Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_pilon, 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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 51 of 51
Found at i:10246946 original size:19 final size:20
Alignment explanation
Indices: 10246873--10246945 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
10246863 TTATGTTCAC
* *
10246873 GGAATATAAGATTACCGGTG
1 GGAATAAAAGATTACCAGTG
10246893 GGAATAAAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
* *
10246913 GAAATAAAAGATTATCAG-G
1 GGAATAAAAGATTACCAGTG
10246932 GGAATAAAAGATTA
1 GGAATAAAAGATTA
10246946 TTAGGAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 14 0.29
20 34 0.71
ACGTcount: A:0.47, C:0.07, G:0.25, T:0.22
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:10247242 original size:28 final size:28
Alignment explanation
Indices: 10247208--10247265 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
10247198 GTAAAAAAAA
* *
10247208 TTTTAACCCCTAAACTTCAAATAAATTT
1 TTTTAACCCATAAACTTCAAATAAAATT
10247236 TTTTAACCCATAAACTTCAAATAAAATT
1 TTTTAACCCATAAACTTCAAATAAAATT
10247264 TT
1 TT
10247266 AATTATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.40
Consensus pattern (28 bp):
TTTTAACCCATAAACTTCAAATAAAATT
Found at i:10251303 original size:140 final size:140
Alignment explanation
Indices: 10251051--10251310 Score: 439
Period size: 140 Copynumber: 1.9 Consensus size: 140
10251041 AACTAAATAT
* * *
10251051 TATAACTTGGGGTATCAATAAATCATTCAAAAGTAGAAAAAAGTTGAAAAGAATCAACCTCGAGG
1 TATAACTTGGGGTATCAATAAATCATTCAAAAGAAGAAAAAACTTAAAAAGAATCAACCTCGAGG
*
10251116 GAAATGGCAGCGGCAGTGGAGAGAAAGTAGAGCTTTCGAATGACCTGAAGACCAAAATAAATCAT
66 GAAATGGCAGCAGCAGTGGAGAGAAAGTAGAGCTTTCGAATGACCTGAAGACCAAAATAAATCAT
10251181 TCAAAAGAAG
131 TCAAAAGAAG
* * *
10251191 TATAACTTGGGGTATCAATAAATCATTCAAAAGAAGAAGACACTTAAAAAGAATCAACCTTGAGG
1 TATAACTTGGGGTATCAATAAATCATTCAAAAGAAGAAAAAACTTAAAAAGAATCAACCTCGAGG
* *
10251256 GGAATGGCAGCAGCAGTGGAGAGAAAGTAGAGCTTTTGAATGACCTGAAGACCAA
66 GAAATGGCAGCAGCAGTGGAGAGAAAGTAGAGCTTTCGAATGACCTGAAGACCAA
10251311 GTGTTCCATG
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
140 111 1.00
ACGTcount: A:0.43, C:0.14, G:0.23, T:0.20
Consensus pattern (140 bp):
TATAACTTGGGGTATCAATAAATCATTCAAAAGAAGAAAAAACTTAAAAAGAATCAACCTCGAGG
GAAATGGCAGCAGCAGTGGAGAGAAAGTAGAGCTTTCGAATGACCTGAAGACCAAAATAAATCAT
TCAAAAGAAG
Found at i:10252276 original size:18 final size:19
Alignment explanation
Indices: 10252255--10252299 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
10252245 GTTGGAAGGT
*
10252255 TTATTTAAGTTTCAAAA-A
1 TTATTTAAATTTCAAAATA
*
10252273 TTATTTAAATTTTAAAATA
1 TTATTTAAATTTCAAAATA
10252292 TT-TTTAAA
1 TTATTTAAA
10252300 ATAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTATTTAAATTTCAAAATA
Found at i:10254446 original size:20 final size:20
Alignment explanation
Indices: 10254391--10254449 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
10254381 TTGTAGCAGG
10254391 TTAAATTTATTATCTA-TAATT
1 TTAAATTTATT-T-TATTAATT
* * *
10254412 TTTATTATTAGTTTATTAATT
1 TTAAAT-TTATTTTATTAATT
10254433 TTAAATTTATTTTATTA
1 TTAAATTTATTTTATTA
10254450 TTTACTATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 12 0.40
21 14 0.47
22 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTAAATTTATTTTATTAATT
Found at i:10259615 original size:2 final size:2
Alignment explanation
Indices: 10259610--10259650 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10259600 ACACACACAA
10259610 AT AT AT AT 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 AT AT AT AT A
10259651 AAAGAAACCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10260135 original size:39 final size:39
Alignment explanation
Indices: 10260016--10260175 Score: 162
Period size: 39 Copynumber: 4.1 Consensus size: 39
10260006 TACACCCAAC
10260016 AAGGACTTACCCTGTGCACAAAGCAGAGGAGCCTGCAGT
1 AAGGACTTACCCTGTGCACAAAGCAGAGGAGCCTGCAGT
* * * *
10260055 AA-GATCTTATCATGTGCATAAAGCAAAGGAGCCTGCAGT
1 AAGGA-CTTACCCTGTGCACAAAGCAGAGGAGCCTGCAGT
* * * ** *
10260094 AAGGTCTTATCCTGTGCACAAAGCAGATGAGCGAGCGGT
1 AAGGACTTACCCTGTGCACAAAGCAGAGGAGCCTGCAGT
** **
10260133 AAGGACTTACCCTGAACACAAAGTC-GAGGAGTTTGCAGT
1 AAGGACTTACCCTGTGCACAAAG-CAGAGGAGCCTGCAGT
10260172 AAGG
1 AAGG
10260176 TCTTGCAAGT
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.02
39 93 0.96
40 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.19
Consensus pattern (39 bp):
AAGGACTTACCCTGTGCACAAAGCAGAGGAGCCTGCAGT
Found at i:10264983 original size:19 final size:19
Alignment explanation
Indices: 10264924--10264983 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
10264914 TCAATAACGT
10264924 TAAAATTTTGACATTTAAAAA
1 TAAAATTTTG--ATTTAAAAA
* * *
10264945 -AAATTCTTTTATTTAGAAA
1 TAAAAT-TTTGATTTAAAAA
10264964 TAAAATTTTGATTTAAAAA
1 TAAAATTTTGATTTAAAAA
10264983 T
1 T
10264984 TATTAGAGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 20 0.65
20 8 0.26
21 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (19 bp):
TAAAATTTTGATTTAAAAA
Found at i:10266660 original size:15 final size:15
Alignment explanation
Indices: 10266640--10266674 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
10266630 AGCAAGGATA
*
10266640 TCCTCAAGGTTATCC
1 TCCTCAAGGATATCC
*
10266655 TCCTCAGGGATATCC
1 TCCTCAAGGATATCC
10266670 TCCTC
1 TCCTC
10266675 CTTATGCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.14, T:0.31
Consensus pattern (15 bp):
TCCTCAAGGATATCC
Found at i:10272865 original size:15 final size:16
Alignment explanation
Indices: 10272829--10272866 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
10272819 GAGCAGTTGC
10272829 AGAAGCAGAAGCTGCA
1 AGAAGCAGAAGCTGCA
*
10272845 A-TAGCAGAAGCTG-A
1 AGAAGCAGAAGCTGCA
10272859 AGAAGCAG
1 AGAAGCAG
10272867 CAAGAGAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 16 0.84
16 1 0.05
ACGTcount: A:0.45, C:0.16, G:0.32, T:0.08
Consensus pattern (16 bp):
AGAAGCAGAAGCTGCA
Found at i:10278532 original size:17 final size:18
Alignment explanation
Indices: 10278502--10278535 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10278492 AAAAACACAC
*
10278502 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
10278520 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
10278536 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:10280602 original size:3 final size:3
Alignment explanation
Indices: 10280596--10280659 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
10280586 AAAAAATATG
* **
10280596 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10280640 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
10280660 CGATAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:10280651 original size:32 final size:32
Alignment explanation
Indices: 10280598--10280665 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
10280588 AAAATATGTA
*
10280598 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAATAAAATAACG
10280630 ATAAT-AATAATAATAATAATAATAAAATAACG
1 ATAATAAATAATAATAA-AATAATAAAATAACG
10280662 ATAA
1 ATAA
10280666 AAAAAAACCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 11 0.32
32 23 0.68
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAATAAAATAACG
Found at i:10280885 original size:43 final size:43
Alignment explanation
Indices: 10280821--10281238 Score: 301
Period size: 43 Copynumber: 9.9 Consensus size: 43
10280811 TGGTGGGGAC
* ** *
10280821 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
*** *
10280864 GACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGAA--AT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
* ** *
10280904 GACACGACTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
*** *
10280947 GACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGAA--AT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
* ** *
10280987 GACACGACTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
*
10281030 GACACGGCTCATACGTGATGAAGAGATCTGG---TCT-GGGGAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGG-T
* * * * * *
10281070 GACACGGTTCCTACATGATGAGGACGGT-TGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGA-GATCTGGTCATCT-AAGG-G-T
* * * * * * * *
10281116 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GATCTGGTCATCTAAGGGT
* * *
10281159 GACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-GGGGAAT
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGG--T
*
10281200 GACACGGCTCATACGTGATGAGGAGATCTGGTCATCTAA
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAA
10281239 AGGAGTTATG
Statistics
Matches: 296, Mismatches: 57, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
39 5 0.02
40 90 0.30
41 37 0.12
42 5 0.02
43 117 0.40
44 3 0.01
45 5 0.02
46 34 0.11
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (43 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAGGGT
Found at i:10281114 original size:83 final size:83
Alignment explanation
Indices: 10280828--10281075 Score: 471
Period size: 83 Copynumber: 3.0 Consensus size: 83
10280818 GACGACACTG
10280828 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
10280893 GGTCGGGAAATGACACGA
66 GGTCGGGAAATGACACGA
10280911 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
10280976 GGTCGGGAAATGACACGA
66 GGTCGGGAAATGACACGA
10280994 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
1 CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
*
10281059 GGTCTGGG-GATGACACG
66 GGTC-GGGAAATGACACG
10281076 GTTCCTACAT
Statistics
Matches: 163, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
83 160 0.98
84 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (83 bp):
CTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCT
GGTCGGGAAATGACACGA
Found at i:10281138 original size:46 final size:43
Alignment explanation
Indices: 10281071--10281182 Score: 134
Period size: 46 Copynumber: 2.5 Consensus size: 43
10281061 TCTGGGGATG
* *
10281071 ACACGGTTCCTACATGATGAGGACGGTTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCT-AAGGT--TA
** * *
10281117 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTAAGGTTA
*
10281160 ACACGGCTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
10281183 GATCTGGTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 23 0.39
45 4 0.07
46 32 0.54
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGCCATCTAAGGTTA
Found at i:10281387 original size:63 final size:62
Alignment explanation
Indices: 10281319--10281436 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
10281309 TTTCAAAAGC
*
10281319 AACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAACGGAA
1 AACTGTCTCAAAAGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAACGGAA
* *
10281382 AACTGTCTCGAATGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
10281437 GTTTTGTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 3 0.06
62 19 0.38
63 28 0.56
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (62 bp):
AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTTAACGGAA
Found at i:10281641 original size:37 final size:36
Alignment explanation
Indices: 10281595--10281712 Score: 102
Period size: 37 Copynumber: 3.3 Consensus size: 36
10281585 TCAAAGATTT
10281595 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAA-TATCTTAAGAGAGACAAAATTTTG
* * * * ***
10281632 TTTCCAAAGAAACAGAC-TCA-A-AG--ATTTTTTTG
1 TTTCAAAAGAAATA-TCTTAAGAGAGACAAAATTTTG
10281664 TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAA-TATCTTAAGAGAGACAAAATTTTG
*
10281701 TTTCCAAAGAAA
1 TTTCAAAAGAAA
10281713 CAAACTCAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
32 18 0.31
33 3 0.05
34 3 0.05
35 3 0.05
36 3 0.05
37 29 0.49
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (36 bp):
TTTCAAAAGAAATATCTTAAGAGAGACAAAATTTTG
Found at i:10281653 original size:64 final size:65
Alignment explanation
Indices: 10281521--10281746 Score: 255
Period size: 69 Copynumber: 3.4 Consensus size: 65
10281511 ATGAACATAT
* * * * * *
10281521 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTTAT-TTT--AAGAAAAACAG
1 TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTT-TGTTTCCAA-AGAAACAG
*
10281583 AT
64 AC
*
10281585 TCAAAGATTT-TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGAC
1 TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGAC
*
10281649 TCAAAGATTTTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAAC
1 TCAAAGA----TTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAAC
*
10281714 AAAC
62 AGAC
*
10281718 TCAAAGATTT-TTTCCAAAAGAAACAATCT
1 TCAAAGATTTATTT-CAAAAGAAACTATCT
10281747 CAAAGATTTT
Statistics
Matches: 142, Mismatches: 11, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
62 1 0.01
63 32 0.23
64 28 0.20
65 19 0.13
68 3 0.02
69 59 0.42
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (65 bp):
TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGAC
Found at i:10281732 original size:27 final size:28
Alignment explanation
Indices: 10281701--10281758 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
10281691 CAAAATTTTG
10281701 TTTCC-AAAGAAACAAACTCAAAGATTT
1 TTTCCAAAAGAAACAAACTCAAAGATTT
*
10281728 TTTCCAAAAGAAACAATCTCAAAGATTT
1 TTTCCAAAAGAAACAAACTCAAAGATTT
10281756 TTT
1 TTT
10281759 TTCACAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (28 bp):
TTTCCAAAAGAAACAAACTCAAAGATTT
Found at i:10281877 original size:26 final size:25
Alignment explanation
Indices: 10281848--10281958 Score: 96
Period size: 28 Copynumber: 4.1 Consensus size: 25
10281838 CAAAACTTTG
* *
10281848 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
10281874 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
10281901 TATTCAAAAGGAACAAACTCCAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
* *
10281929 TATTTAAAAGGAACTAACTCAAAGATT
1 T-TTCAAAAGAAAC-AACTCAAAGATT
10281956 TTT
1 TTT
10281959 TTTCAAGAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
25 8 0.11
26 14 0.19
27 8 0.11
28 35 0.48
29 8 0.11
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:10281915 original size:28 final size:29
Alignment explanation
Indices: 10281863--10281964 Score: 115
Period size: 28 Copynumber: 3.7 Consensus size: 29
10281853 AAATAAATAG
*
10281863 ACTCAAAG--ATTT-TTCAAAAGAAAC-A
1 ACTCAAAGATATTTATTCAAAAGGAACAA
10281888 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
* * *
10281917 ACTCCAAGAT-TTTATTTAAAAGGAACTA
1 ACTCAAAGATATTTATTCAAAAGGAACAA
* *
10281945 ACTCAAAGATTTTTTTTCAA
1 ACTCAAAGATATTTATTCAA
10281965 GAGAAACTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
25 8 0.12
27 4 0.06
28 36 0.55
29 17 0.26
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATATTTATTCAAAAGGAACAA
Found at i:10282295 original size:36 final size:35
Alignment explanation
Indices: 10282211--10282314 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
10282201 GAGAAAATGA
* *
10282211 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGAC-AAATTTGTTTTTAGAGAAAT
* **
10282245 AGTCTCAAATGAGACAACATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAA-ATTTGTTTTTAGAGAAAT
10282281 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAA-TTTGTTTTTAGAGAAA
10282315 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
33 2 0.03
34 17 0.29
35 11 0.19
36 28 0.48
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTGTTTTTAGAGAAAT
Found at i:10286331 original size:31 final size:32
Alignment explanation
Indices: 10286275--10286338 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
10286265 TGACAAAATG
10286275 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
10286307 ACACAAACAAAAGAGAA-AAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
10286338 A
1 A
10286339 AATAAGTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:10286343 original size:14 final size:14
Alignment explanation
Indices: 10286324--10286350 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10286314 CAAAAGAGAA
10286324 AAATAAGTTAGTAT
1 AAATAAGTTAGTAT
10286338 AAATAAGTTAGTA
1 AAATAAGTTAGTA
10286351 CATGTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
AAATAAGTTAGTAT
Found at i:10287833 original size:17 final size:18
Alignment explanation
Indices: 10287803--10287836 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
10287793 AAAAACACAC
*
10287803 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
10287821 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
10287837 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:10289901 original size:3 final size:3
Alignment explanation
Indices: 10289895--10289955 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
10289885 AAAAAATATG
* **
10289895 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10289939 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
10289956 CGATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:10289932 original size:29 final size:30
Alignment explanation
Indices: 10289900--10289962 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
10289890 ATATGTAATA
*
10289900 ATAAATAATAATAA-AATAATAAGATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
10289929 AT-AATAATAATAATAATAATAAAATAACG
1 ATAAATAATAATAATAATAATAAAATAACG
10289958 ATAAA
1 ATAAA
10289963 AAAAAACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 11 0.35
29 18 0.58
30 2 0.06
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (30 bp):
ATAAATAATAATAATAATAATAAAATAACG
Found at i:10299933 original size:31 final size:31
Alignment explanation
Indices: 10299898--10299960 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
10299888 ATTTGGTCGT
* * *
10299898 TTTCGTTTTTATTTAATTAAGATTTGATCAC
1 TTTCGTTTTAATGTAATTAAGATGTGATCAC
*
10299929 TTTCGTTTTAATGTAATTAAGATGTGGTCAC
1 TTTCGTTTTAATGTAATTAAGATGTGATCAC
10299960 T
1 T
10299961 GAGGGTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTCGTTTTAATGTAATTAAGATGTGATCAC
Found at i:10300274 original size:10 final size:9
Alignment explanation
Indices: 10300252--10300281 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
10300242 GTATATATAT
10300252 AAAAATTAG
1 AAAAATTAG
*
10300261 AAAAATTGG
1 AAAAATTAG
10300270 AAAAATTAG
1 AAAAATTAG
10300279 AAA
1 AAA
10300282 GTTTTGGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (9 bp):
AAAAATTAG
Found at i:10304960 original size:12 final size:12
Alignment explanation
Indices: 10304943--10304970 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10304933 AATGAGAGAC
10304943 CAACATCAACTT
1 CAACATCAACTT
10304955 CAACATCAACTT
1 CAACATCAACTT
10304967 CAAC
1 CAAC
10304971 TGTAAAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (12 bp):
CAACATCAACTT
Found at i:10307779 original size:60 final size:60
Alignment explanation
Indices: 10307594--10307781 Score: 218
Period size: 60 Copynumber: 3.1 Consensus size: 60
10307584 TTTGGATGAA
* * * **
10307594 TTTGGGGATGTAATTGGAATATTTAAAAGTTTGGGGACCAATTTAGAAA-GAGAGTCATAG
1 TTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTA-AAATGAGAGTCATAG
* * * * *
10307654 TTTAGGGATGAAATTAAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAG
* * *
10307714 TTTGGGGATGAAATTGAAATATTCAAAAGTTTAATGACCAATCTAAAATAAGAG-CTATAG
1 TTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTC-ATAG
*
10307774 CTTGGGGA
1 TTTGGGGA
10307782 CATATGATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.03
60 104 0.97
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (60 bp):
TTTGGGGATGAAATTGAAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAG
Found at i:10307955 original size:18 final size:18
Alignment explanation
Indices: 10307913--10307961 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
10307903 TTGTTATTAT
*
10307913 AATTTAATAATTCAAAAT
1 AATTTAATAATTCAAAAC
*
10307931 AATTTAATAATTCATTAAC
1 AATTTAATAATTCA-AAAC
*
10307950 AATTAAATAATT
1 AATTTAATAATT
10307962 TAATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAATAATTCAAAAC
Found at i:10308850 original size:14 final size:15
Alignment explanation
Indices: 10308814--10308850 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
10308804 ATAACCACTT
10308814 TATTAATTTAAACAA
1 TATTAATTTAAACAA
10308829 TA-TAATTT-AACAA
1 TATTAATTTAAACAA
*
10308842 TATTTATTT
1 TATTAATTT
10308851 CACCAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 7 0.35
14 11 0.55
15 2 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTAATTTAAACAA
Found at i:10309277 original size:60 final size:61
Alignment explanation
Indices: 10309180--10309296 Score: 191
Period size: 60 Copynumber: 1.9 Consensus size: 61
10309170 CAATCAAATT
* * * *
10309180 ATTAATATAATATTAATTTTATTAAATTATACGTGTCATAATTTGATTGATTGTTATTTTG
1 ATTAATATAATATTAATTTTATTAAATTATACATGTCACAACTTAATTGATTGTTATTTTG
10309241 ATTAATATAATATTAA-TTTATTAAATTATACATGTCACAACTTAATTGATTGTTAT
1 ATTAATATAATATTAATTTTATTAAATTATACATGTCACAACTTAATTGATTGTTAT
10309297 AATAAAAGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 36 0.69
61 16 0.31
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (61 bp):
ATTAATATAATATTAATTTTATTAAATTATACATGTCACAACTTAATTGATTGTTATTTTG
Found at i:10310953 original size:18 final size:19
Alignment explanation
Indices: 10310930--10310984 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
10310920 ATTGCTTGAA
10310930 TATTAATTTAATTAATA-C
1 TATTAATTTAATTAATATC
*
10310948 TATTAATTTTA-TAATTATC
1 TATTAATTTAATTAA-TATC
* *
10310967 AAGTAATTTAATTAATAT
1 TATTAATTTAATTAATAT
10310985 GATTTGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 12 0.40
20 3 0.10
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTAATTTAATTAATATC
Found at i:10313841 original size:3 final size:3
Alignment explanation
Indices: 10313833--10313862 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
10313823 CGGTTCTTGA
10313833 AAG AAG AAG AAG AAG AAG AAG AGAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG A-AG AAG AA
10313863 AAGGGTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10327613 original size:2 final size:2
Alignment explanation
Indices: 10327601--10327638 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
10327591 TGTTTTTATT
*
10327601 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA -A TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10327639 AAGAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10329136 original size:43 final size:44
Alignment explanation
Indices: 10329068--10329222 Score: 210
Period size: 42 Copynumber: 3.6 Consensus size: 44
10329058 CCAACGTCGT
* * *
10329068 AAAAGGTCGATATCTATAGCGGCGTTTTTGGATACAAACGCCGC
1 AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCAC
* * * * *
10329112 GAAAAG-AAAGATCTATAGCTGCGTTTTTGGAT-CAAACGCCTC
1 AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCAC
10329154 AAAAAGTCAATATCTATAGCGGCG-TTTTGGA-ACAAACGCCAC
1 AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCAC
10329196 AAAAAGTCAATATCTATAGCGGCGTTT
1 AAAAAGTCAATATCTATAGCGGCGTTT
10329223 GTATCCACAA
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
42 54 0.56
43 38 0.40
44 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (44 bp):
AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCAC
Found at i:10329234 original size:86 final size:86
Alignment explanation
Indices: 10329068--10329237 Score: 211
Period size: 86 Copynumber: 2.0 Consensus size: 86
10329058 CCAACGTCGT
* * * * *
10329068 AAAAGGTCGATATCTATAGCGGCGTTTTTGGATACAAACGCCGCGAAAAGAAAGATCTATAGCTG
1 AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCACAAAAAGAAAGATCTATAGCGG
**
10329133 CGTTTTTGGATCAAACGCCTC
66 CGTTTTTCCATCAAACGCCTC
* *
10329154 AAAAAGTCAATATCTATAGCGGCG-TTTTGGA-ACAAACGCCACAAAAAGTCAATATCTATAGCG
1 AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCACAAAAAG-AAAGATCTATAGCG
10329217 GCGTTTGTATCCA-CAAACGCC
65 GCGTTT-T-TCCATCAAACGCC
10329238 GCTAATTACC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 15 0.21
85 24 0.33
86 31 0.43
87 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (86 bp):
AAAAAGTCAATATCTATAGCGGCGTTTTTGGATACAAACGCCACAAAAAGAAAGATCTATAGCGG
CGTTTTTCCATCAAACGCCTC
Found at i:10332306 original size:41 final size:41
Alignment explanation
Indices: 10332249--10332668 Score: 357
Period size: 41 Copynumber: 10.3 Consensus size: 41
10332239 TTGTGTTTAC
10332249 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * *
10332290 AAACACCACTGAAGTACAAGTCTTTAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * ** * * *
10332331 AAACGCGACTGAAGTATGAGTCTATAGCGGTGTTTATATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * * * * * *
10332372 AAACGCCACTGAATTACGAGTCTTAAACAGCGTTTGTAAACA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATA-A
*
10332414 CAAACGCCACTAAAGTAC-AGTCGTTAGCGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
** * * * *
10332455 AAACGCCACTAAA-TAACTTGTTTTTAACGACGTTTGTACAAA
1 AAACGCCACTAAAGT-ACAAGTCTTTAGCGGCGTTTGTA-TAA
*
10332497 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * * * *
10332538 AAACCCCACTAAATTACAA-TCTTTAGCAGCATTTATATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * ** * * *
10332578 AAATGCCACTAAAATATGAGTATTTAGCGGC-ATT-TAAAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
* * * * * * *
10332617 AAACACCACTATAGCACATGT-TTTTGTGGCGTTTTTATAA
1 AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
10332657 CAAACGCCACTA
1 -AAACGCCACTA
10332669 TTGATGAACC
Statistics
Matches: 302, Mismatches: 67, Indels: 20
0.78 0.17 0.05
Matches are distributed among these distances:
38 7 0.02
39 20 0.07
40 54 0.18
41 155 0.51
42 50 0.17
43 16 0.05
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAGTCTTTAGCGGCGTTTGTATAA
Found at i:10333501 original size:22 final size:24
Alignment explanation
Indices: 10333475--10333522 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
10333465 TCAAAATAAA
10333475 ATTATTGGATT-AATT-TAATTTT
1 ATTATTGGATTAAATTATAATTTT
*
10333497 ATTATTGTATTAAATTATAATTTT
1 ATTATTGGATTAAATTATAATTTT
10333521 AT
1 AT
10333523 AAAGATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 4 0.17
24 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTATTGGATTAAATTATAATTTT
Found at i:10340505 original size:32 final size:32
Alignment explanation
Indices: 10340464--10340528 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
10340454 GGTCTCTTTG
*
10340464 TGAAACCAATAGT-CATTTTATTTTAGTGCAAA
1 TGAAACCAATAGTGC-TCTTATTTTAGTGCAAA
* **
10340496 TGAACCCAATTTTGCTCTTATTTTAGTGCAAA
1 TGAAACCAATAGTGCTCTTATTTTAGTGCAAA
10340528 T
1 T
10340529 TGATGGGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (32 bp):
TGAAACCAATAGTGCTCTTATTTTAGTGCAAA
Found at i:10345601 original size:72 final size:72
Alignment explanation
Indices: 10345505--10345648 Score: 254
Period size: 72 Copynumber: 2.0 Consensus size: 72
10345495 TTTTCATCCG
10345505 ATAGTTATTTATTTATTTATTTTTTGAATAGTCTGCTATGAATATAATTTAATATTTGTTCAGAA
1 ATAGTTATTTATTTATTTATTTTTTGAATAGTCTGCTATGAATATAATTTAATATTTGTTCAGAA
10345570 ATTTTTT
66 ATTTTTT
*
10345577 ATAGTTATTTTTTTTATTTA-TTTTTGAATAGTCTGCTATGAATATAATTTAATATTTGTTCAGA
1 ATAGTTA-TTTATTTATTTATTTTTTGAATAGTCTGCTATGAATATAATTTAATATTTGTTCAGA
*
10345641 ATTTTTTT
65 AATTTTTT
10345649 TAACAATTAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 58 0.84
73 11 0.16
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (72 bp):
ATAGTTATTTATTTATTTATTTTTTGAATAGTCTGCTATGAATATAATTTAATATTTGTTCAGAA
ATTTTTT
Found at i:10359948 original size:15 final size:15
Alignment explanation
Indices: 10359927--10359966 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
10359917 TCTGTCTTAT
10359927 ATTTTAATTATTGTA
1 ATTTTAATTATTGTA
* * *
10359942 CTTTTAATTTTTTTA
1 ATTTTAATTATTGTA
10359957 ATTTTAATTA
1 ATTTTAATTA
10359967 CTAAACTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (15 bp):
ATTTTAATTATTGTA
Found at i:10360614 original size:23 final size:23
Alignment explanation
Indices: 10360588--10360644 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
10360578 ATCAAGTAAA
10360588 ATAA-CAAATTAGGTACCGCTTAT
1 ATAATCAAA-TAGGTACCGCTTAT
** *
10360611 ATAATGTAATAGGTAGCGCTTAT
1 ATAATCAAATAGGTACCGCTTAT
*
10360634 ATAATAAAATA
1 ATAATCAAATA
10360645 TGTTAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (23 bp):
ATAATCAAATAGGTACCGCTTAT
Found at i:10360922 original size:23 final size:23
Alignment explanation
Indices: 10360896--10360955 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
10360886 ATCAAACACA
*
10360896 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
10360919 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
10360942 ATAATAAAATAGGT
1 ATAACATAATAGGT
10360956 TAATTACTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:10361360 original size:197 final size:198
Alignment explanation
Indices: 10361009--10361682 Score: 925
Period size: 197 Copynumber: 3.4 Consensus size: 198
10360999 CGCTTATATT
* * * *
10361009 GACCTATTATATCATAAAATCGGTATATTTATACC-GGTAACATTGTAAATTTACCTATTATATT
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGT-ACATTGTAAATTTACCTATTACATT
* *
10361073 ATAATTATCGGTTTTGATATTTTTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCG
65 ATAATTATCGGTTTCGAT-TTTTTGGGATCGATAC-ATTTAATAAATGTATCGACACTTTATGTG
* *
10361136 TGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACAT
128 TGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACAT
10361201 TATGTA
193 TATGTA
* *
10361207 GACCTATTTTCTCATAAAACCGGTATATTTCTACCGGGTACATTGTAAATTTACCTATTACATTG
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
* * *
10361272 TAATTATCGGTTTGGATTTTTTGGGATCGATAC-TTTAATAAATGTGTCGACACTTTATGTGTGA
66 TAATTATCGGTTTCGATTTTTTGGGATCGATACATTTAATAAATGTATCGACACTTTATGTGTGC
10361336 ACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTAT
131 ACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTAT
10361401 GTA
196 GTA
* * * * *
10361404 GATCTATTTTCTCAT-AAACCGATATATTTCTACCGAGTACATTGTAAATTTACCTATTACATTG
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
* * * *
10361468 TAATTATCGGTTTCGATGTTTTGGGATCAATACTTTTAATAAATTTATCGACACTTTATGCT-TG
66 TAATTATCGGTTTCGATTTTTTGGGATCGATACATTTAATAAATGTATCGACACTTTATG-TGTG
* * *** *
10361532 CACCTCGTT-TAGCATTCATTCTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACA
130 CACCTCGTTGGA-CATTCATTCTGGA-AAAAAGTATCGACACAAACTTAAA-ATGTGTCGATACA
10361595 TTATGTA
192 TTATGTA
* * * * *
10361602 GACATATTCTCTCATAAAACCGGTATA-TTATACTGGTTATATTGTAAATTTACCTATTACATTA
1 GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
10361666 TAATTATCGGTTTCGAT
66 TAATTATCGGTTTCGAT
10361683 GTAACATATG
Statistics
Matches: 430, Mismatches: 37, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
195 3 0.01
196 78 0.18
197 171 0.40
198 165 0.38
199 13 0.03
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (198 bp):
GACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATTACATTA
TAATTATCGGTTTCGATTTTTTGGGATCGATACATTTAATAAATGTATCGACACTTTATGTGTGC
ACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAATGTGTCGATACATTAT
GTA
Found at i:10361796 original size:16 final size:16
Alignment explanation
Indices: 10361775--10361821 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
10361765 ATTATTCTTA
10361775 TTATAATAAATATAAT
1 TTATAATAAATATAAT
* *
10361791 TTATAAT-AATTTTAT
1 TTATAATAAATATAAT
10361806 TT-TAATAAAATATAAT
1 TTATAAT-AAATATAAT
10361822 AATCATAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATAATAAATATAAT
Found at i:10361820 original size:31 final size:30
Alignment explanation
Indices: 10361772--10361864 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 30
10361762 TATATTATTC
* *
10361772 TTATTATAAT-AAATATAATTTATAATAATT
1 TTATTTTAATAAAATATAA-TAATAATAATT
*
10361802 TTATTTTAATAAAATATAATAATCATAATT
1 TTATTTTAATAAAATATAATAATAATAATT
*
10361832 TT-TTATTTATAAAATTATAGAT-ATAAT-ATT
1 TTATT-TTAATAAAA-TATA-ATAATAATAATT
10361862 TTA
1 TTA
10361865 AAAATAATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 33 0.62
31 16 0.30
32 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTATTTTAATAAAATATAATAATAATAATT
Found at i:10361830 original size:30 final size:31
Alignment explanation
Indices: 10361748--10361846 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 31
10361738 CTCTCATTAT
*
10361748 AATATAATTAATGATATATTATTCTTATTATAAT-A
1 AATATAATTAAT-A-ATA--ATT-TTATTTTAATAA
*
10361783 AATATAATTTATAATAATTTTATTTTAATAA
1 AATATAATTAATAATAATTTTATTTTAATAA
* *
10361814 AATATAA-TAATCATAATTTT-TTATTTATAA
1 AATATAATTAATAATAATTTTATT-TTAATAA
10361844 AAT
1 AAT
10361847 TATAGATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.04
30 29 0.51
31 11 0.19
33 3 0.05
34 1 0.02
35 11 0.19
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (31 bp):
AATATAATTAATAATAATTTTATTTTAATAA
Found at i:10362591 original size:31 final size:31
Alignment explanation
Indices: 10362554--10362647 Score: 86
Period size: 31 Copynumber: 3.0 Consensus size: 31
10362544 TAAAAAATAA
*
10362554 AAAATATAATTTATAATAATTTTATT-TTAAT
1 AAAATATAA-TAATAATAATTTTATTATTAAT
* * *
10362585 AAAATATAATAATCATAATTTTTTTATTTAT
1 AAAATATAATAATAATAATTTTATTATTAAT
* *
10362616 AAAATTATAGAT-ATAAT-ATTTTAATAATAAT
1 AAAA-TATA-ATAATAATAATTTTATTATTAAT
10362647 A
1 A
10362648 TTTACAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 13 0.25
31 28 0.55
32 8 0.16
33 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
AAAATATAATAATAATAATTTTATTATTAAT
Found at i:10362637 original size:29 final size:32
Alignment explanation
Indices: 10362554--10362637 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 32
10362544 TAAAAAATAA
* *
10362554 AAAATATAAT-TTATAATAATTTTATTTTAAT
1 AAAATATAATAATATAATATTTTTATTTTAAT
*
10362585 AAAATATAATAATCATAATTTTTTTA-TTT-AT
1 AAAATATAATAAT-ATAATATTTTTATTTTAAT
10362616 AAAAT-T-ATAGATATAATATTTT
1 AAAATATAATA-ATATAATATTTT
10362638 AATAATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 12 0.26
30 3 0.07
31 17 0.37
32 4 0.09
33 10 0.22
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (32 bp):
AAAATATAATAATATAATATTTTTATTTTAAT
Found at i:10362645 original size:14 final size:14
Alignment explanation
Indices: 10362562--10362682 Score: 52
Period size: 14 Copynumber: 8.6 Consensus size: 14
10362552 AAAAAATATA
**
10362562 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
10362577 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
10362590 ATAATAATCATAATT
1 ATTTTAATAATAA-T
* * * *
10362605 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
10362619 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
10362633 ATTTTAATAATAAT
1 ATTTTAATAATAAT
* *
10362647 ATTTACAAAAATAAT
1 ATTT-TAATAATAAT
* *
10362662 A-TTAAATAA-ATT
1 ATTTTAATAATAAT
10362674 ATTTTAATA
1 ATTTTAATA
10362683 TTTTAAAAAT
Statistics
Matches: 78, Mismatches: 22, Indels: 14
0.68 0.19 0.12
Matches are distributed among these distances:
12 3 0.04
13 20 0.26
14 32 0.41
15 23 0.29
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:10363044 original size:23 final size:23
Alignment explanation
Indices: 10362987--10363059 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
10362977 ACCTATTTTA
*
10362987 TTATATAAGCGATGCCTATTACG
1 TTATATAAGCGCTGCCTATTACG
10363010 TTATATAAGCGCTGCCTATTACG
1 TTATATAAGCGCTGCCTATTACG
* * *
10363033 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTGCCTATTACG
10363056 TTAT
1 TTAT
10363060 TGTGCTTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (23 bp):
TTATATAAGCGCTGCCTATTACG
Found at i:10363115 original size:87 final size:87
Alignment explanation
Indices: 10363011--10363220 Score: 348
Period size: 87 Copynumber: 2.4 Consensus size: 87
10363001 CCTATTACGT
* *
10363011 TATATAAGCGCTGCCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
10363076 TCCAGTAATTAACCTATTTTAG
66 TCCAGTAATTAACCTATTTTAG
*
10363098 TATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGCTTGATAATGTT
1 TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
* *
10363163 TTCAGTAATTAACCTATTTTAT
66 TCCAGTAATTAACCTATTTTAG
* **
10363185 TATATAAGCGATATATATTACATTATATAAGCGCTA
1 TATATAAGCGCTACCTATTACATTATATAAGCGCTA
10363221 ACTATTACAT
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 114 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (87 bp):
TATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATGTT
TCCAGTAATTAACCTATTTTAG
Found at i:10363302 original size:23 final size:23
Alignment explanation
Indices: 10363174--10363293 Score: 177
Period size: 23 Copynumber: 5.2 Consensus size: 23
10363164 TCAGTAATTA
** *
10363174 ACCTATTTTATTATATAAGCGAT
1 ACCTATTACATTATATAAGCGCT
**
10363197 ATATATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
10363220 AACTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
10363243 ACCTATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
*
10363266 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
10363289 ACCTA
1 ACCTA
10363294 ATATGTTATT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 88 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:10367806 original size:45 final size:45
Alignment explanation
Indices: 10367757--10367866 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
10367747 AGCAACTCCG
* *
10367757 CCTCCACCTGCTTCTCCACCTCCCGCCACCCCACCACCTGCTTCT
1 CCTCCACCAGCATCTCCACCTCCCGCCACCCCACCACCTGCTTCT
* * *
10367802 CCTCCACCAGCATCTCCCCCTCCCGCTACTCCACCACCTGCTTCT
1 CCTCCACCAGCATCTCCACCTCCCGCCACCCCACCACCTGCTTCT
*
10367847 CCTCCACCAGCAACTCCACC
1 CCTCCACCAGCATCTCCACC
10367867 ACCTGCAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.15, C:0.59, G:0.06, T:0.20
Consensus pattern (45 bp):
CCTCCACCAGCATCTCCACCTCCCGCCACCCCACCACCTGCTTCT
Found at i:10367808 original size:15 final size:15
Alignment explanation
Indices: 10367760--10367878 Score: 78
Period size: 15 Copynumber: 7.9 Consensus size: 15
10367750 AACTCCGCCT
*
10367760 CCACCTGCTTCTCCA
1 CCACCTGCTACTCCA
* * * *
10367775 CCTCCCGCCACCCCA
1 CCACCTGCTACTCCA
* *
10367790 CCACCTGCTTCTCCT
1 CCACCTGCTACTCCA
* *
10367805 CCACCAGC-ATCTCCC
1 CCACCTGCTA-CTCCA
* *
10367820 CCTCCCGCTACTCCA
1 CCACCTGCTACTCCA
* *
10367835 CCACCTGCTTCTCCT
1 CCACCTGCTACTCCA
* *
10367850 CCACCAGCAACTCCA
1 CCACCTGCTACTCCA
*
10367865 CCACCTGCAACTCC
1 CCACCTGCTACTCC
10367879 TCCAGCTACC
Statistics
Matches: 76, Mismatches: 26, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
15 75 0.99
16 1 0.01
ACGTcount: A:0.16, C:0.58, G:0.07, T:0.19
Consensus pattern (15 bp):
CCACCTGCTACTCCA
Found at i:10367839 original size:63 final size:63
Alignment explanation
Indices: 10367721--10367840 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 63
10367711 CCCAGTTTCA
* * * * * *
10367721 ACCCCTCCACCTAGCTCTCCTCCTCCAGCAACTCCGCCTCCACCTGCTTCTCCACCTCCCGCC
1 ACCCCACCACCTAGCTCTCCTCCACCAGCAACTCCCCCTCCACCTACTCCACCACCTCCCGCC
*
10367784 ACCCCACCACCT-GCTTCTCCTCCACCAGCATCTCCCCCTCC-CGCTACTCCACCACCT
1 ACCCCACCACCTAGC-TCTCCTCCACCAGCAACTCCCCCTCCAC-CTACTCCACCACCT
10367841 GCTTCTCCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
62 3 0.06
63 45 0.94
ACGTcount: A:0.14, C:0.59, G:0.07, T:0.20
Consensus pattern (63 bp):
ACCCCACCACCTAGCTCTCCTCCACCAGCAACTCCCCCTCCACCTACTCCACCACCTCCCGCC
Found at i:10367848 original size:30 final size:30
Alignment explanation
Indices: 10367800--10367878 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
10367790 CCACCTGCTT
* * * * *
10367800 CTCCTCCACCAGCATCTCCCCCTCCCGCTA
1 CTCCACCACCTGCATCTCCCCCACCAGCAA
* *
10367830 CTCCACCACCTGCTTCTCCTCCACCAGCAA
1 CTCCACCACCTGCATCTCCCCCACCAGCAA
*
10367860 CTCCACCACCTGCAACTCC
1 CTCCACCACCTGCATCTCC
10367879 TCCAGCTACC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.57, G:0.06, T:0.19
Consensus pattern (30 bp):
CTCCACCACCTGCATCTCCCCCACCAGCAA
Found at i:10367850 original size:27 final size:27
Alignment explanation
Indices: 10367820--10367900 Score: 81
Period size: 30 Copynumber: 2.9 Consensus size: 27
10367810 AGCATCTCCC
*
10367820 CCTCCCGCTACTCCACCACCTGCTTCT
1 CCTCCCGCTACTCCACCACCTGCTACT
* *
10367847 CCTCCACCAGCAACTCCACCACCTGCAACT
1 CCT-C-CC-GCTACTCCACCACCTGCTACT
* * *
10367877 CCTCCAGCTACCCCACCGCCTGCT
1 CCTCCCGCTACTCCACCACCTGCT
10367901 CCCTTGGCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 17 0.40
28 2 0.05
29 3 0.07
30 21 0.49
ACGTcount: A:0.17, C:0.56, G:0.09, T:0.19
Consensus pattern (27 bp):
CCTCCCGCTACTCCACCACCTGCTACT
Found at i:10367878 original size:45 final size:45
Alignment explanation
Indices: 10367770--10367878 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
10367760 CCACCTGCTT
* * * *
10367770 CTCCACCTCCCGCCACCCCACCACCTGCTTCTCCTCCACCAGCAT
1 CTCCACCACCCGCAACTCCACCACCTGCTTCTCCTCCACCAGCAA
* * *
10367815 CTCCCCCTCCCGCTACTCCACCACCTGCTTCTCCTCCACCAGCAA
1 CTCCACCACCCGCAACTCCACCACCTGCTTCTCCTCCACCAGCAA
*
10367860 CTCCACCACCTGCAACTCC
1 CTCCACCACCCGCAACTCC
10367879 TCCAGCTACC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.17, C:0.59, G:0.06, T:0.18
Consensus pattern (45 bp):
CTCCACCACCCGCAACTCCACCACCTGCTTCTCCTCCACCAGCAA
Found at i:10368910 original size:23 final size:23
Alignment explanation
Indices: 10368880--10368933 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
10368870 ATGAAAAAAA
10368880 CGTTCGGTGAATTATTCGTGAAC
1 CGTTCGGTGAATTATTCGTGAAC
*
10368903 CGTTCGGTGAATTGTTCGTGAAC
1 CGTTCGGTGAATTATTCGTGAAC
10368926 CGTTCGGT
1 CGTTCGGT
10368934 TAAAGCTCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.35
Consensus pattern (23 bp):
CGTTCGGTGAATTATTCGTGAAC
Found at i:10368965 original size:14 final size:14
Alignment explanation
Indices: 10368946--10368972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10368936 AAGCTCGTTC
10368946 ATGTTCGTTTATTT
1 ATGTTCGTTTATTT
10368960 ATGTTCGTTTATT
1 ATGTTCGTTTATT
10368973 AAAGTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (14 bp):
ATGTTCGTTTATTT
Found at i:10375875 original size:23 final size:23
Alignment explanation
Indices: 10375843--10375910 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
10375833 TAAACGAAAA
*
10375843 CTAAATGAATATATTCACGAATG
1 CTAAAAGAATATATTCACGAATG
* *
10375866 -TCAAAAGAATATATTCATGAACG
1 CT-AAAAGAATATATTCACGAATG
* *
10375889 CTAAACGAATATATTCGCGAAT
1 CTAAAAGAATATATTCACGAAT
10375911 ATTTAAACGA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (23 bp):
CTAAAAGAATATATTCACGAATG
Found at i:10375932 original size:12 final size:12
Alignment explanation
Indices: 10375917--10375957 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
10375907 GAATATTTAA
10375917 ACGAACATGTTC
1 ACGAACATGTTC
*
10375929 ACGAAC--GTTAA
1 ACGAACATGTT-C
10375940 ACGAACATGTTC
1 ACGAACATGTTC
10375952 ACGAAC
1 ACGAAC
10375958 GTTAAACGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.12
11 6 0.25
12 12 0.50
13 3 0.12
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (12 bp):
ACGAACATGTTC
Found at i:10375933 original size:24 final size:23
Alignment explanation
Indices: 10375890--10375968 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
10375880 TCATGAACGC
* * * *
10375890 TAAACGAATATATTCGCGAATATT
1 TAAACGAACATGTTCACGAA-AGT
*
10375914 TAAACGAACATGTTCACGAACGT
1 TAAACGAACATGTTCACGAAAGT
*
10375937 TAAACGAACATGTTCACGAACGT
1 TAAACGAACATGTTCACGAAAGT
10375960 TAAACGAAC
1 TAAACGAAC
10375969 TAACACGAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 33 0.66
24 17 0.34
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCACGAAAGT
Found at i:10375943 original size:23 final size:23
Alignment explanation
Indices: 10375913--10375968 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
10375903 TCGCGAATAT
10375913 TTAAACGAACATGTTCACGAACG
1 TTAAACGAACATGTTCACGAACG
10375936 TTAAACGAACATGTTCACGAACG
1 TTAAACGAACATGTTCACGAACG
10375959 TTAAACGAAC
1 TTAAACGAAC
10375969 TAACACGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (23 bp):
TTAAACGAACATGTTCACGAACG
Found at i:10381703 original size:44 final size:43
Alignment explanation
Indices: 10381589--10381789 Score: 185
Period size: 44 Copynumber: 4.7 Consensus size: 43
10381579 TTATTTGTCG
* * * *
10381589 TTTAGTTATAGTTGAATCGGCTTAGAAGGG-ATATCACTTGTCG
1 TTTAGTTATATTTGGATCGGCTTAGATGGGAATATCACTTGT-A
* * ** *
10381632 TTTAGTTATATTTTGATCGACCAAGATGTGG-ATATCACTTATCA
1 TTTAGTTATATTTGGATCGGCTTAGATG-GGAATATCACTTGT-A
* * ** *
10381676 TTTAGTTATATTTGGATTGCCTTAGATGGGTTTTTCACTTGTA
1 TTTAGTTATATTTGGATCGGCTTAGATGGGAATATCACTTGTA
*
10381719 GTTTAGTTATATTTGGACCGGCTTAGATGGGAATATCACTTG--
1 -TTTAGTTATATTTGGATCGGCTTAGATGGGAATATCACTTGTA
* *
10381761 TTTAGTTATATTAGGATTGGCTTAGATGG
1 TTTAGTTATATTTGGATCGGCTTAGATGG
10381790 AGATATAATT
Statistics
Matches: 129, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
41 26 0.20
43 24 0.19
44 79 0.61
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.42
Consensus pattern (43 bp):
TTTAGTTATATTTGGATCGGCTTAGATGGGAATATCACTTGTA
Found at i:10381747 original size:88 final size:85
Alignment explanation
Indices: 10381622--10381789 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 85
10381612 AGAAGGGATA
* * *
10381622 TCACTTGTCGTTTAGTTATATTTTGATCGACCAAGATGTGG-ATATCACTTATCATTTAGTTATA
1 TCACTTGTAGTTTAGTTATATTTGGACCGACCAAGATG-GGAATATCAC-T-T-ATTTAGTTATA
*
10381686 TTTGGATTGCCTTAGATGGGTTTT
62 TTAGGATTGCCTTAGATGGGTTTT
* ** *
10381710 TCACTTGTAGTTTAGTTATATTTGGACCGGCTTAGATGGGAATATCACTTGTTTAGTTATATTAG
1 TCACTTGTAGTTTAGTTATATTTGGACCGACCAAGATGGGAATATCACTTATTTAGTTATATTAG
*
10381775 GATTGGCTTAGATGG
66 GATTGCCTTAGATGG
10381790 AGATATAATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 27 0.39
86 1 0.01
87 3 0.04
88 39 0.56
ACGTcount: A:0.23, C:0.11, G:0.22, T:0.43
Consensus pattern (85 bp):
TCACTTGTAGTTTAGTTATATTTGGACCGACCAAGATGGGAATATCACTTATTTAGTTATATTAG
GATTGCCTTAGATGGGTTTT
Found at i:10394559 original size:15 final size:15
Alignment explanation
Indices: 10394537--10394578 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
10394527 ACTGCTAGAG
10394537 GACTCCAAGGGCGAA
1 GACTCCAAGGGCGAA
*
10394552 GGCTCCAAGGGCGAA
1 GACTCCAAGGGCGAA
10394567 GACTCCAAGGGC
1 GACTCCAAGGGC
10394579 ATCGAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.36, T:0.07
Consensus pattern (15 bp):
GACTCCAAGGGCGAA
Found at i:10403166 original size:14 final size:14
Alignment explanation
Indices: 10403147--10403176 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10403137 GCTTTCCATT
*
10403147 AATTAAACCAAATA
1 AATTAAACAAAATA
10403161 AATTAAACAAAATA
1 AATTAAACAAAATA
10403175 AA
1 AA
10403177 CAATGCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (14 bp):
AATTAAACAAAATA
Found at i:10408469 original size:27 final size:27
Alignment explanation
Indices: 10408433--10408493 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
10408423 TTATTAGCTC
*
10408433 GACACATGTATGCTAAATTTATTTTTA
1 GACACGTGTATGCTAAATTTATTTTTA
10408460 GACACGTGTATGCTAAATTTATTTTTA
1 GACACGTGTATGCTAAATTTATTTTTA
10408487 GACACGT
1 GACACGT
10408494 CACAAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (27 bp):
GACACGTGTATGCTAAATTTATTTTTA
Found at i:10410695 original size:2 final size:2
Alignment explanation
Indices: 10410688--10410730 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10410678 GAATCCTAAC
10410688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10410730 T
1 T
10410731 CATTATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10412228 original size:24 final size:23
Alignment explanation
Indices: 10412176--10412236 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
10412166 GTAATTAAGT
10412176 TTAT-ATTATATTGAATATTGTAA
1 TTATAATTATATT-AATATTGTAA
* *
10412199 TAATAATTATATTAATATTGATCA
1 TTATAATTATATTAATATTG-TAA
*
10412223 TTATAATTTTATTA
1 TTATAATTATATTA
10412237 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (23 bp):
TTATAATTATATTAATATTGTAA
Found at i:10412376 original size:2 final size:2
Alignment explanation
Indices: 10412371--10412405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10412361 ATAAAATGAG
10412371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10412406 TTATCATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10412830 original size:10 final size:10
Alignment explanation
Indices: 10412815--10412874 Score: 66
Period size: 10 Copynumber: 5.8 Consensus size: 10
10412805 ATTCATTTTT
10412815 TAAAAATAAA
1 TAAAAATAAA
*
10412825 TAAAAATGTAA
1 TAAAAAT-AAA
10412836 TAAAAATAAA
1 TAAAAATAAA
*
10412846 TTAAAAATGAA
1 -TAAAAATAAA
* *
10412857 TAAAATTCAA
1 TAAAAATAAA
10412867 TAAAAATA
1 TAAAAATA
10412875 TAATGTAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:10412837 original size:11 final size:10
Alignment explanation
Indices: 10412815--10412878 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
10412805 ATTCATTTTT
*
10412815 TAAAAATAAA
1 TAAAAATTAA
10412825 TAAAAATGTAA
1 TAAAAAT-TAA
*
10412836 TAAAAATAAA
1 TAAAAATTAA
*
10412846 TTAAAAATGAA
1 -TAAAAATTAA
10412857 T-AAAATTCAA
1 TAAAAATT-AA
10412867 TAAAAATATAA
1 TAAAAAT-TAA
10412878 T
1 T
10412879 GTAAAGCTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
9 5 0.11
10 13 0.29
11 26 0.58
12 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:10412839 original size:21 final size:21
Alignment explanation
Indices: 10412815--10412878 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
10412805 ATTCATTTTT
10412815 TAAAAATAAATAAAAATGTAA
1 TAAAAATAAATAAAAATGTAA
10412836 TAAAAATAAATTAAAAATG-AA
1 TAAAAATAAA-TAAAAATGTAA
* * *
10412857 TAAAATTCAATAAAAATATAA
1 TAAAAATAAATAAAAATGTAA
10412878 T
1 T
10412879 GTAAAGCTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.18
21 23 0.61
22 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
TAAAAATAAATAAAAATGTAA
Found at i:10412852 original size:32 final size:32
Alignment explanation
Indices: 10412814--10412883 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
10412804 TATTCATTTT
10412814 TTAAAAATAAATAAAAATGT-AATAAAAATA-AA
1 TTAAAAATAAAT-AAAAT-TCAATAAAAATATAA
*
10412846 TTAAAAATGAATAAAATTCAATAAAAATATAA
1 TTAAAAATAAATAAAATTCAATAAAAATATAA
10412878 TGTAAA
1 T-TAAA
10412884 GCTACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
30 1 0.03
31 15 0.44
32 14 0.41
33 4 0.12
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.27
Consensus pattern (32 bp):
TTAAAAATAAATAAAATTCAATAAAAATATAA
Found at i:10418909 original size:27 final size:27
Alignment explanation
Indices: 10418858--10418909 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
10418848 CACAAGAAGA
*
10418858 TATTATAAATTTATAATCTATATAAGG
1 TATTATAAATTTATAATCTAGATAAGG
*
10418885 TATTATAGATTTATAACTCT-GATAA
1 TATTATAAATTTATAA-TCTAGATAA
10418910 TATTACTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (27 bp):
TATTATAAATTTATAATCTAGATAAGG
Found at i:10423414 original size:2 final size:2
Alignment explanation
Indices: 10423407--10423461 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
10423397 ATTATAAAGC
10423407 AT AT AT AT AT AT AT AT AT AT A- 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 AT AT
10423448 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
10423462 TGCAAATTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.