Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 97 of 125
Found at i:18832005 original size:2 final size:2
Alignment explanation
Indices: 18831998--18832030 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18831988 TAATTTCAGG
18831998 AT AT AT AT 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 AT AT AT AT A
18832031 GTAAGGCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18832359 original size:24 final size:25
Alignment explanation
Indices: 18832323--18832376 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
18832313 GTCAAATTAT
*
18832323 TTATTATTGTATTAAA-TAAT-AAA
1 TTATTATTATATTAAATTAATAAAA
18832346 TTATATATTATATTAAATTAATAAAA
1 TTAT-TATTATATTAAATTAATAAAA
18832372 TTATT
1 TTATT
18832377 TCATAATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 4 0.15
24 11 0.41
25 5 0.19
26 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TTATTATTATATTAAATTAATAAAA
Found at i:18835445 original size:18 final size:18
Alignment explanation
Indices: 18835418--18835459 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
18835408 GAAATCTTAA
*
18835418 ATTTTGAGAAAAAATGTG
1 ATTTTGAGAAAAAATGAG
*
18835436 ATTTTTAGAAAAAATGAG
1 ATTTTGAGAAAAAATGAG
18835454 ATTTTG
1 ATTTTG
18835460 GGAGAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (18 bp):
ATTTTGAGAAAAAATGAG
Found at i:18835941 original size:68 final size:69
Alignment explanation
Indices: 18835869--18836007 Score: 172
Period size: 69 Copynumber: 2.0 Consensus size: 69
18835859 AAAAAAGTAG
* * * * * * *
18835869 TAATTGAGATTTAA-TTTTAAAAAAAATGACAATAAATAATTATTGCGTTTAGTTTCAAAGAAAC
1 TAATTGAGATTAAAGCTATAAAAAAAATGACAATAAACAATTACTACATTTAGTTTCAAAGAAAC
18835933 ACAA
66 ACAA
* * *
18835937 TAATTGATATTAAAGCTATAAAAAAAATGACAATTAACAATTACTATATTTAGTTTCAAAGAAAC
1 TAATTGAGATTAAAGCTATAAAAAAAATGACAATAAACAATTACTACATTTAGTTTCAAAGAAAC
*
18836002 GCAA
66 ACAA
18836006 TA
1 TA
18836008 GTTGGGCTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
68 12 0.20
69 47 0.80
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (69 bp):
TAATTGAGATTAAAGCTATAAAAAAAATGACAATAAACAATTACTACATTTAGTTTCAAAGAAAC
ACAA
Found at i:18837005 original size:19 final size:19
Alignment explanation
Indices: 18836983--18837025 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
18836973 GAGAATTCAT
*
18836983 ATGATTTTAAAGAAAGAAA
1 ATGATTGTAAAGAAAGAAA
*
18837002 ATGAATTGTAAAGAGAGAAA
1 ATG-ATTGTAAAGAAAGAAA
18837022 ATGA
1 ATGA
18837026 ATTGAAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (19 bp):
ATGATTGTAAAGAAAGAAA
Found at i:18837015 original size:20 final size:20
Alignment explanation
Indices: 18836990--18837029 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18836980 CATATGATTT
18836990 TAAAGAAAGAAAATGAATTG
1 TAAAGAAAGAAAATGAATTG
*
18837010 TAAAGAGAGAAAATGAATTG
1 TAAAGAAAGAAAATGAATTG
18837030 AAGATGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (20 bp):
TAAAGAAAGAAAATGAATTG
Found at i:18838411 original size:16 final size:16
Alignment explanation
Indices: 18838390--18838420 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18838380 TAAAACTTAA
*
18838390 TTATTTATTTTTTTAT
1 TTATTTATTATTTTAT
18838406 TTATTTATTATTTTA
1 TTATTTATTATTTTA
18838421 AATCAACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTATTATTTTAT
Found at i:18838446 original size:27 final size:25
Alignment explanation
Indices: 18838406--18838458 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
18838396 ATTTTTTTAT
*
18838406 TTATTTATTA-TTTTAAATCAACAAAA
1 TTATTTAATATTTTTAAAT-AA-AAAA
18838432 TTATTTCAATATTTTTAAATAAAAAA
1 TTATTT-AATATTTTTAAATAAAAAA
18838458 T
1 T
18838459 CAAAATGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 11 0.46
27 5 0.21
28 8 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (25 bp):
TTATTTAATATTTTTAAATAAAAAA
Found at i:18838786 original size:17 final size:17
Alignment explanation
Indices: 18838756--18838790 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18838746 AATTTAAAAT
*
18838756 AAAAAATATGATATTTG
1 AAAAAATATAATATTTG
*
18838773 AAAAAGTATAATATTTG
1 AAAAAATATAATATTTG
18838790 A
1 A
18838791 TATTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (17 bp):
AAAAAATATAATATTTG
Found at i:18839238 original size:25 final size:23
Alignment explanation
Indices: 18839176--18839246 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 23
18839166 CTTTTTAATT
18839176 TTTTTATAAAAAGATTTTTAAAACG
1 TTTTTATAAAAAG--TTTTAAAACG
*
18839201 TTTCTATACAAAAGTTTTAAATGATC-
1 TTTTTATA-AAAAGTTTTAAA--A-CG
*
18839227 TTTTTATAAAAATTTTTAAA
1 TTTTTATAAAAAGTTTTAAA
18839247 GAATCATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 7 0.18
25 18 0.46
26 13 0.33
27 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTTTATAAAAAGTTTTAAAACG
Found at i:18839933 original size:2 final size:2
Alignment explanation
Indices: 18839926--18839965 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
18839916 CATCTAGATG
18839926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18839966 TTGTGTGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18840214 original size:58 final size:58
Alignment explanation
Indices: 18840136--18840246 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
18840126 CGCGCTTCAT
* * *
18840136 GACTCAATCCAGCTATTTGTGCCAGCTTTTTGCTTCCTGTAAATCAACTTCTGACATC
1 GACTCAATCCAGCTACTTGTGCCAGCTTTTCGCTTCCTGAAAATCAACTTCTGACATC
* *
18840194 GACTCAATCCGGCTGCTTGTGCCAGCTTTTCGCTTCCTGAAAATCAACTTCTG
1 GACTCAATCCAGCTACTTGTGCCAGCTTTTCGCTTCCTGAAAATCAACTTCTG
18840247 GTATCGTCCG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (58 bp):
GACTCAATCCAGCTACTTGTGCCAGCTTTTCGCTTCCTGAAAATCAACTTCTGACATC
Found at i:18841998 original size:19 final size:19
Alignment explanation
Indices: 18841970--18842011 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18841960 ACCATAATAC
*
18841970 CATA-CCAGTTCATGTTGA
1 CATATCCAGTTCATATTGA
18841988 CATATCCAGTTCATATTGA
1 CATATCCAGTTCATATTGA
18842007 CATAT
1 CATAT
18842012 ACAGGCAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
CATATCCAGTTCATATTGA
Found at i:18848165 original size:28 final size:28
Alignment explanation
Indices: 18848124--18848180 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
18848114 TGTTTAACAA
*
18848124 TATATATATATGTGTGCATGTGTGTGTG
1 TATATATATATGTGTGCATGTGCGTGTG
* *
18848152 TATATATGTGTGTGTGCATGTGCGTGTG
1 TATATATATATGTGTGCATGTGCGTGTG
18848180 T
1 T
18848181 GTGCTAGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.46
Consensus pattern (28 bp):
TATATATATATGTGTGCATGTGCGTGTG
Found at i:18848178 original size:14 final size:14
Alignment explanation
Indices: 18848134--18848181 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
18848124 TATATATATA
18848134 TGTGTGCATGTGTG
1 TGTGTGCATGTGTG
** *
18848148 TGTGTATATATGTG
1 TGTGTGCATGTGTG
*
18848162 TGTGTGCATGTGCG
1 TGTGTGCATGTGTG
18848176 TGTGTG
1 TGTGTG
18848182 TGCTAGGATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.10, C:0.06, G:0.40, T:0.44
Consensus pattern (14 bp):
TGTGTGCATGTGTG
Found at i:18848464 original size:6 final size:6
Alignment explanation
Indices: 18848447--18848476 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
18848437 CAATAAGCCT
*
18848447 GCAAAA GTAAAA GCAAAA GCAAAA GCAAAA
1 GCAAAA GCAAAA GCAAAA GCAAAA GCAAAA
18848477 AATAAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.67, C:0.13, G:0.17, T:0.03
Consensus pattern (6 bp):
GCAAAA
Found at i:18849212 original size:16 final size:16
Alignment explanation
Indices: 18849191--18849222 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18849181 TAAAATTAAA
*
18849191 TATTATATTTTAATTT
1 TATTATATATTAATTT
18849207 TATTATATATTAATTT
1 TATTATATATTAATTT
18849223 ATGATTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTATATATTAATTT
Found at i:18849912 original size:2 final size:2
Alignment explanation
Indices: 18849907--18849944 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
18849897 GTGCATGAGC
* *
18849907 AT AT AT AT TT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18849945 TGTATCCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:18850264 original size:13 final size:13
Alignment explanation
Indices: 18850246--18850273 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18850236 TCAAGACTAT
18850246 AATCTTGGAGACA
1 AATCTTGGAGACA
18850259 AATCTTGGAGACA
1 AATCTTGGAGACA
18850272 AA
1 AA
18850274 ACTCAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (13 bp):
AATCTTGGAGACA
Found at i:18861589 original size:11 final size:11
Alignment explanation
Indices: 18861573--18861610 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
18861563 GTTTTGTATC
18861573 TATATTTTATA
1 TATATTTTATA
18861584 TATATTTATATA
1 TATATTT-TATA
*
18861596 TATATTTAATA
1 TATATTTTATA
18861607 TATA
1 TATA
18861611 AATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATTTTATA
Found at i:18862144 original size:3 final size:3
Alignment explanation
Indices: 18862136--18862173 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
18862126 AGTGGGCGGA
18862136 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18862174 AACAATATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18862260 original size:27 final size:28
Alignment explanation
Indices: 18862230--18862285 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
18862220 GTTTGATGAA
18862230 TTATTTGTAAATATATTTAATT-TTTAT
1 TTATTTGTAAATATATTTAATTATTTAT
* ** *
18862257 TTATTTTTATTTATATTTATTTATTTAT
1 TTATTTGTAAATATATTTAATTATTTAT
18862285 T
1 T
18862286 AAATTTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (28 bp):
TTATTTGTAAATATATTTAATTATTTAT
Found at i:18862264 original size:10 final size:10
Alignment explanation
Indices: 18862243--18862282 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
18862233 TTTGTAAATA
18862243 TATTTAATTTT
1 TATTT-ATTTT
18862254 TATTTATTTT
1 TATTTATTTT
*
18862264 TATTTATATT
1 TATTTATTTT
18862274 TATTTATTT
1 TATTTATTT
18862283 ATTAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 22 0.81
11 5 0.19
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TATTTATTTT
Found at i:18866586 original size:21 final size:22
Alignment explanation
Indices: 18866556--18866607 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
18866546 AATTAAAACC
* *
18866556 ATGCAACATAATTATT-CAAAT
1 ATGCATCATAATAATTACAAAT
18866577 ATGCATCAT-ATAATTACAAAT
1 ATGCATCATAATAATTACAAAT
*
18866598 AT-AATCATAA
1 ATGCATCATAA
18866608 ATAAGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (22 bp):
ATGCATCATAATAATTACAAAT
Found at i:18866982 original size:28 final size:28
Alignment explanation
Indices: 18866950--18867009 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
18866940 TGGTAATTTC
*
18866950 AAAATCCTCCAATTGTTGTTTAATCCAT
1 AAAATCCTCCAATTGTTATTTAATCCAT
18866978 AAAATCCTCCAATTGTTATTTAATCCAT
1 AAAATCCTCCAATTGTTATTTAATCCAT
18867006 AAAA
1 AAAA
18867010 CTTGAGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
AAAATCCTCCAATTGTTATTTAATCCAT
Found at i:18873538 original size:6 final size:6
Alignment explanation
Indices: 18873527--18873574 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
18873517 AAATTAAACT
**
18873527 ATTTAA ATTTAA ATTT-A ATTTAA AAAT-A A-TTAA A-TTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
18873571 ATTT
1 ATTT
18873575 TATTCTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 1 0.03
5 14 0.39
6 21 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:18873548 original size:11 final size:11
Alignment explanation
Indices: 18873527--18873574 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
18873517 AAATTAAACT
18873527 ATTTAAATTTAA
1 ATTT-AATTTAA
18873539 ATTTAATTTAA
1 ATTTAATTTAA
**
18873550 AAATAA-TTAA
1 ATTTAATTTAA
*
18873560 ATTAAATTTAA
1 ATTTAATTTAA
18873571 ATTT
1 ATTT
18873575 TATTCTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 7 0.24
11 18 0.62
12 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTTAATTTAA
Found at i:18876998 original size:83 final size:83
Alignment explanation
Indices: 18876859--18877034 Score: 282
Period size: 83 Copynumber: 2.1 Consensus size: 83
18876849 GTTAAACAAG
*
18876859 ATAGATTTTTGCAAAGTAAAAGTCATTAAGGTGACAACAAAATAAAAGACAACTTTTGAATATTC
1 ATAGATTTTTGCAAAGTAAAAGCCATTAAGGTGACAACAAAATAAAAGACAACTTTTGAATATTC
* *
18876924 AAAGTTCCAAATTTCTGC
66 AAAGTGCCAAATTTCTAC
* * *
18876942 ATAGATTTTTGCAAAGTCAAAGCCATTAAGGTGGCAACAAAGTAAAA-ATCAACTTTTGAATATT
1 ATAGATTTTTGCAAAGTAAAAGCCATTAAGGTGACAACAAAATAAAAGA-CAACTTTTGAATATT
18877006 CAAAGTGCCAAATTTCTAC
65 CAAAGTGCCAAATTTCTAC
18877025 ATAGATTTTT
1 ATAGATTTTT
18877035 TTTTAAGGGG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
82 1 0.01
83 85 0.99
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (83 bp):
ATAGATTTTTGCAAAGTAAAAGCCATTAAGGTGACAACAAAATAAAAGACAACTTTTGAATATTC
AAAGTGCCAAATTTCTAC
Found at i:18880203 original size:13 final size:13
Alignment explanation
Indices: 18880185--18880221 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
18880175 CTTTTCAATG
18880185 TCTTTATATATGT
1 TCTTTATATATGT
*
18880198 TCTTTAGATATGT
1 TCTTTATATATGT
18880211 TCTTTATATAT
1 TCTTTATATAT
18880222 AGTTAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.59
Consensus pattern (13 bp):
TCTTTATATATGT
Found at i:18881763 original size:160 final size:158
Alignment explanation
Indices: 18881385--18882905 Score: 801
Period size: 161 Copynumber: 9.6 Consensus size: 158
18881375 TTAAAATGTT
* * * * *
18881385 AAAATGTAAAATTACAATTATTGTTTTATTTTAAGAATTTAGATAGCTTTAATATATGATATT-A
1 AAAATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTAA
* * * * * ** * **
18881449 ATTTGT-TCAAATAATTGAATTTAGTTTTCACGGTTGATAGGCATGAAAAAATTGTGGTTTATAT
66 ACTTGTCT-AAATGATTGAACTTAGTTTTCAC-ATTGATATGTGTGAAAAAGTT-ACGTTTATAT
* * * *
18881513 CTATTTAGGA-TTTTTGTGCCGTTGAAAGGA
128 CTATTTAAGACTTTTTGTGTCGTTAAAAGCA
* * *
18881543 AAATAT--AAATTTACAATTATTATTCTACTTTAACAATTTAGATAGCTTCAATACATGATATTA
1 AAA-ATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTA
*
18881606 AACTTGTCTAAATGATTGAACTTAGTTTTCACATTGATATGTGTGAAAAAGCTACGGTTTATATC
65 AACTTGTCTAAATGATTGAACTTAGTTTTCACATTGATATGTGTGAAAAAGTTAC-GTTTATATC
*
18881671 TGTTTAAGACTTTTTGTGTCGTTAAAAAGCA
129 TATTTAAGACTTTTTGTGTCGTT-AAAAGCA
* * * * *
18881702 AAAATGCAAGTTTGCAATTATTGTTCTATTTTAACAGTTTAGATAGCTTAAATGCATGATATTAA
1 AAAATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTAA
* * * * *
18881767 ACTTGTATGAATGATTGAACTTGGTTTTCATAATTGATATGTGTGAAAAAGTTGCAGTTTATATC
66 ACTTGTCTAAATGATTGAACTTAGTTTTCA-CATTGATATGTGTGAAAAAGTTAC-GTTTATATC
* * * * *
18881832 T-TTTTAGAATTTTT-TTTACCATTAAAAAGTA
129 TATTTAAGACTTTTTGTGT--CGTT-AAAAGCA
* * * * *
18881863 AAAATACAAATTTATAGTTATTGTTGTGTTTTAACAATTTAGATAGCTTTAATACATGATATTAA
1 AAAATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTAA
* * * * * * * * *
18881928 ATTTGTTTGAAAT-ATTAAACTTTGTTTCCACAGTTAATATTTGTAAAAAAGTTAC-TATTATGT
66 ACTTGTCT-AAATGATTGAACTTAGTTTTCACA-TTGATATGTGTGAAAAAGTTACGT-TTATAT
* * * *
18881991 C-AGTTTAGGACTTTTTGTGTTGTTAAAGGATA
128 CTA-TTTAAGACTTTTTGTGTCGTTAAAAG-CA
* * ** ** * * *
18882023 AAAAGGTAGTTTTTTAGTTATAT-TTTTATTTTAACAATTTACATAGC-TTAAGTACATGATATT
1 AAAATGCAAATTTACAATTAT-TGTTCTATTTTAACAATTTAGATAGCTTTAA-TACATGATATT
* * * * * * * * *
18882086 AAATTTATC-AGAATGCTTGAACTTAATTTCCATGATTGATATATGTGAAAAA-CTA-ATTGT-T
64 AAACTTGTCTA-AATGATTGAACTTAGTTTTCA-CATTGATATGTGTGAAAAAGTTACGTT-TAT
* * * * *
18882147 GTCTATTTAGGATTTTTTATG-CTATTAAAAGGCA
126 ATCTATTTAAGACTTTTTGTGTC-GTTAAAA-GCA
* * * * * *
18882181 AAAATGCAGAA-TTGCAGTTATTGTTTTATTTTAATAGTTTGGATAGCTTTAATACATGATATTA
1 AAAATGCA-AATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTA
* *
18882245 AACTTGTCTAAATGATTGAACAT-GATTGTCACGATTGATATGTGTGAAAAAGTTA--TTTATAT
65 AACTTGTCTAAATGATTGAACTTAG-TTTTCAC-ATTGATATGTGTGAAAAAGTTACGTTTATAT
* *
18882307 CTATTTAAGACTTTTTGTGTTGTTAAAAGATA
128 CTATTTAAGACTTTTTGTGTCGTTAAAAG-CA
* * * *** *
18882339 AAAATGCAAATTTACTGA-TATTATTCTTTTTTAACAGCCTGGATAGCTTTAATACAT-AGTATT
1 AAAATGCAAATTTAC-AATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGA-TATT
** * * *
18882402 AAACTTGT-TCAAATGATT-AA-TGTTTTTTTCCATAATTAATATGAGTGAAAAAATTGTTA--T
64 AAACTTGTCT-AAATGATTGAACT-TAGTTTT-CA-CATTGATATGTGTG-AAAAA--GTTACGT
* * * * *
18882462 TTATGTCTATTTAGGA-TATTTTATGCCATTAAAAGGCA
122 TTATATCTATTTAAGACT-TTTTGTGTCGTTAAAA-GCA
** ** ** * * * *
18882500 AAAATATAGTTTTTTAGTTCTAT-TTCTATTTTAACAATTTAGATAGCTTAAATACATAATATTA
1 AAAATGCAAATTTACAATTAT-TGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTA
* * * ** *
18882564 AATTTAT-TCGAATGATTGAA-TT--TTATTCCTACAATTGATATAAGTGAAAAAGTTATCATTT
65 AACTTGTCT-AAATGATTGAACTTAGTT-TT-C-AC-ATTGATATGTGTGAAAAAGTTA-CGTTT
* * * *
18882625 ATATATGTTT-AGCACTTTTTATGCCGTTAAAAGGTC-
124 ATATCTATTTAAG-ACTTTTTGTGTCGTTAAAA-G-CA
* * * * * * * * *
18882661 AAAAT-AAAATTTTACAATTAAAT-CTATATTTTAATAATTTATATAGCTTAAATACTTGATTTT
1 AAAATGCAAA-TTTACAATT-ATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATT
* * * * *
18882724 AAACTTGTCCAAATAATTGAACTT-GATTTCCACAATT--TATATGT-AAATAAGTTATGATTTA
64 AAACTTGTCTAAATGATTGAACTTAG-TTTTCAC-ATTGATATGTGTGAAA-AAGTTACG-TTTA
* * * * * *
18882785 TGTTTGTTTAAAACTTTTTATG-CTATTAAAAGGCA
125 TATCTATTTAAGACTTTTTGTGTC-GTTAAAA-GCA
* * * * * * * * *
18882820 AATATGAAAATTTACAGTTATTGTTATGTTTTAATAGTTTAGACA-ATTTCAATACATGATATTA
1 AAAATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTT-AATACATGATATTA
*
18882884 AACTTGTC-AAATGTTTGAACTT
65 AACTTGTCTAAATGATTGAACTT
18882906 CATTATTGCC
Statistics
Matches: 1071, Mismatches: 214, Indels: 156
0.74 0.15 0.11
Matches are distributed among these distances:
157 93 0.09
158 283 0.26
159 135 0.13
160 198 0.18
161 343 0.32
162 16 0.01
163 1 0.00
164 2 0.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (158 bp):
AAAATGCAAATTTACAATTATTGTTCTATTTTAACAATTTAGATAGCTTTAATACATGATATTAA
ACTTGTCTAAATGATTGAACTTAGTTTTCACATTGATATGTGTGAAAAAGTTACGTTTATATCTA
TTTAAGACTTTTTGTGTCGTTAAAAGCA
Found at i:18891440 original size:25 final size:26
Alignment explanation
Indices: 18891402--18891450 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
18891392 CTAATTATCC
18891402 AATGATGAAATTTTTA-AAAATTTCA
1 AATGATGAAATTTTTATAAAATTTCA
18891427 AATGAT-AAATTTTTATAAAATTTC
1 AATGATGAAATTTTTATAAAATTTC
18891451 TAGGTGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (26 bp):
AATGATGAAATTTTTATAAAATTTCA
Found at i:18891462 original size:26 final size:24
Alignment explanation
Indices: 18891402--18891466 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
18891392 CTAATTATCC
18891402 AATGATGAAATTTTTAAAAATTTCA
1 AATGA-GAAATTTTTAAAAATTTCA
*
18891427 AATGATAAATTTTTATAAAATTTCTA
1 AATGAGAAATTTTTA-AAAATTTC-A
**
18891453 GGTGAGAAATTTTT
1 AATGAGAAATTTTT
18891467 TCTAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.26
25 13 0.38
26 12 0.35
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (24 bp):
AATGAGAAATTTTTAAAAATTTCA
Found at i:18891824 original size:52 final size:51
Alignment explanation
Indices: 18891754--18891908 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 51
18891744 AAAAAAAAAG
18891754 AAAAAAAGAAAAAGAATTTCTAAATTGACCAAAATGGTGAAAAATTTAGAAAT
1 AAAAAAA-AAAAAGAATTTCTAAATTGACC-AAATGGTGAAAAATTTAGAAAT
* * *
18891807 AAAAAAAAAAAAGAATTTCTAAATAGGCTCAAATGGTGAAAAATTTAAAAAT
1 AAAAAAAAAAAAGAATTTCTAAATTGAC-CAAATGGTGAAAAATTTAGAAAT
**** * *
18891859 TTTGAAAAAAAA-AATTTCTAAAATTGACCCAAATTGTGGAAAATTTAGAA
1 AAAAAAAAAAAAGAATTTCT-AAATTGA-CCAAATGGTGAAAAATTTAGAA
18891909 CCAAAAAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
51 7 0.08
52 71 0.82
53 9 0.10
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (51 bp):
AAAAAAAAAAAAGAATTTCTAAATTGACCAAATGGTGAAAAATTTAGAAAT
Found at i:18894064 original size:80 final size:81
Alignment explanation
Indices: 18893969--18894123 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 81
18893959 ATTTTTACAT
* * *
18893969 TGTAACTATAG-TTTTTTTATATTGTAAGTAACATTATATTATAACCTATATTATATAATATAAT
1 TGTAACTATAGTTTTTTTTATATTATAAGTAACATTATATTAGAACATATATTATATAATATAAT
18894033 GGTTTTTATATTAGAA
66 GGTTTTTATATTAGAA
* * * * *
18894049 TGTAATTATTGTTTTTTTTTATATTATGAGTAACATTATATTAGAATATATATTGTATAATATAA
1 TGTAACTATAG-TTTTTTTTATATTATAAGTAACATTATATTAGAACATATATTATATAATATAA
18894114 TGGTTTTTAT
65 TGGTTTTTAT
18894124 TAATTGTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
80 9 0.14
82 56 0.86
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (81 bp):
TGTAACTATAGTTTTTTTTATATTATAAGTAACATTATATTAGAACATATATTATATAATATAAT
GGTTTTTATATTAGAA
Found at i:18899119 original size:161 final size:161
Alignment explanation
Indices: 18898717--18900255 Score: 1036
Period size: 161 Copynumber: 9.6 Consensus size: 161
18898707 TATTTTATGC
* * * * * *
18898717 CGTTAAAATGTAAAAATGTAAAATTACAATTATTGTTTTATTTTAAGAATTTAGATAGCTTTAAT
1 CGTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAAT
* * * * ** * ** *
18898782 ATATGATATTAAATTTGT-TCAAATAATTGAATTTAGTTTTCACGGTTGATAGGCATGAAAAAAT
66 ACATGATATTAAACTTGTCT-AAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAGT
** * *
18898846 TGTGGTTTATATCTATTTAGGA-TTTTTGTGC
130 TACGGTTTATATCTATTTAAGACTTTTTGTGT
* * * * * * *
18898877 CGTT-GAAAGGAAAAATATAAATTTACAATTATTATTCTACTTTAACAATTTAGATAGCTTCAAT
1 CGTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAAT
*
18898941 ACATGATATTAAACTTGTCTAAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAGCT
66 ACATGATATTAAACTTGTCTAAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAGTT
*
18899006 ACGGTTTATATCTGTTTAAGACTTTTTGTGT
131 ACGGTTTATATCTATTTAAGACTTTTTGTGT
* * *
18899037 CGTTAAAAAGCAAAAATGCAAGTTTGCAATTATTGTTCTATTTTAACAGTTTAGATAG-TTTGAA
1 CGTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTT-AA
* * * *
18899101 TGCATGATATTAAACTTGTATAAATGATTGAACTT-GTTTTCATAATTGATATGTGTAAAAAAGT
65 TACATGATATTAAACTTGTCTAAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAGT
* * * *
18899165 TACAGTTTATATCT-TTTTAGAATTTTT-TGAA
130 TACGGTTTATATCTATTTAAGACTTTTTGTG-T
* * * * * *
18899196 CTGTTAAAAAGCAAAAATATAAATTTATAGTTATTGTTATGTTTTAATAGTTTAGATAGCTTTAA
1 C-GTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAA
* * * *
18899261 TACATGATATTAAATTTGTCTGAAAT-ATTAAACTTTGTTTTCACAGTTGATATGTGTGAAAAAG
65 TACATGATATTAAACTTGTCT-AAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAG
** * *
18899325 TTACTATTTATGT-TAGTTTAGGACTTTTTGTGT
129 TTACGGTTTATATCTA-TTTAAGACTTTTTGTGT
* * * * ** *
18899358 CGTT-AAAGGATAAAAAGGTAATTTTGTAGTTATAT-TTCTATTTTAACAGTTT-GTATAGC-TT
1 CGTTAAAAAG-CAAAAATGTAAATTTACAATTAT-TGTTCTATTTTAACAGTTTAG-ATAGCTTT
* * ** * * ** *
18899419 AAGTACATGATATTAAATTTATCCGAATGCTTGAACTTAATTTTCATGATTGATATATGTGAAAA
63 AA-TACATGATATTAAACTTGTCTAAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAA
* * * *
18899484 AGTTACCG--T-TGTCTATTTATGACTTTTTATG-
127 AGTTACGGTTTATATCTATTTAAGACTTTTTGTGT
* * * * *
18899515 C-TATTAAAAG-ACAAATGTAGAA-TTGCAGTTATTGTTCTATTTTAATAGTTTAGATAGCTTTA
1 CGT-TAAAAAGCAAAAATGTA-AATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTA
*
18899577 ATACATGATATTAAACTTGTCTAAATGATTGAA-TATGGTTTTCACAATTGATATGTGTGAAAAA
64 ATACATGATATTAAACTTGTCTAAATGATTGAACT-TAGTTTTCACAATTGATATGTGTGAAAAA
*** *
18899641 GTTGTTGTTTATATCTATTTAAGATTTTTTGTGT
128 GTTACGGTTTATATCTATTTAAGACTTTTTGTGT
* * * * * * * *
18899675 TGTTAAAAGGTAAAAATGCAAATTTACTGA-TATTATTCTATTTTAACAGCTTGGATAGCTTTAA
1 CGTTAAAAAGCAAAAATGTAAATTTAC-AATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAA
* ** * * * *
18899739 TACATGATATTAAACTTGT-TCAAATGATT-AATGTTCTTTTTCATAGTTAATATGAGTGAAAAA
65 TACATGATATTAAACTTGTCT-AAATGATTGAA-CTTAGTTTTCACAATTGATATGTGTGAAAAA
**** * * * *
18899802 GTTGTTATTTATGTCTATTTAGGA-TATTTTATGC
128 GTTACGGTTTATATCTATTTAAGACT-TTTTGTGT
* * * * ** * * * * *
18899836 CATTAAAAGGAAAAAAATATAGTTTTTCAGTTATAT-TTCTATTTTAACAATTTAGATAACTTAA
1 CGTTAAAAAG-CAAAAATGTAAATTTACAATTAT-TGTTCTATTTTAACAGTTTAGATAGCTTTA
* * * * **
18899900 ATACATAATATTAAATTTGT-TCGAATGATTGAA-TT--TTATTCCGACGATTGATATAAGTGAA
64 ATACATGATATTAAACTTGTCT-AAATGATTGAACTTAGTT-TT-C-ACAATTGATATGTGTGAA
* * * * *
18899961 AAAGTTATC-ATTTATATATGTTT-AGCACTTTTTATGC
125 AAAGTTA-CGGTTTATATCTATTTAAG-ACTTTTTGTGT
* * * * * * * *
18899998 CGTTAAAAAGTC-AAAA-GGAAATTTTACAATTAAAT-CTATATTTTAATAATTTATATAGCTTA
1 CGTTAAAAAG-CAAAAATGTAAA-TTTACAATT-ATTGTTCTATTTTAACAGTTTAGATAGCTTT
* * * * * *
18900060 AATACTTGATTTTAAACTTGTCCAAATAATTGAACTT-GATTTTCACAATT-TTATATGT-AAAT
63 AATACATGATATTAAACTTGTCTAAATGATTGAACTTAG-TTTTCACAATTGATATGTGTGAAA-
* * * * * *
18900122 AAGTTATGATTTATGTCTGTTTAAAACTTTTCGTG-
126 AAGTTACGGTTTATATCTATTTAAGACTTTTTGTGT
* ** * * * * * * * * *
18900157 CTATTAAAAAATAAATATGAAAATTTACAGTTATTGTTTTGTTTTAATAGTTTAGACAACTTCAA
1 C-GTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAA
* *
18900222 TGA-ATGATATTAAACTTGTC-GAATGTTTGAACTT
65 T-ACATGATATTAAACTTGTCTAAATGATTGAACTT
18900256 CATTATTGCC
Statistics
Matches: 1099, Mismatches: 219, Indels: 123
0.76 0.15 0.09
Matches are distributed among these distances:
155 2 0.00
156 93 0.08
157 8 0.01
158 24 0.02
159 171 0.16
160 248 0.23
161 415 0.38
162 128 0.12
163 8 0.01
164 2 0.00
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (161 bp):
CGTTAAAAAGCAAAAATGTAAATTTACAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAAT
ACATGATATTAAACTTGTCTAAATGATTGAACTTAGTTTTCACAATTGATATGTGTGAAAAAGTT
ACGGTTTATATCTATTTAAGACTTTTTGTGT
Found at i:18899313 original size:321 final size:319
Alignment explanation
Indices: 18898717--18900255 Score: 1197
Period size: 321 Copynumber: 4.8 Consensus size: 319
18898707 TATTTTATGC
* * * * * * *
18898717 CGTTAAAATGTAAAAATGTAAAATTACAATTATTGTTTTATTTTAAGAATTTAGATAGCTTTAAT
1 CGTTAAAAGGTAAAAATGCAAATTTGCAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAAT
* * * * * * *
18898782 ATATGATATTAAATTTGTTCAAATAATTGAATTTAGTTTTCACGGTTGATAGGCATG-AAAAAA-
66 ACATGATATTAAACTTGTTCAAATGATTGAACTTAGTTTTCATGATTGATATG--TGTAAAAAAG
*** * * * * *
18898845 TTGTGGTTTATATCTATTTAGGATTTTTGTGCCGTTGAAAGGAAAAATATAAATTTACAATTATT
129 TTACAGTTTATATCTATTTAGAATTTTTATGCTGTT-AAAAGAAAAATATAAATTTACAGTTATT
* * * * *
18898910 ATTCTACTTTAACAATTTAGATAGCTTCAATACATGATATTAAACTTGTCTAAATGATTGAACTT
193 GTTCTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCTAAATGATTGAACTT
* *
18898975 AGTTTTCACAATTGATATGTGTGAAAAAGCTACGGTTTATATCTGTTTAAGACTTTTTGTGT
258 AGTTTTCACAATTGATATGTGTGAAAAAGTTACTGTTTATATCTGTTTAAGACTTTTTGTGT
* * *
18899037 CGTTAAAAAGCAAAAATGCAAGTTTGCAATTATTGTTCTATTTTAACAGTTTAGATAG-TTTGAA
1 CGTTAAAAGGTAAAAATGCAAATTTGCAATTATTGTTCTATTTTAACAGTTTAGATAGCTTT-AA
* *
18899101 TGCATGATATTAAACTTGTAT-AAATGATTGAACTT-GTTTTCATAATTGATATGTGTAAAAAAG
65 TACATGATATTAAACTTGT-TCAAATGATTGAACTTAGTTTTCATGATTGATATGTGTAAAAAAG
* *
18899164 TTACAGTTTATATCTTTTTAGAATTTTT-TGAACTGTTAAAAAGCAAAAATATAAATTTATAGTT
129 TTACAGTTTATATCTATTTAGAATTTTTATG--CTGTT-AAAAG-AAAAATATAAATTTACAGTT
* * * *
18899228 ATTGTTATGTTTTAATAGTTTAGATAGCTTTAATACATGATATTAAATTTGTCTGAAAT-ATTAA
190 ATTGTTCTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCT-AAATGATTGA
* * * * *
18899292 ACTTTGTTTTCACAGTTGATATGTGTGAAAAAGTTACTATTTATGT-TAGTTTAGGACTTTTTGT
254 ACTTAGTTTTCACAATTGATATGTGTGAAAAAGTTACTGTTTATATCT-GTTTAAGACTTTTTGT
18899356 GT
318 GT
* * * * *
18899358 CGTT-AAAGGATAAAAAGGTAATTTTGTAGTTATAT-TTCTATTTTAACAGTTT-GTATAGC-TT
1 CGTTAAAAGG-TAAAAATGCAAATTTGCAATTAT-TGTTCTATTTTAACAGTTTAG-ATAGCTTT
* * * * * * * *
18899419 AAGTACATGATATTAAATTTATCCGAATGCTTGAACTTAATTTTCATGATTGATATATGTGAAAA
63 AA-TACATGATATTAAACTTGTTCAAATGATTGAACTTAGTTTTCATGATTGATATGTGTAAAAA
* * * * * * *
18899484 AGTTACCG--T-TGTCTATTTATGACTTTTTATGCTATTAAAAGACAAATGTAGAA-TTGCAGTT
127 AGTTACAGTTTATATCTATTTA-GAATTTTTATGCTGTTAAAAGAAAAATATA-AATTTACAGTT
18899545 ATTGTTCTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCTAAATGATTGAA
190 ATTGTTCTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCTAAATGATTGAA
* ** * *
18899610 -TATGGTTTTCACAATTGATATGTGTGAAAAAGTTGTTGTTTATATCTATTTAAGATTTTTTGTG
255 CT-TAGTTTTCACAATTGATATGTGTGAAAAAGTTACTGTTTATATCTGTTTAAGACTTTTTGTG
18899674 T
319 T
* * * * * *
18899675 TGTTAAAAGGTAAAAATGCAAATTTACTGA-TATTATTCTATTTTAACAGCTTGGATAGCTTTAA
1 CGTTAAAAGGTAAAAATGCAAATTTGC-AATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAA
* ** * * *
18899739 TACATGATATTAAACTTGTTCAAATGATT-AATGTTCTTTTTCAT-AGTTAATATGAGTGAAAAA
65 TACATGATATTAAACTTGTTCAAATGATTGAA-CTTAGTTTTCATGA-TTGATATGTGTAAAAAA
** * * ** ** *
18899802 GTTGTTA-TTTATGTCTATTTAGGATATTTTATGCCATTAAAAGGAAAAAAATATAGTTTTTCAG
128 GTT-ACAGTTTATATCTATTTAGAAT-TTTTATGCTGTTAAAA-G--AAAAATATAAATTTACAG
* * * * * * *
18899866 TTATAT-TTCTATTTTAACAATTTAGATAACTTAAATACATAATATTAAATTTGT-TCGAATGAT
188 TTAT-TGTTCTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCT-AAATGAT
* ** * *
18899929 TGAA-TT--TTATTCCGACGATTGATATAAGTGAAAAAGTTA-TCATTTATATATGTTT-AGCAC
251 TGAACTTAGTT-TT-C-ACAATTGATATGTGTGAAAAAGTTACT-GTTTATATCTGTTTAAG-AC
* *
18899989 TTTTTATGC
311 TTTTTGTGT
* * * * * * * * * * *
18899998 CGTTAAAAAGTCAAAA-GGAAATTTTACAATTAAAT-CTATATTTTAATAATTTATATAGCTTAA
1 CGTTAAAAGGTAAAAATGCAAA-TTTGCAATT-ATTGTTCTATTTTAACAGTTTAGATAGCTTTA
* * * * ** * * *
18900061 ATACTTGATTTTAAACTTGTCCAAATAATTGAACTT-GATTTTCACAATT-TTATATGTAAATAA
64 ATACATGATATTAAACTTGTTCAAATGATTGAACTTAG-TTTTCATGATTGATATGTGTAAAAAA
* * * * ** *
18900124 GTTA-TGATTTATGTCTGTTTAAAACTTTTCGTGCTATTAAAA-AATAAATATGAAAATTTACAG
128 GTTACAG-TTTATATCTATTTAGAA-TTTTTATGCTGTTAAAAGAA-AAATAT--AAATTTACAG
* * * * * * *
18900187 TTATTGTTTTGTTTTAATAGTTTAGACAACTTCAATGA-ATGATATTAAACTTGTC-GAATGTTT
188 TTATTGTTCTATTTTAATAGTTTAGATAGCTTTAAT-ACATGATATTAAACTTGTCTAAATGATT
18900250 GAACTT
252 GAACTT
18900256 CATTATTGCC
Statistics
Matches: 981, Mismatches: 177, Indels: 121
0.77 0.14 0.09
Matches are distributed among these distances:
316 9 0.01
317 212 0.22
318 28 0.03
319 61 0.06
320 141 0.14
321 254 0.26
322 85 0.09
323 185 0.19
324 6 0.01
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (319 bp):
CGTTAAAAGGTAAAAATGCAAATTTGCAATTATTGTTCTATTTTAACAGTTTAGATAGCTTTAAT
ACATGATATTAAACTTGTTCAAATGATTGAACTTAGTTTTCATGATTGATATGTGTAAAAAAGTT
ACAGTTTATATCTATTTAGAATTTTTATGCTGTTAAAAGAAAAATATAAATTTACAGTTATTGTT
CTATTTTAATAGTTTAGATAGCTTTAATACATGATATTAAACTTGTCTAAATGATTGAACTTAGT
TTTCACAATTGATATGTGTGAAAAAGTTACTGTTTATATCTGTTTAAGACTTTTTGTGT
Found at i:18899996 original size:162 final size:162
Alignment explanation
Indices: 18899710--18900005 Score: 348
Period size: 162 Copynumber: 1.8 Consensus size: 162
18899700 ACTGATATTA
* * * * *
18899710 TTCTATTTTAACAGCTTGGATAGCTTTAATACATGATATTAAACTTGTTCAAATGATTAATGTTC
1 TTCTATTTTAACAACTTAGATAACTTAAATACATAATATTAAACTTGTTCAAATGATTAATGTTC
* * * * * * * * *
18899775 TTTTTCATAGTTAATATGAGTGAAAAAGTTGTTATTTATGTCTATTTAGGATATTTTATGCCATT
66 TATTCCAGAGTTAATATAAGTGAAAAAGTTATCATTTATATATATTTAGCATATTTTATGCCATT
18899840 AAAAGGAAAAAAATATAGTTTTTCAGTTATAT
131 AAAAGGAAAAAAATATAGTTTTTCAGTTATAT
* * *
18899872 TTCTATTTTAACAATTTAGATAACTTAAATACATAATATTAAATTTGTTCGAATGATTGAAT-TT
1 TTCTATTTTAACAACTTAGATAACTTAAATACATAATATTAAACTTGTTCAAATGATT-AATGTT
* *
18899936 -TATTCC-GACGATTGATATAAGTGAAAAAGTTATCATTTATATATGTTTAGCACT-TTTTATGC
65 CTATTCCAGA-G-TTAATATAAGTGAAAAAGTTATCATTTATATATATTTAGCA-TATTTTATGC
*
18899998 CGTTAAAA
127 CATTAAAA
18900006 AGTCAAAAGG
Statistics
Matches: 110, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
160 1 0.01
161 5 0.05
162 100 0.91
163 4 0.04
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (162 bp):
TTCTATTTTAACAACTTAGATAACTTAAATACATAATATTAAACTTGTTCAAATGATTAATGTTC
TATTCCAGAGTTAATATAAGTGAAAAAGTTATCATTTATATATATTTAGCATATTTTATGCCATT
AAAAGGAAAAAAATATAGTTTTTCAGTTATAT
Found at i:18900963 original size:26 final size:26
Alignment explanation
Indices: 18900923--18900972 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
18900913 TAAGTGGTCT
18900923 ACCAACTCAAATATTATATTTAGTCC
1 ACCAACTCAAATATTATATTTAGTCC
*
18900949 ACCAACTCAAGTATTATATTTAGT
1 ACCAACTCAAATATTATATTTAGT
18900973 ATGATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (26 bp):
ACCAACTCAAATATTATATTTAGTCC
Found at i:18906596 original size:13 final size:13
Alignment explanation
Indices: 18906580--18906615 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
18906570 TTCAAACATA
*
18906580 TATTTCTTAATTT
1 TATTGCTTAATTT
18906593 TATTGCTTAATTT
1 TATTGCTTAATTT
18906606 TATTGCTTAA
1 TATTGCTTAA
18906616 AAACCAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (13 bp):
TATTGCTTAATTT
Found at i:18909132 original size:54 final size:54
Alignment explanation
Indices: 18909065--18909223 Score: 205
Period size: 54 Copynumber: 3.0 Consensus size: 54
18909055 AGTGAACAAA
18909065 AAAAAAAAGAAAAAAAATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAAT
1 AAAAAAAAGAAAAAAAATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAAT
* * * * *
18909119 AAAAAAAAGAAAAAAAAATTCTAAATAGGCTCAAATGGTGAAAAATTTAAAAAT
1 AAAAAAAAGAAAAAAAATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAAT
*** * * *
18909173 -TTTAAAA-AAAAAATATTTCTAAATTGACCCAAATTGTGGAAAATTTAGAAA
1 AAAAAAAAGAAAAAAAATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAA
18909224 CCAAAAAATA
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
52 36 0.40
53 4 0.04
54 49 0.55
ACGTcount: A:0.58, C:0.07, G:0.11, T:0.25
Consensus pattern (54 bp):
AAAAAAAAGAAAAAAAATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAAT
Found at i:18909202 original size:106 final size:111
Alignment explanation
Indices: 18909074--18909309 Score: 310
Period size: 106 Copynumber: 2.1 Consensus size: 111
18909064 AAAAAAAAAG
*
18909074 AAAAAAA-ATTTCTAAATTGACCCAAATGGTGAAAAATTTAG-AA-ATAAAA-AAA-AG-A-AAA
1 AAAAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAACAAAAAATAAATAGAATAAA
18909132 AA-AAATTCTAAATAGG-CTCAAATGGTGAAAAATTTAAAAATTTTAAA
66 AAGAAATTCTAAATAGGTC-CAAATGGTGAAAAATTT-AAAA-TTTAAA
* *
18909179 AAAAAAATATTTCTAAATTGACCCAAATTGTGGAAAATTTAGAAACCAAAAAATAAATAGATAAA
1 AAAAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAA-CAAAAAATAAATAG---AA
*
18909244 TAAAAAGAAATTTTAAATAGGTCCAAATGGTGAAAAATTTAAAATTTAAA
62 TAAAAAGAAATTCTAAATAGGTCCAAATGGTGAAAAATTTAAAATTTAAA
18909294 AAAAAAATATTTCTAA
1 AAAAAAATATTTCTAA
18909310 TTTTGGCTCA
Statistics
Matches: 114, Mismatches: 4, Indels: 16
0.85 0.03 0.12
Matches are distributed among these distances:
105 7 0.06
106 32 0.28
107 2 0.02
109 5 0.04
110 3 0.03
111 2 0.02
115 23 0.20
116 9 0.08
117 30 0.26
118 1 0.01
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (111 bp):
AAAAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAACAAAAAATAAATAGAATAAA
AAGAAATTCTAAATAGGTCCAAATGGTGAAAAATTTAAAATTTAAA
Found at i:18911358 original size:27 final size:28
Alignment explanation
Indices: 18911314--18911366 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
18911304 AACATATATT
18911314 ATATAATATAATGATTTTTTATATTAGA
1 ATATAATATAATGATTTTTTATATTAGA
* *
18911342 ATATAAT-TATTGTTTTTTTATATTA
1 ATATAATATAATGATTTTTTATATTA
18911367 TGAGTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (28 bp):
ATATAATATAATGATTTTTTATATTAGA
Found at i:18915265 original size:17 final size:18
Alignment explanation
Indices: 18915243--18915283 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
18915233 CAATTTGTCT
18915243 AAAAATACGAAATA-AA-A
1 AAAAATA-GAAATACAATA
18915260 AAAAAT-GAAATACAATA
1 AAAAATAGAAATACAATA
18915277 AAAAATA
1 AAAAATA
18915284 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 13 0.62
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAGAAATACAATA
Found at i:18915295 original size:19 final size:19
Alignment explanation
Indices: 18915252--18915307 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
18915242 TAAAAATACG
*
18915252 AAATAA-AAAAAA-ATGAA
1 AAATAATAAAAAATATAAA
* *
18915269 ATACAATAAAAAATATAAA
1 AAATAATAAAAAATATAAA
* *
18915288 AAATAATACAAAATACAAA
1 AAATAATAAAAAATATAAA
18915307 A
1 A
18915308 CAAAATCTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 20 0.67
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (19 bp):
AAATAATAAAAAATATAAA
Found at i:18915338 original size:19 final size:19
Alignment explanation
Indices: 18915316--18915357 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
18915306 AACAAAATCT
18915316 AAAACAAAAAATACAAAAA
1 AAAACAAAAAATACAAAAA
* *
18915335 AAAACAGAAAATAGAAAAA
1 AAAACAAAAAATACAAAAA
18915354 AAAA
1 AAAA
18915358 TAGAGGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.83, C:0.07, G:0.05, T:0.05
Consensus pattern (19 bp):
AAAACAAAAAATACAAAAA
Found at i:18915352 original size:26 final size:26
Alignment explanation
Indices: 18915292--18915353 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
18915282 TATAAAAAAT
* * *
18915292 AATACAAAATACAAAACAAAATCTAA
1 AATAAAAAATACAAAACAAAAACGAA
*
18915318 AACAAAAAATACAAAA-AAAAACAGAA
1 AATAAAAAATACAAAACAAAAAC-GAA
18915344 AATAGAAAAA
1 AATA-AAAAA
18915354 AAAATAGAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 5 0.17
26 19 0.66
27 5 0.17
ACGTcount: A:0.76, C:0.11, G:0.03, T:0.10
Consensus pattern (26 bp):
AATAAAAAATACAAAACAAAAACGAA
Found at i:18915731 original size:22 final size:21
Alignment explanation
Indices: 18915685--18915735 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
18915675 CACGAAGAAG
* *
18915685 AAAAAAAAAGATCAGTTTCAT
1 AAAAAAAAAGATCAGATACAT
18915706 AAAAAAAAAGAGTCAGAATACA-
1 AAAAAAAAAGA-TCAG-ATACAT
18915728 AAAAAAAA
1 AAAAAAAA
18915736 GTCTCACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 12 0.46
23 3 0.12
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.14
Consensus pattern (21 bp):
AAAAAAAAAGATCAGATACAT
Found at i:18922125 original size:18 final size:18
Alignment explanation
Indices: 18922074--18922137 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
18922064 CAATTTGTCT
* *
18922074 AAATATGAATACAATAAA
1 AAATATAAAAACAATAAA
*
18922092 AAA-ATGAAATACAATAAA
1 AAATAT-AAAAACAATAAA
* *
18922110 AAATATAAAAATAATACA
1 AAATATAAAAACAATAAA
*
18922128 AAATACAAAA
1 AAATATAAAA
18922138 CAAATCTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
17 2 0.05
18 35 0.90
19 2 0.05
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATATAAAAACAATAAA
Found at i:18922130 original size:11 final size:11
Alignment explanation
Indices: 18922098--18922186 Score: 55
Period size: 11 Copynumber: 8.3 Consensus size: 11
18922088 TAAAAAAATG
18922098 AAATACAATAAA
1 AAATACAA-AAA
*
18922110 AAATATAAAAA
1 AAATACAAAAA
*
18922121 TAATAC----A
1 AAATACAAAAA
*
18922128 AAATACAAAAC
1 AAATACAAAAA
18922139 AAAT-CTAAAACAA
1 AAATAC--AAA-AA
18922152 AAATACAAAAA
1 AAATACAAAAA
*
18922163 AAAAAC-AAAA
1 AAATACAAAAA
*
18922173 AAATAGAAAAA
1 AAATACAAAAA
18922184 AAA
1 AAA
18922187 ATAAAGGATG
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
7 6 0.10
10 9 0.15
11 25 0.42
12 13 0.22
13 5 0.08
14 1 0.02
ACGTcount: A:0.78, C:0.09, G:0.01, T:0.12
Consensus pattern (11 bp):
AAATACAAAAA
Found at i:18922167 original size:19 final size:20
Alignment explanation
Indices: 18922145--18922187 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
18922135 AAACAAATCT
18922145 AAAAC-AAAAATACAAAAAA
1 AAAACAAAAAATACAAAAAA
*
18922164 AAAACAAAAAAATAGAAAAAA
1 AAAAC-AAAAAATACAAAAAA
18922185 AAA
1 AAA
18922188 TAAAGGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (20 bp):
AAAACAAAAAATACAAAAAA
Found at i:18922539 original size:21 final size:21
Alignment explanation
Indices: 18922513--18922564 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18922503 CACGAAGAAG
**
18922513 AAAAAAAAAGA-TCAGTTTCAT
1 AAAAAAAAAGAGTCAGAAT-AT
18922534 AAAAAAAAAGAGTCAGAATAT
1 AAAAAAAAAGAGTCAGAATAT
18922555 AAAAAAAAAG
1 AAAAAAAAAG
18922565 TCTCACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (21 bp):
AAAAAAAAAGAGTCAGAATAT
Found at i:18924976 original size:9 final size:9
Alignment explanation
Indices: 18924918--18924978 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
18924908 AATACGAAAC
18924918 AAAACAAAA
1 AAAACAAAA
*
18924927 CAAACAAAA
1 AAAACAAAA
**
18924936 AATCTCAAAA
1 AA-AACAAAA
18924946 CACGAAACAAAA
1 -A--AAACAAAA
*
18924958 AAAACTAAA
1 AAAACAAAA
18924967 AAAACAAAA
1 AAAACAAAA
18924976 AAA
1 AAA
18924979 TATTTTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 27 0.68
10 5 0.12
11 2 0.05
12 5 0.12
13 1 0.03
ACGTcount: A:0.77, C:0.16, G:0.02, T:0.05
Consensus pattern (9 bp):
AAAACAAAA
Found at i:18925701 original size:50 final size:49
Alignment explanation
Indices: 18925626--18925767 Score: 194
Period size: 50 Copynumber: 3.0 Consensus size: 49
18925616 AATAATAGAT
18925626 GAGTGGCATAGAAGGGAAAAAGATTGGATCTTCACATGTGATTCAGAAAG
1 GAGTGGCATAGAA-GGAAAAAGATTGGATCTTCACATGTGATTCAGAAAG
18925676 GAGTGGCATAGAAGGAAAAAAGATTGGATCTTCACATGTGATTCAGAAAG
1 GAGTGGCATAGAAGG-AAAAAGATTGGATCTTCACATGTGATTCAGAAAG
18925726 G-GAT-GC-T------AAAAAGATTGGATCTTCACATGTGATTCAGAAAG
1 GAG-TGGCATAGAAGGAAAAAGATTGGATCTTCACATGTGATTCAGAAAG
18925767 G
1 G
18925768 GATGCTCACA
Statistics
Matches: 90, Mismatches: 0, Indels: 13
0.87 0.00 0.13
Matches are distributed among these distances:
41 35 0.39
48 1 0.01
49 5 0.06
50 49 0.54
ACGTcount: A:0.38, C:0.11, G:0.28, T:0.23
Consensus pattern (49 bp):
GAGTGGCATAGAAGGAAAAAGATTGGATCTTCACATGTGATTCAGAAAG
Found at i:18925749 original size:41 final size:41
Alignment explanation
Indices: 18925692--18925773 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
18925682 CATAGAAGGA
18925692 AAAAAGATTGGATCTTCACATGTGATTCAGAAAGGGATGCT
1 AAAAAGATTGGATCTTCACATGTGATTCAGAAAGGGATGCT
18925733 AAAAAGATTGGATCTTCACATGTGATTCAGAAAGGGATGCT
1 AAAAAGATTGGATCTTCACATGTGATTCAGAAAGGGATGCT
18925774 CACATGAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
AAAAAGATTGGATCTTCACATGTGATTCAGAAAGGGATGCT
Found at i:18933210 original size:16 final size:16
Alignment explanation
Indices: 18933180--18933236 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
18933170 TTTAATATTT
*
18933180 TTTTTATGTTATTTTA
1 TTTTTATTTTATTTTA
*
18933196 TTTTT-CTTTATTTTTA
1 TTTTTATTTTA-TTTTA
18933212 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
18933228 -TTTTATTTT
1 TTTTTATTTT
18933237 CTTTAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.33
16 20 0.56
17 4 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:18933211 original size:6 final size:5
Alignment explanation
Indices: 18933175--18933236 Score: 74
Period size: 5 Copynumber: 12.2 Consensus size: 5
18933165 AATTGTTTAA
*
18933175 TATTT T-TTT TATGT TATTT TATTT T-TCTT TATTTT TATTTT TATTT
1 TATTT TATTT TATTT TATTT TATTT TAT-TT TA-TTT TA-TTT TATTT
18933221 TATTT TATTT TATTT T
1 TATTT TATTT TATTT T
18933237 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
4 5 0.10
5 35 0.69
6 10 0.20
7 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:18933218 original size:27 final size:26
Alignment explanation
Indices: 18933180--18933236 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
18933170 TTTAATATTT
18933180 TTTTTATGTTATTTTATTTT-TCTTTA
1 TTTTTATGTTATTTTATTTTAT-TTTA
*
18933206 TTTTTATTTTTATTTTATTTTATTTTA
1 TTTTTA-TGTTATTTTATTTTATTTTA
18933233 TTTT
1 TTTT
18933237 CTTTAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 6 0.21
27 21 0.75
28 1 0.04
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (26 bp):
TTTTTATGTTATTTTATTTTATTTTA
Found at i:18933324 original size:58 final size:56
Alignment explanation
Indices: 18933255--18933535 Score: 327
Period size: 58 Copynumber: 4.9 Consensus size: 56
18933245 AAAATTCAAA
*
18933255 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAGTTTTC
* * * *
18933312 TAAAATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCTTAAA
1 -AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATAAG--TT-TT--C
**
18933375 AAAAAATATTTTTG-GAGAAAAGTTGAAAGTATTGATTTTCCTTAAAAGTAAGTTTTC
1 AAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAA-TAAGTTTTC
*
18933432 -AAAAATA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAACAAGTTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTA-AAATAAGTTTTC
* *
18933487 -AAAAGTGAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAT
1 AAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAT
18933536 TAAAGTTTCA
Statistics
Matches: 194, Mismatches: 17, Indels: 25
0.82 0.07 0.11
Matches are distributed among these distances:
55 44 0.23
56 11 0.06
57 4 0.02
58 82 0.42
59 2 0.01
60 4 0.02
61 7 0.04
62 40 0.21
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (56 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAGTTTTC
Found at i:18933351 original size:27 final size:27
Alignment explanation
Indices: 18933262--18933352 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
18933252 AAAAAAAAAT
*
18933262 ATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTTGAGAAAAAGTTGAAAGTATCA
* * * *
18933289 ATTTTCCTTGAAAATAAATTTTCTAAAATAT--
1 A-TTT--TTGAGAA-AAA-GTT-GAAAGTATCA
18933320 ATTTTTGAGAAAAAGTTGAAAGTATCA
1 ATTTTTGAGAAAAAGTTGAAAGTATCA
18933347 ATTTTT
1 ATTTTT
18933353 CTTGAAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
25 6 0.13
26 2 0.04
27 10 0.21
28 9 0.19
30 8 0.17
31 4 0.09
32 2 0.04
33 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (27 bp):
ATTTTTGAGAAAAAGTTGAAAGTATCA
Found at i:18933383 original size:120 final size:114
Alignment explanation
Indices: 18933252--18933546 Score: 364
Period size: 120 Copynumber: 2.5 Consensus size: 114
18933242 AATAAAATTC
18933252 AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAA-TAAATTTTCTAAA
1 AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAGTAAATTTTC-AAA
* *
18933316 ATATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTT-GAAAATAAGCTTTCTT
64 A-ATA-TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAG-AAACAAG--TT-TT
** *
18933372 AAAAAAAAATATTTTTG-GAGAAAAGTTGAAAGTATTGATTTTCCTTAAAAGTAAGTTTTCAAAA
1 AAAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTCAAAA
*
18933436 ATATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAACAAGTTTT
65 ATATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAACAAGTTTT
* *** * * *
18933486 CAAAAGTGA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCAA
1 AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTCAA
18933547 TTTTCCCTAT
Statistics
Matches: 155, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
113 44 0.28
114 8 0.05
115 2 0.01
117 38 0.25
118 4 0.03
119 9 0.06
120 50 0.32
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (114 bp):
AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTCAAAAA
TATTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAACAAGTTTT
Found at i:18933525 original size:27 final size:27
Alignment explanation
Indices: 18933439--18933526 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
18933429 TTCAAAAATA
18933439 TTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTGAGGAAAAGTTGAAAGTATCAAT
* * * *
18933466 TTTCCTTAGAAACAAGTTTTCAAA--AGTGAAT
1 TTT--TGAGGAA-AAG--TTGAAAGTA-TCAAT
18933497 TTTTGAGGAAAAGTTGAAAGTATCAAT
1 TTTTGAGGAAAAGTTGAAAGTATCAAT
18933524 TTT
1 TTT
18933527 CCTCAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
26 5 0.11
27 10 0.22
28 4 0.09
29 10 0.22
30 4 0.09
31 7 0.16
32 5 0.11
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (27 bp):
TTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:18935347 original size:59 final size:58
Alignment explanation
Indices: 18935248--18935649 Score: 582
Period size: 59 Copynumber: 6.9 Consensus size: 58
18935238 TTTTTTTTAG
***
18935248 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTTG-AAATTTATTTCTAA
*
18935307 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAA-TTT-ATTTCT-AA
*
18935368 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTC-TAA
*
18935425 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
18935483 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAATTTATTTCTAA
* *
18935542 GGAAAATTGATATTTTCAACTTTTTCCC-AAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
*
18935599 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTGAAATTT
18935650 TTTATTTTTA
Statistics
Matches: 315, Mismatches: 14, Indels: 28
0.88 0.04 0.08
Matches are distributed among these distances:
56 9 0.03
57 84 0.27
58 55 0.17
59 106 0.34
60 21 0.07
61 40 0.13
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
Found at i:18935610 original size:174 final size:176
Alignment explanation
Indices: 18935248--18935649 Score: 636
Period size: 174 Copynumber: 2.3 Consensus size: 176
18935238 TTTTTTTTAG
***
18935248 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTTG-AAATTTATTTCTAAGGAAA
18935312 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGGAAAATTG
64 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGGAAAATTG
18935377 ATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTCTTAA
129 ATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTCTTAA
*
18935425 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
* *
18935490 TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAA-TTT-A-TTTCTGAGGAAAATTGA
66 TGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTC-AAGGAAAATTGA
*
18935552 TATTTTCAACTTTTTCCC-AAAAATATTTTTTGGAAATTTATT-TCTAA
130 TACTTTCAAC-TTTTCCCTAAAAATATTTTTTGGAAATTTATTCT-TAA
*
18935599 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAATTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTGAAATTT
18935650 TTTATTTTTA
Statistics
Matches: 212, Mismatches: 8, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
173 5 0.02
174 84 0.40
175 23 0.11
176 60 0.28
177 37 0.17
178 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (176 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGGAAAATTGAT
ACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTCTTAA
Found at i:18935738 original size:12 final size:11
Alignment explanation
Indices: 18935718--18935784 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
18935708 AACCTAATCT
*
18935718 AATAAATAAAA
1 AATAAAAAAAA
18935729 AATAAAATAAACA
1 AATAAAA-AAA-A
*
18935742 AATAAACAAAGA
1 AATAAA-AAAAA
18935754 AATAAAAAAAA
1 AATAAAAAAAA
* *
18935765 ATTCAAAAAAA
1 AATAAAAAAAA
18935776 AA-AAAAAAA
1 AATAAAAAAA
18935785 CCTGGAGTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
10 6 0.13
11 20 0.43
12 10 0.22
13 9 0.20
14 1 0.02
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:18937771 original size:48 final size:50
Alignment explanation
Indices: 18937688--18937782 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
18937678 TCTAAATAGG
*
18937688 CCCAAATGGTAAAAAATTTAGAAATTCCAAAAAAAAAA-AAATAAATTAA
1 CCCAAATGATAAAAAATTTAGAAATTCCAAAAAAAAAATAAATAAATTAA
* *
18937737 CCCAAATGATGAAAAATTTAGAAA-TCCAACAAAAAAATAAATAAAT
1 CCCAAATGATAAAAAATTTAGAAATTCCAAAAAAAAAATAAATAAAT
18937783 AAAGAGAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 12 0.29
49 30 0.71
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.20
Consensus pattern (50 bp):
CCCAAATGATAAAAAATTTAGAAATTCCAAAAAAAAAATAAATAAATTAA
Found at i:18941822 original size:17 final size:18
Alignment explanation
Indices: 18941761--18941827 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 18
18941751 CTAATGGATG
*
18941761 GAAAAAA-TGAAAAAAGA
1 GAAAAAATTAAAAAAAGA
* *
18941778 GAAAAAA-TCAACAAAGA
1 GAAAAAATTAAAAAAAGA
*
18941795 GAAAAATTTAAAAAAAGA
1 GAAAAAATTAAAAAAAGA
18941813 -AAAAAATTAAAAAAA
1 GAAAAAATTAAAAAAA
18941828 TAAAGGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 35 0.81
18 8 0.19
ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10
Consensus pattern (18 bp):
GAAAAAATTAAAAAAAGA
Found at i:18942274 original size:12 final size:12
Alignment explanation
Indices: 18942257--18942281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18942247 TGTATGATTG
18942257 CATTATACTTGT
1 CATTATACTTGT
18942269 CATTATACTTGT
1 CATTATACTTGT
18942281 C
1 C
18942282 CTAATTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (12 bp):
CATTATACTTGT
Found at i:18942432 original size:12 final size:12
Alignment explanation
Indices: 18942415--18942444 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18942405 TTGGAAGGAT
18942415 ATATGGTGATGA
1 ATATGGTGATGA
18942427 ATATGGTGATGA
1 ATATGGTGATGA
18942439 AT-TGGT
1 ATATGGT
18942445 CAACATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:18942540 original size:79 final size:77
Alignment explanation
Indices: 18942453--18942649 Score: 245
Period size: 79 Copynumber: 2.5 Consensus size: 77
18942443 GTCAACATAA
* * * *
18942453 CTTGTGAATTGTGATCGAATGATGAAAATAATATGGATTA-ATGGACATAATTTATTCTTA-AAT
1 CTTGTGAATGGTGATCGAATGATGAAAATAATGTGGATCAGA-GGACATAATTTATT-ATAGAAT
18942516 GGTTAGTGCTGAAAAG
64 GGTTA--GCTGAAAAG
* *
18942532 CTTGTGAATGGTGATTGAATGATGAAAATAATGTGGATCAGAGGACATAATTTATTATAGATTGG
1 CTTGTGAATGGTGATCGAATGATGAAAATAATGTGGATCAGAGGACATAATTTATTATAGAATGG
*
18942597 TTAGCTGAGAAG
66 TTAGCTGAAAAG
* * * *
18942609 CCTATGAATGGTGATCAAATAATGAAAATAATGTGGATCAG
1 CTTGTGAATGGTGATCGAATGATGAAAATAATGTGGATCAG
18942650 GGGATAGCAT
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
77 44 0.42
78 2 0.02
79 57 0.55
80 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (77 bp):
CTTGTGAATGGTGATCGAATGATGAAAATAATGTGGATCAGAGGACATAATTTATTATAGAATGG
TTAGCTGAAAAG
Found at i:18943200 original size:21 final size:21
Alignment explanation
Indices: 18943171--18943578 Score: 381
Period size: 21 Copynumber: 18.8 Consensus size: 21
18943161 ATGAATTCTT
*
18943171 AAATGAGAATCTTTCAGTTTC
1 AAATGAGAATCTTTGAGTTTC
* *
18943192 AAATAAGAATCTTTGGGTTTC
1 AAATGAGAATCTTTGAGTTTC
*
18943213 AAATGAGAATCTTTGGGTTTC
1 AAATGAGAATCTTTGAGTTTC
* *
18943234 AAATGAAAATATTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTC
* * *
18943255 AAATGAGAATCGTTAAGTTTA
1 AAATGAGAATCTTTGAGTTTC
18943276 AAATGAGAATCTTT-AGGTTTC
1 AAATGAGAATCTTTGA-GTTTC
*
18943297 AAATAAGAATCTTTGAGTCTTC
1 AAATGAGAATCTTTGAGT-TTC
* *
18943319 AAATGAGAATTTTTTAGTTTC
1 AAATGAGAATCTTTGAGTTTC
* * *
18943340 AAATAAGAATCTTTAAGATTC
1 AAATGAGAATCTTTGAGTTTC
* *
18943361 AAATGAGAATCTTTAAGATTC
1 AAATGAGAATCTTTGAGTTTC
*
18943382 AAATGAGAATCTTTAAGACATTTTC
1 AAATGAGAATCTTT--G--AGTTTC
* * * *
18943407 ACACGAGAACCTTTGAGTTTT
1 AAATGAGAATCTTTGAGTTTC
*
18943428 AAATGAGAATCTTTAAGACATTTTC
1 AAATGAGAATCTTT--G--AGTTTC
18943453 AAATGAGAA-CTTTGAGTATT-
1 AAATGAGAATCTTTGAGT-TTC
18943473 AAATGAGAATCTTTAAGATGTTTTC
1 AAATGAGAATCTTT--GA-G-TTTC
* *
18943498 AAATAAGAACCTTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTC
* *
18943519 AAATGAGAGTCTTTAAGTTTTC
1 AAATGAGAATCTTTGAG-TTTC
* *
18943541 AAATGAGAATTTTTAAGTTTC
1 AAATGAGAATCTTTGAGTTTC
*
18943562 AAATAAGAATCTTTGAG
1 AAATGAGAATCTTTGAG
18943579 ATGAGAAATT
Statistics
Matches: 320, Mismatches: 48, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
20 12 0.04
21 214 0.67
22 40 0.12
23 6 0.02
24 7 0.02
25 41 0.13
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTTTC
Found at i:18943353 original size:127 final size:127
Alignment explanation
Indices: 18943171--18943578 Score: 394
Period size: 127 Copynumber: 3.1 Consensus size: 127
18943161 ATGAATTCTT
* * * *
18943171 AAATGAGAATCTTTCAGTTTCAAATAAGAATCTTTGGGTTTCAAATGAGAATCTTTGGGTTTCAA
1 AAATAAGAATCTTTGAGTTTCAAATGAGAATCTTTGAGTTTCAAATGAGAATCTTTGGGTTTCAA
* * *
18943236 ATGAAAATATTTGAGTTTCAAATGAGAATCGTTAAG-TTTAAAATGAGAATCTTTAGGTTTC
66 ATGAAAATCTTTGAGTTTCAAATGAGAATCTTTAAGATTTCAAATGAGAATCTTTAGGTTTC
* * * ** *
18943297 AAATAAGAATCTTTGAGTCTTCAAATGAGAATTTTTTAGTTTCAAATAAGAATCTTTAAGATTCA
1 AAATAAGAATCTTTGAGT-TTCAAATGAGAATCTTTGAGTTTCAAATGAGAATCTTTGGGTTTCA
* * * * * *
18943362 AATGAGAATCTTTAAGATTCAAATGAGAATCTTTAAGACATTTTCACACGAGAACCTTT-GAGTT
65 AATGAAAATCTTTGAGTTTCAAATGAGAATCTTTAAG--A-TTTCAAATGAGAATCTTTAG-GTT
*
18943426 TT
126 TC
* *
18943428 AAATGAGAATCTTTAAGACATTTTCAAATGAGAA-CTTTGAGTATT-AAATGAGAATCTTTAAGA
1 AAATAAGAATCTTT--G--AGTTTCAAATGAGAATCTTTGAGT-TTCAAATGAGAATCTTT--G-
* * * * *
18943491 TGTTTTCAAAT-AAGAACCTTTGAGTTTCAAATGAGAGTCTTTAAGTTTTCAAATGAGAATTTTT
58 -GGTTTCAAATGAA-AATCTTTGAGTTTCAAATGAGAATCTTTAAGATTTCAAATGAGAATCTTT
*
18943555 AAGTTTC
121 AGGTTTC
18943562 AAATAAGAATCTTTGAG
1 AAATAAGAATCTTTGAG
18943579 ATGAGAAATT
Statistics
Matches: 222, Mismatches: 43, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
126 16 0.07
127 70 0.32
130 2 0.01
131 31 0.14
132 1 0.00
133 20 0.09
134 45 0.20
135 2 0.01
136 1 0.00
137 34 0.15
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.37
Consensus pattern (127 bp):
AAATAAGAATCTTTGAGTTTCAAATGAGAATCTTTGAGTTTCAAATGAGAATCTTTGGGTTTCAA
ATGAAAATCTTTGAGTTTCAAATGAGAATCTTTAAGATTTCAAATGAGAATCTTTAGGTTTC
Found at i:18943497 original size:91 final size:91
Alignment explanation
Indices: 18943171--18943581 Score: 378
Period size: 85 Copynumber: 4.7 Consensus size: 91
18943161 ATGAATTCTT
* * **
18943171 AAATGAGAATCTTTCAG--TTTCAAATAAGAATCTTTGGGT-TTCAAATGAGAATCTTT--G--G
1 AAATGAGAATCTTTAAGATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGATG
* * **
18943229 GTTTCAAATGAA-AATATTTGAGTTTC
66 TTTTCAAA-CAAGAACCTTTGAGTTTC
* * * *
18943255 AAATGAGAATCGTTAAG--TTTAAAATGAGAATCTTTAGGT-TTCAAATAAGAATCTTT--GA-G
1 AAATGAGAATCTTTAAGATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGATG
* ** ** *
18943314 TCTTCAAATGAGAATTTTTTAGTTTC
66 TTTTCAAACAAGAACCTTTGAGTTTC
* **
18943340 AAATAAGAATCTTTAAGA--TTCAAATGAGAATCTTTAAG-ATTCAAATGAGAATCTTTAAGACA
1 AAATGAGAATCTTTAAGATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGATG
* * *
18943402 TTTTCACACGAGAACCTTTGAGTTTT
66 TTTTCAAACAAGAACCTTTGAGTTTC
*
18943428 AAATGAGAATCTTTAAGACATTTTCAAATGAGAA-CTTTGAGTATT-AAATGAGAATCTTTAAGA
1 AAATGAGAATCTTTAAG--ATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGA
*
18943491 TGTTTTCAAATAAGAACCTTTGAGTTTC
64 TGTTTTCAAACAAGAACCTTTGAGTTTC
* * * *
18943519 AAATGAGAGTCTTTAAG-TTTTCAAATGAGAATTTTTAAGT-TTCAAATAAGAATCTTTGAGATG
1 AAATGAGAATCTTTAAGATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGATG
18943582 AGAAATTTGT
Statistics
Matches: 275, Mismatches: 38, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
84 52 0.19
85 68 0.25
87 2 0.01
88 51 0.19
89 24 0.09
90 1 0.00
91 62 0.23
92 15 0.05
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (91 bp):
AAATGAGAATCTTTAAGATTTTCAAATGAGAATCTTTAAGTATTCAAATGAGAATCTTTAAGATG
TTTTCAAACAAGAACCTTTGAGTTTC
Found at i:18943815 original size:20 final size:20
Alignment explanation
Indices: 18943790--18943830 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18943780 CCCAAATTTG
*
18943790 TCAAATGTGAACCTTTGAAC
1 TCAAATGAGAACCTTTGAAC
*
18943810 TCAAATGAGAAGCTTTGAAC
1 TCAAATGAGAACCTTTGAAC
18943830 T
1 T
18943831 TTTGGATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
TCAAATGAGAACCTTTGAAC
Found at i:18944001 original size:14 final size:14
Alignment explanation
Indices: 18943982--18944018 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18943972 CTTGCATATT
*
18943982 TGAAATTTTGAGAC
1 TGAAATTTTGAGAA
18943996 TGAAATTTTGAGAA
1 TGAAATTTTGAGAA
*
18944010 TCAAATTTT
1 TGAAATTTT
18944019 AGTGATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (14 bp):
TGAAATTTTGAGAA
Found at i:18944270 original size:41 final size:40
Alignment explanation
Indices: 18944155--18944487 Score: 294
Period size: 41 Copynumber: 8.0 Consensus size: 40
18944145 ATTATCAAGG
* * * *
18944155 AGCTTTTATTTTACAAAGTCATTGTGCCTCTGTTTAAAGG
1 AGCTTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
* * * *
18944195 AGTTTTTATTTTTCAAAATCGTTGTGCCTCTGTTTAGAGA
1 AGCTTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
* * *
18944235 AGCTTTTATTTTTCAAAAGTCGTTGAACCTCTGTTTAAATG-
1 AGCTTTTATTTTTC-AAAGTCATTGAGCCTCTGTTTAGA-GA
18944276 AGCCTTTTATTTTTCAAAGTCATTGAGCCTCTG-TTAGA-A
1 AG-CTTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
**
18944315 GAGCTTAATTTATTTTTCAAAGTCATTGAGCCTCTACTTAGAGA
1 -AGC-T--TTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
* * *
18944359 AGCATTATTCATTTTTCAAAATCATTGAGCCTTTGTTTAGAGG
1 AGC-TT-TT-ATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
* * * * *
18944402 AGCCTTTTATTTTTTAAAGCCATTGAACCTCTATTTAGAGG
1 AG-CTTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
* * *
18944443 AGCTTAATTTTATTTTTCAAAGTTATTGAGTCTCTATTTAGAGA
1 AGC----TTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
18944487 A
1 A
18944488 AATCCGAGTA
Statistics
Matches: 243, Mismatches: 33, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.00
40 55 0.23
41 68 0.28
42 44 0.18
43 41 0.17
44 34 0.14
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (40 bp):
AGCTTTTATTTTTCAAAGTCATTGAGCCTCTGTTTAGAGA
Found at i:18944976 original size:20 final size:20
Alignment explanation
Indices: 18944937--18944975 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18944927 TAGAAAATTC
18944937 CTAGATTTTGATGAAATTTT
1 CTAGATTTTGATGAAATTTT
*
18944957 CTAGATTTTGGT-AAATTTT
1 CTAGATTTTGATGAAATTTT
18944976 TTGACATCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.51
Consensus pattern (20 bp):
CTAGATTTTGATGAAATTTT
Found at i:18946071 original size:52 final size:51
Alignment explanation
Indices: 18945966--18946073 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 51
18945956 ATATAAATAT
* * * *
18945966 AAAAAGAATTTCTAAATAGGCCCAAATGGTGAAAATTTTAGAAATTTCAAA
1 AAAAAAAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAATTCCAAA
* * * *
18946017 AAAAAAAATTTCTAAATTGACTCAAATTGTGAAAAATTTAGAAA-TCCAAC
1 AAAAAAAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAATTCCAAA
18946067 AAAAAAA
1 AAAAAAA
18946074 TAAATAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 11 0.22
51 38 0.78
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (51 bp):
AAAAAAAATTTCTAAATAGACCCAAATGGTGAAAAATTTAGAAATTCCAAA
Found at i:18947994 original size:24 final size:24
Alignment explanation
Indices: 18947952--18947998 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18947942 TAATATTAAT
*
18947952 ATTAAAATCAATATCAAAATTTTA
1 ATTAAAATCAATATAAAAATTTTA
18947976 ATTAAAATCAA-ATTAAAAATTTT
1 ATTAAAATCAATA-TAAAAATTTT
18947999 GGGCTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
ATTAAAATCAATATAAAAATTTTA
Found at i:18948593 original size:35 final size:35
Alignment explanation
Indices: 18948484--18948593 Score: 100
Period size: 35 Copynumber: 3.1 Consensus size: 35
18948474 AAAGATTCTA
* * *
18948484 AGATTCACAAAATTTGTAAGATTCTCAGAGGTTCC
1 AGATTCACAAAATTTCTAAGTTTCACAGAGGTTCC
* * * *
18948519 AAATTCACAAAAATTTCAAAATTTGCA-A-AGGTTCT
1 AGATTCAC-AAAATTTCTAAGTTT-CACAGAGGTTCC
*
18948554 AGATTCAC-AAATATTCTAAGTTTCACAGAGATTCC
1 AGATTCACAAAAT-TTCTAAGTTTCACAGAGGTTCC
18948589 AGATT
1 AGATT
18948594 TGCAAATGTT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
33 6 0.10
34 9 0.16
35 30 0.52
36 12 0.21
37 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (35 bp):
AGATTCACAAAATTTCTAAGTTTCACAGAGGTTCC
Found at i:18948831 original size:17 final size:17
Alignment explanation
Indices: 18948806--18948844 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18948796 GAATTTAAAT
* *
18948806 ATTCACAAGGACTTCAG
1 ATTCGCAAGAACTTCAG
*
18948823 ATTCGCAAGAACTTTAG
1 ATTCGCAAGAACTTCAG
18948840 ATTCG
1 ATTCG
18948845 TAGAAACTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (17 bp):
ATTCGCAAGAACTTCAG
Found at i:18949255 original size:23 final size:24
Alignment explanation
Indices: 18949207--18949262 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
18949197 TTTTGCAACT
*
18949207 AAAATTTCAAAGATTCACATTAAA
1 AAAATTTCAAAGATTCACAATAAA
* *
18949231 AAAATTT-AGAGATTCACAAT--C
1 AAAATTTCAAAGATTCACAATAAA
18949252 AAAATTTCAAA
1 AAAATTTCAAA
18949263 TATCCTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.26
22 2 0.07
23 11 0.41
24 7 0.26
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.29
Consensus pattern (24 bp):
AAAATTTCAAAGATTCACAATAAA
Found at i:18949255 original size:24 final size:24
Alignment explanation
Indices: 18949207--18949255 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18949197 TTTTGCAACT
*
18949207 AAAATTTCAAAGATTCACATTAAA
1 AAAATTTCAAAGATTCACATCAAA
*
18949231 AAAATTT-AGAGATTCACAATCAAA
1 AAAATTTCAAAGATTCAC-ATCAAA
18949255 A
1 A
18949256 TTTCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (24 bp):
AAAATTTCAAAGATTCACATCAAA
Found at i:18949256 original size:45 final size:46
Alignment explanation
Indices: 18949066--18949262 Score: 130
Period size: 46 Copynumber: 4.1 Consensus size: 46
18949056 ACATCTAGAA
* ** *
18949066 TTCAAAGATTCTCATTCGAAAAATTTTAGAGATTCACAAAGATTTCAAAAT
1 TTCAAAGATTCACATTAAAAAAAATTTAGAGATTCAC--A-A--TCAAAAT
* * * *
18949117 TTCAAAGATTCACATTTAAAAAAAAAAATTAGAGCTTTAC-ATCCAAATT
1 TTCAAAGATTCACA-TT--AAAAAAAATTTAGAGATTCACAAT-CAAAAT
* ** * * * * **
18949166 TTCAAAGGTTTTCATTCAAAAAATTTTAGGGTTTTGCAA-CTAAAAT
1 TTCAAAGATTCACATTAAAAAAAATTTAGAGATTCACAATC-AAAAT
18949212 TTCAAAGATTCACATT-AAAAAAATTTAGAGATTCACAATCAAAAT
1 TTCAAAGATTCACATTAAAAAAAATTTAGAGATTCACAATCAAAAT
18949257 TTCAAA
1 TTCAAA
18949263 TATCCTCATT
Statistics
Matches: 113, Mismatches: 26, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
45 29 0.26
46 33 0.29
47 1 0.01
48 3 0.03
49 16 0.14
50 1 0.01
51 13 0.12
52 2 0.02
54 15 0.13
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (46 bp):
TTCAAAGATTCACATTAAAAAAAATTTAGAGATTCACAATCAAAAT
Found at i:18949343 original size:15 final size:16
Alignment explanation
Indices: 18949323--18949352 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18949313 ATGATTATTT
18949323 TTTAAA-AAAAGCTCC
1 TTTAAACAAAAGCTCC
18949338 TTTAAACAAAAGCTC
1 TTTAAACAAAAGCTC
18949353 TATAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (16 bp):
TTTAAACAAAAGCTCC
Found at i:18951338 original size:101 final size:100
Alignment explanation
Indices: 18951163--18951366 Score: 264
Period size: 101 Copynumber: 2.0 Consensus size: 100
18951153 ATAGGAAAAG
* * * ** * * * * *
18951163 ATGTAACACGGTAAAAGTATATGATGGAGATTCACATAATCGATGAGGTGTTATAAAAATGCATC
1 ATGTAACAAGGTAAAAGCATATGATGGAGATTCACACAAAAGAGGAGATGTCATAAAAATACACC
* *
18951228 ATATCTGCCATTTTTGTTAAAATAATGAAAAATAAA
66 ATATCTGCCAATTTTATTAAAATAAT-AAAAATAAA
* *
18951264 ATGTAACAAGGTAAAAGCATATGATGGTGATTCACACAAAAGAGGAGATGTCATGAAAATACACC
1 ATGTAACAAGGTAAAAGCATATGATGGAGATTCACACAAAAGAGGAGATGTCATAAAAATACACC
*
18951329 ATATGTGCCAATTTTATTAAAATAATAAAAATAAA
66 ATATCTGCCAATTTTATTAAAATAATAAAAATAAA
18951364 ATG
1 ATG
18951367 AAATTCAAAT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 12 0.14
101 76 0.86
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (100 bp):
ATGTAACAAGGTAAAAGCATATGATGGAGATTCACACAAAAGAGGAGATGTCATAAAAATACACC
ATATCTGCCAATTTTATTAAAATAATAAAAATAAA
Found at i:18957398 original size:16 final size:16
Alignment explanation
Indices: 18957373--18957411 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18957363 AATAGACACG
*
18957373 TAATATATACAAAGAA
1 TAATAAATACAAAGAA
18957389 TAATAAATACAAAGAA
1 TAATAAATACAAAGAA
*
18957405 CAATAAA
1 TAATAAA
18957412 AAAGGTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (16 bp):
TAATAAATACAAAGAA
Found at i:18958664 original size:100 final size:99
Alignment explanation
Indices: 18958526--18958725 Score: 323
Period size: 100 Copynumber: 2.0 Consensus size: 99
18958516 TTTTACAAAA
* *
18958526 TATTTTTTCAAGAAAATTCATTAAGTCATCCAATAGTTTGGTAAGATTTAATTCAAGATTTAAAT
1 TATTTTTTCAAGAAAATTCATTAAGTCATCCAATAGTTTGATAAGACTTAATTCAAGATTTAAAT
18958591 CCTCCAATAGTTTGGTAGGATTGAAAATTTTATTAT
66 CCTCCAATAGTTTGGTAGGATT-AAAATTTT-TTAT
* *
18958627 TATTTTTTACAA-AAAATTCA-TAAGTCCTCCAATAGTTTGATAAGACTTAATTCAATATTTAAA
1 TATTTTTT-CAAGAAAATTCATTAAGTCATCCAATAGTTTGATAAGACTTAATTCAAGATTTAAA
18958690 TCCTCCAATAGTTTGGTAGGATTAAAATTTTTTAT
65 TCCTCCAATAGTTTGGTAGGATTAAAATTTTTTAT
18958725 T
1 T
18958726 TTATCAAAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
98 5 0.05
99 8 0.09
100 62 0.66
101 16 0.17
102 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (99 bp):
TATTTTTTCAAGAAAATTCATTAAGTCATCCAATAGTTTGATAAGACTTAATTCAAGATTTAAAT
CCTCCAATAGTTTGGTAGGATTAAAATTTTTTAT
Found at i:18959916 original size:12 final size:12
Alignment explanation
Indices: 18959899--18959948 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
18959889 GGTTTTCCTC
18959899 TTTTATTTTCAT
1 TTTTATTTTCAT
18959911 TTTTATTTTCTAT
1 TTTTATTTTC-AT
**
18959924 TTAGATTTTCA-
1 TTTTATTTTCAT
18959935 -TTTATTTT-AT
1 TTTTATTTTCAT
18959945 TTTT
1 TTTT
18959949 TAGATTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
9 1 0.03
10 6 0.19
11 3 0.10
12 11 0.35
13 10 0.32
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:18959955 original size:24 final size:27
Alignment explanation
Indices: 18959904--18959976 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 27
18959894 TCCTCTTTTA
*
18959904 TTTTCATTT-TTATT-TTCTATTTAGA-
1 TTTTCATTTATTATTATTAT-TTTAGAT
18959929 TTTTCATTTATT-TTATT-TTTTAGAT
1 TTTTCATTTATTATTATTATTTTAGAT
*
18959954 TTTTCTTTTATTATTATTATTTT
1 TTTTCATTTATTATTATTATTTT
18959977 CATTATTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 6 0.14
25 23 0.55
26 9 0.21
27 4 0.10
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (27 bp):
TTTTCATTTATTATTATTATTTTAGAT
Found at i:18959970 original size:6 final size:6
Alignment explanation
Indices: 18959961--18960030 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
18959951 GATTTTTCTT
* * * *
18959961 TTATTA TTATTA TT-TTCA TTATTA TCATTA TCATTA TCATTA TCATTA
1 TTATTA TTATTA TTATT-A TTATTA TTATTA TTATTA TTATTA TTATTA
* * * *
18960009 TCATCA TTATCA TTATCA TTAT
1 TTATTA TTATTA TTATTA TTAT
18960031 CATCATCATC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
5 2 0.03
6 55 0.93
7 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (6 bp):
TTATTA
Found at i:18959981 original size:15 final size:15
Alignment explanation
Indices: 18959959--18960003 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
18959949 TAGATTTTTC
18959959 TTTT-ATTATTATTA
1 TTTTCATTATTATTA
*
18959973 TTTTCATTATTATCA
1 TTTTCATTATTATTA
* *
18959988 TTATCATTATCATTA
1 TTTTCATTATTATTA
18960003 T
1 T
18960004 CATTATCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 4 0.15
15 22 0.85
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTCATTATTATTA
Found at i:18959991 original size:27 final size:27
Alignment explanation
Indices: 18959961--18960084 Score: 149
Period size: 27 Copynumber: 4.6 Consensus size: 27
18959951 GATTTTTCTT
* * * *
18959961 TTATTATTATTATTTTCATTATTATCA
1 TTATCATTATCATTATCATTATCATCA
18959988 TTATCATTATCATTATCATTATCATCA
1 TTATCATTATCATTATCATTATCATCA
*
18960015 TTATCATTATCATTATCATCATCATCA
1 TTATCATTATCATTATCATTATCATCA
* * * *
18960042 TCATCATCATCATCATCATCATCATCA
1 TTATCATTATCATTATCATTATCATCA
* *
18960069 TCATCATTATTATTAT
1 TTATCATTATCATTAT
18960085 TATTGTTGGT
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (27 bp):
TTATCATTATCATTATCATTATCATCA
Found at i:18960014 original size:21 final size:21
Alignment explanation
Indices: 18959976--18960087 Score: 134
Period size: 21 Copynumber: 5.3 Consensus size: 21
18959966 ATTATTATTT
* *
18959976 TCATTATTATCATTATCATTA
1 TCATTATCATCATCATCATTA
*
18959997 TCATTATCATTATCATCATTA
1 TCATTATCATCATCATCATTA
* *
18960018 TCATTATCATTATCATCATCA
1 TCATTATCATCATCATCATTA
* *
18960039 TCATCATCATCATCATCATCA
1 TCATTATCATCATCATCATTA
* *
18960060 TCATCATCATCATCATTATTA
1 TCATTATCATCATCATCATTA
*
18960081 TTATTAT
1 TCATTAT
18960088 TGTTGGTGGT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (21 bp):
TCATTATCATCATCATCATTA
Found at i:18960031 original size:6 final size:6
Alignment explanation
Indices: 18959981--18960084 Score: 115
Period size: 6 Copynumber: 17.8 Consensus size: 6
18959971 TATTTTCATT
18959981 ATTATC ATTATC ATTATC ATTATC ATTATC ---ATC ATTATC ATTATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
* * * * * * *
18960026 ATTATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
*
18960074 ATTATT ATTAT
1 ATTATC ATTAT
18960085 TATTGTTGGT
Statistics
Matches: 92, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
3 3 0.03
6 89 0.97
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (6 bp):
ATTATC
Found at i:18965027 original size:15 final size:13
Alignment explanation
Indices: 18965009--18965061 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 13
18964999 AAAGTGAGTA
18965009 AAAAAATGAAAAAT
1 AAAAAA-GAAAAAT
18965023 GAAAAAGAGAAAAAT
1 -AAAAA-AGAAAAAT
*
18965038 AAAAAACAAAAA-
1 AAAAAAGAAAAAT
*
18965050 AAAAGAGAAAAA
1 AAAAAAGAAAAA
18965062 AAGAAGACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 10 0.29
13 6 0.18
14 5 0.15
15 12 0.35
16 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (13 bp):
AAAAAAGAAAAAT
Found at i:18966154 original size:21 final size:22
Alignment explanation
Indices: 18966105--18966155 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
18966095 TGAAATGTTA
18966105 AAGTTTTTGCAGGTGAATTTTG
1 AAGTTTTTGCAGGTGAATTTTG
*
18966127 AAATTTTTG-ATGG-GAATCTTT-
1 AAGTTTTTGCA-GGTGAAT-TTTG
18966148 AAGTTTTT
1 AAGTTTTT
18966156 CCAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (22 bp):
AAGTTTTTGCAGGTGAATTTTG
Found at i:18967615 original size:3 final size:3
Alignment explanation
Indices: 18967607--18967661 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
18967597 GGCCTAATAT
18967607 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18967655 TTA TTA T
1 TTA TTA T
18967662 GGTTTATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18968502 original size:24 final size:26
Alignment explanation
Indices: 18968470--18968518 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
18968460 TTCATTTTTG
18968470 TTTACA-TTTTCATTTATT-TTATTT
1 TTTACATTTTTCATTTATTATTATTT
* *
18968494 TTTAGATTTTTCTTTTATTATTATT
1 TTTACATTTTTCATTTATTATTATT
18968519 ATTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 11 0.52
26 5 0.24
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTACATTTTTCATTTATTATTATTT
Found at i:18970103 original size:13 final size:13
Alignment explanation
Indices: 18970085--18970110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18970075 AAAATCAAAA
18970085 CTAAATTAAAATT
1 CTAAATTAAAATT
18970098 CTAAATTAAAATT
1 CTAAATTAAAATT
18970111 AATATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAAATTAAAATT
Found at i:18970155 original size:6 final size:6
Alignment explanation
Indices: 18970069--18970154 Score: 79
Period size: 6 Copynumber: 14.7 Consensus size: 6
18970059 TTTTTTTAAC
* * * *
18970069 AAAATT AAAATC AAAACT -AAATT AAAATT CTAAATT AAAATT AATATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT -AAAATT AAAATT AAAATT
* * *
18970117 AAAATC AAGATC AAAATT AAAATT AAAA-T AAAA-T AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
18970155 AATTTGGGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
5 14 0.21
6 47 0.71
7 5 0.08
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:18971051 original size:25 final size:24
Alignment explanation
Indices: 18971023--18971069 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
18971013 ATATCACAAA
18971023 TTTTTT-TTA-AAAAGTATTATTATT
1 TTTTTTATTATAAAA-TATT-TTATT
18971047 TTTTTTATTATAAAATATTTTAT
1 TTTTTTATTATAAAATATTTTAT
18971070 CACCAAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTTATTATAAAATATTTTATT
Found at i:18971557 original size:16 final size:16
Alignment explanation
Indices: 18971536--18971566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18971526 TTTAGGGTTT
18971536 GATTTTAGAGTTTGGA
1 GATTTTAGAGTTTGGA
*
18971552 GATTTTAGGGTTTGG
1 GATTTTAGAGTTTGG
18971567 GTTTTAAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GATTTTAGAGTTTGGA
Found at i:18971577 original size:14 final size:15
Alignment explanation
Indices: 18971554--18971586 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18971544 AGTTTGGAGA
*
18971554 TTTTAGGGTTT-GGG
1 TTTTAAGGTTTAGGG
18971568 TTTTAAGGTTTAGGG
1 TTTTAAGGTTTAGGG
18971583 TTTT
1 TTTT
18971587 GATTTAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55
Consensus pattern (15 bp):
TTTTAAGGTTTAGGG
Found at i:18971596 original size:14 final size:14
Alignment explanation
Indices: 18971579--18971621 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
18971569 TTTAAGGTTT
18971579 AGGGTTTTGATTTA
1 AGGGTTTTGATTTA
* *
18971593 AGGGTTTGGATTTT
1 AGGGTTTTGATTTA
18971607 AGGGATTTTGGATTT
1 AGGG-TTTT-GATTT
18971622 TTTAGGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 16 0.67
15 3 0.12
16 5 0.21
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.49
Consensus pattern (14 bp):
AGGGTTTTGATTTA
Found at i:18971599 original size:21 final size:21
Alignment explanation
Indices: 18971555--18971595 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18971545 GTTTGGAGAT
*
18971555 TTTAGGGTTTGGGTTTTAAGG
1 TTTAGGGTTTGGGATTTAAGG
*
18971576 TTTAGGGTTT-TGATTTAAGG
1 TTTAGGGTTTGGGATTTAAGG
18971596 GTTTGGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (21 bp):
TTTAGGGTTTGGGATTTAAGG
Found at i:18971606 original size:20 final size:20
Alignment explanation
Indices: 18971569--18971606 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18971559 GGGTTTGGGT
*
18971569 TTTAAGGTTTAGGGTTTTGA
1 TTTAAGGTTTAGGATTTTGA
18971589 TTTAAGGGTTT-GGATTTT
1 TTTAA-GGTTTAGGATTTT
18971607 AGGGATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (20 bp):
TTTAAGGTTTAGGATTTTGA
Found at i:18971618 original size:16 final size:15
Alignment explanation
Indices: 18971576--18971742 Score: 67
Period size: 17 Copynumber: 10.7 Consensus size: 15
18971566 GGTTTTAAGG
18971576 TTTAGGGTTTT-GAT
1 TTTAGGGTTTTGGAT
*
18971590 TTAAGGG-TTTGGAT
1 TTTAGGGTTTTGGAT
18971604 TTTAGGGATTTTGGATTT
1 TTTAGGG-TTTTGGA--T
*
18971622 TTTA-GG-TTTCGAT
1 TTTAGGGTTTTGGAT
* * **
18971635 TTAAGAGTTTAAGA-
1 TTTAGGGTTTTGGAT
* *
18971649 TTT-GGGATTTCGAATT
1 TTTAGGG-TTTTGGA-T
*
18971665 TTTGGGGGTTTTGGAT
1 TTT-AGGGTTTTGGAT
* *
18971681 TTTAGGGGGTTTCGAT
1 TTTA-GGGTTTTGGAT
* *
18971697 TTAAAGGATTTTTGGAT
1 TT-TAGG-GTTTTGGAT
18971714 TTTAAGGGATTTTGGAT
1 TTT-AGGG-TTTTGGAT
18971731 TTTAAGGGTTTT
1 TTT-AGGGTTTT
18971743 AAACAACCTA
Statistics
Matches: 113, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
13 9 0.08
14 22 0.19
15 9 0.08
16 30 0.27
17 35 0.31
18 8 0.07
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (15 bp):
TTTAGGGTTTTGGAT
Found at i:18971688 original size:17 final size:17
Alignment explanation
Indices: 18971669--18971742 Score: 80
Period size: 17 Copynumber: 4.5 Consensus size: 17
18971659 CGAATTTTTG
18971669 GGGGTTTTGGATTTT-A
1 GGGGTTTTGGATTTTAA
* * *
18971685 GGGGGTTTCGATTTAAA
1 GGGGTTTTGGATTTTAA
**
18971702 GGATTTTTGGATTTTAA
1 GGGGTTTTGGATTTTAA
*
18971719 GGGATTTTGGATTTTAA
1 GGGGTTTTGGATTTTAA
18971736 -GGGTTTT
1 GGGGTTTT
18971743 AAACAACCTA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 18 0.39
17 28 0.61
ACGTcount: A:0.19, C:0.01, G:0.32, T:0.47
Consensus pattern (17 bp):
GGGGTTTTGGATTTTAA
Found at i:18973195 original size:13 final size:13
Alignment explanation
Indices: 18973177--18973201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18973167 AGTTTCTGTT
18973177 TTTTTATTTTTTG
1 TTTTTATTTTTTG
18973190 TTTTTATTTTTT
1 TTTTTATTTTTT
18973202 TATTTATTAA
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:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTG
Found at i:18973223 original size:27 final size:27
Alignment explanation
Indices: 18973191--18973273 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
18973181 TATTTTTTGT
18973191 TTTTATTTTTTTATTTATTAATAATTA
1 TTTTATTTTTTTATTTATTAATAATTA
*
18973218 TTTTATTTTATTT-TTTATTAAAATATTAA
1 TTTTATTTT-TTTATTTATTAATA-ATT-A
* *
18973247 TATTATTATTATTA-TTATTAAT-ATTA
1 TTTTATT-TTTTTATTTATTAATAATTA
18973273 T
1 T
18973274 AGTGAAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
26 2 0.04
27 21 0.45
28 6 0.13
29 16 0.34
30 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTATTTTTTTATTTATTAATAATTA
Found at i:18973884 original size:22 final size:23
Alignment explanation
Indices: 18973868--18973918 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
18973858 GAGGTCTTAG
18973868 AAATCATGTTTGGAGGTATTACA
1 AAATCATGTTTGGAGGTATTACA
* * * *
18973891 AAATCATGCTCGAAGGTCTTACA
1 AAATCATGTTTGGAGGTATTACA
18973914 AAATC
1 AAATC
18973919 GACTGGGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
AAATCATGTTTGGAGGTATTACA
Found at i:18973985 original size:133 final size:132
Alignment explanation
Indices: 18973486--18974157 Score: 771
Period size: 133 Copynumber: 5.1 Consensus size: 132
18973476 TTATGCCCGG
* * * * *
18973486 AGGTCTTACA-AATCATG-TCCGGAGGTCTTACAAAATTGATTGGGACAACACCGCAAGTTAAAA
1 AGGTCTTACAGAATCATGCT-CGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAA
* * *** ** * *
18973549 -ATAAAAAATCGATCGGAATAACACCGTAAATCGAATTTATGCCTAAAAGTCATAGAAATCATG-
65 GATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATG-CTGGAGGTCTTAGAAATCATGC
18973612 TTGA
129 TTGA
** * *
18973616 AACTCTTACAGAATCATG-TCCGGAGGTCTTATAGAATCGATTGTGATAACACCACAAGTCAAAA
1 AGGTCTTACAGAATCATGCT-CGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAA
* * *
18973680 GATAAAGAATCGATCTGGATAACACCACGAATCGAATTTATGTTTGGAGGTCTTAGAAATCAAGC
65 GATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATG-CTGGAGGTCTTAGAAATCATGC
18973745 TTGA
129 TTGA
* * * *
18973749 AGGTCTTACAGAATCATGCCCGGAGGTCTTATAGAATCAACT-GGATAACACCACAAGTCAAAAG
1 AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* * *
18973813 ATAAAGAATCGATCGAGATAACACCATGAATCGAATTTATGCCTGGAGGTCTTAGAAATCATGTT
66 ATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATG-CTGGAGGTCTTAGAAATCATGCT
*
18973878 TGG
130 TGA
* * * * * * *
18973881 AGGTATTACAAAATCATGCTCGAAGGTCTTACAAAATCGACTGGGATAACTCCATAAGTCAAAAG
1 AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* * * *
18973946 ATAAAGAATTGATCGGGATAACACCGCGAATAGAATTTATGCTCGGAGGTCTTAAAAATCATGCT
66 ATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATGCT-GGAGGTCTTAGAAATCATGCT
*
18974011 CGA
130 TGA
* *
18974014 AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAATACCATAAGTCAAAAG
1 AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* * * * * * *
18974079 ATAAAGAGTCGATCGGGATAACACAACAAATCAAATTTATGCTCAGAGGTTTTAGAAATCATGCC
66 ATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATGCT-GGAGGTCTTAGAAATCATGCT
* *
18974144 CGG
130 TGA
18974147 AGGTCTTACAG
1 AGGTCTTACAG
18974158 CATCGATTGG
Statistics
Matches: 463, Mismatches: 73, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
130 8 0.02
131 46 0.10
132 168 0.36
133 241 0.52
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (132 bp):
AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
ATAAAGAATCGATCGGGATAACACCACGAATCGAATTTATGCTGGAGGTCTTAGAAATCATGCTT
GA
Found at i:18974018 original size:265 final size:264
Alignment explanation
Indices: 18973486--18974141 Score: 818
Period size: 265 Copynumber: 2.5 Consensus size: 264
18973476 TTATGCCCGG
* * * * * *
18973486 AGGTCTTACA-AATCATGTCCGGAGGTCTTACAAAATTGATTGGGACAACACCGCAAGTTAAAA-
1 AGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* * * * *
18973549 ATAAAAAATCGATCGGAATAACACCGTAAATCGAATTTATGCCTAAAAGTCATAGAAATCATGTT
66 ATAAAGAATCGATCGG-ATAACACCATAAATCGAATTTATGCCTAGAGGTCTTAGAAATCATGTT
* * * * * * *
18973614 GAAACTCTTACAGAATCATGTCCGGAGGTCTTATAGAATCGATTGTGATAACACCACAAGTCAAA
130 GAAACTATTACAAAATCATGTCCGAAGGTCTTACAAAATCGACTGGGATAACACCACAAGTCAAA
* * * * *
18973679 AGATAAAGAATCGATCTGGATAACACCACGAATCGAATTTATGTTTGGAGGTCTTAGAAATCAAG
195 AGATAAAGAATCGATCGGGATAACACCACGAATAGAATTTATGCTCGGAGGTCTTAAAAATCAAG
*
18973744 CTTGA
260 CTCGA
* * *
18973749 AGGTCTTACAGAATCATGCCCGGAGGTCTTATAGAATCAACT-GGATAACACCACAAGTCAAAAG
1 AGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* *
18973813 ATAAAGAATCGATCGAGATAACACCATGAATCGAATTTATGCCTGGAGGTCTTAGAAATCATGTT
66 ATAAAGAATCGATCG-GATAACACCATAAATCGAATTTATGCCTAGAGGTCTTAGAAATCATG-T
* ** * *
18973878 TGGAGGTATTACAAAATCATG-CTCGAAGGTCTTACAAAATCGACTGGGATAACTCCATAAGTCA
129 TGAAACTATTACAAAATCATGTC-CGAAGGTCTTACAAAATCGACTGGGATAACACCACAAGTCA
* *
18973942 AAAGATAAAGAATTGATCGGGATAACACCGCGAATAGAATTTATGCTCGGAGGTCTTAAAAATCA
193 AAAGATAAAGAATCGATCGGGATAACACCACGAATAGAATTTATGCTCGGAGGTCTTAAAAATCA
*
18974007 TGCTCGA
258 AGCTCGA
* * *
18974014 AGGTCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAATACCATAAGTCAAAAG
1 AGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
* * * * *
18974079 ATAAAGAGTCGATCGGGATAACACAACAAATCAAATTTATG-CTCAGAGGTTTTAGAAATCATG
66 ATAAAGAATCGATC-GGATAACACCATAAATCGAATTTATGCCT-AGAGGTCTTAGAAATCATG
18974142 CCCGGAGGTC
Statistics
Matches: 335, Mismatches: 50, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
263 28 0.08
264 80 0.24
265 155 0.46
266 71 0.21
267 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (264 bp):
AGGTCTTACAGAATCATGCCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAG
ATAAAGAATCGATCGGATAACACCATAAATCGAATTTATGCCTAGAGGTCTTAGAAATCATGTTG
AAACTATTACAAAATCATGTCCGAAGGTCTTACAAAATCGACTGGGATAACACCACAAGTCAAAA
GATAAAGAATCGATCGGGATAACACCACGAATAGAATTTATGCTCGGAGGTCTTAAAAATCAAGC
TCGA
Found at i:18974032 original size:23 final size:23
Alignment explanation
Indices: 18973984--18974051 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
18973974 AATAGAATTT
*
18973984 ATGCTCGGAGGTCTTA-AAAATC
1 ATGCTCGGAGGTCTTACAGAATC
*
18974006 ATGCTCGAAGGTCTTACAGAATC
1 ATGCTCGGAGGTCTTACAGAATC
18974029 ATGCTCGGAGGTCTTACAGAATC
1 ATGCTCGGAGGTCTTACAGAATC
18974052 GATTGGGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 15 0.36
23 27 0.64
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
ATGCTCGGAGGTCTTACAGAATC
Found at i:18974292 original size:88 final size:88
Alignment explanation
Indices: 18974143--18974317 Score: 296
Period size: 88 Copynumber: 2.0 Consensus size: 88
18974133 GAAATCATGC
* *
18974143 CCGGAGGTCTTACAGCATCGATTGGGATAACACTACAAATCAAAAGATAAAGAATCGATCGAGAT
1 CCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAATCAAAAGATAAAGAATCGATCGAGAT
* *
18974208 AACACCGTGAATCGAATTTATGT
66 AACACCGTAAATCAAATTTATGT
*
18974231 CCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGAT
1 CCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAATCAAAAGATAAAGAATCGATCGAGAT
*
18974296 AACATCGTAAATCAAATTTATG
66 AACACCGTAAATCAAATTTATG
18974318 CTTGAAGGTC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (88 bp):
CCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAATCAAAAGATAAAGAATCGATCGAGAT
AACACCGTAAATCAAATTTATGT
Found at i:18974394 original size:133 final size:133
Alignment explanation
Indices: 18974235--18974758 Score: 651
Period size: 133 Copynumber: 3.9 Consensus size: 133
18974225 TTATGTCCGG
18974235 AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
1 AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
* * * *
18974300 TCGTAAATCAAATTTATGCTTGAAGGTCTTAGAAATCATGTCCAAAGGTCTTACAGAATAATGCC
66 CCGTAAATCAAATTTATGCTCGAAGGTCTTAGAAATCATGTCCAAAGATCTTACAGAATCATGCC
*
18974365 CGG
131 CGA
* * * * * *
18974368 AGGTCTTATAGAATCGATTGGAATAACACTATAAGTCAAAAGATAAAAAATCGATCGGGATAACA
1 AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
* * * * *
18974433 TCGTGAATCAAATTTATG-TCTGGAGGTCTTAGAAATCATG-CCTGAAGGTCTTACAGAATCATG
66 CCGTAAATCAAATTTATGCTC-GAAGGTCTTAGAAATCATGTCC-AAAGATCTTACAGAATCATG
* *
18974496 CTCAA
129 CCCGA
* *
18974501 AGGTCTTACAGAATCGATCGGGATAACACCATAAGTCAAAAGATAAAGAATCGATC-AGGATAAC
1 AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGA-GATAAC
* * * * * * ** * *
18974565 ACCATGAATCGATTTTATGCCCGGAGGTCTTAGAAATCATACCCGAAGATCTTACAGAATCATGT
65 ACCGTAAATCAAATTTATGCTCGAAGGTCTTAGAAATCATGTCCAAAGATCTTACAGAATCATGC
*
18974630 CTGA
130 CCGA
* * * *
18974634 AAGTTTTACAGAATCGACTGGGATAACATCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
1 AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
* *
18974699 CCGTAAATC-GATTTAATGCTCGAAGGTCTTAGAAATCATGTCCAAAAATCTTACAGAATC
66 CCGTAAATCAAATTT-ATGCTCGAAGGTCTTAGAAATCATGTCCAAAGATCTTACAGAATC
18974759 GACTGGGATA
Statistics
Matches: 337, Mismatches: 47, Indels: 14
0.85 0.12 0.04
Matches are distributed among these distances:
132 6 0.02
133 327 0.97
134 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (133 bp):
AGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA
CCGTAAATCAAATTTATGCTCGAAGGTCTTAGAAATCATGTCCAAAGATCTTACAGAATCATGCC
CGA
Found at i:18974496 original size:23 final size:23
Alignment explanation
Indices: 18974456--18974515 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
18974446 TTATGTCTGG
* *
18974456 AGGTCTTAGA-AATCATGC-CTGA
1 AGGTCTTACAGAATCATGCTC-AA
18974478 AGGTCTTACAGAATCATGCTCAA
1 AGGTCTTACAGAATCATGCTCAA
18974501 AGGTCTTACAGAATC
1 AGGTCTTACAGAATC
18974516 GATCGGGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 9 0.26
23 24 0.71
24 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
AGGTCTTACAGAATCATGCTCAA
Found at i:18974768 original size:597 final size:604
Alignment explanation
Indices: 18973628--18975109 Score: 1857
Period size: 597 Copynumber: 2.4 Consensus size: 604
18973618 CTCTTACAGA
* *
18973628 ATCATGTCCGGAGGTCTTATAGAATCGATTGTGATAACACCACAAGTCAAAAGATAAAGAATCGA
1 ATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGA
* * * * *
18973693 TCTG-GATAACACCACGAATCGAATTTATGTTTGGAGGTCTTAGAAATCAAGCTTGAAGGTCTTA
66 TC-GAGATAACATCACGAATCAAATTTATGCTTGGAGGTCTTAGAAATCATGC-CGAAGGTCTTA
*
18973757 CAGAATCATGCCCGGAGGTCTTATAGAATCAACTGGATAACACCACAAGTCAAAAGATAAAGAAT
129 CAGAATCATGCCCGGAGGTCTTATAGAATCGACTGGATAACACCACAAGTCAAAAGATAAAGAAT
* * * * ** *
18973822 CGATCGAGATAACACCATGAATCGAATTTATGCCTGGAGGTCTTAGAAATCATGTTTGGAGGTAT
194 CGATCGAGATAACATCGTGAATCAAATTTATGACTGGAGGTCTTAGAAATCATGCCTGGAGGTCT
* * *
18973887 TACAAAATCATGCTCGAAGGTCTTACAAAATCGACTGGGATAACTCCATAAGTCAAAAGATAAAG
259 TACAGAATCATGCTCAAAGGTCTTACAAAATCGACTGGGATAACACCATAAGTCAAAAGATAAAG
* * * * * * *
18973952 AATTGATCGGGATAACACCGCGAATAGAATTTATGCTCGGAGGTCTTAAAAATCATGCTCGAAGG
324 AATCGATCAGGATAACACCACGAATAGAATTTATGCCCGGAGGTCTTAAAAATCATACCCGAAGA
* * * * *
18974017 TCTTACAGAATCATGCTCGGAGGTCTTACAGAATCGATTGGGATAATACCATAAGTCAAAAGATA
389 TCTTACAGAATCATGCTCGAAAGTCTTACAGAATCGACTGGGATAACACCACAAGTCAAAAGATA
* * * **
18974082 AAGAGTCGATCGGGATAACACAACAAATCAAATTTATGCTCAGAGGTTTTAGAAATCATGCCCGG
454 AAGAATCGATCGAGATAACACAACAAATCAAATTTATGCTCAGAGGTCTTAGAAATCATGCCCAA
** * * *
18974147 AGGTCTTACAGCATCGATTGGGATAACA-CTACAAATCAAAAGATAAAGAATCGATCGAGATAAC
519 AAATCTTACAGAATCGACTGGGATAACACCT-CAAATCAAAAGATAAAAAATCGATCGAGATAAC
*
18974211 A-C-CG-T-GA-A-TCGAA-TT
583 ATCGCGATAAATATTCGAATTT
18974226 -T-ATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGA
1 ATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGA
*** * *
18974289 TCGAGATAACATCGTAAATCAAATTTATGCTTGAAGGTCTTAGAAATCATGTCCAAAGGTCTTAC
66 TCGAGATAACATCACGAATCAAATTTATGCTTGGAGGTCTTAGAAATCATG-CCGAAGGTCTTAC
* * * * *
18974354 AGAATAATGCCCGGAGGTCTTATAGAATCGATTGGAATAACACTATAAGTCAAAAGATAAAAAAT
130 AGAATCATGCCCGGAGGTCTTATAGAATCGACTGG-ATAACACCACAAGTCAAAAGATAAAGAAT
* * *
18974419 CGATCGGGATAACATCGTGAATCAAATTTATGTCTGGAGGTCTTAGAAATCATGCCTGAAGGTCT
194 CGATCGAGATAACATCGTGAATCAAATTTATGACTGGAGGTCTTAGAAATCATGCCTGGAGGTCT
*
18974484 TACAGAATCATGCTCAAAGGTCTTACAGAATCGA-TCGGGATAACACCATAAGTCAAAAGATAAA
259 TACAGAATCATGCTCAAAGGTCTTACAAAATCGACT-GGGATAACACCATAAGTCAAAAGATAAA
* * * *
18974548 GAATCGATCAGGATAACACCATGAATCGATTTTATGCCCGGAGGTCTTAGAAATCATACCCGAAG
323 GAATCGATCAGGATAACACCACGAATAGAATTTATGCCCGGAGGTCTTAAAAATCATACCCGAAG
* *
18974613 ATCTTACAGAATCATG-TCTGAAAGTTTTACAGAATCGACTGGGATAACATCACAAGTCAAAAGA
388 ATCTTACAGAATCATGCTC-GAAAGTCTTACAGAATCGACTGGGATAACACCACAAGTCAAAAGA
*** * *
18974677 TAAAGAATCGATCGAGATAACACCGTAAATC-GATTTAATGCTC-GAAGGTCTTAGAAATCATGT
452 TAAAGAATCGATCGAGATAACACAACAAATCAAATTT-ATGCTCAG-AGGTCTTAGAAATCATGC
* * * *
18974740 CCAAAAATCTTACAGAATCGACTGGGATAACACCTTAAGTGAAAAGATAAAAAATCGATCGGGAT
515 CCAAAAATCTTACAGAATCGACTGGGATAACACCTCAAATCAAAAGATAAAAAATCGATCGAGAT
18974805 AACATCGCGAATCAAATTTATGTTCGAATGTCTT
580 AACATCGCG-AT-AAA--TA--TTCGAA--T-TT
* * * * *
18974839 AAAAATCATGCCCGAAGGTCTTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAA
1 ----ATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAA
** * * *
18974904 TCGATCGAGATAACATCACGAATCAAATTTATGCCCGGAGGCCTTAAAAATCATGCCTGGAGGTC
62 TCGATCGAGATAACATCACGAATCAAATTTATGCTTGGAGGTCTTAGAAATCATGCC-GAAGGTC
* *
18974969 TTACAGAATCA-GCCTC-GAGGTCTTACAGAATCGACTGGGATAACACCACAAATCAAAAGATAA
126 TTACAGAATCATGCC-CGGAGGTCTTATAGAATCGACT-GGATAACACCACAAGTCAAAAGATAA
* *
18975032 AGAATCGATCGAGATAACATCGTGAATCAAATTTAT-ACCGGAGGCCTTAGAAATCATGCCTGGA
189 AGAATCGATCGAGATAACATCGTGAATCAAATTTATGACTGGAGGTCTTAGAAATCATGCCTGGA
18975096 GGTCTTACAGAATC
254 GGTCTTACAGAATC
18975110 GATTGAGATA
Statistics
Matches: 755, Mismatches: 96, Indels: 47
0.84 0.11 0.05
Matches are distributed among these distances:
595 1 0.00
596 151 0.20
597 353 0.47
598 3 0.00
599 2 0.00
601 1 0.00
603 1 0.00
606 1 0.00
609 5 0.01
613 2 0.00
617 38 0.05
618 79 0.10
619 118 0.16
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (604 bp):
ATCATGTCCGGAGGTCTTACAGAATCGATTGGGATAACACCACAAGTCAAAAGATAAAGAATCGA
TCGAGATAACATCACGAATCAAATTTATGCTTGGAGGTCTTAGAAATCATGCCGAAGGTCTTACA
GAATCATGCCCGGAGGTCTTATAGAATCGACTGGATAACACCACAAGTCAAAAGATAAAGAATCG
ATCGAGATAACATCGTGAATCAAATTTATGACTGGAGGTCTTAGAAATCATGCCTGGAGGTCTTA
CAGAATCATGCTCAAAGGTCTTACAAAATCGACTGGGATAACACCATAAGTCAAAAGATAAAGAA
TCGATCAGGATAACACCACGAATAGAATTTATGCCCGGAGGTCTTAAAAATCATACCCGAAGATC
TTACAGAATCATGCTCGAAAGTCTTACAGAATCGACTGGGATAACACCACAAGTCAAAAGATAAA
GAATCGATCGAGATAACACAACAAATCAAATTTATGCTCAGAGGTCTTAGAAATCATGCCCAAAA
ATCTTACAGAATCGACTGGGATAACACCTCAAATCAAAAGATAAAAAATCGATCGAGATAACATC
GCGATAAATATTCGAATTT
Found at i:18974968 original size:110 final size:108
Alignment explanation
Indices: 18974639--18974978 Score: 441
Period size: 110 Copynumber: 3.1 Consensus size: 108
18974629 TCTGAAAGTT
*
18974639 TTACAGAATCGACTGGGATAACATCACAAGTCAAAAGATAAAGAATCGATCGAGATAACA-CCGT
1 TTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAATCGATCGAGATAACATCCG-
* * * **
18974703 AAATC-GATTTAATGCTCGAAGGTCTTAGAAATCATGTCCAAAAATC
65 -AATCAAATTT-ATGCTCGAAGGTCTTAAAAATCATG-CCGAAGGTC
* * * * *
18974749 TTACAGAATCGACTGGGATAACACCTTAAGTGAAAAGATAAAAAATCGATCGGGATAACATCGCG
1 TTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAATCGATCGAGATAACATC-CG
* *
18974814 AATCAAATTTATGTTCGAATGTCTTAAAAATCATGCCCGAAGGTC
65 AATCAAATTTATGCTCGAAGGTCTTAAAAATCATG-CCGAAGGTC
18974859 TTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAATCGATCGAGATAACATCACG
1 TTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAATCGATCGAGATAACATC-CG
* * * *
18974924 AATCAAATTTATGCCCGGAGGCCTTAAAAATCATGCCTGGAGGTC
65 AATCAAATTTATGCTCGAAGGTCTTAAAAATCATGCC-GAAGGTC
18974969 TTACAGAATC
1 TTACAGAATC
18974979 AGCCTCGAGG
Statistics
Matches: 200, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
109 2 0.01
110 191 0.95
111 5 0.03
112 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (108 bp):
TTACAGAATCGACTGGGATAACATCATAAGTCAAAAGATAAAGAATCGATCGAGATAACATCCGA
ATCAAATTTATGCTCGAAGGTCTTAAAAATCATGCCGAAGGTC
Found at i:18974983 original size:22 final size:23
Alignment explanation
Indices: 18974952--18975000 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
18974942 AGGCCTTAAA
*
18974952 AATCATGCCTGGAGGTCTTACAG
1 AATCATGCCTCGAGGTCTTACAG
18974975 AATCA-GCCTCGAGGTCTTACAG
1 AATCATGCCTCGAGGTCTTACAG
18974997 AATC
1 AATC
18975001 GACTGGGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
AATCATGCCTCGAGGTCTTACAG
Done.