Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 175 of 433
Found at i:54637160 original size:21 final size:21
Alignment explanation
Indices: 54637135--54637189 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
54637125 GTGGCTCAAG
*
54637135 ACACACCCGTGTGACTACTTC
1 ACACACCCGTGTAACTACTTC
*
54637156 ACACACCTGTGTAACTACTTC
1 ACACACCCGTGTAACTACTTC
**
54637177 ACACGTCCGTGTA
1 ACACACCCGTGTA
54637190 CCCTGATCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (21 bp):
ACACACCCGTGTAACTACTTC
Found at i:54646238 original size:21 final size:21
Alignment explanation
Indices: 54646191--54646248 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
54646181 CCACCCCAAT
*
54646191 CCAACCAACACACCACCCGTA
1 CCAACCAACACACCATCCGTA
**
54646212 CCAACCAACACACCATCTTTA
1 CCAACCAACACACCATCCGTA
* *
54646233 CTAACCAGCACACCAT
1 CCAACCAACACACCAT
54646249 GTGGGGATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.47, G:0.03, T:0.12
Consensus pattern (21 bp):
CCAACCAACACACCATCCGTA
Found at i:54646389 original size:28 final size:26
Alignment explanation
Indices: 54646325--54646390 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
54646315 AACAAAGCTG
54646325 CTAATGACAGTAAACGTGGCAAAGCCA
1 CTAAT-ACAGTAAACGTGGCAAAGCCA
* *
54646352 CCAGA-GCAGTAATTACGTGGCAAAGCCA
1 CTA-ATACAGTAA--ACGTGGCAAAGCCA
54646380 CTAATACAGTA
1 CTAATACAGTA
54646391 CTTCCTCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
26 6 0.19
27 3 0.10
28 22 0.71
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CTAATACAGTAAACGTGGCAAAGCCA
Found at i:54647997 original size:139 final size:141
Alignment explanation
Indices: 54647820--54648092 Score: 451
Period size: 139 Copynumber: 1.9 Consensus size: 141
54647810 TCAGCACAAA
*
54647820 ATGGAATGAAAAGAAAGAAGTAGAAACAAGGAACTTCGGCTTAAATCCCGAAGAGGCACGAAAGA
1 ATGGAATGAAAAGAAAGAAGTAGAAACAAGAAACTTCGGCTTAAATCCCGAAGAGGCACGAAAGA
*
54647885 GAGATCGGCACAAGGGAGAAAGATACCAAAAGCGT-AAA-AAAAACCCAAAATGGAAGAGGGAGA
66 GAGATCGGCACAAGGGAGAAAGATACCAAAAGCGTAAAAGAAAAACCCAAAATAGAAGAGGGAGA
54647948 AAATAGCACCT
131 AAATAGCACCT
* * * *
54647959 ATGGAATGAAAAGAAAGAAGTAGAAATAAGAAATTTCGGCTTAAATCCTGAAGTGGCACGAAAGA
1 ATGGAATGAAAAGAAAGAAGTAGAAACAAGAAACTTCGGCTTAAATCCCGAAGAGGCACGAAAGA
*
54648024 GAGATCGGCCCAAGGGAGAAAGATACCAAAAGCGTCAAAAAGAAAAACCCAAAATAGAAGAGGGA
66 GAGATCGGCACAAGGGAGAAAGATACCAAAAGCGT--AAAAGAAAAACCCAAAATAGAAGAGGGA
54648089 GAAA
129 GAAA
54648093 TCAGCCCCTA
Statistics
Matches: 123, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
139 94 0.76
142 3 0.02
143 26 0.21
ACGTcount: A:0.49, C:0.14, G:0.26, T:0.11
Consensus pattern (141 bp):
ATGGAATGAAAAGAAAGAAGTAGAAACAAGAAACTTCGGCTTAAATCCCGAAGAGGCACGAAAGA
GAGATCGGCACAAGGGAGAAAGATACCAAAAGCGTAAAAGAAAAACCCAAAATAGAAGAGGGAGA
AAATAGCACCT
Found at i:54658201 original size:39 final size:39
Alignment explanation
Indices: 54658147--54658309 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
54658137 TGTGAATGAA
54658147 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
54658186 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
54658225 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * **
54658264 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCGTT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
54658304 TGTGCG
1 TGTGCG
54658310 GGTTACCATA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 99 0.86
40 16 0.14
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:54664109 original size:29 final size:29
Alignment explanation
Indices: 54664077--54664208 Score: 237
Period size: 29 Copynumber: 4.5 Consensus size: 29
54664067 ATAGTGAATC
54664077 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
54664106 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
54664136 CGCACACTTAATGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
*
54664165 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
54664194 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54664209 GTACAATTTT
Statistics
Matches: 99, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 71 0.72
30 28 0.28
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:54664218 original size:59 final size:59
Alignment explanation
Indices: 54664077--54664208 Score: 239
Period size: 59 Copynumber: 2.3 Consensus size: 59
54664067 ATAGTGAATC
54664077 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
* *
54664136 CGCACACTTAATGCTATATATTTTCAGCTCGCACACTTAGTGCTATAT-ATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
54664194 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54664209 GTACAATTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
58 23 0.33
59 47 0.67
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (59 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:54666807 original size:39 final size:39
Alignment explanation
Indices: 54666753--54666915 Score: 254
Period size: 39 Copynumber: 4.2 Consensus size: 39
54666743 TGTGAATGAA
54666753 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
54666792 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
54666831 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * **
54666870 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCGTT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
54666910 TGTGCG
1 TGTGCG
54666916 GGTTACCATA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 99 0.86
40 16 0.14
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:54674855 original size:19 final size:19
Alignment explanation
Indices: 54674831--54674869 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54674821 CACACAGCCA
54674831 AGACACACGCCCGTGTTCT
1 AGACACACGCCCGTGTTCT
54674850 AGACACACGCCCGTGTTCT
1 AGACACACGCCCGTGTTCT
54674869 A
1 A
54674870 AGACGTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (19 bp):
AGACACACGCCCGTGTTCT
Found at i:54683253 original size:25 final size:23
Alignment explanation
Indices: 54683199--54683268 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 23
54683189 ATGAAAAATC
54683199 ACTACTAATCAGGATGCTCGTAGGA
1 ACTA-TAA-CAGGATGCTCGTAGGA
*
54683224 ACTATATAACAGGATGCTCG-AGAGG
1 AC--TATAACAGGATGCTCGTAG-GA
*
54683249 GCTATAACAGGATTGCTCGT
1 ACTATAACAGGA-TGCTCGT
54683269 CTGAGCTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 10 0.26
24 8 0.21
25 15 0.39
26 3 0.08
27 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (23 bp):
ACTATAACAGGATGCTCGTAGGA
Found at i:54685714 original size:6 final size:6
Alignment explanation
Indices: 54685703--54685754 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
54685693 TACAATTCGG
54685703 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TATT-TGT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T-TTAT-T TTTATT
54685752 TTT
1 TTT
54685755 CATGTTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:54692074 original size:47 final size:47
Alignment explanation
Indices: 54692005--54692226 Score: 176
Period size: 47 Copynumber: 4.7 Consensus size: 47
54691995 ATTCGTGTGT
*
54692005 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACATT-ATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-G-CACATTGATGA
* *
54692051 GAGCCAGTGTAAGATCATGTCTGGGACATGGCATCG-GCATTGA-GACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCACATTGATG---A
* * * * *
54692099 GGGCTAGTATAA-AACATGTCTGGGACAT-GCATCGGCTACA-AGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GC-ACATTGATGA
* * * *
54692145 TAGTCAATGTAAGACCATGTCTGGGACATGGCATCG-AC-TTGAGATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCACATT--GATGA
*
54692192 GAGCCAGTGTAAGACCGTGTCTGGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
54692227 AGCATTTTAC
Statistics
Matches: 140, Mismatches: 21, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
45 7 0.05
46 26 0.19
47 82 0.59
48 22 0.16
49 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCACATTGATGA
Found at i:54692213 original size:94 final size:94
Alignment explanation
Indices: 54692002--54692229 Score: 278
Period size: 94 Copynumber: 2.4 Consensus size: 94
54691992 GTCATTCGTG
** * *
54692002 TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGATC
1 TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAATGTAAGACC
*
54692067 ATGTCTGGGACATGGCATCGGCATTGAGA
66 ATGTCTGGGACATGGCATCGACATTGAGA
*** * * * * * * *
54692096 CAAGGGCTAGTATAAAACATGTCTGGGACATGCATCGGCTACAAGATGATAGTCAATGTAAGACC
1 TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAATGTAAGACC
54692161 ATGTCTGGGACATGGCATCGAC-TTGAGA
66 ATGTCTGGGACATGGCATCGACATTGAGA
* *
54692189 TGTGAGCCAGTGTAAGACCGTGTCTGGGACATGGCATCAGC
1 TGTGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC
54692230 ATTTTACCCA
Statistics
Matches: 108, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
93 16 0.15
94 85 0.79
95 7 0.06
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (94 bp):
TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGAGAGCCAATGTAAGACC
ATGTCTGGGACATGGCATCGACATTGAGA
Found at i:54697677 original size:29 final size:29
Alignment explanation
Indices: 54697644--54697832 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
54697634 GTGACGAGAT
54697644 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54697673 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54697702 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
54697731 TGGTACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
54697760 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
54697789 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
54697818 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
54697833 GAAATCGAGT
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 135 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:54702890 original size:47 final size:45
Alignment explanation
Indices: 54702813--54703035 Score: 173
Period size: 47 Copynumber: 4.8 Consensus size: 45
54702803 ACTACATTAT
* * *
54702813 AAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGGCATTGAGA
1 AAGAGCCAGTGTAA-AACATGTCTGGGACATGGCATCGGC-TCGAGA
* *
54702860 CAAGGGCTAGTGTAAAACATGTCTGGGACAT-GCATCGGCCTCGAG-
1 -AAGAGCCAGTGTAAAACATGTCTGGGACATGGCATCGG-CTCGAGA
* * *
54702905 AAGTAAGCCAGTGTAAGACATATTTGGGACAT-GCATCGGCTACGAGA
1 AAG--AGCCAGTGTAAAACATGTCTGGGACATGGCATCGGCT-CGAGA
* * * * * *
54702952 TGATAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGA
1 -AAGAGCCAGTGTAA-AACATGTCTGGGACATGGCATCGGCTCGAGA
* * *
54702999 TATGAGCCAGTGTGAGACAGTGTCTGGGACATGGCAT
1 -AAGAGCCAGTGTAAAACA-TGTCTGGGACATGGCAT
54703036 TGGCACCTTA
Statistics
Matches: 140, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
44 3 0.02
45 2 0.01
46 56 0.40
47 58 0.41
48 21 0.15
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (45 bp):
AAGAGCCAGTGTAAAACATGTCTGGGACATGGCATCGGCTCGAGA
Found at i:54702918 original size:46 final size:46
Alignment explanation
Indices: 54702813--54703031 Score: 158
Period size: 46 Copynumber: 4.7 Consensus size: 46
54702803 ACTACATTAT
* * * *
54702813 AAGAGCCAGTGTAAGACCATGTATGGGACATGGCATCGGCATTGAGAC
1 AAGAGCCAGTGTAA-AACATGTCTGGGACAT-GCATCGGCCTCGAGAC
* *
54702861 AAGGGCTAGTGTAAAACATGTCTGGGACATGCATCGGCCTCGAG--
1 AAGAGCCAGTGTAAAACATGTCTGGGACATGCATCGGCCTCGAGAC
* * * *
54702905 AAGTAAGCCAGTGTAAGACATATTTGGGACATGCATCGG-CTACGAGAT
1 AAG--AGCCAGTGTAAAACATGTCTGGGACATGCATCGGCCT-CGAGAC
* * * * * * *
54702953 GATAGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGAT
1 AAGAGCCAGTGTAA-AACATGTCTGGGACAT-GCATCGGCCTCGAGAC
* * *
54703000 ATGAGCCAGTGTGAGACAGTGTCTGGGACATG
1 AAGAGCCAGTGTAAAACA-TGTCTGGGACATG
54703032 GCATTGGCAC
Statistics
Matches: 136, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
44 3 0.02
45 2 0.01
46 58 0.43
47 53 0.39
48 20 0.15
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (46 bp):
AAGAGCCAGTGTAAAACATGTCTGGGACATGCATCGGCCTCGAGAC
Found at i:54709764 original size:95 final size:94
Alignment explanation
Indices: 54709641--54709815 Score: 278
Period size: 95 Copynumber: 1.9 Consensus size: 94
54709631 AGAGTGAGAA
* **
54709641 TCTTATTAACTAATTGAATTTTAGAACAATGGAAATAACTAATTCTTCTAGTTAACTACTCAAAA
1 TCTTATTAACTAATTGAATTTTAAAACAATCAAAATAACTAATTCTTCTAGTTAACTA-TCAAAA
54709706 ACATGCTACCCTAAAAAGAGAACTAATTCT
65 ACATGCTACCCTAAAAAGAGAACTAATTCT
* * *
54709736 TCTTATTAACTATTTGAATTTTAAAACAATCAAAATAACTAATTCTTCTTGTTAACTATTAAAAA
1 TCTTATTAACTAATTGAATTTTAAAACAATCAAAATAACTAATTCTTCTAGTTAACTATCAAAAA
*
54709801 CATGCTACTCTAAAA
66 CATGCTACCCTAAAA
54709816 GAAGAAAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
94 20 0.27
95 53 0.73
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (94 bp):
TCTTATTAACTAATTGAATTTTAAAACAATCAAAATAACTAATTCTTCTAGTTAACTATCAAAAA
CATGCTACCCTAAAAAGAGAACTAATTCT
Found at i:54715231 original size:33 final size:33
Alignment explanation
Indices: 54715193--54715321 Score: 222
Period size: 33 Copynumber: 3.9 Consensus size: 33
54715183 GACTGAGTGG
* *
54715193 GAGTGTTTGGTTGCTGGACAAGAGATGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
*
54715226 GAGTGTTTGATTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
*
54715259 GAGTGTTTGGTTGTTGGACAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
54715292 GAGTGTTTGGTTGCTGGACAGGAGCTGGAA
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAA
54715322 ATAAGATCTC
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.21, C:0.08, G:0.41, T:0.30
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
Found at i:54722368 original size:32 final size:32
Alignment explanation
Indices: 54722314--54722441 Score: 202
Period size: 32 Copynumber: 4.0 Consensus size: 32
54722304 CATAAAAAAT
54722314 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
* * * * *
54722346 ATTATACAGTAGGTTTATATATAAAAAAGTTG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
*
54722378 ATCATACATTAGTTTTGCATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
54722410 ATCATACATTAGTTTTACATATAAAAAAGTAG
1 ATCATACATTAGTTTTACATATAAAAAAGTAG
54722442 TATAGTTATA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (32 bp):
ATCATACATTAGTTTTACATATAAAAAAGTAG
Found at i:54725228 original size:5 final size:5
Alignment explanation
Indices: 54725218--54725277 Score: 84
Period size: 5 Copynumber: 12.0 Consensus size: 5
54725208 AGCTACAATC
* * * *
54725218 ATTAG ATTAG ATTAG ATGAG ATTAG ACTAG ATTAT ATTAG ATTAG AATAG
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG
54725268 ATTAG ATTAG
1 ATTAG ATTAG
54725278 TTGTTTATCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.37
Consensus pattern (5 bp):
ATTAG
Found at i:54727151 original size:35 final size:34
Alignment explanation
Indices: 54727105--54727203 Score: 118
Period size: 29 Copynumber: 3.0 Consensus size: 34
54727095 TTTGGTACCT
54727105 ATACAAGTAGAAATCTCAATGTTAAGTACAGACCC
1 ATACAAGTAGAAATCTCAATGTT-AGTACAGACCC
* *
54727140 ATACAAGTAGAAATCTC-A-GCT--TCCA-ACCC
1 ATACAAGTAGAAATCTCAATGTTAGTACAGACCC
*
54727169 ATACAAGTAGAAATCTCAATGTTAGGTATAGACCC
1 ATACAAGTAGAAATCTCAATGTTA-GTACAGACCC
54727204 CCAATATTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
29 21 0.40
30 4 0.08
31 2 0.04
33 2 0.04
34 3 0.06
35 21 0.40
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.23
Consensus pattern (34 bp):
ATACAAGTAGAAATCTCAATGTTAGTACAGACCC
Found at i:54727372 original size:21 final size:21
Alignment explanation
Indices: 54727346--54727393 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
54727336 ATCGGTCGTC
54727346 GATTGAGGAGGAGTTGACACA
1 GATTGAGGAGGAGTTGACACA
54727367 GATTGAGGAGGAGTTGACACA
1 GATTGAGGAGGAGTTGACACA
*
54727388 GCTTGA
1 GATTGA
54727394 AGCAGAGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (21 bp):
GATTGAGGAGGAGTTGACACA
Found at i:54729828 original size:19 final size:21
Alignment explanation
Indices: 54729778--54729831 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
54729768 GGTGAATCAA
* *
54729778 CTCTTAAGA-CTTCTGTTTAG
1 CTCTTACGAGCTTCTGTTCAG
54729798 CTCTTACGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
54729819 CT-TT-CGAGCTTCT
1 CTCTTACGAGCTTCT
54729832 ATTGGTGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 9 0.29
20 10 0.32
21 12 0.39
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.43
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAG
Found at i:54730674 original size:50 final size:52
Alignment explanation
Indices: 54730571--54730679 Score: 134
Period size: 50 Copynumber: 2.1 Consensus size: 52
54730561 ATGAGTTATT
**
54730571 TAATGCAAGACTTAATTTAATAATGCATACTTAAACTAACATGGGAGTTACA
1 TAATGCAAGACTTAATTTAATAATGCATACTTAAACTAACATGAAAGTTACA
* * * *
54730623 TAATGCAAGTCATT-ATTT-ATGATGCATACTT-AACTACCATTAAAGTTACA
1 TAATGCAAGAC-TTAATTTAATAATGCATACTTAAACTAACATGAAAGTTACA
54730673 TAATGCA
1 TAATGCA
54730680 TTACTTTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 22 0.44
51 12 0.24
52 14 0.28
53 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (52 bp):
TAATGCAAGACTTAATTTAATAATGCATACTTAAACTAACATGAAAGTTACA
Found at i:54737066 original size:55 final size:52
Alignment explanation
Indices: 54736982--54737212 Score: 229
Period size: 55 Copynumber: 4.4 Consensus size: 52
54736972 AGGGTTTAAA
*
54736982 GATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGTCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAG-CAAG
* * * * *
54737037 GATACCATGTAAAACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGAAAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAA-G-CAAG
* * *
54737093 G-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAG-TTCATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-TAA-GCAAG
* * *
54737145 GATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC-AA--AAG
1 GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGCAAG
*
54737194 GATACCACGTAAGACCATG
1 GATACCATGTAAGACCATG
54737213 AAAGTCATGT
Statistics
Matches: 148, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
49 21 0.14
52 7 0.05
53 40 0.27
54 11 0.07
55 64 0.43
56 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (52 bp):
GATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGCAAG
Found at i:54737185 original size:108 final size:110
Alignment explanation
Indices: 54736986--54737186 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
54736976 TTTAAAGATA
*
54736986 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGTCAAGGATACCATGTAAAA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAAA
*
54737051 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGAAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGAAAAGGTC
* *
54737096 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGATACCATGTAAA
* *
54737158 ACCATGTCGAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
54737187 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGATACCATGTAAAA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGAAAAGGTC
Found at i:54737441 original size:16 final size:16
Alignment explanation
Indices: 54737420--54737450 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54737410 ATAAATTTGA
54737420 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
54737436 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
54737451 AGGGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:54741743 original size:21 final size:20
Alignment explanation
Indices: 54741719--54741757 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
54741709 GAGTATTTTG
54741719 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
54741740 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
54741758 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:54743029 original size:22 final size:22
Alignment explanation
Indices: 54742999--54743041 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
54742989 AATTTAGCCA
54742999 TTTGATTTGGCTTGTAAATATC
1 TTTGATTTGGCTTGTAAATATC
* * *
54743021 TTTGGTTTGGTTTGTATATAT
1 TTTGATTTGGCTTGTAAATAT
54743042 AGCCATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (22 bp):
TTTGATTTGGCTTGTAAATATC
Found at i:54745203 original size:23 final size:23
Alignment explanation
Indices: 54745177--54745304 Score: 141
Period size: 23 Copynumber: 5.6 Consensus size: 23
54745167 ATATGTGAAA
* * *
54745177 CCTTTGTGTAATATTCTGTAACG
1 CCTTTGTGTCATATTCTGCAATG
*
54745200 CCTTTGTGGCATATTCTGCAATG
1 CCTTTGTGTCATATTCTGCAATG
* *
54745223 CTTTTATGGT-ATATTCTGCAATG
1 CCTTTGT-GTCATATTCTGCAATG
*
54745246 CCTTTGTGTCATATTTTGCAATG
1 CCTTTGTGTCATATTCTGCAATG
* * *
54745269 CCTTTGTGGCATATTTTGTAATG
1 CCTTTGTGTCATATTCTGCAATG
*
54745292 CCTTTGTGGCATA
1 CCTTTGTGTCATA
54745305 CATATTCTGT
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
22 2 0.02
23 88 0.97
24 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.45
Consensus pattern (23 bp):
CCTTTGTGTCATATTCTGCAATG
Found at i:54745259 original size:46 final size:46
Alignment explanation
Indices: 54745187--54745304 Score: 164
Period size: 46 Copynumber: 2.6 Consensus size: 46
54745177 CCTTTGTGTA
* * *
54745187 ATATTCTGTAACGCCTTTGTGGCATATTCTGCAATGCTTTTATGGT
1 ATATTCTGTAATGCCTTTGTGGCATATTCTGCAATGCCTTTATGGC
* * * *
54745233 ATATTCTGCAATGCCTTTGTGTCATATTTTGCAATGCCTTTGTGGC
1 ATATTCTGTAATGCCTTTGTGGCATATTCTGCAATGCCTTTATGGC
*
54745279 ATATTTTGTAATGCCTTTGTGGCATA
1 ATATTCTGTAATGCCTTTGTGGCATA
54745305 CATATTCTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (46 bp):
ATATTCTGTAATGCCTTTGTGGCATATTCTGCAATGCCTTTATGGC
Found at i:54758853 original size:29 final size:29
Alignment explanation
Indices: 54758820--54758979 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
54758810 GTGACGAGAT
54758820 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54758849 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
54758878 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* ** * ***
54758907 CGGCACTGGGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGC-ATGCTGGAAATATA
* ** * *
54758936 TGGCACTATGTGTGCGGGCT-TAAATCACA
1 TGGCACTAAGTGTGCATGCTGGAAAT-ATA
54758965 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
54758980 GAAATCGAGT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:54764667 original size:27 final size:26
Alignment explanation
Indices: 54764619--54764784 Score: 197
Period size: 27 Copynumber: 6.2 Consensus size: 26
54764609 AGGAAGCGTC
* * *
54764619 CTGGTGGCTATGGCACAAATATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
54764646 CTGGTGGCTCTGCTACATATATCTGCT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
54764673 CTGGTGGCTCTGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
54764700 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
54764727 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
54764755 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
54764781 CTGG
1 CTGG
54764785 CAGCCATGCT
Statistics
Matches: 122, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.07
27 95 0.78
28 19 0.16
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:54764701 original size:54 final size:54
Alignment explanation
Indices: 54764619--54764784 Score: 237
Period size: 54 Copynumber: 3.1 Consensus size: 54
54764609 AGGAAGCGTC
* * * * *
54764619 CTGGTGGCTATGGCACAAATATCTGATCTGGTGGCTCTGCTACATATATCTGCT
1 CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTGCTACATATATCTGTT
*
54764673 CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTGCTACATATATCTGTT
*
54764727 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTG-TCACAT-TATCTGTT
1 CTGGTGGCTCTGCCACGATTATCTG-ATCTGGTGGCTCTGCT-ACATATATCTGTT
54764781 CTGG
1 CTGG
54764785 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 85 0.83
55 17 0.17
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTCTGCCACGATTATCTGATCTGGTGGCTCTGCTACATATATCTGTT
Found at i:54764775 original size:81 final size:81
Alignment explanation
Indices: 54764619--54764784 Score: 219
Period size: 81 Copynumber: 2.0 Consensus size: 81
54764609 AGGAAGCGTC
* * * *
54764619 CTGGTGGCTATGGCACAAATATCTGATCTGGTGGCTCTGCTACATATATCTGCTCTGGTGGCTCT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGATCTGGTGACTCT
54764684 GCCACGATTATCTGAT
66 GCCACGATTATCTGAT
* * *
54764700 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGAT-TATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCAC-ATATATCTG-ATCTGGTGACT
* *
54764764 CTGTCAC-ATTATCTGTT
64 CTGCCACGATTATCTGAT
54764781 CTGG
1 CTGG
54764785 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 57 0.77
82 17 0.23
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (81 bp):
CTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGATCTGGTGACTCT
GCCACGATTATCTGAT
Found at i:54766479 original size:41 final size:41
Alignment explanation
Indices: 54766433--54766527 Score: 190
Period size: 41 Copynumber: 2.3 Consensus size: 41
54766423 TACTTGACAA
54766433 CTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGATAG
1 CTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGATAG
54766474 CTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGATAG
1 CTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGATAG
54766515 CTTGTGTGAGCAG
1 CTTGTGTGAGCAG
54766528 GCCCGTTGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (41 bp):
CTTGTGTGAGCAGCACCGTGTAGCTACGTCTTGACTGATAG
Found at i:54768649 original size:25 final size:25
Alignment explanation
Indices: 54768621--54768677 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
54768611 AACTTTTCTA
54768621 AGCATTTA-AAGTCACAACTCCTGTG
1 AGCATTTACAA-TCACAACTCCTGTG
* **
54768646 AGCATTTACAATCACAGCTTGTGTG
1 AGCATTTACAATCACAACTCCTGTG
54768671 AGCATTT
1 AGCATTT
54768678 TTCCCGCGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCATTTACAATCACAACTCCTGTG
Found at i:54770409 original size:20 final size:19
Alignment explanation
Indices: 54770364--54770410 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54770354 GTGTCTGCCA
* *
54770364 ATAAATGAT-TACATGTGT
1 ATAAATAATGTACATATGT
54770382 ATAAATAATGTACATATGT
1 ATAAATAATGTACATATGT
54770401 ATAAAATAAT
1 AT-AAATAAT
54770411 AAATAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (19 bp):
ATAAATAATGTACATATGT
Found at i:54770491 original size:4 final size:4
Alignment explanation
Indices: 54770460--54770518 Score: 52
Period size: 4 Copynumber: 14.5 Consensus size: 4
54770450 TTATAATAAT
*
54770460 AATA AAGTA AATA AA-A GAATA AACA AATA AATA AATGA AATGA AAT-
1 AATA AA-TA AATA AATA -AATA AATA AATA AATA AAT-A AAT-A AATA
54770506 AA-A AATA AATA AA
1 AATA AATA AATA AA
54770519 AGAATGAACG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 5 0.11
4 28 0.60
5 14 0.30
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:54771376 original size:41 final size:40
Alignment explanation
Indices: 54771322--54771451 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 40
54771312 GACCTCGAGT
*
54771322 CGATGAGACACTGGGTGTCAATCTATTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGATTAATC
** ** *
54771363 CGATGAGGTACTGGGTACCAA-T-TTACTTCGGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGATTAATC
* *
54771400 CGATGAGACATTGGGTGTCAATTTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTAATC
*
54771440 CGATGAGGCACT
1 CGATGAGACACT
54771452 ATGTGCCAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
37 16 0.23
38 13 0.19
39 3 0.04
40 21 0.30
41 17 0.24
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGATTAATC
Found at i:54773788 original size:27 final size:28
Alignment explanation
Indices: 54773729--54773789 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
54773719 TAAAAAGTAA
54773729 AAAAAAATCAATTAAAACTAAAAAAAAT
1 AAAAAAATCAATTAAAACTAAAAAAAAT
* * *
54773757 TAAAAAAT-AGTTAAAA-TAAAAAATCAT
1 AAAAAAATCAATTAAAACTAAAAAA-AAT
54773784 AAAAAA
1 AAAAAA
54773790 TCCAAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.25
27 14 0.50
28 7 0.25
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (28 bp):
AAAAAAATCAATTAAAACTAAAAAAAAT
Found at i:54773846 original size:21 final size:23
Alignment explanation
Indices: 54773804--54773855 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
54773794 AAAAAAATAG
*
54773804 AAAATTATAAAAAAAATCTATTTTT
1 AAAATTAT-AAAAAAA-CTATTTTC
54773829 AAAATTAT-AAAAAA-TATTTTC
1 AAAATTATAAAAAAACTATTTTC
54773850 AAAATT
1 AAAATT
54773856 CTCATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 12 0.46
23 6 0.23
25 8 0.31
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATTATAAAAAAACTATTTTC
Found at i:54776273 original size:26 final size:27
Alignment explanation
Indices: 54776235--54776291 Score: 107
Period size: 26 Copynumber: 2.1 Consensus size: 27
54776225 AGAGTTTGAC
54776235 CATACTTTTTAAACCTTAGTAATACTT
1 CATACTTTTTAAACCTTAGTAATACTT
54776262 CATA-TTTTTAAACCTTAGTAATACTT
1 CATACTTTTTAAACCTTAGTAATACTT
54776288 CATA
1 CATA
54776292 ACCTAGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.44
Consensus pattern (27 bp):
CATACTTTTTAAACCTTAGTAATACTT
Found at i:54781157 original size:19 final size:19
Alignment explanation
Indices: 54781121--54781158 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54781111 TGTACAAAGC
*
54781121 TATCTTTAACTGGTATAAA
1 TATCTTTAACTGCTATAAA
54781140 TATCTTT-ACTGCTAATAAA
1 TATCTTTAACTGCT-ATAAA
54781159 AATGCATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (19 bp):
TATCTTTAACTGCTATAAA
Found at i:54784756 original size:43 final size:43
Alignment explanation
Indices: 54784665--54784759 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
54784655 ATGTGGTTAT
* *
54784665 GTGTAAGACCATGTCTGGGAAATTGGCATCATTATGTGATTAC
1 GTGTAAGACAATGTCTGGGAAATTGGCATCATTATGTAATTAC
* * * *
54784708 ATGTAAGACAATGTCTGGGACATTGGCATCGTTAAT-TAATTTC
1 GTGTAAGACAATGTCTGGGAAATTGGCATCATT-ATGTAATTAC
54784751 GTGTAAGAC
1 GTGTAAGAC
54784760 CATAGTTGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 42 0.95
44 2 0.05
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (43 bp):
GTGTAAGACAATGTCTGGGAAATTGGCATCATTATGTAATTAC
Found at i:54787677 original size:93 final size:93
Alignment explanation
Indices: 54787565--54787736 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
54787555 GCCCATAAGT
* *
54787565 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54787630 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
54787658 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
54787723 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
54787737 CAAATATCCA
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:54787732 original size:46 final size:46
Alignment explanation
Indices: 54787557--54787732 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
54787547 TGTAACCCGC
* * *
54787557 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
54787603 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
54787653 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
54787696 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54787733 TGCCCAAATA
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:54789690 original size:30 final size:30
Alignment explanation
Indices: 54789646--54789734 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
54789636 CAAAGATAAC
54789646 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
54789675 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
54789705 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
54789735 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:54789694 original size:15 final size:15
Alignment explanation
Indices: 54789646--54789725 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
54789636 CAAAGATAAC
*
54789646 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54789660 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54789675 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54789690 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54789705 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54789720 AAGAAA
1 AAGAAA
54789726 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:54789734 original size:15 final size:15
Alignment explanation
Indices: 54789657--54789734 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
54789647 AGAAAACCGA
54789657 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
54789672 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
54789686 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
54789701 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
54789717 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
54789732 ATA
1 ATA
54789735 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:54792707 original size:46 final size:46
Alignment explanation
Indices: 54792640--54792768 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
54792630 TGTAACCCGC
* * *
54792640 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
54792686 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
54792732 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54792769 TGCCCAAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:54797884 original size:41 final size:41
Alignment explanation
Indices: 54797815--54797951 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 41
54797805 GCATACAACC
* * * *
54797815 TGCTAGGC-CTAAGCCTG-TATCATACACCGACACAAGGCC
1 TGCTAGGCTCAAAGCCTGATTTAATACACCGACACAAGGCT
* * * * *
54797854 TGCTAGACTCAAAGTCTGATTTTATACACCGGCA-ATAAGCT
1 TGCTAGGCTCAAAGCCTGATTTAATACACCGACACA-AGGCT
* *
54797895 TGCTAGGCAT-AAAGCCTGATTTAATTCACCAACACAAGGCT
1 TGCTAGGC-TCAAAGCCTGATTTAATACACCGACACAAGGCT
54797936 TGCTAGGCTCAAAGCC
1 TGCTAGGCTCAAAGCC
54797952 CGAATATCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
39 7 0.09
40 9 0.12
41 59 0.77
42 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (41 bp):
TGCTAGGCTCAAAGCCTGATTTAATACACCGACACAAGGCT
Found at i:54806411 original size:24 final size:24
Alignment explanation
Indices: 54806119--54806409 Score: 510
Period size: 24 Copynumber: 12.1 Consensus size: 24
54806109 GCAAAGACCA
*
54806119 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
54806143 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
54806167 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
54806191 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
54806215 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
54806239 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
54806263 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
54806287 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
54806311 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
54806335 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
54806359 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
54806383 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
54806407 TAT
1 TAT
54806410 AGTCACATTC
Statistics
Matches: 260, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 260 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:54814296 original size:29 final size:29
Alignment explanation
Indices: 54814234--54814336 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
54814224 GTGACGAGAT
* * *
54814234 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
54814263 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
54814292 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
54814321 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54814337 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:54816905 original size:32 final size:33
Alignment explanation
Indices: 54816860--54816929 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
54816850 ACAGTACTGC
* * *
54816860 TACTGTATAAGGGCTTGGCCCAGATTGTACGGA
1 TACTGAATAAGGGCATGGCCCAGACTGTACGGA
**
54816893 TACTGAAT-AGGGCATGGCCCAGACTGTATTGA
1 TACTGAATAAGGGCATGGCCCAGACTGTACGGA
54816925 TACTG
1 TACTG
54816930 TGTTGTTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (33 bp):
TACTGAATAAGGGCATGGCCCAGACTGTACGGA
Found at i:54830025 original size:40 final size:39
Alignment explanation
Indices: 54829981--54830173 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
54829971 GTTCAAAACA
* * ** * *
54829981 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
54830021 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
54830061 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54830100 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54830139 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
54830174 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:54830092 original size:39 final size:39
Alignment explanation
Indices: 54830011--54830173 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
54830001 TATGGTAACC
* *
54830011 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54830051 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54830090 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54830129 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
54830168 CGCACA
1 CGCACA
54830174 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54836540 original size:40 final size:39
Alignment explanation
Indices: 54836496--54836688 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
54836486 GTTCAAAACA
* * ** * *
54836496 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
54836536 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
54836576 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54836615 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
54836654 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACA
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACA
54836689 TTCATTCACA
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:54836607 original size:39 final size:39
Alignment explanation
Indices: 54836526--54836688 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
54836516 TATGGTAACC
* *
54836526 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
54836566 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54836605 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
54836644 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
54836683 CGCACA
1 CGCACA
54836689 TTCATTCACA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:54838790 original size:29 final size:29
Alignment explanation
Indices: 54838726--54838862 Score: 134
Period size: 29 Copynumber: 4.8 Consensus size: 29
54838716 TACATATATG
*
54838726 CATATGGCCCACTT-GGCCCAA-TCTCATT
1 CATATGGCCCA-TTAGGCCCAATTCACATT
* * **
54838754 TATATGGCCTATCGGGCCCAATTCACATT
1 CATATGGCCCATTAGGCCCAATTCACATT
* *
54838783 CATATGGCCCATTAGGCCCAATTCATAAT
1 CATATGGCCCATTAGGCCCAATTCACATT
* * *
54838812 CATATTGCCCATTAGGCCCAAATCACCTT
1 CATATGGCCCATTAGGCCCAATTCACATT
* **
54838841 TATATGGCCTGTTAGGCCCAAT
1 CATATGGCCCATTAGGCCCAAT
54838863 CACCTTATAT
Statistics
Matches: 87, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
27 1 0.01
28 16 0.18
29 70 0.80
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCACATT
Found at i:54849559 original size:40 final size:40
Alignment explanation
Indices: 54849502--54849704 Score: 300
Period size: 40 Copynumber: 5.1 Consensus size: 40
54849492 CGGATGATAA
* * *
54849502 CCGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
54849542 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54849582 ACGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
54849622 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* **
54849662 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54849702 CCG
1 CCG
54849705 ATTAAAGCCC
Statistics
Matches: 149, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 148 0.99
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54857049 original size:40 final size:40
Alignment explanation
Indices: 54856949--54857151 Score: 309
Period size: 40 Copynumber: 5.1 Consensus size: 40
54856939 CGGATGATAA
* *
54856949 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54856988 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
54857028 CCGGGATAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
54857068 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
54857108 CTGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
54857148 CCGG
1 CCGG
54857152 TTAAAGCCCA
Statistics
Matches: 148, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 34 0.23
40 114 0.77
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:54860763 original size:75 final size:76
Alignment explanation
Indices: 54860672--54860820 Score: 230
Period size: 76 Copynumber: 2.0 Consensus size: 76
54860662 TATGGAAATT
*
54860672 TATATTCTTTTGGAAAGAATATAATT-CATTTTTCTAACTTTCCATTT-CTCTTCTCTATTAATA
1 TATATTCTTTTAGAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGC-CTTCTCTATTAATA
*
54860735 AGGGAATAATCC
65 AGGAAATAATCC
* * *
54860747 TATATTCTTTTAGAAAGAATATAATTCCTTTTTTCTAATTTTCCATTTGCCTTCTTTATTAATAA
1 TATATTCTTTTAGAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
54860812 GGAAATAAT
66 GGAAATAAT
54860821 ATTGGTTTTC
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 25 0.37
76 41 0.61
77 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (76 bp):
TATATTCTTTTAGAAAGAATATAATTCCATTTTTCTAACTTTCCATTTGCCTTCTCTATTAATAA
GGAAATAATCC
Found at i:54864946 original size:17 final size:18
Alignment explanation
Indices: 54864904--54864952 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
54864894 AGTTGAAAAG
54864904 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
54864923 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
54864940 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
54864953 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:54865841 original size:40 final size:40
Alignment explanation
Indices: 54865775--54865941 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
54865765 AAATTGAATG
* * *
54865775 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
54865814 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
54865854 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
54865894 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
54865934 ATATCCGG
1 ATATCCGG
54865942 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:54872924 original size:17 final size:18
Alignment explanation
Indices: 54872882--54872930 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
54872872 AGTTGAAAAG
54872882 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
54872901 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
54872918 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
54872931 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:54873864 original size:39 final size:36
Alignment explanation
Indices: 54873777--54873888 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 36
54873767 GCTGAAATTA
* * * *
54873777 TATCCGGGTAAGACCCGAAGCATTGTGCTAGTGGTT
1 TATCCGGCTAAGGCCCGAAGCATTGTGCGAGTGATT
*
54873813 TATCCGGGCTAAGGCCCGAAGGCATTCGTGCGAGTTATT
1 TATCC-GGCTAAGGCCCGAA-GCATT-GTGCGAGTGATT
*
54873852 CTATCCGGCTAA-GACCGAAGCATTTGTGC-ACGTGATT
1 -TATCCGGCTAAGGCCCGAAGCA-TTGTGCGA-GTGATT
54873889 ATACCGTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
36 6 0.10
37 24 0.38
38 13 0.21
39 15 0.24
40 5 0.08
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (36 bp):
TATCCGGCTAAGGCCCGAAGCATTGTGCGAGTGATT
Found at i:54881233 original size:29 final size:29
Alignment explanation
Indices: 54881200--54881331 Score: 140
Period size: 29 Copynumber: 4.6 Consensus size: 29
54881190 GTGACGAGAT
*
54881200 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* *
54881229 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * ***
54881258 TGGCACTAAGTGTGCGAGCTCGAAGGGCA
1 TGGCACTAAGTGTGCGTGCTGGAAATACA
* * * *
54881287 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ACA
54881316 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
54881332 AAATCGAGTA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 2 0.02
29 86 0.98
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATACA
Found at i:54887416 original size:40 final size:40
Alignment explanation
Indices: 54887337--54887513 Score: 171
Period size: 40 Copynumber: 4.5 Consensus size: 40
54887327 TGGATGATAA
* * * ** *
54887337 CCGGACTAAGATCTGAAGGCATTCGTGCGACTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
54887377 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-CTATAT
* *
54887417 CTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * *
54887457 CCGAGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
*
54887497 AC-GGCTAA-ATCCCGAAG
1 CCGGGCTAAGA-CCCGAAG
54887514 ATACTTGGGT
Statistics
Matches: 113, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 14 0.12
40 96 0.85
41 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:54887495 original size:80 final size:80
Alignment explanation
Indices: 54887342--54887496 Score: 213
Period size: 80 Copynumber: 1.9 Consensus size: 80
54887332 GATAACCGGA
* * * * * *
54887342 CTAAGATCTGAAGGCATTCGTGCGACTTGCTATATCCGGGCTATGTCCCGAAGGCATTTATGCTA
1 CTAAGACCCGAAGGCATTCGTGCGACTTGCTATATCCGAGCTAAGACCCGAAGGCATTTATGCGA
54887407 GTGATTATATCTGGG
66 GTGATTATATCTGGG
* * *
54887422 CTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGAGCTAAGACCCGAAGGCATTTGTGCGA
1 CTAAGACCCGAAGGCATTCGTGCGACTTGCTATATCCGAGCTAAGACCCGAAGGCATTTATGCGA
54887487 GTTG-TTATAT
66 G-TGATTATAT
54887497 ACGGCTAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
80 63 0.97
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (80 bp):
CTAAGACCCGAAGGCATTCGTGCGACTTGCTATATCCGAGCTAAGACCCGAAGGCATTTATGCGA
GTGATTATATCTGGG
Found at i:54887777 original size:22 final size:22
Alignment explanation
Indices: 54887737--54887778 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
54887727 GAATGTGCAT
*
54887737 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
54887759 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
54887779 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:54893149 original size:127 final size:127
Alignment explanation
Indices: 54892821--54893128 Score: 399
Period size: 127 Copynumber: 2.4 Consensus size: 127
54892811 TATTTAGTTC
* * * *
54892821 AATGAAAAACCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGAACATTGT
1 AATGGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGAATATTGC
* *
54892886 CTTGCTTTAGAATTTATAAAACACGAGTGAAATACTAAAGGAATATTCAATTATTAGGAACA
66 CTTGTTTTAGAATTTAGAAAACACGAGTGAAATACTAAAGGAATATTCAATTATTAGGAACA
* * *
54892948 AACTGG-AAATTGAAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATTGAATATTG
1 AA-TGGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGAATATTG
** * ** * *
54893012 CCTTGTTTTAGAATTTAGAAAGTACG-GATGAAAT-TTCAAAGGAATATTTGATTATTTGG-TCA
65 CCTTGTTTTAGAATTTAGAAAACACGAG-TGAAATACT-AAAGGAATATTCAATTATTAGGAACA
* *
54893074 AATGGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAGTTCCCAAACAT
1 AATGGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACAT
54893129 CAATTATTAC
Statistics
Matches: 156, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
125 3 0.02
126 50 0.32
127 101 0.65
128 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (127 bp):
AATGGAAAATCGAAACCCAGCACGGTAGGGCACGATTCCTCGAATTTCCAAACATTGAATATTGC
CTTGTTTTAGAATTTAGAAAACACGAGTGAAATACTAAAGGAATATTCAATTATTAGGAACA
Found at i:54895213 original size:29 final size:28
Alignment explanation
Indices: 54895179--54895281 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
54895169 TACTCAATCA
*
54895179 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
54895208 CGCACACATAGTGCCATATAGTCTAAACT
1 CGCACACTTAGTGCCATATATTC-AAGCT
* *
54895237 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
54895266 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
54895282 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 3 0.05
29 57 0.93
30 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:54903994 original size:41 final size:41
Alignment explanation
Indices: 54903949--54904065 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 41
54903939 TGAAAGATAA
54903949 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * * *
54903990 ATGTAAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54904019 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
54904060 ATGTAG
1 ATGTAG
54904066 ACAAGAGAGC
Statistics
Matches: 52, Mismatches: 12, Indels: 24
0.59 0.14 0.27
Matches are distributed among these distances:
29 6 0.12
30 10 0.19
31 1 0.02
32 2 0.04
33 2 0.04
34 1 0.02
35 2 0.04
36 1 0.02
37 2 0.04
38 2 0.04
39 1 0.02
40 10 0.19
41 12 0.23
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:54904006 original size:70 final size:71
Alignment explanation
Indices: 54903917--54904079 Score: 310
Period size: 70 Copynumber: 2.3 Consensus size: 71
54903907 GAGATGTATC
*
54903917 CCATGTTGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54903982 AGGACA
66 AGGACA
54903988 CCATGTA-ACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
54904052 AGGACA
66 AGGACA
54904058 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
54904080 AGACAAATCG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
70 70 0.78
71 20 0.22
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:54905958 original size:138 final size:138
Alignment explanation
Indices: 54905646--54906066 Score: 684
Period size: 138 Copynumber: 3.1 Consensus size: 138
54905636 GAGAACATAG
*
54905646 ATATAATTAATATATGAATTTGATTCATGCAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATGCAAAATATTATTTGTATATATTTTACCAAATTTATT
* *
54905711 AATATAAACAGTTATATTAATAAATTTCGGTCAAAATATAAAA-AAATGGAAATTAATATTCTTT
66 AATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
*
54905775 TAGAAACA
131 TAGAAAGA
* * *
54905783 ATATAATTAATATATGAATTTGATTCATACAAAATATTATTTGTATATATTTTACCGAATTTACT
1 ATATAATTAATATATGAATTTGATTCATGCAAAATATTATTTGTATATATTTTACCAAATTTATT
* * * *
54905848 AATATAAGCAGTTATACTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTGTTT
66 AATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
54905913 TAGAAAGA
131 TAGAAAGA
*
54905921 ATATAATTAATATATAAATTTGATTCATGCAAAATATTACTTT-TATATATTTTACCAAATTTAT
1 ATATAATTAATATATGAATTTGATTCATGCAAAATATTA-TTTGTATATATTTTACCAAATTTAT
* *
54905985 TAATATAAACAGTTATATTAATTAATTCCGGTTAAAATATAAAAGACATGGAAATTAATATTCTT
65 TAATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
54906050 TTGGAAAGA
130 TTAGAAAGA
54906059 ATATAATT
1 ATATAATT
54906067 TAGTTTTTTA
Statistics
Matches: 260, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
137 100 0.38
138 157 0.60
139 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATGCAAAATATTATTTGTATATATTTTACCAAATTTATT
AATATAAACAGTTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTT
TAGAAAGA
Found at i:54906927 original size:14 final size:14
Alignment explanation
Indices: 54906908--54906937 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54906898 CATTTAAAAG
*
54906908 TTTTAATAAATATT
1 TTTTAAAAAATATT
54906922 TTTTAAAAAATATT
1 TTTTAAAAAATATT
54906936 TT
1 TT
54906938 ATATAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAAAAAATATT
Found at i:54907994 original size:17 final size:18
Alignment explanation
Indices: 54907961--54907994 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54907951 AGTATTTTTT
54907961 TTTTAAATAACAAAAAAC
1 TTTTAAATAACAAAAAAC
*
54907979 TTTTAAA-AATAAAAAA
1 TTTTAAATAACAAAAAA
54907995 TATTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
TTTTAAATAACAAAAAAC
Found at i:54911474 original size:40 final size:40
Alignment explanation
Indices: 54911392--54911489 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
54911382 TTCGAATACT
* *
54911392 TGAAAAGGTTGAAAAAGAAATATCTAAAAAGGATATCAAA
1 TGAAAAGGTTGAAAAGGAAATATCCAAAAAGGATATCAAA
**
54911432 TGAAAAGGTTGAAAAGGACGTTATCCAAAAAGGATATC-AA
1 TGAAAAGGTTGAAAAGGA-AATATCCAAAAAGGATATCAAA
54911472 TGAAAA-GTTCGAAAAGGA
1 TGAAAAGGTT-GAAAAGGA
54911490 TAGTAATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 3 0.06
40 33 0.63
41 16 0.31
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.19
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGAAATATCCAAAAAGGATATCAAA
Found at i:54922975 original size:89 final size:89
Alignment explanation
Indices: 54922824--54923004 Score: 224
Period size: 89 Copynumber: 2.0 Consensus size: 89
54922814 AGAAAAGACC
* * **
54922824 TGTAGCTTTAATCTGCTCCACTGTAACTTTAGGGAGATAAGACTTTCTAGTTTTGATCTGCTCCA
1 TGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGATAAGACTTTCTAGTTTCAATCTGCTCCA
*
54922889 CTACAACTT-TAAGGAGATAAGGTT
66 CTACAACTTCT-AGGAGATAAGATT
* * *
54922913 TGTAGCTTTAATATGCTCTACTGTAACTTCAGGTAGATAAGA-TTTGCTA-TCTTCAATTTGCTC
1 TGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGATAAGACTTT-CTAGT-TTCAATCTGCTC
* *
54922976 CACTGCAACTTCTGGGAGATAAGATT
64 CACTACAACTTCTAGGAGATAAGATT
54923002 TGT
1 TGT
54923005 TTTATTTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 4 0.05
89 74 0.94
90 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37
Consensus pattern (89 bp):
TGTAGCTTTAATATGCTCCACTGTAACTTCAGGGAGATAAGACTTTCTAGTTTCAATCTGCTCCA
CTACAACTTCTAGGAGATAAGATT
Found at i:54922986 original size:45 final size:44
Alignment explanation
Indices: 54922795--54923170 Score: 281
Period size: 44 Copynumber: 8.7 Consensus size: 44
54922785 CTTCGATCCA
* **
54922795 CTCCACTGTAACTTCAGGGAGAAAAGACCTGTAGCTTTAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * *
54922839 CTCCACTGTAACTTTAGGGAGATAAGACTTTCTAGTTTTGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGA-TTTGTAGCTTTAATCTG
** * * * *
54922884 CTCCACTACAACTTTAAGGAGATAAGGTTTGTAGCTTTAATATG
1 CTCCACTGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
* * * * *
54922928 CTCTACTGTAACTTCAGGTAGATAAGATTTGCTATCTTCAATTTG
1 CTCCACTGTAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTG
* * ** *
54922973 CTCCACTGCAACTTCTGGGAGATAAGATTTGTTTTATTTTTAACCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATTTG---TAGCTTTAATCTG
* * **
54923020 CTCCTCTGTTACTTCAGGGAGATAACG-TTTGTATATTT--T-T-
1 CTCCACTGTAACTTCAGGGAGATAA-GATTTGTAGCTTTAATCTG
* *
54923060 AT-C-C--T-AC-TCAGGGAGATAAGCA-TTGTGGCTTTAATCTG
1 CTCCACTGTAACTTCAGGGAGATAAG-ATTTGTAGCTTTAATCTG
* * * * * *
54923098 CTCCACTGCAACTTCAGAGAGATAAGATTAGTGGCTTCAATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
*
54923142 CTCCACTGTAACTTCAGAGAGATAAGATT
1 CTCCACTGTAACTTCAGGGAGATAAGATT
54923171 CACCATGATA
Statistics
Matches: 263, Mismatches: 51, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
33 1 0.00
34 19 0.07
35 2 0.01
36 2 0.01
37 1 0.00
38 2 0.01
39 2 0.01
40 2 0.01
41 1 0.00
43 3 0.01
44 121 0.46
45 72 0.27
47 34 0.13
48 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTG
Found at i:54923359 original size:46 final size:47
Alignment explanation
Indices: 54923266--54923375 Score: 134
Period size: 46 Copynumber: 2.4 Consensus size: 47
54923256 AAGATTCACT
* * *
54923266 AACTTTAGGGAGATAAGTTTTGTTTTATTTTTAACCTACTCCTCTGC
1 AACTTTAGGGAGATAAGGTTTGTTATATTTTTAACATACTCCTCTGC
* * *
54923313 AACTTTTGGGAGATAAGGTTTG-TATATTTTTATCATACT-TTACTGC
1 AACTTTAGGGAGATAAGGTTTGTTATATTTTTAACATACTCCT-CTGC
*
54923359 AACTTCAGGGAGATAAG
1 AACTTTAGGGAGATAAG
54923376 CATTGTGGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.02
46 33 0.61
47 20 0.37
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (47 bp):
AACTTTAGGGAGATAAGGTTTGTTATATTTTTAACATACTCCTCTGC
Found at i:54923409 original size:44 final size:44
Alignment explanation
Indices: 54923295--54924026 Score: 340
Period size: 44 Copynumber: 15.9 Consensus size: 44
54923285 TTGTTTTATT
* * ** * **
54923295 TTTAACCTACTCCTCTGCAACTTTTGGGAGATAAGGTTTGTATAT
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA-GC
* ** *
54923340 TTTTATCATACTTTACTGCAACTTCAGGGAGATAAGCA-TTGTGGC
1 TTTAATC-TACTCCACTGCAACTTCAGGGAGATAAG-ATTTGTAGC
* * *
54923385 TTTAATCTACTCCACTGCAACTTCAGAGAGATAAGATTAGTGGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * * * * *
54923429 TTCAATCTGCTCTACTGCAACTTTAGAGAGATAAGATTCACCATCGTAGA
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-----T-GTAGC
* * * * * * *
54923479 TTTGATCTGAC-CTAGTACAACTTCAAAGGTATAGGATTTATGACTTGTAGC
1 TTTAATCT-ACTCCACTGCAACTTC--AGG--GA-GA--TAAGATTTGTAGC
* * * *
54923530 -TTGATCTATTCCACTGCAACTTCAGGGATATAAGATTTGCTATC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * * *
54923574 TTCAATTTACTCCACTGCAACATCAGGGAGATAAGATTTATAAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
*
54923618 TTAAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTGTAGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAG-------ATTTGTAGC
* ** * * * *
54923669 CTTAATCTTGTTCCACTGTAACTTCAAGGAGATAATACTTGTTGTAAC
1 TTTAATC-TACTCCACTGCAACTTCAGGGAGATAAGA--T-TTGTAGC
* * * * *
54923717 TTCAACCTACTCCAGTGCAACTTCAGGGAGATAAGGTTTATAGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* * *
54923761 TTTAATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGTTATC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGC
* * * *
54923806 TCTAATCTACTCCATTACAA-TTCAAGGAGATAAGATTTGTAATTTATAGC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-------TAGC
** * ** *
54923856 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTATC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT-TGTAGC
* * * * * *
54923901 TTCAGTCTACTCCACTACAACTTCAGGGAGATAAGACTTATAAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
* ** * * * * *
54923945 TTCAA-CTTGTTCCATTGCAACTTTAGGGAGATAAGGTTAGTGGC
1 TTTAATC-TACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
** * * * *
54923989 TTCGATATGCTTCACTGCAACTTCAAGGAGATAAGATT
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
54924027 CGCCATGCTA
Statistics
Matches: 513, Mismatches: 132, Indels: 85
0.70 0.18 0.12
Matches are distributed among these distances:
43 9 0.02
44 220 0.43
45 99 0.19
46 28 0.05
47 23 0.04
48 13 0.03
49 1 0.00
50 54 0.11
51 32 0.06
52 26 0.05
54 1 0.00
55 2 0.00
57 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGC
Found at i:54923426 original size:296 final size:284
Alignment explanation
Indices: 54922989--54923540 Score: 836
Period size: 296 Copynumber: 1.9 Consensus size: 284
54922979 TGCAACTTCT
* **
54922989 GGGAGATAAGATTTGTTTTATTTTTAACCTGCTCCTCTGTTACTTCAGGGAGATAACGTTTGTAT
1 GGGAGATAAGATTTGTTTTATTTTTAACCTACTCCTCTGCAACTTCAGGGAGATAACGTTTGTAT
*
54923054 ATTTTTATCCTACTCAGGGAGATAAGCATTGTGGCTTTAATCTGCTCCACTGCAACTTCAGAGAG
66 ATTTTTATCCTACTCAGGGAGATAAGCATTGTGGCTTTAATCTACTCCACTGCAACTTCAGAGAG
*
54923119 ATAAGATTAGTGGCTTCAATCTACTCCACTGTAACTTCAGAGAGATAAGATTCACCAT-GATAGA
131 ATAAGATTAGTGGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTCACCATCG-TAGA
* *
54923183 TTTGATCTGACCTACTGCAACTTCAAAGGTATAGGATTTATAACTTGTAGGTTGATCTATTCTAC
195 TTTGATCTGACCTACTACAACTTCAAAGGTATAGGATTTATAACTTGTAGCTTGATCTATTCTAC
54923248 AGGGATATAAGATTCACTAACTTTA
260 AGGGATATAAGATTCACTAACTTTA
* ** *
54923273 GGGAGATAAGTTTTGTTTTATTTTTAACCTACTCCTCTGCAACTTTTGGGAGATAAGGTTTGTAT
1 GGGAGATAAGATTTGTTTTATTTTTAACCTACTCCTCTGCAACTTCAGGGAGATAACGTTTGTAT
54923338 ATTTTTATCATACTTTACTGCAACTTCAGGGAGATAAGCATTGTGGCTTTAATCTACTCCACTGC
66 A-TTTT-T-AT-C----CT---AC-TCAGGGAGATAAGCATTGTGGCTTTAATCTACTCCACTGC
* * *
54923403 AACTTCAGAGAGATAAGATTAGTGGCTTCAATCTGCTCTACTGCAACTTTAGAGAGATAAGATTC
119 AACTTCAGAGAGATAAGATTAGTGGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTC
* *
54923468 ACCATCGTAGATTTGATCTGACCTAGTACAACTTCAAAGGTATAGGATTTATGACTTGTAGCTTG
184 ACCATCGTAGATTTGATCTGACCTACTACAACTTCAAAGGTATAGGATTTATAACTTGTAGCTTG
54923533 ATCTATTC
249 ATCTATTC
54923541 CACTGCAACT
Statistics
Matches: 239, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
284 59 0.25
285 4 0.02
286 1 0.00
287 2 0.01
288 1 0.00
292 2 0.01
295 2 0.01
296 167 0.70
297 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (284 bp):
GGGAGATAAGATTTGTTTTATTTTTAACCTACTCCTCTGCAACTTCAGGGAGATAACGTTTGTAT
ATTTTTATCCTACTCAGGGAGATAAGCATTGTGGCTTTAATCTACTCCACTGCAACTTCAGAGAG
ATAAGATTAGTGGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATTCACCATCGTAGAT
TTGATCTGACCTACTACAACTTCAAAGGTATAGGATTTATAACTTGTAGCTTGATCTATTCTACA
GGGATATAAGATTCACTAACTTTA
Found at i:54923837 original size:187 final size:187
Alignment explanation
Indices: 54923539--54923949 Score: 447
Period size: 187 Copynumber: 2.2 Consensus size: 187
54923529 CTTGATCTAT
* * * * *
54923539 TCCACTGCAACTTCAGGGATATAAGATTTGCTATCTTCAATTTACTCCACTGCAACATCAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGATAGCTTCAATCTACTCCACTGCAACATCAGAGAG
* * * *
54923604 ATAAGATTTATAACTTAAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCACCATTTGTAGC
66 ATAAGATTTATAACTTAAATCTACTCCACTACAACTTCAAGGAGATAAGATTCACAATTTATAGC
* *
54923669 CTTAATCTTGTTCCACTGTAACTTCAAGGAGATAATACTTGTTGTAACTTCAACCTAC
131 CTTAATC-TGTTCCACTGCAACTTCAAGGAAATAATACTTGTTGTAACTTCAACCTAC
* * * * *
54923727 TCCAGTGCAACTTCAGGGAGATAAGGTTT-ATAGCTTTAATCTACTCTACTGCAACTTCAGAGAG
1 TCCACTGCAACTTCAGGGAGATAAGATTTGATAGCTTCAATCTACTCCACTGCAACATCAGAGAG
* * * ***
54923791 ATAAGATTTGTTATCTCT-AATCTACTCCATTACAA-TTCAAGGAGATAAGATTTGTAATTTATA
66 ATAAGATTT-ATAACT-TAAATCTACTCCACTACAACTTCAAGGAGATAAGATTCACAATTTATA
* * * *** * **
54923854 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-CACTATCTTCAGTCTAC
129 GCCTTAATCTGTTCCACTGCAACTTCAAGGAAATAATACTTGTTGTAACTTCAACCTAC
* * *
54923911 TCCACTACAACTTCAGGGAGATAAGACTT-ATAACTTCAA
1 TCCACTGCAACTTCAGGGAGATAAGATTTGATAGCTTCAA
54923950 CTTGTTCCAT
Statistics
Matches: 184, Mismatches: 37, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
184 44 0.24
185 2 0.01
186 25 0.14
187 67 0.36
188 45 0.24
189 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (187 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTGATAGCTTCAATCTACTCCACTGCAACATCAGAGAG
ATAAGATTTATAACTTAAATCTACTCCACTACAACTTCAAGGAGATAAGATTCACAATTTATAGC
CTTAATCTGTTCCACTGCAACTTCAAGGAAATAATACTTGTTGTAACTTCAACCTAC
Found at i:54923873 original size:95 final size:93
Alignment explanation
Indices: 54923584--54923936 Score: 308
Period size: 95 Copynumber: 3.8 Consensus size: 93
54923574 TTCAATTTAC
* * * * *
54923584 TCCACTGCAACATCAGGGAGATAAGATTT-ATAACTTAAATCTACTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGTTAACTTCAATCTACTCCACTACAACTTCAGGGAG
* * *
54923648 ATAAGATTCACCATTTGTAGCCTTAATCTTGT
66 ATAAGATT---GATTTATAGCTTTAATC-TGT
* * * * * *
54923680 TCCACTGTAACTTCA-AGGAGATAATACTTGTTGTAACTTCAACCTACTCCAGTGCAACTTCAGG
1 TCCACTGCAACTTCAGA-GAGATAAGATTTG-T-TAACTTCAATCTACTCCACTACAACTTCAGG
**
54923744 GAGATAAG---G-TTTATAGCTTTAATCTAC
63 GAGATAAGATTGATTTATAGCTTTAATCTGT
* * * *
54923771 TCTACTGCAACTTCAGAGAGATAAGATTTGTTATC-TCTAATCTACTCCATTACAA-TTCAAGGA
1 TCCACTGCAACTTCAGAGAGATAAGATTTGTTAACTTC-AATCTACTCCACTACAACTTCAGGGA
54923834 GATAAGATTTGTAATTTATAGCTTTAATCTGT
65 GATAAGA-TTG--ATTTATAGCTTTAATCTGT
* * *** * *
54923866 TCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTACTCCACTACAACTTCAGGGAG
1 TCCACTGCAACTTCAGAGAGATAAGATTTGTTAACTTCAATCTACTCCACTACAACTTCAGGGAG
54923931 ATAAGA
66 ATAAGA
54923937 CTTATAACTT
Statistics
Matches: 208, Mismatches: 34, Indels: 30
0.76 0.12 0.11
Matches are distributed among these distances:
88 15 0.07
89 17 0.08
90 1 0.00
91 25 0.12
92 15 0.07
95 60 0.29
96 39 0.19
99 36 0.17
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (93 bp):
TCCACTGCAACTTCAGAGAGATAAGATTTGTTAACTTCAATCTACTCCACTACAACTTCAGGGAG
ATAAGATTGATTTATAGCTTTAATCTGT
Found at i:54926038 original size:13 final size:13
Alignment explanation
Indices: 54926017--54926049 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
54926007 AAGGGCACAT
*
54926017 GCCCTTGTGGCCA
1 GCCCGTGTGGCCA
54926030 GCCCGTGTGGCCA
1 GCCCGTGTGGCCA
54926043 GCCCGTG
1 GCCCGTG
54926050 GGCAGTTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.06, C:0.39, G:0.36, T:0.18
Consensus pattern (13 bp):
GCCCGTGTGGCCA
Found at i:54927113 original size:33 final size:33
Alignment explanation
Indices: 54927055--54927192 Score: 156
Period size: 33 Copynumber: 4.2 Consensus size: 33
54927045 TGTACACTTG
* *
54927055 AAGTGTACA-TTCCTTTCCA-AGTGGTACACACA
1 AAGTATACATTTCCTTTCCATA-TGGTATACACA
*
54927087 AAGTATACATTTCCTTTTCATATGGTATACACA
1 AAGTATACATTTCCTTTCCATATGGTATACACA
* *** * *
54927120 AAGTATACCTAAACTTTCCAAAT-GTAAACACA
1 AAGTATACATTTCCTTTCCATATGGTATACACA
*
54927152 AAGTATACATTTCCTTTTCATATGGTATACACA
1 AAGTATACATTTCCTTTCCATATGGTATACACA
54927185 AAGTATAC
1 AAGTATAC
54927193 CTAAGCTTTC
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
32 33 0.38
33 52 0.60
34 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (33 bp):
AAGTATACATTTCCTTTCCATATGGTATACACA
Found at i:54927236 original size:65 final size:65
Alignment explanation
Indices: 54927067--54927220 Score: 263
Period size: 65 Copynumber: 2.4 Consensus size: 65
54927057 GTGTACATTC
54927067 CTTTCCAAGTGGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAA
1 CTTTCCAAGT-GTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAA
54927132 A
65 A
* * *
54927133 CTTTCCAAATGTAAACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAAG
1 CTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAAA
*
54927198 CTTTCCAAGTGTACACAGAAAGT
1 CTTTCCAAGTGTACACACAAAGT
54927221 GTATATAACC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 73 0.89
66 9 0.11
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (65 bp):
CTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAAA
Found at i:54937075 original size:33 final size:33
Alignment explanation
Indices: 54937036--54937166 Score: 151
Period size: 33 Copynumber: 4.0 Consensus size: 33
54937026 GAGGTGTACA
54937036 TTCCTTTCCA-AGTGGTACACACAAAGTATACCT
1 TTCCTTTCCATA-TGGTACACACAAAGTATACCT
* *
54937069 TTCCTTTTCATATGGTATACACAAAGTATACCT
1 TTCCTTTCCATATGGTACACACAAAGTATACCT
** * *
54937102 AACCTTTCCA-A-GTGTACGCACAAAGTATACAT
1 TTCCTTTCCATATG-GTACACACAAAGTATACCT
* *
54937134 TTCCTTTTCATATGGTATACACAAAGTATACCT
1 TTCCTTTCCATATGGTACACACAAAGTATACCT
54937167 AAACTTTCCA
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
31 1 0.01
32 24 0.30
33 53 0.66
34 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (33 bp):
TTCCTTTCCATATGGTACACACAAAGTATACCT
Found at i:54937124 original size:65 final size:65
Alignment explanation
Indices: 54937038--54937191 Score: 254
Period size: 65 Copynumber: 2.4 Consensus size: 65
54937028 GGTGTACATT
*
54937038 CCTTTCCAAGTGGTACACACAAAGTATACCTTTCCTTTTCATATGGTATACACAAAGTATACCTA
1 CCTTTCCAAGT-GTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTA
54937103 A
65 A
*
54937104 CCTTTCCAAGTGTACGCACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAA
1 CCTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAA
* * *
54937169 ACTTTCCAAATGTACACAAAAAG
1 CCTTTCCAAGTGTACACACAAAG
54937192 GGTACATAAC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 71 0.87
66 11 0.13
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (65 bp):
CCTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACAAAGTATACCTAA
Found at i:54937129 original size:32 final size:33
Alignment explanation
Indices: 54937038--54937211 Score: 149
Period size: 33 Copynumber: 5.3 Consensus size: 33
54937028 GGTGTACATT
**
54937038 CCTTTCCAAGTGGTACACACAAAGTATACCTTT
1 CCTTTCCAAGTGGTACACACAAAGTATACCTAA
* *
54937071 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACCTAA
* * **
54937104 CCTTTCCAAGT-GTACGCACAAAGTATACATTT
1 CCTTTCCAAGTGGTACACACAAAGTATACCTAA
* *
54937136 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACCTAA
* * * ** *
54937169 ACTTTCCAAAT-GTACACAAAAAGGGTACATAA
1 CCTTTCCAAGTGGTACACACAAAGTATACCTAA
*
54937201 CCTTTTCAAGT
1 CCTTTCCAAGT
54937212 TATACCATTT
Statistics
Matches: 110, Mismatches: 26, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
32 50 0.45
33 59 0.54
34 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.31
Consensus pattern (33 bp):
CCTTTCCAAGTGGTACACACAAAGTATACCTAA
Found at i:54946064 original size:51 final size:50
Alignment explanation
Indices: 54946002--54946123 Score: 137
Period size: 45 Copynumber: 2.5 Consensus size: 50
54945992 TAATCAATAA
* * *
54946002 CGGTAGCAGTAGCAGTAACAGCAACAATATTCAACACACAAAGTGTTGAAT
1 CGGTAACAGTAGC-GTAACAGTAACAATATTCAACACACAAAGTGTCGAAT
* *
54946053 CTGTAACAGTAGCG-----GTAACAATATTCGACACACAAAGTGTCGAAT
1 CGGTAACAGTAGCGTAACAGTAACAATATTCAACACACAAAGTGTCGAAT
*
54946098 CGGTAACAGTAACTGTAACAGTAACA
1 CGGTAACAGTAGC-GTAACAGTAACA
54946124 GTAGTCAGCA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
45 39 0.67
46 1 0.02
50 1 0.02
51 17 0.29
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (50 bp):
CGGTAACAGTAGCGTAACAGTAACAATATTCAACACACAAAGTGTCGAAT
Found at i:54946073 original size:45 final size:45
Alignment explanation
Indices: 54946014--54946117 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
54946004 GTAGCAGTAG
* * * *
54946014 CAGTAACAGCAACAATATTCAACACACAAAGTGTTGAATCTGTAA
1 CAGTAACGGTAACAATATTCAACACACAAAGTGTCGAATCGGTAA
* *
54946059 CAGTAGCGGTAACAATATTCGACACACAAAGTGTCGAATCGGTAA
1 CAGTAACGGTAACAATATTCAACACACAAAGTGTCGAATCGGTAA
*
54946104 CAGTAACTGTAACA
1 CAGTAACGGTAACA
54946118 GTAACAGTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (45 bp):
CAGTAACGGTAACAATATTCAACACACAAAGTGTCGAATCGGTAA
Found at i:54947431 original size:32 final size:31
Alignment explanation
Indices: 54947394--54947455 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
54947384 ATTATTTAAT
*
54947394 TAATAAATATCT-CTTAATTTTAATAATAATAA
1 TAATAAATATCTAC-TAATTTAAATAA-AATAA
54947426 TAATAAATATCTACTAATTTAAATAAAATA
1 TAATAAATATCTACTAATTTAAATAAAATA
54947456 TTATAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 23 0.82
33 1 0.04
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (31 bp):
TAATAAATATCTACTAATTTAAATAAAATAA
Found at i:54947717 original size:3 final size:3
Alignment explanation
Indices: 54947709--54947817 Score: 95
Period size: 3 Copynumber: 37.3 Consensus size: 3
54947699 TTAATTTATT
*
54947709 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * *
54947756 -AA CCA TAA CAA TTAA TAA TTA TAA TAA TCAA TTA T-A TAA T-A TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
54947800 T-A TAA T-A TAA TATA TAA T
1 TAA TAA TAA TAA TA-A TAA T
54947818 TTAAATAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
2 12 0.14
3 67 0.77
4 8 0.09
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:54947799 original size:5 final size:5
Alignment explanation
Indices: 54947789--54947813 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54947779 ATAATCAATT
54947789 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
54947814 TAATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:54953773 original size:48 final size:48
Alignment explanation
Indices: 54953702--54954038 Score: 532
Period size: 48 Copynumber: 7.0 Consensus size: 48
54953692 AGATAAATAT
* *
54953702 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
54953750 ATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
54953798 ATATATATATGCGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* **
54953846 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
54953894 ATATATATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
54953942 ATATATATATGCGGTAAATCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* *
54953990 -TATGTATATGTGGTAAAGCCGTATGGCTAATGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
54954037 AT
1 AT
54954039 GTGTATATAT
Statistics
Matches: 266, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
47 43 0.16
48 223 0.84
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:54953892 original size:144 final size:144
Alignment explanation
Indices: 54953702--54954046 Score: 602
Period size: 144 Copynumber: 2.4 Consensus size: 144
54953692 AGATAAATAT
* * *
54953702 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
*
54953767 AGCCGAATGGCTAATATGAAATATGTATGAGATATATATATGCGGTAAATCCGAATGGCTAATGT
66 AGCCGAATGGCTAACATGAAATATGTATGAGATATATATATGCGGTAAATCCGAATGGCTAATGT
54953832 GAAATATGTATGAG
131 GAAATATGTATGAG
** *
54953846 ATATGTATATGTGGTAAAGCCGAATGGCTAACATGAAATATGTATGAGATATATATATGTGGTAA
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
54953911 AGCCGAATGGCTAACATGAAATATGTATGAGATATATATATGCGGTAAATCCGAATGGCTAATGT
66 AGCCGAATGGCTAACATGAAATATGTATGAGATATATATATGCGGTAAATCCGAATGGCTAATGT
54953976 GAAATATGTATGAG
131 GAAATATGTATGAG
* *
54953990 -TATGTATATGTGGTAAAGCCGTATGGCTAATGTGAAATATGTATGAGATGTGTATAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATAT
54954047 ATTGTGGCCG
Statistics
Matches: 189, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
143 52 0.28
144 137 0.72
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (144 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAA
AGCCGAATGGCTAACATGAAATATGTATGAGATATATATATGCGGTAAATCCGAATGGCTAATGT
GAAATATGTATGAG
Found at i:54954229 original size:37 final size:37
Alignment explanation
Indices: 54954179--54954249 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
54954169 GGAAATATAT
*
54954179 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
54954216 TCCGGGTAAGACCCGATAACTACGTGTGGGGATT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATT
54954250 ATTCGAGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:54963167 original size:130 final size:130
Alignment explanation
Indices: 54962939--54963327 Score: 616
Period size: 130 Copynumber: 3.0 Consensus size: 130
54962929 TATGTAAAAG
* *
54962939 AGTTAGAGAATGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTAAAGTTGTGAACTGTTC
1 AGTTAGAGAAGGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTTAAGTTGTGAACTGTTC
* * ** * *
54963004 GGTAATACCTTATAACCCTTCCGGCGATAGTTACAGGTTCGGGTGTTACATTTTATTGTTATCAT
66 GGTAATACCTTGTAACCCTTCCGACGACGGTTACGGGTTCGGGTGTTACATTTTATTGGTATCAT
* *
54963069 AGTTAGAAAAGGTTATATTTCTATTAAATGTGTTCTTATGGTGGCTTTTAAGTTGTGAACTGTTC
1 AGTTAGAGAAGGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTTAAGTTGTGAACTGTTC
** * *
54963134 AATAATACCTTGTAACCCTTTCGACGACGGTTACGGGTTCGAGTGTTACATTTTATTGGTATCAT
66 GGTAATACCTTGTAACCCTTCCGACGACGGTTACGGGTTCGGGTGTTACATTTTATTGGTATCAT
*
54963199 AGTTAGAGAAGGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTTAAGTTGTGAACTATTC
1 AGTTAGAGAAGGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTTAAGTTGTGAACTGTTC
* * *
54963264 GGTAATACCTTGTAACCCTTCCGACAACGGTTACGGGTTCAGGTGTTATATTTTATTGGTATCA
66 GGTAATACCTTGTAACCCTTCCGACGACGGTTACGGGTTCGGGTGTTACATTTTATTGGTATCA
54963328 GAGCTACGGT
Statistics
Matches: 235, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 235 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (130 bp):
AGTTAGAGAAGGTTATATTTCTATTAAATGAGTTCTTATGGTGGCTTTTAAGTTGTGAACTGTTC
GGTAATACCTTGTAACCCTTCCGACGACGGTTACGGGTTCGGGTGTTACATTTTATTGGTATCAT
Found at i:54969146 original size:2 final size:2
Alignment explanation
Indices: 54969139--54969170 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54969129 TGATACTTTG
54969139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54969171 GAAACGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54970468 original size:20 final size:20
Alignment explanation
Indices: 54970443--54970483 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54970433 TTCTTTATAT
54970443 ATTTTTCATAATTTTTTTAA
1 ATTTTTCATAATTTTTTTAA
54970463 ATTTTTCATAATTTTTTTAA
1 ATTTTTCATAATTTTTTTAA
54970483 A
1 A
54970484 AATATAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTCATAATTTTTTTAA
Found at i:54970542 original size:19 final size:18
Alignment explanation
Indices: 54970499--54970542 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
54970489 AAATCTTGAA
* *
54970499 AAATTTTATAAATATTTT
1 AAATTTTAAAAATACTTT
*
54970517 GAATTTTAAAAATTACTTT
1 AAATTTTAAAAA-TACTTT
54970536 AAATTTT
1 AAATTTT
54970543 TCTTTTTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTTTAAAAATACTTT
Found at i:54976616 original size:27 final size:26
Alignment explanation
Indices: 54976586--54976644 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
54976576 ATTAATATAA
*
54976586 TTTTATAAAATAAGAAAAAAATTCAT
1 TTTTTTAAAATAAGAAAAAAATTCAT
* * ***
54976612 TTTTTTAGAATTATTTAAAAATTCAT
1 TTTTTTAAAATAAGAAAAAAATTCAT
54976638 TTTTTTA
1 TTTTTTA
54976645 GAATTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (26 bp):
TTTTTTAAAATAAGAAAAAAATTCAT
Found at i:54976631 original size:26 final size:26
Alignment explanation
Indices: 54976602--54976653 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
54976592 AAAATAAGAA
54976602 AAAAATTCATTTTTTTAGAATTATTT
1 AAAAATTCATTTTTTTAGAATTATTT
54976628 AAAAATTCATTTTTTTAGAATTATTT
1 AAAAATTCATTTTTTTAGAATTATTT
54976654 TGTACAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (26 bp):
AAAAATTCATTTTTTTAGAATTATTT
Found at i:54978461 original size:16 final size:17
Alignment explanation
Indices: 54978442--54978482 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
54978432 AGGAGATATC
54978442 AATTTAATTTAAAT-CA
1 AATTTAATTTAAATACA
*
54978458 AATTTTA-TTAAATACA
1 AATTTAATTTAAATACA
54978474 ATATTTAAT
1 A-ATTTAAT
54978483 AAATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.30
16 9 0.45
17 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAATTTAAATACA
Found at i:54978953 original size:17 final size:18
Alignment explanation
Indices: 54978931--54978964 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54978921 AATGTCAAGA
*
54978931 TTACTAAGAAT-ATGCCC
1 TTACTAACAATAATGCCC
54978948 TTACTAACAATAATGCC
1 TTACTAACAATAATGCC
54978965 TTGACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (18 bp):
TTACTAACAATAATGCCC
Found at i:54979795 original size:19 final size:20
Alignment explanation
Indices: 54979771--54979812 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54979761 GTTGCACATA
54979771 CCCGTGTGCTT-GGGACACG
1 CCCGTGTGCTTGGGGACACG
**
54979790 CCCGTGTTTTTGGGGACACG
1 CCCGTGTGCTTGGGGACACG
54979810 CCC
1 CCC
54979813 ATGTCCCACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.24
Consensus pattern (20 bp):
CCCGTGTGCTTGGGGACACG
Found at i:54980867 original size:2 final size:2
Alignment explanation
Indices: 54980860--54980884 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54980850 TTCATCATGT
54980860 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 T
54980885 TTTACCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54994084 original size:48 final size:48
Alignment explanation
Indices: 54994028--54994150 Score: 192
Period size: 48 Copynumber: 2.6 Consensus size: 48
54994018 GTCAGTGCTA
54994028 ATGCCATGTCCCGGACATGGTCTTACACTAGCACACATATCAACGCCG
1 ATGCCATGTCCCGGACATGGTCTTACACTAGCACACATATCAACGCCG
* * * * *
54994076 ATGTCATGTCCCAGACATGGTCTTACACTGGCTCACATATCAACGTCG
1 ATGCCATGTCCCGGACATGGTCTTACACTAGCACACATATCAACGCCG
*
54994124 ATGCCATGTCCTGGACATGGTCTTACA
1 ATGCCATGTCCCGGACATGGTCTTACA
54994151 TTGAATCTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 67 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (48 bp):
ATGCCATGTCCCGGACATGGTCTTACACTAGCACACATATCAACGCCG
Found at i:55000457 original size:27 final size:27
Alignment explanation
Indices: 55000437--55000497 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
55000427 ATTTTTTGAA
55000437 TTTTTAGAAATTTTAATATTTTTAAAAT
1 TTTTTA-AAATTTTAATATTTTTAAAAT
* *
55000465 TTTTTAAAATTTTAACAATTTATTAATAT
1 TTTTTAAAATTTTAA-TATTT-TTAAAAT
55000494 TTTT
1 TTTT
55000498 ATTGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.31
28 10 0.34
29 10 0.34
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTAAAATTTTAATATTTTTAAAAT
Found at i:55000459 original size:9 final size:9
Alignment explanation
Indices: 55000435--55000498 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
55000425 ACATTTTTTG
55000435 AATTTTTAGA
1 AATTTTTA-A
55000445 AA-TTTTAA
1 AATTTTTAA
*
55000453 TATTTTTAA
1 AATTTTTAA
55000462 AATTTTTTAA
1 AA-TTTTTAA
55000472 AA-TTTTAA
1 AATTTTTAA
55000480 CAATTTATTAA
1 -AATTT-TTAA
*
55000491 TATTTTTA
1 AATTTTTA
55000499 TTGAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 8 0.17
9 17 0.37
10 17 0.37
11 4 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (9 bp):
AATTTTTAA
Found at i:55000469 original size:19 final size:18
Alignment explanation
Indices: 55000427--55000498 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 18
55000417 TAAATAACAC
*
55000427 ATTTTTTGAATTTTTAGAA
1 ATTTTTTAAATTTTTA-AA
55000446 A--TTTTAATATTTTTAAA
1 ATTTTTTAA-ATTTTTAAA
*
55000463 ATTTTTTAAAATTTTAACA
1 ATTTTTTAAATTTTTAA-A
*
55000482 ATTTATTAATATTTTTA
1 ATTTTTTAA-ATTTTTA
55000499 TTGAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 8 0.18
18 14 0.32
19 16 0.36
20 6 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTTTAAATTTTTAAA
Found at i:55002632 original size:65 final size:65
Alignment explanation
Indices: 55002524--55002735 Score: 282
Period size: 65 Copynumber: 3.3 Consensus size: 65
55002514 GTTACGACTA
* * *
55002524 CTCTTTGTGAGCATCCTATTTAT-TGATCGGTTGTGATCCTGCATATGTTGCGGATACAAACGCA
1 CTCTTTGTGAGCATCCTA-TTATGCGATCGGTTGTGATCTTGCATATGTTGCGGACACAAACGCA
55002588 G
65 G
* *
55002589 CTCTTTGTGAGCATCCTATTATGCGATTGGTTGTGATCTTGCATATATTGCGGACACAAACGCAG
1 CTCTTTGTGAGCATCCTATTATGCGATCGGTTGTGATCTTGCATATGTTGCGGACACAAACGCAG
** * * * * *
55002654 CTCTTTGTGAGTGTCCTGTTATGCGAACGGTTGTGATCTTGTATATGTTGTGGACACAAATGCAG
1 CTCTTTGTGAGCATCCTATTATGCGATCGGTTGTGATCTTGCATATGTTGCGGACACAAACGCAG
* *
55002719 CTCTTTATGAGCGTCCT
1 CTCTTTGTGAGCATCCT
55002736 GATATACGGC
Statistics
Matches: 130, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
64 4 0.03
65 126 0.97
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (65 bp):
CTCTTTGTGAGCATCCTATTATGCGATCGGTTGTGATCTTGCATATGTTGCGGACACAAACGCAG
Found at i:55004968 original size:19 final size:17
Alignment explanation
Indices: 55004929--55004965 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
55004919 TGATAAATGT
55004929 TATGTTATACGTGTGAA
1 TATGTTATACGTGTGAA
*
55004946 TATGTTATACGTGTGTA
1 TATGTTATACGTGTGAA
55004963 TAT
1 TAT
55004966 ATGAAAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (17 bp):
TATGTTATACGTGTGAA
Found at i:55007715 original size:27 final size:27
Alignment explanation
Indices: 55007697--55007769 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
55007687 ATAGTGAGTC
55007697 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
55007724 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
55007752 CGCACACTTAGTGCTATA
1 CGCACACTTAGTGCTATA
55007770 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.50
28 21 0.50
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:55012725 original size:210 final size:210
Alignment explanation
Indices: 55012356--55012782 Score: 748
Period size: 210 Copynumber: 2.0 Consensus size: 210
55012346 GATCAATTTG
*
55012356 TAAAATTATCAAAGTTTCAAAGTTTTTCCATGGATGAATATGCTGAAATTTTGAAATTTATGGTA
1 TAAAATTATCAAAGTTTCAAAATTTTTCCATGGATGAATATGCTGAAATTTTGAAATTTATGGTA
* *
55012421 GAAAATGAAAGGTTGTTGATAGATAAACAACTTTTACAAAGATAATTTTGATGAAATTATGATTT
66 GAAAATGAAAAGTTGTTGATAGATAAACAACTTTTACAAAGAGAATTTTGATGAAATTATGATTT
55012486 AGGGACTAAATTGTAAAAAATGAAAAAGTCATGGAAAAATTCT-AATTTTTATGAAATACATGGG
131 AGGGACTAAATTGTAAAAAATGAAAAAGTCATGGAAAAATTCTGAA-TTTTATGAAATACATGGG
55012550 CTGTAAATGTTACTTC
195 CTGTAAATGTTACTTC
* * *
55012566 TAAAGTTATCAAATTTTCAAAATTTTTCTATGGATGAATATGCTGAAATTTTGAAATTTATGGTA
1 TAAAATTATCAAAGTTTCAAAATTTTTCCATGGATGAATATGCTGAAATTTTGAAATTTATGGTA
*
55012631 GAAAATGAAAAGTTGTTGATAGATAAACAACTTTTACAAAGAGAATTTTGGTGAAATTATGATTT
66 GAAAATGAAAAGTTGTTGATAGATAAACAACTTTTACAAAGAGAATTTTGATGAAATTATGATTT
* *
55012696 AGGGACTAAATTGTAAAAAATGGAAAAGTCATGGAAAAATTTTGAATTTTATGAAATACATGGGC
131 AGGGACTAAATTGTAAAAAATGAAAAAGTCATGGAAAAATTCTGAATTTTATGAAATACATGGGC
*
55012761 TGTAAATGTTACTTG
196 TGTAAATGTTACTTC
55012776 TAAAATT
1 TAAAATT
55012783 CGACTAGACT
Statistics
Matches: 205, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
210 203 0.99
211 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (210 bp):
TAAAATTATCAAAGTTTCAAAATTTTTCCATGGATGAATATGCTGAAATTTTGAAATTTATGGTA
GAAAATGAAAAGTTGTTGATAGATAAACAACTTTTACAAAGAGAATTTTGATGAAATTATGATTT
AGGGACTAAATTGTAAAAAATGAAAAAGTCATGGAAAAATTCTGAATTTTATGAAATACATGGGC
TGTAAATGTTACTTC
Found at i:55013538 original size:65 final size:65
Alignment explanation
Indices: 55013456--55013600 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 65
55013446 AATACCGTAG
* * * *
55013456 CTCTTCGTGAGCATCCTGTTTAT-TGATC-GATTGTGATCCTGCATATGTTTTAG-ACACAAACA
1 CTCTTTGTGAGCGTCCTG-TTATGCGATCAG-TTGTGATCCTGCATATG-TTGAGAACACAAACA
55013518 CAA
63 CAA
* *
55013521 CTCTTTGTGAGCGTCCTGTTATGCGATCAGTTGTGATCCTGCATATGTTGCGAACACAAACACAG
1 CTCTTTGTGAGCGTCCTGTTATGCGATCAGTTGTGATCCTGCATATGTTGAGAACACAAACACAA
*
55013586 CTCTTTATGAGCGTC
1 CTCTTTGTGAGCGTC
55013601 TTGATATCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
64 7 0.10
65 62 0.89
66 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (65 bp):
CTCTTTGTGAGCGTCCTGTTATGCGATCAGTTGTGATCCTGCATATGTTGAGAACACAAACACAA
Found at i:55013698 original size:23 final size:24
Alignment explanation
Indices: 55013654--55013698 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
55013644 CCGTTACATG
*
55013654 GCTCTTTGTGAGCATTCCTGATAA
1 GCTCTTCGTGAGCATTCCTGATAA
55013678 GCTCTTCGTGAGC-TTCCTGAT
1 GCTCTTCGTGAGCATTCCTGAT
55013699 TAAATGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (24 bp):
GCTCTTCGTGAGCATTCCTGATAA
Done.