Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008797.1 Hibiscus syriacus cultivar Beakdansim tig00111942_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1112200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 4 of 5
Found at i:648847 original size:21 final size:23
Alignment explanation
Indices: 648823--648867 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
648813 TATATTTAAG
648823 ATATATCTAA-AA-ATATTTTTA
1 ATATATCTAATAATATATTTTTA
* *
648844 ATATTTTTAATAATATATTTTTA
1 ATATATCTAATAATATATTTTTA
648867 A
1 A
648868 GTGATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 2 0.10
23 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATATCTAATAATATATTTTTA
Found at i:648909 original size:31 final size:31
Alignment explanation
Indices: 648856--648956 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
648846 ATTTTTAATA
* ** *
648856 ATATATTTTTAAGTGATGATAAAGATAAAAT
1 ATATATTTTTAAGTTAAAATAAAAATAAAAT
648887 ATATATTTTTACA-TTAAAATAAAAATAAAAT
1 ATATATTTTTA-AGTTAAAATAAAAATAAAAT
** * *
648918 ATAT-TTAATAAGTTAAAACAAACATAAAAT
1 ATATATTTTTAAGTTAAAATAAAAATAAAAT
648948 ATATATTTT
1 ATATATTTT
648957 AGATATATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 1 0.02
30 24 0.42
31 31 0.54
32 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (31 bp):
ATATATTTTTAAGTTAAAATAAAAATAAAAT
Found at i:662343 original size:28 final size:27
Alignment explanation
Indices: 662284--662347 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
662274 AACCTGAACT
* *
662284 CGACCCGAATATCACACTTAAAAAATC
1 CGACCCGAATATCAAACTTAAAAAAAC
*
662311 TGACCCGAATATCAAACTTAAAAAAAC
1 CGACCCGAATATCAAACTTAAAAAAAC
662338 ACGACCCGAA
1 -CGACCCGAA
662348 CATGATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (27 bp):
CGACCCGAATATCAAACTTAAAAAAAC
Found at i:663900 original size:13 final size:13
Alignment explanation
Indices: 663882--663907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
663872 AATTTTGAGT
663882 TTTTTAAATTTAA
1 TTTTTAAATTTAA
663895 TTTTTAAATTTAA
1 TTTTTAAATTTAA
663908 ACTTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAAATTTAA
Found at i:665611 original size:21 final size:20
Alignment explanation
Indices: 665579--665617 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
665569 ATTAAAATGA
*
665579 ATTAAAAGTTTAATAATTGT
1 ATTAAAAGTTTAAAAATTGT
*
665599 ATTATAAGCTTTAAAAATT
1 ATTAAAAG-TTTAAAAATT
665618 ATGTGACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (20 bp):
ATTAAAAGTTTAAAAATTGT
Found at i:676500 original size:24 final size:24
Alignment explanation
Indices: 676473--676549 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
676463 AAATCATACC
676473 TAATATTTAATTTTTGTTTTATTT
1 TAATATTTAATTTTTGTTTTATTT
* ** *
676497 TAATATTTCA---CCGTTTTGTTT
1 TAATATTTAATTTTTGTTTTATTT
* * *
676518 AAATGTTTATTTTTTGTTTTATTT
1 TAATATTTAATTTTTGTTTTATTT
676542 TAATATTT
1 TAATATTT
676550 CACCGTTAAA
Statistics
Matches: 37, Mismatches: 13, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 14 0.38
24 23 0.62
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.66
Consensus pattern (24 bp):
TAATATTTAATTTTTGTTTTATTT
Found at i:685564 original size:10 final size:10
Alignment explanation
Indices: 685549--685573 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
685539 TTATAATTTT
685549 TTTAAAAATA
1 TTTAAAAATA
685559 TTTAAAAATA
1 TTTAAAAATA
685569 TTTAA
1 TTTAA
685574 TCTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:686098 original size:20 final size:20
Alignment explanation
Indices: 686073--686112 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
686063 AGTTTCCAAT
*
686073 TTCGTAACGTGATAGTCAAA
1 TTCGTAACGCGATAGTCAAA
686093 TTCGTAACGCGATAGTCAAA
1 TTCGTAACGCGATAGTCAAA
686113 CCATGTGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (20 bp):
TTCGTAACGCGATAGTCAAA
Found at i:686309 original size:18 final size:18
Alignment explanation
Indices: 686288--686324 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
686278 GTAATTGGAG
686288 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
686306 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
686324 T
1 T
686325 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:686331 original size:24 final size:24
Alignment explanation
Indices: 686280--686332 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
686270 TTTCATATGT
* * *
686280 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
686304 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
686328 AATTT
1 AATTT
686333 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:686677 original size:39 final size:39
Alignment explanation
Indices: 686634--686720 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
686624 TCTGATGCTC
686634 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
* *
686673 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
686712 ATCAAAATC
1 ATCAAAATC
686721 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAACAAAAGGAA
Found at i:687002 original size:20 final size:20
Alignment explanation
Indices: 686946--687002 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
686936 GATAGCCAAA
* *
686946 TTCGCGTTGCGAATTTAACT
1 TTCGCGTTACGAATTTGACT
*
686966 TTCGAGTTACGAATTTGACT
1 TTCGCGTTACGAATTTGACT
686986 TTCGCGTTACGAATTTG
1 TTCGCGTTACGAATTTG
687003 TACCTTCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
TTCGCGTTACGAATTTGACT
Found at i:687141 original size:66 final size:60
Alignment explanation
Indices: 687061--687200 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 60
687051 TTTTAGAAAC
*
687061 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACACATC-AATT
687126 A
60 A
* * *
687127 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
687187 AACAAATCAACTTT
1 AACAAATCAACTTT
687201 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 19 0.27
61 22 0.31
62 3 0.04
66 26 0.37
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.31
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACACATCAATTA
Found at i:688597 original size:21 final size:20
Alignment explanation
Indices: 688573--688645 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
688563 GCGGGCGGGA
688573 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGA-AGGGG
* *
688594 CCTCTTGAACGGTGGAAGGGA
1 CCTCTTGAACGAT-GAAGGGG
* * *
688615 CTTCTTCAATGATGAGAGGGG
1 CCTCTTGAACGATGA-AGGGG
688636 CCTCTTGAAC
1 CCTCTTGAAC
688646 AATAGGAGGT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 36 0.90
22 2 0.05
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (20 bp):
CCTCTTGAACGATGAAGGGG
Found at i:688615 original size:42 final size:42
Alignment explanation
Indices: 688553--688645 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
688543 GTGAATCGGG
** *
688553 CTCTTGAACGGCGGGCGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGCGGAAGGGACCTCTTCAACGATGACAGGGGC
* * * *
688595 CTCTTGAACGGTGGAAGGGACTTCTTCAATGATGAGAGGGGC
1 CTCTTGAACGGCGGAAGGGACCTCTTCAACGATGACAGGGGC
688637 CTCTTGAAC
1 CTCTTGAAC
688646 AATAGGAGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGCGGAAGGGACCTCTTCAACGATGACAGGGGC
Found at i:688668 original size:42 final size:41
Alignment explanation
Indices: 688569--688671 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 41
688559 AACGGCGGGC
* **
688569 GGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGAA
1 GGGA-CTCTTGAATGATGACAGGGGCCTCTTGAACAATGGAA
* *
688611 GGGACTTCTTCAATGATGAGAGGGGCCTCTTGAACAATAGG-A
1 GGGAC-TCTTGAATGATGACAGGGGCCTCTTGAACAAT-GGAA
*
688653 GGTGTCTCTTGAATGATGA
1 GG-GACTCTTGAATGATGA
688672 TAGGTGCATC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 46 0.90
43 4 0.08
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (41 bp):
GGGACTCTTGAATGATGACAGGGGCCTCTTGAACAATGGAA
Found at i:688834 original size:12 final size:12
Alignment explanation
Indices: 688815--688856 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
688805 GGGCCGCTGA
688815 AAATAAATTAAT
1 AAATAAATTAAT
* *
688827 ACATAAATTAGT
1 AAATAAATTAAT
*
688839 AAATAAATAAAT
1 AAATAAATTAAT
688851 AAATAA
1 AAATAA
688857 TGCTGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:690867 original size:19 final size:19
Alignment explanation
Indices: 690816--690869 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
690806 AGAAGTTTCT
* *
690816 GAAACTTAAATTCGCAATGC
1 GAAAC-TAAAATCGCAACGC
*
690836 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
690856 GAAACTAAAATCGC
1 GAAACTAAAATCGC
690870 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:691151 original size:22 final size:22
Alignment explanation
Indices: 691114--691168 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
691104 TCTGAGAGAT
*
691114 GGAGATA--GACGGATTTCGTC
1 GGAGATAGGGACGAATTTCGTC
691134 GGAGATAGGGACGAATTTCGTC
1 GGAGATAGGGACGAATTTCGTC
*
691156 GGAGATGGGGACG
1 GGAGATAGGGACG
691169 GATGTCGCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 7 0.23
22 24 0.77
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.20
Consensus pattern (22 bp):
GGAGATAGGGACGAATTTCGTC
Found at i:691324 original size:20 final size:20
Alignment explanation
Indices: 691299--691443 Score: 123
Period size: 20 Copynumber: 7.2 Consensus size: 20
691289 GCGTAAAAAC
*
691299 ATTTGACTTTCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
691319 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * * *
691339 ATTTGACTTTTGTGTCGTG-
1 ATTTGACTTTCGCGTTGCGA
*
691358 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* * *
691379 ATTTGATTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
691399 ATTTGACTATCACGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* **
691419 ATTTGACTATCGCAATGCGA
1 ATTTGACTTTCGCGTTGCGA
691439 ATTTG
1 ATTTG
691444 GAAAATCGCA
Statistics
Matches: 97, Mismatches: 24, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 86 0.89
21 4 0.04
22 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:691453 original size:21 final size:20
Alignment explanation
Indices: 691414--691459 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
691404 ACTATCACGT
**
691414 TGCGAATTTGACTATCGCAA
1 TGCGAATTTGAAAATCGCAA
691434 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTT-GAAAATCGCAA
691455 TGCGA
1 TGCGA
691460 TAGTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCGAATTTGAAAATCGCAA
Found at i:698249 original size:16 final size:16
Alignment explanation
Indices: 698228--698263 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
698218 CCGATTCAAT
698228 AAAGGATTATACTTGA
1 AAAGGATTATACTTGA
*
698244 AAAGGATTATGCTTGA
1 AAAGGATTATACTTGA
698260 AAAG
1 AAAG
698264 TGAGATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (16 bp):
AAAGGATTATACTTGA
Found at i:710357 original size:18 final size:17
Alignment explanation
Indices: 710334--710403 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 17
710324 ATATTCATCG
710334 GTGAATATCCAGCAATTA
1 GTGAAT-TCCAGCAATTA
710352 GTGAATTCCAAGACCATATCATCA
1 GTGAATTCC-AG--CA-AT--T-A
*
710376 GTGAATATCCAGCAATCA
1 GTGAAT-TCCAGCAATTA
710394 GTGAATTCCA
1 GTGAATTCCA
710404 AGACCATATC
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
17 7 0.16
18 15 0.35
20 2 0.05
21 4 0.09
22 2 0.05
23 1 0.02
24 9 0.21
25 3 0.07
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (17 bp):
GTGAATTCCAGCAATTA
Found at i:710374 original size:42 final size:42
Alignment explanation
Indices: 710323--710417 Score: 163
Period size: 42 Copynumber: 2.2 Consensus size: 42
710313 TAAGACCATG
* *
710323 CATATTCATCGGTGAATATCCAGCAATTAGTGAATTCCAAGAC
1 CATA-TCATCAGTGAATATCCAGCAATCAGTGAATTCCAAGAC
710366 CATATCATCAGTGAATATCCAGCAATCAGTGAATTCCAAGAC
1 CATATCATCAGTGAATATCCAGCAATCAGTGAATTCCAAGAC
710408 CATATCATCA
1 CATATCATCA
710418 AAAATGCATC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 46 0.92
43 4 0.08
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (42 bp):
CATATCATCAGTGAATATCCAGCAATCAGTGAATTCCAAGAC
Found at i:728113 original size:10 final size:10
Alignment explanation
Indices: 728098--728148 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
728088 TATTATACTT
*
728098 AAAAAAAAAA
1 AAAAAAAAAG
728108 AAAAAAGTAAATG
1 AAAAAA--AAA-G
*
728121 AAAAAAAATG
1 AAAAAAAAAG
728131 AAAAAAAAAG
1 AAAAAAAAAG
728141 AAAAAAAA
1 AAAAAAAA
728149 TAAATAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 24 0.69
11 2 0.06
12 3 0.09
13 6 0.17
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:729387 original size:87 final size:90
Alignment explanation
Indices: 729223--729434 Score: 286
Period size: 89 Copynumber: 2.4 Consensus size: 90
729213 GTCATCCCCA
* *
729223 GACCAGACCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
729288 GGAACCGTGTTATCA-CCTTTAGAT
66 GGAACCGAGTTATCACCCTAAAGAT
* * *
729312 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
*
729375 TGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGTTATCA-CCCTAAAGAT
* * *
729401 GACCAGATTTCCTCATCACGTAGGAGCCGTGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
729435 CCCTTAGACG
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
87 36 0.33
88 1 0.01
89 71 0.66
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTAAAGAT
Found at i:729646 original size:3 final size:3
Alignment explanation
Indices: 729635--729692 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
729625 TTTTTTCCCG
** *
729635 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
729680 TTA TTA TTTA TTA
1 TTA TTA -TTA TTA
729693 CAATTTTTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:732676 original size:18 final size:18
Alignment explanation
Indices: 732653--732698 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
732643 GAGAAAGTAA
*
732653 TAAAGTAGAGAATTTTAT
1 TAAAGTAGAGAACTTTAT
*
732671 TAAAGT-GAAGTACTTTAT
1 TAAAGTAG-AGAACTTTAT
732689 TAAAGTAGAG
1 TAAAGTAGAG
732699 TGTCTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.35
Consensus pattern (18 bp):
TAAAGTAGAGAACTTTAT
Found at i:732952 original size:41 final size:41
Alignment explanation
Indices: 732900--732978 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
732890 ATGTAAAATC
* *
732900 TTGGTGTTTATTTTATTGGGTGATCATTATGCATGTCGCTA
1 TTGGTGCTTATTTTATTGGGGGATCATTATGCATGTCGCTA
* *
732941 TTGGTGCTTATTTTATTGGGGGATTATTATGTATGTCG
1 TTGGTGCTTATTTTATTGGGGGATCATTATGCATGTCG
732979 TTACCTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.16, C:0.08, G:0.27, T:0.49
Consensus pattern (41 bp):
TTGGTGCTTATTTTATTGGGGGATCATTATGCATGTCGCTA
Found at i:734108 original size:30 final size:30
Alignment explanation
Indices: 734072--734139 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
734062 AAAGGGAAAG
734072 CAGGAACACCGAAACATAATGGATGGTTCA
1 CAGGAACACCGAAACATAATGGATGGTTCA
734102 CAGGAACACCGAAACATAATGGATGGTTCA
1 CAGGAACACCGAAACATAATGGATGGTTCA
734132 CAGGAACA
1 CAGGAACA
734140 GCCGGAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.15
Consensus pattern (30 bp):
CAGGAACACCGAAACATAATGGATGGTTCA
Found at i:735889 original size:36 final size:38
Alignment explanation
Indices: 735831--735914 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
735821 GAAAATATTT
*
735831 TATATATAATTAATATAAAAAATATAAAATATTATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATA
735869 TATATATAATTAATATAAAATATATAAAATATTATATA
1 TATATATAATTAATATAAAATATATAAAATATTATATA
735907 TATATATA
1 TATATATA
735915 TAATCGGGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (38 bp):
TATATATAATTAATATAAAATATATAAAATATTATATA
Found at i:739535 original size:26 final size:26
Alignment explanation
Indices: 739484--739536 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
739474 AAAACATGAC
** *
739484 TTAATTTAAGATTAAATCTTTCAAAA
1 TTAATTTAAGATTAAAAATTTAAAAA
739510 TTAA-TTAAGATTAAAAATTATAAAAA
1 TTAATTTAAGATTAAAAATT-TAAAAA
739536 T
1 T
739537 AAGAAGCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
TTAATTTAAGATTAAAAATTTAAAAA
Found at i:742806 original size:31 final size:31
Alignment explanation
Indices: 742771--742829 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
742761 TTGTGTTCAA
*
742771 ATTTAATTATTTATATATTATA-ATATTACAT
1 ATTTAATTATTAATA-ATTATATATATTACAT
*
742802 ATTTAATTATTAATAATTTTATATATTA
1 ATTTAATTATTAATAATTATATATATTA
742830 AATTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTTAATTATTAATAATTATATATATTACAT
Found at i:742900 original size:18 final size:18
Alignment explanation
Indices: 742877--742921 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
742867 ATTTAATAAT
742877 TAATATAATATTTTTTAA
1 TAATATAATATTTTTTAA
742895 TAATATAAGT-TTTTTTAA
1 TAATATAA-TATTTTTTAA
*
742913 -AAAATAATA
1 TAATATAATA
742922 ATTAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 6 0.25
18 16 0.67
19 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATATAATATTTTTTAA
Found at i:743094 original size:20 final size:21
Alignment explanation
Indices: 743047--743099 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
743037 CCGAAGACCC
*
743047 GGGTACCTGGAACTTCTGGTA
1 GGGTACCTGGAACTTCGGGTA
743068 GGGTACCTGGAACTTCGGGTA
1 GGGTACCTGGAACTTCGGGTA
*
743089 -GGTACCCGGAA
1 GGGTACCTGGAA
743100 TTGAACACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGTACCTGGAACTTCGGGTA
Found at i:745217 original size:17 final size:17
Alignment explanation
Indices: 745195--745231 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
745185 TCATTTATCT
745195 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
745212 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
745229 TTC
1 TTC
745232 TGTTGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCACATTAATCTATAC
Found at i:762866 original size:9 final size:9
Alignment explanation
Indices: 762851--762884 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
762841 TAATATTTTA
762851 TATTTAATT
1 TATTTAATT
*
762860 TATTTAA-G
1 TATTTAATT
762868 TATTTAATT
1 TATTTAATT
762877 TATTTAAT
1 TATTTAAT
762885 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:762895 original size:16 final size:16
Alignment explanation
Indices: 762844--762888 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
762834 ATATTTTTAA
*
762844 TATTTTATATTTAATT
1 TATTTAATATTTAATT
762860 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
762877 TATTTAATATTT
1 TATTTAATATTT
762889 TACTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:765167 original size:11 final size:13
Alignment explanation
Indices: 765091--765163 Score: 62
Period size: 13 Copynumber: 5.8 Consensus size: 13
765081 GATGATTTTG
*
765091 TTTTTTTATTATA
1 TTTTTTTATTGTA
765104 TTTTATTTA--GTA
1 TTTT-TTTATTGTA
*
765116 -CTTTTTATTGTA
1 TTTTTTTATTGTA
* * *
765128 GTTGTTTATTGGA
1 TTTTTTTATTGTA
*
765141 CTTTTTTATTGTA
1 TTTTTTTATTGTA
765154 TTTTTTTATT
1 TTTTTTTATT
765164 ATTTATCATT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
10 4 0.09
11 2 0.04
12 5 0.11
13 32 0.68
14 4 0.09
ACGTcount: A:0.18, C:0.03, G:0.10, T:0.70
Consensus pattern (13 bp):
TTTTTTTATTGTA
Found at i:774119 original size:94 final size:93
Alignment explanation
Indices: 773872--774124 Score: 296
Period size: 94 Copynumber: 2.7 Consensus size: 93
773862 AAGCTAAAAA
* * * *
773872 GGTGCGTGAGCTCTGAGATGTATCCCCTCAGTCGCACCATGATGCTTACCTTATC-TTGTG--TG
1 GGTGCGTGAGCTCTGAGATGTATCCCCTCAGCCGCACCATGATGCCTACCTCAACTTTGTGTTTG
* * *
773934 TCACATAGTACTATAGGTAGGCTAGAGG
66 TTACATAGTACTATAGGTAGGATAGAAG
* * * * * **
773962 GGTACGTGAGCTTTGAGATATAGCCCCTCAGCCACACCATGATGCCTACCTCAGTTTGTGTGTTT
1 GGTGCGTGAGCTCTGAGATGTATCCCCTCAGCCGCACCATGATGCCTACCTCAACTT-TGTGTTT
* * *
774027 GTTGCATAGTAGTATAGGTATGATAGAAG
65 GTTACATAGTACTATAGGTAGGATAGAAG
*
774056 GGTGTGTGAGCTCTGAGATGTATCCCCTCAGCCGCACCATGATGCCTACCTCAACTTATGTGTTA
1 GGTGCGTGAGCTCTGAGATGTATCCCCTCAGCCGCACCATGATGCCTACCTCAACTT-TGTGTT-
774121 TGTT
64 TGTT
774125 TGTGTGTTAC
Statistics
Matches: 133, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
90 45 0.34
91 1 0.01
92 4 0.03
94 79 0.59
95 4 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (93 bp):
GGTGCGTGAGCTCTGAGATGTATCCCCTCAGCCGCACCATGATGCCTACCTCAACTTTGTGTTTG
TTACATAGTACTATAGGTAGGATAGAAG
Found at i:778594 original size:3 final size:3
Alignment explanation
Indices: 778586--778663 Score: 72
Period size: 3 Copynumber: 26.0 Consensus size: 3
778576 TTTATTTTTG
** *
778586 TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA ATA TTA TGTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
778631 TTA -TA ATA TTA TTA TTTA TTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TT-A TTA TTA TTA
778664 CAGGCCCAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
2 6 0.10
3 48 0.77
4 8 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:780439 original size:135 final size:135
Alignment explanation
Indices: 780099--780513 Score: 647
Period size: 135 Copynumber: 3.0 Consensus size: 135
780089 ATTTTCATTA
* *
780099 TTATTATATTAAAATAAATTATTTTTATTTTTAAAGAAAATG-TTTTGGTTATTTA-TTTATTTT
1 TTATTATATTAAAAT-AA--ATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTT
780162 TTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAA
63 TTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATA-TTTT---TAAA
780227 TAAATAAATATC
124 TAAATAAATATC
*
780239 TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAACGTTTTTAGTTATTTATTTTATTTTTTA
1 TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTA
* * * *
780304 ATATCGAATAAAAGAGATGTCTTAAGGCACCTAAAAGCTCTTTTTTGATATTTTTAAATAAATAA
66 ATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAATAA
780369 ATATC
131 ATATC
780374 TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTA
1 TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTA
* * *
780439 ATATCGAAGAAAAGAGCTTTCTTAAAGCACCTAGAAG-TCCTTTTCTGATATTTCTAAATAAATA
66 ATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCT-CTTTTCTGATATTTTTAAATAAATA
780503 AATATC
130 AATATC
780509 TTATT
1 TTATT
780514 TATACATATT
Statistics
Matches: 257, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
134 1 0.00
135 146 0.57
137 20 0.08
138 16 0.06
139 59 0.23
140 15 0.06
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (135 bp):
TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTA
ATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAATAA
ATATC
Found at i:780852 original size:13 final size:13
Alignment explanation
Indices: 780834--780859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
780824 ATGGCGACTC
780834 CCAAATTATTTTA
1 CCAAATTATTTTA
780847 CCAAATTATTTTA
1 CCAAATTATTTTA
780860 AAAACCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
CCAAATTATTTTA
Found at i:784321 original size:24 final size:24
Alignment explanation
Indices: 784289--784336 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
784279 AAACACAATA
*
784289 ATTTGAAAA-TTAATATTTTTTTT
1 ATTTGAAAATTTAAAATTTTTTTT
784312 ATTTCGAAAATTTAAAATTTTTTTT
1 ATTT-GAAAATTTAAAATTTTTTTT
784337 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
ATTTGAAAATTTAAAATTTTTTTT
Found at i:784734 original size:21 final size:21
Alignment explanation
Indices: 784708--784788 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
784698 AGAACCCCAG
*
784708 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
784729 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * * *
784749 CAAAGGGGGAATCGGTTCCCTTAT
1 ---GGGGGGAATCGATTCCCCTGT
784773 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
784789 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 10 0.20
21 22 0.44
23 17 0.34
24 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.37, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:792958 original size:21 final size:22
Alignment explanation
Indices: 792924--792967 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
792914 TTTTCATACA
*
792924 TGCATTTGCCTTTTGCAT-CTT
1 TGCATTTGCATTTTGCATACTT
* *
792945 TGCATTTTCATTTTTCATACTT
1 TGCATTTGCATTTTGCATACTT
792967 T
1 T
792968 TATGTTTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.14, C:0.20, G:0.09, T:0.57
Consensus pattern (22 bp):
TGCATTTGCATTTTGCATACTT
Found at i:795236 original size:2 final size:2
Alignment explanation
Indices: 795229--795254 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
795219 TTATCCTTTA
795229 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
795255 CATTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:795583 original size:12 final size:12
Alignment explanation
Indices: 795562--795596 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
795552 AAAGAAGAAG
795562 AAAA-AAACAAA
1 AAAATAAACAAA
795573 AAAATAAACAAA
1 AAAATAAACAAA
795585 AAAATAAACAAA
1 AAAATAAACAAA
795597 CAAACAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAATAAACAAA
Found at i:795587 original size:20 final size:20
Alignment explanation
Indices: 795562--795606 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
795552 AAAGAAGAAG
*
795562 AAAAAAACAAAAAAATAAAC
1 AAAAAAACAAAAAAACAAAC
* *
795582 AAAAAAATAAACAAACAAAC
1 AAAAAAACAAAAAAACAAAC
795602 AAAAA
1 AAAAA
795607 GGAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.84, C:0.11, G:0.00, T:0.04
Consensus pattern (20 bp):
AAAAAAACAAAAAAACAAAC
Found at i:797930 original size:114 final size:114
Alignment explanation
Indices: 797726--797932 Score: 342
Period size: 114 Copynumber: 1.8 Consensus size: 114
797716 CACGTTCTCG
* * * *
797726 TAGTAGAAATAAGGATACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
*
797791 GGTATGAACCCCAAAACCAAGCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAAGCATTGGATTTGAAAGATGAATTTGCTCA
*
797840 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGCTATTTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
* *
797905 GGTAGGAACCCCAGAACCAATCATTGGA
66 GGTAGGAACCCCAAAACCAAGCATTGGA
797933 ATAGGAAGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAACATCTTCTGGAAGTGTTCTTTGAGCTATCTGATCTGGTTC
GGTAGGAACCCCAAAACCAAGCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:798165 original size:31 final size:31
Alignment explanation
Indices: 798122--798184 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
798112 GCACATATAA
* *
798122 AATCTGTCAACTCTGTAATTGATGAATTCAG
1 AATCCGTCAACTCTGCAATTGATGAATTCAG
798153 AATCCGTCAACTCTGCAATTGATGAATTCAG
1 AATCCGTCAACTCTGCAATTGATGAATTCAG
798184 A
1 A
798185 CCACATCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (31 bp):
AATCCGTCAACTCTGCAATTGATGAATTCAG
Found at i:798988 original size:75 final size:76
Alignment explanation
Indices: 798854--799034 Score: 172
Period size: 75 Copynumber: 2.4 Consensus size: 76
798844 TTGAATCAGA
* * * * * * *
798854 AGCAGATATTGGGGTA-GACTGAAAGCCCATTTCAATTAGAATCAGAAATATTGATGTA-TTCTG
1 AGCAAATATTGGGGCATG-CTGAAAACCCATTTCAATCAGAATAAGAAATATTGAGGTATTTCTA
798917 AACATTTATATC
65 AACATTTATATC
* * *
798929 AGCAAAATGTTGGGGCATGCTGAAAACCC-TTTCAATCAGAATGAAG-AATGTTGAGGTATTTTT
1 AGC-AAATATTGGGGCATGCTGAAAACCCATTTCAATCAGAAT-AAGAAATATTGAGGTATTTCT
* *
798992 AAACATTTGTATT
64 AAACATTTATATC
* * *
799005 AGCCAATATTGGGGCATGTTGAAAGCCCAT
1 AGCAAATATTGGGGCATGCTGAAAACCCAT
799035 ATTATCCTGT
Statistics
Matches: 85, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
75 46 0.54
76 38 0.45
77 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (76 bp):
AGCAAATATTGGGGCATGCTGAAAACCCATTTCAATCAGAATAAGAAATATTGAGGTATTTCTAA
ACATTTATATC
Found at i:800214 original size:22 final size:22
Alignment explanation
Indices: 800182--800258 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
800172 ATCTACATTA
*
800182 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
*
800204 TTCAAATATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
800226 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
800248 TTCAAAGATGA
1 TTCAAAGATGA
800259 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:801058 original size:76 final size:76
Alignment explanation
Indices: 800932--801416 Score: 837
Period size: 76 Copynumber: 6.4 Consensus size: 76
800922 CTATTTCCCA
* *
800932 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
800997 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
801008 CATCTGTAAGTCCTACAGTGCATAATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
801073 AGCCTTAGGGT
66 AGCCTTAGGGT
*
801084 CATCTGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
801149 AGCCTTAGGGT
66 AGCCTTAGGGT
801160 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
801225 AGCCTTAGGGT
66 AGCCTTAGGGT
801236 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
801301 AACCTTTGGGT
66 AGCCTTAGGGT
*
801312 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
801377 AACCTTCGGGT
66 AGCCTTAGGGT
**
801388 CATCTGTAAG-CCTTTTAGTGCATGATGTT
1 CATCTGTAAGTCC-TACAGTGCATGATGTT
801417 GTTAAGACCT
Statistics
Matches: 392, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
75 2 0.01
76 390 0.99
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:801578 original size:3 final size:3
Alignment explanation
Indices: 801570--801647 Score: 63
Period size: 3 Copynumber: 26.0 Consensus size: 3
801560 ATTTTTGTTT
** * *
801570 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA ATA TTA -TA CATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
801618 TTA -TA ATA TTA TTA TTTA TTAA TT- TTA TTA
1 TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA
801648 CAGGCCCAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 47 0.77
4 8 0.13
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:803239 original size:136 final size:134
Alignment explanation
Indices: 803088--803495 Score: 657
Period size: 131 Copynumber: 3.0 Consensus size: 134
803078 ATTTTCATTA
*
803088 TTATTATATTAAAATAAATTATTTTTATTTTTAAAGAAAATG-TTTTGGTTATTTA-TTTATTTT
1 TTATTATATTAAAAT-AA--ATTTTTATTTTT-AAGAAAATGTTTTTAGTTATTTATTTTATTTT
* *
803151 TTAATATCGAAGAAAAGAGCTATCTTAAGGCACCTAGAAGCTATTTTCTGATATTTTTAAATAAA
62 TTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAA
803216 TAAATATC
127 TAAATATC
803224 TTATTATATTAAAATAAA--TTT-TTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTAA
1 TTATTATATTAAAATAAATTTTTATTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTAA
803286 TATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAATAAA
66 TATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAATAAA
803351 TATC
131 TATC
803355 TTATTATATTAAAATAAATTTTTATTTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTT
1 TTATTATATTAAAATAAATTTTTA-TTTTTAAGAAAATGTTTTTAGTTATTTATTTTA-TTTTTT
* * *
803420 AATATCGAAGAAAAGAGTTGTCTTAAAGCACCTAGAAG-TCCTTTTCTGATATTTCTAAATAAAT
64 AATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCT-CTTTTCTGATATTTTTAAATAAAT
803484 AAATATC
128 AAATATC
803491 TTATT
1 TTATT
803496 TATACATATT
Statistics
Matches: 258, Mismatches: 6, Indels: 16
0.92 0.02 0.06
Matches are distributed among these distances:
129 9 0.03
130 17 0.07
131 100 0.39
133 4 0.02
135 36 0.14
136 92 0.36
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (134 bp):
TTATTATATTAAAATAAATTTTTATTTTTAAGAAAATGTTTTTAGTTATTTATTTTATTTTTTAA
TATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGCTCTTTTCTGATATTTTTAAATAAATAAA
TATC
Found at i:803826 original size:13 final size:13
Alignment explanation
Indices: 803808--803833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
803798 ATGGCGACTC
803808 CCAAATTATTTTA
1 CCAAATTATTTTA
803821 CCAAATTATTTTA
1 CCAAATTATTTTA
803834 AAAATCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
CCAAATTATTTTA
Found at i:810040 original size:4 final size:4
Alignment explanation
Indices: 810031--810108 Score: 61
Period size: 4 Copynumber: 18.8 Consensus size: 4
810021 ATGTTAGAAG
* *
810031 AAAT AAAT AAAT AAAT AAAT AAAT AAA- ATACT AAAT AAGT CAAAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT AAAT
* *
810079 AGGAAT AAAT AAATT AATT AAAA AAAT AAA
1 A--AAT AAAT AAA-T AAAT AAAT AAAT AAA
810109 AAAAAATGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 2 0.03
4 47 0.80
5 9 0.15
6 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:811860 original size:14 final size:14
Alignment explanation
Indices: 811841--811918 Score: 88
Period size: 14 Copynumber: 5.4 Consensus size: 14
811831 GCAATAATGT
811841 ATATTATAAAAATA
1 ATATTATAAAAATA
*
811855 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
811871 A-ATTATAAAAATA
1 ATATTATAAAAATA
*
811884 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
811900 A-ATTATAAAAATA
1 ATATTATAAAAATA
811913 ATATTA
1 ATATTA
811919 ATCAAAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.26
14 16 0.30
15 10 0.19
16 14 0.26
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:811885 original size:29 final size:29
Alignment explanation
Indices: 811843--811926 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
811833 AATAATGTAT
811843 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
811872 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
811901 ATTATAAAAATAATATTAATCAAAAG
1 ATTATAAAAATAATATTAATCAAAAG
811927 GGACGAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
ATTATAAAAATAATATTAATCAAAAGTAA
Found at i:812657 original size:98 final size:98
Alignment explanation
Indices: 812423--813092 Score: 1215
Period size: 98 Copynumber: 6.9 Consensus size: 98
812413 AATTGGGAAG
* *
812423 TTGTTTATTGACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTTTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
812488 TCCTTCGTTGTGAAGTTGAAATTGG----GAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
812517 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
812582 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
812615 TTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
812680 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
812713 TTGTTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
812778 TCTTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
*
812811 TTATTTATTGACAACCAGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
812875 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
* *
812908 TTGTTTATTGACAACCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
812973 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
813006 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
813071 TCCTTCGTTGTGAAGTTGAAAT
66 TCCTTCGTTGTGAAGTTGAAAT
813093 CGACTCTGGG
Statistics
Matches: 554, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
94 87 0.16
97 93 0.17
98 374 0.68
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (98 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA
Found at i:812894 original size:43 final size:43
Alignment explanation
Indices: 812833--813090 Score: 129
Period size: 43 Copynumber: 5.4 Consensus size: 43
812823 AACCAGCGGC
812833 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** * *
812876 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGTGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCAAT-AT
*
812930 CCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ** ***
812974 CCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTT-G--C-G---TTG--TCTGGA-GTCCA-ATAT
813028 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
813072 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
813091 ATCGACTCTG
Statistics
Matches: 154, Mismatches: 37, Indels: 48
0.64 0.15 0.20
Matches are distributed among these distances:
43 57 0.37
44 4 0.03
45 7 0.05
46 10 0.06
47 2 0.01
48 6 0.04
50 6 0.04
51 2 0.01
52 10 0.06
53 7 0.05
54 4 0.03
55 39 0.25
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:812924 original size:293 final size:290
Alignment explanation
Indices: 812315--813092 Score: 1297
Period size: 293 Copynumber: 2.6 Consensus size: 290
812305 GGAATTGGGG
* * * *
812315 AATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTGGGGCCCAA
1 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
* *
812380 TCTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT
66 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTG--A-----AA-TTGTTTATTGACAACCAGCGGT
* *
812445 CCATTCGTCGTGAAGTTGAACTTGCGTTTTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
123 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
*
812510 TGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG
188 TGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAG
*
812575 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
253 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGA
*
812613 AATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
1 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
812678 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
66 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
* *
812743 CATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCCCTG
131 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----G
*
812808 AAATTATTTATTGACAACCAGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
192 AAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCA
812872 ATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGA
257 ATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGA
* *
812906 AATTGTTTATTGACAACCAGTGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
1 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
812971 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
66 TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
813036 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
131 CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
813093 CGACTCTGGG
Statistics
Matches: 457, Mismatches: 19, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
290 86 0.19
291 2 0.00
293 254 0.56
294 24 0.05
296 1 0.00
298 90 0.20
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (290 bp):
AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
TATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGT
CGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGAAAT
TATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATAT
CCTTCGTTGTGAAGTTGAAATTGGCCCTGA
Found at i:812939 original size:195 final size:196
Alignment explanation
Indices: 812423--813092 Score: 1224
Period size: 195 Copynumber: 3.4 Consensus size: 196
812413 AATTGGGAAG
* *
812423 TTGTTTATTGACAACCAGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTTTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
812488 TCCTTCGTTGTGAAGTTGAAATTGG----GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCG
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCA
* *
812549 TGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
131 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAA
812614 A
196 A
*
812615 TTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
812680 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCA
*
812745 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCCCTGAA
131 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAA
812810 A
196 A
*
812811 TTATTTATTGACAACCAGCGG-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
812875 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGTGGTCCCTTCGTCA
66 TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCA
812940 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAA
131 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAA
813005 A
196 A
813006 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
813071 TCCTTCGTTGTGAAGTTGAAAT
66 TCCTTCGTTGTGAAGTTGAAAT
813093 CGACTCTGGG
Statistics
Matches: 461, Mismatches: 12, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
192 87 0.19
195 192 0.42
196 182 0.39
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (196 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCA
TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAA
A
Found at i:824298 original size:4 final size:4
Alignment explanation
Indices: 824289--824370 Score: 67
Period size: 4 Copynumber: 19.8 Consensus size: 4
824279 ATGTTAGAAG
* *
824289 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA- ATACT AAAT AAGT CAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT -AAAT
* * * *
824338 GAAAG GAAT AAAT AAATT AATT AAAA AAAT AAA
1 -AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAA
824371 AAAAATGATG
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
3 1 0.02
4 50 0.82
5 10 0.16
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:826122 original size:14 final size:14
Alignment explanation
Indices: 826103--826180 Score: 88
Period size: 14 Copynumber: 5.4 Consensus size: 14
826093 GCAATAATGT
826103 ATATTATAAAAATA
1 ATATTATAAAAATA
*
826117 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
826133 A-ATTATAAAAATA
1 ATATTATAAAAATA
*
826146 ATATTAATCAAAAGTA
1 ATATT-AT-AAAAATA
826162 A-ATTATAAAAATA
1 ATATTATAAAAATA
826175 ATATTA
1 ATATTA
826181 ATCAAAAGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 14 0.26
14 16 0.30
15 10 0.19
16 14 0.26
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATTATAAAAATA
Found at i:826147 original size:29 final size:29
Alignment explanation
Indices: 826105--826188 Score: 168
Period size: 29 Copynumber: 2.9 Consensus size: 29
826095 AATAATGTAT
826105 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
826134 ATTATAAAAATAATATTAATCAAAAGTAA
1 ATTATAAAAATAATATTAATCAAAAGTAA
826163 ATTATAAAAATAATATTAATCAAAAG
1 ATTATAAAAATAATATTAATCAAAAG
826189 GGACGAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (29 bp):
ATTATAAAAATAATATTAATCAAAAGTAA
Found at i:826793 original size:12 final size:12
Alignment explanation
Indices: 826775--826841 Score: 91
Period size: 12 Copynumber: 5.5 Consensus size: 12
826765 CTAATATATT
826775 AAAATATTAATA
1 AAAATATTAATA
*
826787 CAAATATTCAA-A
1 AAAATATT-AATA
826799 AAAATATTAATA
1 AAAATATTAATA
826811 AAAATATTCAATA
1 AAAATATT-AATA
826824 AAAATATTAATA
1 AAAATATTAATA
*
826836 CAAATA
1 AAAATA
826842 GAACACATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
11 2 0.04
12 33 0.67
13 14 0.29
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATATTAATA
Found at i:826807 original size:24 final size:25
Alignment explanation
Indices: 826775--826841 Score: 118
Period size: 24 Copynumber: 2.7 Consensus size: 25
826765 CTAATATATT
826775 AAAATATTAATACAAATATTCAA-A
1 AAAATATTAATACAAATATTCAATA
*
826799 AAAATATTAATAAAAATATTCAATA
1 AAAATATTAATACAAATATTCAATA
826824 AAAATATTAATACAAATA
1 AAAATATTAATACAAATA
826842 GAACACATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 22 0.55
25 18 0.45
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (25 bp):
AAAATATTAATACAAATATTCAATA
Found at i:830389 original size:17 final size:17
Alignment explanation
Indices: 830367--830401 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
830357 TGATGTGAAT
830367 TGTGAAGGCCAAACCGA
1 TGTGAAGGCCAAACCGA
830384 TGTGAAGGCCAAACCGA
1 TGTGAAGGCCAAACCGA
830401 T
1 T
830402 CTTCATCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.29, T:0.14
Consensus pattern (17 bp):
TGTGAAGGCCAAACCGA
Found at i:831859 original size:9 final size:9
Alignment explanation
Indices: 831847--831898 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
831837 TAAAATTTTA
831847 TATTTAATT
1 TATTTAATT
*
831856 TATTTAA-G
1 TATTTAATT
831864 TATTTAATT
1 TATTTAATT
831873 TATTTAA--
1 TATTTAATT
* *
831880 TATTTTACT
1 TATTTAATT
831889 TATTTAATT
1 TATTTAATT
831898 T
1 T
831899 TTTTTGCATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:831891 original size:16 final size:16
Alignment explanation
Indices: 831841--831896 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
831831 TATTTTTAAA
*
831841 ATTTTATATTTAATTT
1 ATTTAATATTTAATTT
831857 ATTTAAGTATTTAATTT
1 ATTTAA-TATTTAATTT
* *
831874 ATTTAATATTTTACTT
1 ATTTAATATTTAATTT
831890 ATTTAAT
1 ATTTAAT
831897 TTTTTTTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
ATTTAATATTTAATTT
Found at i:838780 original size:31 final size:32
Alignment explanation
Indices: 838745--838830 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
838735 ATACATAATA
*
838745 TTTACTTTTTATTTCATTTTAGTA-CCCGGTG
1 TTTACTTTTTATTTCATTTTAGTACCCCAGTG
* *
838776 TTTACTTTTTGTTTCATTTTAGTACCCCATTG
1 TTTACTTTTTATTTCATTTTAGTACCCCAGTG
* *
838808 TTAACTTTTTATTTTATTTTAGT
1 TTTACTTTTTATTTCATTTTAGT
838831 GCTAGGGTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 23 0.48
32 25 0.52
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.59
Consensus pattern (32 bp):
TTTACTTTTTATTTCATTTTAGTACCCCAGTG
Found at i:841609 original size:15 final size:15
Alignment explanation
Indices: 841589--841618 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
841579 TTTGCCAGAT
841589 CCATTTATGAAGAAG
1 CCATTTATGAAGAAG
841604 CCATTTATGAAGAAG
1 CCATTTATGAAGAAG
841619 AGGAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
CCATTTATGAAGAAG
Found at i:845207 original size:37 final size:38
Alignment explanation
Indices: 845122--845207 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 38
845112 ATTAAACTTT
*
845122 TTTTATATTTTTAATTTTGTAAAACAAATTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAACAAATTATATAAATA
*
845161 --TTATGAATTTAATTTTTTAAAGA-AAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAA-ACAAATTATATAAATA
845197 TTTTATAATTT
1 TTTTATAATTT
845208 GTAATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 10 0.24
37 25 0.61
38 6 0.15
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTGTAAAACAAATTATATAAATA
Found at i:849848 original size:2 final size:2
Alignment explanation
Indices: 849841--849870 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
849831 ATAGACACAT
849841 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
849871 ACCTTTGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:857226 original size:20 final size:19
Alignment explanation
Indices: 857201--857296 Score: 120
Period size: 20 Copynumber: 4.9 Consensus size: 19
857191 ATATTGTCCA
*
857201 GGGGTACATATTCCCCACAG
1 GGGGTACAGATTCCCC-CAG
857221 GGGGTACAGATTCCCTCCAG
1 GGGGTACAGATTCCC-CCAG
* *
857241 GGGGTACCGATTCCCCTTAG
1 GGGGTACAGATTCCCC-CAG
*
857261 GGGGAACAGATTCCCCCAG
1 GGGGTACAGATTCCCCCAG
*
857280 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
857297 CCTGTCTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 18 0.27
20 47 0.71
21 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.19
Consensus pattern (19 bp):
GGGGTACAGATTCCCCCAG
Found at i:857280 original size:39 final size:40
Alignment explanation
Indices: 857197--857295 Score: 139
Period size: 40 Copynumber: 2.5 Consensus size: 40
857187 AATCATATTG
** *
857197 TCCA-GGGGTACATATTCCCCACAGGGGGTACAGATTCCC
1 TCCAGGGGGTACCGATTCCCCACAGGGGGAACAGATTCCC
**
857236 TCCAGGGGGTACCGATTCCCCTTAGGGGGAACAGATTCCC
1 TCCAGGGGGTACCGATTCCCCACAGGGGGAACAGATTCCC
857276 -CCAGGGGGTACCGATTCCCC
1 TCCAGGGGGTACCGATTCCCC
857296 CCCTGTCTAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 24 0.44
40 30 0.56
ACGTcount: A:0.20, C:0.32, G:0.28, T:0.19
Consensus pattern (40 bp):
TCCAGGGGGTACCGATTCCCCACAGGGGGAACAGATTCCC
Found at i:860059 original size:21 final size:21
Alignment explanation
Indices: 860015--860098 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
860005 ATCATATTGT
* *
860015 CCAGGGGGTACAGATT-CCCT
1 CCAGGGGGTACCGATTCCCCC
860035 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
860056 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
* *
860077 CAAGGGGGTACCGGTTCCCCC
1 CCAGGGGGTACCGATTCCCCC
860098 C
1 C
860099 TGTCTAACGG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.15, C:0.39, G:0.30, T:0.15
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:860072 original size:41 final size:42
Alignment explanation
Indices: 860015--860098 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
860005 ATCATATTGT
*
860015 CCAGGGGGTACAGATTCCCTCC-AGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCCCAAGGGGGTACCGATTCCCCC
* *
860056 CCAGGGGGTACCGATTCCCCCCAAGGGGGTACCGGTTCCCCC
1 CCAGGGGGTACAGATTCCCCCCAAGGGGGTACCGATTCCCCC
860098 C
1 C
860099 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.15, C:0.39, G:0.30, T:0.15
Consensus pattern (42 bp):
CCAGGGGGTACAGATTCCCCCCAAGGGGGTACCGATTCCCCC
Found at i:860485 original size:34 final size:32
Alignment explanation
Indices: 860446--860515 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
860436 TTTTGTAAAG
* * *
860446 GGGAAAGGTTTTAGCTTAGTCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
*
860480 GGGAAAGGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
860512 GGGA
1 GGGA
860516 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:861845 original size:31 final size:32
Alignment explanation
Indices: 861810--861934 Score: 123
Period size: 31 Copynumber: 3.9 Consensus size: 32
861800 TTAGGTTCAT
*
861810 AAGGAATTACCAGTCGGTG-CTGAACCTATAC
1 AAGGAATTACCAGTCAGTGACTGAACCTATAC
* * *
861841 AAGGAATTACCAG-CAGCGACTGAACCTGCCAAAG
1 AAGGAATTACCAGTCAGTGACTGAACCT---ATAC
* *
861875 ATAGGAATTATCAGTCAGTG-TTGAACCTATAC
1 A-AGGAATTACCAGTCAGTGACTGAACCTATAC
*
861907 AAGGAATTACCAGT-AGGGACTGAACCTA
1 AAGGAATTACCAGTCAGTGACTGAACCTA
861935 CCAGAGTCTT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
30 6 0.08
31 41 0.55
32 3 0.04
34 3 0.04
35 18 0.24
36 4 0.05
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (32 bp):
AAGGAATTACCAGTCAGTGACTGAACCTATAC
Found at i:863701 original size:18 final size:19
Alignment explanation
Indices: 863678--863721 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
863668 CCCAAAAAAA
*
863678 GTCAACGACC-GATCAACG
1 GTCAACGACCTGATCAAAG
863696 GTCAACG-CCTGATCAAAG
1 GTCAACGACCTGATCAAAG
863714 GTCAACGA
1 GTCAACGA
863722 GTTGACTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.34, C:0.30, G:0.23, T:0.14
Consensus pattern (19 bp):
GTCAACGACCTGATCAAAG
Found at i:865085 original size:75 final size:75
Alignment explanation
Indices: 864959--865166 Score: 256
Period size: 76 Copynumber: 2.8 Consensus size: 75
864949 CAAAGCCAAA
* * * * **
864959 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACTGATTCCCCCTGAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
865024 TGGCTCCGAG
66 TGACTCCGAG
*
865034 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
* *
865099 TTTATTCCGAG
65 TTGACTCCGAG
* * * * *
865110 AATTCCAGTATGCTCGTAGGGAACCGATCCCCCCCCA-AGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCCATAGGAGGAACCGATTCCCCCT
865167 TGTACAACGG
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 53 0.46
76 55 0.48
77 7 0.06
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGACTCCGAG
Found at i:870970 original size:21 final size:23
Alignment explanation
Indices: 870944--870994 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
870934 AGGGAATCAA
870944 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
870965 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
*
870988 ACCCCCC
1 TCCCCCC
870995 TGGGGTTCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 8 0.33
22 1 0.04
23 15 0.62
ACGTcount: A:0.22, C:0.41, G:0.22, T:0.16
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:872948 original size:9 final size:8
Alignment explanation
Indices: 872926--872976 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
872916 TGTTTCAACA
872926 TTTTGGAT
1 TTTTGGAT
872934 ATTTTGGAT
1 -TTTTGGAT
872943 TGTTT-GAT
1 T-TTTGGAT
872951 TTTGTGGAT
1 TTT-TGGAT
*
872960 TGTTGGA-
1 TTTTGGAT
872967 TTTTGGAT
1 TTTTGGAT
872975 TT
1 TT
872977 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:872960 original size:17 final size:17
Alignment explanation
Indices: 872928--872971 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
872918 TTTCAACATT
872928 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
872945 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
872962 TTGGATTTTG
1 TTGGATTTTG
872972 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:873753 original size:72 final size:71
Alignment explanation
Indices: 873575--873754 Score: 234
Period size: 72 Copynumber: 2.5 Consensus size: 71
873565 CAAAGCCAAA
* * **
873575 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGTT
1 AATTCCAGA-TGCTCGGAGGGAACCGATT--CCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
873640 TGGCTCGAG
63 TGGCTCGAG
* *
873649 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTG
*
873714 GTTCCGAG
65 GCT-CGAG
*
873722 AATTCCAGTATGCTCGGAGGGAACCGATCCCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCC
873755 CCAAGGGGTA
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
72 34 0.36
73 34 0.36
74 25 0.27
75 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (71 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTGG
CTCGAG
Found at i:873768 original size:73 final size:72
Alignment explanation
Indices: 873575--873773 Score: 242
Period size: 73 Copynumber: 2.7 Consensus size: 72
873565 CAAAGCCAAA
* * **
873575 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGTT
1 AATTCCAGA-TGCTCGGAGGGAACCGA-TCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
873640 TGGCTCGAG
64 TGGCTCGAG
* *
873649 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAG-ATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
873713 TGTTCCGAG
65 GGCT-CGAG
*
873722 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGG-GGTACCGATTCCC
1 AATTCCAG-ATGCTCGGAGGGAACCGAT-CCCCCCATAGGAGGAACCGATTCCC
873774 TCCTTGTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
72 34 0.31
73 43 0.39
74 26 0.24
75 6 0.06
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (72 bp):
AATTCCAGATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTG
GCTCGAG
Found at i:875516 original size:455 final size:452
Alignment explanation
Indices: 874660--875568 Score: 1782
Period size: 455 Copynumber: 2.0 Consensus size: 452
874650 ATTGAACTTT
874660 GGGTTTGTTTACTTAATGTTTATTTTGTGAGAATGTGGAAGATTGGGAAAGGGTTAAAATTTGAA
1 GGGTTTGTTTACTTAATGTTTATTTTGTGAGAATGTGGAAGATTGGGAAAGGGTTAAAATTTGAA
874725 TTTTTTCCGTTTATTTTTTTAATGTGTGGATTAGCAATATAATTATGAAATGGCAATGATGTGTA
66 TTTTTTCCGTTTATTTTTTTAATGTGTGGATTAGCAATATAATTATGAAATGGCAATGATGTGTA
874790 ATTTGGTTAACCTAATGAAGTAATTATTATGTTTTATGTTAGTTATTAGTTTTTGGTAGGTTGGA
131 ATTTGGTTAACCTAATGAAGTAATTATTATGTTTTATGTTAGTTATTAGTTTTTGGTAGGTTGGA
*
874855 CATAAACTATTAAGCAATAACACATTTTATGTCCAACAAAAATAAATAAATAAAATCCAACACTT
196 CATAAACTATTAAGCAATAACACATTTTATGTCCAACAAAAATAAATAAAAAAAATCCAACACTT
874920 CCCACCATGTAACATTAACTAGCCTTAGCTACCTTCCAGCAACTTACTTTACCTTCATTAAATTT
261 CCCACCATGTAACATTAACTAGCCTTAGCTACCTTCCAGCAACTTACTTTACCTTCATTAAATTT
874985 AATTTGACATTTTAAATGGGTGGGAGACCTAACAATAGGTTTTCTTTCATGTGATTTTATGTTTT
326 AATTTGACATTTTAAATGGGTGGGAGACCTAACAATAGGTTTTCTTTCATGTGATTTTATGTTTT
875050 TATTCCCTTGTCCAAATAAGTAATAAAGTTTGGGGTATACTTCAATTTAATCCCACACAAAA
391 TATTCCCTTGTCCAAATAAGTAATAAAGTTTGGGGTATACTTCAATTTAATCCCACACAAAA
875112 GGGTTTGTTTTACTTAATGTTTATTTTGTGAGAATGTGGAAGATTGGGAAAGGGTTAAAATTTGA
1 GGGTTTG-TTTACTTAATGTTTATTTTGTGAGAATGTGGAAGATTGGGAAAGGGTTAAAATTTGA
875177 ATTTTTGTCCGTTTTATTTTTTTAATGTGTGGATTAGCAATATAATTATGAAATGGCAATGATGT
65 ATTTTT-TCCG-TTTATTTTTTTAATGTGTGGATTAGCAATATAATTATGAAATGGCAATGATGT
875242 GTAATTTGGTTAACCTAATGAAGTAATTATTATGTTTTATGTTAGTTATTAGTTTTTGGTAGGTT
128 GTAATTTGGTTAACCTAATGAAGTAATTATTATGTTTTATGTTAGTTATTAGTTTTTGGTAGGTT
875307 GGACATAAACTATTAAGCAATAACACATTTTATGTCCAACAAAAATAAATAAAAAAAATCCAACA
193 GGACATAAACTATTAAGCAATAACACATTTTATGTCCAACAAAAATAAATAAAAAAAATCCAACA
875372 CTTCCCACCATGTAACATTAACTAGCCTTAGCTACCTTCCAGCAACTTACTTTACCTTCATTAAA
258 CTTCCCACCATGTAACATTAACTAGCCTTAGCTACCTTCCAGCAACTTACTTTACCTTCATTAAA
875437 TTTAATTTGACATTTTAAATGGGTGGGAGACCTAACAATAGGTTTTCTTTCATGTGATTTTATGT
323 TTTAATTTGACATTTTAAATGGGTGGGAGACCTAACAATAGGTTTTCTTTCATGTGATTTTATGT
875502 TTTTATTCCCTTGTCCAAATAAGTAATAAAGTTTGGGGTATACTTCAATTTAATCCCACACAAAA
388 TTTTATTCCCTTGTCCAAATAAGTAATAAAGTTTGGGGTATACTTCAATTTAATCCCACACAAAA
875567 GG
1 GG
875569 AATAAAAAAT
Statistics
Matches: 453, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
452 7 0.02
453 63 0.14
454 4 0.01
455 379 0.84
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (452 bp):
GGGTTTGTTTACTTAATGTTTATTTTGTGAGAATGTGGAAGATTGGGAAAGGGTTAAAATTTGAA
TTTTTTCCGTTTATTTTTTTAATGTGTGGATTAGCAATATAATTATGAAATGGCAATGATGTGTA
ATTTGGTTAACCTAATGAAGTAATTATTATGTTTTATGTTAGTTATTAGTTTTTGGTAGGTTGGA
CATAAACTATTAAGCAATAACACATTTTATGTCCAACAAAAATAAATAAAAAAAATCCAACACTT
CCCACCATGTAACATTAACTAGCCTTAGCTACCTTCCAGCAACTTACTTTACCTTCATTAAATTT
AATTTGACATTTTAAATGGGTGGGAGACCTAACAATAGGTTTTCTTTCATGTGATTTTATGTTTT
TATTCCCTTGTCCAAATAAGTAATAAAGTTTGGGGTATACTTCAATTTAATCCCACACAAAA
Found at i:880725 original size:21 final size:21
Alignment explanation
Indices: 880696--880748 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
880686 ATTCTGACTA
880696 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
880717 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
880738 TCGCAATGCGA
1 TCGCATTGCGA
880749 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:880763 original size:20 final size:20
Alignment explanation
Indices: 880738--880828 Score: 155
Period size: 20 Copynumber: 4.5 Consensus size: 20
880728 TTTTCCTAAT
*
880738 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
880758 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
880778 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
880798 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
880818 TCGCAATGCGA
1 TCGCAACGCGA
880829 TTTACATAGC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:881039 original size:18 final size:18
Alignment explanation
Indices: 881016--881051 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
881006 TCCCCATCTC
881016 CGACGA-AATCAGTCTCCA
1 CGACGATAA-CAGTCTCCA
881034 CGACGATAACAGTCTCCA
1 CGACGATAACAGTCTCCA
881052 TCTTCGACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (18 bp):
CGACGATAACAGTCTCCA
Found at i:881423 original size:20 final size:20
Alignment explanation
Indices: 881398--881446 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
881388 CAACGAGTGA
881398 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
881418 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
881438 ATCGCAACG
1 ATCGCAACG
881447 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:883440 original size:20 final size:20
Alignment explanation
Indices: 883415--883498 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
883405 AGAATAGTTT
883415 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
883435 ACTATCACAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
883451 A--ATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
**
883469 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
883489 ACTATCGCAA
1 ACTATCGCAA
883499 CGAAAGAATC
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
14 6 0.12
16 3 0.06
17 4 0.08
18 4 0.08
20 33 0.66
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:883500 original size:54 final size:54
Alignment explanation
Indices: 883415--883519 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
883405 AGAATAGTTT
* *
883415 ACTATCGCAATGCGAAAATGACTATCACAACGAGAGAATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCACAACGAAAGAATCGCAATGCGAAAATG
** *
883469 ACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCGAAA
1 ACTATCGCAATGCGAAAATGACTATCACAACGAAAGAATCGCAATGCGAAA
883520 TGAAAATCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (54 bp):
ACTATCGCAATGCGAAAATGACTATCACAACGAAAGAATCGCAATGCGAAAATG
Found at i:883604 original size:87 final size:87
Alignment explanation
Indices: 883513--883678 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 87
883503 AGAATCGCAA
*
883513 TGCGAAATGAAAATCGCATAGCGATTCTCTCGTTGCAATAGTCAAATTCGCATTGTGATAGTCAT
1 TGCGAAATGAAAATCGCATAGCGATTCTCTCGTTGCAATAGTCAAATTCGCATTGCGATAGTCAT
*
883578 TTTCGCGTTGCGATTTTGTTGT
66 TTTCGCATTGCGATTTTGTTGT
** ** ** * *
883600 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAGTCAT
1 TGCGAAATGAAAATCGCATAGCGATTCTCTCGTTGCAATAGTCAAATTCGCATTGCGATAGTCAT
*
883665 TTTTGCATTGCGAT
66 TTTCGCATTGCGAT
883679 AGTCATTTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (87 bp):
TGCGAAATGAAAATCGCATAGCGATTCTCTCGTTGCAATAGTCAAATTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:883622 original size:33 final size:34
Alignment explanation
Indices: 883569--883738 Score: 108
Period size: 40 Copynumber: 4.7 Consensus size: 34
883559 TTCGCATTGT
* * * * *
883569 GATAGTCATTTTCGCGTTGCGATTTTGTTGTTGC
1 GATAGTCAATTTCGCATTGCGATTCTCTCGTTGC
**
883603 GATTTTC-ATTTCGCATTGCGATTCTCTCGTTGC
1 GATAGTCAATTTCGCATTGCGATTCTCTCGTTGC
* * *
883636 GATAGTCAAATTCGCATTGCGATAGTCATTTTTGCATTGC
1 GATAGTCAATTTCGCATTGCGAT--TC---TCT-CGTTGC
* *
883676 GATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGC
1 GATAGTCAATTTCGCATTGCGAT--TC--TCTCG--TTGC
*
883716 GATAGTCATTTTCGCATTGCGAT
1 GATAGTCAATTTCGCATTGCGAT
883739 AGTCATTTTC
Statistics
Matches: 111, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
33 26 0.23
34 19 0.17
36 2 0.02
38 1 0.01
39 6 0.05
40 57 0.51
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (34 bp):
GATAGTCAATTTCGCATTGCGATTCTCTCGTTGC
Found at i:883657 original size:20 final size:20
Alignment explanation
Indices: 883632--883758 Score: 218
Period size: 20 Copynumber: 6.3 Consensus size: 20
883622 GATTCTCTCG
**
883632 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
883652 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
883672 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
883692 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
883712 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
883732 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
883752 TTGCGAT
1 TTGCGAT
883759 TTTAAGTTTC
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 102 1.00
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:884333 original size:21 final size:21
Alignment explanation
Indices: 884242--884346 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
884232 GGCTCACCTG
*
884242 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
884264 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
884284 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
884305 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
884326 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
884347 ACAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:884346 original size:42 final size:43
Alignment explanation
Indices: 884239--884346 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 43
884229 CCCGGCTCAC
* *
884239 CTGTCATCGTTCAAGAGG--CCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGTCCCT-CCCTACCGTTCAAGAGGCCA
* **
884281 CTATCATCCCTCAAGA-GTCCCCTCCC-ACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGT-CCCTCCCTACCGTTCAAGAGGCCA
*
884323 CTGTCATCGTTGAAGAGGTCCCTC
1 CTGTCATCGTTCAAGAGGTCCCTC
884347 ACAACATTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
41 1 0.02
42 44 0.83
43 5 0.09
44 3 0.06
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.23
Consensus pattern (43 bp):
CTGTCATCGTTCAAGAGGTCCCTCCCTACCGTTCAAGAGGCCA
Found at i:885897 original size:33 final size:33
Alignment explanation
Indices: 885851--885934 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
885841 TCGCAACGCG
**
885851 GAAATGACTATCGCAA-TGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACT-AGAGAATCACAATGC
* *
885884 GAAATGAAAATCGCAACTAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACTAGAGAATCACAATGC
*
885917 GAAAATGAAAATAGCAAC
1 G-AAATGAAAATCGCAAC
885935 GCGTTGCGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
33 28 0.64
34 16 0.36
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (33 bp):
GAAATGAAAATCGCAACTAGAGAATCACAATGC
Found at i:886004 original size:20 final size:21
Alignment explanation
Indices: 885934--886004 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 21
885924 AAAATAGCAA
*
885934 CGCGTTGCGCTAGTCA-ATTC
1 CGCGTTGCGATAGTCATATTC
*
885954 CGCATTGCGATAGTCAT-TTC
1 CGCGTTGCGATAGTCATATTC
*
885974 CGTGTTGCGATAGTCATATT-
1 CGCGTTGCGATAGTCATATTC
*
885994 CGCGTTACGAT
1 CGCGTTGCGAT
886005 TTCTGCGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (21 bp):
CGCGTTGCGATAGTCATATTC
Found at i:888463 original size:24 final size:24
Alignment explanation
Indices: 888436--888489 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
888426 TCTGAAAATC
888436 ATCAAAATCC-GAGTATTGACCAAG
1 ATCAAAATCCTG-GTATTGACCAAG
*
888460 ATCAAAGTCCTGGTATTGACCAAG
1 ATCAAAATCCTGGTATTGACCAAG
888484 ATCAAA
1 ATCAAA
888490 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCTGGTATTGACCAAG
Found at i:889402 original size:20 final size:20
Alignment explanation
Indices: 889349--889409 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
889339 GTCAGAATCT
889349 CGTTGCGATTTACAG-ATTCG
1 CGTTGCGATTTAC-GTATTCG
*
889369 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
889389 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
889409 C
1 C
889410 CGAATTAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:889436 original size:21 final size:21
Alignment explanation
Indices: 889410--889454 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
889400 ACGTAATCGC
889410 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
889431 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
889452 CGA
1 CGA
889455 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:895539 original size:14 final size:14
Alignment explanation
Indices: 895520--895546 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
895510 CTTTTGTTTG
895520 TTTTACTTATTTTA
1 TTTTACTTATTTTA
895534 TTTTACTTATTTT
1 TTTTACTTATTTT
895547 TTATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTACTTATTTTA
Found at i:895554 original size:11 final size:11
Alignment explanation
Indices: 895534--895666 Score: 65
Period size: 11 Copynumber: 11.5 Consensus size: 11
895524 ACTTATTTTA
*
895534 TTTTACTTATT
1 TTTTATTTATT
*
895545 TTTTATTTATA
1 TTTTATTTATT
*
895556 TTGTATTTATCT
1 TTTTATTTAT-T
* *
895568 TGTTTACCTT-TC
1 T-TTTA-TTTATT
895580 TTTTATTTTATT
1 TTTTA-TTTATT
*
895592 ACCTTTATTT-TAT
1 --TTTTATTTAT-T
** *
895605 TTTTACCTATA
1 TTTTATTTATT
895616 TTTTATTTATT
1 TTTTATTTATT
*
895627 TTCTATTTATT
1 TTTTATTTATT
*
895638 TATTATCTTA-T
1 TTTTAT-TTATT
895649 TTTTATTTATGT
1 TTTTATTTAT-T
895661 TTTTAT
1 TTTTAT
895667 CTCTTTTTAT
Statistics
Matches: 89, Mismatches: 22, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
10 3 0.03
11 57 0.64
12 15 0.17
13 8 0.09
14 6 0.07
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.70
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:895595 original size:19 final size:19
Alignment explanation
Indices: 895571--895623 Score: 74
Period size: 17 Copynumber: 2.9 Consensus size: 19
895561 TTTATCTTGT
*
895571 TTACCTTTCTTTTATTTTA
1 TTACCTTTATTTTATTTTA
895590 TTACCTTTATTTTA-TTT-
1 TTACCTTTATTTTATTTTA
*
895607 TTACCTATATTTTATTT
1 TTACCTTTATTTTATTT
895624 ATTTTCTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 13 0.42
18 5 0.16
19 13 0.42
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (19 bp):
TTACCTTTATTTTATTTTA
Found at i:895640 original size:36 final size:36
Alignment explanation
Indices: 895530--895641 Score: 88
Period size: 36 Copynumber: 3.2 Consensus size: 36
895520 TTTTACTTAT
* * * *
895530 TTTA-TTTTACTTATTTTTTATTTATATTGTATTTA
1 TTTATTTTTACCTATATTTTATTTATTTTCTATTTA
* * * * * *
895565 TCT-TGTTTACCTTTCTTTTATTT-TATTAC-CTTTA
1 TTTATTTTTACCTATATTTTATTTAT-TTTCTATTTA
895599 TTTTATTTTTACCTATATTTTATTTATTTTCTATTTA
1 -TTTATTTTTACCTATATTTTATTTATTTTCTATTTA
895636 TTTATT
1 TTTATT
895642 ATCTTATTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 11
0.68 0.18 0.13
Matches are distributed among these distances:
34 5 0.09
35 20 0.36
36 26 0.46
37 5 0.09
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (36 bp):
TTTATTTTTACCTATATTTTATTTATTTTCTATTTA
Found at i:895643 original size:18 final size:18
Alignment explanation
Indices: 895581--895658 Score: 51
Period size: 17 Copynumber: 4.5 Consensus size: 18
895571 TTACCTTTCT
*
895581 TTTATTTTATTACCTT-TA
1 TTTA-TTTATTATCTTATA
*
895599 TTTTATTT-TTA-CCTATA
1 -TTTATTTATTATCTTATA
*
895616 TTTTATTTA-T-T-TTCTA
1 -TTTATTTATTATCTTATA
*
895632 TTTATTTATTATCTTATT
1 TTTATTTATTATCTTATA
895650 TTTATTTAT
1 TTTATTTAT
895659 GTTTTTATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
15 8 0.17
16 6 0.12
17 15 0.31
18 15 0.31
19 4 0.08
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTATTATCTTATA
Found at i:895650 original size:12 final size:11
Alignment explanation
Indices: 895595--895679 Score: 63
Period size: 11 Copynumber: 7.7 Consensus size: 11
895585 TTTTATTACC
*
895595 TTTATTTTATT
1 TTTATCTTATT
*
895606 TTTA-CCTATAT
1 TTTATCTTAT-T
895617 TTTAT-TTATT
1 TTTATCTTATT
895627 TTCTAT-TTATT
1 TT-TATCTTATT
895638 TATTATCTTATT
1 T-TTATCTTATT
895650 TTTAT-TTATGTT
1 TTTATCTTA--TT
*
895662 TTTATC-TCTT
1 TTTATCTTATT
895672 TTTATCTT
1 TTTATCTT
895680 TGTTTCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
10 17 0.28
11 29 0.48
12 15 0.25
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:895666 original size:18 final size:17
Alignment explanation
Indices: 895616--895666 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
895606 TTTACCTATA
*
895616 TTTTATTTATTTTCTA-
1 TTTTATTTATTTTTTAT
*
895632 -TTTATTTATTATCTTAT
1 TTTTATTTATT-TTTTAT
895649 TTTTATTTATGTTTTTAT
1 TTTTATTTAT-TTTTTAT
895667 CTCTTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 10 0.36
16 3 0.11
18 14 0.50
19 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTATTTATTTTTTAT
Found at i:895673 original size:22 final size:22
Alignment explanation
Indices: 895616--895684 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
895606 TTTACCTATA
*
895616 TTTTATTTATTTTCTATTTAT-T
1 TTTTATCTATTTT-TATTTATGT
*
895638 TATTATCTTATTTTTATTTATGT
1 TTTTATC-TATTTTTATTTATGT
*
895661 TTTTATCTCTTTTTATCTT-TGT
1 TTTTATCTATTTTTAT-TTATGT
895683 TT
1 TT
895685 CATTTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 25 0.62
23 15 0.38
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTATCTATTTTTATTTATGT
Found at i:895723 original size:2 final size:2
Alignment explanation
Indices: 895716--895747 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
895706 TTTCTTGTAC
895716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
895748 TATCTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:896901 original size:16 final size:15
Alignment explanation
Indices: 896879--896916 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
896869 TTACTAACTC
*
896879 TTTTCATTTTTGTTT
1 TTTTCATTTTTATTT
896894 TCTTTCATTTTTATTT
1 T-TTTCATTTTTATTT
896910 TTTTCAT
1 TTTTCAT
896917 CATTTGCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTATTT
Found at i:899941 original size:99 final size:99
Alignment explanation
Indices: 899765--899962 Score: 306
Period size: 99 Copynumber: 2.0 Consensus size: 99
899755 TTATAATATC
* * * *
899765 ATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTATGG
1 ATATATATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
* *
899830 ATAAGATTCAGCTAGCTTGATAAAGGTGATTATA
66 ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
* * *
899864 ATATCTATACAATAAAACTTGAGCTGTCTCTCTAAGGCAATTGGTTAAACGCCCCGACTTTATGG
1 ATATATATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
*
899929 ATAAGATTCAGCTAACCTGATAAAGGTGTTTATA
66 ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
899963 TATTGAGCTG
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 89 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAACTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGG
ATAAGATTCAGCTAACCTGATAAAGGTGATTATA
Found at i:900971 original size:64 final size:65
Alignment explanation
Indices: 900870--901036 Score: 234
Period size: 64 Copynumber: 2.6 Consensus size: 65
900860 TGCAGCTTTT
** *
900870 AGAGTCAATTTCAACTTCACAAAG-AAGAATATTGGACTCAACAAATGA-CTTTCCAGTTTCATT
1 AGAGTCAATTTCAACTTCACAGCGAAAGAATATTGGACTCAACAAA-CATCTTTCCAGTTTCATT
900933 C
65 C
* *
900934 AGAGTCAATTTCAATTTCACAGCGAAAG-ATGTTGGACTCAACAAACATCTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAAGAATATTGGACTCAACAAACATCTTTCCAGTTTCATTC
* *
900998 AGAGTCAATTTCAACTTCACAGCG-AAGGATATTGAACTC
1 AGAGTCAATTTCAACTTCACAGCGAAAGAATATTGGACTC
901037 GAAACAATAC
Statistics
Matches: 92, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
63 4 0.04
64 85 0.92
65 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (65 bp):
AGAGTCAATTTCAACTTCACAGCGAAAGAATATTGGACTCAACAAACATCTTTCCAGTTTCATTC
Found at i:901247 original size:109 final size:111
Alignment explanation
Indices: 901056--901380 Score: 368
Period size: 120 Copynumber: 2.9 Consensus size: 111
901046 CAACTCTAGA
* * * * **
901056 TTGGATTTCAACTTCACGACGAATGACATCCACTTCAAATCTCAACTTCACAACGAAGGAGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGG-GCCAT
* *
901121 CCACGATTTCAACTTCACGACGAAGGATATCA-TGC-CA-ACAATCC
65 CCACGATTTCAACTTCACGACGAAGGATATCACAGCACATACAATAC
901165 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCAT
**
901230 CCACGATTTCAACTTCACGATAAAGGATATTGTGCCCACCAGCAACATACAATAC
65 CCACGATTTCAACTTCACGACGAAGGATA---T---CA-CAGC-ACATACAATAC
* * * *
901285 TTGGATTTCAACTTCACGACAAAGAATATCCAATTCAAGGCTCAACTTTAGAACGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAA-GGGCCAT
* ** *
901350 CCAGGATTTCAACTTCATAACGAATGATATC
65 CCACGATTTCAACTTCACGACGAAGGATATC
901381 CGATTCGAGG
Statistics
Matches: 183, Mismatches: 21, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
109 83 0.45
110 2 0.01
112 1 0.01
114 1 0.01
115 2 0.01
117 3 0.02
119 2 0.01
120 89 0.49
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (111 bp):
TTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGCCATC
CACGATTTCAACTTCACGACGAAGGATATCACAGCACATACAATAC
Found at i:901393 original size:66 final size:66
Alignment explanation
Indices: 901287--901752 Score: 283
Period size: 66 Copynumber: 7.4 Consensus size: 66
901277 TACAATACTT
* * * *
901287 GGATTTCAACTTCACGAC-AAAGAATATCCAATTCAAGGCTCAACTTTAGAACGAAGGGGTCATC
1 GGATTTCAACTTCACGACGAATG-ATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATC
901351 CA
65 CA
** * *
901353 GGATTTCAACTTCATAACGAATGATATCCGATTCGAGGCTCAACTTCAAAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
901418 A
66 A
** * * * *
901419 TAATTTTAACTTCACGACGAATGATAT-C-ATGTCCA--C-C-A-GT-AATATAC-AA--TG-C-
1 GGATTTCAACTTCACGACGAATGATATCCAAT-TCAAGGCTCAACTTCAA-A-ACGAAGGGGCCA
*
901471 T--T
63 TCCA
* * *
901473 GGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTTAACTTCACAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
901538 A
66 A
* * * * * *****
901539 CGATTTTAACTTCACGACGAA--AAAT---ATT---GTG-TCCAC--CAGTAAC-ATACAATACA
1 GGATTTCAACTTCACGACGAATGATATCCAATTCAAG-GCTCAACTTCA-AAACGA-AGGGGCCA
901592 T---
63 TCCA
* * * *
901593 GGATTTCAACTTCACGATGAAGGATATCTAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
901658 A
66 A
** * * *
901659 TAATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCC
1 GGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
901724 A
66 A
* * * *
901725 TGATTTCAACTCCACGACGGAGGATATC
1 GGATTTCAACTTCACGACGAATGATATC
901753 GTGCCCACAA
Statistics
Matches: 306, Mismatches: 57, Indels: 74
0.70 0.13 0.17
Matches are distributed among these distances:
54 41 0.13
55 4 0.01
56 9 0.03
57 9 0.03
58 5 0.02
59 9 0.03
60 8 0.03
61 8 0.03
62 7 0.02
63 9 0.03
64 9 0.03
65 4 0.01
66 181 0.59
67 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (66 bp):
GGATTTCAACTTCACGACGAATGATATCCAATTCAAGGCTCAACTTCAAAACGAAGGGGCCATCC
A
Done.