Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 127 of 199
Found at i:42550166 original size:23 final size:24
Alignment explanation
Indices: 42550140--42550193 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
42550130 TTGGTGGGAA
42550140 CATTTTGGT-ACTTCAATGCATAT
1 CATTTTGGTCACTTCAATGCATAT
* *
42550163 CATTCT-GTCACTTCAGTGCATAT
1 CATTTTGGTCACTTCAATGCATAT
42550186 CATTTTGG
1 CATTTTGG
42550194 CATTTTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 2 0.08
23 23 0.88
24 1 0.04
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (24 bp):
CATTTTGGTCACTTCAATGCATAT
Found at i:42555309 original size:22 final size:22
Alignment explanation
Indices: 42555248--42555311 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
42555238 GGGGTAGGAA
*
42555248 TCTGCATCTGTATCTAATATGT
1 TCTGCATCTGTATCTGATATGT
42555270 TCTGCATCTGTATCTGATATGT
1 TCTGCATCTGTATCTGATATGT
* * *
42555292 TTTGCAACTGTATTTGATAT
1 TCTGCATCTGTATCTGATAT
42555312 CCTCTATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (22 bp):
TCTGCATCTGTATCTGATATGT
Found at i:42556640 original size:13 final size:13
Alignment explanation
Indices: 42556618--42556679 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
42556608 TTCTTCATTA
*
42556618 CTTTTTAAAAGTG
1 CTTTTGAAAAGTG
42556631 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
42556644 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
* *
42556657 TTTTTGAGAAGTG
1 CTTTTGAAAAGTG
42556670 CTTTTGAAAA
1 CTTTTGAAAA
42556680 ATTTAAGTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:42556963 original size:21 final size:19
Alignment explanation
Indices: 42556895--42556968 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 19
42556885 AGTAATTAAT
* *
42556895 ATTAATTATTTATTAAATTTA
1 ATTAAATATTTA--AAATATA
*
42556916 ATTAGAATATATAAAATATA
1 ATTA-AATATTTAAAATATA
*
42556936 TTTAAATATTTAAATATAATA
1 ATTAAATATTTAAA-AT-ATA
42556957 ATTAAATATTTA
1 ATTAAATATTTA
42556969 TAATTAGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 9 0.20
20 11 0.25
21 18 0.41
22 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
ATTAAATATTTAAAATATA
Found at i:42568343 original size:17 final size:17
Alignment explanation
Indices: 42568321--42568355 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42568311 TCTCCTTTTG
42568321 AACAGTAGTCTCCC-CTT
1 AACAGTAG-CTCCCACTT
42568338 AACAGTAGCTCCCACTT
1 AACAGTAGCTCCCACTT
42568355 A
1 A
42568356 GACAATGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.34, G:0.11, T:0.26
Consensus pattern (17 bp):
AACAGTAGCTCCCACTT
Found at i:42570007 original size:28 final size:28
Alignment explanation
Indices: 42569967--42570053 Score: 84
Period size: 32 Copynumber: 2.9 Consensus size: 28
42569957 AGAAGTCTAT
*
42569967 ACATAAAAGTAGCCACGAAGGCATCCATA
1 ACATAAAA-TAGCCACAAAGGCATCCATA
* *
42569996 ACATTAAATAGCCACAAAGGCGTCCACATATA
1 ACATAAAATAGCCACAAAGGCAT-C-C--ATA
* *
42570028 ACATCAGATAGCCACAAAGGCATCCA
1 ACATAAAATAGCCACAAAGGCATCCA
42570054 CATATAATAG
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.29
29 8 0.17
30 2 0.04
31 1 0.02
32 23 0.48
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (28 bp):
ACATAAAATAGCCACAAAGGCATCCATA
Found at i:42570039 original size:32 final size:32
Alignment explanation
Indices: 42569993--42570060 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
42569983 GAAGGCATCC
* *
42569993 ATAACATTAAATAGCCACAAAGGCGTCCACAT
1 ATAACATCAAATAGCCACAAAGGCATCCACAT
*
42570025 ATAACATCAGATAGCCACAAAGGCATCCACAT
1 ATAACATCAAATAGCCACAAAGGCATCCACAT
42570057 ATAA
1 ATAA
42570061 TAGGTAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.18
Consensus pattern (32 bp):
ATAACATCAAATAGCCACAAAGGCATCCACAT
Found at i:42571676 original size:40 final size:40
Alignment explanation
Indices: 42571621--42571702 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
42571611 CATTATCGGG
* *
42571621 GTATGCCTTGCATACTTTCAATTAACAGAATTAGTGGCAT
1 GTATGCCTTGCATACTTTCAATTAACAAAATCAGTGGCAT
* *
42571661 GTATGCCTTGTATACTTTCAATTAATAAAATCAGTGGCAT
1 GTATGCCTTGCATACTTTCAATTAACAAAATCAGTGGCAT
42571701 GT
1 GT
42571703 GAACATGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (40 bp):
GTATGCCTTGCATACTTTCAATTAACAAAATCAGTGGCAT
Found at i:42576102 original size:141 final size:140
Alignment explanation
Indices: 42575849--42576111 Score: 384
Period size: 141 Copynumber: 1.9 Consensus size: 140
42575839 GCCTTGGTGG
* * * * *
42575849 CCAAATGAAGTACTTAAGAAAATTTAGAGCTACCTTGGTGAATATGGAAGTAATTTTAGACAATT
1 CCAAATGAAGTACTTAAGAAAACTTAGAGCTACCTTGATAAATATGGAACTAATCTTAGACAATT
* * * *
42575914 TATAGTCTAATAATATTTGAATTTTTAATCTTAAAGGGCTGAGTCAATCTCTTAAGAGTCTCAAT
66 TATAATCTAATAAGATTTGAATTTTTAATCTTAAAGGACTGAGTCAATCCCTTAAGAGTCTCAAT
42575979 TTTATGATGT
131 TTTATGATGT
*
42575989 CCAAATGAAGTACTTAAGAAAACTTAGGGCTACCTTGATAAATATGGAAACTAATCTTAGA-AGA
1 CCAAATGAAGTACTTAAGAAAACTTAGAGCTACCTTGATAAATATGG-AACTAATCTTAGACA-A
* * *
42576053 TTTATAATTTAATAAGATTTGAATTTTTAATCTTAATGGATTGAGTCAATCCCTTAAGA
64 TTTATAATCTAATAAGATTTGAATTTTTAATCTTAAAGGACTGAGTCAATCCCTTAAGA
42576112 ACTTTAATTG
Statistics
Matches: 108, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
140 44 0.41
141 64 0.59
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (140 bp):
CCAAATGAAGTACTTAAGAAAACTTAGAGCTACCTTGATAAATATGGAACTAATCTTAGACAATT
TATAATCTAATAAGATTTGAATTTTTAATCTTAAAGGACTGAGTCAATCCCTTAAGAGTCTCAAT
TTTATGATGT
Found at i:42584972 original size:30 final size:30
Alignment explanation
Indices: 42584938--42584997 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42584928 ACTTTTTTTA
*
42584938 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAGAGGCAT
42584968 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAGAGGCAT
42584998 ATACTTGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAGAGGCAT
Found at i:42591592 original size:24 final size:25
Alignment explanation
Indices: 42591542--42591594 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
42591532 ACAACAGTGA
* * *
42591542 AACAACAATGAAATGGCAGTGGGAC
1 AACAACAATAAAATGGCAGCGGAAC
*
42591567 AACAACAA-AAAATGGTAGCGGAAC
1 AACAACAATAAAATGGCAGCGGAAC
42591591 AACA
1 AACA
42591595 TTAAAAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.51, C:0.17, G:0.23, T:0.09
Consensus pattern (25 bp):
AACAACAATAAAATGGCAGCGGAAC
Found at i:42591623 original size:23 final size:23
Alignment explanation
Indices: 42591597--42591676 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
42591587 GAACAACATT
*
42591597 AAAAACAACAATGAAATAGCACAAA
1 AAAAACAACAATGAAATAGCAC--C
*
42591622 AAAAACAACAATGAAATAACACC
1 AAAAACAACAATGAAATAGCACC
* * *
42591645 AAAAGCAATAAAGAAATAGCACC
1 AAAAACAACAATGAAATAGCACC
*
42591668 AAAAGCAAC
1 AAAAACAAC
42591677 CTAGAAAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 27 0.56
25 21 0.44
ACGTcount: A:0.65, C:0.19, G:0.09, T:0.07
Consensus pattern (23 bp):
AAAAACAACAATGAAATAGCACC
Found at i:42591625 original size:25 final size:25
Alignment explanation
Indices: 42591597--42591648 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
42591587 GAACAACATT
*
42591597 AAAAACAACAATGAAATAGCACAAA
1 AAAAACAACAATGAAATAACACAAA
*
42591622 AAAAACAACAATGAAATAACACCAA
1 AAAAACAACAATGAAATAACACAAA
42591647 AA
1 AA
42591649 GCAATAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (25 bp):
AAAAACAACAATGAAATAACACAAA
Found at i:42595137 original size:17 final size:18
Alignment explanation
Indices: 42595095--42595137 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42595085 TAATAGTGTG
* *
42595095 CATGAAAAGAACAAGGTA
1 CATGAAATGAACAAAGTA
42595113 CATGAAATGAACAAAGTA
1 CATGAAATGAACAAAGTA
42595131 C-TGAAAT
1 CATGAAAT
42595138 ATTTGGTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (18 bp):
CATGAAATGAACAAAGTA
Found at i:42596800 original size:341 final size:340
Alignment explanation
Indices: 42596172--42596862 Score: 1328
Period size: 341 Copynumber: 2.0 Consensus size: 340
42596162 TAGGGAAAAT
* *
42596172 GCTTTTATTTATAGTTGAGCTCCCTCGAACCAACAATATATTTTAATTTACATTGACGATCAATA
1 GCTTTAATTTATAGTTGAGCTCCCTCAAACCAACAATATATTTTAATTTACATTGACGATCAATA
42596237 TCAAAGCCAATATACAAATTGAGATTCTTAAGGGATTTATAAGATCCTCTAAGATTAAAAAAAAT
66 TCAAAGCCAATATACAAATTGAGATTCTTAAGGGATTTATAAGATCCTCTAAGATTAAAAAAAAT
42596302 CAAATCTTCTAAGCTTACAAATCTTATAAGATTATTTTCCATGTTTACCACGATAACTCTAGTTT
131 CAAATCTTCTAAGCTTACAAATCTTATAAGATTATTTTCCATGTTTACCACGATAACTCTAGTTT
42596367 TACTTGAGTGCTTCATTGGGCCACTAAGATTTCAAGTAGATGACTTTTTCCACATGTTTTACAAA
196 TACTTGAGTGCTTCATTGGGCCACTAAGATTTCAAGTAGATGACTTTTTCCACATGTTTTACAAA
42596432 TCAGGTCAGTTTAAGTGGGTTGAATGAACCACATTTAATCAATTGACCTCTATGGGATGCTTTGT
261 TCAGGTCAGTTTAAGTGGGTTGAATGAACCACATTTAATCAATTGACCTCTATGGGATGCTTTGT
42596497 ATGCTTTCTTGACAG
326 ATGCTTTCTTGACAG
42596512 GCTTTAATTTATAGTTGAGCTCCCTCAAACCAACAATATATTTTAATTTACATTGACGATCAATA
1 GCTTTAATTTATAGTTGAGCTCCCTCAAACCAACAATATATTTTAATTTACATTGACGATCAATA
42596577 TCAAAGCCAATATACAAATTGAGATTCTTAAGGGATTTATAAGATCCTCTAAGATTAAAAAAAAA
66 TCAAAGCCAATATACAAATTGAGATTCTTAAGGGATTTATAAGATCCTCTAAGATT-AAAAAAAA
42596642 TCAAATCTTCTAAGCTTACAAATCTTATAAGATTATTTTCCATGTTTACCACGATAACTCTAGTT
130 TCAAATCTTCTAAGCTTACAAATCTTATAAGATTATTTTCCATGTTTACCACGATAACTCTAGTT
*
42596707 TTGCTTGAGTGCTTCATTGGGCCACTAAGATTTCAAGTAGATGACTTTTTCCACATGTTTTACAA
195 TTACTTGAGTGCTTCATTGGGCCACTAAGATTTCAAGTAGATGACTTTTTCCACATGTTTTACAA
*
42596772 ATCAGGTCAGTTTAAGTGGGTTGAATGAACCACATTTAATCAATTGACCTCTATGGGATGTTTTG
260 ATCAGGTCAGTTTAAGTGGGTTGAATGAACCACATTTAATCAATTGACCTCTATGGGATGCTTTG
*
42596837 TGTGCTTTCTTGACAG
325 TATGCTTTCTTGACAG
42596853 GCTTTAATTT
1 GCTTTAATTT
42596863 GAGACTCGTG
Statistics
Matches: 345, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
340 119 0.34
341 226 0.66
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (340 bp):
GCTTTAATTTATAGTTGAGCTCCCTCAAACCAACAATATATTTTAATTTACATTGACGATCAATA
TCAAAGCCAATATACAAATTGAGATTCTTAAGGGATTTATAAGATCCTCTAAGATTAAAAAAAAT
CAAATCTTCTAAGCTTACAAATCTTATAAGATTATTTTCCATGTTTACCACGATAACTCTAGTTT
TACTTGAGTGCTTCATTGGGCCACTAAGATTTCAAGTAGATGACTTTTTCCACATGTTTTACAAA
TCAGGTCAGTTTAAGTGGGTTGAATGAACCACATTTAATCAATTGACCTCTATGGGATGCTTTGT
ATGCTTTCTTGACAG
Found at i:42603943 original size:61 final size:61
Alignment explanation
Indices: 42603870--42603987 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
42603860 AACTCTAGCA
42603870 CTAATTCCTCTTCAGGCATTGATCGTGCATTACAAAATTGATTCAAATTTAATGTATTAAT
1 CTAATTCCTCTTCAGGCATTGATCGTGCATTACAAAATTGATTCAAATTTAATGTATTAAT
*
42603931 CTAATTCCTCTTCAGGCATTGATCGTGCATTACAAAATTGATTCCAATTTAATGTAT
1 CTAATTCCTCTTCAGGCATTGATCGTGCATTACAAAATTGATTCAAATTTAATGTAT
42603988 CAATTTTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (61 bp):
CTAATTCCTCTTCAGGCATTGATCGTGCATTACAAAATTGATTCAAATTTAATGTATTAAT
Found at i:42604674 original size:17 final size:17
Alignment explanation
Indices: 42604649--42604682 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42604639 CCTGTATTGA
*
42604649 AAAATTAAACTGATTAG
1 AAAAGTAAACTGATTAG
42604666 AAAAGTAAACTGATTAG
1 AAAAGTAAACTGATTAG
42604683 TACTTGGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (17 bp):
AAAAGTAAACTGATTAG
Found at i:42615420 original size:14 final size:14
Alignment explanation
Indices: 42615401--42615427 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42615391 TTCGCTTGCA
42615401 CACTTGTATTTTAC
1 CACTTGTATTTTAC
42615415 CACTTGTATTTTA
1 CACTTGTATTTTA
42615428 TTTTATCATG
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:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
CACTTGTATTTTAC
Found at i:42615610 original size:13 final size:13
Alignment explanation
Indices: 42615592--42615616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42615582 ATTGTAAATC
42615592 TAAAAAAATTTAA
1 TAAAAAAATTTAA
42615605 TAAAAAAATTTA
1 TAAAAAAATTTA
42615617 CGGGCTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAAATTTAA
Found at i:42618088 original size:18 final size:19
Alignment explanation
Indices: 42618053--42618090 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
42618043 ATTTAGGTTT
42618053 ATTTAAATCAAAACATTAA
1 ATTTAAATCAAAACATTAA
*
42618072 ATTTAAAT-AAAATATTAA
1 ATTTAAATCAAAACATTAA
42618090 A
1 A
42618091 GATTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTTAAATCAAAACATTAA
Found at i:42621941 original size:21 final size:20
Alignment explanation
Indices: 42621915--42621989 Score: 55
Period size: 20 Copynumber: 3.6 Consensus size: 20
42621905 AGTTAATTAT
42621915 TCCCTGAATTGTACATACGTG
1 TCCCTG-ATTGTACATACGTG
* *
42621936 TCCCTGGTTGTAC-TCCG-G
1 TCCCTGATTGTACATACGTG
* *
42621954 TACCCCTGAATTATACATATGTG
1 T--CCCTG-ATTGTACATACGTG
*
42621977 CCCCTGATTGTAC
1 TCCCTGATTGTAC
42621990 TTCGGTACCC
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 17 0.41
21 16 0.39
22 2 0.05
23 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (20 bp):
TCCCTGATTGTACATACGTG
Found at i:42621982 original size:41 final size:41
Alignment explanation
Indices: 42621916--42622022 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
42621906 GTTAATTATT
* * * *
42621916 CCCTGAATTGTACATACGTGTCCCTGGTTGTACTCCGGTAC
1 CCCTGAATTATACATATGTGCCCCTGATTGTACTCCGGTAC
*
42621957 CCCTGAATTATACATATGTGCCCCTGATTGTACTTCGGTAC
1 CCCTGAATTATACATATGTGCCCCTGATTGTACTCCGGTAC
* *
42621998 CCCTGAATTACACATATGGGCCCCT
1 CCCTGAATTATACATATGTGCCCCT
42622023 TTTTACACTC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.31
Consensus pattern (41 bp):
CCCTGAATTATACATATGTGCCCCTGATTGTACTCCGGTAC
Found at i:42622002 original size:20 final size:20
Alignment explanation
Indices: 42621937--42622003 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
42621927 ACATACGTGT
* *
42621937 CCCTGGTTGTACTCCGGTAC
1 CCCTGATTGTACTTCGGTAC
* * ** *
42621957 CCCTGAATTATACATATGTGC
1 CCCTG-ATTGTACTTCGGTAC
42621978 CCCTGATTGTACTTCGGTAC
1 CCCTGATTGTACTTCGGTAC
42621998 CCCTGA
1 CCCTGA
42622004 ATTACACATA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 21 0.62
21 13 0.38
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (20 bp):
CCCTGATTGTACTTCGGTAC
Found at i:42629519 original size:30 final size:30
Alignment explanation
Indices: 42629458--42629520 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
42629448 TATACTTTTT
* **
42629458 CCCAAAACTTTTACTCTCTCCCATTTTCTC
1 CCCAAAACTTTTACTCCCTCCCATTCCCTC
*
42629488 CCCAAAACTTTTATTCCCCTCCCA-TCCCTC
1 CCCAAAACTTTTACT-CCCTCCCATTCCCTC
42629518 CCC
1 CCC
42629521 CTTCTACCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (30 bp):
CCCAAAACTTTTACTCCCTCCCATTCCCTC
Found at i:42629641 original size:19 final size:19
Alignment explanation
Indices: 42629609--42629645 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42629599 CTACCTCAAG
42629609 CCCCAAAACTTTTTATTTT
1 CCCCAAAACTTTTTATTTT
42629628 CCCCTAAAAC-TTTTATTT
1 CCCC-AAAACTTTTTATTT
42629646 CCCTCCCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (19 bp):
CCCCAAAACTTTTTATTTT
Found at i:42630743 original size:47 final size:49
Alignment explanation
Indices: 42630672--42630798 Score: 150
Period size: 47 Copynumber: 2.6 Consensus size: 49
42630662 CATGGTAATA
*
42630672 TGTGATATGTGATTTCTGTATAAGACCATAGCTAGGCTATAGCATT-G-G
1 TGTGATATGTGA-TTCTGTGTAAGACCATAGCTAGGCTATAGCATTGGTG
* * * * * *
42630720 TGTGATATGTGCTTCTGTGTAAGACCATGGTTGGGCTATGGCTTTGGTG
1 TGTGATATGTGATTCTGTGTAAGACCATAGCTAGGCTATAGCATTGGTG
* *
42630769 TGTGATATGTGATTATGTGCAAGACCATAG
1 TGTGATATGTGATTCTGTGTAAGACCATAG
42630799 TTATACTATG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 27 0.41
48 12 0.18
49 27 0.41
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (49 bp):
TGTGATATGTGATTCTGTGTAAGACCATAGCTAGGCTATAGCATTGGTG
Found at i:42631373 original size:24 final size:25
Alignment explanation
Indices: 42631346--42631408 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
42631336 GAACCTTAGC
* **
42631346 GTGCTCT-TTATTATTAGCACATTA
1 GTGCTCTCTAATTATTAAAACATTA
*
42631370 GTGCTCTCTAATTATTAAAACGTTA
1 GTGCTCTCTAATTATTAAAACATTA
*
42631395 GTGCTCTCCAATTA
1 GTGCTCTCTAATTA
42631409 GCACATCTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (25 bp):
GTGCTCTCTAATTATTAAAACATTA
Found at i:42633337 original size:22 final size:23
Alignment explanation
Indices: 42633312--42633362 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
42633302 AATAAAAAAT
*
42633312 AAATTCTT-TTTAAAAATT-TAGA
1 AAATTCTTGTATAAAAATTCTA-A
42633334 AAATT-TTGTATAAAAATTCTAA
1 AAATTCTTGTATAAAAATTCTAA
42633356 AAATTCT
1 AAATTCT
42633363 AAAACTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 20 0.80
23 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTCTTGTATAAAAATTCTAA
Found at i:42633961 original size:21 final size:19
Alignment explanation
Indices: 42633935--42633973 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
42633925 TCGTTGCAAG
42633935 AATAACTACAATCAATTAGAC
1 AATAAC-ACAATC-ATTAGAC
*
42633956 AATAACATAATCATTAGA
1 AATAACACAATCATTAGA
42633974 ACATACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (19 bp):
AATAACACAATCATTAGAC
Found at i:42635290 original size:10 final size:11
Alignment explanation
Indices: 42635272--42635300 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
42635262 TTAATTTATC
42635272 ATTTCTTATTT
1 ATTTCTTATTT
42635283 ATTT-TTATTT
1 ATTTCTTATTT
42635293 ATTTCTTA
1 ATTTCTTA
42635301 CTGTTTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTCTTATTT
Found at i:42640389 original size:13 final size:13
Alignment explanation
Indices: 42640371--42640395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42640361 AGCAAATATT
42640371 TCTAATTATAAAA
1 TCTAATTATAAAA
42640384 TCTAATTATAAA
1 TCTAATTATAAA
42640396 CTCTTGTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TCTAATTATAAAA
Found at i:42640986 original size:45 final size:45
Alignment explanation
Indices: 42640927--42641014 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
42640917 CTTAATGATC
* *
42640927 ATATAAATTTCTCTTTTAATTAGTTTCTAACATTTGTCTCTCATA
1 ATATAAATGTCTCTTTTAATTAGTTTCTAACATTTATCTCTCATA
*
42640972 ATATAAATGTCTCTTTTACTTAGTTTCTAACATTTATCTCTCA
1 ATATAAATGTCTCTTTTAATTAGTTTCTAACATTTATCTCTCA
42641015 CAACATTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (45 bp):
ATATAAATGTCTCTTTTAATTAGTTTCTAACATTTATCTCTCATA
Found at i:42644883 original size:16 final size:16
Alignment explanation
Indices: 42644859--42644905 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
42644849 TTATAATTTA
*
42644859 AGAACAACTCTTGTTG
1 AGAATAACTCTTGTTG
**
42644875 AGAATAACTAATGTATG
1 AGAATAACTCTTGT-TG
42644892 A-AATAACTCTTGTT
1 AGAATAACTCTTGTT
42644906 TAGAGCAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 1 0.04
16 21 0.84
17 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (16 bp):
AGAATAACTCTTGTTG
Found at i:42645978 original size:68 final size:69
Alignment explanation
Indices: 42645820--42645997 Score: 200
Period size: 68 Copynumber: 2.6 Consensus size: 69
42645810 CAACATGCAC
* * *
42645820 TTCTCA-CTTTCTTAAAGAATATATAAAAACATGTTCTTCCTACTAATTTTAAGAAACACAAAAA
1 TTCTCACCTTT-TTAAAGAA-ATA-AAGAGCATGTTCTTCCCACTAATTTTAAGAAACACAAAAA
* *
42645884 TAGGTCG
63 GAGGTCA
* * **
42645891 TTCTCACCTTTTTAGAGAAATAAAGAGCATGTTCTTCCCACTATTTTTAAGAAACAC-AATGGAG
1 TTCTCACCTTTTTAAAGAAATAAAGAGCATGTTCTTCCCACTAATTTTAAGAAACACAAAAAGAG
42645955 GTCA
66 GTCA
* *
42645959 TTCTC-CCTTGTTTAAAGAAATAAGGAGCATGCTCTTCCC
1 TTCTCACCTT-TTTAAAGAAATAAAGAGCATGTTCTTCCC
42645998 TTTTTTTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
67 4 0.04
68 38 0.41
69 31 0.33
70 3 0.03
71 13 0.14
72 4 0.04
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (69 bp):
TTCTCACCTTTTTAAAGAAATAAAGAGCATGTTCTTCCCACTAATTTTAAGAAACACAAAAAGAG
GTCA
Found at i:42646234 original size:16 final size:17
Alignment explanation
Indices: 42646213--42646244 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42646203 TGATGTCATT
42646213 ATTTTTCT-TTTCTTTC
1 ATTTTTCTATTTCTTTC
42646229 ATTTTTCTATTTCTTT
1 ATTTTTCTATTTCTTT
42646245 TTGTCCTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTCTATTTCTTTC
Found at i:42648674 original size:20 final size:20
Alignment explanation
Indices: 42648651--42648829 Score: 137
Period size: 20 Copynumber: 9.0 Consensus size: 20
42648641 CACGAATGTG
* * *
42648651 CAAATAGGAATACCGAAATA
1 CAAACAGGAGTACCGAAGTA
*
42648671 CAAACAGGGGTA-CGAAGTA
1 CAAACAGGAGTACCGAAGTA
* * **
42648690 CATACAAGAGTATTGAAGTA
1 CAAACAGGAGTACCGAAGTA
* *
42648710 CAAATAGGGGTACCGAAGTA
1 CAAACAGGAGTACCGAAGTA
*
42648730 CAAACAGGAATACCGAAGTA
1 CAAACAGGAGTACCGAAGTA
* * * * *
42648750 CATATAGGAGTATCTAAATA
1 CAAACAGGAGTACCGAAGTA
* * **
42648770 CATACAAGAGTATTGAAGTA
1 CAAACAGGAGTACCGAAGTA
*
42648790 CAAACATGG-GTACCAAAGTA
1 CAAACA-GGAGTACCGAAGTA
*
42648810 CAAACAAGAGTACCGAAGTA
1 CAAACAGGAGTACCGAAGTA
42648830 TATTCACATA
Statistics
Matches: 121, Mismatches: 35, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
19 16 0.13
20 104 0.86
21 1 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (20 bp):
CAAACAGGAGTACCGAAGTA
Found at i:42648748 original size:40 final size:40
Alignment explanation
Indices: 42648661--42648829 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
42648651 CAAATAGGAA
* *
42648661 TACCGAAATACAAACAGGGGTA-CGAAGTACATACAAGAG
1 TACCGAAGTACAAACAGGGGTACCGAAGTACAAACAAGAG
** * * *
42648700 TATTGAAGTACAAATAGGGGTACCGAAGTACAAACAGGAA
1 TACCGAAGTACAAACAGGGGTACCGAAGTACAAACAAGAG
* * * * * * *
42648740 TACCGAAGTACATATAGGAGTATCTAAATACATACAAGAG
1 TACCGAAGTACAAACAGGGGTACCGAAGTACAAACAAGAG
** * *
42648780 TATTGAAGTACAAACATGGGTACCAAAGTACAAACAAGAG
1 TACCGAAGTACAAACAGGGGTACCGAAGTACAAACAAGAG
42648820 TACCGAAGTA
1 TACCGAAGTA
42648830 TATTCACATA
Statistics
Matches: 100, Mismatches: 29, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
39 18 0.18
40 82 0.82
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (40 bp):
TACCGAAGTACAAACAGGGGTACCGAAGTACAAACAAGAG
Found at i:42648788 original size:80 final size:79
Alignment explanation
Indices: 42648651--42648829 Score: 241
Period size: 80 Copynumber: 2.3 Consensus size: 79
42648641 CACGAATGTG
* * * * *
42648651 CAAATAGGAATACCGAAATACAAACAGGGGTACGAAGTACATACAAGAGTATTGAAGTACAAATA
1 CAAACAGGAATACCGAAGTACAAACAGGAGTACGAAATACATACAAGAGTATTGAAGTACAAACA
*
42648716 GGGGTACCGAAGTA
66 GGGGTACCAAAGTA
* * *
42648730 CAAACAGGAATACCGAAGTACATATAGGAGTATCTAAATACATACAAGAGTATTGAAGTACAAAC
1 CAAACAGGAATACCGAAGTACAAACAGGAGTA-CGAAATACATACAAGAGTATTGAAGTACAAAC
*
42648795 ATGGGTACCAAAGTA
65 AGGGGTACCAAAGTA
* *
42648810 CAAACAAGAGTACCGAAGTA
1 CAAACAGGAATACCGAAGTA
42648830 TATTCACATA
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
79 27 0.31
80 60 0.69
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (79 bp):
CAAACAGGAATACCGAAGTACAAACAGGAGTACGAAATACATACAAGAGTATTGAAGTACAAACA
GGGGTACCAAAGTA
Found at i:42653393 original size:17 final size:17
Alignment explanation
Indices: 42653371--42653403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42653361 AACTAAGATT
*
42653371 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
42653388 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
42653404 GTTCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:42663105 original size:33 final size:33
Alignment explanation
Indices: 42663063--42663130 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
42663053 AGATTGATAC
42663063 TTAAACTATATCGTGATTTCCATATTAGTTTTT
1 TTAAACTATATCGTGATTTCCATATTAGTTTTT
*
42663096 TTAAACTATATCGTGGTTTCCATATTAGTTTTT
1 TTAAACTATATCGTGATTTCCATATTAGTTTTT
42663129 TT
1 TT
42663131 TTCTCATAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (33 bp):
TTAAACTATATCGTGATTTCCATATTAGTTTTT
Found at i:42663407 original size:24 final size:21
Alignment explanation
Indices: 42663380--42663426 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
42663370 AACACTTAAT
*
42663380 TTTTTAATTTTATTTCTTTCTTTC
1 TTTTT-ATCTTATTTC--TCTTTC
42663404 -TTTTATCTTATTTCTCTTTC
1 TTTTTATCTTATTTCTCTTTC
42663424 TTT
1 TTT
42663427 ACCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 9 0.43
23 4 0.19
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTATCTTATTTCTCTTTC
Found at i:42663423 original size:28 final size:26
Alignment explanation
Indices: 42663392--42663449 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 26
42663382 TTTAATTTTA
42663392 TTTCTTT-CTTTCTTTTATCTTATTTCTC
1 TTTCTTTACTTT-TTTTAT-TTATTTC-C
42663420 TTTCTTTACCTTTTTTTATTTATTTCC
1 TTTCTTTA-CTTTTTTTATTTATTTCC
42663447 TTT
1 TTT
42663450 TTTTTCTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 4 0.14
28 14 0.50
29 6 0.21
30 4 0.14
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTCTTTACTTTTTTTATTTATTTCC
Found at i:42663438 original size:24 final size:21
Alignment explanation
Indices: 42663387--42663440 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
42663377 AATTTTTTAA
42663387 TTTTA-TTTCTTTCTTTCTTT
1 TTTTATTTTCTTTCTTTCTTT
42663407 TATCTTATTTCTCTTTCTTTACCTTT
1 T-T-TTATTT-TCTTTCTTT--CTTT
42663433 TTTTATTT
1 TTTTATTT
42663441 ATTTCCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 3 0.11
23 2 0.07
24 15 0.54
25 1 0.04
26 5 0.18
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTATTTTCTTTCTTTCTTT
Found at i:42666287 original size:4 final size:4
Alignment explanation
Indices: 42666268--42666303 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
42666258 GTTGTAAAGT
42666268 TTTA TTT- TTATA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
42666304 CTTAGTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 2 0.07
4 26 0.87
5 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:42685760 original size:13 final size:13
Alignment explanation
Indices: 42685742--42685767 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42685732 GCAATTGCTA
42685742 AACTTTAGTAAAT
1 AACTTTAGTAAAT
42685755 AACTTTAGTAAAT
1 AACTTTAGTAAAT
42685768 TTTTTAGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTTTAGTAAAT
Found at i:42686669 original size:22 final size:22
Alignment explanation
Indices: 42686641--42686685 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42686631 ATAGCAACGA
42686641 ATCAGATAAAATCACAGAACAG
1 ATCAGATAAAATCACAGAACAG
* *
42686663 ATCAGATAAGATCGCAGAACAG
1 ATCAGATAAAATCACAGAACAG
42686685 A
1 A
42686686 CCAGGTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.13
Consensus pattern (22 bp):
ATCAGATAAAATCACAGAACAG
Found at i:42689377 original size:40 final size:40
Alignment explanation
Indices: 42689272--42689454 Score: 187
Period size: 40 Copynumber: 4.6 Consensus size: 40
42689262 TTGAATGCTG
* * * *
42689272 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
42689311 ATCCGGACTAAGAT-CCGAA-GTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
42689351 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
42689391 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
42689431 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
42689455 GAATGAGTTA
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 1 0.01
39 21 0.17
40 98 0.81
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:42689408 original size:79 final size:81
Alignment explanation
Indices: 42689272--42689451 Score: 212
Period size: 80 Copynumber: 2.3 Consensus size: 81
42689262 TTGAATGCTG
* * *
42689272 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAA-GTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
42689335 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
42689351 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
42689412 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
42689431 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
42689452 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
78 2 0.02
79 41 0.47
80 45 0.51
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:42689475 original size:39 final size:38
Alignment explanation
Indices: 42689352--42689501 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
42689342 GTTATTAATT
* ** * *
42689352 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
42689392 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
42689431 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
42689471 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
42689502 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:42703784 original size:22 final size:22
Alignment explanation
Indices: 42703723--42703785 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
42703713 TTATAGCAAT
* **
42703723 AGATCACATAAGATCACAGAAC
1 AGATCAAATAAGATTGCAGAAC
* *
42703745 ATATCAGATAAGATTGCAGAAC
1 AGATCAAATAAGATTGCAGAAC
42703767 AGATCAAATACAGA-TGCAG
1 AGATCAAATA-AGATTGCAG
42703786 TTTCCTACCC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (22 bp):
AGATCAAATAAGATTGCAGAAC
Found at i:42714026 original size:52 final size:50
Alignment explanation
Indices: 42713937--42714035 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 50
42713927 ACTTTGTAGA
* * *
42713937 TTAATTCAAACATTTGCTAATGATAAAGACTATTAAAAATATTATTAAATTT
1 TTAATTCAAACATTTGCTAATAATAAAAACTAATAAAAA-ATT-TTAAATTT
* * *
42713989 TTAATTCAAATATTTGTTAATAATAAAAAGTAATAAAAAATTTTAAA
1 TTAATTCAAACATTTGCTAATAATAAAAACTAATAAAAAATTTTAAA
42714036 ATACAATAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 5 0.12
51 3 0.07
52 33 0.80
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (50 bp):
TTAATTCAAACATTTGCTAATAATAAAAACTAATAAAAAATTTTAAATTT
Found at i:42725809 original size:26 final size:26
Alignment explanation
Indices: 42725774--42725825 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
42725764 AAATGAAAAG
*
42725774 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
42725800 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
42725826 TTCAGTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:42725847 original size:102 final size:102
Alignment explanation
Indices: 42725595--42725856 Score: 404
Period size: 103 Copynumber: 2.6 Consensus size: 102
42725585 TGTATATAAA
** * * *
42725595 AGGGGTTGCTGTGTGCTGATTCCCTGATTCATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGT-ATCCACCGTATCTTT
*
42725660 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 GAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
42725698 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT-GTGCTAAGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TATCCACCGTATCTT
42725762 TGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCCG
64 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
42725799 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCGTATCCACCG
42725857 ATAACGGTTA
Statistics
Matches: 148, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
101 48 0.32
102 36 0.24
103 59 0.40
104 5 0.03
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTATCCACCGTATCTTTG
AAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:42740741 original size:30 final size:30
Alignment explanation
Indices: 42740707--42740763 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42740697 ATTTGAATTG
*
42740707 GATTAACTTTAATCTTTGTACTTTTAACTT
1 GATTAACTTTAATCTTTATACTTTTAACTT
*
42740737 GATTAATTTTAATCTTTATACTTTTAA
1 GATTAACTTTAATCTTTATACTTTTAA
42740764 AATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (30 bp):
GATTAACTTTAATCTTTATACTTTTAACTT
Found at i:42740761 original size:15 final size:15
Alignment explanation
Indices: 42740714--42740763 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
42740704 TTGGATTAAC
*
42740714 TTTAATCTTTGTACT
1 TTTAATCTTTATACT
* *
42740729 TTTAA-CTTGATTAAT
1 TTTAATCTTTA-TACT
42740744 TTTAATCTTTATACT
1 TTTAATCTTTATACT
42740759 TTTAA
1 TTTAA
42740764 AATATTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 3 0.11
15 21 0.75
16 4 0.14
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (15 bp):
TTTAATCTTTATACT
Found at i:42742211 original size:363 final size:363
Alignment explanation
Indices: 42741536--42742261 Score: 1087
Period size: 363 Copynumber: 2.0 Consensus size: 363
42741526 TTTGTAAACC
* **
42741536 CCTTTGGGTTCTCCTTGGAGTAGGGAGAGAAAAACTCGAGGCTAAAATCGAGCATAGACACCTTG
1 CCTTTGGGCTCTCCTCAGAGTAGGGAGAGAAAAACTCGAGGCTAAAATCGAGCATAGACACCTTG
*
42741601 GGAACAATACTTTACTGTTGAGGGAGTGAGACACTACAAAGTAGATACTCGCCCTTAACATAAAA
66 GGAACAATACTTTACTGTTGAGGGAGTGAGACACTACAAAGTAGATACTCACCCTTAACATAAAA
* * * *
42741666 GGTGGCTTTAATGGGTTTGAATCCCACCAAAGCTAAATTATAAAATATTTTCTTGGTGGACCTAA
131 GGTGGCTCTAATGGGTTTGAATCCCACCAAAGCTAAATTATAAAACATTTCCTTGGTGCACCTAA
* * * * *
42741731 ACGCTCCCACTGAAACTTCGTGAACTCCTTTGGGCTCTCCTCGGAGTATAAAAACAAAAACTCGA
196 ACGCTCCCACTGAAACCTCGTGAACACCTTTGGGCTCTCCTCAGAGTAGAAAAACAAAAACTCAA
* * *
42741796 GGCTAAAATCAAGTATAGACATCTCGGAACAATATTTCCACCCTTGAGGAAGTAAGGCACTCTAG
261 GGCTAAAATCAAGTAAAGACATCTCGGAACAATATCTCCACCCTTGAGGAAGTAAGACACTCTAG
* * *
42741861 AGCAAATACTCACCTTCAACAAGCTTAATGCAAGAACT
326 AGCAAATACTCACCCTCAACAAACATAATGCAAGAACT
*
42741899 CCTTTGGGCTCTCCTCAGAGTAGGGAGAGAAAAACTCGAGGTTAAAATCGAGCATAGACACCTTG
1 CCTTTGGGCTCTCCTCAGAGTAGGGAGAGAAAAACTCGAGGCTAAAATCGAGCATAGACACCTTG
42741964 GGAACAATACATTTACTGTTGAGGGAGTGAGACACTACAAAGTAGATACTCACCCTTAACATAAA
66 GGAACAATAC-TTTACTGTTGAGGGAGTGAGACACTACAAAGTAGATACTCACCCTTAACATAAA
* * *
42742029 AGGTGGCTCTAATGGGTTTGAATCCCACCAAGGTTAAATTATAAAACATTTCCTTGGTGCATCTA
130 AGGTGGCTCTAATGGGTTTGAATCCCACCAAAGCTAAATTATAAAACATTTCCTTGGTGCACCTA
* * * *
42742094 GATGCTCCTATTGAAACCT-GTGAACACCTTTGGGCTCTCCTCAGAGTAGAAAAA-AAAAACTCA
195 AACGCTCCCACTGAAACCTCGTGAACACCTTTGGGCTCTCCTCAGAGTAGAAAAACAAAAACTCA
** * * * * *
42742157 AGGCTAAAATTGAGTAAAGACATCTTGGGAACAATATCTCTACTCTTGAGGAAGTTAGACACTTT
260 AGGCTAAAATCAAGTAAAGACATC-TCGGAACAATATCTCCACCCTTGAGGAAGTAAGACACTCT
* * *
42742222 AGAGCATATACTCGCCCTCAACAAACATAATGTAAGAACT
324 AGAGCAAATACTCACCCTCAACAAACATAATGCAAGAACT
42742262 AATAATAGCA
Statistics
Matches: 324, Mismatches: 37, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
362 29 0.09
363 170 0.52
364 125 0.39
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (363 bp):
CCTTTGGGCTCTCCTCAGAGTAGGGAGAGAAAAACTCGAGGCTAAAATCGAGCATAGACACCTTG
GGAACAATACTTTACTGTTGAGGGAGTGAGACACTACAAAGTAGATACTCACCCTTAACATAAAA
GGTGGCTCTAATGGGTTTGAATCCCACCAAAGCTAAATTATAAAACATTTCCTTGGTGCACCTAA
ACGCTCCCACTGAAACCTCGTGAACACCTTTGGGCTCTCCTCAGAGTAGAAAAACAAAAACTCAA
GGCTAAAATCAAGTAAAGACATCTCGGAACAATATCTCCACCCTTGAGGAAGTAAGACACTCTAG
AGCAAATACTCACCCTCAACAAACATAATGCAAGAACT
Found at i:42749868 original size:15 final size:15
Alignment explanation
Indices: 42749848--42749878 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42749838 CCAAATGGAA
42749848 ACTGAAGCATAGTTC
1 ACTGAAGCATAGTTC
42749863 ACTGAAGCATAGTTC
1 ACTGAAGCATAGTTC
42749878 A
1 A
42749879 AGTTTGCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (15 bp):
ACTGAAGCATAGTTC
Found at i:42756895 original size:12 final size:12
Alignment explanation
Indices: 42756878--42756902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42756868 CTCTCGGCCT
42756878 TTAATTGGTTAA
1 TTAATTGGTTAA
42756890 TTAATTGGTTAA
1 TTAATTGGTTAA
42756902 T
1 T
42756903 ACTTGCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTAATTGGTTAA
Found at i:42762019 original size:9 final size:9
Alignment explanation
Indices: 42762002--42762038 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
42761992 TGATTTTTTG
42762002 AATTCGAAT
1 AATTCGAAT
*
42762011 AATTAGAAT
1 AATTCGAAT
*
42762020 AACTCGAAT
1 AATTCGAAT
42762029 AATTCGAAT
1 AATTCGAAT
42762038 A
1 A
42762039 TCAAACTATA
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:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42762300 original size:30 final size:31
Alignment explanation
Indices: 42762252--42762311 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
42762242 AAACCTTTTA
*
42762252 TTTTCACCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCACCCAAAACTTTTACTCCCTTCCCAC
*
42762282 TTTTC-CCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCACCC-AAAACTTTTACTCCCTTCCCA
42762312 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCACCCAAAACTTTTACTCCCTTCCCAC
Found at i:42762446 original size:18 final size:16
Alignment explanation
Indices: 42762398--42762446 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
42762388 TATTTACTTT
42762398 CCCTCAAACTTTTATTC
1 CCCT-AAACTTTTATTC
*
42762415 CCCAAAACTTTTTATTTCC
1 CCCTAAAC-TTTTA-TT-C
42762434 CCCTAAACTTTTA
1 CCCTAAACTTTTA
42762447 CTTCTCACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 8 0.30
18 7 0.26
19 8 0.30
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.41
Consensus pattern (16 bp):
CCCTAAACTTTTATTC
Found at i:42765388 original size:354 final size:353
Alignment explanation
Indices: 42764910--42765619 Score: 1127
Period size: 354 Copynumber: 2.0 Consensus size: 353
42764900 GGATCAAATG
*
42764910 TTTCATGAGTGGACAAAGCACATTGACGTTCAGTATCATTTTGTGTGTGATATTATTGCTCGTGG
1 TTTCATGAGAGGACAAAGCACATTGACGTTCAGTATCATTTTGTGTGTGATATTATTGCTCGTGG
* * ** *
42764975 TGATCTTGTTGTGAGAAAAGTTAGTAGTCATAATACTCTTGTAGATATGATGACTAAGTCACTTC
66 TGATATTGTTGTGAGAAAAGTTAGTACTCATAATAAACTTGTAGATATGATAACTAAGTCACTTC
* * *
42765040 CTATAACCAAATTTGAGCATTGCTTGGACTTAGTTAGTGTTCATTGTTTAAGAATATCCTTAAGG
131 CTATAACCAAATTTGAGCATTGCTTGGACTTAGTTAGTGTTCATTGTTGAAGAATACCCTTAAGA
* * * * *
42765105 GTTTTGTGGGAGAGGTGGAGAACTTGTTCGTTGAGAATTCGTATCAAGGTGAGGATCGTTAGAGT
196 GTTTTGTGGAAAAGGTGGAGAACTTGGTCGTTGAGAATGCGTATCAAGGTGAAGATCGTTAGAGT
* *
42765170 TGTGTAACCCAAATTCTAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATATATTTAT-TCTTCT
261 TGTGCAACCCAAATTCTAAGAGATTGCTTGCAAGTCAAATTAAACAAAATATATTT-TCT-TTCT
42765234 AGAAGATTTAGTATTTATTAGTATAATATA
324 AGAAGATTTAGTATTTATTAGTATAATATA
* **
42765264 TTTCATGAGAGGGCAAAGCACATTGACGTTTGGTATCATTTCT-TGTGTGATATTATTGCTCGTG
1 TTTCATGAGAGGACAAAGCACATTGACGTTCAGTATCATTT-TGTGTGTGATATTATTGCTCGTG
*
42765328 GTGATATTGTTGTGAGAAAAGTTAGTACTCATGATAAACTTGTAGATATGATAACTAAGTCACTT
65 GTGATATTGTTGTGAGAAAAGTTAGTACTCATAATAAACTTGTAGATATGATAACTAAGTCACTT
** *
42765393 CCTATAAGTAATTTTGAGCATTGCTTGGACTTAGTTAGTGTTCATTGTTGAAGAATACCCTTAAG
130 CCTATAACCAAATTTGAGCATTGCTTGGACTTAGTTAGTGTTCATTGTTGAAGAATACCCTTAAG
* * *
42765458 AGTTTTGTGGAAAAGGTGGAGAACTTGGTCGTTGAGAATGCGTGTTAAGGTGAAGATTGTTAGAG
195 AGTTTTGTGGAAAAGGTGGAGAACTTGGTCGTTGAGAATGCGTATCAAGGTGAAGATCGTTAGAG
* *
42765523 TTGTGCAACCCAAATTCTAAGAGATTTCTTGCAAGTCAAATTAAACAATATATATTTTCTTTCTA
260 TTGTGCAACCCAAATTCTAAGAGATTGCTTGCAAGTCAAATTAAACAAAATATATTTTCTTTCTA
42765588 GAAGATTTAGTATTTATTAGTATAATATA
325 GAAGATTTAGTATTTATTAGTATAATATA
42765617 TTT
1 TTT
42765620 AGCATTTATT
Statistics
Matches: 326, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
353 38 0.12
354 287 0.88
355 1 0.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (353 bp):
TTTCATGAGAGGACAAAGCACATTGACGTTCAGTATCATTTTGTGTGTGATATTATTGCTCGTGG
TGATATTGTTGTGAGAAAAGTTAGTACTCATAATAAACTTGTAGATATGATAACTAAGTCACTTC
CTATAACCAAATTTGAGCATTGCTTGGACTTAGTTAGTGTTCATTGTTGAAGAATACCCTTAAGA
GTTTTGTGGAAAAGGTGGAGAACTTGGTCGTTGAGAATGCGTATCAAGGTGAAGATCGTTAGAGT
TGTGCAACCCAAATTCTAAGAGATTGCTTGCAAGTCAAATTAAACAAAATATATTTTCTTTCTAG
AAGATTTAGTATTTATTAGTATAATATA
Found at i:42765649 original size:24 final size:24
Alignment explanation
Indices: 42765592--42765643 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
42765582 TTTCTAGAAG
* * *
42765592 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCACAATAT
42765616 ATTTAGCATTTATTAGCACAATAT
1 ATTTAGCATTTATTAGCACAATAT
42765640 ATTT
1 ATTT
42765644 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCACAATAT
Found at i:42768898 original size:95 final size:95
Alignment explanation
Indices: 42768784--42768974 Score: 256
Period size: 95 Copynumber: 2.0 Consensus size: 95
42768774 AAATGCTTGG
** ** ** *
42768784 GCAAAATTTTAGGCCCATTTTTGGGGTCGGGCTGGGCCCGGGCCTAATTGACGAGCCTAAATTTT
1 GCAAAATTTTAGGCCCATTTTTCAGGTCGGGCTGAACCCAAGCCTAATTAACGAGCCTAAATTTT
*
42768849 TAGTTTGGCTCGACCTATGAACACCTCTAA
66 TAGTTGGGCTCGACCTATGAACACCTCTAA
* * * *
42768879 GCAAAATTTTAGGCCCATTTTTCAGGTTGGGTTGAACCCAAGCCTAGTTAACGAGCCTGAATTTT
1 GCAAAATTTTAGGCCCATTTTTCAGGTCGGGCTGAACCCAAGCCTAATTAACGAGCCTAAATTTT
* *
42768944 TAGTTGGGCTTGACCTATGATCACCTCTAA
66 TAGTTGGGCTCGACCTATGAACACCTCTAA
42768974 G
1 G
42768975 TGTTACTGAT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (95 bp):
GCAAAATTTTAGGCCCATTTTTCAGGTCGGGCTGAACCCAAGCCTAATTAACGAGCCTAAATTTT
TAGTTGGGCTCGACCTATGAACACCTCTAA
Found at i:42770021 original size:25 final size:25
Alignment explanation
Indices: 42769973--42770021 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
42769963 CATAGCTTTA
* **
42769973 ATAAAATGAGGTTGATAATGAATGC
1 ATAAAATGAGGTTCATAACAAATGC
42769998 ATAAAATGAGGTTCATAACAAATG
1 ATAAAATGAGGTTCATAACAAATG
42770022 GGGGTATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (25 bp):
ATAAAATGAGGTTCATAACAAATGC
Found at i:42774429 original size:24 final size:24
Alignment explanation
Indices: 42774378--42774430 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
42774368 TTTAATATTT
* * *
42774378 ATTAGTATAATTTATTTAGCATTT
1 ATTAGCATAATATATTTAGCATTG
42774402 ATTAGCATAATATATTT-GACATTG
1 ATTAGCATAATATATTTAG-CATTG
42774426 ATTAG
1 ATTAG
42774431 AATTAGGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (24 bp):
ATTAGCATAATATATTTAGCATTG
Found at i:42776276 original size:21 final size:21
Alignment explanation
Indices: 42776250--42776291 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42776240 CAACGCCAAT
42776250 CTTTGGAGATTGACATCAAAG
1 CTTTGGAGATTGACATCAAAG
42776271 CTTTGGAGATTGACATCAAAG
1 CTTTGGAGATTGACATCAAAG
42776292 AAATGATGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
CTTTGGAGATTGACATCAAAG
Found at i:42777666 original size:21 final size:18
Alignment explanation
Indices: 42777634--42777673 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
42777624 ATTTAGATGC
42777634 ATAATGGAATAATAAACATG
1 ATAATGGAATAA-AAA-ATG
42777654 ATAATGTGAATAAAAAATG
1 ATAATG-GAATAAAAAATG
42777673 A
1 A
42777674 ACAAAACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (18 bp):
ATAATGGAATAAAAAATG
Found at i:42779530 original size:98 final size:98
Alignment explanation
Indices: 42779345--42780214 Score: 1317
Period size: 98 Copynumber: 8.9 Consensus size: 98
42779335 CGAGGAAATA
* * * *
42779345 AGATTCGCCGTTGCAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCC-AGAAGTAAGATTCGCCGTTGTGG
* * *
42779410 CTTTGAACTTTTAAATTGCAATGTCGGGGAAGAG
65 CTTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * * * * * *
42779444 AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACATCGCCAGAAGTAAGATTCACTGCTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
*
42779509 TTCGATCTTTTAAATTGCAATGTTGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* *
42779542 AGATTCGCTATTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGGTTCGCCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
*
42779607 TTCGATCTTTTAAATTGCAATGTCAGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
*** *
42779640 AGATTTATTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCGGAAGTAAGATTCGCCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
*
42779705 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTA
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * * * * *
42779738 AGATTCACTGTTGTAGCTTCAATCTGTTCCACTGCATCGCTAGAAGTAAGATTCACCGTTGTTGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
* *
42779803 TTCGATCCTTTAAATTGCAATGTTGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * * *
42779836 AGATTCGCTGTTGTAGCTTCAATTTGCTCTGCTGCATCGCCAGAAGTAAGATTCACTGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
42779901 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * * *
42779934 AGATTCGCTATTGTAGCTTCAATCTGTTCCGCTGTATCGCCAGAAATAAGATTCGCCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
* *
42779999 TTCGATCCTTTAAATTGCAATGTCGGGGAAGTA
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
*
42780032 AGATTCGCTGTTGTAGCTTCGATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
*
42780097 TTCGATCCTTTAAATTGCAATGTCGGGGAAGTG
66 TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
* * *
42780130 AAATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCTGCTGTGGC
1 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
42780195 TTCGATCTTTTAAATTGCAA
66 TTCGATCTTTTAAATTGCAA
42780215 ACTATGGTTT
Statistics
Matches: 699, Mismatches: 72, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
98 661 0.95
99 38 0.05
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (98 bp):
AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGC
TTCGATCTTTTAAATTGCAATGTCGGGGAAGTG
Found at i:42792255 original size:21 final size:18
Alignment explanation
Indices: 42792223--42792262 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
42792213 ATTTAGATGC
42792223 ATAATGGAATAATAAACATG
1 ATAATGGAATAA-AAA-ATG
42792243 ATAATGTGAATAAAAAATG
1 ATAATG-GAATAAAAAATG
42792262 A
1 A
42792263 ACAAAACGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (18 bp):
ATAATGGAATAAAAAATG
Found at i:42795471 original size:43 final size:43
Alignment explanation
Indices: 42795418--42795643 Score: 244
Period size: 42 Copynumber: 5.3 Consensus size: 43
42795408 TTTTAAAAAT
*
42795418 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* ** *
42795461 AAACGCCGCTAAAGACCAAGACCTATAATGGCAC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
42795503 AAACGCCACTAAAGACCATGATCTTTAGCGGCGC-TTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
42795545 AAGCGCCGCTAAAGACTATGACCTTTAGCGGCGCTTTTTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCCAC
* * * * **
42795589 AAATGCCACTATAGA--ATAGACCTTTAGTGGCGCTTTTAACAC
1 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCCAC
42795631 AAACGCCGCTAAA
1 AAACGCCGCTAAA
42795644 AATATATCTT
Statistics
Matches: 152, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 90 0.59
43 44 0.29
44 18 0.12
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:42799496 original size:14 final size:14
Alignment explanation
Indices: 42799479--42799506 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42799469 ATAGTTTTTT
42799479 ATAAAAAAAACGCC
1 ATAAAAAAAACGCC
42799493 ATAAAAAAAACGCC
1 ATAAAAAAAACGCC
42799507 GCTATTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.07, T:0.07
Consensus pattern (14 bp):
ATAAAAAAAACGCC
Found at i:42800102 original size:21 final size:21
Alignment explanation
Indices: 42800078--42800125 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
42800068 AATTTAGTCT
42800078 TATCCAAAATAGATAGTTACC
1 TATCCAAAATAGATAGTTACC
42800099 TATCCAAAATAGATAGTTACC
1 TATCCAAAATAGATAGTTACC
42800120 TATCCA
1 TATCCA
42800126 CATGTTACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (21 bp):
TATCCAAAATAGATAGTTACC
Found at i:42800648 original size:16 final size:17
Alignment explanation
Indices: 42800612--42800653 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
42800602 CACTATAATC
42800612 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
42800630 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
42800646 ATTATTTA
1 ATTATTTA
42800654 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:42800775 original size:7 final size:7
Alignment explanation
Indices: 42800759--42800955 Score: 69
Period size: 7 Copynumber: 28.0 Consensus size: 7
42800749 ACTAATTAAT
42800759 CTAAACC
1 CTAAACC
*
42800766 CTAAATC
1 CTAAACC
42800773 CTAAACCC
1 CTAAA-CC
*
42800781 CT-AACT
1 CTAAACC
* *
42800787 ATTAACC
1 CTAAACC
*
42800794 CTCAACCC
1 CT-AAACC
*
42800802 CTAACCC
1 CTAAACC
42800809 CTAAACC
1 CTAAACC
*
42800816 TTAAACC
1 CTAAACC
*
42800823 C-CAACC
1 CTAAACC
* *
42800829 CTTAA-T
1 CTAAACC
42800835 CTATAACC
1 CTA-AACC
*
42800843 TTAAACC
1 CTAAACC
*
42800850 ATAAACC
1 CTAAACC
* *
42800857 ATAACCC
1 CTAAACC
*
42800864 CTAAATC
1 CTAAACC
42800871 CTAAACC
1 CTAAACC
*
42800878 TTAAACC
1 CTAAACC
* *
42800885 ATAAACT
1 CTAAACC
*
42800892 GTAAACC
1 CTAAACC
*
42800899 AT-AACC
1 CTAAACC
42800905 CTTAAACC
1 C-TAAACC
* *
42800913 CATAATCT
1 C-TAAACC
*
42800921 ATAAACC
1 CTAAACC
* *
42800928 TTAAACT
1 CTAAACC
*
42800935 CTATACC
1 CTAAACC
* *
42800942 ATATACC
1 CTAAACC
42800949 CTAAACC
1 CTAAACC
42800956 AAAAACCTTA
Statistics
Matches: 138, Mismatches: 44, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
6 13 0.09
7 106 0.77
8 19 0.14
ACGTcount: A:0.41, C:0.36, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:42800856 original size:14 final size:14
Alignment explanation
Indices: 42800839--42800968 Score: 88
Period size: 14 Copynumber: 9.2 Consensus size: 14
42800829 CTTAATCTAT
* *
42800839 AACCTTAAACCATA
1 AACCATAAACCTTA
* *
42800853 AACCATAACCCCTA
1 AACCATAAACCTTA
42800867 AATCC-TAAACCTTA
1 AA-CCATAAACCTTA
42800881 AACCATAAA-CTGTA
1 AACCATAAACCT-TA
*
42800895 AACCATAACCCTTA
1 AACCATAAACCTTA
*
42800909 AACCCAT-AATCTATA
1 AA-CCATAAACCT-TA
*
42800924 AACCTTAAA-CTCTA
1 AACCATAAACCT-TA
* * *
42800938 TACCATATACCCTA
1 AACCATAAACCTTA
*
42800952 AACCAAAAACCTTA
1 AACCATAAACCTTA
42800966 AAC
1 AAC
42800969 TATAGAGATA
Statistics
Matches: 90, Mismatches: 18, Indels: 16
0.73 0.15 0.13
Matches are distributed among these distances:
13 4 0.04
14 71 0.79
15 15 0.17
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (14 bp):
AACCATAAACCTTA
Found at i:42800896 original size:28 final size:28
Alignment explanation
Indices: 42800839--42800968 Score: 102
Period size: 28 Copynumber: 4.6 Consensus size: 28
42800829 CTTAATCTAT
* * *
42800839 AACCTTAAACCATAAACCATAACCCCTA
1 AACCATAAACCTTAAACCATAAACCCTA
**
42800867 AATCC-TAAACCTTAAACCATAAACTGTA
1 AA-CCATAAACCTTAAACCATAAACCCTA
* * **
42800895 AACCATAACCCTTAAACCCATAATCTATA
1 AACCATAAACCTTAAA-CCATAAACCCTA
* * *
42800924 AACCTTAAA-CTCTATACCATATACCCTA
1 AACCATAAACCT-TAAACCATAAACCCTA
*
42800952 AACCAAAAACCTTAAAC
1 AACCATAAACCTTAAAC
42800969 TATAGAGATA
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
27 2 0.03
28 54 0.68
29 24 0.30
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (28 bp):
AACCATAAACCTTAAACCATAAACCCTA
Found at i:42800968 original size:7 final size:7
Alignment explanation
Indices: 42800839--42800968 Score: 75
Period size: 7 Copynumber: 18.4 Consensus size: 7
42800829 CTTAATCTAT
*
42800839 AACCTTA
1 AACCATA
42800846 AACCATA
1 AACCATA
42800853 AACCATA
1 AACCATA
* *
42800860 ACCCCTA
1 AACCATA
42800867 AATCC-TA
1 AA-CCATA
*
42800874 AACCTTA
1 AACCATA
42800881 AACCATA
1 AACCATA
**
42800888 AACTGTA
1 AACCATA
42800895 AACCATA
1 AACCATA
* *
42800902 ACCCTTA
1 AACCATA
42800909 AACCCATA
1 AA-CCATA
* *
42800917 ATCTATA
1 AACCATA
*
42800924 AACCTTA
1 AACCATA
42800931 AACTC-TA
1 AAC-CATA
*
42800938 TACCATA
1 AACCATA
* *
42800945 TACCCTA
1 AACCATA
*
42800952 AACCAAA
1 AACCATA
*
42800959 AACCTTA
1 AACCATA
42800966 AAC
1 AAC
42800969 TATAGAGATA
Statistics
Matches: 93, Mismatches: 25, Indels: 10
0.73 0.20 0.08
Matches are distributed among these distances:
6 3 0.03
7 82 0.88
8 8 0.09
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (7 bp):
AACCATA
Found at i:42801242 original size:22 final size:22
Alignment explanation
Indices: 42801190--42801242 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
42801180 ATCTATTTTT
42801190 AACAAATATTTAATTAAAAATAA
1 AACAAAT-TTTAATTAAAAATAA
***
42801213 ATTGAATTTTAATTAATAAA-AA
1 AACAAATTTTAATTAA-AAATAA
42801235 AACAAATT
1 AACAAATT
42801243 AAATAGTAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (22 bp):
AACAAATTTTAATTAAAAATAA
Found at i:42801361 original size:42 final size:42
Alignment explanation
Indices: 42801273--42801425 Score: 256
Period size: 42 Copynumber: 3.7 Consensus size: 42
42801263 AAATGTTTTT
* * * *
42801273 GCGGCGCTTTTACAAAAACGCCGCTAATG--CTTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
42801313 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
42801355 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
42801397 GCGGCGCTTCTCCAAAAACGCCGCTAAAG
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAG
42801426 GCCTGAAAGG
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
40 26 0.24
42 81 0.76
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (42 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
Found at i:42801534 original size:40 final size:40
Alignment explanation
Indices: 42801469--42801603 Score: 173
Period size: 40 Copynumber: 3.2 Consensus size: 40
42801459 TAGGTTTTTT
*
42801469 GCGGCGTTTTCCT-TAAAGCGCCGCTAATGCTCGATCTTTA
1 GCGGCGTTTT-ATATAAAGCGCCGCTAATGCTCGATCTTTA
* *
42801509 GCGGTGTTTTATATAAAGCGGCGCTAATGCTCGATCTTTAGTTTA
1 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATC-----TTTA
*
42801554 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATTTTTA
1 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATCTTTA
42801594 GCGGCGTTTT
1 GCGGCGTTTT
42801604 TTATGCAAAC
Statistics
Matches: 83, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
39 1 0.01
40 45 0.54
45 37 0.45
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (40 bp):
GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATCTTTA
Found at i:42801556 original size:45 final size:45
Alignment explanation
Indices: 42801469--42801594 Score: 165
Period size: 45 Copynumber: 2.9 Consensus size: 45
42801459 TAGGTTTTTT
*
42801469 GCGGCGTTTTCCT-TAAAGCGCCGCTAATGCTCGATC-----TTTA
1 GCGGCGTTTT-ATATAAAGCGCCGCTAATGCTCGATCTTTAGTTTA
* *
42801509 GCGGTGTTTTATATAAAGCGGCGCTAATGCTCGATCTTTAGTTTA
1 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATCTTTAGTTTA
*
42801554 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATTTTTAG
1 GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATCTTTAG
42801595 CGGCGTTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
39 1 0.01
40 31 0.42
45 42 0.57
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (45 bp):
GCGGCGTTTTATATAAAGCGCCGCTAATGCTCGATCTTTAGTTTA
Found at i:42803357 original size:9 final size:9
Alignment explanation
Indices: 42803343--42803398 Score: 78
Period size: 9 Copynumber: 6.2 Consensus size: 9
42803333 GTAGTGATTC
42803343 AATTCGGTT
1 AATTCGGTT
42803352 AATTCGAG-T
1 AATTCG-GTT
42803361 AATTCGGTT
1 AATTCGGTT
*
42803370 AATTCGGGT
1 AATTCGGTT
*
42803379 AATTAGGTT
1 AATTCGGTT
42803388 AATTCGGTT
1 AATTCGGTT
42803397 AA
1 AA
42803399 GTTTTAACCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (9 bp):
AATTCGGTT
Found at i:42803394 original size:18 final size:18
Alignment explanation
Indices: 42803343--42803394 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
42803333 GTAGTGATTC
*
42803343 AATTCGGTTAATTCGAGT
1 AATTCGGTTAATTCGGGT
42803361 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
42803379 AATTAGGTTAATTCGG
1 AATTCGGTTAATTCGG
42803395 TTAAGTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:42804101 original size:29 final size:29
Alignment explanation
Indices: 42804034--42804104 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
42804024 GATCATCGAA
* *
42804034 TATGAAAAGAGATAGCTTCCGCTATTAAT
1 TATGAAAAGGGATAACTTCCGCTATTAAT
* * * *
42804063 TATGAAAAGGGATAACTTTCGTTGTTGAT
1 TATGAAAAGGGATAACTTCCGCTATTAAT
42804092 TATGAAAAGGGAT
1 TATGAAAAGGGAT
42804105 GGTGATGACC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (29 bp):
TATGAAAAGGGATAACTTCCGCTATTAAT
Found at i:42804152 original size:28 final size:29
Alignment explanation
Indices: 42804092--42804243 Score: 159
Period size: 29 Copynumber: 5.3 Consensus size: 29
42804082 CGTTGTTGAT
*
42804092 TATGAAAAGGGATGGTGATGACCATC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* *
42804120 CTATGAAAA-GGATAGTGACGACTATCGAA
1 -TATGAAAAGGGATGGTGACGACCATCGAA
*
42804149 TATGAAAAGGGATGGTGACAACCATC-AA
1 TATGAAAAGGGATGGTGACGACCATCGAA
* *
42804177 CTATGAAAAGGGAT-GTGATGACCATCGAT
1 -TATGAAAAGGGATGGTGACGACCATCGAA
* ** *
42804206 TAATGAAAATGGATGGTTTCGATCATCGAA
1 T-ATGAAAAGGGATGGTGACGACCATCGAA
42804236 TATGAAAA
1 TATGAAAA
42804244 AGGACGGGTA
Statistics
Matches: 102, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
28 35 0.34
29 56 0.55
30 11 0.11
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (29 bp):
TATGAAAAGGGATGGTGACGACCATCGAA
Found at i:42804243 original size:58 final size:57
Alignment explanation
Indices: 42804092--42804222 Score: 183
Period size: 57 Copynumber: 2.3 Consensus size: 57
42804082 CGTTGTTGAT
** *
42804092 TATGAAAAGGGATGGTGATGACCATCAACTATGAAAAGGATAGTGACGACTATCGAA
1 TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGATAGTGACGACCATCGAA
* *
42804149 TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGAT-GTGATGACCATCGAT
1 TATGAAAAGGGATGGTGACAACCATCAACTATGAAAA-GGATAGTGACGACCATCGAA
*
42804206 TAATGAAAATGGATGGT
1 T-ATGAAAAGGGATGGT
42804223 TTCGATCATC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 48 0.73
58 18 0.27
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (57 bp):
TATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGATAGTGACGACCATCGAA
Found at i:42812450 original size:39 final size:39
Alignment explanation
Indices: 42812403--42812489 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
42812393 ATTGTAATAC
*
42812403 ATGCTTAAATGTTATGTGATTATATGAGTATTATGATAT
1 ATGCTTAAATGTTATGTGATTATATGAGTAATATGATAT
* * *
42812442 ATGTTTAAATGTTATGTGATTATATGTGTAATGTGATAT
1 ATGCTTAAATGTTATGTGATTATATGAGTAATATGATAT
42812481 ATGCTTAAA
1 ATGCTTAAA
42812490 AGTGAATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.46
Consensus pattern (39 bp):
ATGCTTAAATGTTATGTGATTATATGAGTAATATGATAT
Found at i:42818414 original size:3 final size:3
Alignment explanation
Indices: 42818406--42818474 Score: 54
Period size: 3 Copynumber: 24.0 Consensus size: 3
42818396 AAAATGAGGA
* * * * *
42818406 AAT AAT AAT AAT AAT AGT AGT AGT AAT AAT AAT AGT -GT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
42818452 AGT AAT AAT AAT ATT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
42818475 TAATTTAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:42818452 original size:13 final size:15
Alignment explanation
Indices: 42818414--42818464 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
42818404 GAAATAATAA
*
42818414 TAATAATAGTAGTAG
1 TAATAATAATAGTAG
42818429 TAATAATAATAGT-G
1 TAATAATAATAGTAG
*
42818443 TAAT-ATAATAGTAA
1 TAATAATAATAGTAG
42818457 TAATAATA
1 TAATAATA
42818465 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 8 0.25
14 9 0.28
15 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
TAATAATAATAGTAG
Found at i:42819862 original size:35 final size:35
Alignment explanation
Indices: 42819817--42819885 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
42819807 GGGTGTGTGA
42819817 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
42819852 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
42819886 AGAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:42820474 original size:44 final size:44
Alignment explanation
Indices: 42820425--42820780 Score: 161
Period size: 44 Copynumber: 8.2 Consensus size: 44
42820415 CTTCGACCTG
* *
42820425 CTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTA
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* * ** * * ** * *
42820469 TTCCACTGTTGCCCAAGGAGAT-AGAACTACCAGCTTCAATGTA
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* ** * * * * * * *
42820512 CTCCACT-GTAATCAGGGAGGTAAAATCTGCCGTCTTCAACCTG
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* *
42820555 CTCCACTATTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTA
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* * * * ** *
42820599 TTCCACTGCCAAATAC--AGGGAGAT-AGAGT-TATCGGCTTCAATGTA
1 CTCCACT----ATTGCTTAGGGAGATAAGA-TCTGTCATCTTCAATCTA
* * * * * * * * *
42820644 CTCCACTGTAG-TCAGGGAGGTAAAATCTGCCATCTTCGACCTG
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* *
42820687 CTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCGATCTA
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
* * * * ** * *
42820731 TTCCACTGTTGCCTAGGGAGAT-AGAACTACCAGCTTCAATGTA
1 CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
42820774 CTCCACT
1 CTCCACT
42820781 GTAATCAGGG
Statistics
Matches: 217, Mismatches: 83, Indels: 25
0.67 0.26 0.08
Matches are distributed among these distances:
42 16 0.07
43 79 0.36
44 91 0.42
45 20 0.09
46 8 0.04
48 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCCACTATTGCTTAGGGAGATAAGATCTGTCATCTTCAATCTA
Found at i:42820490 original size:130 final size:130
Alignment explanation
Indices: 42820328--42820812 Score: 781
Period size: 130 Copynumber: 3.7 Consensus size: 130
42820318 AATGTTGTTT
*
42820328 TCTTCGATCTATTCCACTGTTGTCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
1 TCTTCGATCTATTCCACTGTTGCCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
* *
42820393 TCAGGGAGGTAAAATCCGCCGTCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAA
66 TCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAA
*
42820458 TCTTCGATCTATTCCACTGTTGCCCAAGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
1 TCTTCGATCTATTCCACTGTTGCCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
* * *
42820523 TCAGGGAGGTAAAATCTGCCGTCTTCAACCTGCTCCACTATTGCTTAAGGAGATAAGATCTGTAA
66 TCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAA
* ***** ** * *
42820588 TCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGT
1 TCTTCGATCTATTCCACTG--TTGCCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGT
*
42820653 AGTCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
64 AATCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGT
42820718 AA
129 AA
*
42820720 TCTTCGATCTATTCCACTGTTGCCTAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
1 TCTTCGATCTATTCCACTGTTGCCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
42820785 TCAGGGAGGTAAAATCTGCCATCTTCGA
66 TCAGGGAGGTAAAATCTGCCATCTTCGA
42820813 TCTTCAATCT
Statistics
Matches: 321, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
130 206 0.64
132 115 0.36
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (130 bp):
TCTTCGATCTATTCCACTGTTGCCCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAA
TCAGGGAGGTAAAATCTGCCATCTTCGACCTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAA
Found at i:42821030 original size:97 final size:95
Alignment explanation
Indices: 42820745--42821102 Score: 608
Period size: 95 Copynumber: 3.7 Consensus size: 95
42820735 ACTGTTGCCT
** * * *
42820745 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
42820810 CGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
*
42820840 AAGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
42820905 CGATCTTCAATCTATTCCACTGCCAAATAC
66 CGATCTTCAATCTATTCCACTGCCAAATAC
*
42820935 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATC
* *
42821000 TTTGATATTCAATCTATTCCACTGCCAAATAC
64 TTCGATCTTCAATCTATTCCACTGCCAAATAC
42821032 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
1 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
*
42821097 TGATCT
66 CGATCT
42821103 GCTTCGCTGC
Statistics
Matches: 249, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
95 157 0.63
97 92 0.37
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (95 bp):
AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTT
CGATCTTCAATCTATTCCACTGCCAAATAC
Found at i:42821070 original size:192 final size:190
Alignment explanation
Indices: 42820745--42821102 Score: 608
Period size: 192 Copynumber: 1.9 Consensus size: 190
42820735 ACTGTTGCCT
42820745 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTT
1 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTT
*
42820810 CGATCTTCAATCTATTCCACTGCCAAATACAAGGAGATAGAGTTATCGGCTTCAATGTACTCCAC
66 CGATATTCAATCTATTCCACTGCCAAATACAAGGAGATAGAGTTATCGGCTTCAATGTACTCCAC
42820875 TGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAATAC
131 TGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAATAC
** * * * *
42820935 AGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATC
1 AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAAT--CAGGGAGGTAAAATCTGCCATC
* *
42821000 TTTGATATTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCC
64 TTCGATATTCAATCTATTCCACTGCCAAATACAAGGAGATAGAGTTATCGGCTTCAATGTACTCC
*
42821065 ACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCT
129 ACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCT
42821103 GCTTCGCTGC
Statistics
Matches: 156, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
190 36 0.23
192 120 0.77
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (190 bp):
AGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTT
CGATATTCAATCTATTCCACTGCCAAATACAAGGAGATAGAGTTATCGGCTTCAATGTACTCCAC
TGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTTCAATCTATTCCACTGCCAAATAC
Found at i:42821218 original size:86 final size:87
Alignment explanation
Indices: 42821099--42821269 Score: 272
Period size: 86 Copynumber: 2.0 Consensus size: 87
42821089 GCCATCTTTG
* **
42821099 ATCTGCTTCGCTGCCAAATACAGGAATGCAAGATCTGCAATCTTCAACTTGCTCTGCTACAAACG
1 ATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTGCTACAAACG
42821164 AGAGAGGCAAGGTTTGTCTTCT
66 AGAGAGGCAAGGTTTGTCTTCT
* * * *
42821186 ATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATTTGCTATCTTCAACCAGCTCTGCTACAAACG
1 ATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTGCTACAAACG
42821250 AGAGAGGCAAGGTTTGTCTT
66 AGAGAGGCAAGGTTTGTCTT
42821270 TGATTTTTAC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 63 0.82
87 14 0.18
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (87 bp):
ATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTGCTACAAACG
AGAGAGGCAAGGTTTGTCTTCT
Found at i:42821260 original size:44 final size:43
Alignment explanation
Indices: 42821126--42821265 Score: 110
Period size: 44 Copynumber: 3.2 Consensus size: 43
42821116 ATACAGGAAT
* *
42821126 GCAAGATCTGCAATCTTCAACTTGCTCTGCTACAAACGAGAGAG
1 GCAAGATTTGC-ATCTTCAACCTGCTCTGCTACAAACGAGAGAG
* * * * *
42821170 GCAAGGTTTG--TCTTCTATCTGCT-TCGCTGTC-AATGCAG-GAAG
1 GCAAGATTTGCATCTTCAACCTGCTCT-GCT-ACAAACG-AGAG-AG
*
42821212 GCAAGATTTGCTATCTTCAACCAGCTCTGCTACAAACGAGAGAG
1 GCAAGATTTGC-ATCTTCAACCTGCTCTGCTACAAACGAGAGAG
*
42821256 GCAAGGTTTG
1 GCAAGATTTG
42821266 TCTTTGATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
40 1 0.01
41 17 0.24
42 14 0.19
44 22 0.31
45 17 0.24
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (43 bp):
GCAAGATTTGCATCTTCAACCTGCTCTGCTACAAACGAGAGAG
Found at i:42825403 original size:19 final size:20
Alignment explanation
Indices: 42825379--42825422 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
42825369 CGTGAAAGTC
* *
42825379 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
42825398 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
42825418 -AATGC
1 TAATGC
42825423 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:42827641 original size:3 final size:3
Alignment explanation
Indices: 42827633--42827701 Score: 54
Period size: 3 Copynumber: 24.0 Consensus size: 3
42827623 AAAATGAGGA
* * * * *
42827633 AAT AAT AAT AAT AAT AGT AGT AGT AAT AAT AAT AGT -GT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
42827679 AGT AAT AAT AAT ATT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
42827702 TAATTTAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 6 0.11
3 49 0.89
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:42827679 original size:13 final size:15
Alignment explanation
Indices: 42827641--42827691 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
42827631 GAAATAATAA
*
42827641 TAATAATAGTAGTAG
1 TAATAATAATAGTAG
42827656 TAATAATAATAGT-G
1 TAATAATAATAGTAG
*
42827670 TAAT-ATAATAGTAA
1 TAATAATAATAGTAG
42827684 TAATAATA
1 TAATAATA
42827692 TTAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 8 0.25
14 9 0.28
15 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (15 bp):
TAATAATAATAGTAG
Found at i:42829086 original size:35 final size:35
Alignment explanation
Indices: 42829041--42829109 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
42829031 GGGTGTGAGA
42829041 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
42829076 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
42829110 AAAGGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.12, G:0.51, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
Found at i:42833457 original size:32 final size:32
Alignment explanation
Indices: 42833420--42833483 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
42833410 TGAAATCGTG
*
42833420 CATTGGAGTTTTTACTTTTTATTTTTATTACT
1 CATTGGAGTCTTTACTTTTTATTTTTATTACT
42833452 CATTGGAGTCTTTACTTTTTATTTTTATTACT
1 CATTGGAGTCTTTACTTTTTATTTTTATTACT
42833484 TAGTTAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (32 bp):
CATTGGAGTCTTTACTTTTTATTTTTATTACT
Found at i:42835869 original size:55 final size:55
Alignment explanation
Indices: 42835808--42835916 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
42835798 ATTTATATGA
42835808 AATCTTTAAAATAATCTACTTATAAATACAATACTAACATTCCAAACCTTAAATT
1 AATCTTTAAAATAATCTACTTATAAATACAATACTAACATTCCAAACCTTAAATT
*
42835863 AATCTTTAAAATAATCTATTTATAAATACAATACTAACATTCCAAACCTTAAAT
1 AATCTTTAAAATAATCTACTTATAAATACAATACTAACATTCCAAACCTTAAAT
42835917 CTTAAAGTAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (55 bp):
AATCTTTAAAATAATCTACTTATAAATACAATACTAACATTCCAAACCTTAAATT
Found at i:42839997 original size:16 final size:17
Alignment explanation
Indices: 42839978--42840009 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42839968 TTTATAAATC
42839978 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
42839994 ATATATTTAATATTAA
1 ATATATTTAATATTAA
42840010 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:42840072 original size:66 final size:63
Alignment explanation
Indices: 42840002--42840214 Score: 194
Period size: 61 Copynumber: 3.4 Consensus size: 63
42839992 AAATATATTT
42840002 AATATTAATTATTTAA-AATTTTATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATA
1 AATATTAATTA-TTAAGAATTTTA--TTA-AGTATCATATATTATGATTTGAGTAAATTCATATA
42840066 AG
62 AG
* * * * * * *
42840068 AATATTAATTATTAAGAATTTTATTAA--ATTATATATTTTAATTAT-ATTATATTTA-ATAAT
1 AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATT-TGAGTAAATTCATATAAG
* * * *
42840128 AATTATGTTATT-TT-A-TATTTTA--CAGTATCATATATTATGGTTTGAGTAAATTCATATAAG
1 AA-TAT-TAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
42840188 AATATTAATTATTAAGAATTTTATTAA
1 AATATTAATTATTAAGAATTTTATTAA
42840215 ATTATATATT
Statistics
Matches: 113, Mismatches: 21, Indels: 29
0.69 0.13 0.18
Matches are distributed among these distances:
57 1 0.01
58 5 0.04
59 30 0.27
60 14 0.12
61 31 0.27
62 5 0.04
63 2 0.02
64 3 0.03
65 4 0.04
66 18 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAGAATTTTATTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:42840099 original size:54 final size:54
Alignment explanation
Indices: 42840041--42840219 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
42840031 AGTATCATAT
42840041 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
42840095 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
42840158 TA
54 -A
*
42840160 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
42840215 ATTAT
1 ATTAT
42840220 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:42840103 original size:120 final size:120
Alignment explanation
Indices: 42839965--42840256 Score: 473
Period size: 120 Copynumber: 2.4 Consensus size: 120
42839955 AATTATTTTA
* * *
42839965 AATTTTA-TAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
42840027 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
42840084 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
42840149 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
42840204 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
42840257 TAAATATGAT
Statistics
Matches: 160, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
119 11 0.07
120 147 0.92
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:42840116 original size:18 final size:17
Alignment explanation
Indices: 42840085--42840119 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42840075 ATTATTAAGA
42840085 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
42840102 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
42840120 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:42840233 original size:18 final size:17
Alignment explanation
Indices: 42840205--42840239 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42840195 ATTATTAAGA
*
42840205 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42840222 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42840240 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42840251 original size:54 final size:54
Alignment explanation
Indices: 42840068--42840253 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
42840058 TTCATATAAG
* *
42840068 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
42840122 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
42840185 AAG
53 -TT
* *
42840188 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
42840242 AATAATAATTAT
1 AATAATAATTAT
42840254 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:42840353 original size:147 final size:149
Alignment explanation
Indices: 42840193--42840467 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
42840183 ATAAGAATAT
*
42840193 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
42840258 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
42840321 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
42840340 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
42840405 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
42840468 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:42840380 original size:18 final size:17
Alignment explanation
Indices: 42840352--42840386 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42840342 ATTATTAAGA
*
42840352 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42840369 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42840387 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42840597 original size:44 final size:45
Alignment explanation
Indices: 42840548--42840642 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
42840538 TTACACCTCT
* *
42840548 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
42840592 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
42840637 ATTACA
1 ATTACA
42840643 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:42840642 original size:16 final size:16
Alignment explanation
Indices: 42840623--42840674 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
42840613 GATTTGCTAT
* *
42840623 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
42840639 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42840655 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
42840671 TACA
1 TACA
42840675 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:42844101 original size:14 final size:13
Alignment explanation
Indices: 42844061--42844111 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
42844051 TTAAGTATAT
*
42844061 TATTATTTTATTA
1 TATTATTATATTA
* *
42844074 TATT-GTAAATTA
1 TATTATTATATTA
42844086 TATTAATTATATTA
1 TATT-ATTATATTA
42844100 TATTATTATATT
1 TATTATTATATT
42844112 TTAAATAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.29
13 12 0.39
14 10 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:42848606 original size:20 final size:19
Alignment explanation
Indices: 42848581--42848618 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
42848571 TGGAAATTAA
42848581 TCAATTCACAAACATATAAT
1 TCAATTCA-AAACATATAAT
*
42848601 TCAATTTAAAACATATAA
1 TCAATTCAAAACATATAA
42848619 ATATACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (19 bp):
TCAATTCAAAACATATAAT
Found at i:42851819 original size:9 final size:9
Alignment explanation
Indices: 42851805--42851844 Score: 53
Period size: 9 Copynumber: 4.1 Consensus size: 9
42851795 CCCCTAACAG
42851805 TCAACTCTT
1 TCAACTCTT
42851814 TCAACTATGCTT
1 TCAAC--T-CTT
42851826 TCAACTCTT
1 TCAACTCTT
42851835 TCAACTCTT
1 TCAACTCTT
42851844 T
1 T
42851845 AGGAGCCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 18 0.64
10 1 0.04
11 1 0.04
12 8 0.29
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.45
Consensus pattern (9 bp):
TCAACTCTT
Found at i:42858275 original size:13 final size:13
Alignment explanation
Indices: 42858257--42858281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42858247 AGAAATTTGA
42858257 AACACGAAAAATT
1 AACACGAAAAATT
42858270 AACACGAAAAAT
1 AACACGAAAAAT
42858282 CAAAACATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (13 bp):
AACACGAAAAATT
Found at i:42858889 original size:29 final size:29
Alignment explanation
Indices: 42858826--42858904 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
42858816 CCCATATCGT
* *
42858826 CAAAATTACTTTTTCAGAGCCCATCCCCA
1 CAAAATTATTTTTTCAGAACCCATCCCCA
**
42858855 CAAAATTATTTTTTCAGAACCCATCCTGTA
1 CAAAATTATTTTTTCAGAACCCATCC-CCA
42858885 C-AAATTATTTTTT-AGAACCC
1 CAAAATTATTTTTTCAGAACCC
42858905 CTAAAAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 7 0.16
29 36 0.80
30 2 0.04
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
CAAAATTATTTTTTCAGAACCCATCCCCA
Found at i:42858937 original size:26 final size:26
Alignment explanation
Indices: 42858906--42858961 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
42858896 TTAGAACCCC
* *
42858906 TAAAAATTAAATAAAACCCTAAACACT
1 TAAAAACTAAAAAAAACCCTAAAC-CT
*
42858933 TAAAAACTAAAAAAAACCTTAAACCT
1 TAAAAACTAAAAAAAACCCTAAACCT
42858959 TAA
1 TAA
42858962 TTGGTACTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (26 bp):
TAAAAACTAAAAAAAACCCTAAACCT
Done.