Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 122 of 222
Found at i:39600774 original size:74 final size:72
Alignment explanation
Indices: 39600653--39600788 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 72
39600643 TAGAAAGATA
* *
39600653 AAAATGCAAGAAAAGTAAAAAAGACAAGAGAAGCCAGAGTAAATGCTAAGTAATTTCTATTACTC
1 AAAATGAAAGAAAAGTAAAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCTATTACTC
39600718 AACAATT
66 AACAATT
* *
39600725 AAAATGAAAGAATAGTAAAAAAAAGACAAGAGAAGCAAGAGTAATTGCTAAGTAATTTCTATTA
1 AAAATGAAAGAAAAGT--AAAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCTATTA
39600789 AAATGCAAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
72 14 0.24
74 44 0.76
ACGTcount: A:0.53, C:0.10, G:0.16, T:0.21
Consensus pattern (72 bp):
AAAATGAAAGAAAAGTAAAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCTATTACTC
AACAATT
Found at i:39600793 original size:63 final size:60
Alignment explanation
Indices: 39600722--39600848 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 60
39600712 TTACTCAACA
* *
39600722 ATTAAAATGAAAGAATAGTAAAAAAAAGACAAGAGAAGCAAGAGTAATTGCTAAGTAATTTCT
1 ATTAAAATGAAAGAACAGT---AAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCT
* *
39600785 ATTAAAATGCAAGAACAGTAAAAAGACAAGAGAAGCCAGAGTAAATGCTAAGTAATTTCT
1 ATTAAAATGAAAGAACAGTAAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCT
39600845 ATTA
1 ATTA
39600849 CTCAAGAATG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 43 0.72
63 17 0.28
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (60 bp):
ATTAAAATGAAAGAACAGTAAAAAGACAAGAGAAGCAAGAGTAAATGCTAAGTAATTTCT
Found at i:39605237 original size:42 final size:43
Alignment explanation
Indices: 39605105--39605246 Score: 160
Period size: 43 Copynumber: 3.3 Consensus size: 43
39605095 TCCCGGACTT
* * * *
39605105 GGTCTTACATGTAATCAAATAATGAAGCCATTGTCCCAGACAG
1 GGTCTTACACGTAATTAAATAACGAAGCCAATGTCCCAGACAG
* * * *
39605148 GGTTTTACATGTAATTAAATAACGATGCCACTGTCCCAGACAG
1 GGTCTTACACGTAATTAAATAACGAAGCCAATGTCCCAGACAG
* * * **
39605191 GGTCTTACACGTAATTATAT-ACGACGCCAATATCCCAGACTT
1 GGTCTTACACGTAATTAAATAACGAAGCCAATGTCCCAGACAG
39605233 GGTCTTACACGTAA
1 GGTCTTACACGTAA
39605247 ATCTCAAATT
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 31 0.36
43 55 0.64
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGTAATTAAATAACGAAGCCAATGTCCCAGACAG
Found at i:39611108 original size:49 final size:49
Alignment explanation
Indices: 39610994--39611136 Score: 189
Period size: 49 Copynumber: 2.9 Consensus size: 49
39610984 GTACATGTAT
* * *
39610994 GCTCATATGAGCT-ACGAATCGGTATGCTTTCACGAGCTGTAAATCGGTAA
1 GCTCATATGAGCTGA-GAATCGGTAAGCTCTCACGAGCTG-AAATCGATAA
* *
39611044 GCTCATATGAACTGAGAATCGATAAGCTCTCACGAGCTGAAATCGATAA
1 GCTCATATGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGATAA
* * *
39611093 GCTCATACGAGCTGAGAATCGGTAAGCTCTCATGAGCTAAAATC
1 GCTCATATGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATC
39611137 AGTAATCCCT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
49 48 0.59
50 33 0.40
51 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (49 bp):
GCTCATATGAGCTGAGAATCGGTAAGCTCTCACGAGCTGAAATCGATAA
Found at i:39611129 original size:25 final size:25
Alignment explanation
Indices: 39611009--39611130 Score: 126
Period size: 25 Copynumber: 4.9 Consensus size: 25
39610999 TATGAGCTAC
* *
39611009 GAATCGGTATGCTTTCACGAGCTGTA
1 GAATCGGTAAGCTCTCACGAGCTG-A
* *
39611035 -AATCGGTAAGCTCAT-ATGAACTGA
1 GAATCGGTAAGCTC-TCACGAGCTGA
*
39611059 GAATCGATAAGCTCTCACGAGCTGA
1 GAATCGGTAAGCTCTCACGAGCTGA
*
39611084 -AATCGATAAGCTCAT-ACGAGCTGA
1 GAATCGGTAAGCTC-TCACGAGCTGA
*
39611108 GAATCGGTAAGCTCTCATGAGCT
1 GAATCGGTAAGCTCTCACGAGCT
39611131 AAAATCAGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
24 25 0.31
25 55 0.68
26 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (25 bp):
GAATCGGTAAGCTCTCACGAGCTGA
Found at i:39611141 original size:24 final size:23
Alignment explanation
Indices: 39611060--39611141 Score: 76
Period size: 24 Copynumber: 3.3 Consensus size: 23
39611050 ATGAACTGAG
*
39611060 AATCGATAAGCTCTCACGAGCTGA
1 AATCG-TAAGCTCTCACGAGCTAA
*
39611084 AATCGATAAGCTCAT-ACGAGCTGAG
1 AATCG-TAAGCTC-TCACGAGCT-AA
*
39611109 AATCGGTAAGCTCTCATGAGCTAA
1 AATC-GTAAGCTCTCACGAGCTAA
39611133 AATCAGTAA
1 AATC-GTAA
39611142 TCCCTAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 30 0.61
25 18 0.37
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (23 bp):
AATCGTAAGCTCTCACGAGCTAA
Found at i:39616237 original size:2 final size:2
Alignment explanation
Indices: 39616230--39616254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39616220 TAAAAGCAAA
39616230 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39616255 GCAATCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39650188 original size:39 final size:39
Alignment explanation
Indices: 39650144--39650241 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
39650134 ATTTAAGGAA
39650144 AATGTGATAAAAATTACTAAATAAAATAAAGCATAAATT
1 AATGTGATAAAAATTACTAAATAAAATAAAGCATAAATT
*
39650183 AATGTGATAAAAATTAATAAATAAAATAAAGCATAAATT
1 AATGTGATAAAAATTACTAAATAAAATAAAGCATAAATT
* *
39650222 AA-GTAAAAAAAATTAGCTAA
1 AATGTGATAAAAATTA-CTAA
39650242 TGGAATGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 11 0.20
39 43 0.80
ACGTcount: A:0.61, C:0.04, G:0.08, T:0.27
Consensus pattern (39 bp):
AATGTGATAAAAATTACTAAATAAAATAAAGCATAAATT
Found at i:39655431 original size:14 final size:14
Alignment explanation
Indices: 39655408--39655444 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
39655398 CAATATATCA
*
39655408 TGGTCATTCATTAT
1 TGGTCGTTCATTAT
*
39655422 TGGTTGTTCATTAT
1 TGGTCGTTCATTAT
39655436 TGGTCGTTC
1 TGGTCGTTC
39655445 TTGAGCTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (14 bp):
TGGTCGTTCATTAT
Found at i:39661934 original size:37 final size:37
Alignment explanation
Indices: 39661893--39661994 Score: 127
Period size: 37 Copynumber: 2.7 Consensus size: 37
39661883 TGAACATCAG
*
39661893 TCAGTATATCGATAAGATTTGCTC-AGTTAAGC-TCAAT
1 TCAGTATAACGATAAGATTTGCTCGA-TTAAGCTTC-AT
* *
39661930 TCAGTATAACGATATGACTTGCTCGATTAAGCTTCAT
1 TCAGTATAACGATAAGATTTGCTCGATTAAGCTTCAT
*
39661967 TCAGTATAACAATAAGATTTGGCTCGAT
1 TCAGTATAACGATAAGATTT-GCTCGAT
39661995 AGAGCATATT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 46 0.82
38 10 0.18
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (37 bp):
TCAGTATAACGATAAGATTTGCTCGATTAAGCTTCAT
Found at i:39665902 original size:79 final size:82
Alignment explanation
Indices: 39665791--39665975 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
39665781 GCTACTCGTT
* * *
39665791 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
39665854 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
**
39665871 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
39665934 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
39665951 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39665976 CATCATTCGA
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:39665975 original size:40 final size:40
Alignment explanation
Indices: 39665772--39665975 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
39665762 CGGAATTTAA
** * *
39665772 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGTCATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39665812 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
39665852 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
39665891 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39665931 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39665971 CCGGA
1 CCGGA
39665976 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 94 0.66
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:39667168 original size:56 final size:56
Alignment explanation
Indices: 39667101--39667220 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
39667091 TATTAGTTTA
39667101 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
39667157 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
39667213 TTGCCCAT
1 TTGCCCAT
39667221 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:39673132 original size:79 final size:82
Alignment explanation
Indices: 39673021--39673205 Score: 211
Period size: 79 Copynumber: 2.3 Consensus size: 82
39673011 GCTACTCGTT
* * * *
39673021 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTC-GGATCTTAACCC
* **
39673084 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAACA
* **
39673101 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCACACAAATGCCTTCGGATCTTATTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
* *
39673164 GATATGGTCACTTAACA
66 GATATAGTAACTTAACA
39673181 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39673206 CATCATTCGA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCACACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAACA
Found at i:39673142 original size:39 final size:40
Alignment explanation
Indices: 39673021--39673205 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
39673011 GCTACTCGTT
* *
39673021 CAAATGCCTTCGGGTCATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
39673061 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
39673101 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
** * * * **
39673140 CAAATGCCTTC-GGATCTTATTCCGGATATGGTCACTTAACA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
39673181 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39673206 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39674399 original size:56 final size:56
Alignment explanation
Indices: 39674332--39674451 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
39674322 TATTAGTTTA
39674332 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
39674388 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
39674444 TTGCCCAT
1 TTGCCCAT
39674452 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:39675498 original size:21 final size:21
Alignment explanation
Indices: 39675454--39675551 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
39675444 CAAATACACC
39675454 AACAGAAGCTCGTGAGAG-TG
1 AACAGAAGCTCGTGAGAGCTG
*
39675474 AACAAAAGCTCGTGAGAGCTG
1 AACAGAAGCTCGTGAGAGCTG
* *
39675495 AACAAAAGCTCGTGAGAGCAG
1 AACAGAAGCTCGTGAGAGCTG
*** *
39675516 AACAGAAGCTCAAAAGAGCTT
1 AACAGAAGCTCGTGAGAGCTG
39675537 AACAGAAGCTCGTGA
1 AACAGAAGCTCGTGA
39675552 AAGTTGATCC
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
20 17 0.26
21 49 0.74
ACGTcount: A:0.41, C:0.18, G:0.28, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCGTGAGAGCTG
Found at i:39680473 original size:32 final size:32
Alignment explanation
Indices: 39680437--39680501 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
39680427 TTGGGCTTCG
39680437 GAGCATTTCGTACACTTCCCACACTATCAGCA
1 GAGCATTTCGTACACTTCCCACACTATCAGCA
39680469 GAGCATTTCGTACACTTCCCACACTATCAGCA
1 GAGCATTTCGTACACTTCCCACACTATCAGCA
39680501 G
1 G
39680502 GTTTAGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.25
Consensus pattern (32 bp):
GAGCATTTCGTACACTTCCCACACTATCAGCA
Found at i:39683444 original size:39 final size:40
Alignment explanation
Indices: 39683327--39683507 Score: 208
Period size: 40 Copynumber: 4.5 Consensus size: 40
39683317 GCTACTCGTT
* *
39683327 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCTCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
39683367 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
39683407 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
39683446 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
39683487 CAAA-GCCTTTGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
39683508 TGGACATCAT
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 73 0.60
41 13 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:39683471 original size:79 final size:81
Alignment explanation
Indices: 39683327--39683507 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 81
39683317 GCTACTCGTT
* * *
39683327 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCTCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
39683392 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* **
39683407 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* *
39683469 GGATATGGTCACTTAGCA
64 GGATATAGTAACTTAGCA
*
39683487 CAAA-GCCTTTGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
39683508 TGGACATCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
78 4 0.05
79 53 0.62
80 29 0.34
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:39691442 original size:79 final size:79
Alignment explanation
Indices: 39691331--39691554 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
39691321 GCTACTCGTT
* * *
39691331 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
39691396 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
39691411 CAAATGCCTTCGGGCTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
39691474 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * *
39691489 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
39691553 GA
64 GA
39691555 CATCATTCAA
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 36 0.28
79 57 0.45
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGCTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:39691448 original size:39 final size:40
Alignment explanation
Indices: 39691331--39691554 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
39691321 GCTACTCGTT
* *
39691331 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
39691371 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
39691411 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
39691450 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
39691489 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
39691530 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39691555 CATCATTCAA
Statistics
Matches: 166, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 77 0.46
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:39694039 original size:21 final size:21
Alignment explanation
Indices: 39694010--39694052 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39694000 TGAATACGCC
39694010 AACAAAAGCTCGTAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTG
*
39694031 AACAGAAGCTCGTAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTG
39694052 A
1 A
39694053 TCCTCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTG
Found at i:39701789 original size:10 final size:10
Alignment explanation
Indices: 39701774--39701818 Score: 74
Period size: 10 Copynumber: 4.5 Consensus size: 10
39701764 AAAAAATAAC
39701774 TTTTTTATAT
1 TTTTTTATAT
39701784 TTTTTTATAT
1 TTTTTTATAT
39701794 ATTTTTTA-AT
1 -TTTTTTATAT
39701804 TTTTTTATAT
1 TTTTTTATAT
39701814 TTTTT
1 TTTTT
39701819 AAAATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.21
10 19 0.58
11 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:39703177 original size:71 final size:71
Alignment explanation
Indices: 39703079--39703240 Score: 216
Period size: 71 Copynumber: 2.3 Consensus size: 71
39703069 ACTGTGTTGT
* * * * **
39703079 AAAATACCGCAAACTATATTTACAGAAATGCCGCAAAATGTATTGTAGAATTACTGTGAACTGCA
1 AAAATACTGCAAACTGTATTTACAGAAATGCCACAAAATATATTGTAGAATTACAATGAACTGCA
39703144 TTTACA
66 TTTACA
* ** * *
39703150 AAAATATTGTGAACTGTATTTATAGAAATGCCACAAAATATATTGTAGAATTACAATGAACTGTA
1 AAAATACTGCAAACTGTATTTACAGAAATGCCACAAAATATATTGTAGAATTACAATGAACTGCA
39703215 TTTACA
66 TTTACA
*
39703221 GAAATACTGCAAACTGTATT
1 AAAATACTGCAAACTGTATT
39703241 GTAATACCCA
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (71 bp):
AAAATACTGCAAACTGTATTTACAGAAATGCCACAAAATATATTGTAGAATTACAATGAACTGCA
TTTACA
Found at i:39703178 original size:24 final size:24
Alignment explanation
Indices: 39703124--39703178 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
39703114 AAATGTATTG
*
39703124 TAGAATTACTGTGAACTGCATTTA
1 TAGAAATACTGTGAACTGCATTTA
* * * *
39703148 CAAAAATATTGTGAACTGTATTTA
1 TAGAAATACTGTGAACTGCATTTA
39703172 TAGAAAT
1 TAGAAAT
39703179 GCCACAAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (24 bp):
TAGAAATACTGTGAACTGCATTTA
Found at i:39716827 original size:44 final size:44
Alignment explanation
Indices: 39716759--39717229 Score: 636
Period size: 44 Copynumber: 10.7 Consensus size: 44
39716749 AAATCATAAA
39716759 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* * *
39716803 CCCTAGTTCCCTAACCAGCTGTGGAATAGGTGGAAGACTGCAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* *
39716847 CCCTAGTTCCCTAACCAGTAGTGGAATAGGTGGAAGACTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* *
39716891 CCCTAGTTCCTTGACCAGCAGTGGAATAGGTGGAAGACTGCAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* * * *
39716935 CCCTAGTTCCCTGACTATCAGTGGAACAAGTGGAAGACTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
**
39716979 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTAAAAGACTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* *
39717023 CCCTAGTTCCCTAACCAGCAGTGGAATAGGTGGAAGATTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
** * * * * *
39717067 TTCTAGCTCCCTGAACAGCAGTGGAATAGGCGGAAGATTGTAAA
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* *
39717111 TCCTAGCTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* * * * *
39717155 TCCTAGCTCCCTGACCAACAGTGGAATAGGTAGAAGATTGTAAG
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
* * * * *
39717199 TCCTAGCTCCCTGAGCAGCTGTGGAGTAGGT
1 CCCTAGTTCCCTGACCAGCAGTGGAATAGGT
39717230 TGAAAATTAC
Statistics
Matches: 382, Mismatches: 45, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 382 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (44 bp):
CCCTAGTTCCCTGACCAGCAGTGGAATAGGTGGAAGACTGTAAG
Found at i:39720764 original size:54 final size:54
Alignment explanation
Indices: 39720526--39720765 Score: 284
Period size: 54 Copynumber: 4.4 Consensus size: 54
39720516 ATAAGATTGC
* * *
39720526 AAAAGGTCGTGATCGTAAATCAGCGGACTGTGAGATTCGTAAAATCCCGTAAGT
1 AAAAGGTTGTGATCATAAATCAGCGGACTGCGAGATTCGTAAAATCCCGTAAGT
** ** *
39720580 AAAAGGTTGTGATTGTAAATCAATGGACTGCAAGATTCGTAAAATCCCGTAAGT
1 AAAAGGTTGTGATCATAAATCAGCGGACTGCGAGATTCGTAAAATCCCGTAAGT
* * * ** * * *
39720634 AAAAGATCGTGATCATAAATCAACATA-TCACGAGATTCGTAAAATCTCATAAGT
1 AAAAGGTTGTGATCATAAATCAGCGGACT-GCGAGATTCGTAAAATCCCGTAAGT
* * **
39720688 AAAAGGTTGTGATCATAAATCAGCGGACTGTGAGATTCATAAAATCTTGTAAGT
1 AAAAGGTTGTGATCATAAATCAGCGGACTGCGAGATTCGTAAAATCCCGTAAGT
39720742 AAAAGGTTGTGATCATAAATCAGC
1 AAAAGGTTGTGATCATAAATCAGC
39720766 AAACCATAAG
Statistics
Matches: 157, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 155 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (54 bp):
AAAAGGTTGTGATCATAAATCAGCGGACTGCGAGATTCGTAAAATCCCGTAAGT
Found at i:39720800 original size:39 final size:39
Alignment explanation
Indices: 39720744--39720966 Score: 232
Period size: 39 Copynumber: 5.7 Consensus size: 39
39720734 TTGTAAGTAA
* * *
39720744 AAGGTTGTGATCATAAATCAGCAAACCATAAGAAAGTCG
1 AAGGTCGTGATCGTAAATCAGCAAACCATAAGAAAGCCG
* * *
39720783 AAGGTCGTGATCGTAAATCAGCAGACTATAAGAAAGCCA
1 AAGGTCGTGATCGTAAATCAGCAAACCATAAGAAAGCCG
*
39720822 AAGGTCGTGATCGTAAACCAGCAAACCATAAGAAAGCCG
1 AAGGTCGTGATCGTAAATCAGCAAACCATAAGAAAGCCG
* * * * * *
39720861 -ATGACTGTGACCGTAAATCAACAGACCATAAGAAAGCCA
1 AAGGTC-GTGATCGTAAATCAGCAAACCATAAGAAAGCCG
* * * ****
39720900 AAGTTTGTGATCGTAAATCAACGGGTCATAAGAAAGCCG
1 AAGGTCGTGATCGTAAATCAGCAAACCATAAGAAAGCCG
* *
39720939 AAGGTCGTGGTCATAAATCAGCAAACCA
1 AAGGTCGTGATCGTAAATCAGCAAACCA
39720967 CGAAATTCAT
Statistics
Matches: 147, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
38 3 0.02
39 143 0.97
40 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (39 bp):
AAGGTCGTGATCGTAAATCAGCAAACCATAAGAAAGCCG
Found at i:39721034 original size:54 final size:54
Alignment explanation
Indices: 39720939--39721121 Score: 233
Period size: 54 Copynumber: 3.4 Consensus size: 54
39720929 AAGAAAGCCG
* * * *
39720939 AAGGTCGTGGTCATAAATCAGCAAACCACGAAATTCATAAAATCCCGTAAGTAA
1 AAGGTCGTGATCGTAAATCAGCAGACCACGAGATTCATAAAATCCCGTAAGTAA
* * *
39720993 AAAGTCGTGATTGTAAATCAGCAGACCACGAGATTCGTAAAATCCCGTAAGTAA
1 AAGGTCGTGATCGTAAATCAGCAGACCACGAGATTCATAAAATCCCGTAAGTAA
** * **
39721047 AAGGTCGTGATCGTAAATCAGC-GAACTGCGAGACTCATAAAATCTTGTAAGTAA
1 AAGGTCGTGATCGTAAATCAGCAG-ACCACGAGATTCATAAAATCCCGTAAGTAA
*
39721101 AAGGCCGTGATCGTAAATCAG
1 AAGGTCGTGATCGTAAATCAG
39721122 TGAACCATAA
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 111 0.99
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.22
Consensus pattern (54 bp):
AAGGTCGTGATCGTAAATCAGCAGACCACGAGATTCATAAAATCCCGTAAGTAA
Found at i:39721289 original size:357 final size:357
Alignment explanation
Indices: 39720614--39721313 Score: 865
Period size: 357 Copynumber: 2.0 Consensus size: 357
39720604 GGACTGCAAG
* * *
39720614 ATTCGTAAAATCCCGTAAGTAAAAGATCGTGATCATAAATCAACATATCACGAGATTCGTAAAAT
1 ATTCATAAAATCCCGTAAGTAAAAGATCGTGATCATAAATCAACAGACCACGAGATTCGTAAAAT
* * * * *
39720679 CTCATAAGTAAAAGGTTGTGATCATAAATCAGCGGACTGTGAGATTCATAAAATCTTGTAAGTAA
66 CCCATAAGTAAAAGGTCGTGATCATAAATCAGCGAACTGCGAGACTCATAAAATCTTGTAAGTAA
** * * *
39720744 AAGGTTGTGATCATAAATCAGCAAACCATAAGAAAGTCGAAGGTCGTGATCGTAAATCAGCAGAC
131 AAGGCCGTGATCATAAATCAGCAAACCATAAGAAAGGCGAAAGTCATGATCGTAAATCAGCAGAC
* * * * * *
39720809 TATAAGAAAGCCAAAGGTCGTGATCGTAAACCAGCAAACCATAAGAAAGCCGATGACTGTGACCG
196 CATAAGAAAGCCAAAGGTCATGATCGTAAACCAACAAACCATAAGAAAGCAGAGGACTGTGACCA
* **
39720874 TAAATCAACAGACCATAAGAAAGCCAAAGTTTGTGATCGTAAATCAACGGGTCATAAGAAAGCCG
261 TAAATCAACAGACCATAAGAAAGCCAAAGGTCATGATCGTAAATCAACGGGTCATAAGAAAGCCG
*
39720939 AAGGTCGTGGTCATAAATCAGCAAACCACGAA
326 AAGGTCGTGATCATAAATCAGCAAACCACGAA
** *
39720971 ATTCATAAAATCCCGTAAGTAAAA-AGTCGTGATTGTAAATCAGCAGACCACGAGATTCGTAAAA
1 ATTCATAAAATCCCGTAAGTAAAAGA-TCGTGATCATAAATCAACAGACCACGAGATTCGTAAAA
* *
39721035 TCCCGTAAGTAAAAGGTCGTGATCGTAAATCAGCGAACTGCGAGACTCATAAAATCTTGTAAGTA
65 TCCCATAAGTAAAAGGTCGTGATCATAAATCAGCGAACTGCGAGACTCATAAAATCTTGTAAGTA
* **
39721100 AAAGGCCGTGATCGTAAATCAGTGAACCATAAGAAAGGCGAAAGTCATGATCGTAAATCA--ATG
130 AAAGGCCGTGATCATAAATCAGCAAACCATAAGAAAGGCGAAAGTCATGATCGTAAATCAGCA-G
* * ** * *
39721163 AACCGTAAGAAAGCCGAAA-GTCATGATCGTAAATCAATGAACCGTAAGAAAGTCAGAGGTC-GT
194 -ACCATAAGAAAGCC-AAAGGTCATGATCGTAAACCAACAAACCATAAGAAAG-CAGAGGACTGT
* *** * * * *
39721226 GATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCTTAAAT-AA-GTGTACCATAAG
256 GACCATAAATCAACAGACCATAAGAAAGCCAAAGGTCATGATCGTAAATCAACGGGT--CATAAG
* *
39721289 AAAGTCGAAGGTTGTGATCATAAAT
319 AAAGCCGAAGGTCGTGATCATAAAT
39721314 TAGCGGACTA
Statistics
Matches: 289, Mismatches: 47, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
355 4 0.01
356 4 0.01
357 273 0.94
358 8 0.03
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.22
Consensus pattern (357 bp):
ATTCATAAAATCCCGTAAGTAAAAGATCGTGATCATAAATCAACAGACCACGAGATTCGTAAAAT
CCCATAAGTAAAAGGTCGTGATCATAAATCAGCGAACTGCGAGACTCATAAAATCTTGTAAGTAA
AAGGCCGTGATCATAAATCAGCAAACCATAAGAAAGGCGAAAGTCATGATCGTAAATCAGCAGAC
CATAAGAAAGCCAAAGGTCATGATCGTAAACCAACAAACCATAAGAAAGCAGAGGACTGTGACCA
TAAATCAACAGACCATAAGAAAGCCAAAGGTCATGATCGTAAATCAACGGGTCATAAGAAAGCCG
AAGGTCGTGATCATAAATCAGCAAACCACGAA
Found at i:39721298 original size:39 final size:39
Alignment explanation
Indices: 39721101--39721508 Score: 300
Period size: 39 Copynumber: 10.5 Consensus size: 39
39721091 TTGTAAGTAA
* * * *
39721101 AAGGCCGTGATCGTAAATCAGTGAACCATAAGAAAGGCG
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * * * *
39721140 AAAGTCATGATCGTAAATCAA-TGAACCGTAAGAAAGCCG
1 AAGGTCGTGATCGTAAAT-AAGTGGACCATAAGAAAGTCG
* * * *
39721179 AAAGTCATGATCGTAAATCAA-TGAACCGTAAGAAAGTC-
1 AAGGTCGTGATCGTAAAT-AAGTGGACCATAAGAAAGTCG
* *
39721217 AGAGGTCGTGATCATAAATCAGTGGACCATAAGAAAGTCG
1 A-AGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * *
39721257 AAGGTCATGATCTTAAATAAGTGTACCATAAGAAAGTCG
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * * * * *
39721296 AAGGTTGTGATCATAAATTAGCGGACTATAAGAAAGTTG
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* ** * * * *
39721335 AAGGCCGTGATAATAAATCAGTGGACCGTAAGAAAATCA
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * * *
39721374 AAGGTCGTGATCGTAAATAAGCGGACCATAAAAAAATTG
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * *** * *
39721413 AAGGTCGTGATCGTAAATTAGCGGATTGTAAAAAAGTCA
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
* * * * *** ** *
39721452 AAGATCATGATCATAAATTAGCATATTATAAAAAAGTCG
1 AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
39721491 AAGGTCGTGATCGTAAAT
1 AAGGTCGTGATCGTAAAT
39721509 CAACAAATCA
Statistics
Matches: 304, Mismatches: 61, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
38 2 0.01
39 300 0.99
40 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (39 bp):
AAGGTCGTGATCGTAAATAAGTGGACCATAAGAAAGTCG
Found at i:39721313 original size:117 final size:117
Alignment explanation
Indices: 39721095--39721430 Score: 361
Period size: 117 Copynumber: 2.9 Consensus size: 117
39721085 AAAATCTTGT
* * * * *
39721095 AAGTAAAAGGCCGTGATCGTAAATCAGTGAACCATAAGAAAGGCGAAAGTCATGATCGTAAATCA
1 AAGTAGAAGGCCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCGTAAAT-A
* * * * * *
39721160 A-TGAACCGTAAGAAAGCCGAAAGTCATGATCGTAAATCAATGAACCGTAAGA
65 AGTGAACCATAAGAAAGTCGAAGGTCGTGATCGTAAATCAACGAACCATAAGA
* *
39721212 AAGTCAG-AGGTCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCTTAAATA
1 AAGT-AGAAGGCCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCGTAAATA
* * * * * * *
39721276 AGTGTACCATAAGAAAGTCGAAGGTTGTGATCATAAATTAGCGGACTATAAGA
65 AGTGAACCATAAGAAAGTCGAAGGTCGTGATCGTAAATCAACGAACCATAAGA
* * * * * *
39721329 AAGTTGAAGGCCGTGATAATAAATCAGTGGACCGTAAGAAAATCAAAGGTCGTGATCGTAAATAA
1 AAGTAGAAGGCCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCGTAAATAA
* * * * *
39721394 GCGGACCATAAAAAAATTGAAGGTCGTGATCGTAAAT
66 GTGAACCATAAGAAAGTCGAAGGTCGTGATCGTAAAT
39721431 TAGCGGATTG
Statistics
Matches: 181, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
116 3 0.02
117 177 0.98
118 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (117 bp):
AAGTAGAAGGCCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCGTAAATAA
GTGAACCATAAGAAAGTCGAAGGTCGTGATCGTAAATCAACGAACCATAAGA
Found at i:39721327 original size:78 final size:78
Alignment explanation
Indices: 39721101--39721508 Score: 343
Period size: 78 Copynumber: 5.2 Consensus size: 78
39721091 TTGTAAGTAA
* * * * * * * * ** *
39721101 AAGGCCGTGATCGTAAATCAGTGAACCATAAGAAAGGCGAAA-GTCATGATCGTAAATCAATGAA
1 AAGGTCGTGATCGTAAATAAGTGGACCGTAAGAAAGTC-AAAGGTCGTGATCATAAATTAGCGGA
* *
39721165 CCGTAAGAAAGCCG
65 CCATAAGAAAGTCG
* * * * * *
39721179 AAAGTCATGATCGTAAATCAA-TGAACCGTAAGAAAGTCAGAGGTCGTGATCATAAATCAGTGGA
1 AAGGTCGTGATCGTAAAT-AAGTGGACCGTAAGAAAGTCAAAGGTCGTGATCATAAATTAGCGGA
39721243 CCATAAGAAAGTCG
65 CCATAAGAAAGTCG
* * * * * *
39721257 AAGGTCATGATCTTAAATAAGTGTACCATAAGAAAGTCGAAGGTTGTGATCATAAATTAGCGGAC
1 AAGGTCGTGATCGTAAATAAGTGGACCGTAAGAAAGTCAAAGGTCGTGATCATAAATTAGCGGAC
* *
39721322 TATAAGAAAGTTG
66 CATAAGAAAGTCG
* ** * * * *
39721335 AAGGCCGTGATAATAAATCAGTGGACCGTAAGAAAATCAAAGGTCGTGATCGTAAATAAGCGGAC
1 AAGGTCGTGATCGTAAATAAGTGGACCGTAAGAAAGTCAAAGGTCGTGATCATAAATTAGCGGAC
* * *
39721400 CATAAAAAAATTG
66 CATAAGAAAGTCG
* * ** * * * ** *
39721413 AAGGTCGTGATCGTAAATTAGCGGATTGTAAAAAAGTCAAAGATCATGATCATAAATTAGCATAT
1 AAGGTCGTGATCGTAAATAAGTGGACCGTAAGAAAGTCAAAGGTCGTGATCATAAATTAGCGGAC
* *
39721478 TATAAAAAAGTCG
66 CATAAGAAAGTCG
39721491 AAGGTCGTGATCGTAAAT
1 AAGGTCGTGATCGTAAAT
39721509 CAACAAATCA
Statistics
Matches: 269, Mismatches: 58, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
77 4 0.01
78 264 0.98
79 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (78 bp):
AAGGTCGTGATCGTAAATAAGTGGACCGTAAGAAAGTCAAAGGTCGTGATCATAAATTAGCGGAC
CATAAGAAAGTCG
Found at i:39721468 original size:117 final size:117
Alignment explanation
Indices: 39721095--39721469 Score: 340
Period size: 117 Copynumber: 3.2 Consensus size: 117
39721085 AAAATCTTGT
* * * * **
39721095 AAGTAAAAGGCCGTGATCGTAAATCAGTGAACCATAAGAAAGGCGAAA-GTCATGATCGTAAATC
1 AAGTCAAAGGTCGTGATCATAAATCAGTGGACCATAAGAAAATC-AAAGGTCATGATCGTAAAT-
* * * * ** * * * * ** * *
39721159 AA-TGAACCGTAAGAAAGCCGAAAGTCATGATCGTAAATCAATGAACCGTAAGA
64 AAGCGGACCATAAAAAAATCGAAGGTCGTGATCATAAATTAGCGGACTGTAAGA
* * * *
39721212 AAGTCAGAGGTCGTGATCATAAATCAGTGGACCATAAGAAAGTCGAAGGTCATGATCTTAAATAA
1 AAGTCAAAGGTCGTGATCATAAATCAGTGGACCATAAGAAAATCAAAGGTCATGATCGTAAATAA
* * * * * *
39721277 GTGTACCATAAGAAAGTCGAAGGTTGTGATCATAAATTAGCGGACTATAAGA
66 GCGGACCATAAAAAAATCGAAGGTCGTGATCATAAATTAGCGGACTGTAAGA
** * * * *
39721329 AAGTTGAAGGCCGTGATAATAAATCAGTGGACCGTAAGAAAATCAAAGGTCGTGATCGTAAATAA
1 AAGTCAAAGGTCGTGATCATAAATCAGTGGACCATAAGAAAATCAAAGGTCATGATCGTAAATAA
* * * *
39721394 GCGGACCATAAAAAAATTGAAGGTCGTGATCGTAAATTAGCGGATTGTAAAA
66 GCGGACCATAAAAAAATCGAAGGTCGTGATCATAAATTAGCGGACTGTAAGA
* *
39721446 AAGTCAAAGATCATGATCATAAAT
1 AAGTCAAAGGTCGTGATCATAAAT
39721470 TAGCATATTA
Statistics
Matches: 209, Mismatches: 47, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
116 4 0.02
117 205 0.98
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.22
Consensus pattern (117 bp):
AAGTCAAAGGTCGTGATCATAAATCAGTGGACCATAAGAAAATCAAAGGTCATGATCGTAAATAA
GCGGACCATAAAAAAATCGAAGGTCGTGATCATAAATTAGCGGACTGTAAGA
Found at i:39736128 original size:41 final size:41
Alignment explanation
Indices: 39736083--39736188 Score: 167
Period size: 41 Copynumber: 2.6 Consensus size: 41
39736073 GGTTTTAAAA
39736083 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* *
39736124 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
* * *
39736165 CCTAACAAGCTAAGTGCCAGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGAA
39736189 TCTGTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
Found at i:39738523 original size:24 final size:25
Alignment explanation
Indices: 39738477--39738523 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
39738467 TTACGTGCTT
*
39738477 ATTTTTAATTAGTTTTAAATAATGC
1 ATTTTTAATTAGTTCTAAATAATGC
*
39738502 ATTTTTAATTA-TTCTAATTAAT
1 ATTTTTAATTAGTTCTAAATAAT
39738524 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (25 bp):
ATTTTTAATTAGTTCTAAATAATGC
Found at i:39740509 original size:20 final size:20
Alignment explanation
Indices: 39740479--39740516 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39740469 TGATCCATGT
39740479 AATTAAAATGTATGGTATAAG
1 AATTAAAATGT-TGGTATAAG
39740500 AATT-AAATGTTGGTATA
1 AATTAAAATGTTGGTATA
39740517 TGGCATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (20 bp):
AATTAAAATGTTGGTATAAG
Found at i:39742457 original size:18 final size:18
Alignment explanation
Indices: 39742431--39742479 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
39742421 CAAATATGCC
39742431 CAAGCCCAAACTAATAAA
1 CAAGCCCAAACTAATAAA
* * * *
39742449 TAGGCCCAAACCATTAAA
1 CAAGCCCAAACTAATAAA
39742467 CAAGCCCAAACTA
1 CAAGCCCAAACTA
39742480 TCCCAAGCCC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.49, C:0.31, G:0.08, T:0.12
Consensus pattern (18 bp):
CAAGCCCAAACTAATAAA
Found at i:39743957 original size:12 final size:13
Alignment explanation
Indices: 39743929--39743957 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39743919 TTTGCAAATT
39743929 TACTTGTATATTA
1 TACTTGTATATTA
39743942 TACTTGTATA-TA
1 TACTTGTATATTA
39743954 TACT
1 TACT
39743958 GGCAATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (13 bp):
TACTTGTATATTA
Found at i:39745653 original size:13 final size:13
Alignment explanation
Indices: 39745635--39745659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39745625 AAGAGATTTC
39745635 TTTTCTAGTAAAG
1 TTTTCTAGTAAAG
39745648 TTTTCTAGTAAA
1 TTTTCTAGTAAA
39745660 AAAAATGAAC
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:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
TTTTCTAGTAAAG
Found at i:39745730 original size:19 final size:20
Alignment explanation
Indices: 39745693--39745732 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
39745683 TCTTTTCGCA
* *
39745693 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
39745713 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
39745732 T
1 T
39745733 AAACACGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:39747666 original size:19 final size:20
Alignment explanation
Indices: 39747626--39747666 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39747616 GCAAATGTTC
39747626 TTTCATTCTTTACAATTTTT
1 TTTCATTCTTTACAATTTTT
39747646 TTTCATTCTTT-CAGATTTTT
1 TTTCATTCTTTACA-ATTTTT
39747666 T
1 T
39747667 CTGCCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.17, C:0.15, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTACAATTTTT
Found at i:39748795 original size:42 final size:42
Alignment explanation
Indices: 39748734--39748833 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
39748724 GAAAAGGGCG
* *
39748734 GCTCAAATATTGATTAGAATGGGGTATGAGATTATCGAAGTA
1 GCTCAAATATTGATCAGAATGGGGCATGAGATTATCGAAGTA
* * *
39748776 GCTCAAATATTGATCAGAATGTGGCATGAGATTATTGGAGTA
1 GCTCAAATATTGATCAGAATGGGGCATGAGATTATCGAAGTA
*
39748818 GCTCAAATACTGATCA
1 GCTCAAATATTGATCA
39748834 TCATGAGGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (42 bp):
GCTCAAATATTGATCAGAATGGGGCATGAGATTATCGAAGTA
Found at i:39748844 original size:42 final size:42
Alignment explanation
Indices: 39748734--39748845 Score: 134
Period size: 42 Copynumber: 2.7 Consensus size: 42
39748724 GAAAAGGGCG
* * * *
39748734 GCTCAAATATTGATTAGAATGGGGTATGAGATTATCGAAGTA
1 GCTCAAATACTGATCAGAATGAGGCATGAGATTATCGAAGTA
* * * *
39748776 GCTCAAATATTGATCAGAATGTGGCATGAGATTATTGGAGTA
1 GCTCAAATACTGATCAGAATGAGGCATGAGATTATCGAAGTA
**
39748818 GCTCAAATACTGATCATCATGAGGCATG
1 GCTCAAATACTGATCAGAATGAGGCATG
39748846 CAGTGGTCTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (42 bp):
GCTCAAATACTGATCAGAATGAGGCATGAGATTATCGAAGTA
Found at i:39750014 original size:45 final size:45
Alignment explanation
Indices: 39749946--39751228 Score: 691
Period size: 44 Copynumber: 28.2 Consensus size: 45
39749936 GTGGAGTAGC
* * ** *
39749946 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGA-
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** **
39749990 AAGCAGATCTTGTCTTCATGTACTGG-CATGAAGTAGATCAAAGAT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* *
39750035 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA-
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** *
39750079 AAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * * *
39750124 AAAAGATCTTG-CATTCCCATACTGGTGGTGAAGCAGATCGAAGGAAA
1 AACAGATCTTGTC-TTCACATACTGGTGGTGAAGTAGATC-AAAG-AT
* ** * *
39750171 AAGCAGATTTTGTCTTCATGTATTGGT-GTGAAGTAGATCAAAGAC
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * *
39750216 AACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAG
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** * * *
39750261 AACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAT
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * * * * * * *
39750305 TATAGATCTTATC-TC-CCTAAGC-AGTAGTGGAGCAGATCGAAGAT
1 AACAGATCTTGTCTTCACAT-A-CTGGTGGTGAAGTAGATCAAAGAT
** * * * ** * **
39750349 GGCAGATTTTACCTCTCTGAGGC-TACAGTGGACTACATTGAAGCCAGTAATTCTATCGA-
1 AACAGATCTT--GTCT-TCA--CATAC--TGG--T--GGTGAAG-TAG--A-TC-AAAGAT
* ** * * * ** * * * * *
39750408 AGA-AAATAGATAT-TGTCTTCAT-GTACTGGCG-TGAAG-T-AGATCAAAG
1 A-ACAGAT-CTTGTCT-TC-ACATACTGGTGGTGAAGTAGATCA-A--AGAT
* * ** *
39750454 ATAACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGA-
1 A--ACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* ** * *
39750500 AAGCAGATCTTATCTTCATGTACTGG-CGTGAAATAGATCAAAGAT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* ** *
39750545 AACAGATCTTGTCTTCCCATACTGGTGACGAAGTAAATCAAAGAT
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * *
39750590 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAA
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* ** *
39750635 AACAGATTTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * ** *
39750679 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCAAAGAA
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** * *
39750724 AACAGATCTTGTCTTCATGTACTAG-CGTGAAGTAGATCAAAGAT
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * **
39750768 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAA-A-
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC-AAAGAT
* ** *
39750812 AAGTAGATCTTGTCTTCATGTACTGGT-GTGAAGTAGATCAAAGGT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * *
39750857 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAA
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC-AA-AGAT
** *
39750904 AAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * **
39750949 AACAGATTTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGA-
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** *
39750993 AAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
1 AA-CAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * * *
39751038 AACAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAA
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATC-AA--AGAT
* ** * * *
39751086 AATAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGAC
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
* * * * * *
39751130 AGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAG
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
** * * * *
39751175 AACAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAATAT
1 AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
*
39751219 TACAGATCTT
1 AACAGATCTT
39751229 ATCTCCCTAA
Statistics
Matches: 927, Mismatches: 242, Indels: 140
0.71 0.18 0.11
Matches are distributed among these distances:
42 2 0.00
43 8 0.01
44 370 0.40
45 370 0.40
46 24 0.03
47 52 0.06
48 67 0.07
49 5 0.01
50 2 0.00
51 2 0.00
52 1 0.00
53 1 0.00
54 1 0.00
55 5 0.01
56 4 0.00
57 3 0.00
58 2 0.00
59 5 0.01
60 3 0.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (45 bp):
AACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCAAAGAT
Found at i:39750097 original size:89 final size:89
Alignment explanation
Indices: 39749946--39751228 Score: 1137
Period size: 89 Copynumber: 14.1 Consensus size: 89
39749936 GTGGAGTAGC
* **
39749946 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGAAAGCAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
39750011 ACTGGCATGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
39750035 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
39750100 ACTGGCGTGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* * *
39750124 AAAAGATCTTG-CATTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAAGCAGATTTTGTCTTC
1 AACAGATCTTGTC-TTCCCATACTGGTGGTGAAGTAGATCGAA-G--AAAGCAGATCTTGTCTTC
* * *
39750188 ATGTATTGGTGTGAAGTAGATCAAAGAC
62 ATGTACTGGCGTGAAGTAGATCAAAGAT
* * *
39750216 AACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCAAAGAGAA-CAGATCTTGTCTTCATG
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATG
* *
39750280 TATTGGCGTGAAGTAGATCGAAGAT
65 TACTGGCGTGAAGTAGATCAAAGAT
* * * * * * * ** * **
39750305 TATAGATCTTATC-TCCC-TAAGC-AGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCTC-
1 AACAGATCTTGTCTTCCCAT-A-CTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCT-TCA
* **
39750366 TG-A--GGC-T-ACAGTGGACTACATTGA-
63 TGTACTGGCGTGA-AGTAGA-T-CAAAGAT
* ** ** * * * ** *** * *
39750390 AGCCAG-TAAT-TCTATCGAAGAAAATAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAA
1 A-ACAGATCTTGTCT-TC--CCATACT-GGTGGTGAAGT-A-G-A-T--C--GAAG-AAAGC--A
* * * * * ** *
39750453 GATAAC-AGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGA-
50 GAT--CTTG-TC-T-TCAT---GTACTGG-CGTGAAGTAGATCAAAGAT
* *** * * * **
39750500 AAGCAGATCTTATCTTCATGTACTGG-CGTGAAATAGATCAAAGATAA-CAGATCTTGTCTTCCC
1 AA-CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCAT
* * * *
39750563 ATACTGGTGACGAAGTAAATCAAAGAT
64 GTACTGGCG-TGAAGTAGATCAAAGAT
* * *
39750590 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATTTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
39750655 ACTGGCGTGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* ** * *
39750679 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCAAAGAAAACAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
*
39750744 ACTAGCGTGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* ** * *
39750768 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAAAAAGTAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
* *
39750833 ACTGGTGTGAAGTAGATCAAAGGT
66 ACTGGCGTGAAGTAGATCAAAGAT
*
39750857 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAAAAGCAGATCTTGTCTTCA
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAG---AAAGCAGATCTTGTCTTCA
39750922 TGTACTGGCGTGAAGTAGATCAAAGAT
63 TGTACTGGCGTGAAGTAGATCAAAGAT
* *
39750949 AACAGATTTTGTCTTCCCATACTGGTGGTGAAGTAGATTGAAGAAAGCAGATCTTGTCTTCATGT
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
39751014 ACTGGCGTGAAGTAGATCAAAGAT
66 ACTGGCGTGAAGTAGATCAAAGAT
* * **
39751038 AACAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAAATAGATCTTGTCTTCA
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAA-G--AAAGCAGATCTTGTCTTCA
* *
39751103 TGTATTGGCGTGAAGTAGATCAAAGAC
63 TGTACTGGCGTGAAGTAGATCAAAGAT
* * *
39751130 AGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAGAA-CAGATCTTGTCTTCATG
1 AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCATG
* * *
39751194 TATTGGCGTGAAGTAGATCGAATAT
65 TACTGGCGTGAAGTAGATCAAAGAT
*
39751219 TACAGATCTT
1 AACAGATCTT
39751229 ATCTCCCTAA
Statistics
Matches: 985, Mismatches: 147, Indels: 124
0.78 0.12 0.10
Matches are distributed among these distances:
83 1 0.00
84 8 0.01
85 6 0.01
86 7 0.01
87 2 0.00
88 35 0.04
89 571 0.58
90 43 0.04
91 3 0.00
92 242 0.25
93 3 0.00
94 3 0.00
95 2 0.00
96 4 0.00
97 4 0.00
98 4 0.00
99 4 0.00
100 4 0.00
101 1 0.00
102 1 0.00
103 4 0.00
104 2 0.00
105 1 0.00
106 1 0.00
107 3 0.00
108 2 0.00
109 3 0.00
110 9 0.01
111 5 0.01
112 6 0.01
113 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGT
ACTGGCGTGAAGTAGATCAAAGAT
Found at i:39750253 original size:181 final size:178
Alignment explanation
Indices: 39749946--39751228 Score: 1241
Period size: 181 Copynumber: 7.1 Consensus size: 178
39749936 GTGGAGTAGC
* *
39749946 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAA-G-AAAGCAGATCTTGTCTTCAT
1 AACAGATCTTG-CTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAGCAGATCTTGTCTTCAT
*
39750009 GTACTGGCATGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
65 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
39750074 GAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
130 GAAGAAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
* *
39750124 AAAAGATCTTGCATTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAAGCAGATTTTGTCTTCA
1 AACAGATCTTGC-TTCCCATACTGGTGGTGAAGCAGATCGAAGG-AAAAGCAGATCTTGTCTTCA
* * * * *
39750189 TGTATTGGTGTGAAGTAGATCAAAGACAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGAT
64 TGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
* * *
39750254 CAAAGAGAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT
129 CGAAGA-AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
* * * * * * ** * *
39750305 TATAGATCTT-ATCTCCC-TAAGC-AGTAGTGGAGCAGATCGAA-G-ATGGCAGATTTTACCTCT
1 AACAGATCTTGCT-TCCCAT-A-CTGGTGGTGAAGCAGATCGAAGGAAAAGCAGATCTT--GTCT
* * * * ** * ** * *
39750365 CTGAGGCTACAGTGGACTACATTGAAGCCAGTAATTCTATCGA-AGA-AAATAGATAT-TGTCTT
61 -TCATG-TAC--TGG----C-GTGAAG-TAG--A-TC-AAAGATA-ACAGAT-CTTGTCT-TC-C
* ** * *** * * **
39750427 CAT-GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAACA
108 CATACTGGT-G-GTGAAGTAGATCGAAGA-AACAGATCTTGTCTTCATGTACTGG-CGTGAAGTA
*
39750491 GATCGAAGA-
169 GATCAAAGAT
* *** * ** * * *
39750500 AAGCAGATCTTATCTTCATGTACTGG-CGTGAAATAGATC-AAAGATAA-CAGATCTTGTCTTCC
1 AA-CAGATCTT-GCTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAGCAGATCTTGTCTTCA
** * * * *
39750562 CATACTGGTGACGAAGTAAATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
64 TGTACTGGCG-TGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGA
*
39750627 TCGAAGAAAACAGATTTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
128 TCGAAG-AAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
* * *
39750679 AACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATC-AAAGAAAA-CAGATCTTGTCTTCAT
1 AACAGATCTTG-CTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAGCAGATCTTGTCTTCAT
* * **
39750742 GTACTAGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATC
65 GTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
* * * *
39750807 GAAAAAAGTAGATCTTGTCTTCATGTACTGGTGTGAAGTAGATCAAAGGT
130 GAAGAAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
* * *
39750857 AACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAAAAGCAGATCTTGTCTTCA
1 AACAGATCTTG-CTTCCCATACTGGTGGTGAAGCAGATCGAAG-GAAAAGCAGATCTTGTCTTCA
*
39750922 TGTACTGGCGTGAAGTAGATCAAAGATAACAGATTTTGTCTTCCCATACTGGTGGTGAAGTAGAT
64 TGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
*
39750987 TGAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
129 CGAAGAAA-CAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
**
39751038 AACAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAAATAGATCTTGTCTTCA
1 AACAGATCTTG-CTTCCCATACTGGTGGTGAAGCAGATCGAAGG-AAAAGCAGATCTTGTCTTCA
* * * * *
39751103 TGTATTGGCGTGAAGTAGATCAAAGACAGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGAT
64 TGTACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGAT
* * *
39751168 CGAAGAGAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAATAT
129 CGAAGA-AACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
*
39751219 TACAGATCTT
1 AACAGATCTT
39751229 ATCTCCCTAA
Statistics
Matches: 905, Mismatches: 147, Indels: 103
0.78 0.13 0.09
Matches are distributed among these distances:
177 14 0.02
178 198 0.22
179 83 0.09
180 33 0.04
181 434 0.48
182 11 0.01
183 4 0.00
185 1 0.00
186 4 0.00
188 5 0.01
189 2 0.00
190 3 0.00
191 1 0.00
192 10 0.01
193 10 0.01
194 7 0.01
195 40 0.04
196 39 0.04
197 4 0.00
198 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (178 bp):
AACAGATCTTGCTTCCCATACTGGTGGTGAAGCAGATCGAAGGAAAAGCAGATCTTGTCTTCATG
TACTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCG
AAGAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT
Found at i:39751364 original size:44 final size:44
Alignment explanation
Indices: 39751316--39751507 Score: 140
Period size: 44 Copynumber: 4.4 Consensus size: 44
39751306 CCAGTAATTA
39751316 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
** * ** ** ** *
39751360 TATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTT
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
* * * ** * *
39751404 TACCTCCCTGAGGTTA-CAGT-GAAGTACATTGAAG-CCA-ATATTT
1 TATCTCCCTG-GG-CAGCAGTGGAA-TAGATTGAAGATTACAGATCT
* *
39751447 CTATCTCCCTGGGCAACAGTGGAATAGATTGAAGAATACAGATCT
1 -TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
*
39751492 TATCTCCCTAGGCAGC
1 TATCTCCCTGGGCAGC
39751508 GAAGTAGATC
Statistics
Matches: 107, Mismatches: 33, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
42 1 0.01
43 20 0.19
44 71 0.66
45 14 0.13
46 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
Found at i:39751377 original size:132 final size:132
Alignment explanation
Indices: 39751207--39751506 Score: 501
Period size: 132 Copynumber: 2.3 Consensus size: 132
39751197 TGGCGTGAAG
* * *
39751207 TAGATCGAATATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGCGGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGCAGATTT
* * *
39751272 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTATATCTCCCTGGGCAGCAGTGG
66 TACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAATAATTATATCTCCCTGGGCAACAGTGG
39751337 AA
131 AA
*
39751339 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTT
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGCAGATTT
* *
39751404 TACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAATATTTCTATCTCCCTGGGCAACAGTGG
66 TACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAATAATTATATCTCCCTGGGCAACAGTGG
39751469 AA
131 AA
* *
39751471 TAGATTGAAGAATACAGATCTTATCTCCCTAGGCAG
1 TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
39751507 CGAAGTAGAT
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 157 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (132 bp):
TAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGCAGATTT
TACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAATAATTATATCTCCCTGGGCAACAGTGG
AA
Found at i:39751690 original size:44 final size:44
Alignment explanation
Indices: 39751594--39751750 Score: 164
Period size: 44 Copynumber: 3.7 Consensus size: 44
39751584 AAAATGGCGA
* *
39751594 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTAAAGATAATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAA-ATCACAG
* *
39751638 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
* * * ***
39751682 ATCTTATCTCTCTGAAGTTGCAGAGG-GCAGA-TCGCATC-CAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
39751723 -TCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
39751751 AGACAGAACT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
40 23 0.24
41 5 0.05
42 3 0.03
43 9 0.09
44 56 0.58
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
Found at i:39754513 original size:21 final size:22
Alignment explanation
Indices: 39754483--39754538 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
39754473 CCTTGGTACT
39754483 TCAAAAA-TTTTGAAAATTTTA
1 TCAAAAATTTTTGAAAATTTTA
* *
39754504 TCAAAGATTTTTGAAAGTTTTTA
1 TCAAAAATTTTTGAAA-ATTTTA
*
39754527 TTAGAAAATTTT
1 TCA-AAAATTTT
39754539 ATCAAAGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 6 0.21
22 8 0.29
23 7 0.25
24 7 0.25
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (22 bp):
TCAAAAATTTTTGAAAATTTTA
Found at i:39754551 original size:12 final size:12
Alignment explanation
Indices: 39754498--39754551 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
39754488 AATTTTGAAA
39754498 ATTTTATCAAAG
1 ATTTTATCAAAG
*
39754510 ATTTT-TGAAAG
1 ATTTTATCAAAG
* * *
39754521 TTTTTATTAGAAA
1 ATTTTATCA-AAG
39754534 ATTTTATCAAAG
1 ATTTTATCAAAG
39754546 ATTTTA
1 ATTTTA
39754552 AAAGTTTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
11 9 0.27
12 15 0.45
13 9 0.27
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (12 bp):
ATTTTATCAAAG
Found at i:39756954 original size:10 final size:10
Alignment explanation
Indices: 39756939--39756976 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
39756929 TTCTTGATGT
39756939 ATTTTATAAA
1 ATTTTATAAA
39756949 ATTTTA-ATAA
1 ATTTTATA-AA
*
39756959 TTTTTATAAA
1 ATTTTATAAA
39756969 ATTTTATA
1 ATTTTATA
39756977 TTTTTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:39756965 original size:20 final size:18
Alignment explanation
Indices: 39756940--39756998 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 18
39756930 TCTTGATGTA
39756940 TTTTATAAAATTTTAATAAT
1 TTTTATAAAATTTT-AT-AT
39756960 TTTTATAAAATTTTATAT
1 TTTTATAAAATTTTATAT
* *
39756978 TTTTAT-GATTTTTATAT
1 TTTTATAAAATTTTATAT
39756995 TTTT
1 TTTT
39756999 TTTTCTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 13 0.35
18 8 0.22
19 2 0.05
20 14 0.38
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTATAAAATTTTATAT
Found at i:39757046 original size:26 final size:26
Alignment explanation
Indices: 39757007--39757058 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39756997 TTTTTTCTAA
39757007 TTTTAATAAAATTTAA-ATATTTTTAT
1 TTTTAATAAAATTTAATA-ATTTTTAT
* *
39757033 TTTTATTAATATTTAATAATTTTTAT
1 TTTTAATAAAATTTAATAATTTTTAT
39757059 AACTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTAATAAAATTTAATAATTTTTAT
Found at i:39757056 original size:57 final size:57
Alignment explanation
Indices: 39756948--39757056 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
39756938 TATTTTATAA
** * * *
39756948 AATTTTAATAATTTTTATAAAATTTTATATTTTTATGATTTTTATATTTTTTTTTCT
1 AATTTTAATAAAATTTATAAAATTTTATATTTTTATAATTTTAATAATTTTTTTTCT
*
39757005 AATTTTAATAAAATTTA-AATATTTT-TATTTTTATTAATATTTAATAATTTTT
1 AATTTTAATAAAATTTATAAAATTTTATATTTTTA-TAAT-TTTAATAATTTTT
39757057 ATAACTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
55 8 0.18
56 10 0.23
57 26 0.59
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (57 bp):
AATTTTAATAAAATTTATAAAATTTTATATTTTTATAATTTTAATAATTTTTTTTCT
Found at i:39757065 original size:10 final size:9
Alignment explanation
Indices: 39756948--39757090 Score: 66
Period size: 9 Copynumber: 15.8 Consensus size: 9
39756938 TATTTTATAA
*
39756948 AATTTTAAT
1 AATTTTTAT
39756957 AATTTTTAT
1 AATTTTTAT
*
39756966 AAAATTTTAT
1 -AATTTTTAT
39756976 -ATTTTTAT
1 AATTTTTAT
*
39756984 GATTTTTAT
1 AATTTTTAT
* *
39756993 ATTTTTTTTTCT
1 A---ATTTTTAT
*
39757005 AATTTTAAT
1 AATTTTTAT
**
39757014 AAAATTTA-
1 AATTTTTAT
39757022 AATATTTT-T
1 AAT-TTTTAT
39757031 -ATTTTTATT
1 AATTTTTA-T
*
39757040 AATATTTAAT
1 AAT-TTTTAT
39757050 AATTTTTAT
1 AATTTTTAT
*
39757059 AACTTTTATT
1 AATTTTTA-T
*
39757069 GATTTTTAT
1 AATTTTTAT
39757078 --TTTTTAT
1 AATTTTTAT
39757085 -ATTTTT
1 AATTTTT
39757091 TTTGTCACAT
Statistics
Matches: 102, Mismatches: 19, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
7 11 0.11
8 16 0.16
9 43 0.42
10 21 0.21
11 4 0.04
12 7 0.07
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
AATTTTTAT
Found at i:39770931 original size:30 final size:31
Alignment explanation
Indices: 39770885--39770942 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
39770875 ATTTTTATAT
* *
39770885 TAAAATATTTAAAATATTTTTTTATATTTTC
1 TAAAATATTAAAAATATTATTTTATATTTTC
39770916 TAAAA-ATTAAAAATATTATTTTATATT
1 TAAAATATTAAAAATATTATTTTATATT
39770943 AAATCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
TAAAATATTAAAAATATTATTTTATATTTTC
Found at i:39773525 original size:25 final size:24
Alignment explanation
Indices: 39773484--39773531 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
39773474 TTATAAATTA
* *
39773484 GAAAAATATCTTTAGAAATTTTTT
1 GAAAAATATCTTCAGAAAATTTTT
*
39773508 GAAATAATCTCTTCAGAAAATTTT
1 GAAA-AATATCTTCAGAAAATTTT
39773532 CTCTCAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (24 bp):
GAAAAATATCTTCAGAAAATTTTT
Found at i:39773769 original size:62 final size:63
Alignment explanation
Indices: 39773642--39773822 Score: 230
Period size: 62 Copynumber: 2.9 Consensus size: 63
39773632 AATCACTTTA
* * * *
39773642 ATATTAAATTAATATAATATTTATC-T-ATATATAAACATTATATTATTTTAATA--AGATTT
1 ATATTAAATTAATATAATATTTATCTTGATAGATAAACATTATATTAATTTAATATTAAATCT
*
39773701 AATATTAAATTAATATAATATTTATCTTGATAGATAAATATTATATTAATTTAATATTAAATCT
1 -ATATTAAATTAATATAATATTTATCTTGATAGATAAACATTATATTAATTTAATATTAAATCT
* * *
39773765 -TATTAAAATAATATAATGTTTATCTTG-TAGATAAACATTAAATTGAATTTAATATTAA
1 ATATTAAATTAATATAATATTTATCTTGATAGATAAACATTATATT-AATTTAATATTAA
39773823 GATAACCACT
Statistics
Matches: 107, Mismatches: 9, Indels: 8
0.86 0.07 0.06
Matches are distributed among these distances:
60 25 0.23
61 16 0.15
62 62 0.58
64 4 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (63 bp):
ATATTAAATTAATATAATATTTATCTTGATAGATAAACATTATATTAATTTAATATTAAATCT
Found at i:39776339 original size:40 final size:40
Alignment explanation
Indices: 39776256--39776558 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
39776246 TTGAATGCTG
* * * * * *
39776256 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
39776296 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
39776336 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
39776376 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
39776416 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
39776456 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
39776496 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
39776535 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39776559 TGAACGAGGA
Statistics
Matches: 241, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 35 0.15
40 198 0.82
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:39784329 original size:40 final size:40
Alignment explanation
Indices: 39784246--39784548 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
39784236 TTGAATGCTG
* * * * * *
39784246 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
39784286 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
39784326 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
39784366 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
39784406 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
39784446 TCCGAGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
39784486 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
39784525 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
39784549 TGAACGAGGA
Statistics
Matches: 239, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
39 35 0.15
40 196 0.82
41 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:39789328 original size:13 final size:13
Alignment explanation
Indices: 39789310--39789356 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
39789300 TCTGAAACTT
*
39789310 TGTTTTCAATATA
1 TGTTTTAAATATA
* *
39789323 TGTTTTTAAGATA
1 TGTTTTAAATATA
39789336 TGATTTTAAATATA
1 TG-TTTTAAATATA
39789350 TGTTTTA
1 TGTTTTA
39789357 CGCCTGCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (13 bp):
TGTTTTAAATATA
Found at i:39789423 original size:14 final size:13
Alignment explanation
Indices: 39789377--39789426 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
39789367 TAAGCGAGCA
39789377 TATG-TTTT-AAG
1 TATGTTTTTAAAG
39789388 ATATGTTTTTAAAG
1 -TATGTTTTTAAAG
39789402 TATGGTTTTGTAAAG
1 TAT-GTTTT-TAAAG
*
39789417 TGTGTTTTTA
1 TATGTTTTTA
39789427 GGCACTTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 4 0.12
13 9 0.27
14 13 0.39
15 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.20, T:0.54
Consensus pattern (13 bp):
TATGTTTTTAAAG
Found at i:39797020 original size:20 final size:19
Alignment explanation
Indices: 39796981--39797020 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
39796971 AAATAGTGAG
*
39796981 AATTTATTTTCTGAGTATA
1 AATTTATTTTCTGAGAATA
*
39797000 AATTCTATTTTCTGGGAATA
1 AATT-TATTTTCTGAGAATA
39797020 A
1 A
39797021 CAATTCTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTTATTTTCTGAGAATA
Found at i:39807684 original size:12 final size:12
Alignment explanation
Indices: 39807669--39807699 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
39807659 GATGAAAATG
39807669 TAAATAAAGAAA
1 TAAATAAAGAAA
39807681 TAAATAAAGAAA
1 TAAATAAAGAAA
*
39807693 TGAATAA
1 TAAATAA
39807700 GATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (12 bp):
TAAATAAAGAAA
Found at i:39807724 original size:2 final size:2
Alignment explanation
Indices: 39807719--39807752 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
39807709 AAGGTAAAAG
* *
39807719 AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39807753 GCATAGAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39807822 original size:30 final size:32
Alignment explanation
Indices: 39807778--39807863 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 32
39807768 AAGATAAGAA
*
39807778 ATACGTATAAGTATATATATGTTAGCAAAAATAA-
1 ATACGTAT--GTATATATATATTA-CAAAAATAAT
*
39807812 A-A-GTATGTATATAGATATATTATAAAAATAAT
1 ATACGTATGTATAT--ATATATTACAAAAATAAT
39807844 ATACGTATGTATATATATAT
1 ATACGTATGTATATATATAT
39807864 GTATGTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
30 6 0.13
31 8 0.18
32 18 0.40
33 2 0.04
34 11 0.24
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.37
Consensus pattern (32 bp):
ATACGTATGTATATATATATTACAAAAATAAT
Found at i:39808148 original size:3 final size:3
Alignment explanation
Indices: 39808134--39808214 Score: 60
Period size: 3 Copynumber: 27.3 Consensus size: 3
39808124 GAATGAGTAG
* *
39808134 ATA ATT ATA ATA ATA ATA A-A GTA AGTA ATA ATA ATA A-A TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -ATA ATA
* * * * *
39808179 CTA ATA ATA GTA ATA GTA GTA GTA ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
39808215 ATGAAAGGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.06
3 55 0.87
4 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39808164 original size:18 final size:17
Alignment explanation
Indices: 39808140--39808193 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
39808130 GTAGATAATT
39808140 ATAATAATAATAAAGTA
1 ATAATAATAATAAAGTA
39808157 AGTAATAATAATAAA-T-
1 A-TAATAATAATAAAGTA
*
39808173 ATAATACTAATAATAGTA
1 ATAATAATAATAA-AGTA
39808191 ATA
1 ATA
39808194 GTAGTAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 2 0.06
17 3 0.09
18 16 0.50
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (17 bp):
ATAATAATAATAAAGTA
Found at i:39809309 original size:15 final size:17
Alignment explanation
Indices: 39809289--39809326 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
39809279 TACAGTGTAC
39809289 GGAGGCG-TGTG-GCGT
1 GGAGGCGTTGTGCGCGT
39809304 GGAGGCGTTGTGCGCGT
1 GGAGGCGTTGTGCGCGT
39809321 GCGAGG
1 G-GAGG
39809327 GCAGAGGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.35
16 4 0.20
17 5 0.25
18 4 0.20
ACGTcount: A:0.08, C:0.16, G:0.58, T:0.18
Consensus pattern (17 bp):
GGAGGCGTTGTGCGCGT
Found at i:39816260 original size:17 final size:18
Alignment explanation
Indices: 39816240--39816278 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39816230 TGGATTACAC
39816240 GGGT-GTGTAGGCCACAT
1 GGGTCGTGTAGGCCACAT
*
39816257 GGGTGCGTGTGGGCCACAT
1 GGGT-CGTGTAGGCCACAT
39816276 GGG
1 GGG
39816279 CTGCCCAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
19 15 0.79
ACGTcount: A:0.13, C:0.18, G:0.49, T:0.21
Consensus pattern (18 bp):
GGGTCGTGTAGGCCACAT
Found at i:39816697 original size:25 final size:28
Alignment explanation
Indices: 39816668--39816719 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
39816658 TATATTAGTA
39816668 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
39816693 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
39816720 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:39818662 original size:41 final size:41
Alignment explanation
Indices: 39818617--39818802 Score: 327
Period size: 41 Copynumber: 4.5 Consensus size: 41
39818607 AACTTTAAGT
39818617 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
39818658 CTAGCAGGCTACGTGCCGGTGATCTGAATCAAGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
39818699 CTAGCAGGCTACGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
39818740 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
*
39818781 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTACGTGCCGGTGA
39818803 ATATGTTAAA
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:39820736 original size:13 final size:13
Alignment explanation
Indices: 39820720--39820744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39820710 GTCTGTGAAA
39820720 AAATACTTTTGAG
1 AAATACTTTTGAG
39820733 AAATACTTTTGA
1 AAATACTTTTGA
39820745 AAAGTTTGGT
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
AAATACTTTTGAG
Found at i:39829848 original size:24 final size:23
Alignment explanation
Indices: 39829816--39829883 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
39829806 GATGTTTAGC
39829816 CTTTCACCTTTCATCTTCCTTAAA
1 CTTTCACCTTTCATCTTCCTT-AA
**
39829840 CTTTCACCTTTTGTCTTCCTTAA
1 CTTTCACCTTTCATCTTCCTTAA
*
39829863 CTCTTCACATTTCATC-TCCTT
1 CT-TTCACCTTTCATCTTCCTT
39829884 GTAATCCCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
23 9 0.24
24 29 0.76
ACGTcount: A:0.16, C:0.34, G:0.01, T:0.49
Consensus pattern (23 bp):
CTTTCACCTTTCATCTTCCTTAA
Found at i:39836204 original size:27 final size:26
Alignment explanation
Indices: 39836174--39836225 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39836164 TTAAAATAAA
*
39836174 AAGGTTAATGAATAGAGTTCCTGTCAC
1 AAGGTTAATG-ACAGAGTTCCTGTCAC
* *
39836201 AAGGTTATTGCCAGAGTTCCTGTCA
1 AAGGTTAATGACAGAGTTCCTGTCA
39836226 ATCACAGCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (26 bp):
AAGGTTAATGACAGAGTTCCTGTCAC
Found at i:39838400 original size:23 final size:23
Alignment explanation
Indices: 39838335--39838414 Score: 108
Period size: 24 Copynumber: 3.4 Consensus size: 23
39838325 ATCCCTTAAT
39838335 CTTTCATCTTCTTTAAC-CTTTCAC
1 CTTTCATCTTC-TTAACTCTTT-AC
*
39838359 CTTTCATATTCCTTAACTCTTTAC
1 CTTTCATCTT-CTTAACTCTTTAC
*
39838383 CTTTCATCTTCTTAACTCTTCAC
1 CTTTCATCTTCTTAACTCTTTAC
39838406 CTTTCATCT
1 CTTTCATCT
39838415 CCTTGTATCC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
23 21 0.41
24 25 0.49
25 5 0.10
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (23 bp):
CTTTCATCTTCTTAACTCTTTAC
Found at i:39839179 original size:18 final size:17
Alignment explanation
Indices: 39839148--39839193 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
39839138 AGAATAGGGT
39839148 TTTAAAATAAATAAAAATA
1 TTTAAAA-AAATAAAAA-A
39839167 TTTAAAAAAATAAAAAA
1 TTTAAAAAAATAAAAAA
*
39839184 TCTAAAAAAA
1 TTTAAAAAAA
39839194 AAGATTTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 10 0.38
18 9 0.35
19 7 0.27
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
TTTAAAAAAATAAAAAA
Found at i:39839194 original size:18 final size:18
Alignment explanation
Indices: 39839149--39839194 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
39839139 GAATAGGGTT
*
39839149 TTAAAATAAATAAAAATA
1 TTAAAAAAAATAAAAATA
*
39839167 TTTAAAAAAATAAAAA-A
1 TTAAAAAAAATAAAAATA
39839184 TCTAAAAAAAA
1 T-TAAAAAAAA
39839195 AGATTTCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 22 0.92
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
TTAAAAAAAATAAAAATA
Found at i:39840038 original size:18 final size:20
Alignment explanation
Indices: 39840025--39840062 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
39840015 ATTTTTATTT
39840025 TTTTAAA-ATATTTTATTAA
1 TTTTAAATATATTTTATTAA
39840044 TTTTAAATATATTTT-TTAA
1 TTTTAAATATATTTTATTAA
39840063 ATTATGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAAATATATTTTATTAA
Found at i:39844739 original size:20 final size:20
Alignment explanation
Indices: 39844716--39844756 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39844706 AATATCGCGA
39844716 ACAAGCTACCAAAATCGCAG
1 ACAAGCTACCAAAATCGCAG
39844736 ACAAGCTACCAAAATCGCAG
1 ACAAGCTACCAAAATCGCAG
39844756 A
1 A
39844757 TAAACTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.29, G:0.15, T:0.10
Consensus pattern (20 bp):
ACAAGCTACCAAAATCGCAG
Found at i:39849036 original size:18 final size:18
Alignment explanation
Indices: 39848999--39849045 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
39848989 CAAAATTGCG
*
39848999 AGTTGCGAGCTCACTTGA
1 AGTTGCAAGCTCACTTGA
39849017 AGTTGCAAGCTCA-TTGGA
1 AGTTGCAAGCTCACTT-GA
*
39849035 AGCTGCAAGCT
1 AGTTGCAAGCT
39849046 GTCAAGACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (18 bp):
AGTTGCAAGCTCACTTGA
Found at i:39852740 original size:41 final size:40
Alignment explanation
Indices: 39852683--39852833 Score: 143
Period size: 41 Copynumber: 3.9 Consensus size: 40
39852673 GACCTTTCGA
* *
39852683 GGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGG
1 GGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-G
39852724 GGCTTTAACGGCGTTTTTGAAAAAGCGCCGC---T-CT-G
1 GGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * * *
39852759 GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCTAATGTTCTG
1 GGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTC-G
* * * *
39852800 GTCTTTAGA-AGCGTTTTTGAATAAGCGTCGCTAA
1 GGCTTTA-ACGGCGTTTTTGAAAAAGCGCCGCTAA
39852834 AAAACATTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
35 29 0.32
37 2 0.02
38 2 0.02
39 1 0.01
41 56 0.62
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.31
Consensus pattern (40 bp):
GGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
Found at i:39852775 original size:35 final size:37
Alignment explanation
Indices: 39852683--39852790 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 37
39852673 GACCTTTCGA
*
39852683 GGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGG
1 GGCTTTAGCGGAGTTTTTGAAAAAGCGCCGC---TGCTC-G
* *
39852724 GGCTTTAACGGCGTTTTTGAAAAAGCGCCGCT-CT-G
1 GGCTTTAGCGGAGTTTTTGAAAAAGCGCCGCTGCTCG
*
39852759 GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCT
1 GGCTTTAGCGGAGTTTTTGAAAAAGCGCCGCT
39852791 AATGTTCTGG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 30 0.48
37 2 0.03
38 1 0.02
41 29 0.47
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (37 bp):
GGCTTTAGCGGAGTTTTTGAAAAAGCGCCGCTGCTCG
Found at i:39852814 original size:76 final size:76
Alignment explanation
Indices: 39852683--39852831 Score: 210
Period size: 76 Copynumber: 2.0 Consensus size: 76
39852673 GACCTTTCGA
* * *
39852683 GGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGCTTTAACGGCGTTTTTGAAAAA
1 GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGCTTTAACAGCGTTTTTGAAAAA
39852748 GCGCCGCTCTG
66 GCGCCGCTCTG
* * * *
39852759 GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCTAATGTTCTGGTCTTTAGA-AGCGTTTTTGAATA
1 GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGCTTTA-ACAGCGTTTTTGAAAA
*
39852823 AGCGTCGCT
65 AGCGCCGCT
39852832 AAAAAACATT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
76 63 0.98
77 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (76 bp):
GGCTTTAGCGGAGTTTTTAAAAAAGCGCCGCTAATGCTCGGGGCTTTAACAGCGTTTTTGAAAAA
GCGCCGCTCTG
Found at i:39853197 original size:14 final size:15
Alignment explanation
Indices: 39853161--39853203 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39853151 TTTAAGGCCG
*
39853161 ATTTAGGGAGTATGA
1 ATTTAGGGATTATGA
*
39853176 ATTTAGGGATTATGC
1 ATTTAGGGATTATGA
39853191 A-TTAGGGATTATG
1 ATTTAGGGATTATG
39853204 GTTTAAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.37
Consensus pattern (15 bp):
ATTTAGGGATTATGA
Found at i:39853229 original size:21 final size:21
Alignment explanation
Indices: 39853195--39853247 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
39853185 TTATGCATTA
* *
39853195 GGGA-TTATGGTTTAAGTGTT
1 GGGATTTAAGGTTTAAGGGTT
39853215 GGGATTTAAGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
*
39853236 GAGGGTTTAAGG
1 G-GGATTTAAGG
39853248 GTTAGACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.38
Consensus pattern (21 bp):
GGGATTTAAGGTTTAAGGGTT
Found at i:39858974 original size:102 final size:102
Alignment explanation
Indices: 39858854--39859039 Score: 347
Period size: 102 Copynumber: 1.8 Consensus size: 102
39858844 TCAAAAATAA
39858854 AACATAATATAATATTTATCATAGAAATAAATATTATTTAATTAAAATATTTTTTTAAAAGTCAT
1 AACATAATATAATATTTATCATAGAAATAAATATTATTTAATTAAAATATTTTTTTAAAAGTCAT
39858919 GTTTTTAGCT-GCGTTTGTGAAAAAGCGCCACTAAAAG
66 GTTTTTAG-TAGCGTTTGTGAAAAAGCGCCACTAAAAG
*
39858956 AACATAATATAATATTTATCATAGAAATAAATATTATTTAATTAAAATATTTTTTTAAAATTCAT
1 AACATAATATAATATTTATCATAGAAATAAATATTATTTAATTAAAATATTTTTTTAAAAGTCAT
39859021 GTTTTTAGTAGCGTTTGTG
66 GTTTTTAGTAGCGTTTGTG
39859040 GTAAAAGTGT
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
101 1 0.01
102 81 0.99
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (102 bp):
AACATAATATAATATTTATCATAGAAATAAATATTATTTAATTAAAATATTTTTTTAAAAGTCAT
GTTTTTAGTAGCGTTTGTGAAAAAGCGCCACTAAAAG
Found at i:39859068 original size:42 final size:43
Alignment explanation
Indices: 39859017--39859113 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 43
39859007 TTTTTAAAAT
*
39859017 TCATG-TTTTTAGTAGCGTTTGTGGTAAAAGTGTCGTTAAA-G
1 TCATGATTTTTAGTAGCGTTTGTGGTAAAAGTGCCGTTAAAGG
* *
39859058 TCATGATTTTTAGTGGCGTTTGTGGTAGAAGTGCCGTTAAAGG
1 TCATGATTTTTAGTAGCGTTTGTGGTAAAAGTGCCGTTAAAGG
*
39859101 TCATGATATTTAG
1 TCATGATTTTTAG
39859114 CGGCGTTGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 5 0.10
42 32 0.64
43 13 0.26
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (43 bp):
TCATGATTTTTAGTAGCGTTTGTGGTAAAAGTGCCGTTAAAGG
Found at i:39860252 original size:15 final size:15
Alignment explanation
Indices: 39860232--39860264 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39860222 GTTTAAGGAG
39860232 GACCAGTTAGAAATA
1 GACCAGTTAGAAATA
39860247 GACCAGTTAGAAATA
1 GACCAGTTAGAAATA
39860262 GAC
1 GAC
39860265 ATGTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (15 bp):
GACCAGTTAGAAATA
Found at i:39872128 original size:6 final size:6
Alignment explanation
Indices: 39872117--39872148 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39872107 CATATAACTG
39872117 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
39872149 ATATTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:39872160 original size:18 final size:18
Alignment explanation
Indices: 39872117--39872152 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39872107 CATATAACTG
*
39872117 ATCTATATCTATATCTAT
1 ATCTATATCTATATATAT
39872135 ATCTATATCTATATATAT
1 ATCTATATCTATATATAT
39872153 TCTTATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (18 bp):
ATCTATATCTATATATAT
Found at i:39901663 original size:6 final size:6
Alignment explanation
Indices: 39901652--39901683 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39901642 CATATAACTG
39901652 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
39901684 ATATTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:39901695 original size:18 final size:18
Alignment explanation
Indices: 39901652--39901687 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39901642 CATATAACTG
*
39901652 ATCTATATCTATATCTAT
1 ATCTATATCTATATATAT
39901670 ATCTATATCTATATATAT
1 ATCTATATCTATATATAT
39901688 TCTTATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (18 bp):
ATCTATATCTATATATAT
Found at i:39913746 original size:4 final size:4
Alignment explanation
Indices: 39913739--39913775 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
39913729 AATATGTGTG
39913739 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
39913776 TGTTTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:39913829 original size:23 final size:23
Alignment explanation
Indices: 39913802--39913882 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
39913792 ACATTGTTCG
*
39913802 TGAACATGTTGGATTAAGTTAAA
1 TGAACATGTTCGATTAAGTTAAA
* **
39913825 TGAACATGTTCGTTTAATGTT-TG
1 TGAACATGTTCGATTAA-GTTAAA
*
39913848 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATTAAGTTAAA
39913871 TGAACATGTTCG
1 TGAACATGTTCG
39913883 TGAACATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.04
23 43 0.90
24 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (23 bp):
TGAACATGTTCGATTAAGTTAAA
Found at i:39913870 original size:46 final size:46
Alignment explanation
Indices: 39913796--39913883 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
39913786 TTATTAACAT
* *
39913796 TGTTCGTGAACATGTTGGATTAAGTTAAATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAAATTAAATGAACATGTTCGTTTAA
*
39913842 TGTTTGTGAACATGTTCGATTAAATTAAATGAACATGTTCGT
1 TGTTCGTGAACATGTTCGATTAAATTAAATGAACATGTTCGT
39913884 GAACATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (46 bp):
TGTTCGTGAACATGTTCGATTAAATTAAATGAACATGTTCGTTTAA
Found at i:39913891 original size:23 final size:23
Alignment explanation
Indices: 39913802--39913893 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 23
39913792 ACATTGTTCG
* * *
39913802 TGAACATGTTGGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
** ***
39913825 TGAACATGTTCG-TTTAATGTTTG
1 TGAACATGTTCGATGAAAT-TAAA
*
39913848 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATGAAATTAAA
39913871 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
39913894 CAAACGAACA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
22 7 0.13
23 43 0.78
24 5 0.09
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:39914115 original size:31 final size:31
Alignment explanation
Indices: 39914077--39914154 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
39914067 ATGTTTGCAT
* * *
39914077 TTTCATTTTGGTCACCTAACTTCTAGGTCGC
1 TTTCATTTTGATCACCCAACTTCTAAGTCGC
*
39914108 TTTCATTTTGATCACCCAACTTTTAAGTCGC
1 TTTCATTTTGATCACCCAACTTCTAAGTCGC
39914139 TTTCATTTTGATCACC
1 TTTCATTTTGATCACC
39914155 AAAAAAATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.44
Consensus pattern (31 bp):
TTTCATTTTGATCACCCAACTTCTAAGTCGC
Found at i:39914885 original size:13 final size:13
Alignment explanation
Indices: 39914867--39914942 Score: 84
Period size: 13 Copynumber: 5.8 Consensus size: 13
39914857 TTGACAATGT
39914867 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
39914880 TTTTGAAAAGTG-
1 TTTTGAAAAGTGC
*
39914892 TTGTGAAAAAGTGC
1 TTTTG-AAAAGTGC
* *
39914906 TGTGGAAAAGTGC
1 TTTTGAAAAGTGC
39914919 TTTTGAGAAA-TGC
1 TTTTGA-AAAGTGC
*
39914932 TTTTAAAAAGT
1 TTTTGAAAAGT
39914943 TTAGTTTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
12 7 0.13
13 40 0.77
14 5 0.10
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:39915224 original size:8 final size:8
Alignment explanation
Indices: 39915211--39915237 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
39915201 TAAACTATAT
39915211 TTTAAATA
1 TTTAAATA
39915219 TTTAAATA
1 TTTAAATA
39915227 TTTAAATA
1 TTTAAATA
39915235 TTT
1 TTT
39915238 GTAATTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTAAATA
Found at i:39916106 original size:31 final size:31
Alignment explanation
Indices: 39916064--39916122 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
39916054 CAATTTGGTC
39916064 ACTGAAATATTCAAAAGTTTTCATTTAAATT
1 ACTGAAATATTCAAAAGTTTTCATTTAAATT
* *
39916095 ACTGAATTATTCAAAAGTTTTTATTTAA
1 ACTGAAATATTCAAAAGTTTTCATTTAA
39916123 GTCACTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (31 bp):
ACTGAAATATTCAAAAGTTTTCATTTAAATT
Found at i:39916136 original size:31 final size:31
Alignment explanation
Indices: 39916062--39916128 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
39916052 TACAATTTGG
*
39916062 TCACTGAAATATTCAAAAGTTTTCATTTAAA
1 TCACTGAATTATTCAAAAGTTTTCATTTAAA
* * *
39916093 TTACTGAATTATTCAAAAGTTTTTATTTAAG
1 TCACTGAATTATTCAAAAGTTTTCATTTAAA
39916124 TCACT
1 TCACT
39916129 AGGTTATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (31 bp):
TCACTGAATTATTCAAAAGTTTTCATTTAAA
Found at i:39917484 original size:25 final size:25
Alignment explanation
Indices: 39917450--39917499 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39917440 AAACCTCCAA
39917450 AGTCATATAAAAGAAGAGTTGGGAT
1 AGTCATATAAAAGAAGAGTTGGGAT
39917475 AGTCATATAAAAGAAGAGTTGGGAT
1 AGTCATATAAAAGAAGAGTTGGGAT
39917500 GCTCCGCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.24
Consensus pattern (25 bp):
AGTCATATAAAAGAAGAGTTGGGAT
Found at i:39928613 original size:47 final size:47
Alignment explanation
Indices: 39928535--39928917 Score: 540
Period size: 47 Copynumber: 8.1 Consensus size: 47
39928525 CCCTTCGGGA
* * * *
39928535 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
39928582 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
39928629 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39928676 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928725 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39928774 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928821 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39928870 CTTATCACATATAT--A--TACACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928913 CTTAT
1 CTTAT
39928918 GTGACAGCCC
Statistics
Matches: 310, Mismatches: 22, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
43 31 0.10
45 1 0.00
47 142 0.46
49 136 0.44
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39928709 original size:49 final size:49
Alignment explanation
Indices: 39928535--39928917 Score: 542
Period size: 49 Copynumber: 8.1 Consensus size: 49
39928525 CCCTTCGGGA
* * *
39928535 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * *
39928582 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
39928629 CTTATCAC--ATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39928676 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928725 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39928774 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928821 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39928870 CTTATCACATATATAT--A----CACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39928913 CTTAT
1 CTTAT
39928918 GTGACAGCCC
Statistics
Matches: 310, Mismatches: 20, Indels: 16
0.90 0.06 0.05
Matches are distributed among these distances:
43 30 0.10
46 1 0.00
47 135 0.44
49 144 0.46
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39928732 original size:96 final size:95
Alignment explanation
Indices: 39928535--39928917 Score: 562
Period size: 96 Copynumber: 4.1 Consensus size: 95
39928525 CCCTTCGGGA
* * * * * *
39928535 CTTATCAC-ATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
39928599 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
** *
39928629 CTTATCAC-ATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATATA
1 CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATA
* * *
39928693 CACTTTCACATTCATCACATTGGTCATTCGGC
64 CACTTTCACATTCATCACATCGGCCATTAGGC
39928725 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
39928790 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
39928821 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAT--
1 CTTATCACA-ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
* *
39928884 A--TACACATTCATCACATTGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
39928913 CTTAT
1 CTTAT
39928918 GTGACAGCCC
Statistics
Matches: 265, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
92 31 0.12
94 47 0.18
96 143 0.54
98 44 0.17
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACAATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39928807 original size:145 final size:145
Alignment explanation
Indices: 39928535--39928917 Score: 615
Period size: 145 Copynumber: 2.7 Consensus size: 145
39928525 CCCTTCGGGA
* * * * *
39928535 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
*
39928596 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
39928661 CATCAGCCATTAGGC
131 CATCAGCCATTAGGC
*
39928676 CTTATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
*
39928741 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
39928806 CATCGGCCATTAGGC
131 CATCAGCCATTAGGC
39928821 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
39928886 --A----CACATTCATCACATTGGCCATTAGGCCTTAT
66 ACACTTTCACATTCATCACATTGGCCATTAGGCCTTAT
39928918 GTGACAGCCC
Statistics
Matches: 227, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
139 30 0.13
141 10 0.04
142 1 0.00
143 39 0.17
145 147 0.65
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (145 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAT
ACACTTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
CATCAGCCATTAGGC
Found at i:39930667 original size:27 final size:27
Alignment explanation
Indices: 39930636--39930813 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
39930626 TAAATTGTAC
39930636 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39930663 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39930689 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39930717 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
39930745 AGCACTAAGTGTGGGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39930772 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39930799 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39930814 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 105 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39930750 original size:82 final size:81
Alignment explanation
Indices: 39930637--39930792 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
39930627 AAATTGTACA
* *
39930637 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39930701 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
39930718 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGGGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39930783 TGCGAGTTGA
65 TGCGAATTGA
39930793 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39930804 original size:82 final size:81
Alignment explanation
Indices: 39930633--39930813 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
39930623 GATTAAATTG
* *
39930633 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39930698 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
39930714 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGGGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39930778 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39930796 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39930814 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39944497 original size:21 final size:22
Alignment explanation
Indices: 39944449--39944497 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
39944439 TCTACCAACT
*
39944449 TACTTACCTTGAATAATTTTCA
1 TACTTACCTTGAATAATTTTAA
*
39944471 TGCTTACCTT-AAT-ATTTTAAA
1 TACTTACCTTGAATAATTTT-AA
39944492 TACTTA
1 TACTTA
39944498 TATTACTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 9 0.39
22 9 0.39
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (22 bp):
TACTTACCTTGAATAATTTTAA
Found at i:39950839 original size:27 final size:28
Alignment explanation
Indices: 39950755--39950852 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
39950745 CATGAGATTG
* * *
39950755 GCACTAAGTGTGCGGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
39950784 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
39950812 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39950839 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
39950853 GACTTAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 24 0.38
28 21 0.33
29 19 0.30
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:39950866 original size:29 final size:27
Alignment explanation
Indices: 39950783--39950866 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
39950773 TAAATTGTTC
* *
39950783 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
39950811 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
39950838 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
39950867 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:39955375 original size:31 final size:31
Alignment explanation
Indices: 39955316--39955375 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
39955306 GTCACCGAAA
* *
39955316 TATTCAAAAGTTTTCATTTAATTTACTAAAC
1 TATTCAAAAGTTTTCATTTAACTCACTAAAC
*
39955347 TATTCAAAAGTTTTTATTTAACTCACTAA
1 TATTCAAAAGTTTTCATTTAACTCACTAA
39955376 GTTGTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.45
Consensus pattern (31 bp):
TATTCAAAAGTTTTCATTTAACTCACTAAAC
Found at i:39976931 original size:18 final size:18
Alignment explanation
Indices: 39976908--39976942 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39976898 GCATAAAAAA
39976908 AATTCAACTAA-AAATATT
1 AATTCAA-TAAGAAATATT
39976926 AATTCAATAAGAAATAT
1 AATTCAATAAGAAATAT
39976943 AAATGTGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.57, C:0.09, G:0.03, T:0.31
Consensus pattern (18 bp):
AATTCAATAAGAAATATT
Found at i:39978890 original size:35 final size:35
Alignment explanation
Indices: 39978844--39978912 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
39978834 TTTTGGACAG
39978844 AGACTCGATAATGTATATAGTGAACTTAAACCCTA
1 AGACTCGATAATGTATATAGTGAACTTAAACCCTA
39978879 AGACTCGATAATGTATATAGTGAACTTAAACCCT
1 AGACTCGATAATGTATATAGTGAACTTAAACCCT
39978913 TGGGCATGCA
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:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (35 bp):
AGACTCGATAATGTATATAGTGAACTTAAACCCTA
Found at i:39979396 original size:27 final size:26
Alignment explanation
Indices: 39979339--39979396 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
39979329 TCTAACGGGC
*
39979339 TTACCCGTGTTTAATGTCCTGGTGGA
1 TTACCCGTGTTTAATGTCCTGGTAGA
* *
39979365 CTACCCTGTGTTTACTGT-CTAGGTAGA
1 TTACCC-GTGTTTAATGTCCT-GGTAGA
39979392 TTACC
1 TTACC
39979397 TATGCTTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TTACCCGTGTTTAATGTCCTGGTAGA
Done.