Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 148 of 210
Found at i:49243197 original size:8 final size:8
Alignment explanation
Indices: 49243184--49243212 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
49243174 TTTTAAATGA
49243184 TATTTTAT
1 TATTTTAT
49243192 TATTTTAT
1 TATTTTAT
49243200 TATTTTAT
1 TATTTTAT
49243208 TATTT
1 TATTT
49243213 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:49243623 original size:12 final size:12
Alignment explanation
Indices: 49243606--49243630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49243596 TGTTCTTGAT
49243606 ATATTAGTGAAG
1 ATATTAGTGAAG
49243618 ATATTAGTGAAG
1 ATATTAGTGAAG
49243630 A
1 A
49243631 GAAATAAGTG
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
ATATTAGTGAAG
Found at i:49245819 original size:50 final size:48
Alignment explanation
Indices: 49245752--49245936 Score: 183
Period size: 50 Copynumber: 3.7 Consensus size: 48
49245742 AAAGTGAAAG
**
49245752 TGATGGTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
1 TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-A
* * *
49245801 TGATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGA
1 TGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA
* * * * * *
49245850 TAACTTCGATCACGTGTGTAGTAC-ATGTGTAGACTACTACGTGTATCGGA
1 TGA--T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA
*
49245900 TGGAAATGGTCACATGTGTAGTACTATGTGTAGGCTA
1 T-G--ATGGTCACATGTGTAGTACTATGTGCAGGCTA
49245937 TTATGTGAAC
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
49 7 0.06
50 75 0.68
51 27 0.25
53 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (48 bp):
TGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA
Found at i:49246021 original size:44 final size:45
Alignment explanation
Indices: 49245956--49246045 Score: 137
Period size: 44 Copynumber: 2.0 Consensus size: 45
49245946 CTGAGTACAC
*
49245956 CATTGACTATAAAGGTGGTTGCTATGTGCTGAATCCATCGAGTAT
1 CATTGACTATAAAGGTGGTTGCTATGTGCTGAATCCACCGAGTAT
* * *
49246001 CATTGATTAT-AAGGTGGTTGCTATGTGCTGATTCCACCGTGTAT
1 CATTGACTATAAAGGTGGTTGCTATGTGCTGAATCCACCGAGTAT
49246045 C
1 C
49246046 TGTTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.78
45 9 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (45 bp):
CATTGACTATAAAGGTGGTTGCTATGTGCTGAATCCACCGAGTAT
Found at i:49251876 original size:45 final size:45
Alignment explanation
Indices: 49251795--49251970 Score: 198
Period size: 45 Copynumber: 4.0 Consensus size: 45
49251785 AACCATTAGA
* * *
49251795 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAACAACCACCTTTATAATCAATGATATT
* **
49251838 CGATGGAATCAGCACATAACAACCACCTTTATTTTCAATGAT-TT
1 CGGTGGAATCAGCACATAACAACCACCTTTATAATCAATGATATT
* * * **
49251882 CCGGTGGAGTCAGCACATAGA-AACCACCTTTATAATCAGTGGTACC
1 -CGGTGGAATCAGCACATA-ACAACCACCTTTATAATCAATGATATT
*
49251928 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATA
1 CGGTGGAATCAGCACATAACAACCACCTTTATAATCAATGATA
49251971 CTCAGTACAC
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
43 5 0.05
44 14 0.13
45 89 0.82
46 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAACAACCACCTTTATAATCAATGATATT
Found at i:49251954 original size:90 final size:88
Alignment explanation
Indices: 49251795--49251969 Score: 233
Period size: 90 Copynumber: 2.0 Consensus size: 88
49251785 AACCATTAGA
* * **
49251795 CGGTGGATCAGCACATAGCACCACCCTTATAATCAATTATATTCGATGGAATCAGCACATAACAA
1 CGGTGGATCAGCACATAGAACCACCCTTATAATCAATGATACCCGATGGAATCAGCACATAACAA
**
49251860 CCACCTTTATTTTCAATGATTTC
66 CCACCTTTATAATCAATGATTTC
* * * * *
49251883 CGGTGGAGTCAGCACATAGAAACCACCTTTATAATCAGTGGTACCCGGTGGAATCAGCACATAGC
1 CGGTGGA-TCAGCACATAG-AACCACCCTTATAATCAATGATACCCGATGGAATCAGCACATAAC
49251948 AACCACCTTTATAATCAATGAT
64 AACCACCTTTATAATCAATGAT
49251970 ACTCAGTACA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
88 7 0.09
89 11 0.15
90 56 0.76
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (88 bp):
CGGTGGATCAGCACATAGAACCACCCTTATAATCAATGATACCCGATGGAATCAGCACATAACAA
CCACCTTTATAATCAATGATTTC
Found at i:49252287 original size:30 final size:29
Alignment explanation
Indices: 49252251--49252307 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
49252241 ACACTTTAGA
*
49252251 AAAATTACATTTTTGCCCCTAGAGTTTCAC
1 AAAATTACAATTTTGCCCCTAG-GTTTCAC
*
49252281 AAAATTACAATTTTGGCCCTAGGTTTC
1 AAAATTACAATTTTGCCCCTAGGTTTC
49252308 GTAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (29 bp):
AAAATTACAATTTTGCCCCTAGGTTTCAC
Found at i:49254423 original size:29 final size:29
Alignment explanation
Indices: 49254391--49254463 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
49254381 AGCTCCGGCT
* *
49254391 ATCGATCATGAAAAGGGATAGTGACGACC
1 ATCGATTATGAAAAGGGATAGTGACAACC
* *
49254420 ATCGATTATGGAAAGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATAGTGACAACC
*
49254449 ACCGAATTATGAAAA
1 ATCG-ATTATGAAAA
49254464 AGGACGGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 28 0.76
30 9 0.24
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATAGTGACAACC
Found at i:49254514 original size:30 final size:29
Alignment explanation
Indices: 49254398--49254523 Score: 96
Period size: 30 Copynumber: 4.2 Consensus size: 29
49254388 GCTATCGATC
* * *
49254398 ATGAAAAGGGATAGTGACGACCATC-GATT
1 ATGAAAAGGGATGGTGAC-AACATCAAATT
* * *
49254427 ATGGAAAGGGATGGTGACAACCACCGAATT
1 ATGAAAAGGGATGGTGACAA-CATCAAATT
* * *
49254457 ATGAAAAAGGACGGCTTTAGC-A-ATCAAATT
1 ATGAAAAGGGATGG--TGA-CAACATCAAATT
49254487 ATGAAAAGGGATGGTGACAACAGTCAAATT
1 ATGAAAAGGGATGGTGACAACA-TCAAATT
49254517 ATGAAAA
1 ATGAAAA
49254524 TGAATAGTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
27 1 0.01
28 4 0.05
29 20 0.27
30 46 0.61
32 3 0.04
33 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (29 bp):
ATGAAAAGGGATGGTGACAACATCAAATT
Found at i:49271294 original size:36 final size:36
Alignment explanation
Indices: 49271247--49271317 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
49271237 AAGTAACTCC
49271247 TTAGAATATGGAATGAAGGATTGGGAATTTAGGGTA
1 TTAGAATATGGAATGAAGGATTGGGAATTTAGGGTA
49271283 TTAGAATATGGAATGAAGGATTGGGAATTTAGGGT
1 TTAGAATATGGAATGAAGGATTGGGAATTTAGGGT
49271318 TTGAGTAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.34, T:0.31
Consensus pattern (36 bp):
TTAGAATATGGAATGAAGGATTGGGAATTTAGGGTA
Found at i:49274878 original size:25 final size:25
Alignment explanation
Indices: 49274850--49274958 Score: 98
Period size: 25 Copynumber: 4.4 Consensus size: 25
49274840 AGAAGTTGTA
49274850 AATCGGTAAGCTCATACGAGCTAAG
1 AATCGGTAAGCTCATACGAGCTAAG
*
49274875 AATCGGTAAGCTCATATGAGCTAAG
1 AATCGGTAAGCTCATACGAGCTAAG
* *** *
49274900 AGTCAACAAGTTCTCA-A-GATCTACA-
1 AATCGGTAAG--CTCATACGAGCTA-AG
* *
49274925 AATCGATAAGCTTATACGAGCTAAG
1 AATCGGTAAGCTCATACGAGCTAAG
49274950 AATCGGTAA
1 AATCGGTAA
49274959 CCCTAATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
23 3 0.05
24 2 0.03
25 55 0.83
26 2 0.03
27 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (25 bp):
AATCGGTAAGCTCATACGAGCTAAG
Found at i:49286449 original size:70 final size:70
Alignment explanation
Indices: 49286355--49286505 Score: 257
Period size: 70 Copynumber: 2.2 Consensus size: 70
49286345 ACAGGACCTA
*
49286355 TGTCGTGACATAGCAACCAACATGTTTCTCTATAGCCATCTTCAGGGGTAGACGCAAAACCCTCA
1 TGTCGTGACATAGCAACCAACATGTTTCTCTATAGCCATCTTCAGGGGTAGACACAAAACCCTCA
49286420 GACTG
66 GACTG
* * * *
49286425 TGTCATGACGTAGCAACCAGCATGTTTCTCTATAGCCATCTTCAGGGGTAGACACAACACCCTCA
1 TGTCGTGACATAGCAACCAACATGTTTCTCTATAGCCATCTTCAGGGGTAGACACAAAACCCTCA
49286490 GACTG
66 GACTG
49286495 TGTCGTGACAT
1 TGTCGTGACAT
49286506 TGAAGGCAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (70 bp):
TGTCGTGACATAGCAACCAACATGTTTCTCTATAGCCATCTTCAGGGGTAGACACAAAACCCTCA
GACTG
Found at i:49308646 original size:26 final size:27
Alignment explanation
Indices: 49308617--49308673 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
49308607 TAAAACGATA
*
49308617 ATTTTACTCGCT-AGGGTATTTTGGTC
1 ATTTTACCCGCTGAGGGTATTTTGGTC
** *
49308643 ATTTTACCCTTTGAGGGTATTTTGGTT
1 ATTTTACCCGCTGAGGGTATTTTGGTC
49308670 ATTT
1 ATTT
49308674 AACAACCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (27 bp):
ATTTTACCCGCTGAGGGTATTTTGGTC
Found at i:49312517 original size:27 final size:29
Alignment explanation
Indices: 49312487--49312540 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
49312477 AAGGAAATCT
* *
49312487 AAAGCCCTTTTAA-A-AATTTAATCCCTC
1 AAAGCCCTTATAACATAATTAAATCCCTC
*
49312514 AAAGGCCTTATAACATAATTAAATCCC
1 AAAGCCCTTATAACATAATTAAATCCC
49312541 AGAATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 1 0.05
29 10 0.45
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAGCCCTTATAACATAATTAAATCCCTC
Found at i:49328480 original size:24 final size:24
Alignment explanation
Indices: 49328448--49328494 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
49328438 AATTAAAGAA
49328448 AAGAAAGATTAAACCCAATTCAGG
1 AAGAAAGATTAAACCCAATTCAGG
49328472 AAGAAAGATTAAACCCAATTCAG
1 AAGAAAGATTAAACCCAATTCAG
49328495 AGTGGCTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
AAGAAAGATTAAACCCAATTCAGG
Found at i:49330568 original size:24 final size:26
Alignment explanation
Indices: 49330520--49330568 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
49330510 AACATTATTT
* *
49330520 ATTAAAATATACTTATGAAAGAAATG
1 ATTAAAACATACTTATGAAAAAAATG
49330546 ATTAAAACATAC-T-TGAAAAAAAT
1 ATTAAAACATACTTATGAAAAAAAT
49330569 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 1 0.05
26 11 0.52
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (26 bp):
ATTAAAACATACTTATGAAAAAAATG
Found at i:49345518 original size:49 final size:49
Alignment explanation
Indices: 49345452--49345546 Score: 138
Period size: 49 Copynumber: 1.9 Consensus size: 49
49345442 TGCAGTCGAG
* *
49345452 CTGCTAGAAACAAAATATTATGGTCGAGCGACCAGATAA-TGCAGATATA
1 CTGCCAGAAACAAAATATTATGGTCAAGCGACCAGA-AATTGCAGATATA
* *
49345501 CTGCCAGATACAAAATATTATGGTCAAGCTACCAGAAATTGCAGAT
1 CTGCCAGAAACAAAATATTATGGTCAAGCGACCAGAAATTGCAGAT
49345547 TATTAAACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 2 0.05
49 39 0.95
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (49 bp):
CTGCCAGAAACAAAATATTATGGTCAAGCGACCAGAAATTGCAGATATA
Found at i:49346033 original size:26 final size:26
Alignment explanation
Indices: 49345970--49346120 Score: 149
Period size: 26 Copynumber: 5.7 Consensus size: 26
49345960 GTCATTATTA
* * * *
49345970 GCCACAAAGGCATCCATTTCCATAGACC
1 GCCACAAAGGCTTCAATTT-CAGATA-C
*
49345998 GCCACAAAGGGTTCAATTTCAGATAC
1 GCCACAAAGGCTTCAATTTCAGATAC
**
49346024 GCCACAAAGGCTTCAATTTCAGATTT
1 GCCACAAAGGCTTCAATTTCAGATAC
* *
49346050 GCCACAAAGGCTTCTATTTTAGATAC
1 GCCACAAAGGCTTCAATTTCAGATAC
* * *
49346076 GCCACAAAGACTTCCATTTCAAATAC
1 GCCACAAAGGCTTCAATTTCAGATAC
** *
49346102 AACACAAAGGCTTCCATTT
1 GCCACAAAGGCTTCAATTT
49346121 TCATACATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 84 0.81
27 4 0.04
28 16 0.15
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (26 bp):
GCCACAAAGGCTTCAATTTCAGATAC
Found at i:49348278 original size:18 final size:16
Alignment explanation
Indices: 49348257--49348295 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
49348247 AATTTAATTT
49348257 TGATATTAAAACTTGAAA
1 TGAT-TTAAAACTTG-AA
*
49348275 TGATTTTAAACTTGAA
1 TGATTTAAAACTTGAA
49348291 TGATT
1 TGATT
49348296 CAAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (16 bp):
TGATTTAAAACTTGAA
Found at i:49353656 original size:25 final size:24
Alignment explanation
Indices: 49353620--49353666 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
49353610 ATAAATTCAT
*
49353620 AAAATATAAAATATCATCTATTTGA
1 AAAATATAAAATATAATC-ATTTGA
49353645 AAAATA-ATAAATATAATCATTT
1 AAAATATA-AAATATAATCATTT
49353667 TGATGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATATAAAATATAATCATTTGA
Found at i:49355493 original size:11 final size:11
Alignment explanation
Indices: 49355477--49355506 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49355467 AAATGGTAAC
49355477 AAGAAAAAAAA
1 AAGAAAAAAAA
49355488 AAGAAAAAAAA
1 AAGAAAAAAAA
*
49355499 CAGAAAAA
1 AAGAAAAA
49355507 GAGGGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:49356310 original size:20 final size:22
Alignment explanation
Indices: 49356284--49356333 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
49356274 AATTTGTTTA
*
49356284 ATATTAG-TTTATTTTTATTAT
1 ATATTAGCTTTATTATTATTAT
49356305 -TATTAGCCTTTTATTATTATTAT
1 ATATTAG-C-TTTATTATTATTAT
49356328 ATATTA
1 ATATTA
49356334 TTACTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 6 0.25
23 13 0.54
24 5 0.21
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (22 bp):
ATATTAGCTTTATTATTATTAT
Found at i:49356357 original size:25 final size:25
Alignment explanation
Indices: 49356300--49356359 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
49356290 GTTTATTTTT
* *
49356300 ATTATTATTAGCCTTTTATTATTATT
1 ATTATTATTA-CCTCTTATTATTATG
49356326 ATATATTATTA-CTCTTATTATTATAG
1 AT-TATTATTACCTCTTATTATTAT-G
49356352 ATTATTAT
1 ATTATTAT
49356360 ATTTATCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 18 0.60
26 4 0.13
27 8 0.27
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.58
Consensus pattern (25 bp):
ATTATTATTACCTCTTATTATTATG
Found at i:49361021 original size:12 final size:12
Alignment explanation
Indices: 49361006--49361033 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49360996 AATCAAAGTC
49361006 AAAATGAAAATG
1 AAAATGAAAATG
49361018 AAAATGAAAATG
1 AAAATGAAAATG
49361030 AAAA
1 AAAA
49361034 AAGAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAATGAAAATG
Found at i:49361049 original size:15 final size:14
Alignment explanation
Indices: 49361018--49361062 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
49361008 AATGAAAATG
* *
49361018 AAAATGAAAATGAA
1 AAAAGGAAAAAGAA
*
49361032 AAAAGAGAGAAAGAA
1 AAAAG-GAAAAAGAA
49361047 AAAAGGAAAAAGAA
1 AAAAGGAAAAAGAA
49361061 AA
1 AA
49361063 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (14 bp):
AAAAGGAAAAAGAA
Found at i:49361889 original size:13 final size:13
Alignment explanation
Indices: 49361873--49361899 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49361863 CAAAAAAAAG
49361873 ATGAAAAATGAAA
1 ATGAAAAATGAAA
49361886 ATGAAAAATGAAA
1 ATGAAAAATGAAA
49361899 A
1 A
49361900 AATGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:49361892 original size:21 final size:21
Alignment explanation
Indices: 49361868--49361917 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
49361858 CAATTCAAAA
49361868 AAAAGATG-AAAAATGAAAATG
1 AAAA-ATGAAAAAATGAAAATG
*
49361889 AAAAATGAAAAAATGAAAAAG
1 AAAAATGAAAAAATGAAAATG
49361910 TAAAAATG
1 -AAAAATG
49361918 GAGAGGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 3 0.12
21 16 0.62
22 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAAATGAAAATG
Found at i:49361902 original size:8 final size:7
Alignment explanation
Indices: 49361868--49361917 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
49361858 CAATTCAAAA
49361868 AAAAGATG
1 AAAA-ATG
49361876 AAAAATG
1 AAAAATG
49361883 -AAAATG
1 AAAAATG
49361889 AAAAATG
1 AAAAATG
49361896 AAAAAATG
1 -AAAAATG
49361904 AAAAA-G
1 AAAAATG
49361910 TAAAAATG
1 -AAAAATG
49361918 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 19 0.50
8 12 0.32
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:49363455 original size:128 final size:128
Alignment explanation
Indices: 49363208--49364137 Score: 1409
Period size: 128 Copynumber: 7.2 Consensus size: 128
49363198 GCTCCTTGAC
*
49363208 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCTTAAGCAGTAGCGGAGCAGATCAAA
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAA
* * *
49363273 -A-GTGAAAAATCTTATCTTCAAGAGTAAGGAAGAAGATTTAAGCCACAAGTCTTATATCCCTGG
65 GACG-G-CAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGG
49363336 T
128 T
* * *
49363337 CAGCAGTGGAATAGGTTTGAAATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGTAGATCGAAA
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATC-AAA
* *
49363402 G-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTAGT
65 GACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
* * * *
49363465 CAACAGTGGAATAGATTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAG-TGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
** * *
49363529 ACGGTGAATCTTATCTTCAAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGT
66 ACGGCAAATCTTATCTTC-AAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
* * * * *
49363593 CAGCAGTGGAATAGGTTAGAAATTACAGATCTTATCTTCCTAAGCAATAGCAGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
* * *
49363658 ACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
66 ACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
* * *
49363721 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCATAAGCAATAGCAGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
* *
49363786 ACGGAAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGT
66 ACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
49363849 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAA
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAA
* * * *
49363914 GACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
65 GACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
* * * *
49363978 CAGTAGTGGAATAGGTTGGAAATTATAGATCTTGTCTCCCTAAGCAATAGCGGAGCTGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
* *
49364043 ACGGCAAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
66 ACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
49364106 CAGCAGTGGAATAGGTTAGGAAATTACAGATC
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATC
49364138 CAATCTCCCT
Statistics
Matches: 736, Mismatches: 57, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
126 4 0.01
127 19 0.03
128 535 0.73
129 177 0.24
130 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (128 bp):
CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
ACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
Found at i:49364147 original size:257 final size:257
Alignment explanation
Indices: 49363208--49364147 Score: 1442
Period size: 257 Copynumber: 3.7 Consensus size: 257
49363198 GCTCCTTGAC
* * *
49363208 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCTTAAGCAGTAGCGGAGCAGATCAAA
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAA
* *
49363273 -A-GTGAAAAATCTTATCTTCAAGAGTAAGGAAGAAGATTTAAGCCACAAGTCTTATATCCCTGG
65 GACG-G-AAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGG
* * * *
49363336 TCAGCAGTGGAATAGGTT-TGAAATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGTAGATCGA
128 TCAGCAGTGGAATAGGTTAGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATC-A
* * * * *
49363400 AAG-CGGCAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCTTATATCCCTAG
192 AAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGG
49363464 T
257 T
* * * *
49363465 CAACAGTGGAATAGATTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCAGAG-TGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAG
** * *
49363529 ACGGTGAATCTTATCTTCAAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTC
66 ACGGAAAATCTTATCTTC-AAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTC
* * *
49363594 AGCAGTGGAATAGGTTA-GAAATTACAGATCTTATCTTCCTAAGCAATAGCAGAGCAGATCAAAG
130 AGCAGTGGAATAGGTTAGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
49363658 ACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
195 ACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
*
49363721 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCATAAGCAATAGCAGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAG
*
49363786 ACGGAAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGTCA
66 ACGGAAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCA
* *
49363851 GCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGA
131 GCAGTGGAATAGGTTAGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGA
*
49363916 CGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
196 CGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
* * * *
49363978 CAGTAGTGGAATAGGTTGGAAATTATAGATCTTGTCTCCCTAAGCAATAGCGGAGCTGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAG
* * *
49364043 ACGGCAAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCA
66 ACGGAAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCA
**
49364108 GCAGTGGAATAGGTTAGGAAATTACAGATCCAATCTCCCT
131 GCAGTGGAATAGGTTAGGAAATTACAGATCTTATCTCCCT
49364148 GAAGTTGTAG
Statistics
Matches: 625, Mismatches: 51, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
255 23 0.04
256 300 0.48
257 302 0.48
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (257 bp):
CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAATAGCAGAGCAGATCAAAG
ACGGAAAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCA
GCAGTGGAATAGGTTAGGAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCAAAGA
CGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTTCCTGGT
Found at i:49364325 original size:44 final size:44
Alignment explanation
Indices: 49364258--49364383 Score: 162
Period size: 44 Copynumber: 2.9 Consensus size: 44
49364248 TAGACCGAAG
* * *
49364258 AATCTTATCTCCCTGAGGTTACAGCGGAGTAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGA
* *
49364302 AATTTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGA
* * * **
49364346 AATCCTATTTCCTTGAGATTACAATGGAGCAGATTAAA
1 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAA
49364384 ATAAATGATC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGA
Found at i:49364656 original size:132 final size:132
Alignment explanation
Indices: 49364503--49364862 Score: 551
Period size: 132 Copynumber: 2.7 Consensus size: 132
49364493 AATAGAGCAG
* * * *
49364503 ATTGAAGCCAGTAATTCTATCTCCTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATC
1 ATTGAAGCCAGTAATTCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTACAGATCTTATC
* * *
49364568 TCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATTGTGCCTCCCTGAGGTTATAGTGGAGT
66 TCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATTGTACCTCCCTAAGGTTACAGTGGAGT
*
49364633 AT
131 AC
49364635 ATTGAAGCCAGTAATTCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTACAGATCTTATC
1 ATTGAAGCCAGTAATTCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTACAGATCTTATC
* * *
49364700 TCCCTAAGTAGTAGTGGAATAGATCGAAGATGGTGAATTTTACCTCCCTAAGGTTACAGTGGAGT
66 TCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATTGTACCTCCCTAAGGTTACAGTGGAGT
49364765 AC
131 AC
* *
49364767 ATTGAAGCTAGTAATTCTATCTCCCTGGTCAGCAGTTGGAATAGGTTAGAA-ATTACAGATCTTA
1 ATTGAAGCCAGTAATTCTATCTCCCTGGTCAGCAG-TGGAATAGATT-GAAGATTACAGATCTTA
* * *
49364831 TCTCCCTAAGCAGTAGCGAAGCAGATCGAAGA
64 TCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA
49364863 CGGCGAATCT
Statistics
Matches: 208, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
132 155 0.75
133 50 0.24
134 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (132 bp):
ATTGAAGCCAGTAATTCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTACAGATCTTATC
TCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATTGTACCTCCCTAAGGTTACAGTGGAGT
AC
Found at i:49364747 original size:44 final size:43
Alignment explanation
Indices: 49364536--49364751 Score: 136
Period size: 44 Copynumber: 4.9 Consensus size: 43
49364526 CTTGGGCAAC
* * *
49364536 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCA-ATTTTATCTCCCTAAGTAGT
* * * * ** *
49364580 AGTGGAGTAGATCGAAGATGGTGAATTGTGCCTCCCTGAGGTTA-T
1 AGTGGAATAGATTGAAGAT-GTCAATTTTATCTCCCT-AAG-TAGT
* * * * *
49364625 AGTGGAGTATATTGAAGCCA-GT-AATTCTATCTCCCT-GGTCAGC
1 AGTGGAATAGATTGAAG--ATGTCAATTTTATCTCCCTAAGT-AGT
*
49364668 AGTGGAATAGATTGAAGAT-TACAGATCTTATCTCCCTAAGTAGT
1 AGTGGAATAGATTGAAGATGT-CA-ATTTTATCTCCCTAAGTAGT
* * *
49364712 AGTGGAATAGATCGAAGATGGTGAATTTTACCTCCCTAAG
1 AGTGGAATAGATTGAAGAT-GTCAATTTTATCTCCCTAAG
49364752 GTTACAGTGG
Statistics
Matches: 132, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
41 3 0.02
42 3 0.02
43 16 0.12
44 82 0.62
45 25 0.19
46 2 0.02
47 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (43 bp):
AGTGGAATAGATTGAAGATGTCAATTTTATCTCCCTAAGTAGT
Found at i:49364791 original size:44 final size:45
Alignment explanation
Indices: 49364611--49364810 Score: 132
Period size: 44 Copynumber: 4.6 Consensus size: 45
49364601 TGAATTGTGC
* * * * *
49364611 CTCCCTGAGGTTA-TAGTGGAGTATATTGAAGCCAGTAATTCTAT
1 CTCCCTAAGGTTAGCAGTGGAATAGATTGAAGCTAGTAATTCTAT
* * *
49364655 CTCCCT--GGTCAGCAGTGGAATAGATTGAAG--ATTACAGATCTTAT
1 CTCCCTAAGGTTAGCAGTGGAATAGATTGAAGCTAGTA-A-TTC-TAT
* * * * * *
49364699 CTCCCTAA-G-TAGTAGTGGAATAGATCGAAGATGGTGAATTTTAC
1 CTCCCTAAGGTTAGCAGTGGAATAGATTGAAGCTAGT-AATTCTAT
* *
49364743 CTCCCTAAGGTTA-CAGTGGAGTACATTGAAGCTAGTAATTCTAT
1 CTCCCTAAGGTTAGCAGTGGAATAGATTGAAGCTAGTAATTCTAT
*
49364787 CTCCCT--GGTCAGCAGTTGGAATAG
1 CTCCCTAAGGTTAGCAG-TGGAATAG
49364811 GTTAGAAATT
Statistics
Matches: 118, Mismatches: 25, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
41 3 0.03
42 9 0.08
43 20 0.17
44 61 0.52
45 20 0.17
46 4 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.30
Consensus pattern (45 bp):
CTCCCTAAGGTTAGCAGTGGAATAGATTGAAGCTAGTAATTCTAT
Found at i:49368723 original size:21 final size:19
Alignment explanation
Indices: 49368697--49368735 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
49368687 GTATATGATT
49368697 AAAAATGGAAGAACAAAAAAG
1 AAAAATGG-A-AACAAAAAAG
*
49368718 AAAAATTGAAACAAAAAA
1 AAAAATGGAAACAAAAAA
49368736 ACTAAAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAATGGAAACAAAAAAG
Found at i:49370175 original size:15 final size:15
Alignment explanation
Indices: 49370155--49370192 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
49370145 CACTACAGGG
49370155 GTCACACGGCCGTGT
1 GTCACACGGCCGTGT
*
49370170 GTCACAGGGCCGTGT
1 GTCACACGGCCGTGT
49370185 GTCACACG
1 GTCACACG
49370193 TGGCTGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (15 bp):
GTCACACGGCCGTGT
Found at i:49371957 original size:26 final size:26
Alignment explanation
Indices: 49371921--49371989 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
49371911 TTTACATTGT
*
49371921 TGCTCACACGAGCTGTGAAATGGGTA
1 TGCTCACACGAGCTGTGAAATGGGCA
*
49371947 TGCTCACACGAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATGGGCA
*
49371973 TGCTCATACGAGCTGTG
1 TGCTCACACGAGCTGTG
49371990 GGTCAGAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGCA
Found at i:49373455 original size:20 final size:20
Alignment explanation
Indices: 49373430--49373507 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
49373420 TTGTACAGGT
49373430 TTGCAC-TTTGGTGCCTTTGA
1 TTGCACATTT-GTGCCTTTGA
**
49373450 TTGCACATTTGTGCCTTTTC
1 TTGCACATTTGTGCCTTTGA
*
49373470 TTGCAC-TTTGGTGCCTCTGA
1 TTGCACATTT-GTGCCTTTGA
49373490 TTGCACATTTGTGCCTTT
1 TTGCACATTTGTGCCTTT
49373508 TTCTACACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.06
20 40 0.82
21 6 0.12
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (20 bp):
TTGCACATTTGTGCCTTTGA
Found at i:49373485 original size:40 final size:40
Alignment explanation
Indices: 49373430--49373508 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
49373420 TTGTACAGGT
*
49373430 TTGCACTTTGGTGCCTTTGATTGCACATTTGTGCCTTTTC
1 TTGCACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTTC
49373470 TTGCACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTT
1 TTGCACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTT
49373509 TCTACACTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (40 bp):
TTGCACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTTC
Found at i:49373517 original size:40 final size:40
Alignment explanation
Indices: 49373433--49373517 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
49373423 TACAGGTTTG
* *
49373433 CACTTTGGTGCCTTTGATTGCACATTTGTGCCTTTTCTTG
1 CACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTTCTTA
49373473 CACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTT-TCTA
1 CACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTTCT-TA
49373513 CACTT
1 CACTT
49373518 CGTTTCCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.98
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.46
Consensus pattern (40 bp):
CACTTTGGTGCCTCTGATTGCACATTTGTGCCTTTTCTTA
Found at i:49382801 original size:12 final size:12
Alignment explanation
Indices: 49382784--49382843 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
49382774 GTTCACTAAC
*
49382784 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
49382796 AAGCTCATTTAT
1 AAGCTCGTTTAT
**
49382808 TGGCTCGTTTAT
1 AAGCTCGTTTAT
49382820 AAGCTCGTTTATT
1 AAGCTCGTTTA-T
49382833 AA-CTCGTTTAT
1 AAGCTCGTTTAT
49382844 TTATTAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
11 1 0.03
12 36 0.90
13 3 0.08
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:49382813 original size:24 final size:24
Alignment explanation
Indices: 49382785--49382842 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
49382775 TTCACTAACA
49382785 AGCTCGTTTAAAAGCTCATTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
* * *
49382809 GGCTCGTTTATAAGCTCGTTTATT
1 AGCTCGTTTAAAAGCTCATTTATT
*
49382833 AACTCGTTTA
1 AGCTCGTTTA
49382843 TTTATTAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (24 bp):
AGCTCGTTTAAAAGCTCATTTATT
Found at i:49384241 original size:20 final size:19
Alignment explanation
Indices: 49384206--49384243 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
49384196 TTACTAGAGG
49384206 TTTTTCTTTTGATTCTTCT
1 TTTTTCTTTTGATTCTTCT
49384225 TTTTTCTTTTG-TT-TTCT
1 TTTTTCTTTTGATTCTTCT
49384242 TT
1 TT
49384244 GTCCTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTGATTCTTCT
Found at i:49387540 original size:51 final size:51
Alignment explanation
Indices: 49387478--49387578 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
49387468 GATGTCCAGG
* * *
49387478 TGGCTTTTAATCAAGGTGTCTCGACTTCTAGTCAAAGTCAGA-ACGTACAGT
1 TGGCTTGTAATCAAGGTGTCTCAACTGCTAGTCAAAGTCAGACA-GTACAGT
49387529 TGGCTTGTAATCAAGGTGTCTCAACTGCTAGTCAAAGTCAGACAGTACAG
1 TGGCTTGTAATCAAGGTGTCTCAACTGCTAGTCAAAGTCAGACAGTACAG
49387579 GTGTCATGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (51 bp):
TGGCTTGTAATCAAGGTGTCTCAACTGCTAGTCAAAGTCAGACAGTACAGT
Found at i:49392945 original size:41 final size:41
Alignment explanation
Indices: 49392868--49392945 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
49392858 GATTTTTATC
* * * *
49392868 AAATCTATTTTACAATCATTAGCTATTTACGCTATGTTAAG
1 AAATCTATTTTACAATAATTACCTACTTACGATATGTTAAG
*
49392909 AAATCTATTTTACAATAATTACCTACTTATGATATGT
1 AAATCTATTTTACAATAATTACCTACTTACGATATGT
49392946 CTGTTTTCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (41 bp):
AAATCTATTTTACAATAATTACCTACTTACGATATGTTAAG
Found at i:49398209 original size:29 final size:29
Alignment explanation
Indices: 49398177--49398238 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
49398167 GCCACGTGTT
*
49398177 ATGTTAGTCTTGAGAGAGAAAGTTGTGAG
1 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
49398206 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
1 ATGTTAGTCTTGAGAGAGAAAATTGTGAG
49398235 ATGT
1 ATGT
49398239 AAATATCAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.32
Consensus pattern (29 bp):
ATGTTAGTCTTGAGAGAGAAAATTGTGAG
Found at i:49402762 original size:13 final size:13
Alignment explanation
Indices: 49402744--49402801 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
49402734 TCATCGGGTG
49402744 GAAATGGATATAT
1 GAAATGGATATAT
* * *
49402757 GAAATGGTTCTAC
1 GAAATGGATATAT
*
49402770 GAAATGGTTATAT
1 GAAATGGATATAT
*
49402783 GACATGGATATAT
1 GAAATGGATATAT
49402796 GAAATG
1 GAAATG
49402802 AACATTTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.31
Consensus pattern (13 bp):
GAAATGGATATAT
Found at i:49405272 original size:40 final size:39
Alignment explanation
Indices: 49405158--49405317 Score: 153
Period size: 39 Copynumber: 4.1 Consensus size: 39
49405148 ACCTATGTCA
* * * * *
49405158 TATATTACTCGAGAATTCT-CAA-CAAGGTTGGATCTTAT
1 TATATTACCCGAGAA-TCTGCAATAAAGGCTAGATCTCAT
* * * *
49405196 TATATTATCTGAGAATCTGCAATAGAGGATAGATCTCAT
1 TATATTACCCGAGAATCTGCAATAAAGGCTAGATCTCAT
* *
49405235 TATATTACCCCGAGAATCTGCAACAAAGGCTAAATCTCAT
1 TATATTA-CCCGAGAATCTGCAATAAAGGCTAGATCTCAT
* * * *
49405275 TATATTTCCCGAGAATCTGTAATAAATGCTAGATCTCGT
1 TATATTACCCGAGAATCTGCAATAAAGGCTAGATCTCAT
49405314 TATA
1 TATA
49405318 ATCTATAATA
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
37 3 0.03
38 15 0.15
39 49 0.49
40 32 0.32
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (39 bp):
TATATTACCCGAGAATCTGCAATAAAGGCTAGATCTCAT
Found at i:49413301 original size:4 final size:4
Alignment explanation
Indices: 49413292--49413332 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
49413282 TCTATTTATA
* *
49413292 TATG TATG TATG TATG TATG TATG CATG CATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
49413333 TAGATTAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (4 bp):
TATG
Found at i:49416600 original size:14 final size:15
Alignment explanation
Indices: 49416578--49416654 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
49416568 CAATCAAACA
49416578 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
49416592 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
49416607 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
49416627 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
49416641 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
49416655 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:49416619 original size:20 final size:20
Alignment explanation
Indices: 49416594--49416633 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
49416584 AATATTTTCC
*
49416594 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
49416614 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
49416634 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:49416639 original size:34 final size:35
Alignment explanation
Indices: 49416582--49416648 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49416572 CAAACACCAG
*
49416582 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
49416617 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
49416649 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:49419222 original size:99 final size:99
Alignment explanation
Indices: 49419051--49419252 Score: 377
Period size: 99 Copynumber: 2.0 Consensus size: 99
49419041 AAATCTATTG
*
49419051 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCGGCTAGATGGAGGAAA
1 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCAGCTAGATGGAGGAAA
*
49419116 GAATCCTTCATTTGTTGGCAGATCTGGCACTCAA
66 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
*
49419150 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCAGCTGGATGGAGGAAA
1 AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCAGCTAGATGGAGGAAA
49419215 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
66 GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
49419249 AAAT
1 AAAT
49419253 GAAGTGATGA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (99 bp):
AAATACCCTCAAAGACCAACTCCGAAATTGGTAATGGTTGTAATAGGTCAGCTAGATGGAGGAAA
GAATCCTTCATTTGTTGGCAGATCTGACACTCAA
Found at i:49425131 original size:36 final size:36
Alignment explanation
Indices: 49425080--49425159 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
49425070 ATATAATTAT
* * *
49425080 TGTCACATGGCATGAATAACATACCCACATATTTAC
1 TGTCACATGGCATGAACAACACACCCACATATTCAC
** *
49425116 TGTCACATGTTATGAACAACACACCCTCATATTCAC
1 TGTCACATGGCATGAACAACACACCCACATATTCAC
*
49425152 TTTCACAT
1 TGTCACAT
49425160 CAGTCATCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.30
Consensus pattern (36 bp):
TGTCACATGGCATGAACAACACACCCACATATTCAC
Found at i:49437279 original size:26 final size:25
Alignment explanation
Indices: 49437250--49437300 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
49437240 TTATTATTAT
*
49437250 TTTTAATAAAATATATTTAACAATAA
1 TTTTAATAAAATATA-ATAACAATAA
* *
49437276 TTTTATTAAAATTTAATAACAATAA
1 TTTTAATAAAATATAATAACAATAA
49437301 CAATAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTAATAAAATATAATAACAATAA
Found at i:49437476 original size:16 final size:16
Alignment explanation
Indices: 49437455--49437506 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
49437445 TGAATTACTG
*
49437455 ATTACAGCTCTATTCC
1 ATTACAACTCTATTCC
*
49437471 ATTACAACTCTATTCA
1 ATTACAACTCTATTCC
*
49437487 ATTACAACCCTATTCC
1 ATTACAACTCTATTCC
49437503 ATTA
1 ATTA
49437507 TAGTGAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.33, C:0.29, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:49454175 original size:44 final size:42
Alignment explanation
Indices: 49454068--49454914 Score: 410
Period size: 44 Copynumber: 19.7 Consensus size: 42
49454058 NNNCACCAGG
* * ** *
49454068 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AATAG-A-A
*
49454114 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAG-AA
* * *
49454158 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT--AA-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAGAA
* * * * * *
49454197 TCTTATCTCTCTGA-AGTTACAGTAGAGCAGATCGCACTAG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAGAA
* * * * ** *
49454238 TCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AA-TAGA-A
*
49454284 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAG-AA
* * *
49454328 TCCTATCTCCCTGAGATTACAGTGGAGCGGATT--AA-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAGAA
* * * * * *
49454367 TCTTATCTCTCTGA-AGTTACAGTAGAGCAGATCGCACTAG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAATAGAA
* * * * ** *
49454408 TCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTG-A-AA-TAGA-A
*
49454454 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAG-AA
* *
49454498 TCCTATCTCCCTGAGATTACAGTGGAGCAGATT--AA-AGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAGAA
* * * ** *
49454537 TCTTATCTCTCTGA-AGTTACAGTAGAGCAGA-TCACACCAG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AATAGAA
* * **
49454578 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGGATTTCAGAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA--A--T-AGAA
*
49454625 -CTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAACTAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAA-TAG-AA
* * * * * * * *
49454668 TCCTATCGCCTTGAGATTACAATTGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAT--AGAA
* * * * * *
49454712 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-TATCAG-G
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAAT-AGAA
* * ** *
49454753 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAG-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAG---ATTGAA-AT-AGAA
* * * * **
49454799 TCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG-TGTCAG-A
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAAT-AGAA
* *
49454840 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAA-ATAG-AA
* *
49454884 TCCTATCTCCCTGAGATTACAGTGGAACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGA
49454915 CCAAAGAACT
Statistics
Matches: 604, Mismatches: 142, Indels: 112
0.70 0.17 0.13
Matches are distributed among these distances:
38 4 0.01
39 81 0.13
40 6 0.01
41 136 0.23
42 21 0.03
43 12 0.02
44 188 0.31
45 14 0.02
46 142 0.24
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (42 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAATAGAA
Found at i:49454347 original size:170 final size:170
Alignment explanation
Indices: 49454065--49454876 Score: 1235
Period size: 170 Copynumber: 4.8 Consensus size: 170
49454055 NNNNNNCACC
*
49454065 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTGAGA
1 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
49454130 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
66 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
49454195 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
131 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
* *
49454235 AGGTCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
1 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
49454300 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
66 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
49454365 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
131 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
* *
49454405 AGGTCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
1 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
*
49454470 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG
66 TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
* *
49454535 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCACACC
131 GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
* * *
49454575 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGGATTTCAGAACTTATCTCCCTGAGA
1 AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
* * * *
49454640 TTACAGCGGAGCAGATTGAA-ACTAGTAATCCTATCGCCTTGAGATTACAATTGAGCGGATTAAA
66 TTACAGCGGAGCAGATTGAATA-TAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGA-T---
* *
49454704 ATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTA-T
126 -TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
* *
49454749 CAGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTT-CAGATCTTATCTCTCTGA
1 -AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAA-TTACAGATCTTATCTCCCTGA
** * * * * * *
49454813 -AGTTACAGTAGAGTAGATCG--TGTCAG--ATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
64 GA-TTACAGCGGAGCAGATTGAATAT-AGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
49454873 AAAG
127 AAAG
49454877 ATAGTAATCC
Statistics
Matches: 595, Mismatches: 36, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
167 5 0.01
169 1 0.00
170 446 0.75
171 2 0.00
172 25 0.04
173 1 0.00
174 3 0.01
175 110 0.18
176 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (170 bp):
AGGTCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTGAGA
TTACAGCGGAGCAGATTGAATATAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG
GATCTTATCTCTCTGAAGTTACAGTAGAGCAGATCGCACT
Found at i:49454757 original size:41 final size:41
Alignment explanation
Indices: 49454710--49454861 Score: 137
Period size: 41 Copynumber: 3.6 Consensus size: 41
49454700 TAAAATAAAG
*
49454710 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTATCA
1 GATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATCGTATCA
* * * ** * *
49454751 GGTCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCA
1 GATCTTATCTCCCTGAGATTACAGTAGAGTAGATC---GTA--TCA
* *
49454797 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGTGTCA
1 GATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATCGTATCA
49454838 GATCTTATCTCCCTGAGATTACAG
1 GATCTTATCTCCCTGAGATTACAG
49454862 CGGAGCAGAT
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
41 50 0.59
42 2 0.02
43 1 0.01
44 2 0.02
45 1 0.01
46 29 0.34
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
GATCTTATCTCCCTGAGATTACAGTAGAGTAGATCGTATCA
Found at i:49454811 original size:87 final size:86
Alignment explanation
Indices: 49454068--49454870 Score: 512
Period size: 87 Copynumber: 9.4 Consensus size: 86
49454058 NNNCACCAGG
* * *
49454068 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGCAGATCTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT-CAGATCTTATCTCTCTGAAG-TT
** *
49454132 ACAGCGGAGCAGATTGAATAT-AGTAA
64 ACAGTAGAGCAGATCG--TATCAG--A
* * * **
49454158 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG------GATCTTATCTCTCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCTTATCTCTCTGAAGTTAC
* *
49454217 AGTAGAGCAGATCGCA-CTAGG
66 AGTAGAGCAGATCGTATC-AGA
* * * * *
49454238 TCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT-CAGATCTTATCTCTCTGAAG-TT
** *
49454302 ACAGCGGAGCAGATTGAATAT-AGTAA
64 ACAGTAGAGCAGATCG--TATCAG--A
* * * **
49454328 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAG------GATCTTATCTCTCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCTTATCTCTCTGAAGTTAC
* *
49454387 AGTAGAGCAGATCGCA-CTAGG
66 AGTAGAGCAGATCGTATC-AGA
* * * * *
49454408 TCTTATTTCCCTAAGATTACGGTGGAACAGACCGAAGAATTACAGATCTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATT-CAGATCTTATCTCTCTGAAG-TT
** *
49454472 ACAGCGGAGCAGATTGAATAT-AGTAA
64 ACAGTAGAGCAGATCG--TATCAG--A
* * **
49454498 TCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAG------GATCTTATCTCTCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCTTATCTCTCTGAAGTTAC
** * *
49454557 AGTAGAGCAGATCACACCAGG
66 AGTAGAGCAGATCGTATCAGA
* * * * *
49454578 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGGATTTCAGAACTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACC-AAAGAATTCAGATCTTATCTCTCTGAAG-TT
** * * *
49454642 ACAGCGGAGCAGATTGAAACTAGTAA
64 ACAGTAGAGCAGATCGTATC-AG--A
* * * * * * * ** **
49454668 TCCTATCGCCTTGAGATTACAATTGAGCGGA-TTAA-AATAAAGGATCTTATCTCTCTGAAGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCA-GATCTTATCTCTCTGAAGTTA
* *
49454731 CAGTAGAGTAGATCGTATCAGG
65 CAGTAGAGCAGATCGTATCAGA
*
49454753 TCTTATTTCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAA-TTCAGATCTTATCTCTCTGAAGTTA
* *
49454818 CAGTAGAGTAGATCGTGTCAGA
65 CAGTAGAGCAGATCGTATCAGA
* *
49454840 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGA
49454871 TTAAAGATAG
Statistics
Matches: 534, Mismatches: 129, Indels: 103
0.70 0.17 0.13
Matches are distributed among these distances:
80 84 0.16
81 6 0.01
82 6 0.01
83 86 0.16
84 6 0.01
85 23 0.04
86 8 0.01
87 163 0.31
88 38 0.07
89 4 0.01
90 110 0.21
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (86 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCTTATCTCTCTGAAGTTAC
AGTAGAGCAGATCGTATCAGA
Found at i:49454922 original size:131 final size:129
Alignment explanation
Indices: 49454760--49455151 Score: 438
Period size: 131 Copynumber: 3.1 Consensus size: 129
49454750 AGGTCTTATT
49454760 TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTACAGTAGA
1 TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTACAGTAGA
* * *
49454825 GTAGATCGTGTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGATAGTAATCCTAT
66 GTAGATCG-GTCAG-TCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTAT
49454890 C
129 C
49454891 TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTACAGTAGA
1 TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTACAGTAGA
*********
49454956 GTAGATC-GT---NNNNNNNNNCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
66 GTAGATCGGTCAGTCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
* * ** ** *
49455016 TCCCTGAGATTACAGTGGAGCGGA-TTAA-AAC-AAAGGATCTTATCTCACTGAAGTTACAGTAG
1 TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCA-GATCTTATCTCTCTGAAGTTACAGTAG
* * * * * * * * *
49455078 AGTAGATCGCATCAGGTTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
65 AGTAGATCG-GTCA-GTCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTA
49455143 TC
128 TC
49455145 TCCCTGA
1 TCCCTGA
49455152 CGTTGCGGAG
Statistics
Matches: 219, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
122 1 0.00
123 37 0.17
124 2 0.01
125 63 0.29
129 44 0.20
131 72 0.33
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.27
Consensus pattern (129 bp):
TCCCTGAGATTACAGTGGAACAGACCAAAGAACTTCAGATCTTATCTCTCTGAAGTTACAGTAGA
GTAGATCGGTCAGTCTTACCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATC
Found at i:49460396 original size:2 final size:2
Alignment explanation
Indices: 49460389--49460419 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49460379 ATAATTTTAA
49460389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49460420 AAAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49464250 original size:22 final size:22
Alignment explanation
Indices: 49464196--49464251 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
49464186 TATGCGCATT
49464196 TTCAAATTAAAATAATAAAAAA
1 TTCAAATTAAAATAATAAAAAA
* *
49464218 TTGCCAA-TAAAATACAT-AAGAA
1 TT-CAAATTAAAATA-ATAAAAAA
49464240 TTCAAATTAAAA
1 TTCAAATTAAAA
49464252 AAAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 5 0.18
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.27
Consensus pattern (22 bp):
TTCAAATTAAAATAATAAAAAA
Found at i:49464709 original size:3 final size:3
Alignment explanation
Indices: 49464701--49464739 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
49464691 GGCCGCCCAA
49464701 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49464740 CTAGCATGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49466905 original size:159 final size:161
Alignment explanation
Indices: 49466675--49467025 Score: 458
Period size: 159 Copynumber: 2.2 Consensus size: 161
49466665 GTTCTTTTCT
* * * * *
49466675 TTTTATATAGAAAAAAGATGAATCCAACAAATCA--CTAGGACATCAAAATCTTTCTTTCTTCTC
1 TTTTATAT--AAAGAAGATAAATCCAACAAATCATTGTA-AACATCAAAATCTTTATTTCTTCTC
* * * * **
49466738 AACGATGTTTATTCTTTACCTTGAGGCATCTGCGTTCAATTCAAAATCAAACCAAGCGAATATTA
63 AACAATGTTCATTCTTTACCTTGAGGCATCTACATTCAATTCAAAATCAAACCAAGAAAATATTA
* * *
49466803 AACCTTACAATGTTCCCTTTTAATC-ACTCTTTA
128 AACCCTAAAATGATCCCTTTTAATCAACTCTTTA
49466836 TTTTATATAAAGAA-ATAAATCCAACAAATCATTGTAAACATCAAAATCTTTATTTCTTCTCAAC
1 TTTTATATAAAGAAGATAAATCCAACAAATCATTGTAAACATCAAAATCTTTATTTCTTCTCAAC
*
49466900 AATGTTCATTCTTTACCTTGAGGTATCTACATTCAATTCAAAATCAAACCAAGAAAATATTAAAC
66 AATGTTCATTCTTTACCTTGAGGCATCTACATTCAATTCAAAATCAAACCAAGAAAATATTAAAC
* *
49466965 CCTAAAATGATCCCTTTTATTCATATTCTTTA
131 CCTAAAATGATCCCTTTTAATCA-ACTCTTTA
* *
49466997 TTTTCTATAAAGAAGGATGAATCCAACAA
1 TTTTATATAAAGAA-GATAAATCCAACAA
49467026 CCCACAGTAA
Statistics
Matches: 165, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
158 16 0.10
159 107 0.65
160 2 0.01
161 28 0.17
163 12 0.07
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (161 bp):
TTTTATATAAAGAAGATAAATCCAACAAATCATTGTAAACATCAAAATCTTTATTTCTTCTCAAC
AATGTTCATTCTTTACCTTGAGGCATCTACATTCAATTCAAAATCAAACCAAGAAAATATTAAAC
CCTAAAATGATCCCTTTTAATCAACTCTTTA
Found at i:49467107 original size:170 final size:164
Alignment explanation
Indices: 49466745--49467156 Score: 437
Period size: 159 Copynumber: 2.5 Consensus size: 164
49466735 CTCAACGATG
* * * *
49466745 TTTATTCTTTACCTTGAGGCATCTGCGTTCAATTCAAAATCAAACCAAGCGAATATTAAACCTTA
1 TTTA-TCTTTA-CTTGAGGTATCTGCATTCAATTCAAAATCAAACCAAGCAAATATTAAACCCTA
* * **
49466810 CAATGTTCCCTTTTAATCACTCTTTATTTTATATAAAGAAATAAATCCAACAAATCATTGTAAAC
64 AAATGTTCCCTTTTAATCACTCTTTATTTTATATAAAGAAATAAATCCAACAAACCACAGTAAAC
* *
49466875 ATCAAAATCTTTATTTCTTCTCAACAATGTTCATTC
129 ATCAAAACCTTTATTTCTACTCAACAATGTTCATTC
* *
49466911 TTTA-C----CTTGAGGTATCTACATTCAATTCAAAATCAAACCAAGAAAATATTAAACCCTAAA
1 TTTATCTTTACTTGAGGTATCTGCATTCAATTCAAAATCAAACCAAGCAAATATTAAACCCTAAA
* * * * * *
49466971 ATGATCCCTTTTATTCATATTCTTTATTTTCTATAAAGAAGGATGAATCCAACAACCCACAGTAA
66 ATGTTCCCTTTTAATC--ACTCTTTATTTTATATAAAGAA--ATAAATCCAACAAACCACAGTAA
* * * *
49467036 GCATCAAAACCTTTCTTTC-ACGT-AA-ATTGTATTTATTC
127 ACATCAAAACCTTTATTTCTAC-TCAACAATG--TTCATTC
**
49467074 TTTACTCTTTACGTTGAGGTATCTGCATTCAATT-AAAAAAAAACCAAGCAAATATTAAACCCTA
1 TTTA-TCTTTAC-TTGAGGTATCTGCATTCAATTCAAAATCAAACCAAGCAAATATTAAACCCTA
*
49467138 AAATGTTCCTTTTTAATCA
64 AAATGTTCCCTTTTAATCA
49467157 GCAAGAAAAT
Statistics
Matches: 203, Mismatches: 29, Indels: 27
0.78 0.11 0.10
Matches are distributed among these distances:
159 62 0.31
161 23 0.11
162 3 0.01
163 45 0.22
164 1 0.00
165 1 0.00
166 4 0.02
167 1 0.00
169 43 0.21
170 20 0.10
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.36
Consensus pattern (164 bp):
TTTATCTTTACTTGAGGTATCTGCATTCAATTCAAAATCAAACCAAGCAAATATTAAACCCTAAA
ATGTTCCCTTTTAATCACTCTTTATTTTATATAAAGAAATAAATCCAACAAACCACAGTAAACAT
CAAAACCTTTATTTCTACTCAACAATGTTCATTC
Found at i:49467394 original size:22 final size:19
Alignment explanation
Indices: 49467353--49467390 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
49467343 CGAGTTACTT
49467353 CTCCTCCAATTTTCTCAAC
1 CTCCTCCAATTTTCTCAAC
49467372 CTCCTCCAATTTTCTCAAC
1 CTCCTCCAATTTTCTCAAC
49467391 AACCAAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCCTCCAATTTTCTCAAC
Found at i:49468367 original size:18 final size:19
Alignment explanation
Indices: 49468344--49468388 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
49468334 AAGTCATATA
49468344 TTATAAATTAA-T-AAAATT
1 TTATAAA-TAATTCAAAATT
49468362 TTATAAATAATTCAAAATT
1 TTATAAATAATTCAAAATT
49468381 TATATAAA
1 T-TATAAA
49468389 AATAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
19 7 0.29
20 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATAAATAATTCAAAATT
Found at i:49468396 original size:18 final size:19
Alignment explanation
Indices: 49468344--49468398 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
49468334 AAGTCATATA
49468344 TTATAAATTAA-T-AAAATT
1 TTATAAA-TAATTAAAAATT
*
49468362 TTATAAATAATTCAAAATT
1 TTATAAATAATTAAAAATT
49468381 TATATAAA-AA-TAAAAATT
1 T-TATAAATAATTAAAAATT
49468399 ATAAACATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.09
18 15 0.45
19 9 0.27
20 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATAAATAATTAAAAATT
Found at i:49468625 original size:14 final size:14
Alignment explanation
Indices: 49468603--49468637 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
49468593 TTAGTAAAAA
49468603 ACACGCTGACGTGG
1 ACACGCTGACGTGG
*
49468617 ACGCGCTGACGTGG
1 ACACGCTGACGTGG
49468631 ACACGCT
1 ACACGCT
49468638 TTGCTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.31, G:0.34, T:0.14
Consensus pattern (14 bp):
ACACGCTGACGTGG
Found at i:49468865 original size:34 final size:33
Alignment explanation
Indices: 49468834--49468931 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 33
49468824 GAATTTTATA
49468834 AAAATTAATTAAATTAGGTTTTAGGGGTTTTAAG
1 AAAATTAATTAAATTAGGTTTTA-GGGTTTTAAG
* *
49468868 TAAATTAATTAAATTAGGGTTTAAGGGTTTTAAG
1 AAAATTAATTAAATTA-GGTTTTAGGGTTTTAAG
49468902 AAAATTAATTAAATTAAGGTTTT-GGGTTTT
1 AAAATTAATTAAATT-AGGTTTTAGGGTTTT
49468932 TAAAAATAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
33 7 0.12
34 44 0.76
35 7 0.12
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGTTTTAGGGTTTTAAG
Found at i:49472087 original size:14 final size:14
Alignment explanation
Indices: 49472050--49472098 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
49472040 TTTAAACTCG
*
49472050 AACCTCGAACCCTA
1 AACCTCAAACCCTA
* *
49472064 AAGCTTAAACCCTA
1 AACCTCAAACCCTA
*
49472078 AACCTCAAA-CTTA
1 AACCTCAAACCCTA
49472091 AACCTCAA
1 AACCTCAA
49472099 GTTTAGGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.18
Consensus pattern (14 bp):
AACCTCAAACCCTA
Found at i:49475765 original size:27 final size:27
Alignment explanation
Indices: 49475722--49475774 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
49475712 AGACCACTCG
*
49475722 TGTTTAATGCCCTAGTGGGCTACCCCA
1 TGTTTAATGCCCTAGTGGACTACCCCA
49475749 TGTTTAATGTCCC-AGTGGACTACCCC
1 TGTTTAATG-CCCTAGTGGACTACCCC
49475775 GTCTTCACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (27 bp):
TGTTTAATGCCCTAGTGGACTACCCCA
Found at i:49488338 original size:24 final size:24
Alignment explanation
Indices: 49488306--49488351 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
49488296 AGAAGGGAAT
49488306 GAGCATGTGGAAGCAATAGCGAAG
1 GAGCATGTGGAAGCAATAGCGAAG
*
49488330 GAGCATGTGGAAGTAATAGCGA
1 GAGCATGTGGAAGCAATAGCGA
49488352 TTGACCGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.37, T:0.15
Consensus pattern (24 bp):
GAGCATGTGGAAGCAATAGCGAAG
Found at i:49488904 original size:230 final size:230
Alignment explanation
Indices: 49488501--49488961 Score: 805
Period size: 230 Copynumber: 2.0 Consensus size: 230
49488491 CTAGAGATAG
* * * * *
49488501 AAACAATTAAAGATTCTGCTGTTGCAAAGATACCGTACCCTTCAAGGTTAGAAGAGAAATAAAAG
1 AAACAATTAAAGATTCTACCGTTGCAAAGATACCATACCCTTCAAGGCTAAAAGAGAAATAAAAG
49488566 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTACATTT
66 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTACATTT
49488631 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
131 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
49488696 AGGTAAGAGAACAAGTTAACATGAGCACTTATTGT
196 AGGTAAGAGAACAAGTTAACATGAGCACTTATTGT
*
49488731 AAACAATTAAAGATTCTACCGTTGTAAAGATACCATACCCTTCAAGGCTAAAAGAGAAATAAAAG
1 AAACAATTAAAGATTCTACCGTTGCAAAGATACCATACCCTTCAAGGCTAAAAGAGAAATAAAAG
* **
49488796 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAACATTAGATGTCAACCTGTATTT
66 TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTACATTT
*
49488861 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCGTAGGAAAATTA
131 GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
* * *
49488926 AGGTAGGAGAACAAGTTAACATGAGCTCTTCTTGT
196 AGGTAAGAGAACAAGTTAACATGAGCACTTATTGT
49488961 A
1 A
49488962 GTGTTCTTAT
Statistics
Matches: 218, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
230 218 1.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (230 bp):
AAACAATTAAAGATTCTACCGTTGCAAAGATACCATACCCTTCAAGGCTAAAAGAGAAATAAAAG
TGGGATGGAAACGAGGTTGTAAGTTTTTTAAACTTGTTCAAAAAATTAGATGTCAACCTACATTT
GATTGAAAAAGTTCCTAAGTATGCCAAAATTTTAAAGGAAATCATGTCTAGGCATAGGAAAATTA
AGGTAAGAGAACAAGTTAACATGAGCACTTATTGT
Found at i:49491892 original size:13 final size:13
Alignment explanation
Indices: 49491870--49491904 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
49491860 CCGTGTGCCA
49491870 CACATAGCCTACT
1 CACATAGCCTACT
*
49491883 CACATGGCCTACT
1 CACATAGCCTACT
*
49491896 CACACAGCC
1 CACATAGCC
49491905 GTGTGCCTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.29, C:0.43, G:0.11, T:0.17
Consensus pattern (13 bp):
CACATAGCCTACT
Found at i:49494046 original size:17 final size:17
Alignment explanation
Indices: 49494024--49494059 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
49494014 GGGCTAAACG
49494024 AATTAAAGAGTGGAACA
1 AATTAAAGAGTGGAACA
49494041 AATTAAAGAGTGGAACA
1 AATTAAAGAGTGGAACA
49494058 AA
1 AA
49494060 CGCAATAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (17 bp):
AATTAAAGAGTGGAACA
Found at i:49495825 original size:63 final size:63
Alignment explanation
Indices: 49495726--49495852 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
49495716 TGATCTATCC
49495726 TAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTAG
1 TAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTAG
49495789 TAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTAG
1 TAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTAG
49495852 T
1 T
49495853 TAAGTTTTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (63 bp):
TAATTCGGTGTAGTAGATTAAACTAGTTTTTGCACTTTAGGAGCTTGAACATAAGCATTTTAG
Found at i:49497362 original size:22 final size:21
Alignment explanation
Indices: 49497328--49497369 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
49497318 CAGCTGATGC
*
49497328 AAAAAGGATGAAGAAAATGAG
1 AAAAAGGAGGAAGAAAATGAG
*
49497349 AAAAAGGGAGGAAGAGAATGA
1 AAAAA-GGAGGAAGAAAATGA
49497370 AGGAAGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.07
Consensus pattern (21 bp):
AAAAAGGAGGAAGAAAATGAG
Found at i:49499291 original size:23 final size:22
Alignment explanation
Indices: 49499265--49499329 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
49499255 CCCCTCCGCC
* *
49499265 TTTTAATTTATTTTCAATTAGGT
1 TTTTAATTTATTTTAAATT-CGT
*
49499288 TTTT-TTTTATTTTTAAATTCGT
1 TTTTAATTTA-TTTTAAATTCGT
49499310 TCTTTAATTTATTTTAAATT
1 T-TTTAATTTATTTTAAATT
49499330 TCAATATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 7 0.20
23 24 0.69
24 4 0.11
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTTAATTTATTTTAAATTCGT
Found at i:49510001 original size:44 final size:44
Alignment explanation
Indices: 49509944--49510373 Score: 286
Period size: 44 Copynumber: 9.8 Consensus size: 44
49509934 AAGATGGCAG
*
49509944 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA
* * * *
49509988 ATCCTATCTCCCTGAAGTTGCAG-AGAGCAGA-T--CGCAT-CTA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-TGATA
* * *
49510028 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTATG-TA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAG-CTGATA
* * * *
49510075 TTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-A
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCT-G-ATA
* * * *
49510120 ATCTTATCTCCCTGAAGTTGCAGTAGAGAAAATTAAAGCCGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA
* * *
49510164 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCT--TA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCTGATA
* * * * *
49510207 GATCTTATTTCTCTGAAGTTGC-G-GAGAGCAGATCACATCT-AT-
1 -ATCTTATCTCCCTGAAGTTGCAGTG-GAGCAGATTAAAGCTGATA
* * *
49510249 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-A
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCT-G-ATA
* * *
49510293 ATCTTATCTCCTTGAAGTTACAGTGGAGCAGATTAAAGCCGATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA
* **
49510337 ATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
49510374 ACCTTGGATC
Statistics
Matches: 297, Mismatches: 55, Indels: 68
0.71 0.13 0.16
Matches are distributed among these distances:
39 1 0.00
40 43 0.14
41 16 0.05
42 6 0.02
43 22 0.07
44 109 0.37
45 61 0.21
46 9 0.03
47 30 0.10
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATA
Found at i:49510300 original size:173 final size:173
Alignment explanation
Indices: 49509900--49510454 Score: 746
Period size: 173 Copynumber: 3.2 Consensus size: 173
49509890 ACAGATCGGG
* * *
49509900 TCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAGATCTTATCTCCCTGAAGTTGT
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
* * * *** *
49509965 AGTGGAGCAGATTAAAGCTGATAATCCTATCTCCCTGAAGTTGCAG-AGAGCAGA-TCGCATC-T
66 AGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
* * * * *
49510027 AG-TCTTATCTCCCTGAAGTTGCAGTG-GAGCAGACTAAGTAAGTATGTAT
131 AGATCTTATTTCTCTGAAGTTGC-G-GAGAGCAG----A-TCA-CATCTAT
49510076 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
* * *
49510141 AGTAGAGAAAATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
66 AGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
49510206 AGATCTTATTTCTCTGAAGTTGCGGAGAGCAGATCACATCTAT
131 AGATCTTATTTCTCTGAAGTTGCGGAGAGCAGATCACATCTAT
* *
49510249 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCTTGAAGTTAC
1 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
*
49510314 AGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTT
66 AGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
* * *
49510379 GGATCTTATTTCTCTGAAGTTACGGAGAGCAGATCGCATCTAT
131 AGATCTTATTTCTCTGAAGTTGCGGAGAGCAGATCACATCTAT
*
49510422 TCTTAT-TTCCCTGAAGTTGCAGTG-GAGCAGACT
1 TCTTATCCT-CCTGAAGTTGCAGTGAG-GCAGACT
49510455 AATAGATTAA
Statistics
Matches: 344, Mismatches: 28, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
172 2 0.01
173 197 0.57
174 2 0.01
175 1 0.00
176 104 0.30
177 6 0.02
178 4 0.01
179 10 0.03
180 18 0.05
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (173 bp):
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTT
AGATCTTATTTCTCTGAAGTTGCGGAGAGCAGATCACATCTAT
Found at i:49510444 original size:84 final size:83
Alignment explanation
Indices: 49510172--49510448 Score: 244
Period size: 84 Copynumber: 3.2 Consensus size: 83
49510162 TAATCCTATC
* *
49510172 TCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATTTCTCTGAAGTTGCGGAGAGCA
1 TCCCTGAAGTTGCAGTGGAG-GGATTAAAACCTTGGATCTTATTTCTCTGAAGTTACGGAGAGCA
*
49510237 GATCACATCTATTCTTA-T
65 GATCGCATCTATTCTTATT
* * * *
49510255 CCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGA---TGGCAAATCTTATCTC-CTTGAAGTTACA
1 TC-CCTGAAGTTGCAGTGGAGG--GA-TTAAAACCTTGG---ATCTTATTTCTC-TGAAGTTAC-
* *** * * *
49510315 GTG-GAGCAGATTAAAGCCGATAATCCTATC
57 G-GAGAGCAGA-T--CGCATCTATTCTTATT
49510345 TCCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGGATCTTATTTCTCTGAAGTTACGGAGAGCA
1 TCCCTGAAGTTGCAGTGGAG-GGATTAAAACCTTGGATCTTATTTCTCTGAAGTTACGGAGAGCA
49510410 GATCGCATCTATTCTTATT
65 GATCGCATCTATTCTTATT
49510429 TCCCTGAAGTTGCAGTGGAG
1 TCCCTGAAGTTGCAGTGGAG
49510449 CAGACTAATA
Statistics
Matches: 148, Mismatches: 25, Indels: 41
0.69 0.12 0.19
Matches are distributed among these distances:
82 3 0.02
83 4 0.03
84 46 0.31
85 21 0.14
86 10 0.07
87 10 0.07
88 22 0.15
89 24 0.16
90 4 0.03
91 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (83 bp):
TCCCTGAAGTTGCAGTGGAGGGATTAAAACCTTGGATCTTATTTCTCTGAAGTTACGGAGAGCAG
ATCGCATCTATTCTTATT
Found at i:49519120 original size:18 final size:18
Alignment explanation
Indices: 49519097--49519296 Score: 193
Period size: 18 Copynumber: 11.1 Consensus size: 18
49519087 TAAGACACGT
*
49519097 ATAATAACATATGTTCAC
1 ATAATAACATAGGTTCAC
***
49519115 ATAATAACATAGGTTTGT
1 ATAATAACATAGGTTCAC
*
49519133 ATGATAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
* *
49519151 ATAACAACATAGGTTCCC
1 ATAATAACATAGGTTCAC
**
49519169 ATAATAACATAGGTTCGT
1 ATAATAACATAGGTTCAC
* * *
49519187 ATGATAACATAAGCTCAC
1 ATAATAACATAGGTTCAC
* **
49519205 ATGATAACATAGGTTTGC
1 ATAATAACATAGGTTCAC
*
49519223 ATAACAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
* **
49519241 ATAATATCATAGGTTCGT
1 ATAATAACATAGGTTCAC
* **
49519259 ATAATAACATAAGTTTGC
1 ATAATAACATAGGTTCAC
*
49519277 ATAAGAACATAGGTTCAC
1 ATAATAACATAGGTTCAC
49519295 AT
1 AT
49519297 GAAATATGGG
Statistics
Matches: 143, Mismatches: 39, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 143 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (18 bp):
ATAATAACATAGGTTCAC
Found at i:49519179 original size:54 final size:54
Alignment explanation
Indices: 49519097--49519292 Score: 221
Period size: 54 Copynumber: 3.6 Consensus size: 54
49519087 TAAGACACGT
* * *
49519097 ATAATAACATATGTTCACATAATAACATAGGTTTGTATGATAACATAGGTTCAC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * * *
49519151 ATAACAACATAGGTTCCCATAATAACATAGGTTCGTATGATAACATAAGCTCAC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * * ** * * **
49519205 ATGATAACATAGGTTTGCATAACAACATAGGTTCACATAATATCATAGGTTCGT
1 ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
* * *
49519259 ATAATAACATAAGTTTGCATAAGAACATAGGTTC
1 ATAATAACATAGGTTCGCATAATAACATAGGTTC
49519293 ACATGAAATA
Statistics
Matches: 120, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (54 bp):
ATAATAACATAGGTTCGCATAATAACATAGGTTCGTATGATAACATAGGTTCAC
Found at i:49527828 original size:28 final size:29
Alignment explanation
Indices: 49527719--49527832 Score: 133
Period size: 30 Copynumber: 3.9 Consensus size: 29
49527709 GGCATACAAC
* * *
49527719 ATACAGTATC-AGTCTGGGCCTGAGCCCT
1 ATACAGTATCAAGTGTGGGCCTTAGCCCA
* *
49527747 ATACAGTAGCAGAGTGTGGGCCATAGCCCA
1 ATACAGTATCA-AGTGTGGGCCTTAGCCCA
* *
49527777 ATACTGTAACAGAGTGTGGGCCTTAGCCCA
1 ATACAGTATCA-AGTGTGGGCCTTAGCCCA
49527807 ATACAGTATC-AGTGTGGGCCTTAGCC
1 ATACAGTATCAAGTGTGGGCCTTAGCC
49527833 GAAAATAGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 25 0.34
30 49 0.66
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (29 bp):
ATACAGTATCAAGTGTGGGCCTTAGCCCA
Found at i:49527842 original size:28 final size:29
Alignment explanation
Indices: 49527759--49527848 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
49527749 ACAGTAGCAG
* * *
49527759 AGTGTGGGCCATAGCCCAATACTGTAA-C
1 AGTGTGGGCCTTAGCCCAAAACAGTAATC
*
49527787 AGAGTGTGGGCCTTAGCCCAATACAGT-ATC
1 --AGTGTGGGCCTTAGCCCAAAACAGTAATC
* *
49527817 AGTGTGGGCCTTAGCCGAAAATAGTAATC
1 AGTGTGGGCCTTAGCCCAAAACAGTAATC
49527846 AGT
1 AGT
49527849 ACAAATGTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 22 0.42
29 7 0.13
30 24 0.45
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (29 bp):
AGTGTGGGCCTTAGCCCAAAACAGTAATC
Found at i:49528274 original size:27 final size:27
Alignment explanation
Indices: 49528227--49528313 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 27
49528217 TATAACGGTC
49528227 ATTTTACCCTAT--AGGGCTATTTTAGTA
1 ATTTTACCCT-TCGAGGG-TATTTTAGTA
* *
49528254 GTTTTACCCTTCGAGGGTA-TTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTAG-TA
*
49528281 ATTTTACCCTTCGAGGGTATTTGAGTA
1 ATTTTACCCTTCGAGGGTATTTTAGTA
49528308 ATTTTA
1 ATTTTA
49528314 GTGGCCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 5 0.10
27 39 0.76
28 7 0.14
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTTAGTA
Found at i:49531031 original size:73 final size:73
Alignment explanation
Indices: 49530946--49531171 Score: 452
Period size: 73 Copynumber: 3.1 Consensus size: 73
49530936 GGAATCTCTT
49530946 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
49531011 GGAAACTA
66 GGAAACTA
49531019 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
49531084 GGAAACTA
66 GGAAACTA
49531092 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
1 AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
49531157 GGAAACTA
66 GGAAACTA
49531165 AAAAATT
1 AAAAATT
49531172 TATAGACTTT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 153 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (73 bp):
AAAAATTAAATTCTTTTGTAAGTTAGCATTACTTGAGATGAGAAATGAATTAAGTTTAGGGGTGT
GGAAACTA
Found at i:49531936 original size:27 final size:26
Alignment explanation
Indices: 49531900--49531950 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
49531890 CTCATCCATT
49531900 TCTCTCATTTTCTC-TTCTCCCATTTGC
1 TCTCTCATTTTC-CATT-TCCCATTTGC
*
49531927 TCTCTTATTTTCCATTTCCCATTT
1 TCTCTCATTTTCCATTTCCCATTT
49531951 TTGATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.10, C:0.33, G:0.02, T:0.55
Consensus pattern (26 bp):
TCTCTCATTTTCCATTTCCCATTTGC
Found at i:49563628 original size:15 final size:16
Alignment explanation
Indices: 49563608--49563637 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49563598 TACTCATTAA
49563608 AAATTTTAA-ACATAT
1 AAATTTTAACACATAT
49563623 AAATTTTAACACATA
1 AAATTTTAACACATA
49563638 ATTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTTTAACACATAT
Found at i:49582222 original size:12 final size:11
Alignment explanation
Indices: 49582180--49582238 Score: 72
Period size: 10 Copynumber: 5.6 Consensus size: 11
49582170 AGTTTTTTTC
49582180 AAAAATT-AAA
1 AAAAATTCAAA
49582190 AAAAA--CAAA
1 AAAAATTCAAA
*
49582199 AAAAACTC-AA
1 AAAAATTCAAA
49582209 AAAAATTCAAA
1 AAAAATTCAAA
49582220 AAAAATTCGAAA
1 AAAAATTC-AAA
49582232 AAAAATT
1 AAAAATT
49582239 AGTTTCCATT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
9 8 0.19
10 14 0.33
11 11 0.26
12 10 0.23
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (11 bp):
AAAAATTCAAA
Found at i:49598154 original size:42 final size:42
Alignment explanation
Indices: 49598080--49598265 Score: 207
Period size: 42 Copynumber: 4.4 Consensus size: 42
49598070 ACGTCGCTAA
*
49598080 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCT-AAAGATCATGTT
1 CTTTAGCGGCGCTTA-AG-AAAAAACGCCGCTAAAAG-TCATGTT
*
49598124 CTTTAACGGCGCTTAAGAAAAAACGCCGCT-AAAGATCATGTT
1 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAAG-TCATGTT
** * *
49598166 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAAGAA-AAAACGCCGCTAAAAGTCATGTT
* ***
49598209 CTATAGCGGCGCTTATTCAAAAACGCCGCTAAAAGT-AGTGTT
1 CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAAGTCA-TGTT
49598251 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
49598266 TTTCACAAAC
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 75 0.60
43 32 0.26
44 17 0.14
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAAGAAAAAACGCCGCTAAAAGTCATGTT
Found at i:49598278 original size:85 final size:85
Alignment explanation
Indices: 49598101--49598264 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
49598091 CTTACAGAAA
* *
49598101 AAAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTT
1 AAAACGCCGCTAAAGATAATGTTCTATAACGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTT
49598166 CTTTAGCGGCGCTTTGGAAG
66 CTTTAGCGGCGCTTTGGAAG
* * ***
49598186 AAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATTCAAAAACGCCGCTAAA-AGT-AGT
1 AAAACGCCGCTAAAGA-TAATGTTCTATAACGGCGCTTAAGAAAAAACGCCGCTAAAGA-TCA-T
49598248 GTTCTTTAGCGGCGCTT
63 GTTCTTTAGCGGCGCTT
49598265 ATTTCACAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 3 0.04
85 66 0.96
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (85 bp):
AAAACGCCGCTAAAGATAATGTTCTATAACGGCGCTTAAGAAAAAACGCCGCTAAAGATCATGTT
CTTTAGCGGCGCTTTGGAAG
Found at i:49602640 original size:21 final size:22
Alignment explanation
Indices: 49602614--49602658 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
49602604 CAAAATCTAA
49602614 ATGCAAAATCA-TTTTTTACGG
1 ATGCAAAATCATTTTTTTACGG
49602635 ATGCAAAATCATTTTTTTACGG
1 ATGCAAAATCATTTTTTTACGG
49602657 AT
1 AT
49602659 ACATAGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ATGCAAAATCATTTTTTTACGG
Found at i:49603118 original size:172 final size:170
Alignment explanation
Indices: 49602816--49603158 Score: 460
Period size: 172 Copynumber: 2.0 Consensus size: 170
49602806 TGATTGTTGC
* *
49602816 GGCAGAGGAGACCGATGGAGGGAGACGGTGATACGCCAGAGGAAACGGCAACGTTGCAAGAGGTC
1 GGCAGAGGAGACCCACGGAGGGAGACGGTGATACGCCAGAGGAAACGGCAACGTTGCAAGAGGTC
* * * *
49602881 GGGTTTGGGAAAATGTGGATTAGGGGAATTTCTCAATATTTCAGGGAGAAATGGATTTTGGGGAT
66 GGCTTTGGGAAAATCTGGATTAGGGGAAATTCTCAAGATTTCAGGGAGAAATGGATTTTGGGGAT
* * *
49602946 AAGTCACAATAGTTGGGG-TTTAAGTTTCGGTTAAATGTATGG
131 AAGTCAC--GA-TTGGGGCTCTAAGTTTCGGTAAAATGTATGG
* * *
49602988 GGCAGAGGAGACCCACGGAGGGAGACGGTGATGCGGCAGAGGAAATGGCAACGTTGCAAGAGGTC
1 GGCAGAGGAGACCCACGGAGGGAGACGGTGATACGCCAGAGGAAACGGCAACGTTGCAAGAGGTC
* * **
49603053 GGCTTTGGGGAAATCTGGATTAGGGGAAATT-T-AGGGATTTGGGGGAG-AATGGGATTTTGGGG
66 GGCTTTGGGAAAATCTGGATTAGGGGAAATTCTCA-AGATTTCAGGGAGAAAT-GGATTTT-GGG
49603115 GATAAGTCACGATTGGGGCTCTAAGTTTCGGTAAAATGTATGG
128 GATAAGTCACGATTGGGGCTCTAAGTTTCGGTAAAATGTATGG
49603158 G
1 G
49603159 AAAAAAACGA
Statistics
Matches: 151, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
169 6 0.04
170 28 0.19
171 17 0.11
172 100 0.66
ACGTcount: A:0.28, C:0.11, G:0.38, T:0.23
Consensus pattern (170 bp):
GGCAGAGGAGACCCACGGAGGGAGACGGTGATACGCCAGAGGAAACGGCAACGTTGCAAGAGGTC
GGCTTTGGGAAAATCTGGATTAGGGGAAATTCTCAAGATTTCAGGGAGAAATGGATTTTGGGGAT
AAGTCACGATTGGGGCTCTAAGTTTCGGTAAAATGTATGG
Found at i:49603744 original size:25 final size:23
Alignment explanation
Indices: 49603702--49603751 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
49603692 TTACATCAAT
49603702 ATATTTTTATATTGAATAAATATAA
1 ATATTTTTATATTGAAT--ATATAA
*
49603727 ATATTTTTGTA-TGCAATATATAA
1 ATATTTTTATATTG-AATATATAA
49603750 AT
1 AT
49603752 GAAAAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.35
24 2 0.09
25 13 0.57
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
ATATTTTTATATTGAATATATAA
Found at i:49604054 original size:14 final size:13
Alignment explanation
Indices: 49604030--49604085 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 13
49604020 CCTAAACGCC
49604030 AAACCTAAAACTC-T
1 AAACCT-AAAC-CAT
*
49604044 AAACTCTAAACCGT
1 AAAC-CTAAACCAT
49604058 AAACCCTAAACCAT
1 AAA-CCTAAACCAT
49604072 AAACCTAAACCAT
1 AAACCTAAACCAT
49604085 A
1 A
49604086 TTTTTGAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
13 12 0.32
14 23 0.61
15 3 0.08
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (13 bp):
AAACCTAAACCAT
Found at i:49604054 original size:21 final size:20
Alignment explanation
Indices: 49604020--49604080 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
49604010 AATCTTAAAT
*
49604020 CCTAAACGCCAAACCTAAAAC
1 CCTAAAC-CTAAACCTAAAAC
*
49604041 TCTAAACTCTAAACCGT-AAAC
1 CCTAAAC-CTAAACC-TAAAAC
49604062 CCTAAACCATAAACCTAAA
1 CCTAAACC-TAAACCTAAA
49604081 CCATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.48, C:0.33, G:0.03, T:0.16
Consensus pattern (20 bp):
CCTAAACCTAAACCTAAAAC
Found at i:49604444 original size:16 final size:15
Alignment explanation
Indices: 49604423--49604455 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
49604413 CCCTAACTGT
49604423 AACCCCTAATCCCCTA
1 AACCCCTAA-CCCCTA
49604439 AACCCCTAACCCCTA
1 AACCCCTAACCCCTA
49604454 AA
1 AA
49604456 GCATAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.15
Consensus pattern (15 bp):
AACCCCTAACCCCTA
Found at i:49604451 original size:7 final size:7
Alignment explanation
Indices: 49604422--49604475 Score: 54
Period size: 7 Copynumber: 7.4 Consensus size: 7
49604412 ACCCTAACTG
49604422 TAACCCC
1 TAACCCC
49604429 TAATCCCC
1 TAA-CCCC
49604437 TAAACCCC
1 T-AACCCC
49604445 TAACCCC
1 TAACCCC
** *
49604452 TAAAGCA
1 TAACCCC
*
49604459 TAACACC
1 TAACCCC
49604466 TAACCCC
1 TAACCCC
49604473 TAA
1 TAA
49604476 ACTTTAAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 26 0.68
8 10 0.26
9 2 0.05
ACGTcount: A:0.37, C:0.44, G:0.02, T:0.17
Consensus pattern (7 bp):
TAACCCC
Found at i:49604974 original size:75 final size:77
Alignment explanation
Indices: 49604832--49604975 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 77
49604822 CCGCTAAAGT
* * * *
49604832 AAGCATTAGCGGCGCTTTACTAGAAAACGCTGCTAACGCCATTGAAAGTTAAGAAAACGGTGCCG
1 AAGCATTAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCATCGAAAGATAAGAAAACGGTGCCG
49604897 TTGGGCACCCCC
66 TTGGGCACCCCC
* ** *
49604909 AAGCATTAGCGGCGCTTCACTA-AAAACGCCGCTAAGGCC-TCGAAAGATCTGAAAACGGTGTCG
1 AAGCATTAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCATCGAAAGATAAGAAAACGGTGCCG
49604972 TTGG
66 TTGG
49604976 ACATATGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
75 23 0.39
76 15 0.25
77 21 0.36
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (77 bp):
AAGCATTAGCGGCGCTTCACTAGAAAACGCCGCTAACGCCATCGAAAGATAAGAAAACGGTGCCG
TTGGGCACCCCC
Found at i:49605181 original size:72 final size:72
Alignment explanation
Indices: 49605074--49605220 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 72
49605064 AAAGCTGAGA
* * * *
49605074 AAACAACACCGTTTGGCTTAGGTTTTTTAGCGGCGCTTCCCCAAAAACGCCGCTAAAT-CCCAAA
1 AAACAACACCGTTTGGCTTAGGATTATTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAA
49605138 AACTACGG
66 AAC-ACGG
* * * ** *
49605146 AAACGACACCGTTTGGCTTAGGATTATTAGTGGCGCTTGATTAAAAACGTCACTAAATCCCCAAA
1 AAACAACACCGTTTGGCTTAGGATTATTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAA
49605211 AACACGG
66 AACACGG
49605218 AAA
1 AAA
49605221 TGGTGTCGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 55 0.86
73 9 0.14
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (72 bp):
AAACAACACCGTTTGGCTTAGGATTATTAGCGGCGCTTCACCAAAAACGCCACTAAATCCCCAAA
AACACGG
Found at i:49607938 original size:12 final size:12
Alignment explanation
Indices: 49607921--49607964 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
49607911 AACTAATCCT
49607921 CTCTCAAATTTC
1 CTCTCAAATTTC
49607933 CTCTCAAATTTC
1 CTCTCAAATTTC
49607945 CT-TCAAAATTT-
1 CTCTC-AAATTTC
49607956 CTCTCAAAT
1 CTCTCAAAT
49607965 CCATATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:49608162 original size:14 final size:15
Alignment explanation
Indices: 49608130--49608161 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49608120 ATTTTTAAAA
49608130 TTTATTTAAGAATTT
1 TTTATTTAAGAATTT
*
49608145 TTTATTTATGAATTT
1 TTTATTTAAGAATTT
49608160 TT
1 TT
49608162 AGATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTATTTAAGAATTT
Found at i:49608241 original size:107 final size:107
Alignment explanation
Indices: 49608111--49608319 Score: 312
Period size: 107 Copynumber: 2.0 Consensus size: 107
49608101 ATGGTAAGCG
*
49608111 TTAAATATAATTTTTAAAATTTATTTAAGA-ATTTTTTATTTATGAATTTTTAGATAATTATTAA
1 TTAAATATAAATTTTAAAATTTATTTAAGATA-TTTTTATTTATGAATTTTTAGATAATTATTAA
* * **
49608175 TTTATTATTTGTTATAAAAGTCTGTAGATCGGGTATTGAAGTA
65 ATTATTATTTGTTATAAAAGGCTAAAGATCGGGTATTGAAGTA
* * * *
49608218 TTAAATTTAAATTTTAAATTTTATTTAAGATATTTTTATTTATGTATTTTTAGATATTTATTAAA
1 TTAAATATAAATTTTAAAATTTATTTAAGATATTTTTATTTATGAATTTTTAGATAATTATTAAA
*
49608283 TTATTTTTTGTTATAAAAGGCTAAAGATCGGGTATTG
66 TTATTATTTGTTATAAAAGGCTAAAGATCGGGTATTG
49608320 GAATGCAATA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 90 0.99
108 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (107 bp):
TTAAATATAAATTTTAAAATTTATTTAAGATATTTTTATTTATGAATTTTTAGATAATTATTAAA
TTATTATTTGTTATAAAAGGCTAAAGATCGGGTATTGAAGTA
Found at i:49608265 original size:14 final size:15
Alignment explanation
Indices: 49608236--49608269 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49608226 AAATTTTAAA
49608236 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
49608251 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
49608265 TTTTA
1 TTTTA
49608270 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:49609921 original size:18 final size:18
Alignment explanation
Indices: 49609888--49609922 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49609878 AGGTATGTTT
* *
49609888 CCTAACCCTTATATGTAC
1 CCTAACCCGTACATGTAC
49609906 CCTAACCCGTACATGTA
1 CCTAACCCGTACATGTA
49609923 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (18 bp):
CCTAACCCGTACATGTAC
Found at i:49610429 original size:22 final size:23
Alignment explanation
Indices: 49610396--49610444 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
49610386 ATTTGATTAA
49610396 AATTAAAAACCCTAACCTAATTC
1 AATTAAAAACCCTAACCTAATTC
*
49610419 AATT-AAAACCCTAACCTAATTT
1 AATTAAAAACCCTAACCTAATTC
49610441 AATT
1 AATT
49610445 TAATTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (23 bp):
AATTAAAAACCCTAACCTAATTC
Found at i:49610447 original size:23 final size:23
Alignment explanation
Indices: 49610396--49610568 Score: 105
Period size: 23 Copynumber: 6.9 Consensus size: 23
49610386 ATTTGATTAA
* *
49610396 AATTAAAAACCCTAACCTAATTC
1 AATTTAAAACCCTAACCTAATTT
49610419 AA-TTAAAACCCTAACCTAATTT
1 AATTTAAAACCCTAACCTAATTT
**** **
49610441 AATTTAATTTAATTAAAAACCATAACCT
1 AATTTAA---AA-CCCTAACC-TAATTT
49610469 AATTTAATTTAAAACCCTAACCTAATTT
1 AATTT-A---A-AACCCTAACCTAATTT
* *
49610497 AATTAAAAACCCTAACCTAAATT
1 AATTTAAAACCCTAACCTAATTT
*
49610520 AATTTAATTACAAACTCTAACCTAATTT
1 AA--T--TTA-AAACCCTAACCTAATTT
49610548 AATTTAAAACCCTAACCTAAT
1 AATTTAAAACCCTAACCTAAT
49610569 NNNNNNNNNN
Statistics
Matches: 114, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
22 20 0.18
23 37 0.32
24 4 0.04
25 1 0.01
26 3 0.03
27 7 0.06
28 34 0.30
29 5 0.04
30 2 0.02
32 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (23 bp):
AATTTAAAACCCTAACCTAATTT
Found at i:49610467 original size:33 final size:32
Alignment explanation
Indices: 49610413--49610480 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
49610403 AACCCTAACC
*
49610413 TAATTCAATTAAAACCCTAACCTAATTTAATT
1 TAATTCAATTAAAACCATAACCTAATTTAATT
*
49610445 TAATTTAATTAAAAACCATAACCTAATTTAATT
1 TAATTCAATT-AAAACCATAACCTAATTTAATT
49610478 TAA
1 TAA
49610481 AACCCTAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (32 bp):
TAATTCAATTAAAACCATAACCTAATTTAATT
Found at i:49610471 original size:28 final size:28
Alignment explanation
Indices: 49610440--49610554 Score: 124
Period size: 28 Copynumber: 4.5 Consensus size: 28
49610430 TAACCTAATT
*
49610440 TAATTTAATTTAATTAAAAACCATAACC
1 TAATTTAATTTAATTAAAAACCCTAACC
49610468 TAATTTAA--T--TT-AAAACCCTAACC
1 TAATTTAATTTAATTAAAAACCCTAACC
49610491 -----TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTTAATTAAAAACCCTAACC
* * *
49610514 TAAATTAATTTAATTACAAACTCTAACC
1 TAATTTAATTTAATTAAAAACCCTAACC
49610542 TAATTTAATTTAA
1 TAATTTAATTTAA
49610555 AACCCTAACC
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.04
20 1 0.01
22 2 0.03
23 23 0.32
24 2 0.03
26 1 0.01
28 41 0.56
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATTTAATTTAATTAAAAACCCTAACC
Found at i:49610497 original size:56 final size:55
Alignment explanation
Indices: 49610396--49610500 Score: 183
Period size: 56 Copynumber: 1.9 Consensus size: 55
49610386 ATTTGATTAA
*
49610396 AATTAAAAACCCTAACCTAATTCAATTAAAACCCTAACCTAATTTAATTTAATTT
1 AATTAAAAACCATAACCTAATTCAATTAAAACCCTAACCTAATTTAATTTAATTT
*
49610451 AATTAAAAACCATAACCTAATTTAATTTAAAACCCTAACCTAATTTAATT
1 AATTAAAAACCATAACCTAATTCAA-TTAAAACCCTAACCTAATTTAATT
49610501 AAAAACCCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 23 0.49
56 24 0.51
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (55 bp):
AATTAAAAACCATAACCTAATTCAATTAAAACCCTAACCTAATTTAATTTAATTT
Found at i:49610523 original size:51 final size:49
Alignment explanation
Indices: 49610445--49610568 Score: 166
Period size: 51 Copynumber: 2.6 Consensus size: 49
49610435 TAATTTAATT
*
49610445 TAATTTAATTAAAAACCATAACC---TAATTTAATTTA-AAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCTAATAATTTAA-TTACAAACCCTAACC
*
49610491 TAATTTAATTAAAAACCCTAACCTAAATTAATTTAATTACAAACTCTAACC
1 TAATTTAATTAAAAACCCTAACCT-AA-TAATTTAATTACAAACCCTAACC
*
49610542 TAATTTAATTTAAAACCCTAACCTAAT
1 TAATTTAATTAAAAACCCTAACCTAAT
49610569 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
46 22 0.32
49 1 0.01
50 5 0.07
51 41 0.59
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (49 bp):
TAATTTAATTAAAAACCCTAACCTAATAATTTAATTACAAACCCTAACC
Found at i:49611056 original size:23 final size:24
Alignment explanation
Indices: 49611030--49611149 Score: 109
Period size: 23 Copynumber: 4.8 Consensus size: 24
49611020 AAACCCTAAC
*
49611030 CTAATTTAATTTAATTAAAAACTCTAA
1 CTAATTTAATTTAATT-AAAA-TC-CA
49611057 CCTAATTTAATTTAATTAAAATCCCTAA
1 -CTAATTTAATTTAATTAAAAT-CC--A
49611085 CCTAATTTAATTTAATTAAAATCC-
1 -CTAATTTAATTTAATTAAAATCCA
**
49611109 CTAACCTAATTTAATTAAAATCC-
1 CTAATTTAATTTAATTAAAATCCA
**
49611132 CTAACCTAATTTAATTAA
1 CTAATTTAATTTAATTAA
49611150 TGTAAAAACC
Statistics
Matches: 86, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
23 39 0.45
26 1 0.01
27 7 0.08
28 39 0.45
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (24 bp):
CTAATTTAATTTAATTAAAATCCA
Found at i:49611056 original size:28 final size:28
Alignment explanation
Indices: 49611012--49611164 Score: 219
Period size: 28 Copynumber: 5.6 Consensus size: 28
49611002 NNNNNNNNNN
49611012 TTAATTAAAAACCCTAACCTAATTTAAT
1 TTAATTAAAAACCCTAACCTAATTTAAT
*
49611040 TTAATTAAAAACTCTAACCTAATTTAAT
1 TTAATTAAAAACCCTAACCTAATTTAAT
*
49611068 TTAATTAAAATCCCTAACCTAATTTAAT
1 TTAATTAAAAACCCTAACCTAATTTAAT
*
49611096 TTAATTAAAATCCCTAACC-----TAAT
1 TTAATTAAAAACCCTAACCTAATTTAAT
*
49611119 TTAATTAAAATCCCTAACCTAATTTAA-
1 TTAATTAAAAACCCTAACCTAATTTAAT
49611146 TTAATGTAAAAACCCTAAC
1 TTAAT-TAAAAACCCTAAC
49611165 ATAACTCAGC
Statistics
Matches: 115, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
23 23 0.20
27 5 0.04
28 87 0.76
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (28 bp):
TTAATTAAAAACCCTAACCTAATTTAAT
Found at i:49611091 original size:51 final size:49
Alignment explanation
Indices: 49611012--49611164 Score: 171
Period size: 51 Copynumber: 2.9 Consensus size: 49
49611002 NNNNNNNNNN
* **
49611012 TTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACTCTAACCTAATTTAAT
1 TTAATTAAAATCCCTAACCTAATTTAA-TTAA-T-AAAA-TC---CCTAACCTAAT
49611068 TTAATTAAAATCCCTAACCTAATTTAATTTAATTAAAATCCCTAACCTAAT
1 TTAATTAAAATCCCTAACCTAATTTAA-TTAA-TAAAATCCCTAACCTAAT
*
49611119 TTAATTAAAATCCCTAACCTAATTTAATTAATGTAAAAACCCTAAC
1 TTAATTAAAATCCCTAACCTAATTTAATTAA--TAAAATCCCTAAC
49611165 ATAACTCAGC
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
50 4 0.04
51 48 0.53
54 2 0.02
55 4 0.04
56 33 0.36
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (49 bp):
TTAATTAAAATCCCTAACCTAATTTAATTAATAAAATCCCTAACCTAAT
Found at i:49611248 original size:56 final size:56
Alignment explanation
Indices: 49611177--49611285 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 56
49611167 AACTCAGCGG
* ** *
49611177 ATTTGATAATCTTACTAACCATTAACACACTTTTTTGGGCT-TAATAATTTTACATA
1 ATTTGATAATCTTACTAACCA-TAACAAAAGTTTTTGGGATGTAATAATTTTACATA
49611233 ATTTGATAAGT-TTACTAACCATAACAAAAGTTTTTGGGATGTAATAATTTTAC
1 ATTTGATAA-TCTTACTAACCATAACAAAAGTTTTTGGGATGTAATAATTTTAC
49611286 CTAGTTTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
55 15 0.32
56 31 0.66
57 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (56 bp):
ATTTGATAATCTTACTAACCATAACAAAAGTTTTTGGGATGTAATAATTTTACATA
Found at i:49614066 original size:126 final size:125
Alignment explanation
Indices: 49613842--49614086 Score: 409
Period size: 126 Copynumber: 2.0 Consensus size: 125
49613832 CCACGAGGGC
*
49613842 GCGATTTGACACTATTTGCTCAGAAACGCCAAAAAATAATTATTTCCTACATGACCAATTATAGC
1 GCGATTTGACACTATTTGCTCAGAAACGCCAAAAAATAATTATTTCCTACATGACCAACTATAGC
* *
49613907 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
* * * *
49613967 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTGACACTATTTGCTCAG-AAACGCCAAAAAATAATTATTTCCTACATGACCAACTATAG
*
49614032 CGAAATCGCGTCCATGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTG
65 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTG
49614087 CTGGAGGCGA
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
125 21 0.19
126 90 0.81
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (125 bp):
GCGATTTGACACTATTTGCTCAGAAACGCCAAAAAATAATTATTTCCTACATGACCAACTATAGC
GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTATCA
Found at i:49614097 original size:126 final size:125
Alignment explanation
Indices: 49613842--49614124 Score: 408
Period size: 126 Copynumber: 2.3 Consensus size: 125
49613832 CCACGAGGGC
* * *
49613842 GCGATTTGACACTATTTGCTCAGAAACGCCAAAAAATAATTATTTCCTACATGACCAATTATAGC
1 GCGATTTCACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAGC
* * * *
49613907 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
* * *
49613967 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAATAATTATTTCCTACATGACCAACTGTAG
1 GCGATTTCACACTATTTGCTCAG-AAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAG
* *
49614032 CGAAATCGCGTCCATGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCT-GGA
65 CGAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
*
49614092 GGCGATTTCCCACTATTTGAC-CAGAAACGTCAA
1 -GCGATTTCACACTATTTG-CTCAGAAACGTCAA
49614125 CTTAAAAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
125 31 0.22
126 109 0.77
127 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (125 bp):
GCGATTTCACACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCCTACATGACCAACTATAGC
GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGCTAGCA
Done.