Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 49 of 62
Found at i:11390717 original size:18 final size:18
Alignment explanation
Indices: 11390694--11390732 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
11390684 CTTTAGACGA
*
11390694 CCGACCAGTTGACCAGAC
1 CCGACCAGTTAACCAGAC
* *
11390712 CCGACCCGTTAACCCGAC
1 CCGACCAGTTAACCAGAC
11390730 CCG
1 CCG
11390733 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.46, G:0.21, T:0.10
Consensus pattern (18 bp):
CCGACCAGTTAACCAGAC
Found at i:11390726 original size:13 final size:13
Alignment explanation
Indices: 11390710--11390734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11390700 AGTTGACCAG
11390710 ACCCGACCCGTTA
1 ACCCGACCCGTTA
11390723 ACCCGACCCGTT
1 ACCCGACCCGTT
11390735 GACCGTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:11393391 original size:57 final size:57
Alignment explanation
Indices: 11393303--11393475 Score: 249
Period size: 57 Copynumber: 3.0 Consensus size: 57
11393293 TATAGTTGGA
11393303 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG
* *
11393360 GGAAGAATACTTGCAAGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGA
1 GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG
** ** * * *
11393417 GGTTG-ATAACTTTTAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGG
1 GGAAGAAT-ACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG
11393474 GG
1 GG
11393476 TTGTATGATT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
56 2 0.02
57 102 0.98
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (57 bp):
GGAAGAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGG
Found at i:11397968 original size:24 final size:24
Alignment explanation
Indices: 11397905--11397968 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
11397895 ATTTATGATT
11397905 TGAATTCTGTTATGATACCTGACA
1 TGAATTCTGTTATGATACCTGACA
* * * * *
11397929 TGGATTCTGATCTGATACTTGACC
1 TGAATTCTGTTATGATACCTGACA
* *
11397953 TGAATTATGTTTTGAT
1 TGAATTCTGTTATGAT
11397969 TTTTTATATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (24 bp):
TGAATTCTGTTATGATACCTGACA
Found at i:11398252 original size:57 final size:57
Alignment explanation
Indices: 11398026--11398254 Score: 332
Period size: 57 Copynumber: 4.0 Consensus size: 57
11398016 GATGGAGGAA
* * **
11398026 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCATGACGAGGAA
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * *
11398083 GAATACTTGCAGGTTCCTCGGCTTTGTACTGAGAGCCTTACTGTTTGTAACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* **
11398140 GAATACTTGCAGGTTCCTTGGCTTTGTGCTGAGAGCCTTACTGTTCGTGGTGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
* * * *
11398197 GATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
11398254 G
1 G
11398255 TATGATTATG
Statistics
Matches: 154, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 154 1.00
ACGTcount: A:0.15, C:0.20, G:0.31, T:0.34
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTT
Found at i:11403045 original size:26 final size:23
Alignment explanation
Indices: 11403022--11403065 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11403012 ATAATTTAGA
*
11403022 AATATAATAACTAATGATTTTTT
1 AATAAAATAACTAATGATTTTTT
*
11403045 ATTAAAATAACTAATGATTTT
1 AATAAAATAACTAATGATTTT
11403066 AAAATACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (23 bp):
AATAAAATAACTAATGATTTTTT
Found at i:11405448 original size:60 final size:60
Alignment explanation
Indices: 11405371--11405483 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
11405361 AATGATCTCC
* * **
11405371 AATTATATGGTGATATTTTA-TCGAGTTCATTGACTATTAAAAGTTACAAAATGATCAATT
1 AATTATAGGGTGATA-TTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATGATCAATT
* *
11405431 AATTATAGGGT-ATTATTTAGTTGAGTCCCCCGACTATTAAAAGTTACAAAATG
1 AATTATAGGGTGA-TATTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATG
11405484 GTCACCCGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (60 bp):
AATTATAGGGTGATATTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATGATCAATT
Found at i:11408369 original size:31 final size:30
Alignment explanation
Indices: 11408315--11408396 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
11408305 GTATATTGAG
* *
11408315 CAAAATATAAATTTTG-AAAGTTT-AGTGGC
1 CAAAGTATAAATTTAGAAAAGTTTAAG-GGC
11408344 CAAAGTATAAACTTTAGAAAAGTTTAAGGGC
1 CAAAGTATAAA-TTTAGAAAAGTTTAAGGGC
* *
11408375 CAAAGTGTAATTTTA-AAAAGTT
1 CAAAGTATAAATTTAGAAAAGTT
11408397 ATGTAATCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 17 0.37
30 8 0.17
31 19 0.41
32 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (30 bp):
CAAAGTATAAATTTAGAAAAGTTTAAGGGC
Found at i:11409430 original size:48 final size:48
Alignment explanation
Indices: 11409378--11409473 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
11409368 GGAGCACGAT
11409378 ACTAGGGCAAGTAAAAAATGGTAAAGAGTCAGTTTTTTGGGAAAAAGA
1 ACTAGGGCAAGTAAAAAATGGTAAAGAGTCAGTTTTTTGGGAAAAAGA
11409426 ACTAGGGCAAGTAAAAAATGGTAAAGAGTCAGTTTTTTGGGAAAAAGA
1 ACTAGGGCAAGTAAAAAATGGTAAAGAGTCAGTTTTTTGGGAAAAAGA
11409474 TTAGATTATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.06, G:0.27, T:0.23
Consensus pattern (48 bp):
ACTAGGGCAAGTAAAAAATGGTAAAGAGTCAGTTTTTTGGGAAAAAGA
Found at i:11421226 original size:38 final size:38
Alignment explanation
Indices: 11421184--11421260 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
11421174 TGCCCGAAAA
11421184 TGTCACAAATGTCAGATTTATGGAGATAGGATACATAC
1 TGTCACAAATGTCAGATTTATGGAGATAGGATACATAC
11421222 TGTCACAAATGTCAGATTTATGGAGATAGGATACATAC
1 TGTCACAAATGTCAGATTTATGGAGATAGGATACATAC
11421260 T
1 T
11421261 TCTCCTCATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (38 bp):
TGTCACAAATGTCAGATTTATGGAGATAGGATACATAC
Found at i:11422204 original size:14 final size:15
Alignment explanation
Indices: 11422176--11422299 Score: 63
Period size: 15 Copynumber: 8.5 Consensus size: 15
11422166 AAATAAAAGA
11422176 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
11422191 GAAAAAA-GAAAAATGAT
1 GAAAAAATG-AAAA--AT
*
11422208 GGAAAAAACG-AAAA-
1 -GAAAAAATGAAAAAT
*
11422222 GAAAAAA--AAGAA-
1 GAAAAAATGAAAAAT
*
11422234 GAAAAAATGGAAAAGGGAA
1 GAAAAAAT-GAAAA---AT
11422253 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
*
11422268 G--AAAA--AAAGA-
1 GAAAAAATGAAAAAT
11422278 GAAAAAATGAAAAAT
1 GAAAAAATGAAAAAT
11422293 GAAAAAA
1 GAAAAAA
11422300 AGAGAAATAA
Statistics
Matches: 86, Mismatches: 5, Indels: 36
0.68 0.04 0.28
Matches are distributed among these distances:
10 1 0.01
11 4 0.05
12 14 0.16
13 11 0.13
14 5 0.06
15 24 0.28
17 5 0.06
18 13 0.15
19 9 0.10
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (15 bp):
GAAAAAATGAAAAAT
Found at i:11422247 original size:19 final size:18
Alignment explanation
Indices: 11422185--11422284 Score: 68
Period size: 17 Copynumber: 5.7 Consensus size: 18
11422175 AGAAAAAATG
11422185 AAAAATGAAAAAAGAA-A
1 AAAAATGAAAAAAGAAGA
** * *
11422202 AATGATGGAAAAA-ACGA
1 AAAAATGAAAAAAGAAGA
11422219 AAAGAA--AAAAAAGAAGA
1 AAA-AATGAAAAAAGAAGA
**
11422236 AAAAATGGAAAAGGGAAGA
1 AAAAAT-GAAAAAAGAAGA
*
11422255 AAAAATGAAAAATGAA-A
1 AAAAATGAAAAAAGAAGA
11422272 AAAAGA-GAAAAAA
1 AAAA-ATGAAAAAA
11422285 TGAAAAATGA
Statistics
Matches: 63, Mismatches: 13, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
16 8 0.13
17 30 0.48
18 10 0.16
19 15 0.24
ACGTcount: A:0.74, C:0.01, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAATGAAAAAAGAAGA
Found at i:11422271 original size:25 final size:23
Alignment explanation
Indices: 11422166--11422302 Score: 109
Period size: 26 Copynumber: 5.6 Consensus size: 23
11422156 CTTGAAGAAG
11422166 AAAT-AAAAG-AGAAAAAATGAA
1 AAATGAAAAGAAGAAAAAATGAA
11422187 AAATGAAAA-AAGAAAAATGATGGAAA
1 AAATGAAAAGAAGAAAAA--AT-G-AA
* * *
11422213 AAACGAAAAGAAAAAAAAGAAGAAA
1 AAATGAAAAGAAGAAAAA-ATG-AA
11422238 AAATGGAAAAGGGAAGAAAAAATGAA
1 AAAT-GAAAA--GAAGAAAAAATGAA
*
11422264 AAATGAAAAAAAGAGAAAAAATGAA
1 AAATG-AAAAGA-AGAAAAAATGAA
*
11422289 AAATGAAAAAAAGA
1 AAATGAAAAGAAGA
11422303 GAAATAAAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.04
22 11 0.11
23 3 0.03
24 9 0.09
25 26 0.27
26 27 0.28
27 9 0.09
28 8 0.08
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (23 bp):
AAATGAAAAGAAGAAAAAATGAA
Found at i:11422303 original size:25 final size:25
Alignment explanation
Indices: 11422165--11422306 Score: 132
Period size: 25 Copynumber: 5.6 Consensus size: 25
11422155 GCTTGAAGAA
11422165 GAAATAAAAGAGAAAAAATGAAAAAT
1 GAAA-AAAAGAGAAAAAATGAAAAAT
* *
11422191 G-AAAAAAGA-AAAATGATGGAAAAAAC
1 GAAAAAAAGAGAAAA-AAT-G-AAAAAT
11422217 GAAAAGAAA-A-AAAAGAA-GAAAAAAT
1 GAAAA-AAAGAGAAAA-AATG-AAAAAT
* **
11422242 GGAAAAGGGAAGAAAAAATGAAAAAT
1 GAAAAAAAG-AGAAAAAATGAAAAAT
11422268 GAAAAAAAGAGAAAAAATGAAAAAT
1 GAAAAAAAGAGAAAAAATGAAAAAT
11422293 GAAAAAAAGAGAAA
1 GAAAAAAAGAGAAA
11422307 TAAAATGAGG
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
23 4 0.04
24 9 0.09
25 44 0.46
26 22 0.23
27 14 0.15
28 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (25 bp):
GAAAAAAAGAGAAAAAATGAAAAAT
Found at i:11422307 original size:15 final size:15
Alignment explanation
Indices: 11422176--11422311 Score: 64
Period size: 18 Copynumber: 8.3 Consensus size: 15
11422166 AAATAAAAGA
*
11422176 GAAAAAATGAAAAAT
1 GAAAAAAAGAAAAAT
11422191 G-AAAAAAGAAAAAT
1 GAAAAAAAGAAAAAT
*
11422205 GATGGAAAAAACGAAAAGAA
1 GA---AAAAAA-GAAAA-AT
*
11422225 AAAAAAGAAGAAAAAAT
1 GAAAAA-AAG-AAAAAT
*
11422242 GGAAAAGGGAAGAAAAAAT
1 -GAAAA--AAAG-AAAAAT
11422261 GAAAAATGAA-AAAAA-
1 GAAAAA--AAGAAAAAT
11422276 GAGAAAAAATGAAAAAT
1 GA-AAAAAA-GAAAAAT
*
11422293 GAAAAAAAGAGAAAT
1 GAAAAAAAGAAAAAT
11422308 -AAAA
1 GAAAA
11422312 TGAGGGTTCA
Statistics
Matches: 96, Mismatches: 8, Indels: 35
0.69 0.06 0.25
Matches are distributed among these distances:
14 19 0.20
15 9 0.09
16 20 0.21
17 8 0.08
18 23 0.24
19 15 0.16
20 2 0.02
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (15 bp):
GAAAAAAAGAAAAAT
Found at i:11423611 original size:55 final size:55
Alignment explanation
Indices: 11423528--11424010 Score: 555
Period size: 55 Copynumber: 8.9 Consensus size: 55
11423518 GAAGCAAACT
* *
11423528 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * *
11423579 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
** *
11423634 CGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
*
11423689 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
11423744 CGTTT-TATGAAGATTGCTCGAGTTCTATACTCTCTGAAGGAATAGGGAGTGAACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * * *
11423799 CGTTTGTTAAAGA---TT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGTAC-
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* *
11423849 CTGTTTATTGAAGATT-TTCCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 C-GTTTGTTGAAGATTGTT-CGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
* * * *
11423905 CGTTTTATTGAAGATTGTTCAAG-TCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACA
* *
11423961 CATTT-TATGAAGATTGTTCGAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 CGTTTGT-TGAAGATTGTTCGAGTTC-TATACTCT-CTGAAGGAATAGAGAGC
11424011 AGGCTCGTCA
Statistics
Matches: 375, Mismatches: 40, Indels: 30
0.84 0.09 0.07
Matches are distributed among these distances:
50 1 0.00
51 52 0.14
52 1 0.00
53 2 0.01
54 5 0.01
55 266 0.71
56 46 0.12
57 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
Found at i:11423741 original size:110 final size:110
Alignment explanation
Indices: 11423543--11424010 Score: 612
Period size: 110 Copynumber: 4.3 Consensus size: 110
11423533 GTTGAAGATT
* * * *
11423543 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
*
11423608 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTCATGAAGATTGTTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
*
11423653 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
*
11423718 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGCTC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
* * *
11423763 GAGTTCTATACTCTCTGAAGGAATAGGGAGTGAACACGTTTGTTAAAGA---TT-GAGTCCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
* * * *
11423824 CTCTCTGAAAGAATAGGGAGCGTACCTG-TTTATTGAAGATT-TTCC
66 CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA-TGAAGATTGTT-C
* * * * *
11423869 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCAAG-TCTTA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACG-TTTGTTGAAGATTGTTCGAGTTC-TA
* * * *
11423933 TACTCTCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTC
64 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
11423980 GAG-TCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTTC-TATACTCT-CTGAAGGAATAGGGAGC
11424011 AGGCTCGTCA
Statistics
Matches: 314, Mismatches: 32, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
105 5 0.02
106 76 0.24
107 11 0.04
110 155 0.49
111 61 0.19
112 6 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (110 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTTCTATA
CTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:11424051 original size:55 final size:53
Alignment explanation
Indices: 11423883--11424052 Score: 137
Period size: 55 Copynumber: 3.1 Consensus size: 53
11423873 TCTATACTCT
* * * *
11423883 CTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTCAAGTCTTA-TACTC
1 CTGAAGGAATAGAGAGCAGACAC-ATAT-TTGAAGATTGTTCAAGTCTTATTA-TC
* * *
11423938 TCTGAATGAATAGAGAGCAGACACATTTTATGAAGATTGTTCGAGTCTTA-TACTTC
1 -CTGAAGGAATAGAGAGCAGACACATATT-TGAAGATTGTTCAAGTCTTATTA--TC
* * * * *
11423994 CTGAAGGAATAGGGAGCAGGCTCGTCATTTGAAGATTTTTCAAGTCTTATTTATC
1 CTGAAGGAATAGAGAGCAGACACAT-ATTTGAAGATTGTTCAAGTCTTA-TTATC
11424049 CTGA
1 CTGA
11424053 CATAACAGTG
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
54 1 0.01
55 68 0.72
56 24 0.25
57 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (53 bp):
CTGAAGGAATAGAGAGCAGACACATATTTGAAGATTGTTCAAGTCTTATTATC
Found at i:11429406 original size:15 final size:14
Alignment explanation
Indices: 11429340--11429447 Score: 62
Period size: 15 Copynumber: 8.4 Consensus size: 14
11429330 ACATGTAAAC
*
11429340 ATGTGATATAAACT
1 ATGTGATATGAACT
11429354 ATGTGATATCGAACT
1 ATGTGATAT-GAACT
*
11429369 A--CG---TGAAC-
1 ATGTGATATGAACT
11429377 ATGTGATAT-AACT
1 ATGTGATATGAACT
11429390 ATGTGATATCGAACT
1 ATGTGATAT-GAACT
11429405 A--TG---TGAAC-
1 ATGTGATATGAACT
*
11429413 ATGTGATATAAACT
1 ATGTGATATGAACT
*
11429427 ATGTGATACTAAACT
1 ATGTGATA-TGAACT
11429442 ATGTGA
1 ATGTGA
11429448 AAATATGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 31
0.68 0.04 0.28
Matches are distributed among these distances:
8 2 0.03
9 8 0.11
10 5 0.07
12 3 0.04
13 17 0.23
14 17 0.23
15 22 0.30
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (14 bp):
ATGTGATATGAACT
Found at i:11429429 original size:22 final size:23
Alignment explanation
Indices: 11429390--11429432 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
11429380 TGATATAACT
*
11429390 ATGTGATATCGAACTATGTGAAC
1 ATGTGATATCAAACTATGTGAAC
11429413 ATGTGATAT-AAACTATGTGA
1 ATGTGATATCAAACTATGTGA
11429433 TACTAAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (23 bp):
ATGTGATATCAAACTATGTGAAC
Found at i:11429442 original size:37 final size:37
Alignment explanation
Indices: 11429328--11429448 Score: 185
Period size: 36 Copynumber: 3.3 Consensus size: 37
11429318 CGAACTACAT
*
11429328 GAAC-ATGTAAACATGTGATATAAACTATGTGATATC
1 GAACTATGTGAACATGTGATATAAACTATGTGATATC
*
11429364 GAACTACGTGAACATGTGATAT-AACTATGTGATATC
1 GAACTATGTGAACATGTGATATAAACTATGTGATATC
11429400 GAACTATGTGAACATGTGATATAAACTATGTGATA-C
1 GAACTATGTGAACATGTGATATAAACTATGTGATATC
*
11429436 TAAACTATGTGAA
1 -GAACTATGTGAA
11429449 AATATGAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
36 40 0.51
37 38 0.49
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (37 bp):
GAACTATGTGAACATGTGATATAAACTATGTGATATC
Found at i:11429722 original size:23 final size:23
Alignment explanation
Indices: 11429604--11429705 Score: 114
Period size: 23 Copynumber: 4.4 Consensus size: 23
11429594 AGAGTTCTAC
*
11429604 GTGGTCCTTCAGGACAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
* *
11429627 GTGGTCATTCGGGAAAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
* * *** *
11429650 GTGGTACTTCGGGACATTTGGAC
1 GTGGTCCTTCGGGACAATACTAT
*
11429673 GCGGTCCTTCGGGACAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
11429696 GTGGTCCTTC
1 GTGGTCCTTC
11429706 AGGATATTTC
Statistics
Matches: 60, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
GTGGTCCTTCGGGACAATACTAT
Found at i:11429729 original size:46 final size:47
Alignment explanation
Indices: 11429604--11429730 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 47
11429594 AGAGTTCTAC
* *
11429604 GTGGTCCTTCAGGACAATACTATGTGGTCA-TTCGGGAAAATACTAT
1 GTGGTCCTTCAGGACATTTCTATGTGGTCACTTCGGGAAAATACTAT
* * ** * * *
11429650 GTGGTACTTCGGGACATTTGGACGCGGTC-CTTCGGGACAATACTAT
1 GTGGTCCTTCAGGACATTTCTATGTGGTCACTTCGGGAAAATACTAT
*
11429696 GTGGTCCTTCAGGATATTTCTATGTGG-CACTTCGG
1 GTGGTCCTTCAGGACATTTCTATGTGGTCACTTCGG
11429731 TGCAATTTAT
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
45 1 0.02
46 62 0.98
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (47 bp):
GTGGTCCTTCAGGACATTTCTATGTGGTCACTTCGGGAAAATACTAT
Found at i:11429858 original size:6 final size:6
Alignment explanation
Indices: 11429849--11429914 Score: 87
Period size: 6 Copynumber: 11.0 Consensus size: 6
11429839 TGACCAGTTT
* * *
11429849 ATGATA ATGATA ATGATG TTGATA ATGATA ATGATA ATGATA GTGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* *
11429897 ATGATG ATGATG ATGATA
1 ATGATA ATGATA ATGATA
11429915 TGTATATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (6 bp):
ATGATA
Found at i:11429871 original size:18 final size:18
Alignment explanation
Indices: 11429849--11429914 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
11429839 TGACCAGTTT
11429849 ATGATAATGATAATGATG
1 ATGATAATGATAATGATG
* *
11429867 TTGATAATGATAATGATA
1 ATGATAATGATAATGATG
*
11429885 ATGATAGTGATAATGATG
1 ATGATAATGATAATGATG
*
11429903 ATGATGATGATA
1 ATGATAATGATA
11429915 TGTATATATA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (18 bp):
ATGATAATGATAATGATG
Found at i:11429932 original size:2 final size:2
Alignment explanation
Indices: 11429927--11429952 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11429917 TATATATATA
11429927 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
11429953 CATATATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11433952 original size:20 final size:20
Alignment explanation
Indices: 11433927--11434247 Score: 147
Period size: 20 Copynumber: 14.2 Consensus size: 20
11433917 TTTATTTATG
* *
11433927 GCATCCTTTTATGCCTTACT
1 GCATCCTTTCATGCCTTAAT
11433947 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
** *
11433967 GCATTATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
11433992 GGCATCCTTTTATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
11434013 GCATCCGTTCATACATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
11434038 GGCATCCTTTCATGCCTTAAC
1 -GCATCCTTTCATGCCTTAAT
*
11434059 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
11434084 AGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
11434105 GCATACGTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
11434130 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
11434151 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
11434176 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
11434197 GCATCCGTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
11434222 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
11434243 TCATC
1 GCATC
11434248 TGTTCATTCA
Statistics
Matches: 230, Mismatches: 35, Indels: 72
0.68 0.10 0.21
Matches are distributed among these distances:
20 97 0.42
21 11 0.05
22 18 0.08
24 18 0.08
25 11 0.05
26 75 0.33
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:11433992 original size:66 final size:66
Alignment explanation
Indices: 11433915--11434164 Score: 222
Period size: 66 Copynumber: 3.7 Consensus size: 66
11433905 TTGTTCGTTA
* *
11433915 ATTTTATTTATGGCATCCTTTTATGCCTTACTGCATCCTTTCATGCCTTAATGCATTATTTCATG
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATTATTTCATG
11433980 C
66 C
* * * * * **
11433981 ATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCCGTTCATACATT--T-TATTTATGGCAT
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCA-TTATTTCAT
11434043 -C
65 GC
* * ** *
11434044 CTTTCATGCCTTAACGCATCCTTTCATGCATTTTATTTATAGCATCCTTTCATGCCTTAATGCA-
1 ATTTTAT---TTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCCTTAATGCAT
*
11434108 TACGTTCATGC
57 TA-TTTCATGC
*
11434119 ATTTTATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
11434165 ATTTTATTTA
Statistics
Matches: 143, Mismatches: 26, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
63 7 0.05
64 8 0.06
66 75 0.52
67 2 0.01
68 3 0.02
70 3 0.02
71 2 0.01
72 30 0.21
73 2 0.01
74 4 0.03
75 7 0.05
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (66 bp):
ATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCCTTAATGCATTATTTCATG
C
Found at i:11433998 original size:46 final size:46
Alignment explanation
Indices: 11433947--11434268 Score: 518
Period size: 46 Copynumber: 7.0 Consensus size: 46
11433937 ATGCCTTACT
***
11433947 GCATCCTTTCATGCCTTAATGCATTATTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
* *
11433993 GCATCCTTTTATGCCTTAATGCATCCGTTCATACATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
* * *
11434039 GCATCCTTTCATGCCTTAACGCATCCTTTCATGCATTTTATTTATA
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
*
11434085 GCATCCTTTCATGCCTTAATGCATACGTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
* *
11434131 GTATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
11434177 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
* * *
11434223 GCATCCTTTCATGCCTTAATTCATCTGTTCATTCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
11434269 TATTTGATTT
Statistics
Matches: 254, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 254 1.00
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATG
Found at i:11436393 original size:24 final size:24
Alignment explanation
Indices: 11436330--11436393 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
11436320 ATTTATGATT
11436330 TGAATTCTGTTATGATACCTGACA
1 TGAATTCTGTTATGATACCTGACA
* * * * *
11436354 TGGATTCTGATCTGATACTTGACC
1 TGAATTCTGTTATGATACCTGACA
* *
11436378 TGAATTATGTTTTGAT
1 TGAATTCTGTTATGAT
11436394 TTTTTATATA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (24 bp):
TGAATTCTGTTATGATACCTGACA
Found at i:11436677 original size:57 final size:57
Alignment explanation
Indices: 11436452--11436679 Score: 321
Period size: 57 Copynumber: 4.0 Consensus size: 57
11436442 TTGGAGGAAA
* * * * **
11436452 AATAGTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCATGATGAGGAAG
1 AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
*
11436509 AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTAACGGGGTTG
1 AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
* * **
11436566 AATACTTGCAAGTTCCTCGACTTTGTGCTGAGAGCCTTACTGTTCGTGGTGGGGTTG
1 AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
* * * *
11436623 ATTACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACGGGGTTG
1 AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
11436680 TATGATTATG
Statistics
Matches: 151, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 151 1.00
ACGTcount: A:0.16, C:0.20, G:0.30, T:0.34
Consensus pattern (57 bp):
AATACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
Found at i:11443268 original size:60 final size:60
Alignment explanation
Indices: 11443191--11443303 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
11443181 AATGATCTCC
* * **
11443191 AATTATATGGTGATATTTTA-TCGAGTTCATTGACTATTAAAAGTTACAAAATGATCAATT
1 AATTATAGGGTGATA-TTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATGATCAATT
* *
11443251 AATTATAGGGT-ATTATTTAGTTGAGTCCCCCGACTATTAAAAGTTACAAAATG
1 AATTATAGGGTGA-TATTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATG
11443304 GTCACCGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (60 bp):
AATTATAGGGTGATATTTAGTCGAGTCCACCGACTATTAAAAGTTACAAAATGATCAATT
Found at i:11446186 original size:31 final size:30
Alignment explanation
Indices: 11446132--11446213 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
11446122 GTATATTGAG
* *
11446132 CAAAATATAAATTTTG-AAAGTTT-AGTGGC
1 CAAAGTATAAATTTAGAAAAGTTTAAG-GGC
11446161 CAAAGTATAAACTTTAGAAAAGTTTAAGGGC
1 CAAAGTATAAA-TTTAGAAAAGTTTAAGGGC
* *
11446192 CAAAGTGTAATTTTA-AAAAGTT
1 CAAAGTATAAATTTAGAAAAGTT
11446214 ATGTAATCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 17 0.37
30 8 0.17
31 19 0.41
32 2 0.04
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (30 bp):
CAAAGTATAAATTTAGAAAAGTTTAAGGGC
Found at i:11449574 original size:17 final size:18
Alignment explanation
Indices: 11449552--11449585 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11449542 TTGAAAGGTC
*
11449552 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
11449569 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
11449586 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:11459986 original size:44 final size:44
Alignment explanation
Indices: 11459868--11459996 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 44
11459858 TATGAGAAAA
* * * *
11459868 TGATATAAGCTATATGATACCGAACTACATGAACATGTAAACATG
1 TGATATAA-CTATGTGATATCGAACTACGTGAACATGTGAACATG
11459913 TGATATAAACTATGTGATATCGAACTACGTGAACATGTGAACATG
1 TGATAT-AACTATGTGATATCGAACTACGTGAACATGTGAACATG
* *
11459958 TGATATAACTATGTGACATCGAAGTACGTGAACATGTGA
1 TGATATAACTATGTGATATCGAACTACGTGAACATGTGA
11459997 TATAAACTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 31 0.40
45 44 0.57
46 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (44 bp):
TGATATAACTATGTGATATCGAACTACGTGAACATGTGAACATG
Found at i:11460021 original size:15 final size:14
Alignment explanation
Indices: 11459986--11460025 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
11459976 TCGAAGTACG
11459986 TGAAC-ATGTGATA
1 TGAACTATGTGATA
*
11459999 TAAACTATGTGATA
1 TGAACTATGTGATA
11460013 CTGAACTATGTGA
1 -TGAACTATGTGA
11460026 AAATATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 11 0.48
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (14 bp):
TGAACTATGTGATA
Found at i:11460026 original size:37 final size:35
Alignment explanation
Indices: 11459942--11460026 Score: 109
Period size: 37 Copynumber: 2.4 Consensus size: 35
11459932 TCGAACTACG
11459942 TGAAC-ATGTGAACATGTGATATAACTATGTGACA
1 TGAACTATGTGAACATGTGATATAACTATGTGACA
* * *
11459976 TCGAAGTACGTGAACATGTGATATAAACTATGTGATA
1 T-GAACTATGTGAACATGTGATAT-AACTATGTGACA
11460013 CTGAACTATGTGAA
1 -TGAACTATGTGAA
11460027 AATATGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.07
36 16 0.38
37 21 0.50
38 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (35 bp):
TGAACTATGTGAACATGTGATATAACTATGTGACA
Found at i:11460213 original size:23 final size:23
Alignment explanation
Indices: 11460182--11460299 Score: 146
Period size: 23 Copynumber: 5.1 Consensus size: 23
11460172 AGGGTTCTAC
*
11460182 GTGGTCCTTCAGGACAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
* *
11460205 ATGGTCCTTCGGGAAAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
* ** *
11460228 GTGGTCCTTCGGGACATTTGTAC
1 GTGGTCCTTCGGGACAATACTAT
*
11460251 GCGGTCCTTCGGGACAATACTAT
1 GTGGTCCTTCGGGACAATACTAT
* *
11460274 GTGGTCCTTCGGGACATTTCTAT
1 GTGGTCCTTCGGGACAATACTAT
11460297 GTG
1 GTG
11460300 TGTGTGTATA
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
GTGGTCCTTCGGGACAATACTAT
Found at i:11460303 original size:2 final size:2
Alignment explanation
Indices: 11460296--11460331 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
11460286 GACATTTCTA
* *
11460296 TG TG TG TG TG TA TA TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11460332 CGCGCGCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (2 bp):
TG
Found at i:11461344 original size:31 final size:31
Alignment explanation
Indices: 11461306--11461523 Score: 366
Period size: 31 Copynumber: 7.0 Consensus size: 31
11461296 CCCGAAGGAC
* * *
11461306 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
**
11461337 CAGTCCATATGTCCCGAAGGGCATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
11461368 CAGTCCATATGTCTCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11461399 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11461430 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11461461 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11461492 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
11461523 C
1 C
11461524 CCTCGACCCT
Statistics
Matches: 177, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 176 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:11462473 original size:21 final size:21
Alignment explanation
Indices: 11462449--11462492 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11462439 TGTTGTTCGT
* *
11462449 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
11462470 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
11462491 TT
1 TT
11462493 ACCCAGAAAT
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:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:11466959 original size:20 final size:20
Alignment explanation
Indices: 11466934--11467196 Score: 144
Period size: 20 Copynumber: 12.2 Consensus size: 20
11466924 TTTATTTATG
* *
11466934 GCATCCTTTTATGCCTTACT
1 GCATCCTTTCATGCCTTAAT
11466954 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
11466974 GCATCATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
11466999 GGCATCCTTTCATGCCTTAAC
1 -GCATCCTTTCATGCCTTAAT
*
11467020 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
11467045 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
11467066 GCATACGTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
11467091 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
11467112 GCATCCTTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
11467137 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
11467158 GCAT--TTT-AT---TT-AT
1 GCATCCTTTCATGCCTTAAT
*
11467171 GGCATCCTTTCATTCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
11467192 GCATC
1 GCATC
11467197 TGTTCATTCA
Statistics
Matches: 191, Mismatches: 20, Indels: 64
0.69 0.07 0.23
Matches are distributed among these distances:
13 2 0.01
14 6 0.03
16 3 0.02
17 4 0.02
18 3 0.02
20 81 0.42
21 9 0.05
22 12 0.06
24 12 0.06
25 7 0.04
26 52 0.27
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:11467005 original size:46 final size:46
Alignment explanation
Indices: 11466954--11467161 Score: 355
Period size: 46 Copynumber: 4.5 Consensus size: 46
11466944 ATGCCTTACT
11466954 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
* *
11467000 GCATCCTTTCATGCCTTAACGCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
*
11467046 GCATCCTTTCATGCCTTAATGCAT-ACGTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCA-TTTCATGCATTTTATTTATG
* *
11467092 GTATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
11467138 GCATCCTTTCATGCCTTAATGCAT
1 GCATCCTTTCATGCCTTAATGCAT
11467162 TTTATTTATG
Statistics
Matches: 151, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
46 151 1.00
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATG
Found at i:11467010 original size:26 final size:26
Alignment explanation
Indices: 11466974--11467151 Score: 158
Period size: 26 Copynumber: 7.5 Consensus size: 26
11466964 ATGCCTTAAT
*
11466974 GCATCATTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCATTTTATTTATG
* *
11467000 GCATCCTTTCATGC--CTTA---A-C
1 GCATCCTTTCATGCATTTTATTTATG
11467020 GCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCATTTTATTTATG
*
11467046 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTATTTATG
* *
11467066 GCATACGTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCATTTTATTTATG
* *
11467092 GTATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTATTTATG
11467112 GCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGCATTTTATTTATG
11467138 GCATCCTTTCATGC
1 GCATCCTTTCATGC
11467152 CTTAATGCAT
Statistics
Matches: 119, Mismatches: 15, Indels: 36
0.70 0.09 0.21
Matches are distributed among these distances:
20 39 0.33
21 5 0.04
22 9 0.08
24 9 0.08
25 5 0.04
26 52 0.44
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTATTTATG
Found at i:11467165 original size:34 final size:34
Alignment explanation
Indices: 11467122--11467195 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
11467112 GCATCCTTTC
11467122 ATGCATTTTATTTATGGCATCCTTTCATGCCTTA
1 ATGCATTTTATTTATGGCATCCTTTCATGCCTTA
*
11467156 ATGCATTTTATTTATGGCATCCTTTCATTCCTTA
1 ATGCATTTTATTTATGGCATCCTTTCATGCCTTA
11467190 ATGCAT
1 ATGCAT
11467196 CTGTTCATTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (34 bp):
ATGCATTTTATTTATGGCATCCTTTCATGCCTTA
Found at i:11470776 original size:23 final size:23
Alignment explanation
Indices: 11470737--11470817 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
11470727 GTATAAAATG
* *
11470737 CACCGAAGTGCCACGTATAATCA
1 CACCGAAGTGCCGCGTAGAATCA
* * *
11470760 CACTGAAGTGTCGCGTAGAATTA
1 CACCGAAGTGCCGCGTAGAATCA
* **
11470783 TACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCGCGTAGAATCA
11470806 CACCGAAGTGCC
1 CACCGAAGTGCC
11470818 ATATAAAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCGCGTAGAATCA
Found at i:11472404 original size:20 final size:20
Alignment explanation
Indices: 11472379--11472447 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
11472369 TTCATTTAGG
11472379 GGGTATCGATACCCTCCTTA
1 GGGTATCGATACCCTCCTTA
11472399 GGGTATCGATACCCT-C---
1 GGGTATCGATACCCTCCTTA
*
11472415 ---TATCGGTACCCTCCTTA
1 GGGTATCGATACCCTCCTTA
11472432 GGGTATCGATACCCTC
1 GGGTATCGATACCCTC
11472448 TATCGGTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
19 1 0.03
20 27 0.68
ACGTcount: A:0.19, C:0.32, G:0.20, T:0.29
Consensus pattern (20 bp):
GGGTATCGATACCCTCCTTA
Found at i:11472425 original size:33 final size:33
Alignment explanation
Indices: 11472382--11472460 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
11472372 ATTTAGGGGG
*
11472382 TATCGATACCCTCCTTAGGGTATCGATACCCTC
1 TATCGGTACCCTCCTTAGGGTATCGATACCCTC
11472415 TATCGGTACCCTCCTTAGGGTATCGATACCCTC
1 TATCGGTACCCTCCTTAGGGTATCGATACCCTC
11472448 TATCGGTACCCTC
1 TATCGGTACCCTC
11472461 ATTGCATTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.19, C:0.34, G:0.16, T:0.30
Consensus pattern (33 bp):
TATCGGTACCCTCCTTAGGGTATCGATACCCTC
Found at i:11483569 original size:5 final size:5
Alignment explanation
Indices: 11483559--11483594 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
11483549 TCAAGGTACC
* *
11483559 TTGCA TTGCA TTGCA TTGCA TTACA TTGCA TAGCA T
1 TTGCA TTGCA TTGCA TTGCA TTGCA TTGCA TTGCA T
11483595 GTAGTCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (5 bp):
TTGCA
Found at i:11486234 original size:41 final size:41
Alignment explanation
Indices: 11486189--11486269 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
11486179 TATTTTCACA
11486189 ACCATATTTAGTAGTCACAATTCGCAAACAACAAGTTAAAC
1 ACCATATTTAGTAGTCACAATTCGCAAACAACAAGTTAAAC
11486230 ACCATATTTAGTAGTCACAATTCGCAAACAACAAGTTAAA
1 ACCATATTTAGTAGTCACAATTCGCAAACAACAAGTTAAA
11486270 ACATCGTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (41 bp):
ACCATATTTAGTAGTCACAATTCGCAAACAACAAGTTAAAC
Found at i:11488311 original size:16 final size:15
Alignment explanation
Indices: 11488280--11488328 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 15
11488270 ATATGTTTTT
*
11488280 AAAATAATTATTTTAA
1 AAAAT-ATTATATTAA
11488296 CAAAATATTATATT-A
1 -AAAATATTATATTAA
*
11488311 AAAATATTAAATTAA
1 AAAATATTATATTAA
11488326 AAA
1 AAA
11488329 TTTATCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 12 0.41
15 5 0.17
16 7 0.24
17 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATATTATATTAA
Found at i:11488314 original size:14 final size:14
Alignment explanation
Indices: 11488297--11488344 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
11488287 TTATTTTAAC
11488297 AAAATATTATATTA
1 AAAATATTATATTA
*
11488311 AAAATATTAAATTA
1 AAAATATTATATTA
*
11488325 AAAAT-TTATCTTTA
1 AAAATATTAT-ATTA
11488339 AAAATA
1 AAAATA
11488345 GATTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 3 0.10
14 26 0.90
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATATTATATTA
Found at i:11490167 original size:14 final size:16
Alignment explanation
Indices: 11490148--11490180 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11490138 CGGGTCTTTC
11490148 TTCA-TTTCTAT-ATT
1 TTCATTTTCTATGATT
11490162 TTCATTTTCTATGATT
1 TTCATTTTCTATGATT
11490178 TTC
1 TTC
11490181 TCGGTTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 7 0.41
16 6 0.35
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (16 bp):
TTCATTTTCTATGATT
Found at i:11490880 original size:13 final size:13
Alignment explanation
Indices: 11490862--11490886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11490852 TTTCAGAACT
11490862 TATATATATATAA
1 TATATATATATAA
11490875 TATATATATATA
1 TATATATATATA
11490887 TTTTGCTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:11494824 original size:2 final size:2
Alignment explanation
Indices: 11494817--11494851 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
11494807 AAACAAGGAA
* *
11494817 AT AT AT AT AT GT AT AT GT 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 A
11494852 ACTAATCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11498475 original size:97 final size:98
Alignment explanation
Indices: 11498364--11498559 Score: 385
Period size: 97 Copynumber: 2.0 Consensus size: 98
11498354 ATTTGAAAGA
11498364 TATGAATAAAATAAATTATTCCATTGTTGCATAAATGTGTGGATAAGGATTTTAAATTATGTTAT
1 TATGAATAAAATAAATTATTCCATTGTTGCATAAATGTGTGGATAAGGATTTTAAATTATGTTAT
11498429 CTGTGTGCTAATATATTTTCAGAAGTGAAAGTG
66 CTGTGTGCTAATATATTTTCAGAAGTGAAAGTG
11498462 TATGAAT-AAATAAATTATTCCATTGTTGCATAAATGTGTGGATAAGGATTTTAAATTATGTTAT
1 TATGAATAAAATAAATTATTCCATTGTTGCATAAATGTGTGGATAAGGATTTTAAATTATGTTAT
11498526 CTGTGTGCTAATATATTTTCAGAAGTGAAAGTG
66 CTGTGTGCTAATATATTTTCAGAAGTGAAAGTG
11498559 T
1 T
11498560 GTGGTTGCTA
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 91 0.93
98 7 0.07
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.40
Consensus pattern (98 bp):
TATGAATAAAATAAATTATTCCATTGTTGCATAAATGTGTGGATAAGGATTTTAAATTATGTTAT
CTGTGTGCTAATATATTTTCAGAAGTGAAAGTG
Found at i:11502976 original size:11 final size:11
Alignment explanation
Indices: 11502960--11502984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11502950 ACTTTATTTT
11502960 TTCGAAATCTG
1 TTCGAAATCTG
11502971 TTCGAAATCTG
1 TTCGAAATCTG
11502982 TTC
1 TTC
11502985 AGAACTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (11 bp):
TTCGAAATCTG
Found at i:11503431 original size:91 final size:91
Alignment explanation
Indices: 11503324--11503508 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
11503314 ACTACATGTC
11503324 AAGAAAGAGTGTCGATTCAAAAATTAAAATATTAAAATAAAAAATATTTTTATTAAAAAGTCCAA
1 AAGAAAGAGTGTCGATTCAAAAATTAAAATATTAAAATAAAAAATATTTTTATTAAAAAGTCCAA
11503389 TAAAAACATGTCACGCATAGTGTAGT
66 TAAAAACATGTCACGCATAGTGTAGT
11503415 AAGAAAGAGTGTCGATTCAAAAATTAAAATATTAAAATAAAAAATATTTTTATTAAAAAGTCCAA
1 AAGAAAGAGTGTCGATTCAAAAATTAAAATATTAAAATAAAAAATATTTTTATTAAAAAGTCCAA
11503480 TAAAAACATGTCACGCATAGTGTAGT
66 TAAAAACATGTCACGCATAGTGTAGT
11503506 AAG
1 AAG
11503509 CTTTGACTAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (91 bp):
AAGAAAGAGTGTCGATTCAAAAATTAAAATATTAAAATAAAAAATATTTTTATTAAAAAGTCCAA
TAAAAACATGTCACGCATAGTGTAGT
Found at i:11507687 original size:2 final size:2
Alignment explanation
Indices: 11507680--11507755 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
11507670 ATTTTCCGCA
11507680 AT 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 AT
11507722 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
11507756 TTGCATGCAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11519913 original size:12 final size:12
Alignment explanation
Indices: 11519892--11519930 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
11519882 TGAAGATTTT
*
11519892 ATATTTAAAAAA
1 ATATTAAAAAAA
11519904 ATATTAAAAAAA
1 ATATTAAAAAAA
*
11519916 TATTTTAAAAAAA
1 -ATATTAAAAAAA
11519929 AT
1 AT
11519931 TCCCCCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATTAAAAAAA
Found at i:11519923 original size:13 final size:12
Alignment explanation
Indices: 11519892--11519928 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
11519882 TGAAGATTTT
11519892 ATATTTAAAAAA
1 ATATTTAAAAAA
11519904 ATA-TTAAAAAA
1 ATATTTAAAAAA
11519915 ATATTTTAAAAAA
1 ATA-TTTAAAAAA
11519928 A
1 A
11519929 ATTCCCCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATTTAAAAAA
Found at i:11520154 original size:16 final size:16
Alignment explanation
Indices: 11520112--11520154 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
11520102 GGGTATTTGT
11520112 GATTTAAGGAATTTAGG
1 GATTTAA-GAATTTAGG
*
11520129 GATTTGAGAATTTAGG
1 GATTTAAGAATTTAGG
*
11520145 GGTTTAAGAA
1 GATTTAAGAA
11520155 GACGACAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (16 bp):
GATTTAAGAATTTAGG
Found at i:11528549 original size:67 final size:67
Alignment explanation
Indices: 11528470--11528603 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
11528460 TATGAAACAG
11528470 CCTAAATAAAATCTTAAGATTGCAATTACATGAAAGTCATCCAAATCGGTCTCAACATTATAACC
1 CCTAAATAAAATCTTAAGATTGCAATTACATGAAAGTCATCCAAATCGGTCTCAACATTATAACC
11528535 AA
66 AA
11528537 CCTAAATAAAATCTTAAGATTGCAATTACATGAAAGTCATCCAAATCGGTCTCAACATTATAACC
1 CCTAAATAAAATCTTAAGATTGCAATTACATGAAAGTCATCCAAATCGGTCTCAACATTATAACC
11528602 AA
66 AA
11528604 GTCCAAGAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (67 bp):
CCTAAATAAAATCTTAAGATTGCAATTACATGAAAGTCATCCAAATCGGTCTCAACATTATAACC
AA
Found at i:11529656 original size:18 final size:16
Alignment explanation
Indices: 11529636--11529666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11529626 GTGTAAAGAA
11529636 AAAAAATCTATTAAAG
1 AAAAAATCTATTAAAG
*
11529652 TAAAAATCTATTAAA
1 AAAAAATCTATTAAA
11529667 ATTGTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAAAATCTATTAAAG
Found at i:11532333 original size:21 final size:21
Alignment explanation
Indices: 11532291--11532333 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11532281 TTTCTGGGCT
* *
11532291 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
11532312 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
11532333 A
1 A
11532334 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:11532406 original size:23 final size:22
Alignment explanation
Indices: 11532362--11532406 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
11532352 AATCTCATAG
*
11532362 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
11532384 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
11532407 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:11533913 original size:103 final size:103
Alignment explanation
Indices: 11533688--11533905 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
11533678 GTCGAGGGTC
* *
11533688 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGCGAGACACGTAC
1 TATGTGGTCCTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGCGAGACACATAC
* * *
11533753 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
*
11533791 TATGTGGTCCTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGCGAGACACATAC
*
11533856 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
11533894 TATGTGGTCCTT
1 TATGTGGTCCTT
11533906 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCATTGGAACATGTGTGAAGTCTGGCGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:11533956 original size:23 final size:23
Alignment explanation
Indices: 11533930--11533989 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
11533920 ATGGCACTAG
11533930 GGTGCAATTCTACGCGGCAC-TC
1 GGTGCAATTCTACGCGGCACTTC
*
11533952 TGGTGCAATTCTACGTGGCACTTC
1 -GGTGCAATTCTACGCGGCACTTC
*
11533976 GGTGCAATTATACG
1 GGTGCAATTCTACG
11533990 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTTC
Found at i:11534958 original size:20 final size:20
Alignment explanation
Indices: 11534913--11534970 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
11534903 GCATGTGTAG
11534913 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
11534937 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
11534957 TGCATCGATGCACT
1 TGCATCGATGCACT
11534971 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:11538818 original size:19 final size:19
Alignment explanation
Indices: 11538796--11538847 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
11538786 AATGCAATTG
*
11538796 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGAA
11538815 GTGCATCGATGCATAAGAA
1 GTGCATCGATGCATAAGAA
11538834 GTGCATCGATGCAT
1 GTGCATCGATGCAT
11538848 CCCTTTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCATAAGAA
Found at i:11543519 original size:20 final size:20
Alignment explanation
Indices: 11543494--11543549 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
11543484 AGAATGTAAT
11543494 GAGGGTACCGATACCCTAAG
1 GAGGGTACCGATACCCTAAG
11543514 GAGGGTACCGATACCCTAAG
1 GAGGGTACCGATACCCTAAG
* *
11543534 AAGGGTATCGATACCC
1 GAGGGTACCGATACCC
11543550 CCTAAAGGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (20 bp):
GAGGGTACCGATACCCTAAG
Found at i:11544283 original size:19 final size:21
Alignment explanation
Indices: 11544238--11544288 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
11544228 TATGTTATTT
*
11544238 TATATGCTATGTGATGTATGCA
1 TATAAGCTATGTGA-GTATGCA
11544260 T-TAAGCTATGTGA-TATG-A
1 TATAAGCTATGTGAGTATGCA
11544278 TATAAGCTATG
1 TATAAGCTATG
11544289 AGACATGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.07
19 13 0.48
21 11 0.41
22 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (21 bp):
TATAAGCTATGTGAGTATGCA
Found at i:11544296 original size:19 final size:19
Alignment explanation
Indices: 11544261--11544297 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11544251 ATGTATGCAT
* *
11544261 TAAGCTATGTGATATGATA
1 TAAGCTATGAGACATGATA
11544280 TAAGCTATGAGACATGAT
1 TAAGCTATGAGACATGAT
11544298 CTACGTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (19 bp):
TAAGCTATGAGACATGATA
Found at i:11544468 original size:22 final size:22
Alignment explanation
Indices: 11544440--11544500 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
11544430 GGGTCTACGC
*
11544440 GGTCCTTCGGGACATATACAGA
1 GGTCCTTCGGGACAAATACAGA
*
11544462 GGTCCTTCGGGACAAATACATA
1 GGTCCTTCGGGACAAATACAGA
*
11544484 GGTCCTTCTGGACAAAT
1 GGTCCTTCGGGACAAAT
11544501 TTCACATGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGA
Found at i:11546247 original size:18 final size:18
Alignment explanation
Indices: 11546224--11546258 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11546214 GACCTATGAA
11546224 TATGTCCCGAAGGACCAT
1 TATGTCCCGAAGGACCAT
*
11546242 TATGTCCCGAATGACCA
1 TATGTCCCGAAGGACCA
11546259 CGTAGAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAT
Found at i:11547051 original size:23 final size:23
Alignment explanation
Indices: 11547014--11547077 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
11547004 CAGCTCATAT
11547014 AAATGCACCGAAGTGCCA-CGTAG
1 AAATGCACC-AAGTGCCAGCGTAG
* *
11547037 AATTGCACCATAGTG-CAGTGTAG
1 AAATGCACCA-AGTGCCAGCGTAG
11547060 AAATGCACCAAAGTGCCA
1 AAATGCACC-AAGTGCCA
11547078 TATAAAATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.09
23 28 0.82
24 3 0.09
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.17
Consensus pattern (23 bp):
AAATGCACCAAGTGCCAGCGTAG
Found at i:11547812 original size:21 final size:21
Alignment explanation
Indices: 11547786--11547830 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11547776 GATTTCTGGG
* *
11547786 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
11547807 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
11547828 CAA
1 CAA
11547831 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:11548730 original size:31 final size:31
Alignment explanation
Indices: 11548692--11548845 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
11548682 GGGTCGAGGG
11548692 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
11548723 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
11548754 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
11548785 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
11548816 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
11548846 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:11549614 original size:21 final size:21
Alignment explanation
Indices: 11549590--11549633 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
11549580 ATATACATAT
**
11549590 TCCAAGGACCAAGTATGTGTC
1 TCCAAGGACCAAAAATGTGTC
11549611 TCCAAGGACCAAAAATGTGTC
1 TCCAAGGACCAAAAATGTGTC
11549632 TC
1 TC
11549634 AAAGCACCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TCCAAGGACCAAAAATGTGTC
Found at i:11550823 original size:23 final size:23
Alignment explanation
Indices: 11550793--11550853 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
11550783 CTCGTATAAA
11550793 TGCACCGAAGTGCCACGCAGAAT
1 TGCACCGAAGTGCCACGCAGAAT
* *
11550816 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGCAGAAT
* *
11550839 TGCATCAAAGTGCCA
1 TGCACCGAAGTGCCA
11550854 TATAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGCAGAAT
Found at i:11552555 original size:21 final size:21
Alignment explanation
Indices: 11552517--11552557 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11552507 GTTCATTTAT
*
11552517 TTGAAAGTGTATCAATACACA
1 TTGAAAGTGCATCAATACACA
* *
11552538 TTGAATGTGCATCGATACAC
1 TTGAAAGTGCATCAATACAC
11552558 TTTGCCCATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (21 bp):
TTGAAAGTGCATCAATACACA
Found at i:11553458 original size:20 final size:20
Alignment explanation
Indices: 11553416--11553458 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
11553406 ATTCAGAGTC
* *
11553416 ATCTATATATATATCTATCT
1 ATCTATATATATATCCATAT
11553436 ATCTATATATATATACCA-AT
1 ATCTATATATATAT-CCATAT
11553456 ATC
1 ATC
11553459 ATTTTACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (20 bp):
ATCTATATATATATCCATAT
Found at i:11555913 original size:20 final size:20
Alignment explanation
Indices: 11555876--11555914 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11555866 AGATTGAGTG
* * *
11555876 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
11555896 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
11555915 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:11556140 original size:22 final size:23
Alignment explanation
Indices: 11556091--11556150 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
11556081 ATTCACCTGT
11556091 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
11556114 AGGGGGAATCGGTT-CCCTT-AT
1 GGGGGGAATCGGTTCCCCTTCAA
*
11556135 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
11556151 TCTGAACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 8 0.25
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:11565199 original size:23 final size:23
Alignment explanation
Indices: 11565169--11565227 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
11565159 CCTATAAATA
11565169 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
11565192 CACCGAAGTGCCGCGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
11565215 CACCGTAGTGCCA
1 CACCGAAGTGCCA
11565228 TATAAGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:11570791 original size:64 final size:64
Alignment explanation
Indices: 11570717--11570859 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
11570707 CCCTTGACGG
* *
11570717 GTGCATCGATGCACTA-TCTATGCATCGATACA-TAAATCCTATTCGATGTTTTCA-TTTAAGGG
1 GTGCATCGATGCACTACT-TATGCATCGATACACT-AATCCGATTCGATGTTTTCATTTTAA-AG
11570779 GA
63 GA
* * ** *
11570781 GTGCATCGATGCACTACTTGTGCATCGATACACTGATGGGATTCGATGTTTTTATTTTAAAGGA
1 GTGCATCGATGCACTACTTATGCATCGATACACTAATCCGATTCGATGTTTTCATTTTAAAGGA
11570845 GTGCATCGATGCACT
1 GTGCATCGATGCACT
11570860 TCATGTGTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 62 0.90
65 7 0.10
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACTTATGCATCGATACACTAATCCGATTCGATGTTTTCATTTTAAAGGA
Found at i:11570875 original size:64 final size:64
Alignment explanation
Indices: 11570757--11570877 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 64
11570747 CATAAATCCT
* * *
11570757 ATTCGATGTTTTCATTTAAGGGGAGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGG
1 ATTCGATGTTTTCATTTAAGAGGAGTGCATCGATGCACTACATGTGCATAGATACACTGATGGG
* * *
11570821 ATTCGATGTTTTTATTTTAA-AGGAGTGCATCGATGCACTTCATGTGTATAGATACAC
1 ATTCGATGTTTTCA-TTTAAGAGGAGTGCATCGATGCACTACATGTGCATAGATACAC
11570878 CTTGAATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 45 0.90
65 5 0.10
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (64 bp):
ATTCGATGTTTTCATTTAAGAGGAGTGCATCGATGCACTACATGTGCATAGATACACTGATGGG
Found at i:11575261 original size:44 final size:45
Alignment explanation
Indices: 11575212--11575313 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
11575202 GCACTATCTA
* * *
11575212 TGCATCGATACA-TAAATCCTATTCGATGTTTGTA-TTTAAGGGGG
1 TGCATCGATACACT-AATCCAATTCGATGTTTGTATTTTAAAGGAG
* ** *
11575256 TGCATCGATACACTGATGGAATTCGATGTTTTTATTTTAAAGGAG
1 TGCATCGATACACTAATCCAATTCGATGTTTGTATTTTAAAGGAG
11575301 TGCATCGATACAC
1 TGCATCGATACAC
11575314 CTTGAACAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 27 0.55
45 22 0.45
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (45 bp):
TGCATCGATACACTAATCCAATTCGATGTTTGTATTTTAAAGGAG
Found at i:11578066 original size:23 final size:23
Alignment explanation
Indices: 11577996--11578057 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
11577986 CTCGTATAAA
11577996 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
**
11578019 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCATGTAGAAT
*
11578042 TGCACCGTAGTGCCAT
1 TGCACCGAAGTGCCAT
11578058 ATAAGATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATGTAGAAT
Found at i:11583875 original size:20 final size:20
Alignment explanation
Indices: 11583850--11583901 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
11583840 TTTCAAGGGG
11583850 GTATCGATACACTCCTTAAT
1 GTATCGATACACTCCTTAAT
11583870 GTATCGATACACTCCTTAAT
1 GTATCGATACACTCCTTAAT
11583890 GTATCGATACAC
1 GTATCGATACAC
11583902 CATGAAGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATACACTCCTTAAT
Found at i:11588324 original size:42 final size:42
Alignment explanation
Indices: 11588254--11588373 Score: 127
Period size: 42 Copynumber: 2.9 Consensus size: 42
11588244 CTATTGCTGA
* ** *
11588254 AGACATACCACCAAA-AGTACTACAGCCTGTGCTTTTAGTTGC
1 AGACGTACCACCAAAGA-TACTATTGCCTGTGCTTGTAGTTGC
* *
11588296 AGATGTACCACCAAAGATAAC-ATTGCCTGTGCTGGTAGTTGC
1 AGACGTACCACCAAAGAT-ACTATTGCCTGTGCTTGTAGTTGC
* * *
11588338 AGACGTGCCACCGAAGATACTATTGCCTTTGCTTGT
1 AGACGTACCACCAAAGATACTATTGCCTGTGCTTGT
11588374 CACTGTGGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 2 0.03
42 59 0.92
43 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (42 bp):
AGACGTACCACCAAAGATACTATTGCCTGTGCTTGTAGTTGC
Found at i:11596432 original size:11 final size:11
Alignment explanation
Indices: 11596407--11596442 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
11596397 AGCAAATAAA
11596407 ACATAATAA-T
1 ACATAATAATT
11596417 ACATAATAATT
1 ACATAATAATT
11596428 ACATAATAATT
1 ACATAATAATT
11596439 ACAT
1 ACAT
11596443 GCCACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (11 bp):
ACATAATAATT
Found at i:11597778 original size:29 final size:30
Alignment explanation
Indices: 11597694--11597782 Score: 83
Period size: 29 Copynumber: 3.0 Consensus size: 30
11597684 ATTATATAGC
* * *
11597694 ACTTACACAATAATCCCTCAATTTTTCTAGA
1 ACTTACAAAATGATCCCT-AATTTTTCTAAA
* * * *
11597725 ATTTACGAATTGATCTCC-AACTTTTC-AAA
1 ACTTACAAAATGATC-CCTAATTTTTCTAAA
11597754 ACTTACAAAATGATCCCTAATTTTTCTAA
1 ACTTACAAAATGATCCCTAATTTTTCTAA
11597783 GGCTTGTATA
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
28 2 0.05
29 21 0.48
30 9 0.20
31 10 0.23
32 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.37
Consensus pattern (30 bp):
ACTTACAAAATGATCCCTAATTTTTCTAAA
Found at i:11602600 original size:19 final size:19
Alignment explanation
Indices: 11602578--11602626 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
11602568 CCCTTCAATG
*
11602578 GTATTGATACCCTCCTGCA
1 GTATTGATACCCTCCTACA
11602597 GTATTGATACCCTCCTACA
1 GTATTGATACCCTCCTACA
*
11602616 GTACTGATACC
1 GTATTGATACC
11602627 ATTTTTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (19 bp):
GTATTGATACCCTCCTACA
Found at i:11611034 original size:13 final size:13
Alignment explanation
Indices: 11611016--11611048 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
11611006 AATCATACCT
11611016 CTCCAAGCTGGAA
1 CTCCAAGCTGGAA
11611029 CTCCAAGCTGGAA
1 CTCCAAGCTGGAA
11611042 CTCCAAG
1 CTCCAAG
11611049 GTTGAGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (13 bp):
CTCCAAGCTGGAA
Found at i:11616588 original size:13 final size:13
Alignment explanation
Indices: 11616570--11616602 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
11616560 AATCATACCT
11616570 CTCCAAGCTGGAA
1 CTCCAAGCTGGAA
11616583 CTCCAAGCTGGAA
1 CTCCAAGCTGGAA
11616596 CTCCAAG
1 CTCCAAG
11616603 GTTGAGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (13 bp):
CTCCAAGCTGGAA
Found at i:11623659 original size:20 final size:20
Alignment explanation
Indices: 11623622--11623662 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
11623612 TAAATTAATC
*
11623622 AAACCAAATTCAATCATTCA
1 AAACCAAATTCAAACATTCA
11623642 AAACCAAATAT-AAACATTCA
1 AAACCAAAT-TCAAACATTCA
11623662 A
1 A
11623663 GTTCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (20 bp):
AAACCAAATTCAAACATTCA
Found at i:11623721 original size:24 final size:22
Alignment explanation
Indices: 11623674--11623738 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
11623664 TTCAAATTAA
* *
11623674 AAATTCAAATCATTC-AAACAC
1 AAATCCAAATCATCCAAAACAC
11623695 AAATATCCAAATCATCCAAAACAC
1 -AA-ATCCAAATCATCCAAAACAC
*
11623719 AAATCCAAAAACATCCAAAA
1 AAATCC-AAATCATCCAAAA
11623739 TATTTTAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.16
23 25 0.68
24 6 0.16
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (22 bp):
AAATCCAAATCATCCAAAACAC
Found at i:11625680 original size:44 final size:44
Alignment explanation
Indices: 11625617--11625719 Score: 170
Period size: 44 Copynumber: 2.3 Consensus size: 44
11625607 AAACCCGATG
* * *
11625617 AGTGTATCGATGCACATTCAAGGAATGCATCGGTGCCCTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCAGTACACTTTCAT
*
11625661 AGTGTATCGATGCATATTCAAGGAATGCATCAGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCAGTACACTTTCAT
11625705 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
11625720 TTTTCACAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCAGTACACTTTCAT
Found at i:11629935 original size:15 final size:15
Alignment explanation
Indices: 11629915--11629955 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
11629905 TGCCATCTCT
*
11629915 TCATCATCATCGTCG
1 TCATCATAATCGTCG
11629930 TCATCATAATCGTCG
1 TCATCATAATCGTCG
11629945 TCATCATAATC
1 TCATCATAATC
11629956 ACTCTCAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (15 bp):
TCATCATAATCGTCG
Found at i:11632398 original size:124 final size:124
Alignment explanation
Indices: 11632178--11632433 Score: 494
Period size: 124 Copynumber: 2.1 Consensus size: 124
11632168 AAATCCTCAA
*
11632178 GTCTTTAACCAGTTTACTACTAACATAGGAATAATTCAATCTCGGATCAATCAAAACTAAAACAT
1 GTCTTTAACCAGTTTACTACTAACATAGGAATAATTCAATCTCGGATCAATCAAAACTAAAACAG
*
11632243 ATTTACCAGCTATCCGAAAAGTACCTACAATGATTTCAGGATCATCACAATCTTCACTG
66 ATTTACCAACTATCCGAAAAGTACCTACAATGATTTCAGGATCATCACAATCTTCACTG
11632302 GTCTTTAACCAGTTTACTACTAACATAGGAATAATTCAATCTCGGATCAATCAAAACTAAAACAG
1 GTCTTTAACCAGTTTACTACTAACATAGGAATAATTCAATCTCGGATCAATCAAAACTAAAACAG
11632367 ATTTACCAACTATCCGAAAAGTACCTACAATGATTTCAGGATCATCACAATCTTCACTG
66 ATTTACCAACTATCCGAAAAGTACCTACAATGATTTCAGGATCATCACAATCTTCACTG
11632426 GTCTTTAA
1 GTCTTTAA
11632434 ATTATACCTT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 130 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (124 bp):
GTCTTTAACCAGTTTACTACTAACATAGGAATAATTCAATCTCGGATCAATCAAAACTAAAACAG
ATTTACCAACTATCCGAAAAGTACCTACAATGATTTCAGGATCATCACAATCTTCACTG
Found at i:11642742 original size:19 final size:21
Alignment explanation
Indices: 11642705--11642747 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
11642695 TAACTTTTTC
11642705 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
11642725 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
11642745 TTT
1 TTT
11642748 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:11642753 original size:19 final size:20
Alignment explanation
Indices: 11642704--11642753 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11642694 TTAACTTTTT
*
11642704 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
11642724 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
11642743 CTTTTACCTTT
1 CTTTTACCTTT
11642754 TCTCTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:11652128 original size:23 final size:23
Alignment explanation
Indices: 11652075--11652128 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
11652065 ACATTTTATA
* *
11652075 TGGCACTTCGGTGCAATTCTATG
1 TGGCACTTCGGTACAATTCTACG
* *
11652098 CGGTACTTCGGTACAATTCTACG
1 TGGCACTTCGGTACAATTCTACG
11652121 TGGCACTT
1 TGGCACTT
11652129 ATGTGCATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTACAATTCTACG
Found at i:11653133 original size:19 final size:18
Alignment explanation
Indices: 11653106--11653142 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
11653096 AAATTTAATC
11653106 TTTTCCTTATTTTAATTTT
1 TTTTCCTTATTTT-ATTTT
*
11653125 TTTTTCTTATTTTATTTT
1 TTTTCCTTATTTTATTTT
11653143 GTAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCCTTATTTTATTTT
Found at i:11653494 original size:21 final size:23
Alignment explanation
Indices: 11653428--11653495 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 23
11653418 TCTCAAATAT
11653428 TTTTTAACTTTTTATTCTCTCTTTCA
1 TTTTTAACTTTTTA--CTCT-TTTCA
*
11653454 TTATTAACTTTTT-CTCTTTT-A
1 TTTTTAACTTTTTACTCTTTTCA
11653475 TTTTTAACTTTTTACT-TTTTC
1 TTTTTAACTTTTTACTCTTTTC
11653496 TCTCTCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 17 0.45
22 5 0.13
23 4 0.11
26 12 0.32
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTAACTTTTTACTCTTTTCA
Found at i:11654806 original size:18 final size:18
Alignment explanation
Indices: 11654783--11654821 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11654773 GTTGAATAAA
11654783 CACCCAGTCTCATTCCTG
1 CACCCAGTCTCATTCCTG
**
11654801 CACCCAGTCTTGTTCCTG
1 CACCCAGTCTCATTCCTG
11654819 CAC
1 CAC
11654822 TTGATCCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.44, G:0.13, T:0.28
Consensus pattern (18 bp):
CACCCAGTCTCATTCCTG
Found at i:11661375 original size:18 final size:19
Alignment explanation
Indices: 11661352--11661390 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11661342 ATCGATACTG
11661352 ATTGAA-GGAGGTATCGAT
1 ATTGAAGGGAGGTATCGAT
*
11661370 ATTGAAGTGGGGGTATCGAT
1 ATTGAAG-GGAGGTATCGAT
11661390 A
1 A
11661391 CCATGGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.28
Consensus pattern (19 bp):
ATTGAAGGGAGGTATCGAT
Found at i:11662080 original size:23 final size:23
Alignment explanation
Indices: 11662050--11662104 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
11662040 GTCGAGGGTT
11662050 CTATGTGGTCC-TTCAGGAAAAAA
1 CTATGTGGTCCTTTC-GGAAAAAA
*
11662073 CTATGTGGTCCTTTCGGATAAAA
1 CTATGTGGTCCTTTCGGAAAAAA
*
11662096 TTATGTGGT
1 CTATGTGGT
11662105 TATTCGGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (23 bp):
CTATGTGGTCCTTTCGGAAAAAA
Found at i:11662928 original size:23 final size:23
Alignment explanation
Indices: 11662902--11662946 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11662892 CACCACAGCT
*
11662902 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
11662925 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
11662947 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:11663089 original size:25 final size:25
Alignment explanation
Indices: 11663061--11663129 Score: 138
Period size: 25 Copynumber: 2.8 Consensus size: 25
11663051 TATATATATA
11663061 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
11663086 TCCCGAAGGACCGCGTAGAATATTG
1 TCCCGAAGGACCGCGTAGAATATTG
11663111 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCGTAGA
11663130 CCCTCTACTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCGTAGAATATTG
Found at i:11664796 original size:64 final size:63
Alignment explanation
Indices: 11664698--11664858 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
11664688 TAATGAAGGT
* * *
11664698 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT--
*
11664761 AG
62 AC
*
11664763 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
* *
11664827 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
11664859 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
Found at i:11668105 original size:23 final size:23
Alignment explanation
Indices: 11668079--11668123 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11668069 CACCACAGCT
*
11668079 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
11668102 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
11668124 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:11668299 original size:25 final size:25
Alignment explanation
Indices: 11668238--11668306 Score: 111
Period size: 25 Copynumber: 2.8 Consensus size: 25
11668228 TATATATATA
* *
11668238 TCCCGAAGGACAGCATAGAATATTG
1 TCCCGAAGGACCGCATAGAATATTC
11668263 TCCCGAAGGACCGCATAGAATATTC
1 TCCCGAAGGACCGCATAGAATATTC
*
11668288 TCCCGAAGGACCGCGTAGA
1 TCCCGAAGGACCGCATAGA
11668307 CCCTCTACTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (25 bp):
TCCCGAAGGACCGCATAGAATATTC
Found at i:11669973 original size:64 final size:63
Alignment explanation
Indices: 11669875--11670035 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
11669865 TAATGAAGGT
* * *
11669875 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT--
*
11669938 AG
62 AC
*
11669940 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
* *
11670004 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
11670036 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATAC
Found at i:11675898 original size:20 final size:20
Alignment explanation
Indices: 11675869--11675907 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11675859 ATTCCACTAC
*
11675869 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
11675889 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
11675908 CATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:11679982 original size:18 final size:18
Alignment explanation
Indices: 11679959--11680035 Score: 93
Period size: 18 Copynumber: 4.2 Consensus size: 18
11679949 ATGTGTTATC
*
11679959 AGTGGTCCTTCAGGACGT
1 AGTGGTCCTTCAGGACAT
*
11679977 AGTGGTCCTTCAGAACAT
1 AGTGGTCCTTCAGGACAT
*
11679995 AAGTGG-CCATTCGGGACAT
1 -AGTGGTCC-TTCAGGACAT
*
11680014 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACAT
11680032 AGTG
1 AGTG
11680036 ATCATACGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
18 37 0.71
19 15 0.29
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:11683365 original size:12 final size:12
Alignment explanation
Indices: 11683350--11683374 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11683340 GATAATAATA
11683350 GATAAAATATAT
1 GATAAAATATAT
11683362 GATAAAATATAT
1 GATAAAATATAT
11683374 G
1 G
11683375 TGAAAGTGAT
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (12 bp):
GATAAAATATAT
Found at i:11686849 original size:2 final size:2
Alignment explanation
Indices: 11686842--11686887 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
11686832 AGTTCCAACA
* * *
11686842 AG AG AG AG AG AA AG AG AG AG AG AA AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
11686884 AG AG
1 AG AG
11686888 TAAATTAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (2 bp):
AG
Found at i:11686858 original size:12 final size:12
Alignment explanation
Indices: 11686841--11686887 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
11686831 AAGTTCCAAC
11686841 AAGAGAGAGAGA
1 AAGAGAGAGAGA
11686853 AAGAGAGAGAGA
1 AAGAGAGAGAGA
*
11686865 AAGAGAGAAAGA
1 AAGAGAGAGAGA
*
11686877 GAGAGAGAGAG
1 AAGAGAGAGAG
11686888 TAAATTAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AAGAGAGAGAGA
Done.