Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 35 of 187
Found at i:10201638 original size:44 final size:44
Alignment explanation
Indices: 10201545--10201930 Score: 266
Period size: 44 Copynumber: 8.8 Consensus size: 44
10201535 TCCTATACTG
* * ** * *
10201545 GTAGTGAAGCAGATCGAAGCCACCAG-TCTTATCTCCCTGAGCA
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
* ** * *
10201588 GCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCA
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
* * * * *
10201632 GTAGTGGAGCAGATCGAAGATAGAAAATCTTATCTTCCTAAGGTA
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAA-GCA
* * ** * * *
10201677 GCAG-GGAAGCAGATTTAAGCCACCAG-CCTTATCTCCCTGAGCA
1 GTAGTGG-AGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
* * * *
10201720 GCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCA
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
** * *
10201764 GTAGTGGAGCAGATTGAAGACGGC-GAATCTTATCTTGCC-AAGGTA
1 GTAGTGGAGCAGATTGAAGATAGCAG-ATCTTATC-TCCCTAA-GCA
* * * *
10201809 GTAG-GGAAGCAGATTTAAG-TCACCAG-CCTTATCTCCCTGAGCA
1 GTAGTGG-AGCAGATTGAAGAT-AGCAGATCTTATCTCCCTAAGCA
* * * *
10201852 GTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCA
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
* ** *
10201896 GTAGTGGAGCAGATCGAAGACGGCAAATCTTATCT
1 GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCT
10201931 TCCCAAGGTA
Statistics
Matches: 256, Mismatches: 72, Indels: 29
0.72 0.20 0.08
Matches are distributed among these distances:
43 55 0.21
44 162 0.63
45 38 0.15
46 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (44 bp):
GTAGTGGAGCAGATTGAAGATAGCAGATCTTATCTCCCTAAGCA
Found at i:10201663 original size:88 final size:88
Alignment explanation
Indices: 10201486--10201930 Score: 287
Period size: 88 Copynumber: 5.1 Consensus size: 88
10201476 CCACCAGTCC
* * * * * * * *
10201486 TATCTCCCTGAACAACAGCGGAATAGGTCGAAGATTGTAGATCTTGTCTTCCTATA-CTGGTAGT
1 TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTA-AGC-AGTAGT
* ** * *
10201550 GAAGCAGATCGAAGCCA-CCAGTCT
64 GGAGCAGATCGAAGATAGCAAATCT
10201574 TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
*
10201639 AGCAGATCGAAGATAGAAAATCT
66 AGCAGATCGAAGATAGCAAATCT
* * * * * * **** * * *
10201662 TATCTTCCTAAGGTAGCAG-GGAAGCAGATTTAAGCCACCAG-CCTTATCTCCCTGAGCAGCAGT
1 TATCTCCCTGA-GCAGCAGTGGAA-TAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGT
* * * * *
10201725 GGAGTAGGTTGAAGATTGCAGATCT
64 GGAGCAGATCGAAGATAGCAAATCT
* * ** * ** * *
10201750 TATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGC-GAATCTTATCTTGCC-AAGGTAGTAG
1 TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAG-ATCTTATC-TCCCTAA-GCAGTAG
** * **
10201813 -GGAAGCAGATTTAAG-TCA-CCAGCCT
63 TGG-AGCAGATCGAAGAT-AGCAAATCT
* * *
10201838 TATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
**
10201903 AGCAGATCGAAGACGGCAAATCT
66 AGCAGATCGAAGATAGCAAATCT
10201926 TATCT
1 TATCT
10201931 TCCCAAGGTA
Statistics
Matches: 272, Mismatches: 69, Indels: 32
0.73 0.18 0.09
Matches are distributed among these distances:
86 1 0.00
87 55 0.20
88 182 0.67
89 34 0.12
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATCGAAGATAGCAAATCT
Found at i:10201723 original size:132 final size:131
Alignment explanation
Indices: 10201545--10201978 Score: 697
Period size: 132 Copynumber: 3.3 Consensus size: 131
10201535 TCCTATACTG
* ** * *
10201545 GTAGTGAAGCAGATCGAAGCCACCAGTCTTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAGATT
1 GTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
** *
10201610 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGAAAATCTTATCTTCCTAAGG
66 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCC-AAGG
10201675 TA
130 TA
*
10201677 GCAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
1 GTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
* *
10201742 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGAATCTTATCTTGCCAAGG
66 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTT-CCAAGG
10201807 TA
130 TA
* *
10201809 GTAGGGAAGCAGATTTAAGTCACCAGCCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAGATT
1 GTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
*
10201874 GTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCAAGG
66 GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTT-CCAAGG
10201939 TA
130 TA
* *
10201941 GTAGGGAAGTAGATTTAAGCCACCAACCTTATCTCCCT
1 GTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCT
10201979 AAAGTTGCAA
Statistics
Matches: 280, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 278 0.99
133 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (131 bp):
GTAGGGAAGCAGATTTAAGCCACCAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
GCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCAAGGT
A
Found at i:10201972 original size:88 final size:86
Alignment explanation
Indices: 10201616--10201980 Score: 211
Period size: 88 Copynumber: 4.2 Consensus size: 86
10201606 GATTGCAGAT
* * * * *
10201616 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGAAAATCTTATCTTCCTAAGGTAGCAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGCAAATCTTATC-TCCCAAGGCAGTAG
* *
10201681 -GGAAGCAGATTTAAGCCACCAGC
64 TGG-AGCAGATTGAAGCCACCAAC
* * * * * * *
10201704 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCTTATCTCCCTAA-GCAGTAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-CGCAAATCTTATCTCCC-AAGGCAGTAG
** * *
10201768 TGGAGCAGATTGAAGACGGCGAAT
64 TGGAGCAGATTGAAG-CCACCAAC
* * ** * * * ** *
10201792 CTTATCTTGCC-AAGGTAGTAG-GGAAGCAGATTTAAGTCACCAGCCTTATCTCCC-TGAGCAGT
1 CTTATC-TCCCTAA-GCAGTAGTGG-AGCAGATCGAAGACGCAAATCTTATCTCCCAAG-GCAGT
* * ***** *
10201854 AGTGGAGTAGGTTGAAGATTGTAGAT
62 AGTGGAGCAGATTGAAGCCACCA-AC
*
10201880 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC-GCAAATCTTATC-TCCCAAGGCAGTAG
* *
10201945 -GGAAGTAGATTTAAGCCACCAAC
64 TGG-AGCAGATTGAAGCCACCAAC
10201968 CTTATCTCCCTAA
1 CTTATCTCCCTAA
10201981 AGTTGCAATG
Statistics
Matches: 204, Mismatches: 58, Indels: 30
0.70 0.20 0.10
Matches are distributed among these distances:
87 40 0.20
88 125 0.61
89 38 0.19
90 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (86 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGCAAATCTTATCTCCCAAGGCAGTAGTG
GAGCAGATTGAAGCCACCAAC
Found at i:10202066 original size:44 final size:43
Alignment explanation
Indices: 10201968--10202209 Score: 149
Period size: 44 Copynumber: 5.7 Consensus size: 43
10201958 AGCCACCAAC
* * * * *
10201968 CTTATCTCCCTAAAGTTGCAATGGAG-A-ATAAAAAAACCA-AT
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGAT-TAAAATCCAGAT
* * **
10202009 CCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGAT
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATC-CAGAT
* * ***
10202053 CTTATCTATCTGAAGTTGCAGTAGAGCAGA-TCGCATCCAG-T
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCCAGAT
* * * * *
10202094 CTTATCTCCCTAAAGTTGCAGCGGAGTAGATTGAAGAAACCA-AT
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATT-AA-AATCCAGAT
* * * *
10202138 CCTATCT-TCCTGAAGTTGCAGTGAAGCGGATTAAAAT-TATGGAT
1 CTTATCTCT-CTGAAGTTGCAGTGGAGCAGATTAAAATCCA--GAT
*
10202182 CTTATCTCTCTGAAGTTGCAGTAGAGCA
1 CTTATCTCTCTGAAGTTGCAGTGGAGCA
10202210 CATCGCATCA
Statistics
Matches: 150, Mismatches: 38, Indels: 23
0.71 0.18 0.11
Matches are distributed among these distances:
41 49 0.33
42 11 0.07
43 10 0.07
44 79 0.53
45 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAATCCAGAT
Found at i:10202134 original size:129 final size:126
Alignment explanation
Indices: 10201968--10202218 Score: 367
Period size: 129 Copynumber: 2.0 Consensus size: 126
10201958 AGCCACCAAC
* *
10201968 CTTATCTCCCTAAAGTTGCAATGGAGAATAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGG
1 CTTATCTCCCTAAAGTTGCAACGGAGAATAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGA
* *
10202033 AGTGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCCAGT
66 AGCGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGTAGAGCACATCGCATCCAGT
* * * *
10202094 CTTATCTCCCTAAAGTTGCAGCGGAGTAGATTGAAGAAACCAATCCTATCTTCCTGAAGTTGCAG
1 CTTATCTCCCTAAAGTTGCAACGGAG-A-A-TAAAAAAACCAATCCTATCTCCCTGAAGTTGCAG
* ** *
10202159 TGAAGCGGATTAAAATTATGGATCTTATCTCTCTGAAGTTGCAGTAGAGCACATCGCATC
63 TGAAGCGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGTAGAGCACATCGCATC
10202219 AGATTTTATT
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
126 24 0.22
127 1 0.01
128 1 0.01
129 84 0.76
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (126 bp):
CTTATCTCCCTAAAGTTGCAACGGAGAATAAAAAAACCAATCCTATCTCCCTGAAGTTGCAGTGA
AGCGGATTAAAATCACAGATCTTATCTATCTGAAGTTGCAGTAGAGCACATCGCATCCAGT
Found at i:10202482 original size:44 final size:44
Alignment explanation
Indices: 10202322--10202539 Score: 226
Period size: 44 Copynumber: 4.9 Consensus size: 44
10202312 CTCGAAGAGC
* * * *
10202322 TACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCACACCA
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA-A-GA
* *
10202367 TA-ATAAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGA
1 TACA-AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * *
10202412 TGACAAACCTTATC-CCCTTGAAGTTGCAGTGGAGCAGGTTGAAAA
1 T-ACAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTGAAGA
* * *
10202457 TACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
* * *
10202501 TACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATT
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
10202540 AAAACGACGA
Statistics
Matches: 146, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
44 72 0.49
45 39 0.27
46 32 0.22
47 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
Found at i:10204192 original size:21 final size:20
Alignment explanation
Indices: 10204152--10204202 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
10204142 ACTTACTCTT
*
10204152 TTTTCTTTCTTTCTTTTTTA
1 TTTTCTTTCTTTCTTATTTA
10204172 TTTTCTATTC-TTCATTATTTA
1 TTTTCT-TTCTTTC-TTATTTA
10204193 --TTCTTTCTTT
1 TTTTCTTTCTTT
10204203 TCGCATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.11
19 6 0.22
20 9 0.33
21 9 0.33
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTTCTTTCTTATTTA
Found at i:10204340 original size:21 final size:21
Alignment explanation
Indices: 10204316--10204361 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
10204306 TAAACTTTGT
*
10204316 TATAGACATATATTTCTTTTA
1 TATAGACATATATTTCTTATA
* *
10204337 TATATATATATATTTCTTATA
1 TATAGACATATATTTCTTATA
10204358 TATA
1 TATA
10204362 TTTATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (21 bp):
TATAGACATATATTTCTTATA
Found at i:10204345 original size:17 final size:17
Alignment explanation
Indices: 10204323--10204366 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
10204313 TGTTATAGAC
*
10204323 ATATATTTCTTT-TATAT
1 ATATATTTATTTCT-TAT
*
10204340 ATATATATATTTCTTAT
1 ATATATTTATTTCTTAT
10204357 ATATATTTAT
1 ATATATTTAT
10204367 AATTTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATATTTATTTCTTAT
Found at i:10204362 original size:21 final size:21
Alignment explanation
Indices: 10204323--10204371 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
10204313 TGTTATAGAC
*
10204323 ATATATTTCTTTTATATATAT
1 ATATATTTCTTATATATATAT
*
10204344 ATATATTTCTTATATATATTT
1 ATATATTTCTTATATATATAT
10204365 ATA-ATTT
1 ATATATTT
10204372 TTTCTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTCTTATATATATAT
Found at i:10204367 original size:19 final size:20
Alignment explanation
Indices: 10204323--10204367 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
10204313 TGTTATAGAC
10204323 ATATATTTCTTTTATATATAT
1 ATATATTTC-TTTATATATAT
10204344 ATATATTTC-TTATATATAT
1 ATATATTTCTTTATATATAT
*
10204363 TTATA
1 ATATA
10204368 ATTTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.61
21 9 0.39
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTCTTTATATATAT
Found at i:10206207 original size:23 final size:23
Alignment explanation
Indices: 10206175--10206250 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
10206165 AGTGTTATTG
*
10206175 ATCAGAGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
10206198 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
10206221 ATCAGTGGTAGCTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
10206244 ATCAGTG
1 ATCAGTG
10206251 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:10211381 original size:16 final size:16
Alignment explanation
Indices: 10211360--10211395 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
10211350 GCTGAACTGG
10211360 ACCTTGAACCCTAATA
1 ACCTTGAACCCTAATA
*
10211376 ACCTTGAACCCTAATG
1 ACCTTGAACCCTAATA
10211392 ACCT
1 ACCT
10211396 AGTACAACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.33, G:0.08, T:0.25
Consensus pattern (16 bp):
ACCTTGAACCCTAATA
Found at i:10213091 original size:3 final size:3
Alignment explanation
Indices: 10213083--10213107 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10213073 ATTTCACAAT
10213083 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
10213108 CAACAACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10214363 original size:67 final size:67
Alignment explanation
Indices: 10214247--10214381 Score: 225
Period size: 67 Copynumber: 2.0 Consensus size: 67
10214237 TTCAATTCAG
* * *
10214247 AGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATCACCAGTCCAGGCTAAATCCCCTGCA
1 AGAGCACACTACCGCGAACCTCATTTCTTACAACGGGATCACCAATCCAGGCTAAATCCCCTGCA
10214312 AT
66 AT
* *
10214314 AGAGCACACTACCGCGAACCTCATTTCTTACAACGGGATTACCAATCCAGGCTAAATCCCCTGTA
1 AGAGCACACTACCGCGAACCTCATTTCTTACAACGGGATCACCAATCCAGGCTAAATCCCCTGCA
10214379 AT
66 AT
10214381 A
1 A
10214382 TAAACTCATA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (67 bp):
AGAGCACACTACCGCGAACCTCATTTCTTACAACGGGATCACCAATCCAGGCTAAATCCCCTGCA
AT
Found at i:10220440 original size:18 final size:17
Alignment explanation
Indices: 10220399--10220440 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
10220389 ATACGTTTTG
*
10220399 GTATCTATTATTCTGTT
1 GTATCTAATATTCTGTT
*
10220416 ATATCTAATATTCTGTTT
1 GTATCTAATATTCTG-TT
10220434 GTATCTA
1 GTATCTA
10220441 GCTATGGGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (17 bp):
GTATCTAATATTCTGTT
Found at i:10221621 original size:51 final size:50
Alignment explanation
Indices: 10221541--10221640 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 50
10221531 AGAGTAAGAC
* *
10221541 CTTTAGCGGCGCTTTAGTGGAAGCGCCGCTAAAGACCCTGATCTTTAGCT
1 CTTTAGCGGCGCTTTAGGGGAAGCGCCGCTAAAGACCCTGATCTATAGCT
* *
10221591 CTTTAGCGGCGTTTTTGGGAGAAGCGCCGCTAAAGACCCTGATCTATAGC
1 CTTTAGCGGCGCTTTAGGG-GAAGCGCCGCTAAAGACCCTGATCTATAGC
10221641 GGCATTTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 16 0.36
51 29 0.64
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (50 bp):
CTTTAGCGGCGCTTTAGGGGAAGCGCCGCTAAAGACCCTGATCTATAGCT
Found at i:10221702 original size:43 final size:42
Alignment explanation
Indices: 10221654--10221746 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
10221644 ATTTATACCA
10221654 CAAACGCCACTAAAGAACCTATTCTTTAACGGCGCTTTGACCCT
1 CAAACGCCACTAAAG-ACCTATTCTTTAACGGCGCTTT-ACCCT
* *
10221698 -AAACGCCACTAAAGACCTATTCTTTAGCGGCGCTTTCCCCT
1 CAAACGCCACTAAAGACCTATTCTTTAACGGCGCTTTACCCT
10221739 CAAACGCC
1 CAAACGCC
10221747 GCAATAGACT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 28 0.61
43 14 0.30
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (42 bp):
CAAACGCCACTAAAGACCTATTCTTTAACGGCGCTTTACCCT
Found at i:10221772 original size:85 final size:84
Alignment explanation
Indices: 10221651--10221880 Score: 216
Period size: 85 Copynumber: 2.7 Consensus size: 84
10221641 GGCATTTATA
* * * * *
10221651 CCACAAACGCCACTAAAGAACC-TATTCTTTAACGGCGCTTTGACCCTAAACGCCACTAAAGACC
1 CCACAAACGCCGCTAAAGACCCTTA-TCTATAGCGGCGCTTTGACCC-AAACACCACTAAAGACC
10221715 -TATTCTTTAGCGGCGCTTTCC
64 ATA-TCTTTAGCGGCGCTTTCC
* * ** * *
10221736 CCTCAAACGCCGC-AATAGA-CTTTGATCTATAGCGGCGCTTTCTCACAAACACCACCAAAGACC
1 CCACAAACGCCGCTAA-AGACCCTT-ATCTATAGCGGCGCTTTGACCCAAACACCACTAAAGACC
* **
10221799 ATGATCTTTAGTGGCGCTTTTT
64 AT-ATCTTTAGCGGCGCTTTCC
* * *
10221821 CCACAAATGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACACCACTAAA
1 CCACAAACGCCGCTAAAGACCCTTATCTATAGCGGCGCTTTGACC-CAAACACCACTAAA
10221881 AAGGCCAACA
Statistics
Matches: 115, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
84 18 0.16
85 78 0.68
86 19 0.17
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (84 bp):
CCACAAACGCCGCTAAAGACCCTTATCTATAGCGGCGCTTTGACCCAAACACCACTAAAGACCAT
ATCTTTAGCGGCGCTTTCC
Found at i:10221840 original size:43 final size:42
Alignment explanation
Indices: 10221615--10221861 Score: 191
Period size: 43 Copynumber: 5.8 Consensus size: 42
10221605 TTGGGAGAAG
* * *
10221615 CGCCGCTAAAGACCCTGATCTATAGCGGC-ATTTATACCACAAA
1 CGCCGCTAAAGA-CCTGATCTTTAGCGGCGCTTTCT-CCACAAA
* * **
10221658 CGCCACTAAAGAACCT-ATTCTTTAACGGCGCTTTGACC-CTAAA
1 CGCCGCTAAAG-ACCTGA-TCTTTAGCGGCGCTTTCTCCAC-AAA
* * *
10221701 CGCCACTAAAGACCT-ATTCTTTAGCGGCGCTTTCCCCTCAAA
1 CGCCGCTAAAGACCTGA-TCTTTAGCGGCGCTTTCTCCACAAA
* *
10221743 CGCCGC-AATAGACTTTGATCTATAGCGGCGCTTTCT-CACAAA
1 CGCCGCTAA-AGAC-CTGATCTTTAGCGGCGCTTTCTCCACAAA
* * * * *
10221785 CACCACCAAAGACCATGATCTTTAGTGGCGCTTTTTCCACAAA
1 CGCCGCTAAAGACC-TGATCTTTAGCGGCGCTTTCTCCACAAA
* *
10221828 TGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTT
1 CGCCGCTAAAGA-CCTGATCTTTAGCGGCGCTTT
10221862 GACCAAAAAC
Statistics
Matches: 166, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
41 2 0.01
42 68 0.41
43 89 0.54
44 7 0.04
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (42 bp):
CGCCGCTAAAGACCTGATCTTTAGCGGCGCTTTCTCCACAAA
Found at i:10222307 original size:21 final size:21
Alignment explanation
Indices: 10222235--10222326 Score: 76
Period size: 21 Copynumber: 4.4 Consensus size: 21
10222225 TTTGACGCTG
**
10222235 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
10222256 CTCTGCTTCCCTCGTTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
10222277 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
10222298 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
10222319 ATCTGCTT
1 CTCTGCTT
10222327 TAAGCTACTG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.04, C:0.40, G:0.17, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:10222387 original size:66 final size:66
Alignment explanation
Indices: 10222297--10222463 Score: 203
Period size: 66 Copynumber: 2.5 Consensus size: 66
10222287 CTCGCTGCCG
* * *
10222297 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTTCTTCATA-CTTTCATT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG-TACTAGCTGGAGTTCTTCATATCTTT-ATT
10222360 GAA
64 GAA
* ** *
10222363 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTATTGA
10222428 A
66 A
* * * *
10222429 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGT
10222464 TGTGTAATTT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 2 0.02
66 81 0.93
67 4 0.05
ACGTcount: A:0.14, C:0.29, G:0.17, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTATTGA
A
Found at i:10227921 original size:16 final size:16
Alignment explanation
Indices: 10227900--10227953 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
10227890 ATTAAGCTAC
10227900 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
10227916 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* *
10227932 GAAAATTATGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
10227950 GTAA
1 GTAA
10227954 TTTACGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 23 0.74
17 1 0.03
18 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:10227949 original size:9 final size:9
Alignment explanation
Indices: 10227900--10227953 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
10227890 ATTAAGCTAC
10227900 GTAAGTTAT
1 GTAAGTTAT
10227909 GT-A-TTAT
1 GTAAGTTAT
10227916 GTAAGTTAT
1 GTAAGTTAT
*
10227925 -TTA-TTAT
1 GTAAGTTAT
* *
10227932 GAAAATTAT
1 GTAAGTTAT
10227941 GTAAGTTAT
1 GTAAGTTAT
10227950 GTAA
1 GTAA
10227954 TTTACGAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
7 10 0.28
8 5 0.14
9 21 0.58
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:10227952 original size:34 final size:34
Alignment explanation
Indices: 10227905--10227987 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
10227895 GCTACGTAAG
*** *
10227905 TTATGT-A-TTATGTAAGTTATTTATTATGAAAA
1 TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
* *
10227937 TTATGTAAGTTATGTAATTTACGAATAATTAAAA
1 TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
*
10227971 ATATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
10227988 AATGTAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 6 0.14
33 1 0.02
34 35 0.83
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
Found at i:10228000 original size:25 final size:24
Alignment explanation
Indices: 10227900--10228036 Score: 66
Period size: 25 Copynumber: 5.5 Consensus size: 24
10227890 ATTAAGCTAC
**
10227900 GTAAGTTATGTATTATGTAAGTTAT
1 GTAA-TTATGTAAAATGTAAGTTAT
* *
10227925 -TTATTATGAAAATTATGTAAGTTAT
1 GTAATTATGTAAA--ATGTAAGTTAT
* **
10227950 GTAATTTACG-AATAAT-TAAAAATAT
1 GTAA-TTATGTAA-AATGT-AAGTTAT
10227975 GTAAGTTATGTAAAATGTAAGTTAT
1 GTAA-TTATGTAAAATGTAAGTTAT
* **
10228000 GTATAATAT-TAAATAACTAAGTTAT
1 GTA-ATTATGTAAA-ATGTAAGTTAT
10228025 GTAATTTATGTA
1 GTAA-TTATGTA
10228037 TAATATTAAT
Statistics
Matches: 84, Mismatches: 16, Indels: 23
0.68 0.13 0.19
Matches are distributed among these distances:
23 6 0.07
24 8 0.10
25 55 0.65
26 10 0.12
27 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.14, T:0.43
Consensus pattern (24 bp):
GTAATTATGTAAAATGTAAGTTAT
Found at i:10228055 original size:22 final size:22
Alignment explanation
Indices: 10228023--10228067 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10228013 TAACTAAGTT
*
10228023 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228045 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228067 A
1 A
10228068 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:10228055 original size:31 final size:31
Alignment explanation
Indices: 10227989--10228838 Score: 936
Period size: 31 Copynumber: 28.2 Consensus size: 31
10227979 GTTATGTAAA
* * *
10227989 ATGTAAGTTATGTATAATATTAAATAACTAAGTT
1 ATGTAATTTATGTAT-A-A-TAACTAATTAAGTT
*
10228023 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
*
10228054 ATGT-ATAATAT-TA-AATAAC----TAAGTT
1 ATGTAAT-TTATGTATAATAACTAATTAAGTT
*
10228079 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
* * *
10228110 ATGT-A--TA---ATATTAATTAACTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
* * *
10228135 ATGTAATTTCTGTATAAT-ATTAATGTATGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
*
10228166 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228197 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
*
10228228 ATGT-ATAATAT-TA-AATAAC----TAAGTT
1 ATGTAAT-TTATGTATAATAACTAATTAAGTT
*
10228253 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
*
10228284 ATGT-ATAATAT-TA-AATAAC----TAAGTT
1 ATGTAAT-TTATGTATAATAACTAATTAAGTT
* * *
10228309 ATGTAATTTCTGTATAAT-ATTAATGTATGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
10228340 ATGTAATTTATGTATAATTAACTAATTAAGTT
1 ATGTAATTTATGTATAA-TAACTAATTAAGTT
10228372 ATGTAATTTATGTA-AATTAACTAATTAAGTT
1 ATGTAATTTATGTATAA-TAACTAATTAAGTT
*
10228403 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228434 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228465 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228496 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228527 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228558 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228589 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228620 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228651 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
* *
10228682 ATGTAATTTATGTATATTAACTAATTATGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228713 ATGTAATTTATGTATATTAACTAATTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228744 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
* * *
10228775 ATGT-A--TA---ATATTAATTAACTAAGTT
1 ATGTAATTTATGTATAATAACTAATTAAGTT
*
10228800 ATGTAATTTATGTATATTAACTAATGTAAGTT
1 ATGTAATTTATGTATAATAACTAAT-TAAGTT
10228832 ATGTAAT
1 ATGTAAT
10228839 ATCTTATATT
Statistics
Matches: 722, Mismatches: 41, Indels: 108
0.83 0.05 0.12
Matches are distributed among these distances:
25 66 0.09
26 27 0.04
27 9 0.01
28 7 0.01
29 9 0.01
30 36 0.05
31 508 0.70
32 40 0.06
33 6 0.01
34 14 0.02
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (31 bp):
ATGTAATTTATGTATAATAACTAATTAAGTT
Found at i:10228111 original size:22 final size:22
Alignment explanation
Indices: 10228079--10228124 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
10228069 TAACTAAGTT
*
10228079 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228101 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228123 AT
1 AT
10228125 TAACTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:10228170 original size:22 final size:22
Alignment explanation
Indices: 10228145--10228241 Score: 73
Period size: 22 Copynumber: 4.6 Consensus size: 22
10228135 ATGTAATTTC
10228145 TGTATAATATTAATGTATGTTA
1 TGTATAATATTAATGTATGTTA
*
10228167 TG--TAAT-TT-ATGTATATTA
1 TGTATAATATTAATGTATGTTA
** *
10228185 ACTAATTAA-GTT-ATGTAAT-TTA
1 TGT-A-TAATATTAATGT-ATGTTA
*
10228207 TGTATAATATTAATGTAAGTTA
1 TGTATAATATTAATGTATGTTA
10228229 TGTATAATATTAA
1 TGTATAATATTAA
10228242 ATAACTAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
18 9 0.15
19 2 0.03
20 7 0.12
21 4 0.07
22 35 0.59
23 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.48
Consensus pattern (22 bp):
TGTATAATATTAATGTATGTTA
Found at i:10228285 original size:22 final size:22
Alignment explanation
Indices: 10228253--10228297 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10228243 TAACTAAGTT
*
10228253 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228275 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228297 A
1 A
10228298 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:10228769 original size:22 final size:22
Alignment explanation
Indices: 10228744--10228789 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
10228734 TAATTAAGTT
*
10228744 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228766 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
10228788 AT
1 AT
10228790 TAACTAAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:10228803 original size:25 final size:22
Alignment explanation
Indices: 10228751--10228804 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
10228741 GTTATGTAAT
*
10228751 TTATGTATAATATTAATGTAAG
1 TTATGTATAATATTAATCTAAG
10228773 TTATGTATAATATTAATTAACTAAG
1 TTATGTATAATATTAA-T--CTAAG
10228798 TTATGTA
1 TTATGTA
10228805 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 16 0.57
23 1 0.04
25 11 0.39
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATGTATAATATTAATCTAAG
Found at i:10231733 original size:35 final size:36
Alignment explanation
Indices: 10231685--10231754 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
10231675 CAACTTTTAA
* *
10231685 TTTGTAATATTATAATATTT-ATTTTTTTGTATAAAG
1 TTTGAAATATTATAATATTTAATTTTATTG-ATAAAG
10231721 TTTGAAAT-TTATAATATTTAATTTTATTGATAAA
1 TTTGAAATATTATAATATTTAATTTTATTGATAAA
10231755 TAAATAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 16 0.52
36 15 0.48
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (36 bp):
TTTGAAATATTATAATATTTAATTTTATTGATAAAG
Found at i:10234067 original size:14 final size:14
Alignment explanation
Indices: 10234048--10234074 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10234038 TACTAATTAA
10234048 CCATATATATATAG
1 CCATATATATATAG
10234062 CCATATATATATA
1 CCATATATATATA
10234075 TCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
CCATATATATATAG
Found at i:10234358 original size:15 final size:15
Alignment explanation
Indices: 10234338--10234375 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
10234328 TTGAAATTAA
10234338 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
10234353 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
10234368 CCCTAAAT
1 CCCTAAAT
10234376 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:10234518 original size:24 final size:24
Alignment explanation
Indices: 10234457--10234520 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
10234447 TAAATGTTTA
10234457 ATATATATAATTAA-TCATAAAAT
1 ATATATATAATTAATTCATAAAAT
**
10234480 ATAGTCA-ATAATTAATTGTTAAAAT
1 ATA-T-ATATAATTAATTCATAAAAT
*
10234505 ATATATATATTTAATT
1 ATATATATAATTAATT
10234521 TCTATAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 4 0.12
24 19 0.56
25 11 0.32
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (24 bp):
ATATATATAATTAATTCATAAAAT
Found at i:10234940 original size:41 final size:42
Alignment explanation
Indices: 10234895--10235213 Score: 226
Period size: 41 Copynumber: 7.8 Consensus size: 42
10234885 AGGTAAATAC
* * * *
10234895 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGA-CAAGCGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
* * * * *
10234936 ATTAGTGGCGCTCAGTTAGAAACGCCGCTAAAGATC-CGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
* *
10234977 ATTAGCGGCGCTT-GTATAAAAACGCCGCTAAAGACC-CAAGC
1 ATTAGCGGCGCTTAG-ATAAAAACGCCGCTAAAGACCACGAGA
* * * *
10235018 ATTAGCGGCGCATAGA-CAAAACGCTGCTAAAGATC-CGAGA
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
* * * *
10235058 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGA-TACGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
* ** * * * *
10235099 ATTAGCGGCACTTAGACGAAATCACCGCTAAAGA--TCGAGGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGA-GA
** * * * * *
10235140 ATTAGCGGCGCTTTCACAAAAACGCCGCGAAAGATC-GGAGC
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
* * *
10235181 ATTAGCAGCGCTTACACAAAAACGCCGCTAAAG
1 ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAG
10235214 GTTTAAAAAA
Statistics
Matches: 229, Mismatches: 41, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
40 39 0.17
41 186 0.81
42 4 0.02
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (42 bp):
ATTAGCGGCGCTTAGATAAAAACGCCGCTAAAGACCACGAGA
Found at i:10235000 original size:82 final size:79
Alignment explanation
Indices: 10234895--10235213 Score: 284
Period size: 82 Copynumber: 3.9 Consensus size: 79
10234885 AGGTAAATAC
* * * **
10234895 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGA-CAAGCGAATTAGTGGCGC-TCAGTTAGAAA
1 ATTAGCGGCGCTT-GATAAAAACGCCGCTAAAGACCAAGC--ATTAGCGGCGCAT-AGACA-AAA
10234958 CGCCGCTAAAGATCCGAGA
61 CGCCGCTAAAGATCCGAGA
10234977 ATTAGCGGCGCTTGTATAAAAACGCCGCTAAAGACCCAAGCATTAGCGGCGCATAGACAAAACGC
1 ATTAGCGGCGCTTG-ATAAAAACGCCGCTAAAGA-CCAAGCATTAGCGGCGCATAGACAAAACGC
*
10235042 TGCTAAAGATCCGAGA
64 CGCTAAAGATCCGAGA
* * * * * * * *
10235058 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGATACGAGCATTAGCGGCACTTAGACGAAATCA
1 ATTAGCGGCGC-TTGATAAAAACGCCGCTAAAGA-CCAAGCATTAGCGGCGCATAGAC-AAAACG
*
10235123 CCGCTAAAGAT-CGAGGC
63 CCGCTAAAGATCCGA-GA
* * * ** * * *
10235140 ATTAGCGGCGCTTTCACAAAAACGCCGCGAAAGATCGGAGCATTAGCAGCGCTTACACAAAAACG
1 ATTAGCGGCGC-TTGATAAAAACGCCGCTAAAGA-CCAAGCATTAGCGGCGCATAGAC-AAAACG
10235205 CCGCTAAAG
63 CCGCTAAAG
10235214 GTTTAAAAAA
Statistics
Matches: 201, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
81 73 0.36
82 122 0.61
83 1 0.00
84 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (79 bp):
ATTAGCGGCGCTTGATAAAAACGCCGCTAAAGACCAAGCATTAGCGGCGCATAGACAAAACGCCG
CTAAAGATCCGAGA
Found at i:10235319 original size:39 final size:40
Alignment explanation
Indices: 10235270--10235368 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 40
10235260 GGCGCTTTAT
* * ** *
10235270 ATAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTTCGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCACTTT-GG
*
10235310 AT-AATCGCCGCTGATGCTCTACCTTTAGCGGCACTTTGG
1 ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCACTTTGG
*
10235349 CTAAATCGCCGCTAATGCTC
1 ATAAATCGCCGCTAATGCTC
10235369 AATTTTTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 15 0.31
40 34 0.69
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.30
Consensus pattern (40 bp):
ATAAATCGCCGCTAATGCTCTACCTTTAGCGGCACTTTGG
Found at i:10237321 original size:24 final size:24
Alignment explanation
Indices: 10237236--10237325 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 24
10237226 AAATGTATAA
* * * *
10237236 AATAATACATAATAAATTT-GAAG
1 AATAATATATGATAAATTTAAAAT
*
10237259 AATAATATATGA-AAACTTAAAAT
1 AATAATATATGATAAATTTAAAAT
10237282 AAT--TATATGATAAATTTAAAAT
1 AATAATATATGATAAATTTAAAAT
*
10237304 AATAATATGTGATAAATTTAAA
1 AATAATATATGATAAATTTAAA
10237326 CAACATTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
21 7 0.12
22 18 0.32
23 15 0.27
24 16 0.29
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (24 bp):
AATAATATATGATAAATTTAAAAT
Found at i:10241418 original size:20 final size:20
Alignment explanation
Indices: 10241370--10241407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10241360 GTGAGAAAAT
10241370 AAATATTTTGAGTTAATTAA
1 AAATATTTTGAGTTAATTAA
* *
10241390 AAAAATTTTGATTTAATT
1 AAATATTTTGAGTTAATT
10241408 TTTAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
AAATATTTTGAGTTAATTAA
Found at i:10249864 original size:13 final size:14
Alignment explanation
Indices: 10249846--10249874 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10249836 TTAATTTAAA
10249846 TATATTTTA-TATT
1 TATATTTTATTATT
10249859 TATATTTTATTATT
1 TATATTTTATTATT
10249873 TA
1 TA
10249875 ATATGTACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATATTTTATTATT
Found at i:10250340 original size:32 final size:31
Alignment explanation
Indices: 10250304--10250377 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 31
10250294 TAGTTTTTTT
*
10250304 ATTTTTTATATATT-ATTTTTTATAATTTTAAA
1 ATTTTTTATATATTAATTTATT-TAATTTT-AA
*
10250336 ATTTTTTATATATTAATTTATTTAATTTTTA
1 ATTTTTTATATATTAATTTATTTAATTTTAA
10250367 ATTTATTTATA
1 ATTT-TTTATA
10250378 ATTTCTTGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 5 0.13
32 27 0.71
33 6 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
ATTTTTTATATATTAATTTATTTAATTTTAA
Found at i:10250359 original size:16 final size:15
Alignment explanation
Indices: 10250304--10250377 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
10250294 TAGTTTTTTT
10250304 ATTTTTTATATATT-
1 ATTTTTTATATATTA
*
10250318 ATTTTTTATAATTTTAAA
1 ATTTTTTAT-ATATT--A
10250336 ATTTTTTATATATTA
1 ATTTTTTATATATTA
*
10250351 ATTTATTTA-ATTTTTA
1 ATTT-TTTATA-TATTA
10250367 ATTTATTTATA
1 ATTT-TTTATA
10250378 ATTTCTTGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
14 9 0.18
15 10 0.20
16 17 0.34
17 5 0.10
18 9 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTTATATATTA
Found at i:10257036 original size:17 final size:19
Alignment explanation
Indices: 10257001--10257037 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
10256991 TAAATATCTA
10257001 TTTTTACAATATTTAATTT
1 TTTTTACAATATTTAATTT
*
10257020 TTTTTA-AAT-TTTCATTT
1 TTTTTACAATATTTAATTT
10257037 T
1 T
10257038 AAATTATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTACAATATTTAATTT
Found at i:10257637 original size:15 final size:16
Alignment explanation
Indices: 10257615--10257648 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
10257605 CAAAATATAT
10257615 CAAAAAAACTAAAA-AA
1 CAAAAAAA-TAAAAGAA
10257631 CAAAAAAATAAAAGAA
1 CAAAAAAATAAAAGAA
10257647 CA
1 CA
10257649 GGAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.79, C:0.12, G:0.03, T:0.06
Consensus pattern (16 bp):
CAAAAAAATAAAAGAA
Found at i:10257756 original size:27 final size:27
Alignment explanation
Indices: 10257698--10257765 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
10257688 GAGGGAAGCA
**
10257698 GGTTGGCGGCACCAAACAAGGAGAGGG
1 GGTTGGCGGCACCAAACAAGGAGACCG
* *
10257725 GGTTGGCGGCACCAAACAAGGAGTCCT
1 GGTTGGCGGCACCAAACAAGGAGACCG
* *
10257752 TGTTGGTGGCACCA
1 GGTTGGCGGCACCA
10257766 CCCTTAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.38, T:0.15
Consensus pattern (27 bp):
GGTTGGCGGCACCAAACAAGGAGACCG
Found at i:10257829 original size:4 final size:4
Alignment explanation
Indices: 10257820--10257889 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
10257810 GGGGAAGAAG
*
10257820 AAGA AAGA AATG- AAGA AAG- AA-A AAGA AGGAA AAGGA AAGA AGAGGA
1 AAGA AAGA AA-GA AAGA AAGA AAGA AAGA AAG-A AA-GA AAGA A-A-GA
10257866 AAGA AAG- AA-A AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
10257890 AGGAAAGGGG
Statistics
Matches: 54, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
3 9 0.17
4 33 0.61
5 8 0.15
6 4 0.07
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:10257845 original size:10 final size:10
Alignment explanation
Indices: 10257814--10257896 Score: 64
Period size: 10 Copynumber: 8.3 Consensus size: 10
10257804 AGGAGAGGGG
*
10257814 AAGAAGAAGA
1 AAGAAAAAGA
10257824 AAGAAATGAAGA
1 AAGAAA--AAGA
10257836 AAGAAAAAGA
1 AAGAAAAAGA
* *
10257846 AGGAAAAGGA
1 AAGAAAAAGA
* *
10257856 AAGAAGAGGA
1 AAGAAAAAGA
10257866 AAG--AAAGA
1 AAGAAAAAGA
10257874 AA-AAGAAAGA
1 AAGAA-AAAGA
*
10257884 AAGAAAAGGA
1 AAGAAAAAGA
10257894 AAG
1 AAG
10257897 GGGAAGAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
8 5 0.08
10 42 0.71
11 2 0.03
12 10 0.17
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:10257858 original size:14 final size:14
Alignment explanation
Indices: 10257834--10257896 Score: 74
Period size: 14 Copynumber: 4.4 Consensus size: 14
10257824 AAGAAATGAA
10257834 GAAAGAAA-AAGAAG
1 GAAAGAAAGAA-AAG
*
10257848 GAAAAGGAAAGAAGAG
1 G-AAA-GAAAGAAAAG
*
10257864 GAAAGAAAGAAAAA
1 GAAAGAAAGAAAAG
10257878 GAAAGAAAGAAAAG
1 GAAAGAAAGAAAAG
10257892 GAAAG
1 GAAAG
10257897 GGGAAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
14 27 0.64
15 6 0.14
16 7 0.17
17 2 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGAAAAG
Found at i:10257904 original size:34 final size:34
Alignment explanation
Indices: 10257831--10257912 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
10257821 AGAAAGAAAT
* *
10257831 GAAGAAAGAAAAAGAAGGAAAAGGAAAGAAGAGG
1 GAAGAAAGAAAAAGAAAGAAAAGAAAAGAAGAGG
*
10257865 AAAGAAAGAAAAAGAAAG-AAAGAAAAGGAA-AGGG
1 GAAGAAAGAAAAAGAAAGAAAAGAAAA-GAAGA-GG
*
10257899 GAAGAAAAAAAAAG
1 GAAGAAAGAAAAAG
10257913 CAGTTTATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 8 0.20
34 33 0.80
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (34 bp):
GAAGAAAGAAAAAGAAAGAAAAGAAAAGAAGAGG
Found at i:10257957 original size:27 final size:24
Alignment explanation
Indices: 10257921--10257991 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 24
10257911 AGCAGTTTAT
10257921 AAGGAA-AGAAAAATAAGAAAAGGA
1 AAGGAAGAGAAAAA-AAGAAAAGGA
* *
10257945 AAGGAGAAGAGAAAAAAAAAAAGAGGG
1 AA-G-GAAGAGAAAAAAAGAAA-AGGA
10257972 AAGGAAG-GAAAAAAAGAAAA
1 AAGGAAGAGAAAAAAAGAAAA
10257992 TAAGGTAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.03
24 13 0.32
25 5 0.12
26 9 0.22
27 12 0.30
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (24 bp):
AAGGAAGAGAAAAAAAGAAAAGGA
Found at i:10258520 original size:18 final size:18
Alignment explanation
Indices: 10258497--10258531 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10258487 TATTTTAAAA
*
10258497 AAAGTAATGAAATAATAT
1 AAAGTAATAAAATAATAT
10258515 AAAGTAATAAAATAATA
1 AAAGTAATAAAATAATA
10258532 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAGTAATAAAATAATAT
Found at i:10258694 original size:18 final size:18
Alignment explanation
Indices: 10258671--10258718 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
10258661 AAAATATATA
*
10258671 TAATATTTTGGTTTTTTT-
1 TAATATTTT-ATTTTTTTG
10258689 TAATATTTTATTTTTTTG
1 TAATATTTTATTTTTTTG
*
10258707 TAATGTTTTATT
1 TAATATTTTATT
10258719 ATGGGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (18 bp):
TAATATTTTATTTTTTTG
Found at i:10258795 original size:52 final size:53
Alignment explanation
Indices: 10258738--10258848 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 53
10258728 ATACAAAAAT
**
10258738 AATATAAAAAATAAAAAATTACCAAAATATTAT-AAATTTTTTTATTTACCGA
1 AATATAAAAAATAAAAAATTACCAAAATATTATAAAAAATTTTTATTTACCGA
* * * **** *
10258790 AATATATATATTTTTTATTTACCAAAATATTATAAAAAATTTTTATTTACCGA
1 AATATAAAAAATAAAAAATTACCAAAATATTATAAAAAATTTTTATTTACCGA
10258843 AATATA
1 AATATA
10258849 TTTTTTTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
52 25 0.52
53 23 0.48
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (53 bp):
AATATAAAAAATAAAAAATTACCAAAATATTATAAAAAATTTTTATTTACCGA
Found at i:10258799 original size:28 final size:27
Alignment explanation
Indices: 10258756--10258900 Score: 169
Period size: 28 Copynumber: 5.5 Consensus size: 27
10258746 AAATAAAAAA
10258756 TTACCAAAATAT-TATAAATTTTTTTAT
1 TTACCAAAATATATAT-AATTTTTTTAT
*
10258783 TTACCGAAATATATAT-A-TTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
* **
10258808 TTACCAAAATATTATAAAAAATTTTTAT
1 TTACCAAAATA-TATATAATTTTTTTAT
*
10258836 TTACC-GAA-ATATAT--TTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
10258859 TTACCAAAATATATATAATTTTGTTTAT
1 TTACCAAAATATATATAATTTT-TTTAT
10258887 TTACCAAAATATAT
1 TTACCAAAATATAT
10258901 CAAAAAAAAC
Statistics
Matches: 100, Mismatches: 9, Indels: 17
0.79 0.07 0.13
Matches are distributed among these distances:
23 12 0.12
24 2 0.02
25 28 0.28
26 6 0.06
27 18 0.18
28 34 0.34
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:10258867 original size:51 final size:53
Alignment explanation
Indices: 10258756--10258900 Score: 217
Period size: 51 Copynumber: 2.8 Consensus size: 53
10258746 AAATAAAAAA
10258756 TTACCAAAATATTAT-AAATTTTTTTATTTACCGAAATATATATATTTTTTAT
1 TTACCAAAATATTATAAAATTTTTTTATTTACCGAAATATATATATTTTTTAT
**
10258808 TTACCAAAATATTATAAAAAATTTTTATTTACCGAAATATAT-T-TTTTTTAT
1 TTACCAAAATATTATAAAATTTTTTTATTTACCGAAATATATATATTTTTTAT
* *
10258859 TTACCAAAATA-TATATAATTTTGTTTATTTACCAAAATATAT
1 TTACCAAAATATTATAAAATTTT-TTTATTTACCGAAATATAT
10258901 CAAAAAAAAC
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
50 8 0.09
51 37 0.44
52 16 0.19
53 24 0.28
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (53 bp):
TTACCAAAATATTATAAAATTTTTTTATTTACCGAAATATATATATTTTTTAT
Found at i:10260263 original size:216 final size:216
Alignment explanation
Indices: 10259889--10260321 Score: 848
Period size: 216 Copynumber: 2.0 Consensus size: 216
10259879 GCCGTGCTAG
10259889 CAGTCTTGTATCGAGAGCTTTGTCGGGCGACAGATCCGAAAGTTCGCGACATTGGCGGATGCCTC
1 CAGTCTTGTATCGAGAGCTTTGTCGGGCGACAGATCCGAAAGTTCGCGACATTGGCGGATGCCTC
10259954 TCACTGCTGCAGTCCTGGGCGCTGTATCGGATGCCATTTTTGGCATCGGTTAGACACCAACCGTA
66 TCACTGCTGCAGTCCTGGGCGCTGTATCGGATGCCATTTTTGGCATCGGTTAGACACCAACCGTA
10260019 TGTTTATCCACTGCTGAGCAGGTGATAAAATATAACTTCTCATTATTTGTAGTCATAATATATTG
131 TGTTTATCCACTGCTGAGCAGGTGATAAAATATAACTTCTCATTATTTGTAGTCATAATATATTG
10260084 ACTAATGTTACCAACTCTAAA
196 ACTAATGTTACCAACTCTAAA
*
10260105 CAGTCTTGTATCGAGAGCTTTGTCGGGCGACAGATCCGAAAGTTTGCGACATTGGCGGATGCCTC
1 CAGTCTTGTATCGAGAGCTTTGTCGGGCGACAGATCCGAAAGTTCGCGACATTGGCGGATGCCTC
*
10260170 TCACTGCTGCAGTCCTGGGCGCTGTATCGGATGTCATTTTTGGCATCGGTTAGACACCAACCGTA
66 TCACTGCTGCAGTCCTGGGCGCTGTATCGGATGCCATTTTTGGCATCGGTTAGACACCAACCGTA
10260235 TGTTTATCCACTGCTGAGCAGGTGATAAAATATAACTTCTCATTATTTGTAGTCATAATATATTG
131 TGTTTATCCACTGCTGAGCAGGTGATAAAATATAACTTCTCATTATTTGTAGTCATAATATATTG
10260300 ACTAATGTTACCAACTCTAAA
196 ACTAATGTTACCAACTCTAAA
10260321 C
1 C
10260322 CCTATATTTG
Statistics
Matches: 215, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
216 215 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (216 bp):
CAGTCTTGTATCGAGAGCTTTGTCGGGCGACAGATCCGAAAGTTCGCGACATTGGCGGATGCCTC
TCACTGCTGCAGTCCTGGGCGCTGTATCGGATGCCATTTTTGGCATCGGTTAGACACCAACCGTA
TGTTTATCCACTGCTGAGCAGGTGATAAAATATAACTTCTCATTATTTGTAGTCATAATATATTG
ACTAATGTTACCAACTCTAAA
Found at i:10263854 original size:18 final size:18
Alignment explanation
Indices: 10263828--10263865 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10263818 ATCCCAATGA
* *
10263828 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
10263846 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
10263864 TC
1 TC
10263866 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:10263872 original size:18 final size:18
Alignment explanation
Indices: 10263831--10263872 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
10263821 CCAATGATCG
* *
10263831 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
10263849 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
10263867 CCACCA
1 CCACCA
10263873 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:10264622 original size:3 final size:3
Alignment explanation
Indices: 10264614--10264642 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10264604 AGTAACATCT
10264614 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
10264643 CTATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10265128 original size:28 final size:28
Alignment explanation
Indices: 10265096--10265149 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
10265086 TTAGTTTTTT
10265096 TATATATTTTGATAAATAAAAAAATTTA
1 TATATATTTTGATAAATAAAAAAATTTA
*
10265124 TATATATTTTGGTAAATAAAAAAATT
1 TATATATTTTGATAAATAAAAAAATT
10265150 ATAACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
TATATATTTTGATAAATAAAAAAATTTA
Found at i:10265158 original size:26 final size:28
Alignment explanation
Indices: 10265096--10265164 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
10265086 TTAGTTTTTT
* *
10265096 TATATATTTTGATAAATAAAAAAATTTA
1 TATACATTTTGGTAAATAAAAAAATTTA
*
10265124 TATATATTTTGGTAAATAAAAAAA-TTA
1 TATACATTTTGGTAAATAAAAAAATTTA
10265151 TA-ACATTTTGGTAA
1 TATACATTTTGGTAA
10265165 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 11 0.28
27 5 0.13
28 23 0.59
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (28 bp):
TATACATTTTGGTAAATAAAAAAATTTA
Found at i:10265680 original size:18 final size:19
Alignment explanation
Indices: 10265641--10265681 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
10265631 ATTGTTTGTA
*
10265641 TATTGTATAATTCTTATTT
1 TATTGTATAATTCTTATAT
10265660 TATTGT-TAATT-TTACTAT
1 TATTGTATAATTCTTA-TAT
10265678 TATT
1 TATT
10265682 TTAGAGGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 3 0.15
18 11 0.55
19 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTCTTATAT
Found at i:10276664 original size:110 final size:110
Alignment explanation
Indices: 10276471--10276691 Score: 415
Period size: 110 Copynumber: 2.0 Consensus size: 110
10276461 TCCCTTAGTG
*
10276471 CAATGTCTGTGTTCATACAACCAAACACTATAAGTAAGTGCCTTTTTCATTCATTGAAATTAGTC
1 CAATGTCTATGTTCATACAACCAAACACTATAAGTAAGTGCCTTTTTCATTCATTGAAATTAGTC
10276536 CCATTAAGCATAAGTATAGAATTTATATTAGCAGATATTATTAAC
66 CCATTAAGCATAAGTATAGAATTTATATTAGCAGATATTATTAAC
*
10276581 CAATGTCTATGTTCATACAACCAAACACTATAAGTAAGTGCCTTTTTCATTCATTGAAATTAGTT
1 CAATGTCTATGTTCATACAACCAAACACTATAAGTAAGTGCCTTTTTCATTCATTGAAATTAGTC
*
10276646 CCATTAAGCATAAGTATAGAATTTATATTAGTAGATATTATTAAC
66 CCATTAAGCATAAGTATAGAATTTATATTAGCAGATATTATTAAC
10276691 C
1 C
10276692 TTCATTTGGC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 108 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (110 bp):
CAATGTCTATGTTCATACAACCAAACACTATAAGTAAGTGCCTTTTTCATTCATTGAAATTAGTC
CCATTAAGCATAAGTATAGAATTTATATTAGCAGATATTATTAAC
Found at i:10277601 original size:15 final size:15
Alignment explanation
Indices: 10277583--10277611 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10277573 ATATGCATAT
10277583 AATATATATACACAC
1 AATATATATACACAC
10277598 AATATATATACACA
1 AATATATATACACA
10277612 ATTATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATATATACACAC
Found at i:10278426 original size:22 final size:22
Alignment explanation
Indices: 10278401--10278442 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10278391 TATAAAATTA
10278401 AAAAAGAA-AAACGAATCAATCC
1 AAAAAGAATAAA-GAATCAATCC
*
10278423 AAAAATAATAAAGAATCAAT
1 AAAAAGAATAAAGAATCAAT
10278443 TCATTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.67, C:0.12, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAAAGAATAAAGAATCAATCC
Found at i:10284321 original size:24 final size:24
Alignment explanation
Indices: 10284287--10284481 Score: 87
Period size: 25 Copynumber: 8.0 Consensus size: 24
10284277 TTTAGCTCTT
*
10284287 ATGAGCATCCCGTTACATGGCTCC
1 ATGAGCTTCCCGTTACATGGCTCC
* *
10284311 ATGAGCTTCCCGATA-TTGGCTCGC
1 ATGAGCTTCCCGTTACATGGCTC-C
* * *
10284335 ATGAGCTTCCCAATTACA--GATCTT
1 ATGAGCTTCCC-GTTACATGGCTC-C
*
10284359 ATGAGCTTCCCGATTA-ATGGCTCT
1 ATGAGCTTCCCG-TTACATGGCTCC
* * * * *
10284383 ATGGAGCTTCCTGAT-CTTTGGTTGTC
1 AT-GAGCTTCCCGTTAC-ATGGCT-CC
* * * *
10284409 TTGAGCTTCCTGATA-ATTGGCTTGC
1 ATGAGCTTCCCGTTACA-TGGC-TCC
* * *
10284434 AAGAGCTTCCCATTATATGGCTCAC
1 ATGAGCTTCCCGTTACATGGCTC-C
10284459 ATGAGCTTCCCGTTACATGGCTC
1 ATGAGCTTCCCGTTACATGGCTC
10284482 GAAAGAGCTT
Statistics
Matches: 126, Mismatches: 30, Indels: 29
0.68 0.16 0.16
Matches are distributed among these distances:
23 7 0.06
24 47 0.37
25 69 0.55
26 3 0.02
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (24 bp):
ATGAGCTTCCCGTTACATGGCTCC
Found at i:10284454 original size:25 final size:25
Alignment explanation
Indices: 10284426--10284503 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
10284416 TCCTGATAAT
* *
10284426 TGGCTTGCAAGAGCTTCCCATTATA
1 TGGCTCGCAAGAGCTTCCCATTACA
* * *
10284451 TGGCTCACATGAGCTTCCCGTTACA
1 TGGCTCGCAAGAGCTTCCCATTACA
* *
10284476 TGGCTCGAAAGAGCTTCCTGATTACA
1 TGGCTCGCAAGAGCTTCC-CATTACA
10284502 TG
1 TG
10284504 CTCATATGGG
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
25 35 0.83
26 7 0.17
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (25 bp):
TGGCTCGCAAGAGCTTCCCATTACA
Found at i:10285482 original size:30 final size:30
Alignment explanation
Indices: 10285447--10285514 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
10285437 TCTGTCTCAA
10285447 CCGTGTGTGACACACGACCATATGACACGG
1 CCGTGTGTGACACACGACCATATGACACGG
*
10285477 TCGTGTGTGACACACGACCATATGACACGG
1 CCGTGTGTGACACACGACCATATGACACGG
10285507 CCGTGTGT
1 CCGTGTGT
10285515 CCCCTGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (30 bp):
CCGTGTGTGACACACGACCATATGACACGG
Found at i:10291952 original size:22 final size:22
Alignment explanation
Indices: 10291926--10292009 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 22
10291916 AAACATTTAC
10291926 AAATATAAACATAATTATATCA
1 AAATATAAACATAATTATATCA
* * * *
10291948 AAATATATACATCATTTACCAAGATTCT
1 AAATATAAACAT-AATT----ATA-TCA
10291976 AAATATAAACATAATTATATCA
1 AAATATAAACATAATTATATCA
*
10291998 AAATATATACAT
1 AAATATAAACAT
10292010 CATTTACCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
22 24 0.51
23 5 0.11
27 5 0.11
28 13 0.28
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (22 bp):
AAATATAAACATAATTATATCA
Found at i:10291984 original size:50 final size:50
Alignment explanation
Indices: 10291926--10292027 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
10291916 AAACATTTAC
10291926 AAATATAAACATAATTATATCAAAATATATACATCATTTACCAAGATTCT
1 AAATATAAACATAATTATATCAAAATATATACATCATTTACCAAGATTCT
10291976 AAATATAAACATAATTATATCAAAATATATACATCATTTACCAAGATTCT
1 AAATATAAACATAATTATATCAAAATATATACATCATTTACCAAGATTCT
10292026 AA
1 AA
10292028 CTTATATATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (50 bp):
AAATATAAACATAATTATATCAAAATATATACATCATTTACCAAGATTCT
Found at i:10292896 original size:21 final size:21
Alignment explanation
Indices: 10292870--10292916 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
10292860 TAATTTTTTA
10292870 ATTAAA-TGGAAATTAAAACAT
1 ATTAAAGT-GAAATTAAAACAT
10292891 ATTAAAGTGAAATTAAAACAT
1 ATTAAAGTGAAATTAAAACAT
*
10292912 TTTAA
1 ATTAA
10292917 TTTCATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (21 bp):
ATTAAAGTGAAATTAAAACAT
Found at i:10295947 original size:35 final size:34
Alignment explanation
Indices: 10295856--10295957 Score: 116
Period size: 34 Copynumber: 3.0 Consensus size: 34
10295846 GTGAAAGAGT
* *
10295856 TTGCGCCCTGCGCTAGTCAGATAAACCGAC-AAA
1 TTGCGCCCAGCGCTAGTCAGATAAACTGACGAAA
* * * *
10295889 TGTGTGTCCAGCACTAGTCAGATAAACTGACGGAAG
1 T-TGCGCCCAGCGCTAGTCAGATAAACTGAC-GAAA
*
10295925 TTGCGCCCAGCGCTAGTAAGATAAACTGACGAA
1 TTGCGCCCAGCGCTAGTCAGATAAACTGACGAA
10295958 TAAATAGTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
33 1 0.02
34 27 0.48
35 25 0.45
36 3 0.05
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (34 bp):
TTGCGCCCAGCGCTAGTCAGATAAACTGACGAAA
Found at i:10300340 original size:29 final size:31
Alignment explanation
Indices: 10300304--10300371 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
10300294 TTTTAGTCCT
10300304 TCAACTTTTCAAAT-TT-ACACTATAAC-CCA
1 TCAACTTTT-AAATATTCACACTATAACTCCA
* *
10300333 TCAACTTTTAAATATTCACACTTTGACTCCA
1 TCAACTTTTAAATATTCACACTATAACTCCA
10300364 TC-ACTTTT
1 TCAACTTTT
10300372 TTACTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 11 0.32
30 14 0.41
31 5 0.15
ACGTcount: A:0.32, C:0.26, G:0.01, T:0.40
Consensus pattern (31 bp):
TCAACTTTTAAATATTCACACTATAACTCCA
Found at i:10300457 original size:12 final size:12
Alignment explanation
Indices: 10300432--10300470 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
10300422 ATACCATATG
10300432 TTTTATTA-TTA
1 TTTTATTATTTA
10300443 TTTTATTATTTA
1 TTTTATTATTTA
10300455 -TTTATTTATTTA
1 TTTTA-TTATTTA
10300467 TTTT
1 TTTT
10300471 TAGACCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 12 0.48
12 10 0.40
13 3 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:10305435 original size:55 final size:55
Alignment explanation
Indices: 10305351--10305459 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
10305341 GCCCTCGACT
**
10305351 GATTTGCAGACAGGGTTGAAGAAATTTGTAAGATGGTATCTCAGCTACTATTCTA
1 GATTTGCAGACAGGGACGAAGAAATTTGTAAGATGGTATCTCAGCTACTATTCTA
10305406 GATTTGCAGACAGGGACGAAGAAATTTGTAAGATGGTATCTCAGCTACTATTCT
1 GATTTGCAGACAGGGACGAAGAAATTTGTAAGATGGTATCTCAGCTACTATTCT
10305460 GGTGGGAACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (55 bp):
GATTTGCAGACAGGGACGAAGAAATTTGTAAGATGGTATCTCAGCTACTATTCTA
Found at i:10314419 original size:23 final size:22
Alignment explanation
Indices: 10314358--10314429 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 22
10314348 TACATTATTT
10314358 TAATTTAATATTTAATAATTTTATA
1 TAATTTAATA-TTAAT--TTTTATA
* *
10314383 TATTTTTATTTATTAATTTTTATA
1 TA-ATTTA-ATATTAATTTTTATA
*
10314407 TAATTATAATATT-ATTTTAATA
1 TAATT-TAATATTAATTTTTATA
10314429 T
1 T
10314430 GTAGATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 9 0.23
23 6 0.15
24 11 0.28
25 2 0.05
26 9 0.23
27 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATTTAATATTAATTTTTATA
Found at i:10315573 original size:13 final size:14
Alignment explanation
Indices: 10315555--10315583 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10315545 TCTATAATTA
10315555 TTTTAAA-TTTGAT
1 TTTTAAATTTTGAT
10315568 TTTTAAATTTTGAT
1 TTTTAAATTTTGAT
10315582 TT
1 TT
10315584 ATTTAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTTAAATTTTGAT
Found at i:10315600 original size:23 final size:23
Alignment explanation
Indices: 10315582--10315627 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
10315572 AAATTTTGAT
10315582 TTATTTAGTGATAATATTTAGGA
1 TTATTTAGTGATAATATTTAGGA
10315605 TTATTTAGTGATAATATTTAGGA
1 TTATTTAGTGATAATATTTAGGA
10315628 AAAATCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (23 bp):
TTATTTAGTGATAATATTTAGGA
Found at i:10315601 original size:13 final size:13
Alignment explanation
Indices: 10315583--10315625 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
10315573 AATTTTGATT
10315583 TATTTAGTGATAA
1 TATTTAGTGATAA
10315596 TATTTAG-GAT--
1 TATTTAGTGATAA
10315606 TATTTAGTGATAA
1 TATTTAGTGATAA
10315619 TATTTAG
1 TATTTAG
10315626 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:10321077 original size:25 final size:25
Alignment explanation
Indices: 10321040--10321093 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
10321030 TTCTGTTATA
*
10321040 GCTCAGATAAGCTTCCTGTTACATG
1 GCTCACATAAGCTTCCTGTTACATG
* * *
10321065 GCTCACATGAGCTTCTTGTTATATG
1 GCTCACATAAGCTTCCTGTTACATG
10321090 GCTC
1 GCTC
10321094 GAAAGAGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (25 bp):
GCTCACATAAGCTTCCTGTTACATG
Found at i:10321833 original size:27 final size:27
Alignment explanation
Indices: 10321802--10321856 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
10321792 GTTTAAGTAA
*
10321802 GTATATGATCATTTGAGTAAGTTGGAT
1 GTATAAGATCATTTGAGTAAGTTGGAT
10321829 GTATAAGATCATTTGAGTAAGTTGGAT
1 GTATAAGATCATTTGAGTAAGTTGGAT
10321856 G
1 G
10321857 ATTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (27 bp):
GTATAAGATCATTTGAGTAAGTTGGAT
Found at i:10335080 original size:40 final size:40
Alignment explanation
Indices: 10334994--10335080 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
10334984 TAATTGTAAT
* *
10334994 TAAATAGGACAATTAAATTAATTAATCATCATAATTTTAC
1 TAAATAGGACAATTAAATTAATTAATCATCATAATCTTAA
* *
10335034 TAAATAGGACAATTAAATTTATTTA-C-TCATATATCTTAA
1 TAAATAGGACAATTAAATTAATTAATCATCATA-ATCTTAA
10335073 TACAATAG
1 TA-AATAG
10335081 TTGTAATGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 5 0.12
39 8 0.20
40 28 0.68
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (40 bp):
TAAATAGGACAATTAAATTAATTAATCATCATAATCTTAA
Found at i:10335345 original size:13 final size:13
Alignment explanation
Indices: 10335277--10335347 Score: 97
Period size: 13 Copynumber: 5.5 Consensus size: 13
10335267 TCTTCATTGT
* *
10335277 TTTTGAAAAGTAC
1 TTTTGAGAAGTGC
10335290 TTTTGAGAAGTGC
1 TTTTGAGAAGTGC
*
10335303 TTTTGAGAAGTGA
1 TTTTGAGAAGTGC
*
10335316 TTTTGAGAAGTGA
1 TTTTGAGAAGTGC
*
10335329 TTTTGAGAAGCGC
1 TTTTGAGAAGTGC
10335342 TTTTGA
1 TTTTGA
10335348 AAAATTTGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.28, C:0.06, G:0.27, T:0.39
Consensus pattern (13 bp):
TTTTGAGAAGTGC
Found at i:10341026 original size:21 final size:21
Alignment explanation
Indices: 10340974--10341043 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
10340964 TCGTGTTTAC
*
10340974 TTTCCGTTTAGCTT-TCATGAG
1 TTTCCGTTTAACTTAT-ATGAG
* *
10340995 GTTCTG-TTAACTTATATGAG
1 TTTCCGTTTAACTTATATGAG
*
10341015 TTTCCGTTTAACCTTA-ATGGG
1 TTTCCGTTTAA-CTTATATGAG
10341036 TTTCCGTT
1 TTTCCGTT
10341044 CAGCTCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 15 0.38
21 21 0.52
22 4 0.10
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (21 bp):
TTTCCGTTTAACTTATATGAG
Found at i:10341101 original size:42 final size:42
Alignment explanation
Indices: 10341024--10341165 Score: 185
Period size: 42 Copynumber: 3.4 Consensus size: 42
10341014 GTTTCCGTTT
*
10341024 AACCTTAATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTC
1 AACCCTAATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTC
* * * *
10341066 AACCCTAATAGGTTCCCGTTCAGCTCTTTTGAGCTTCAGTTT
1 AACCCTAATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTC
* * ** *
10341108 AACCCTTATGGGTTTCCGTTTAGCTCTTACAAGCTTCCGTTC
1 AACCCTAATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTC
*
10341150 AACCCTTATGGGTTTC
1 AACCCTAATGGGTTTC
10341166 TGTTTAGCAC
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (42 bp):
AACCCTAATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTC
Found at i:10341136 original size:21 final size:21
Alignment explanation
Indices: 10341009--10341165 Score: 66
Period size: 21 Copynumber: 7.5 Consensus size: 21
10340999 TGTTAACTTA
*
10341009 TATGAGTTTCCGTTTAA-CCT
1 TATGAGTTTCCGTTCAACCCT
* * *
10341029 TAATGGGTTTCCGTTCAGCTCT
1 T-ATGAGTTTCCGTTCAACCCT
* * * *
10341051 TTTAAGCTTCAGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
10341072 AAT-AGGTTCCCGTTCAGCTCT
1 TATGA-GTTTCCGTTCAACCCT
* * * *
10341093 TTTGAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
10341114 TATGGGTTTCCGTTTAGCTCT
1 TATGAGTTTCCGTTCAACCCT
** *
10341135 TACAAGCTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
*
10341156 TATGGGTTTC
1 TATGAGTTTC
10341166 TGTTTAGCAC
Statistics
Matches: 90, Mismatches: 43, Indels: 7
0.64 0.31 0.05
Matches are distributed among these distances:
20 2 0.02
21 84 0.93
22 4 0.04
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:10342564 original size:37 final size:37
Alignment explanation
Indices: 10342507--10342658 Score: 173
Period size: 37 Copynumber: 3.9 Consensus size: 37
10342497 TATGATCACT
*
10342507 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
10342542 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
10342579 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCAC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGC-----C-A-C-C
*
10342624 TTATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 -TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
10342659 GAAGCTATCA
Statistics
Matches: 100, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
35 6 0.06
36 4 0.04
37 54 0.54
41 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 32 0.32
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:10342642 original size:46 final size:46
Alignment explanation
Indices: 10342575--10342843 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
10342565 TAAGTGTAGC
* **
10342575 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
10342621 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
10342667 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
10342719 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
10342765 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
10342817 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
10342844 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:10342694 original size:52 final size:52
Alignment explanation
Indices: 10342618--10342837 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
10342608 TAGCTAAAGC
* *
10342618 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
10342671 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
10342723 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
10342769 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
10342821 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
10342838 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:10342740 original size:98 final size:98
Alignment explanation
Indices: 10342575--10342843 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
10342565 TAAGTGTAGC
* * *
10342575 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
10342640 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
10342674 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
10342739 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
10342772 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
10342837 GATCAGA
66 GATCAGA
10342844 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:10362404 original size:14 final size:14
Alignment explanation
Indices: 10362385--10362411 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10362375 CCAAACTGTG
10362385 TAAATATAGTGGAT
1 TAAATATAGTGGAT
10362399 TAAATATAGTGGA
1 TAAATATAGTGGA
10362412 ATTACTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (14 bp):
TAAATATAGTGGAT
Found at i:10368585 original size:22 final size:22
Alignment explanation
Indices: 10368557--10368615 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
10368547 AATGGTTTTG
*
10368557 ATTAAATAATATTAATAT-TAAA
1 ATTAAATAA-ATTAAAATGTAAA
*
10368579 ATTAAATTAATTAAAATGTAAA
1 ATTAAATAAATTAAAATGTAAA
*
10368601 A-TATATAAATTAAAA
1 ATTAAATAAATTAAAA
10368616 CAATATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTAAATAAATTAAAATGTAAA
Found at i:10373595 original size:33 final size:34
Alignment explanation
Indices: 10373557--10373633 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
10373547 TAAGTTATTA
*
10373557 TTTAGGTATGATTGGAACATGTTTTT-GAGCATG
1 TTTAGGTATGATTGGAACATGTTTTTCAAGCATG
* * *
10373590 TTTAGGCATGATTTGAACATGTTTTTCAAGGATG
1 TTTAGGTATGATTGGAACATGTTTTTCAAGCATG
*
10373624 TTTTGGTATG
1 TTTAGGTATG
10373634 GTTGATAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.23, C:0.06, G:0.26, T:0.44
Consensus pattern (34 bp):
TTTAGGTATGATTGGAACATGTTTTTCAAGCATG
Found at i:10374234 original size:19 final size:20
Alignment explanation
Indices: 10374206--10374257 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
10374196 ATGGTTCCTA
*
10374206 ATGATTAATTAAGA-AAATT
1 ATGATTAATTAAGATAAAAT
10374225 AT-ATTTAATTAAGATAAAAT
1 ATGA-TTAATTAAGATAAAAT
10374245 ATGATTAATTAAG
1 ATGATTAATTAAG
10374258 GCTAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 15 0.52
21 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGATTAATTAAGATAAAAT
Found at i:10379462 original size:19 final size:18
Alignment explanation
Indices: 10379434--10379469 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
10379424 CTTTATATAC
*
10379434 AACTTTAAATTTCAACAAG
1 AACTTCAAATTT-AACAAG
10379453 AACTTCAAATTTAACAA
1 AACTTCAAATTTAACAA
10379470 CTTCGAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (18 bp):
AACTTCAAATTTAACAAG
Found at i:10382209 original size:13 final size:13
Alignment explanation
Indices: 10382191--10382217 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10382181 AATAAAACTC
10382191 TACTTGGAGATGA
1 TACTTGGAGATGA
10382204 TACTTGGAGATGA
1 TACTTGGAGATGA
10382217 T
1 T
10382218 TTTCCATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (13 bp):
TACTTGGAGATGA
Found at i:10391974 original size:62 final size:61
Alignment explanation
Indices: 10391869--10391997 Score: 222
Period size: 62 Copynumber: 2.1 Consensus size: 61
10391859 TTCTATTTCC
* *
10391869 CAAAATAAACATCTTAATATTTTTCCATTAAATAATCTTCTCAACTCAGTTCTAGTTTTGT
1 CAAAATAAACATCTTAATATTTTTCCATAAAATAATCTTCTCAACTCAGTTATAGTTTTGT
10391930 CAAAATAAACATCTTAATATTTTTTCCATAAAATAATCTTCTCAACTCAGTTATAGTTTTGT
1 CAAAATAAACATCTTAATA-TTTTTCCATAAAATAATCTTCTCAACTCAGTTATAGTTTTGT
*
10391992 TAAAAT
1 CAAAAT
10391998 CATGACGACT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
61 19 0.30
62 45 0.70
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (61 bp):
CAAAATAAACATCTTAATATTTTTCCATAAAATAATCTTCTCAACTCAGTTATAGTTTTGT
Found at i:10392248 original size:17 final size:17
Alignment explanation
Indices: 10392226--10392267 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10392216 AAACAATAAT
10392226 CATTTCTAAATGTTTC-C
1 CATTTCTAAAT-TTTCAC
**
10392243 CATTTCTCCATTTTCAC
1 CATTTCTAAATTTTCAC
10392260 CATTTCTA
1 CATTTCTA
10392268 TTCATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CATTTCTAAATTTTCAC
Found at i:10396011 original size:41 final size:41
Alignment explanation
Indices: 10395966--10396047 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
10395956 ATAGGGACTA
10395966 AGTCAAAAACTCAAAAAAAATTCAGAAATATTTAAAATTTT
1 AGTCAAAAACTCAAAAAAAATTCAGAAATATTTAAAATTTT
10396007 AGTCAAAAACTCAAAAAAAATTCAGAAATATTTAAAATTTT
1 AGTCAAAAACTCAAAAAAAATTCAGAAATATTTAAAATTTT
10396048 CAACACTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (41 bp):
AGTCAAAAACTCAAAAAAAATTCAGAAATATTTAAAATTTT
Found at i:10402684 original size:3 final size:3
Alignment explanation
Indices: 10402676--10402744 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
10402666 ATATATAGGT
10402676 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA ATGA A-A ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
*
10402721 ATA AT- ATCA ATA CTA ATA A-A ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA A
10402745 ACTAAAAAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
2 8 0.14
3 42 0.74
4 7 0.12
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10410559 original size:30 final size:30
Alignment explanation
Indices: 10410523--10410583 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
10410513 AGCTTATCAC
10410523 ATATTGAATAGAGTTCCTAATAAGGAAACT
1 ATATTGAATAGAGTTCCTAATAAGGAAACT
10410553 ATATTGAATAGAGTTCCTAATAAGGAAACT
1 ATATTGAATAGAGTTCCTAATAAGGAAACT
10410583 A
1 A
10410584 AAATAACCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (30 bp):
ATATTGAATAGAGTTCCTAATAAGGAAACT
Found at i:10420231 original size:21 final size:22
Alignment explanation
Indices: 10420205--10420251 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
10420195 CTCTGCTCAA
*
10420205 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
10420226 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
10420248 ACTC
1 ACTC
10420252 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:10423523 original size:15 final size:16
Alignment explanation
Indices: 10423488--10423524 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10423478 ATTTAGTGTT
*
10423488 TATT-TTTTATTTTGA
1 TATTGTTTTATTTTAA
10423503 TATTGTTTTATTTTAA
1 TATTGTTTTATTTTAA
10423519 T-TTGTT
1 TATTGTT
10423525 ATTCTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (16 bp):
TATTGTTTTATTTTAA
Found at i:10430547 original size:44 final size:43
Alignment explanation
Indices: 10430447--10430568 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 43
10430437 AGCTCGTACT
*
10430447 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCCAACATCCCAGACGTGGTCTTACACGTAATCAAACATCG
* * *
10430490 ATGCC-ACTGTCCCAAACAG-GGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAAC-ATCCCAGAC-GTGGTCTTACACGT-AATC-AAACATCG
10430534 ATGCCAACATCCCAGACGTGGTCTTACACGATAAT
1 ATGCCAACATCCCAGACGTGGTCTTACACG-TAAT
10430569 TCATATCAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
42 2 0.03
43 24 0.36
44 35 0.53
45 5 0.08
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
ATGCCAACATCCCAGACGTGGTCTTACACGTAATCAAACATCG
Found at i:10441349 original size:49 final size:49
Alignment explanation
Indices: 10441293--10441439 Score: 276
Period size: 49 Copynumber: 3.0 Consensus size: 49
10441283 GCACAAGGCA
*
10441293 TGTGATTTCACTCAGTAGTGCTAAAGCTTATTTGCATCTTTCAATATGC
1 TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGCATCTTTCAATATGC
10441342 TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGCATCTTTCAATATGC
1 TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGCATCTTTCAATATGC
10441391 TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGCTATCTTTCAATATG
1 TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGC-ATCTTTCAATATG
10441440 TTCATATTGT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
49 83 0.86
50 13 0.14
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.41
Consensus pattern (49 bp):
TGTGATTTCACTCACTAGTGCTAAAGCTTATTTGCATCTTTCAATATGC
Found at i:10449378 original size:18 final size:18
Alignment explanation
Indices: 10449308--10449384 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
10449298 TGTCACTATG
* *
10449308 TATTTTAGAATTAAAAAA
1 TATTTTAAAATTAAAAAT
*
10449326 TATATT-AAATGTAAAAAT
1 TATTTTAAAAT-TAAAAAT
**
10449344 ATGATTTTCTTAA-TAAAAAT
1 -T-ATTTT-AAAATTAAAAAT
10449364 TATTTTAAAATTAAAATAT
1 TATTTTAAAATTAAAA-AT
10449383 TA
1 TA
10449385 AAATTGATAC
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
17 5 0.11
18 21 0.47
19 6 0.13
20 11 0.24
22 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (18 bp):
TATTTTAAAATTAAAAAT
Found at i:10449983 original size:26 final size:27
Alignment explanation
Indices: 10449954--10450008 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
10449944 GGGGAGAAAG
**
10449954 TGGGAAAGAGAG-GGGAGTAAAAGTTT
1 TGGGAAAGAGAGAAAGAGTAAAAGTTT
*
10449980 TGGGAAAGTGAGAAAGAGTAAAAGTTT
1 TGGGAAAGAGAGAAAGAGTAAAAGTTT
10450007 TG
1 TG
10450009 AGGGAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (27 bp):
TGGGAAAGAGAGAAAGAGTAAAAGTTT
Found at i:10449995 original size:34 final size:36
Alignment explanation
Indices: 10449926--10449997 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 36
10449916 GAAGGGAGGG
*
10449926 GAGGGGAGTAAAAGTTTTGGGGAGAAAGTGGGAAAGA
1 GAGGGGAGTAAAAGTTTT-GGGAGAAAGTGAGAAAGA
10449963 GAGGGGAGTAAAAGTTTT-GG-GAAAGTGAGAAAGA
1 GAGGGGAGTAAAAGTTTTGGGAGAAAGTGAGAAAGA
10449997 G
1 G
10449998 TAAAAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 14 0.41
35 2 0.06
37 18 0.53
ACGTcount: A:0.39, C:0.00, G:0.44, T:0.17
Consensus pattern (36 bp):
GAGGGGAGTAAAAGTTTTGGGAGAAAGTGAGAAAGA
Found at i:10450081 original size:9 final size:9
Alignment explanation
Indices: 10450067--10450103 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
10450057 TATAGTTTGA
10450067 TATTCGAAT
1 TATTCGAAT
10450076 TATTCGAAT
1 TATTCGAAT
* *
10450085 TATTTGAGT
1 TATTCGAAT
10450094 TATTCGAAT
1 TATTCGAAT
10450103 T
1 T
10450104 CAAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:10459236 original size:24 final size:25
Alignment explanation
Indices: 10459195--10459251 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
10459185 ATTACAACTA
10459195 CGGGAAGCTCATAAGAGCC-ATAAT
1 CGGGAAGCTCATAAGAGCCAATAAT
**
10459219 CGGGAAGCTCATGTGAGCCAATAAT
1 CGGGAAGCTCATAAGAGCCAATAAT
*
10459244 -GGGTAGCT
1 CGGGAAGCT
10459252 TTGAAGAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATAAGAGCCAATAAT
Found at i:10466953 original size:23 final size:23
Alignment explanation
Indices: 10466923--10466966 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10466913 AACTTTTTTT
10466923 TAAAGAATAT-TCACTATTCATTC
1 TAAAGAATATGT-ACTATTCATTC
*
10466946 TAAAGAATCTGTACTATTCAT
1 TAAAGAATATGTACTATTCAT
10466967 CGCAGGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
TAAAGAATATGTACTATTCATTC
Found at i:10468581 original size:15 final size:15
Alignment explanation
Indices: 10468561--10468592 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
10468551 ATTTTGGTAA
10468561 CAAAATTGGTGTGGT
1 CAAAATTGGTGTGGT
10468576 CAAAATTGGTGTGGT
1 CAAAATTGGTGTGGT
10468591 CA
1 CA
10468593 CTTGTCTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.31
Consensus pattern (15 bp):
CAAAATTGGTGTGGT
Found at i:10472662 original size:6 final size:6
Alignment explanation
Indices: 10472651--10472679 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10472641 GTTTGTATTA
10472651 AACTTT AACTTT AACTTT AACTTT AACTT
1 AACTTT AACTTT AACTTT AACTTT AACTT
10472680 ACTGTAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.48
Consensus pattern (6 bp):
AACTTT
Found at i:10472983 original size:40 final size:39
Alignment explanation
Indices: 10472907--10472995 Score: 106
Period size: 40 Copynumber: 2.3 Consensus size: 39
10472897 ATACAACTAT
** * *
10472907 TTTCATATAATCGATTTGTATAATCATTTCAAATATTTG
1 TTTCATATAATCGATTCATATAATCATTCCAAATATTTA
* **
10472946 TTTCCATATAATTGATTCATATAATCATTCCGTATATTTA
1 TTT-CATATAATCGATTCATATAATCATTCCAAATATTTA
10472986 TTTCATATAA
1 TTTCATATAA
10472996 CCATTTCATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTCATATAATCGATTCATATAATCATTCCAAATATTTA
Found at i:10473515 original size:15 final size:16
Alignment explanation
Indices: 10473484--10473516 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
10473474 ACTAACCTTT
10473484 AACTTAATTAGCATTTC
1 AACTTAATTA-CATTTC
10473501 AACTTAATT-CATTTC
1 AACTTAATTACATTTC
10473516 A
1 A
10473517 TTGCTTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (16 bp):
AACTTAATTACATTTC
Found at i:10478851 original size:14 final size:14
Alignment explanation
Indices: 10478832--10478865 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
10478822 TGGAAGTGTA
10478832 TGAAAA-TAATAATT
1 TGAAAATTAA-AATT
10478846 TGAAAATTAAAATT
1 TGAAAATTAAAATT
10478860 TGAAAA
1 TGAAAA
10478866 ACTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (14 bp):
TGAAAATTAAAATT
Done.