 TTAATTT
1 TTAATTT
28967058 AATCCGTATT
Statistics
Matches: 72, Mismatches: 11, Indels: 28
0.65 0.10 0.25
Matches are distributed among these distances:
41 9 0.12
42 11 0.15
43 7 0.10
44 8 0.11
45 8 0.11
46 8 0.11
47 7 0.10
48 12 0.17
49 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (40 bp):
TTAATTTCTTAGAATATTTGTATTTTTTTATATTGTAAAT
Found at i:28966979 original size:90 final size:90
Alignment explanation
Indices: 28966838--28967055 Score: 373
Period size: 90 Copynumber: 2.4 Consensus size: 90
28966828 TATTTTTTAT
* *
28966838 TTAGAATGTTTGTATTTTTTTATATATATAAATTTAATATAGTTGTTTAGGATTTAAGGTATCAT
1 TTAGAATATTTGTATTTTTTTATATATGTAAATTTAATATAGTTGTTTAGGATTTAAGGTATCAT
*
28966903 TTTTATATTTTCGTGTATTAATTTC
66 TTTTATATTTTCATGTATTAATTTC
* *
28966928 TTAGAATATTTGTATTTTTTTATATATGTAAATTTAATATAGTTGTTTAGGATTTAATGTTTCAT
1 TTAGAATATTTGTATTTTTTTATATATGTAAATTTAATATAGTTGTTTAGGATTTAAGGTATCAT
28966993 TTTTATATTTTCATGTATTAATTTC
66 TTTTATATTTTCATGTATTAATTTC
* *
28967018 TTAGAATATTTGTATTTTTTTGTATCTGTAAATTTAAT
1 TTAGAATATTTGTATTTTTTTATATATGTAAATTTAAT
28967056 TTAATCCGTA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 121 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (90 bp):
TTAGAATATTTGTATTTTTTTATATATGTAAATTTAATATAGTTGTTTAGGATTTAAGGTATCAT
TTTTATATTTTCATGTATTAATTTC
Found at i:28969424 original size:40 final size:40
Alignment explanation
Indices: 28969350--28969491 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
28969340 CCGCACCAAG
* * * * * *
28969350 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
28969390 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * * *
28969430 GCCTTCGGGTCTTGGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
28969470 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
28969492 GTAATTTTCA
Statistics
Matches: 85, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:28977543 original size:40 final size:40
Alignment explanation
Indices: 28977469--28977610 Score: 167
Period size: 40 Copynumber: 3.5 Consensus size: 40
28977459 CCGCACCAAG
* * * * * *
28977469 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
28977509 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
28977549 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
28977589 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
28977611 GTAATTTTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:28977629 original size:40 final size:40
Alignment explanation
Indices: 28977501--28977652 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
28977491 ATCACGATTT
* * * * *
28977501 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
28977541 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * * **
28977581 GCACAATTGCCTTCGGGTCTTAACCCGGATGTA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
28977621 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
28977653 CATTCAATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.04
40 89 0.94
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:28979876 original size:6 final size:5
Alignment explanation
Indices: 28979848--28979945 Score: 65
Period size: 5 Copynumber: 18.6 Consensus size: 5
28979838 TCACTTGTTT
* * * *
28979848 TTTCA TTTTA TTTATA TTTCA TTTGCA TTTCG TTTC- -TTCT TGTTCA
1 TTTCA TTTCA TTT-CA TTTCA TTT-CA TTTCA TTTCA TTTCA T-TTCA
* *
28979894 TTTCA TTTGTA TTTTCA TTTCA TTTCA TTTCG TTTACA TTTACA TTTCA
1 TTTCA TTT-CA -TTTCA TTTCA TTTCA TTTCA TTT-CA TTT-CA TTTCA
28979943 TTT
1 TTT
28979946 AAATTACTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.04
5 45 0.58
6 26 0.34
7 3 0.04
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.62
Consensus pattern (5 bp):
TTTCA
Found at i:28979877 original size:11 final size:10
Alignment explanation
Indices: 28979848--28979945 Score: 65
Period size: 11 Copynumber: 9.3 Consensus size: 10
28979838 TCACTTGTTT
*
28979848 TTTCATTTTA
1 TTTCATTTCA
*
28979858 TTTATATTTCA
1 TTT-CATTTCA
*
28979869 TTTGCATTTCG
1 TTT-CATTTCA
*
28979880 TTTC--TTCT
1 TTTCATTTCA
28979888 TGTTCATTTCA
1 T-TTCATTTCA
*
28979899 TTTGTATTTTCA
1 TTT-CA-TTTCA
28979911 TTTCATTTCA
1 TTTCATTTCA
*
28979921 TTTCGTTTACA
1 TTTCATTT-CA
28979932 TTTACATTTCA
1 TTT-CATTTCA
28979943 TTT
1 TTT
28979946 AAATTACTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
8 4 0.06
9 3 0.04
10 18 0.26
11 32 0.46
12 12 0.17
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.62
Consensus pattern (10 bp):
TTTCATTTCA
Found at i:28979934 original size:27 final size:27
Alignment explanation
Indices: 28979890--28979945 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
28979880 TTTCTTCTTG
** *
28979890 TTCATTTCATTTGTATTTTCATTTCAT
1 TTCATTTCATTTACATTTACATTTCAT
*
28979917 TTCATTTCGTTTACATTTACATTTCAT
1 TTCATTTCATTTACATTTACATTTCAT
28979944 TT
1 TT
28979946 AAATTACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (27 bp):
TTCATTTCATTTACATTTACATTTCAT
Found at i:28979952 original size:22 final size:21
Alignment explanation
Indices: 28979890--28979974 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 21
28979880 TTTCTTCTTG
* * *
28979890 TTCATTTCATTTGTATTTTCAT
1 TTCATTTCATTT-AAATTACAT
***
28979912 TTCATTTCATTTCGTTTACAT
1 TTCATTTCATTTAAATTACAT
28979933 TTACATTTCATTTAAATTAC-T
1 TT-CATTTCATTTAAATTACAT
*
28979954 TT--TTTCCATTTAAATTTCAT
1 TTCATTT-CATTTAAATTACAT
28979974 T
1 T
28979975 ATTTCTCATT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 3 0.06
19 11 0.21
20 2 0.04
21 11 0.21
22 26 0.49
ACGTcount: A:0.24, C:0.15, G:0.02, T:0.59
Consensus pattern (21 bp):
TTCATTTCATTTAAATTACAT
Found at i:28980060 original size:5 final size:5
Alignment explanation
Indices: 28980031--28980152 Score: 50
Period size: 5 Copynumber: 22.4 Consensus size: 5
28980021 TAATTTAAAC
* * *
28980031 TTTCA TTCCA TTTCA TAATCA --TCA TTTCA TTTTA TATTCA TTTAACA
1 TTTCA TTTCA TTTCA T-TTCA TTTCA TTTCA TTTCA T-TTCA TTT--CA
* * * **
28980078 TTTCA TTTAA TTTCA TATTCA TTACAAA TTACA TTTCA TTTTT TATTCATA
1 TTTCA TTTCA TTTCA T-TTCA TTTC--A TTTCA TTTCA TTTCA T-TTC--A
28980129 TTTCA TTTAACA TTTCA TTTCA TT
1 TTTCA TTT--CA TTTCA TTTCA TT
28980153 AATTTTTTTC
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
3 3 0.03
5 54 0.60
6 14 0.16
7 18 0.20
8 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTCA
Found at i:28980084 original size:28 final size:29
Alignment explanation
Indices: 28980052--28980127 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
28980042 TTCATAATCA
*
28980052 TCATTTCATTTTATATTCATTTA-ACATT
1 TCATTTCATTTTATATTCATTTACAAATT
* *
28980080 TCATTTAATTTCATATTCA-TTACAAATT
1 TCATTTCATTTTATATTCATTTACAAATT
* *
28980108 ACATTTCATTTTTTATTCAT
1 TCATTTCATTTTATATTCAT
28980128 ATTTCATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.55
Consensus pattern (29 bp):
TCATTTCATTTTATATTCATTTACAAATT
Found at i:28980148 original size:35 final size:33
Alignment explanation
Indices: 28980075--28980157 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 33
28980065 TATTCATTTA
28980075 ACATTTCATTTAATTTCATATTCATTACAAATT
1 ACATTTCATTTAATTTCATATTCATTACAAATT
** *
28980108 ACATTTCATTTTTTATTCATATTTCATTTA-ACATT
1 ACATTTCATTTAAT-TTCATA-TTCA-TTACAAATT
*
28980143 TCATTTCA-TTAATTT
1 ACATTTCATTTAATTT
28980158 TTTTCATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
33 14 0.34
34 9 0.22
35 15 0.37
36 3 0.07
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (33 bp):
ACATTTCATTTAATTTCATATTCATTACAAATT
Found at i:28980267 original size:14 final size:14
Alignment explanation
Indices: 28980225--28980267 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
28980215 AGTAGTCTCA
*
28980225 TTTCAATTTATCTTT
1 TTTCAATTCAT-TTT
*
28980240 TTTTAATTCAATTTT
1 TTTCAATTC-ATTTT
28980255 TTTCAATTCATTT
1 TTTCAATTCATTT
28980268 CATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 18 0.75
16 2 0.08
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTCAATTCATTTT
Found at i:28985237 original size:2 final size:2
Alignment explanation
Indices: 28985230--28985256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28985220 TCATGACATG
28985230 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
28985257 GACTAGTCTC
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:28989386 original size:19 final size:19
Alignment explanation
Indices: 28989354--28989399 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28989344 ACAACATATA
* * *
28989354 ATAATGTCACATTATTTAC
1 ATAATATCAAATTATTCAC
28989373 ATAATATCAAATTATTCAC
1 ATAATATCAAATTATTCAC
28989392 ATATATAT
1 ATA-ATAT
28989400 ATATACTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAATATCAAATTATTCAC
Found at i:28990331 original size:26 final size:27
Alignment explanation
Indices: 28990278--28990331 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
28990268 TTAATAATAA
* **
28990278 TATTTTGAGGTGATTAAAGTGTAGTTT
1 TATTTTGAGGTGATTAAAATACAGTTT
*
28990305 TATTTTGAGGTG-TTAAAATACATTTT
1 TATTTTGAGGTGATTAAAATACAGTTT
28990331 T
1 T
28990332 TATTATTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (27 bp):
TATTTTGAGGTGATTAAAATACAGTTT
Found at i:28992607 original size:53 final size:47
Alignment explanation
Indices: 28992491--28992633 Score: 169
Period size: 47 Copynumber: 2.9 Consensus size: 47
28992481 CACGGATCAC
** * *
28992491 ATATCACACCGATGCCATATCCCAGATATGGTCTTATACAGTAGCAC
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATATGGAAGCAA
*
28992538 ATATCACACCAATGCCATATCCCAGATATGGTCTTATATGGAAGCAA
1 ATATCACACCGATGCCATATCCCAGATATGGTCTTATATGGAAGCAA
* *
28992585 ATAATCACATCTCTCCGATGCCATAGCCCAGCTATGGTCTTATATGGAA
1 AT-ATCACA-----CCGATGCCATATCCCAGATATGGTCTTATATGGAA
28992634 ATCACATATC
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
47 44 0.54
48 6 0.07
53 32 0.39
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (47 bp):
ATATCACACCGATGCCATATCCCAGATATGGTCTTATATGGAAGCAA
Found at i:29011176 original size:38 final size:36
Alignment explanation
Indices: 29011110--29011215 Score: 95
Period size: 37 Copynumber: 2.8 Consensus size: 36
29011100 ATACTCCTTT
* * * * *
29011110 TTTGGTGTGTTTTTGGTTGGACTAGCTCTTCGGAGCAA
1 TTTGGTGTGTTTCTGG-TGGATTGGCTCTTAGGAAC-A
*
29011148 TTTGGTGTGTTATCTGGTGGATTGGCTCTTATGAACA
1 TTTGGTGTGTT-TCTGGTGGATTGGCTCTTAGGAACA
* * *
29011185 TTTGGCGTGTTCTCAGGTGGATTGCCTCTTA
1 TTTGGTGTGTT-TCTGGTGGATTGGCTCTTA
29011216 TGAGCATCTG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
37 28 0.49
38 25 0.44
39 4 0.07
ACGTcount: A:0.13, C:0.14, G:0.30, T:0.42
Consensus pattern (36 bp):
TTTGGTGTGTTTCTGGTGGATTGGCTCTTAGGAACA
Found at i:29011204 original size:37 final size:37
Alignment explanation
Indices: 29011147--29011234 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
29011137 CTTCGGAGCA
* * *
29011147 ATTTGGTGTGTTATCTGGTGGATTGGCTCTTATGAAC
1 ATTTGGCGTGTTATCAGGTGGATTGCCTCTTATGAAC
* *
29011184 ATTTGGCGTGTTCTCAGGTGGATTGCCTCTTATGAGC
1 ATTTGGCGTGTTATCAGGTGGATTGCCTCTTATGAAC
* *
29011221 ATCTGGCATGTTAT
1 ATTTGGCGTGTTAT
29011235 TGAGTGGATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.16, C:0.15, G:0.28, T:0.41
Consensus pattern (37 bp):
ATTTGGCGTGTTATCAGGTGGATTGCCTCTTATGAAC
Found at i:29011242 original size:37 final size:36
Alignment explanation
Indices: 29011155--29011252 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 36
29011145 CAATTTGGTG
* *
29011155 TGTTATCTG-GTGGATTGGCTCTTATGAACATTTGGCG
1 TGTTAT-TGAGTGGATT-GCTCTTATGAACATCTGGCA
* * *
29011192 TGTT-CTCAGGTGGATTGCCTCTTATGAGCATCTGGCA
1 TGTTATTGA-GTGGATTG-CTCTTATGAACATCTGGCA
29011229 TGTTATTGAGTGGATTAGCTCTTA
1 TGTTATTGAGTGGATT-GCTCTTA
29011253 CGAGTGATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
35 1 0.02
36 1 0.02
37 44 0.90
38 3 0.06
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (36 bp):
TGTTATTGAGTGGATTGCTCTTATGAACATCTGGCA
Found at i:29019479 original size:29 final size:29
Alignment explanation
Indices: 29019458--29019516 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
29019448 AAACATCGGT
* *
29019458 AATAACTGGTTAAACCCCAAAAGCTTCTA
1 AATAACTGGCTAAACCCCAAAAGCATCTA
*
29019487 AATAACTGGCTAAACCCCAAAAGCTTCTA
1 AATAACTGGCTAAACCCCAAAAGCATCTA
29019516 A
1 A
29019517 CTTCAGATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.22
Consensus pattern (29 bp):
AATAACTGGCTAAACCCCAAAAGCATCTA
Found at i:29033600 original size:123 final size:123
Alignment explanation
Indices: 29033381--29033719 Score: 597
Period size: 123 Copynumber: 2.8 Consensus size: 123
29033371 GAATTATGTG
*
29033381 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
29033446 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
29033504 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
29033569 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
29033627 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
29033692 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
29033720 AATTATATGG
Statistics
Matches: 207, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 207 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:29033792 original size:40 final size:39
Alignment explanation
Indices: 29033688--29033929 Score: 274
Period size: 40 Copynumber: 6.1 Consensus size: 39
29033678 TGAATGATAC
* * * *
29033688 CCGGGCTAAGT-CCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAA-TACCCGAAGGCATTTGTGCAAGT-GTTATAT
* * * * *
29033728 --GGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATAT
1 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTG-TTATAT
29033766 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAATACCCGAAGGCATTTGTGCAAG-TGTTATAT
29033806 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAATACCCGAAGGCATTTGTGCAAG-TGTTATAT
29033846 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAATACCCGAAGGCATTTGTGCAAGT-GTTATAT
* * * **
29033886 CCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAATACCCGAAGGCATTTGTGCAAGT-GTTATAT
29033926 CCGG
1 CCGG
29033930 TTGTATTCCG
Statistics
Matches: 178, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
38 29 0.16
39 1 0.01
40 146 0.82
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CCGGGCTAATACCCGAAGGCATTTGTGCAAGTGTTATAT
Found at i:29040574 original size:22 final size:22
Alignment explanation
Indices: 29040549--29040599 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
29040539 CGAAAATGAA
*
29040549 ATATGGTGTGTAATGATTA-TTG
1 ATATGGTGTGT-ATGAGTATTTG
*
29040571 ATATATGTGTGTATGAGTATTTG
1 ATAT-GGTGTGTATGAGTATTTG
29040594 A-ATGGT
1 ATATGGT
29040600 ACCCGGGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.08
22 12 0.50
23 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (22 bp):
ATATGGTGTGTATGAGTATTTG
Found at i:29040653 original size:122 final size:123
Alignment explanation
Indices: 29040419--29040756 Score: 588
Period size: 122 Copynumber: 2.8 Consensus size: 123
29040409 GAATTATGTG
*
29040419 AAATGAAATATGGATGTGTAATGATTATTGACATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
*
29040484 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
29040542 AAATGAAATATGG-TGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
29040606 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
* * * * *
29040664 AAATGAAATATGGATGTGTAATGATTATTGATTTATGTGTGCATGAGCAATTGAATGATACCCGG
1 AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
* *
29040729 GCTAAGTCCCGAAGACATTTATGCTAGT
66 GCTAAGTCCCGAAGGCAATTATGCTAGT
29040757 AATTATATCC
Statistics
Matches: 205, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
122 120 0.59
123 85 0.41
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (123 bp):
AAATGAAATATGGATGTGTAATGATTATTGATATATGTGTGTATGAGTATTTGAATGGTACCCGG
GCTAAGTCCCGAAGGCAATTATGCTAGTGATATGTTTGTGTTCGAGCCTTAGTAACGA
Found at i:29040780 original size:40 final size:40
Alignment explanation
Indices: 29040725--29040968 Score: 274
Period size: 40 Copynumber: 6.1 Consensus size: 40
29040715 TGAATGATAC
* * * * **
29040725 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * *
29040765 CCGGGTTAAGACCCGAAGGCAATTGTGCTAG-TGACTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTG-TTATAT
* *
29040805 CCGGGATAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
*
29040845 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * *
29040885 CCGGGCCAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
* * * ** *
29040925 TCGGGCTAAGACCCGAGGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
29040965 CCGG
1 CCGG
29040969 TTGTATTCCG
Statistics
Matches: 177, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
40 175 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
Found at i:29042835 original size:33 final size:33
Alignment explanation
Indices: 29042757--29042866 Score: 168
Period size: 33 Copynumber: 3.3 Consensus size: 33
29042747 TTGTACTGAT
* *
29042757 ACTGATACTGTTACTG-AATTGGGCTAAGGCCCA
1 ACTGATACTGGTACTGTAA-TGGGCTAATGCCCA
*
29042790 CATTGATACTGGTACTGTAATGGGCTAATGCCCA
1 -ACTGATACTGGTACTGTAATGGGCTAATGCCCA
29042824 ACTGATACTGGTACTGTAATGGGCTAATGCCCA
1 ACTGATACTGGTACTGTAATGGGCTAATGCCCA
29042857 ACTGATACTG
1 ACTGATACTG
29042867 AATTGTACTG
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
33 42 0.59
34 27 0.38
35 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (33 bp):
ACTGATACTGGTACTGTAATGGGCTAATGCCCA
Found at i:29050441 original size:48 final size:48
Alignment explanation
Indices: 29050370--29050465 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
29050360 ATGTTATTAG
* *
29050370 GAGATTCATTGAGTTGGCTTTGGGCCATGATATTGGCACTTCAGGTGC
1 GAGATTCAATGAGTTGGATTTGGGCCATGATATTGGCACTTCAGGTGC
* *
29050418 GAGATTCAATGAGTTGTATTTGGGCCATGATATTGGCACTTCGGGTGC
1 GAGATTCAATGAGTTGGATTTGGGCCATGATATTGGCACTTCAGGTGC
29050466 AAGACTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (48 bp):
GAGATTCAATGAGTTGGATTTGGGCCATGATATTGGCACTTCAGGTGC
Found at i:29054688 original size:31 final size:31
Alignment explanation
Indices: 29054650--29054713 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29054640 CCTTTTCACA
29054650 TTTCACATTTCATAACACTGGGCCGAAGCCT
1 TTTCACATTTCATAACACTGGGCCGAAGCCT
** * *
29054681 TTTCACATTTCATATTATTGGGCTGAAGCCT
1 TTTCACATTTCATAACACTGGGCCGAAGCCT
29054712 TT
1 TT
29054714 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCACATTTCATAACACTGGGCCGAAGCCT
Found at i:29054958 original size:24 final size:24
Alignment explanation
Indices: 29054920--29055071 Score: 227
Period size: 24 Copynumber: 6.4 Consensus size: 24
29054910 CTGGAGGCCT
*
29054920 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
* *
29054945 AGCCCTTTTTATAATTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29054969 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
29054992 AGCCCTTTTGATAACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
29055016 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29055040 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
29055063 AGCCCTTTT
1 AGCCCTTTT
29055072 TCACTTCCTC
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
23 43 0.37
24 69 0.59
25 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:29055013 original size:71 final size:71
Alignment explanation
Indices: 29054920--29055071 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 71
29054910 CTGGAGGCCT
* * *
29054920 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAATTGGGGCATAAGCCCTTTAATAACTG
1 AGCC-CTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTG
29054985 GGGCATA
65 GGGCATA
* *
29054992 AGCCCTTTTGATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
1 AGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
29055057 GGCATA
66 GGCATA
29055063 AGCCCTTTT
1 AGCCCTTTT
29055072 TCACTTCCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 71 0.95
72 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (71 bp):
AGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
GGCATA
Found at i:29055071 original size:47 final size:48
Alignment explanation
Indices: 29054920--29055071 Score: 227
Period size: 47 Copynumber: 3.2 Consensus size: 48
29054910 CTGGAGGCCT
* * *
29054920 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAATTGGGGCATA
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
* *
29054969 AGCCC-TTTAATAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
*
29055016 AGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
29055063 AGCCCTTTT
1 AGCCCTTTT
29055072 TCACTTCCTC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
47 68 0.72
48 23 0.24
49 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (48 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
Found at i:29055145 original size:20 final size:20
Alignment explanation
Indices: 29055120--29055186 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
29055110 TTATGATTAC
29055120 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
29055140 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29055160 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29055180 ACCATGT
1 ATCATGT
29055187 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29055151 original size:11 final size:11
Alignment explanation
Indices: 29055120--29055175 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29055110 TTATGATTAC
29055120 ATCATGTGCAT
1 ATCATGTGCAT
*
29055131 ATCA--TACAT
1 ATCATGTGCAT
29055140 ATCATGTGCAT
1 ATCATGTGCAT
*
29055151 ATCA--TACAT
1 ATCATGTGCAT
*
29055160 GTCATGTGCAT
1 ATCATGTGCAT
29055171 ATCAT
1 ATCAT
29055176 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:29055269 original size:25 final size:25
Alignment explanation
Indices: 29055223--29055270 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29055213 ATACATAAAC
* * * *
29055223 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29055248 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29055271 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29059746 original size:28 final size:27
Alignment explanation
Indices: 29059683--29059752 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
29059673 ATAGTGAGTC
*
29059683 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
29059710 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
29059738 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29059753 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29065925 original size:31 final size:31
Alignment explanation
Indices: 29065884--29065947 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29065874 CCTTTTCACA
*
29065884 TTTCACATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
29065915 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
29065946 TT
1 TT
29065948 ACTGTAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:29066187 original size:24 final size:24
Alignment explanation
Indices: 29066154--29066305 Score: 209
Period size: 24 Copynumber: 6.4 Consensus size: 24
29066144 CTGGAGGCCT
*
29066154 AGCCTCTTTTAATAACTAGGGCAAA
1 AGCC-CTTTTAATAACTAGGGCATA
* *
29066179 AGCCCTTTTTATAACTGGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
*
29066203 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
*
29066226 AGCCCTTTTGATAACTAGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
* *
29066250 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
*
29066274 AGCCC-TTTAATAACTATGGCATA
1 AGCCCTTTTAATAACTAGGGCATA
29066297 AGCCCTTTT
1 AGCCCTTTT
29066306 TCACTTCCTC
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
23 42 0.37
24 69 0.60
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTAGGGCATA
Found at i:29066240 original size:71 final size:71
Alignment explanation
Indices: 29066154--29066305 Score: 250
Period size: 71 Copynumber: 2.1 Consensus size: 71
29066144 CTGGAGGCCT
* *
29066154 AGCCTCTTTTAATAACTAGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTTAATAACTG
1 AGCC-CTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTA
29066219 GGGCATA
65 GGGCATA
* * *
29066226 AGCCCTTTTGATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTAT
1 AGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTAG
29066291 GGCATA
66 GGCATA
29066297 AGCCCTTTT
1 AGCCCTTTT
29066306 TCACTTCCTC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 71 0.95
72 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (71 bp):
AGCCCTTTTAATAACTAGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTAG
GGCATA
Found at i:29066305 original size:47 final size:48
Alignment explanation
Indices: 29066154--29066305 Score: 218
Period size: 47 Copynumber: 3.2 Consensus size: 48
29066144 CTGGAGGCCT
* * * *
29066154 AGCCTCTTTTAATAACTAGGGCAAAAGCCCTTTTTATAACTGGGGCATA
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCATA
*
29066203 AGCCC-TTTAATAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCATA
* *
29066250 AGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTATGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCATA
29066297 AGCCCTTTT
1 AGCCCTTTT
29066306 TCACTTCCTC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
47 68 0.72
48 23 0.24
49 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (48 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCATA
Found at i:29066399 original size:20 final size:20
Alignment explanation
Indices: 29066354--29066419 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
29066344 TTATGATTAC
29066354 ATCATGTGCATATCATA-AT
1 ATCATGTGCATATCATACAT
29066373 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29066393 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29066413 ACCATGT
1 ATCATGT
29066420 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 17 0.40
20 26 0.60
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29072854 original size:26 final size:26
Alignment explanation
Indices: 29072817--29072897 Score: 101
Period size: 26 Copynumber: 3.1 Consensus size: 26
29072807 TTTGCCACAT
*
29072817 ATACTGATACTGGCAGCTTTGTTGCG
1 ATACTGTTACTGGCAGCTTTGTTGCG
* *
29072843 TTACTGTTACTGGTAGCTTTGTTGCG
1 ATACTGTTACTGGCAGCTTTGTTGCG
* *
29072869 ATA-TGATTACTAGCAGCTTTGCTGCG
1 ATACTG-TTACTGGCAGCTTTGTTGCG
29072895 ATA
1 ATA
29072898 TTGGTGTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 2 0.04
26 45 0.96
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGTTGCG
Found at i:29075802 original size:29 final size:29
Alignment explanation
Indices: 29075769--29075930 Score: 155
Period size: 29 Copynumber: 5.6 Consensus size: 29
29075759 GTGACGAGAT
29075769 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
29075798 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
29075827 TGGCACTAAGTGTGGCATGCTGGAAATATA
1 TGGCACTAAGTGT-GCGTGCTGGAAATATA
* * ** * * ***
29075857 CGACACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
29075886 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
29075915 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
29075931 AAATCGAGTA
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.02
29 83 0.75
30 25 0.23
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Done.