Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 29
Found at i:5937150 original size:10 final size:10
Alignment explanation
Indices: 5937135--5937173 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
5937125 AAATTATATT
5937135 TTCATTTATG
1 TTCATTTATG
*
5937145 TTCATTTACG
1 TTCATTTATG
*
5937155 TTCGTTTATG
1 TTCATTTATG
*
5937165 TTTATTTAT
1 TTCATTTAT
5937174 TGTGTTCATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (10 bp):
TTCATTTATG
Found at i:5954462 original size:15 final size:16
Alignment explanation
Indices: 5954442--5954474 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5954432 ATGTATCTAA
*
5954442 TTATGTTTATTT-ATT
1 TTATGTTCATTTAATT
5954457 TTATGTTCATTTAATT
1 TTATGTTCATTTAATT
5954473 TT
1 TT
5954475 CGTCCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATGTTCATTTAATT
Found at i:5956317 original size:44 final size:48
Alignment explanation
Indices: 5956251--5956347 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 48
5956241 TTATTTTCGT
5956251 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
5956298 TTTTT-GAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
5956343 TTTTT
1 TTTTT
5956348 ATGGATAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
44 28 0.60
45 10 0.21
46 4 0.09
47 5 0.11
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:5966012 original size:9 final size:8
Alignment explanation
Indices: 5965998--5966156 Score: 71
Period size: 8 Copynumber: 19.5 Consensus size: 8
5965988 TCGCTTGAAG
5965998 AAGAAATAA
1 AAGAAA-AA
5966007 AAGAAAAA
1 AAGAAAAA
5966015 AA-AACGAAA
1 AAGAA--AAA
5966024 AATGAAAAA
1 AA-GAAAAA
* *
5966033 ATA-ATAAT
1 A-AGAAAAA
*
5966041 AATAAAAA
1 AAGAAAAA
*
5966049 TGAGAAAAA
1 -AAGAAAAA
5966058 AA-AAAGAA
1 AAGAAA-AA
*
5966066 AAGAAGAA
1 AAGAAAAA
5966074 AAGAAAAA
1 AAGAAAAA
* *
5966082 ATGAGAAA
1 AAGAAAAA
*
5966090 AA-ATAAA
1 AAGAAAAA
*
5966097 AAG-GAAA
1 AAGAAAAA
*
5966104 TA-AAAAA
1 AAGAAAAA
5966111 AAGAAAAAA
1 AAG-AAAAA
5966120 AAGAAAGAA
1 AAGAAA-AA
*
5966129 AA-ATAAA
1 AAGAAAAA
5966136 AAGAGAAAA
1 AAGA-AAAA
*
5966145 ATGAAAAA
1 AAGAAAAA
5966153 AAGA
1 AAGA
5966157 GAAATAAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 33
0.68 0.13 0.20
Matches are distributed among these distances:
7 24 0.21
8 45 0.40
9 41 0.36
10 1 0.01
11 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:5966025 original size:11 final size:10
Alignment explanation
Indices: 5965995--5966168 Score: 55
Period size: 12 Copynumber: 15.4 Consensus size: 10
5965985 ATTTCGCTTG
5965995 AAGAAGAAATAA
1 AAGAA-AAA-AA
5966007 AAGAAAAAAA
1 AAGAAAAAAA
*
5966017 AACGAAAAATGA
1 AA-GAAAAA-AA
* *
5966029 AA-AAATAAT
1 AAGAAAAAAA
*
5966038 AATAATAAAAA
1 AAGAA-AAAAA
*
5966049 TGAGAAAAAAAA
1 -AAG-AAAAAAA
5966061 AAGAAAAGAAGAA
1 AAG-AAA-AA-AA
5966074 AAGAAAAAATGA
1 AAGAAAAAA--A
5966086 GAA-AAAATAAA
1 -AAGAAAA-AAA
5966097 AAGGAAATAAAA
1 AA-GAAA-AAAA
*
5966109 AAAAGAAAAAA
1 AAGA-AAAAAA
5966120 AAGAAAGAAAA
1 AAGAAA-AAAA
*
5966131 ATAAAAAGAGAAA
1 A-AGAAA-A-AAA
5966144 AATGAAAAAAA
1 AA-GAAAAAAA
* *
5966155 GAGAAATAAA
1 AAGAAAAAAA
5966165 AAGA
1 AAGA
5966169 GGGTTCAAGA
Statistics
Matches: 126, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
9 2 0.02
10 25 0.20
11 38 0.30
12 42 0.33
13 19 0.15
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:5966082 original size:34 final size:34
Alignment explanation
Indices: 5966044--5966166 Score: 117
Period size: 34 Copynumber: 3.5 Consensus size: 34
5966034 TAATAATAAT
5966044 AAAAATGAGAAAAAAAAAAGAAA-AGAAGAAAAGA
1 AAAAATGAGAAAAAAAAAAGAAAGAGAA-AAAAGA
* *
5966078 AAAAATGAGAAAAAATAAAAAGGAAATAAAAAAAAGA
1 AAAAATGAG-AAAAA-AAAAA-GAAAGAGAAAAAAGA
* *
5966115 AAAAA-AAGAAAGAAAAATAA-AAAGAGAAAAATGA
1 AAAAATGAGAAA-AAAAA-AAGAAAGAGAAAAAAGA
* *
5966149 AAAAAAGAGAAATAAAAA
1 AAAAATGAGAAAAAAAAA
5966167 GAGGGTTCAA
Statistics
Matches: 75, Mismatches: 7, Indels: 15
0.77 0.07 0.15
Matches are distributed among these distances:
33 1 0.01
34 29 0.39
35 16 0.21
36 11 0.15
37 15 0.20
38 3 0.04
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (34 bp):
AAAAATGAGAAAAAAAAAAGAAAGAGAAAAAAGA
Found at i:5966090 original size:28 final size:25
Alignment explanation
Indices: 5966059--5966145 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 25
5966049 TGAGAAAAAA
5966059 AAAAGAAAAGAAGAAAAGAAAAAATGAG
1 AAAA-AAAAGAAGAAAA-AAAAAA-GAG
*
5966087 AAAAAATAAAAAGGAAATAAAAAAA-AG
1 AAAAAA-AAGAA-GAAA-AAAAAAAGAG
5966114 AAAAAAAAGAAAGAAAAATAAAAAGAG
1 AAAAAAAAG-AAGAAAAA-AAAAAGAG
5966141 AAAAA
1 AAAAA
5966146 TGAAAAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
25 2 0.04
26 11 0.22
27 19 0.37
28 8 0.16
29 10 0.20
30 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (25 bp):
AAAAAAAAGAAGAAAAAAAAAAGAG
Found at i:5966090 original size:29 final size:27
Alignment explanation
Indices: 5966058--5966166 Score: 89
Period size: 28 Copynumber: 3.9 Consensus size: 27
5966048 ATGAGAAAAA
*
5966058 AAAAAGAAAAGAAGAAAAGAAAAAATGAG
1 AAAAA-AAAAGAAGAAAATAAAAAA-GAG
* *
5966087 AAAAAATAAA-AAGGAAATAAAAAAAAG
1 AAAAAA-AAAGAAGAAAATAAAAAAGAG
5966114 -AAAAAAAAGAAAGAAAA-ATAAAAAGAG
1 AAAAAAAAAG-AAGAAAATA-AAAAAGAG
*
5966141 AAAAATGAAAAAAAGAGAAATAAAAA
1 AAAAA--AAAAGAAGA-AAATAAAAA
5966167 GAGGGTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
25 3 0.05
26 6 0.09
27 15 0.23
28 17 0.26
29 12 0.18
30 11 0.17
31 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (27 bp):
AAAAAAAAAGAAGAAAATAAAAAAGAG
Found at i:5966091 original size:43 final size:43
Alignment explanation
Indices: 5966008--5966091 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
5965998 AAGAAATAAA
* * *
5966008 AGAAAAAAAAACGAAAAATGAAAAAATAATAATAATAAAAATG
1 AGAAAAAAAAAAGAAAAAAGAAAAAATAATAATAAGAAAAATG
*
5966051 AGAAAAAAAAAAGAAAAGAAGAAAAGAA-AA-AATGAGAAAAA
1 AGAAAAAAAAAAGAAAA-AAGAAAA-AATAATAATAAGAAAAA
5966092 ATAAAAAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
43 25 0.71
44 8 0.23
45 2 0.06
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (43 bp):
AGAAAAAAAAAAGAAAAAAGAAAAAATAATAATAAGAAAAATG
Found at i:5966142 original size:54 final size:55
Alignment explanation
Indices: 5966053--5966166 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 55
5966043 TAAAAATGAG
* *
5966053 AAAAAAAAAAGAAAAGAAGAAAAGAAAAAATGAGAAAAA-ATAAAAAG-GAAATA
1 AAAAAAAAAAAAAAAGAAGAAAAGAAAAAATGAGAAAAAGAAAAAAAGAGAAATA
5966106 AAAAAAAGAAAAAAAAGAAAGAAAA-ATAAAAA-GAGAAAAATGAAAAAAAGAGAAATA
1 AAAAAAA-AAAAAAAAG-AAGAAAAGA-AAAAATGAGAAAAA-GAAAAAAAGAGAAATA
5966163 AAAA
1 AAAA
5966167 GAGGGTTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
53 7 0.13
54 17 0.32
55 12 0.23
56 7 0.13
57 10 0.19
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (55 bp):
AAAAAAAAAAAAAAAGAAGAAAAGAAAAAATGAGAAAAAGAAAAAAAGAGAAATA
Found at i:5966146 original size:14 final size:14
Alignment explanation
Indices: 5966064--5966169 Score: 89
Period size: 13 Copynumber: 7.5 Consensus size: 14
5966054 AAAAAAAAAG
5966064 AAAAGAAGAAAAGA-A
1 AAAAG-AGAAAA-ATA
5966079 AAAATGAGAAAAAATA
1 AAAA-GAG-AAAAATA
5966095 AAAAG-GAAATAA-A
1 AAAAGAGAAA-AATA
5966108 AAAA-AGAAAAA-A
1 AAAAGAGAAAAATA
5966120 AAGAA-AGAAAAATA
1 AA-AAGAGAAAAATA
5966134 AAAAGAGAAAAATGA
1 AAAAGAGAAAAAT-A
* *
5966149 AAAAAAGAGAAATA
1 AAAAGAGAAAAATA
5966163 AAAAGAG
1 AAAAGAG
5966170 GGTTCAAGAC
Statistics
Matches: 79, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
12 5 0.06
13 23 0.29
14 21 0.27
15 20 0.25
16 10 0.13
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (14 bp):
AAAAGAGAAAAATA
Found at i:5967354 original size:51 final size:51
Alignment explanation
Indices: 5967293--5967704 Score: 671
Period size: 51 Copynumber: 8.0 Consensus size: 51
5967283 TGAAGCAAAT
5967293 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
5967344 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
5967395 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
5967446 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
5967497 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
* *
5967548 AAGTTCGTTGGAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
* * *
5967599 TAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
** ** * * * *
5967650 CTGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
1 AAGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
5967705 CCGTTTTATT
Statistics
Matches: 342, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
51 310 0.91
54 2 0.01
55 30 0.09
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (51 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
Found at i:5967425 original size:102 final size:102
Alignment explanation
Indices: 5967293--5967811 Score: 673
Period size: 102 Copynumber: 5.0 Consensus size: 102
5967283 TGAAGCAAAT
5967293 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
*
5967358 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
5967395 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
*
5967460 TTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
*
5967497 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGGAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
5967562 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
66 TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
* * * ** **
5967599 TAGTTCGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTTATTGAAGA
1 AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
* * *
5967664 TTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
66 ---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
** ** * * * * * *
5967705 CCGTTTTATTAAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTT-TTA
1 AAG-TTCGTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGT-
*
5967769 TGAAGATTATTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGC
60 TGAAG---ATT-GAGTCCTATACTCT-CTGAAGGAATAGGGAGC
5967812 AGGCTCGTCA
Statistics
Matches: 373, Mismatches: 30, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
102 259 0.69
105 2 0.01
106 33 0.09
107 11 0.03
110 2 0.01
111 65 0.17
114 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (102 bp):
AAGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGA
TTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGAC
Found at i:5967737 original size:56 final size:56
Alignment explanation
Indices: 5967309--5967811 Score: 246
Period size: 51 Copynumber: 9.6 Consensus size: 56
5967299 GTTGAAGATT
* * * ** **
5967309 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * ** **
5967360 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * ** **
5967411 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * ** **
5967462 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * ** ** *
5967513 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTG--GA-GATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * ** **
5967564 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * * * *
5967615 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * *
5967670 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
* * * *
5967726 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTATTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
*
5967781 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
5967812 AGGCTCGTCA
Statistics
Matches: 413, Mismatches: 27, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.00
51 289 0.70
53 1 0.00
54 3 0.01
55 67 0.16
56 51 0.12
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTATTC
Found at i:5967805 original size:55 final size:55
Alignment explanation
Indices: 5967564--5967813 Score: 212
Period size: 55 Copynumber: 4.6 Consensus size: 55
5967554 GTTGGAGATT
* * * * **
5967564 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAG---ATT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTATTC
* * * * * *
5967615 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTATTC
* * * *
5967670 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTATTC
* *
5967726 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTATTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTATTC
*
5967781 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
5967814 GCTCGTCATT
Statistics
Matches: 165, Mismatches: 22, Indels: 20
0.80 0.11 0.10
Matches are distributed among these distances:
51 41 0.25
54 3 0.02
55 67 0.41
56 52 0.32
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTATTC
Found at i:5967828 original size:55 final size:55
Alignment explanation
Indices: 5967616--5967839 Score: 179
Period size: 55 Copynumber: 4.1 Consensus size: 55
5967606 TTGAAGATTG
* * * * * * *
5967616 AGTCCTATACTCCCTGAAAGAATAGGGAGCGGAC-CTGT-TTATTGAAGATTTTTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC-GTATTA-TGAAGATTATTCA
* * * * * *
5967671 AGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTCA
1 AGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACGTATTA-TGAAGATTATTCA
* * *
5967727 AGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTATGAAGATTATTCG
1 AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTATTCA
* * * *
5967782 AGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCGTCATT-TGAAGATTTTTCA
1 AGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACGT-ATTATGAAGATTATTCA
5967837 AGT
1 AGT
5967840 ATTTATCCTG
Statistics
Matches: 141, Mismatches: 22, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
54 1 0.01
55 86 0.61
56 53 0.38
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (55 bp):
AGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGTATTATGAAGATTATTCA
Found at i:5969397 original size:15 final size:16
Alignment explanation
Indices: 5969377--5969409 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5969367 ATGTATCTAA
*
5969377 TTATGTTTATTT-ATT
1 TTATGTTCATTTAATT
5969392 TTATGTTCATTTAATT
1 TTATGTTCATTTAATT
5969408 TT
1 TT
5969410 CGTCCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATGTTCATTTAATT
Found at i:5979565 original size:8 final size:8
Alignment explanation
Indices: 5979554--5979627 Score: 51
Period size: 8 Copynumber: 9.1 Consensus size: 8
5979544 AAAATATTTA
5979554 AATAAAAT
1 AATAAAAT
*
5979562 AATAAAAA
1 AATAAAAT
*
5979570 AATTAAAT
1 AATAAAAT
*
5979578 AATACAAT
1 AATAAAAT
*
5979586 AATTAAAT
1 AATAAAAT
*
5979594 AA-AATATT
1 AATAA-AAT
*
5979602 AACAAAAT
1 AATAAAAT
*
5979610 ATTAAATAT
1 AATAAA-AT
*
5979619 AACAAAAT
1 AATAAAAT
5979627 A
1 A
5979628 TATTTTATAA
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
7 1 0.02
8 40 0.82
9 8 0.16
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (8 bp):
AATAAAAT
Found at i:5979565 original size:21 final size:21
Alignment explanation
Indices: 5979536--5979579 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5979526 AATAACTACA
* *
5979536 AAAAAAATAAAATATTTAAAT
1 AAAAAAATAAAAAAATTAAAT
*
5979557 AAAATAATAAAAAAATTAAAT
1 AAAAAAATAAAAAAATTAAAT
5979578 AA
1 AA
5979580 TACAATAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAAAATAAAAAAATTAAAT
Found at i:5979572 original size:16 final size:16
Alignment explanation
Indices: 5979553--5979595 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
5979543 TAAAATATTT
*
5979553 AAATAAAATAATAAAA
1 AAATTAAATAATAAAA
*
5979569 AAATTAAATAATACAA
1 AAATTAAATAATAAAA
*
5979585 TAATTAAATAA
1 AAATTAAATAA
5979596 AATATTAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTAAATAATAAAA
Found at i:5979593 original size:21 final size:21
Alignment explanation
Indices: 5979536--5979587 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
5979526 AATAACTACA
* * *
5979536 AAAAAAATAAAATATTTAAAT
1 AAAACAATAAAAAAATTAAAT
*
5979557 AAAATAATAAAAAAATTAAAT
1 AAAACAATAAAAAAATTAAAT
*
5979578 AATACAATAA
1 AAAACAATAA
5979588 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAACAATAAAAAAATTAAAT
Found at i:5979593 original size:37 final size:39
Alignment explanation
Indices: 5979541--5979617 Score: 113
Period size: 37 Copynumber: 2.0 Consensus size: 39
5979531 CTACAAAAAA
*
5979541 AATAAAATATTTAAATAAAATAATAA-AAAA-ATTAAAT
1 AATAAAATAATTAAATAAAATAATAACAAAATATTAAAT
* *
5979578 AATACAATAATTAAATAAAATATTAACAAAATATTAAAT
1 AATAAAATAATTAAATAAAATAATAACAAAATATTAAAT
5979617 A
1 A
5979618 TAACAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 23 0.66
38 4 0.11
39 8 0.23
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (39 bp):
AATAAAATAATTAAATAAAATAATAACAAAATATTAAAT
Found at i:5979598 original size:21 final size:21
Alignment explanation
Indices: 5979536--5979617 Score: 57
Period size: 21 Copynumber: 4.0 Consensus size: 21
5979526 AATAACTACA
* * *
5979536 AAAAAAATAAAATATTTAAAT
1 AAAATAATACAATAATTAAAT
5979557 AAAATAAT--AA-AA--AAAT
1 AAAATAATACAATAATTAAAT
*
5979573 TAAATAATACAATAATTAAAT
1 AAAATAATACAATAATTAAAT
* *
5979594 AAAATATTAACAAAATATTAAAT
1 AAAATAAT-ACAATA-ATTAAAT
5979617 A
1 A
5979618 TAACAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.23
18 3 0.06
19 4 0.08
21 17 0.35
22 5 0.10
23 8 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAATACAATAATTAAAT
Found at i:5979623 original size:17 final size:18
Alignment explanation
Indices: 5979595--5979628 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5979585 TAATTAAATA
5979595 AAATATTAACAAAATATT
1 AAATATTAACAAAATATT
5979613 AAATA-TAACAAAATAT
1 AAATATTAACAAAATAT
5979629 ATTTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATTAACAAAATATT
Found at i:5987274 original size:40 final size:40
Alignment explanation
Indices: 5987219--5987328 Score: 202
Period size: 40 Copynumber: 2.8 Consensus size: 40
5987209 CAAAGTGGGA
*
5987219 TGAATTCGGAGTTTTGGTCCCTACTTAGCACACAATCGAT
1 TGAATTTGGAGTTTTGGTCCCTACTTAGCACACAATCGAT
*
5987259 TGAATTTGGAGTTTTGGTCCCTACTTAGTACACAATCGAT
1 TGAATTTGGAGTTTTGGTCCCTACTTAGCACACAATCGAT
5987299 TGAATTTGGAGTTTTGGTCCCTACTTAGCA
1 TGAATTTGGAGTTTTGGTCCCTACTTAGCA
5987329 ACTCCATAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
TGAATTTGGAGTTTTGGTCCCTACTTAGCACACAATCGAT
Found at i:5988432 original size:29 final size:29
Alignment explanation
Indices: 5988397--5988470 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
5988387 ATCGGACCGT
*
5988397 AAACCGGTTGAAAACTGATAGAACCGGTA
1 AAACCGGTTGAAAACCGATAGAACCGGTA
*
5988426 AAACCGGTTGAAAACCGATAGAATCGGTA
1 AAACCGGTTGAAAACCGATAGAACCGGTA
*
5988455 AAACCGG-TGTAAACCG
1 AAACCGGTTGAAAACCG
5988471 CCAGTTCTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (29 bp):
AAACCGGTTGAAAACCGATAGAACCGGTA
Found at i:5990254 original size:19 final size:18
Alignment explanation
Indices: 5990217--5990258 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5990207 ATCTCCTTTA
*
5990217 AAATATAATTTTATAATT
1 AAATATAATTTAATAATT
5990235 AGAATAT-ATTTAATATATT
1 A-AATATAATTTAATA-ATT
5990254 AAATA
1 AAATA
5990259 ACATTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AAATATAATTTAATAATT
Found at i:5990536 original size:23 final size:19
Alignment explanation
Indices: 5990488--5990529 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5990478 TCTACTACAC
*
5990488 TGAAACCTAACATTGTGAA
1 TGAAACCCAACATTGTGAA
5990507 TGAAACCCAACATTGTGAA
1 TGAAACCCAACATTGTGAA
5990526 TGAA
1 TGAA
5990530 GAAAACCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (19 bp):
TGAAACCCAACATTGTGAA
Found at i:5993606 original size:17 final size:17
Alignment explanation
Indices: 5993584--5993617 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5993574 AATATAAATT
5993584 TATAAAATTCTAAATAA
1 TATAAAATTCTAAATAA
*
5993601 TATAAAATTTTAAATAA
1 TATAAAATTCTAAATAA
5993618 AATGCCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAATTCTAAATAA
Found at i:5995067 original size:34 final size:34
Alignment explanation
Indices: 5994980--5995079 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 34
5994970 ATTTTTCAAC
* * *
5994980 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCA--TTTCAAAA
*
5995017 AAACATTTACCGAACTTTGAAAACCATTT-AAAA
1 AAACATTTACCAAACTTTGAAAACCATTTCAAAA
*
5995050 AAATCATTTACCAAACTTTGAAAATCATTT
1 AAA-CATTTACCAAACTTTGAAAACCATTT
5995080 TTTCAAAGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
33 6 0.11
34 27 0.48
36 6 0.11
37 17 0.30
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (34 bp):
AAACATTTACCAAACTTTGAAAACCATTTCAAAA
Found at i:5999629 original size:37 final size:36
Alignment explanation
Indices: 5999571--5999692 Score: 147
Period size: 38 Copynumber: 3.3 Consensus size: 36
5999561 TCCCATTATC
* *
5999571 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAAAAACATTTACCAAACTTT-AAAAACT
*
5999607 ATTTTTCAAAGAAACATTTACCAAACTTTAAAAACCAT
1 ATTTTTCAAAAAAACATTTACCAAACTTTAAAAA-C-T
* * *
5999645 TTTTTTTAAAAAAACATTTACCAAACTTTAAAAATT
1 ATTTTTCAAAAAAACATTTACCAAACTTTAAAAACT
5999681 ATTTTTTCAAAA
1 A-TTTTTCAAAA
5999693 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
36 13 0.18
37 29 0.39
38 32 0.43
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (36 bp):
ATTTTTCAAAAAAACATTTACCAAACTTTAAAAACT
Found at i:6002785 original size:20 final size:20
Alignment explanation
Indices: 6002760--6002820 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
6002750 TGGAGGTTCG
6002760 AGTCCTCTTCAAGGAATAAT
1 AGTCCTCTTCAAGGAATAAT
6002780 AGTCCTCTTCAAGGAATAAT
1 AGTCCTCTTCAAGGAATAAT
6002800 AGTCCTCTTCAAGGAATAAT
1 AGTCCTCTTCAAGGAATAAT
6002820 A
1 A
6002821 TAGAGAATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTCCTCTTCAAGGAATAAT
Found at i:6005021 original size:15 final size:17
Alignment explanation
Indices: 6005001--6005032 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
6004991 TATCGATTCA
6005001 AATTTAA-T-AAAATTT
1 AATTTAACTCAAAATTT
6005016 AATTTAACTCAAAATTT
1 AATTTAACTCAAAATTT
6005033 GATCTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAACTCAAAATTT
Found at i:6007034 original size:2 final size:2
Alignment explanation
Indices: 6007029--6007055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6007019 ATAGAAATGG
6007029 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 A
6007056 CTACATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6007524 original size:21 final size:21
Alignment explanation
Indices: 6007498--6007575 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
6007488 GGGTTTCATA
*
6007498 GGTCCTTCGGGACAATACAGT
1 GGTCCTTTGGGACAATACAGT
6007519 GGTCCTTTGGGACAATACAGT
1 GGTCCTTTGGGACAATACAGT
6007540 GGTCCTTTGGGACAATACAGT
1 GGTCCTTTGGGACAATACAGT
6007561 GGTCCTTTGGGACAA
1 GGTCCTTTGGGACAA
6007576 ATTTCATATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTCCTTTGGGACAATACAGT
Found at i:6010305 original size:45 final size:47
Alignment explanation
Indices: 6010249--6010402 Score: 185
Period size: 45 Copynumber: 3.4 Consensus size: 47
6010239 TGCACCAATC
**
6010249 CATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
* *
6010294 CATGCATCGATGCACTCA--GAGTTTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTT-TG-AAACATCGAATGCATTT
* *
6010341 GATGCATCGATGCACTC-TGG-CTATTTTGAAACATCGAATGCATTT
1 CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
*
6010386 TATGCATCGATGCACTC
1 CATGCATCGATGCACTC
6010403 TTAGTGCACC
Statistics
Matches: 95, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
44 4 0.04
45 50 0.53
46 4 0.04
47 36 0.38
48 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (47 bp):
CATGCATCGATGCACTCATGGAATATTTTGAAACATCGAATGCATTT
Found at i:6010403 original size:45 final size:47
Alignment explanation
Indices: 6010278--6010403 Score: 186
Period size: 47 Copynumber: 2.7 Consensus size: 47
6010268 GAATAAATTG
* *
6010278 AACATCGAATGCATTTCATGCATCGATGCACTCAGAGTTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGAGTATTTATGAA
*
6010325 AACATCGAATGCATTTGATGCATCGATGCACTCTG-GCTATTT-TG-A
1 AACATCGAATGCATTTCATGCATCGATGCACTCTGAG-TATTTATGAA
*
6010370 AACATCGAATGCATTTTATGCATCGATGCACTCT
1 AACATCGAATGCATTTCATGCATCGATGCACTCT
6010404 TAGTGCACCG
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
45 34 0.46
46 3 0.04
47 37 0.50
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (47 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTGAGTATTTATGAA
Found at i:6022911 original size:20 final size:20
Alignment explanation
Indices: 6022886--6022931 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6022876 AAAAAATCTA
*
6022886 TAGGTATCTAAAGTTAATTT
1 TAGGTAACTAAAGTTAATTT
6022906 TAGGTAACTAAAGTTAATTT
1 TAGGTAACTAAAGTTAATTT
6022926 TAGGTA
1 TAGGTA
6022932 CAGTTTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (20 bp):
TAGGTAACTAAAGTTAATTT
Found at i:6023848 original size:2 final size:2
Alignment explanation
Indices: 6023841--6023870 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6023831 ATATGAGATC
6023841 AT AT AT 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
6023871 GCTTACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6025487 original size:29 final size:31
Alignment explanation
Indices: 6025440--6025501 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
6025430 TATGTCTGTT
*
6025440 TTTTCAGTTTAGTGTCTAACG-TTTATTTTG
1 TTTTCAGTTTAGTGCCTAACGTTTTATTTTG
* *
6025470 TTTT-AGTTTGGTGCCTAATGTTTTATTTTG
1 TTTTCAGTTTAGTGCCTAACGTTTTATTTTG
6025500 TT
1 TT
6025502 ACTCAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.46
30 15 0.54
ACGTcount: A:0.15, C:0.08, G:0.18, T:0.60
Consensus pattern (31 bp):
TTTTCAGTTTAGTGCCTAACGTTTTATTTTG
Found at i:6027422 original size:38 final size:37
Alignment explanation
Indices: 6027349--6027422 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
6027339 ATCTGTAATG
**
6027349 AAAAAGATAGTTGTTATCTTTGAGGTTTTCATATTTA
1 AAAAAGATAGTTGTTATCTTAAAGGTTTTCATATTTA
6027386 AAAAAGATAGTTGTTATCATTAAAGGTTCTT-ATATTT
1 AAAAAGATAGTTGTTATC-TTAAAGGTT-TTCATATTT
6027423 GAGTATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 18 0.55
38 13 0.39
39 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (37 bp):
AAAAAGATAGTTGTTATCTTAAAGGTTTTCATATTTA
Found at i:6035160 original size:2 final size:2
Alignment explanation
Indices: 6035153--6035192 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6035143 ATTAATATTG
6035153 AT AT AT AT AT AT AT AT 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 AT
6035193 TGGAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6035407 original size:21 final size:20
Alignment explanation
Indices: 6035321--6035478 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
6035311 AAATGACCAA
**
6035321 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
6035340 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
6035360 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
6035380 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
6035401 GAAAATCGTAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
6035422 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
6035442 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
6035463 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
6035479 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 41 0.40
21 45 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:6035491 original size:40 final size:40
Alignment explanation
Indices: 6035445--6035599 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
6035435 CGATTTTCCA
* ** *
6035445 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
6035485 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
6035525 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
6035565 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
6035600 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:6035507 original size:20 final size:20
Alignment explanation
Indices: 6035445--6035598 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
6035435 CGATTTTCCA
* ** *
6035445 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
6035465 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
6035485 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6035505 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6035525 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
6035545 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
6035565 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
6035586 AAATCGCAACGCG
1 AAATCGCAACGCG
6035599 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:6035770 original size:22 final size:22
Alignment explanation
Indices: 6035745--6035787 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6035735 CTCTCTACGG
*
6035745 CGAAGAAATCTGTCCCCATCTT
1 CGAAGAAATCCGTCCCCATCTT
**
6035767 CGAAGATTTCCGTCCCCATCT
1 CGAAGAAATCCGTCCCCATCT
6035788 CCGGCGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (22 bp):
CGAAGAAATCCGTCCCCATCTT
Found at i:6036020 original size:33 final size:33
Alignment explanation
Indices: 6035981--6036051 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6035971 TTCACTTAGA
*
6035981 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
6036014 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
6036047 TTTCA
1 TTTCA
6036052 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:6036188 original size:41 final size:41
Alignment explanation
Indices: 6036130--6036207 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
6036120 TTGCAGAAGA
*
6036130 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
6036171 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
6036208 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:6036204 original size:21 final size:21
Alignment explanation
Indices: 6036131--6036206 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
6036121 TGCAGAAGAG
*
6036131 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
6036152 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
6036172 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
6036193 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
6036207 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:6036210 original size:14 final size:14
Alignment explanation
Indices: 6036191--6036247 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
6036181 GAGAAATGAA
6036191 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
6036205 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
6036224 AATCGCAACTAGAG
1 AATCGCAACGAGAG
6036238 AATCGCAACG
1 AATCGCAACG
6036248 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:6036223 original size:33 final size:33
Alignment explanation
Indices: 6036183--6036263 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
6036173 CGCAACGAGA
6036183 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
6036216 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
6036249 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
6036264 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:6036281 original size:19 final size:19
Alignment explanation
Indices: 6036259--6036356 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
6036249 GAAACCAAAA
*
6036259 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6036278 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
6036292 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6036311 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
6036325 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6036344 TCGAGTTGCGATT
1 TCGCGTTGCGATT
6036357 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 19 0.30
16 6 0.10
17 6 0.10
19 32 0.51
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6036300 original size:14 final size:14
Alignment explanation
Indices: 6036281--6036370 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
6036271 TTTCATTTCG
6036281 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6036295 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6036314 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
6036328 AGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
6036345 CGAGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
6036361 CGTTGCGATT
1 CGTTGCGATT
6036371 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 26 0.43
16 9 0.15
17 8 0.13
19 17 0.28
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6036306 original size:33 final size:33
Alignment explanation
Indices: 6036264--6036378 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
6036254 CAAAATCGCA
6036264 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
6036297 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
6036330 TTGCGATTTTCATTTCGAGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6036363 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
6036379 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:6038232 original size:93 final size:93
Alignment explanation
Indices: 6038073--6038448 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
6038063 TAGATTGCTT
* *
6038073 AGTAAATTTATTCGGTTGTTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6038138 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6038166 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6038231 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
6038259 AGTAAATTTGTTCGGTTGCTGCCAATTCTGATAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6038324 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6038352 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6038417 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6038444 AGTAA
1 AGTAA
6038449 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 273 0.98
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6038536 original size:19 final size:19
Alignment explanation
Indices: 6038496--6038624 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
6038486 TAGTTTACTT
* *
6038496 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
6038516 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
6038535 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
6038554 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
6038568 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
6038587 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
6038601 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
6038620 TCGCA
1 TCGCA
6038625 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:6038575 original size:33 final size:32
Alignment explanation
Indices: 6038532--6038624 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
6038522 CGCGAAACCA
**
6038532 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
6038564 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
6038597 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
6038625 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:6038622 original size:52 final size:52
Alignment explanation
Indices: 6038496--6038624 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
6038486 TAGTTTACTT
**
6038496 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
6038548 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
6038601 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
6038625 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:6038642 original size:19 final size:18
Alignment explanation
Indices: 6038620--6038719 Score: 99
Period size: 19 Copynumber: 5.8 Consensus size: 18
6038610 GAAACCAAAA
6038620 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
6038639 TCGCGTTGCGA--TTC-TT
1 TCGC-TTGCGATTTTCATT
6038655 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
6038672 TCGCATTGCGA--TTC-TG
1 TCGC-TTGCGATTTTCATT
6038688 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
6038705 TCGCGTTGCGATTTT
1 TCGC-TTGCGATTTT
6038720 AAGTTTCGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
14 12 0.18
16 15 0.22
17 15 0.22
19 26 0.38
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:6038661 original size:14 final size:14
Alignment explanation
Indices: 6038642--6038698 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6038632 TTTCATTTCG
6038642 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
6038656 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
6038673 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
6038689 CGTTGCGATT
1 CGTTGCGATT
6038699 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:6038667 original size:33 final size:33
Alignment explanation
Indices: 6038625--6038717 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
6038615 CAAAATCGCA
*
6038625 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
6038658 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
6038691 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
6038718 TTAAGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:6038732 original size:20 final size:19
Alignment explanation
Indices: 6038620--6038735 Score: 72
Period size: 19 Copynumber: 6.6 Consensus size: 19
6038610 GAAACCAAAA
* *
6038620 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
*
6038639 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAATT
*
6038655 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
* * *
6038672 TCGCATTGCGA--TT-CTG
1 TCGCGTTGCGATTTTAATT
*
6038688 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
6038705 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTAA-TT
*
6038725 TCGTGTTGCGA
1 TCGCGTTGCGA
6038736 AAGTAAACTA
Statistics
Matches: 75, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 15 0.20
16 9 0.12
17 9 0.12
19 30 0.40
20 12 0.16
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:6040680 original size:14 final size:14
Alignment explanation
Indices: 6040661--6040696 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6040651 ATTGTTTAAT
6040661 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
6040675 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
6040689 TGATTTGT
1 TGATTTGT
6040697 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6040827 original size:19 final size:19
Alignment explanation
Indices: 6040803--6040900 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
6040793 AAAATTGACT
6040803 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6040822 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6040841 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6040855 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6040874 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
6040894 ATCGCAA
1 ATCGCAA
6040901 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6040932 original size:53 final size:53
Alignment explanation
Indices: 6040803--6040919 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
6040793 AAAATTGACT
6040803 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
6040855 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
6040908 ATCGCAATGCGA
1 ATCGCAATGCGA
6040920 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:6040937 original size:19 final size:19
Alignment explanation
Indices: 6040909--6041188 Score: 348
Period size: 19 Copynumber: 15.7 Consensus size: 19
6040899 AACGGGAGAA
* *
6040909 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
6040928 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
6040944 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6040961 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
6040980 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
6040996 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041013 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041032 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041051 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
6041071 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
6041087 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041104 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041123 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041142 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
6041160 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
6041176 TCGCATTGCGATT
1 TCGCATTGCGATT
6041189 CTCTCGTTGC
Statistics
Matches: 229, Mismatches: 10, Indels: 44
0.81 0.04 0.16
Matches are distributed among these distances:
14 29 0.13
16 23 0.10
17 21 0.09
18 1 0.00
19 120 0.52
20 35 0.15
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:6040972 original size:52 final size:52
Alignment explanation
Indices: 6040909--6041188 Score: 343
Period size: 52 Copynumber: 5.2 Consensus size: 52
6040899 AACGGGAGAA
* *
6040909 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
6040961 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
6041013 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
* * * * *
6041071 TCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
* *
6041123 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
6041176 TCGCATTGCGATT
1 TCGCATTGCGATT
6041189 CTCTCGTTGC
Statistics
Matches: 199, Mismatches: 15, Indels: 27
0.83 0.06 0.11
Matches are distributed among these distances:
50 4 0.02
51 6 0.03
52 111 0.56
53 28 0.14
54 4 0.02
55 3 0.02
56 2 0.01
57 2 0.01
58 27 0.14
59 3 0.02
60 9 0.05
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:6041077 original size:91 final size:91
Alignment explanation
Indices: 6040915--6041160 Score: 432
Period size: 91 Copynumber: 2.8 Consensus size: 91
6040905 AGAATCGCAA
* *
6040915 TGCGATTTTAATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
6040974 TTCATTTCGCATTGCGATTCTCTCGT
66 TTCATTTCGCATTGCGATTCTCTCGT
6041000 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
6041065 TTCATTTCGCATTGCGATTCTCTCGT
66 TTCATTTCGCATTGCGATTCTCTCGT
6041091 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
6041156 TTCAT
66 TTCAT
6041161 GTTGGGATTT
Statistics
Matches: 153, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
85 23 0.15
87 3 0.02
88 4 0.03
90 15 0.10
91 108 0.71
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (91 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
TTCATTTCGCATTGCGATTCTCTCGT
Found at i:6043667 original size:24 final size:24
Alignment explanation
Indices: 6043633--6043679 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6043623 CTGAAACATC
6043633 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
6043657 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
6043680 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:6044389 original size:20 final size:20
Alignment explanation
Indices: 6044361--6044630 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
6044351 AAATTTCAGT
* * *
6044361 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6044381 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
6044401 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6044421 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
6044441 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
6044461 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
6044481 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6044501 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6044521 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
6044541 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
6044561 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
6044581 GTTGCAATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
6044601 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
6044621 GTTGCGATTT
1 GTTGCGATTT
6044631 TGGAAAATCG
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:6044647 original size:21 final size:21
Alignment explanation
Indices: 6044617--6044699 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
6044607 ATTTTCATAT
*
6044617 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
6044638 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
6044659 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
6044680 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
6044700 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:6044690 original size:42 final size:43
Alignment explanation
Indices: 6044597--6044695 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
6044587 ATTTATGTGT
* *
6044597 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
6044638 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
6044680 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
6044696 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:6045143 original size:15 final size:15
Alignment explanation
Indices: 6045123--6045189 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
6045113 TTTCGGAAAA
*
6045123 TGAATTACTGCAATT
1 TGAATTACTGGAATT
**
6045138 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
6045153 TGAATTATTGGAATT
1 TGAATTACTGGAATT
**
6045168 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
6045182 TGAATTAC
1 TGAATTAC
6045190 ACATTTATGA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 11 0.26
15 31 0.74
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:6045187 original size:29 final size:30
Alignment explanation
Indices: 6045117--6045189 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
6045107 TTGGTTTTTC
6045117 GGAAAATGAATTACTGCAATTTGAATTACT
1 GGAAAATGAATTACTGCAATTTGAATTACT
* *
6045147 GGAAAATGAATTATTGGAATTTGAATT-CT
1 GGAAAATGAATTACTGCAATTTGAATTACT
6045176 GGAAAATGAATTAC
1 GGAAAATGAATTAC
6045190 ACATTTATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 25 0.62
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (30 bp):
GGAAAATGAATTACTGCAATTTGAATTACT
Found at i:6045560 original size:25 final size:28
Alignment explanation
Indices: 6045533--6045603 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
6045523 TTACTAAAAT
6045533 ATTATTTAAATATATAAATAA-TATTATTC
1 ATTA-TTAAATATATAAA-AATTATTATTC
6045562 ATTATTAAATATATAAAAATTATTA-T-
1 ATTATTAAATATATAAAAATTATTATTC
6045588 ATTATTAAA-ATA-AAAA
1 ATTATTAAATATATAAAA
6045604 TATAATATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.10
25 3 0.07
26 9 0.22
27 3 0.07
28 18 0.44
29 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTATTAAATATATAAAAATTATTATTC
Found at i:6045571 original size:28 final size:27
Alignment explanation
Indices: 6045531--6045707 Score: 106
Period size: 29 Copynumber: 6.5 Consensus size: 27
6045521 CTTTACTAAA
6045531 ATATTATTTAAATATATAAATAA-TATT
1 ATATTA-TTAAATATATAAATAATTATT
6045558 ATTCATTATTAAATATATAAA-AATTATT
1 A-T-ATTATTAAATATATAAATAATTATT
* *
6045586 ATATTATTAAA-ATAAAAATATAATATCT
1 ATATTATTAAATATATAAATA-ATTAT-T
*
6045614 -TA-TATTATATTATTATAATATAATTGATT
1 ATATTATTA-AATA-TATAA-ATAATT-ATT
* * *
6045643 ATTTTA-TATAATATTAAAAATATAATATT
1 ATATTATTA-AATA-TATAAATA-ATTATT
*
6045672 ATATTATTAAA-ATATTAATAA--A-T
1 ATATTATTAAATATATAAATAATTATT
6045695 ATATT-TTAAATAT
1 ATATTATTAAATAT
6045708 TTTAATAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 36
0.72 0.07 0.21
Matches are distributed among these distances:
22 5 0.04
23 8 0.07
24 1 0.01
25 6 0.05
26 16 0.13
27 17 0.14
28 22 0.18
29 24 0.20
30 21 0.17
31 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATTATTAAATATATAAATAATTATT
Found at i:6045674 original size:22 final size:22
Alignment explanation
Indices: 6045649--6045691 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6045639 GATTATTTTA
6045649 TATAATATTAAAA-ATATAATAT
1 TATAATATTAAAATAT-TAATAT
*
6045671 TATATTATTAAAATATTAATA
1 TATAATATTAAAATATTAATA
6045692 AATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATAATATTAAAATATTAATAT
Found at i:6045712 original size:23 final size:22
Alignment explanation
Indices: 6045659--6045725 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
6045649 TATAATATTA
*
6045659 AAAATA-TAAT-ATTATATTATT
1 AAAATATTAATAAATATATT-TT
6045680 AAAATATTAATAAATATATTTT
1 AAAATATTAATAAATATATTTT
*
6045702 AAATATTTTAATAAATAATATTTT
1 AAA-ATATTAATAAAT-ATATTTT
6045726 GATGAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.15
22 9 0.22
23 18 0.45
24 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATTAATAAATATATTTT
Found at i:6045720 original size:52 final size:52
Alignment explanation
Indices: 6045615--6045762 Score: 135
Period size: 52 Copynumber: 2.9 Consensus size: 52
6045605 ATAATATCTT
* ** *
6045615 ATATTATATTATTATAATATAATTGATTATTTTATATAATATTAAAAATATA
1 ATATTATATTATTAAAATATAATAAATTATTTTAAATAATATTAAAAATATA
* *
6045667 ATATTATATTATTAAAATATTAATAAATATATTTTAAAT-ATTTTAATAA-ATA
1 ATATTATATTATTAAAATA-TAATAAAT-TATTTTAAATAATATTAAAAATATA
* * * * *
6045719 ATATT-T-TGATGAAAATGATATTAAAATATTTT-ATTAATATTAAA
1 ATATTATATTATTAAAAT-ATAATAAATTATTTTAAATAATATTAAA
6045763 TTCATAAAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
48 2 0.03
49 12 0.15
50 14 0.18
51 2 0.03
52 26 0.33
53 14 0.18
54 9 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (52 bp):
ATATTATATTATTAAAATATAATAAATTATTTTAAATAATATTAAAAATATA
Found at i:6045954 original size:42 final size:42
Alignment explanation
Indices: 6045897--6046053 Score: 242
Period size: 42 Copynumber: 3.7 Consensus size: 42
6045887 ATGAATTACA
* *
6045897 TTCCGGAAAATGAATTACGTAAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
* *
6045939 TTCCGGAAAACGAATTACGTGAAACAAACACGAGAAAATATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
*
6045981 TTCCGAAAAACGAATTACGTAAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
* * *
6046023 TTTCGGAAAACGAATTACATGAAACAAACAC
1 TTCCGGAAAACGAATTACGTAAAACAAACAC
6046054 AGAATTTCAG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 104 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
Found at i:6046003 original size:84 final size:83
Alignment explanation
Indices: 6045897--6046057 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 83
6045887 ATGAATTACA
* * *
6045897 TTCCGGAAAATGAATTACGTAAAACAAACACGGGAAAACATTTTCCGGAAAACGAATTACGTGAA
1 TTCCGAAAAACGAATTACGTAAAACAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAA
6045962 ACAAACACGAGAAAATATT
66 ACAAACAC-AGAAAATATT
* *
6045981 TTCCGAAAAACGAATTACGTAAAACAAACACGGGAAAATATTTTTCGGAAAACGAATTACATGAA
1 TTCCGAAAAACGAATTACGTAAAACAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAA
6046046 ACAAACACAGAA
66 ACAAACACAGAA
6046058 TTTCAGGAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
83 4 0.06
84 68 0.94
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.19
Consensus pattern (83 bp):
TTCCGAAAAACGAATTACGTAAAACAAACACGGGAAAACATTTTCCGGAAAACGAATTACATGAA
ACAAACACAGAAAATATT
Found at i:6047036 original size:30 final size:30
Alignment explanation
Indices: 6047000--6047060 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
6046990 CTTTCAAGTT
6047000 ATAATTTACGAC-TGTATAATTATAA-TCAAA
1 ATAATTTACGACTTGTA-AATTA-AAGTCAAA
*
6047030 ATAATTTATGACTTGTAAATTAAAGTCAAA
1 ATAATTTACGACTTGTAAATTAAAGTCAAA
6047060 A
1 A
6047061 CCGAGACCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 22 0.79
31 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
ATAATTTACGACTTGTAAATTAAAGTCAAA
Found at i:6047282 original size:23 final size:22
Alignment explanation
Indices: 6047235--6047288 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6047225 CAATCCGATT
* *
6047235 AAATATATCATATCTCTTAAAA
1 AAATATATCATATCTATAAAAA
6047257 AAATAATATCATAT-TATAAAATAA
1 AAAT-ATATCATATCTAT-AAA-AA
6047281 AAATATAT
1 AAATATAT
6047289 ACGATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 6 0.22
23 15 0.56
24 6 0.22
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATATCATATCTATAAAAA
Found at i:6057314 original size:29 final size:29
Alignment explanation
Indices: 6057270--6057327 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
6057260 CTAAGATAGA
6057270 ACTCACATTGTAGAAGATATTGTGAACAT
1 ACTCACATTGTAGAAGATATTGTGAACAT
*
6057299 ACTCACATTGTTGAAGATATTGTGAACAT
1 ACTCACATTGTAGAAGATATTGTGAACAT
6057328 TCACCCAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (29 bp):
ACTCACATTGTAGAAGATATTGTGAACAT
Found at i:6061181 original size:14 final size:14
Alignment explanation
Indices: 6061162--6061188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6061152 GATTAAAATG
6061162 TTTTTTTAATTAAA
1 TTTTTTTAATTAAA
6061176 TTTTTTTAATTAA
1 TTTTTTTAATTAA
6061189 GGTTTGAGAA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTTAATTAAA
Found at i:6061442 original size:21 final size:21
Alignment explanation
Indices: 6061416--6061468 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
6061406 CCAAAATAAT
* *
6061416 AATAAAAATATTTTTTTATTC
1 AATAAAAATATTATTTAATTC
6061437 AAT-AAAATAGTTATTTAATTC
1 AATAAAAATA-TTATTTAATTC
6061458 AA-AAAATATAT
1 AATAAAA-ATAT
6061469 ATATAGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.22
21 18 0.67
22 3 0.11
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (21 bp):
AATAAAAATATTATTTAATTC
Found at i:6061445 original size:20 final size:19
Alignment explanation
Indices: 6061419--6061466 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
6061409 AAATAATAAT
* *
6061419 AAAAATATTTTTTTATTCA
1 AAAAATATTATTTAATTCA
6061438 ATAAAATAGTTATTTAATTCA
1 A-AAAATA-TTATTTAATTCA
6061459 AAAAATAT
1 AAAAATAT
6061467 ATATATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.08
20 12 0.48
21 11 0.44
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAAATATTATTTAATTCA
Found at i:6073700 original size:4 final size:4
Alignment explanation
Indices: 6073691--6073760 Score: 77
Period size: 4 Copynumber: 17.5 Consensus size: 4
6073681 TAAAACTTTG
* * * *
6073691 CTCT CTCT CTCT CTCT CGCT CGCT CACT CTCT CTCT CTCT CTCT CGCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
* * *
6073739 CGCT CACT CTCT CTGT CTCT CT
1 CTCT CTCT CTCT CTCT CTCT CT
6073761 TCTTGGCTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.03, C:0.49, G:0.07, T:0.41
Consensus pattern (4 bp):
CTCT
Found at i:6073725 original size:24 final size:24
Alignment explanation
Indices: 6073693--6073752 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
6073683 AAACTTTGCT
6073693 CTCTCTCTCTCTCTCGCTCGCTCA
1 CTCTCTCTCTCTCTCGCTCGCTCA
* *
6073717 CTCTCTCTCTCTCTCTCTCGCTCG
1 CTCTCTCTCTCTCTCGCTCGCTCA
*
6073741 CTCACTCTCTCT
1 CTCTCTCTCTCT
6073753 GTCTCTCTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.03, C:0.50, G:0.07, T:0.40
Consensus pattern (24 bp):
CTCTCTCTCTCTCTCGCTCGCTCA
Found at i:6073731 original size:28 final size:28
Alignment explanation
Indices: 6073691--6073760 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
6073681 TAAAACTTTG
6073691 CTCTCTCTCTCTCTCTCGCTCGCTCACT
1 CTCTCTCTCTCTCTCTCGCTCGCTCACT
6073719 CTCTCTCTCTCTCTCTCGCTCGCTCACT
1 CTCTCTCTCTCTCTCTCGCTCGCTCACT
*
6073747 CTCTCTGTCTCTCT
1 CTCTCTCTCTCTCT
6073761 TCTTGGCTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.03, C:0.49, G:0.07, T:0.41
Consensus pattern (28 bp):
CTCTCTCTCTCTCTCTCGCTCGCTCACT
Found at i:6073757 original size:24 final size:24
Alignment explanation
Indices: 6073697--6073759 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
6073687 TTTGCTCTCT
* *
6073697 CTCTCTCTCTCGCTCGCTCACTCT
1 CTCTCTCTCTCTCTCGCTCACTCA
*
6073721 CTCTCTCTCTCTCTCGCTCGCTCA
1 CTCTCTCTCTCTCTCGCTCACTCA
*
6073745 CTCTCTCTGTCTCTC
1 CTCTCTCTCTCTCTC
6073760 TTCTTGGCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.03, C:0.49, G:0.08, T:0.40
Consensus pattern (24 bp):
CTCTCTCTCTCTCTCGCTCACTCA
Found at i:6079873 original size:33 final size:33
Alignment explanation
Indices: 6079827--6079892 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
6079817 ATTTTAATGC
*
6079827 TTTAAAACTTAATCAAGAAGATCAATATAAAAT
1 TTTAAAACATAATCAAGAAGATCAATATAAAAT
6079860 TTTAAAACATAATCAAGAAGATCAATATAAAAT
1 TTTAAAACATAATCAAGAAGATCAATATAAAAT
6079893 ATAAAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.29
Consensus pattern (33 bp):
TTTAAAACATAATCAAGAAGATCAATATAAAAT
Found at i:6080911 original size:2 final size:2
Alignment explanation
Indices: 6080904--6080931 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6080894 TCTCTAATGA
6080904 AT AT 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
6080932 TGCAGGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6083202 original size:28 final size:28
Alignment explanation
Indices: 6083167--6083224 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6083157 AACCATATAT
6083167 AAAACATATATATTTCTTCATATATTAA
1 AAAACATATATATTTCTTCATATATTAA
6083195 AAAACATATATATTTCTTCATATATTAA
1 AAAACATATATATTTCTTCATATATTAA
6083223 AA
1 AA
6083225 GAAAGCCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAACATATATATTTCTTCATATATTAA
Found at i:6088153 original size:19 final size:20
Alignment explanation
Indices: 6088114--6088153 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6088104 TGGTTCACGG
*
6088114 AATGTAAAATTACTAGTGGA
1 AATGTAAAATTACCAGTGGA
*
6088134 AATGTAAGATTACCAG-GGA
1 AATGTAAAATTACCAGTGGA
6088153 A
1 A
6088154 TAGGATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (20 bp):
AATGTAAAATTACCAGTGGA
Found at i:6089151 original size:37 final size:37
Alignment explanation
Indices: 6089075--6089151 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
6089065 TTTTTATATT
*
6089075 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
6089112 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
6089149 TTT
1 TTT
6089152 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:6091683 original size:21 final size:20
Alignment explanation
Indices: 6091657--6091696 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
6091647 AAACCTCAAA
6091657 TAAAACTCA-ACTCGACTATAC
1 TAAAACT-ATACTCGA-TATAC
6091678 TAAAACTATACTCGATATA
1 TAAAACTATACTCGATATA
6091697 TGTCCGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAACTATACTCGATATAC
Found at i:6091901 original size:171 final size:173
Alignment explanation
Indices: 6091599--6091943 Score: 660
Period size: 171 Copynumber: 2.0 Consensus size: 173
6091589 TGTACTTTAA
6091599 ATTACGCTGAGTTCAAAACGATTTAAACCTAGAATGATTAGAAAATGTAAACCTCAAATAAAACT
1 ATTACGCTGAGTTCAAAACGATTTAAACCTAGAATGATTAGAAAATGTAAACCTCAAATAAAACT
6091664 CAACTCGACTATACTAAAACTATACTCGATATATGTCCGCACAGACATGATAAAGTTAGGAAATG
66 CAACTCGACTATACTAAAACTATACTCGATATATGTCCGCACAGACATGATAAAGTTAGGAAATG
6091729 AAGGTGTTAAATTAGTTACCTTAAGA-TAACATATCTAAAACC
131 AAGGTGTTAAATTAGTTACCTTAAGATTAACATATCTAAAACC
6091771 ATTACGCTGAGTTCAAAACGATTTAAACCTAGAATGATTAGAAAATGTAAACCTCAAAT-AAACT
1 ATTACGCTGAGTTCAAAACGATTTAAACCTAGAATGATTAGAAAATGTAAACCTCAAATAAAACT
6091835 CAACTCGACTATACTAAAACTATACTCGA-ATATGTCCGACACAGACATGATAAAGTTAGGAAAT
66 CAACTCGACTATACTAAAACTATACTCGATATATGTCCG-CACAGACATGATAAAGTTAGGAAAT
6091899 GAAGGTGTTAAATTAGTTACCTTAAGATTAACATATCTAAAACC
130 GAAGGTGTTAAATTAGTTACCTTAAGATTAACATATCTAAAACC
6091943 A
1 A
6091944 GGACTGCCTG
Statistics
Matches: 171, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
170 9 0.05
171 86 0.50
172 76 0.44
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (173 bp):
ATTACGCTGAGTTCAAAACGATTTAAACCTAGAATGATTAGAAAATGTAAACCTCAAATAAAACT
CAACTCGACTATACTAAAACTATACTCGATATATGTCCGCACAGACATGATAAAGTTAGGAAATG
AAGGTGTTAAATTAGTTACCTTAAGATTAACATATCTAAAACC
Found at i:6092516 original size:2 final size:2
Alignment explanation
Indices: 6092509--6092537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6092499 TATGCTGCAA
6092509 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 A
6092538 GGCAAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6092595 original size:42 final size:42
Alignment explanation
Indices: 6092536--6092619 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6092526 TATATATATA
6092536 TAGGCAAAACTTTCGAGATAATGTTCTGGAAAAAATTAATTC
1 TAGGCAAAACTTTCGAGATAATGTTCTGGAAAAAATTAATTC
6092578 TAGGCAAAACTTTCGAGATAATGTTCTGGAAAAAATTAATTC
1 TAGGCAAAACTTTCGAGATAATGTTCTGGAAAAAATTAATTC
6092620 ACGAGATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (42 bp):
TAGGCAAAACTTTCGAGATAATGTTCTGGAAAAAATTAATTC
Found at i:6092789 original size:10 final size:10
Alignment explanation
Indices: 6092776--6092846 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 10
6092766 ACACGCTGGG
6092776 CATCCGAGGC
1 CATCCGAGGC
6092786 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
6092800 CATCCGAGAG-
1 CATCCGAG-GC
6092810 CATCCGAGGC
1 CATCCGAGGC
6092820 CATCCGAGAG-
1 CATCCGAG-GC
*
6092830 CATCCGATGC
1 CATCCGAGGC
6092840 CATCCGA
1 CATCCGA
6092847 CCGAGGCCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
9 2 0.04
10 36 0.69
11 4 0.08
13 2 0.04
14 8 0.15
ACGTcount: A:0.24, C:0.38, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:6092798 original size:14 final size:14
Alignment explanation
Indices: 6092779--6092806 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6092769 CGCTGGGCAT
6092779 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
6092793 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
6092807 GAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:6092818 original size:20 final size:20
Alignment explanation
Indices: 6092793--6092846 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
6092783 GGCCATCCGA
6092793 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
6092813 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
*
6092833 CCGATGCCATCCGA
1 CCGAGGCCATCCGA
6092847 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.37, G:0.28, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:6092860 original size:10 final size:10
Alignment explanation
Indices: 6092793--6092846 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
6092783 GGCCATCCGA
6092793 CCGAGGCCAT
1 CCGAGGCCAT
6092803 CCGAGAG-CAT
1 CCGAG-GCCAT
6092813 CCGAGGCCAT
1 CCGAGGCCAT
6092823 CCGAGAG-CAT
1 CCGAG-GCCAT
*
6092833 CCGATGCCAT
1 CCGAGGCCAT
6092843 CCGA
1 CCGA
6092847 CCGAGGCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 2 0.05
10 35 0.90
11 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.28, T:0.11
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:6092886 original size:10 final size:10
Alignment explanation
Indices: 6092871--6092940 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 10
6092861 ACGAGCTATG
6092871 CGAGGGCATC
1 CGAGGGCATC
*
6092881 CGAGGGCAAC
1 CGAGGGCATC
6092891 CGAGCGAGCTATC
1 CGAG-G-GC-ATC
*
6092904 CGAGGGCAAC
1 CGAGGGCATC
*
6092914 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
6092927 CGAGGGAATC
1 CGAGGGCATC
6092937 CGAG
1 CGAG
6092941 AGAAGCCGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
10 25 0.53
11 5 0.11
12 6 0.13
13 11 0.23
ACGTcount: A:0.26, C:0.27, G:0.39, T:0.09
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:6092899 original size:33 final size:33
Alignment explanation
Indices: 6092846--6092917 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
6092836 ATGCCATCCG
* *
6092846 ACCGAGGCCATCCGAACGAGCTATGCGAGGGCA
1 ACCGAGGCCAACCGAACGAGCTATCCGAGGGCA
* * *
6092879 TCCGAGGGCAACCGAGCGAGCTATCCGAGGGCA
1 ACCGAGGCCAACCGAACGAGCTATCCGAGGGCA
6092912 ACCGAG
1 ACCGAG
6092918 CGAGCTATGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.31, G:0.35, T:0.08
Consensus pattern (33 bp):
ACCGAGGCCAACCGAACGAGCTATCCGAGGGCA
Found at i:6092904 original size:23 final size:23
Alignment explanation
Indices: 6092878--6092940 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
6092868 ATGCGAGGGC
6092878 ATCCGAGGGCAACCGAGCGAGCT
1 ATCCGAGGGCAACCGAGCGAGCT
6092901 ATCCGAGGGCAACCGAGCGAGCT
1 ATCCGAGGGCAACCGAGCGAGCT
*
6092924 ATGCGAGGG-AATCCGAG
1 ATCCGAGGGCAA-CCGAG
6092941 AGAAGCCGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (23 bp):
ATCCGAGGGCAACCGAGCGAGCT
Found at i:6092924 original size:56 final size:56
Alignment explanation
Indices: 6092847--6092954 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
6092837 TGCCATCCGA
* * *
6092847 CCGAGGCCATCCGAACGAGCTATGCGAGGGCATCCGAGGGCAA-CCGAGCGAGCTAT
1 CCGAGGCCAACCGAACGAGCTATGCGAGGGAATCCGAGAG-AAGCCGAGCGAGCTAT
* *
6092903 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAATCCGAGAGAAGCCGAGCGAG
1 CCGAGGCCAACCGAACGAGCTATGCGAGGGAATCCGAGAGAAGCCGAGCGAG
6092955 GGTAGGTCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 2 0.04
56 44 0.96
ACGTcount: A:0.27, C:0.28, G:0.37, T:0.08
Consensus pattern (56 bp):
CCGAGGCCAACCGAACGAGCTATGCGAGGGAATCCGAGAGAAGCCGAGCGAGCTAT
Found at i:6093041 original size:29 final size:29
Alignment explanation
Indices: 6092958--6093041 Score: 109
Period size: 28 Copynumber: 2.9 Consensus size: 29
6092948 GAGCGAGGGT
*
6092958 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
***
6092987 AGGAT-GCCC-TCCGGCATGGCGACCTACA
1 AGG-TCGCCCGGAGGGCATGGCGACCTACA
6093015 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
6093042 TGTGTTGGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 22 0.49
29 21 0.47
30 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.35, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:6095838 original size:83 final size:83
Alignment explanation
Indices: 6095748--6095917 Score: 261
Period size: 83 Copynumber: 2.0 Consensus size: 83
6095738 TGCACATGGC
* * *
6095748 GAATGATATATACACTAGGCTTGGTATTACAAATTGATCCCTAAATTTTAAAGA-TTTTAAATTA
1 GAATGATATATACACTAGGCTTGATATTACAAATTGATCCCTAAA-TTTAAACATTTTTAAACTA
6095812 GATACTCAAGTATTTATTG
65 GATACTCAAGTATTTATTG
* * *
6095831 GAATGATATATACACTTGGCTTGATATTACAAATTGATCCCTAAATTTAATCATTTTTAAACTAT
1 GAATGATATATACACTAGGCTTGATATTACAAATTGATCCCTAAATTTAAACATTTTTAAACTAG
*
6095896 ATACTCAAGTTTTTATTG
66 ATACTCAAGTATTTATTG
6095914 GAAT
1 GAAT
6095918 AATTTGATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 6 0.08
83 73 0.92
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (83 bp):
GAATGATATATACACTAGGCTTGATATTACAAATTGATCCCTAAATTTAAACATTTTTAAACTAG
ATACTCAAGTATTTATTG
Found at i:6098069 original size:12 final size:12
Alignment explanation
Indices: 6098052--6098076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6098042 CCCAACTACC
6098052 ATGATAAAATTG
1 ATGATAAAATTG
6098064 ATGATAAAATTG
1 ATGATAAAATTG
6098076 A
1 A
6098077 AAATCTCCTC
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGATAAAATTG
Found at i:6101903 original size:29 final size:30
Alignment explanation
Indices: 6101860--6101925 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
6101850 TTAAATTTTT
* *
6101860 TATTTTAAATTAATCCTTAAATT-TTAAAA
1 TATTTTAAATCAATCATTAAATTATTAAAA
* *
6101889 TATTTTATATCAATCATTAAATTATTAATA
1 TATTTTAAATCAATCATTAAATTATTAAAA
6101919 TCATTTT
1 T-ATTTT
6101926 TTTTATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.65
30 6 0.19
31 5 0.16
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.52
Consensus pattern (30 bp):
TATTTTAAATCAATCATTAAATTATTAAAA
Found at i:6107961 original size:34 final size:34
Alignment explanation
Indices: 6107923--6107999 Score: 129
Period size: 34 Copynumber: 2.3 Consensus size: 34
6107913 TATAATTAAA
6107923 AAATATATAG-AGATAAATTATAGTAATTATATCT
1 AAATATATAGAAG-TAAATTATAGTAATTATATCT
*
6107957 AAATATATAGAAGTCAATTATAGTAATTATATCT
1 AAATATATAGAAGTAAATTATAGTAATTATATCT
6107991 AAATATATA
1 AAATATATA
6108000 TATAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 39 0.95
35 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.38
Consensus pattern (34 bp):
AAATATATAGAAGTAAATTATAGTAATTATATCT
Found at i:6109616 original size:22 final size:22
Alignment explanation
Indices: 6109591--6109635 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
6109581 CTGGATTTAA
*
6109591 ATTTTTTATTTTAAGTT-TTTTT
1 ATTTTTCATTTTAA-TTATTTTT
6109613 ATTTTTCATTTTAATTATTTTT
1 ATTTTTCATTTTAATTATTTTT
6109635 A
1 A
6109636 AATTAAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTCATTTTAATTATTTTT
Found at i:6109618 original size:16 final size:15
Alignment explanation
Indices: 6109586--6109636 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
6109576 TTCAACTGGA
*
6109586 TTTAAATTTTTTA-T
1 TTTAATTTTTTTATT
6109600 TTTAAGTTTTTTTATT
1 TTTAA-TTTTTTTATT
* *
6109616 TTTCATTTTAATTATT
1 TTTAATTTT-TTTATT
6109632 TTTAA
1 TTTAA
6109637 ATTAAGGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.17
15 11 0.37
16 14 0.47
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTAATTTTTTTATT
Found at i:6110951 original size:14 final size:14
Alignment explanation
Indices: 6110932--6110960 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6110922 CCTATAATTG
6110932 ATCAAAAGTATTTT
1 ATCAAAAGTATTTT
6110946 ATCAAAAGTATTTT
1 ATCAAAAGTATTTT
6110960 A
1 A
6110961 GGTCTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATCAAAAGTATTTT
Found at i:6112171 original size:247 final size:246
Alignment explanation
Indices: 6111761--6112230 Score: 666
Period size: 247 Copynumber: 1.9 Consensus size: 246
6111751 ATTATTTCGA
* * *
6111761 GTCGGTTTCTAATTTATATATTTGGGTCGGGTGAAACTTTATTTTGGTCGAGTCGAGTCGGTTTT
1 GTCGGTTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGGT---GTCGAGTCGGGTTT
* * *
6111826 TTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAAT
63 TTTAAGTGTGATATTCGGGTC-GG-CGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCAAAAAA
* *
6111891 ATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATA-CACCTTTCTATATATATATT
126 ATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATATC-CC--TATATAAATATATT
*
6111955 TTTCAATTAAGTCAATGTTTTTATTGAATAATTTTTTTTATTATTTCGGGTCGGGTCGG
188 TTTCAATTAAGTCAATGTTTTTATTAAATAATTTTTTTTATTATTTCGGGTCGGGTCGG
*
6112014 GTCGGATTTCTAATTCATTTATTCGGGTCGGGTGAAACTTTATTTT-GT-TCGA-TCGGGTTTTT
1 GTCGG-TTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGGTGTCGAGTCGGGTTTTT
6112076 TAAGTGTGATATTCGGGTC-G-G-GTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCAAAAAA
65 TAAGTGTGATATTCGGGTCGGCGAGTTCGGGTTTAGGGTGAAAAAAA-C---CCGACCCAAAAAA
* *
6112138 ATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATATCCCTATATAAATATTTTTTT
126 ATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATATCCCTATATAAATATATTTTT
6112203 CAATTAAGTCAATGTTTTTATTAAATAA
191 CAATTAAGTCAATGTTTTTATTAAATAA
6112231 AAATAATGTT
Statistics
Matches: 199, Mismatches: 12, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
243 22 0.11
244 2 0.01
245 41 0.21
246 1 0.01
247 56 0.28
248 29 0.15
249 4 0.02
253 7 0.04
254 37 0.19
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (246 bp):
GTCGGTTTCTAATTCATATATTCGGGTCGGGTGAAACTTTATTTTGGTGTCGAGTCGGGTTTTTT
AAGTGTGATATTCGGGTCGGCGAGTTCGGGTTTAGGGTGAAAAAAACCCGACCCAAAAAAATATA
TAATTTTACCTTATATATTTAAGAATAATTACAATAATATCCCTATATAAATATATTTTTCAATT
AAGTCAATGTTTTTATTAAATAATTTTTTTTATTATTTCGGGTCGGGTCGG
Found at i:6121406 original size:36 final size:36
Alignment explanation
Indices: 6121359--6121447 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
6121349 TGATATAGGG
* *
6121359 CATTATAGTATTTATCTCTAAATATTTAGAGAGGAA
1 CATTATAGTATTTATCTCTAAATATATAGAGAAGAA
6121395 CATTATAGTATTTATCTCTAAATATATAGAGAAGAA
1 CATTATAGTATTTATCTCTAAATATATAGAGAAGAA
* *
6121431 CATTATAATAATTATCT
1 CATTATAGTATTTATCT
6121448 GGGTTGGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (36 bp):
CATTATAGTATTTATCTCTAAATATATAGAGAAGAA
Found at i:6122586 original size:12 final size:12
Alignment explanation
Indices: 6122569--6122593 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6122559 TACTAACAAC
6122569 ATAACCTAATAA
1 ATAACCTAATAA
6122581 ATAACCTAATAA
1 ATAACCTAATAA
6122593 A
1 A
6122594 CCTCTGTGCA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAACCTAATAA
Found at i:6134154 original size:19 final size:18
Alignment explanation
Indices: 6134130--6134169 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
6134120 CTATTAAAAG
*
6134130 TTATAAAATGATCTTTTGA
1 TTATAAAATGATATTTT-A
*
6134149 TTATAAGATGATATTTTA
1 TTATAAAATGATATTTTA
6134167 TTA
1 TTA
6134170 AATCCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (18 bp):
TTATAAAATGATATTTTA
Done.