Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 51
Found at i:5413275 original size:42 final size:44
Alignment explanation
Indices: 5413194--5413275 Score: 132
Period size: 42 Copynumber: 1.9 Consensus size: 44
5413184 AAATTATCAG
*
5413194 TTTTTAATTCCATATTTATGACTAATTATAATTATAATTACATA
1 TTTTTAATTCCATATTGATGACTAATTATAATTATAATTACATA
*
5413238 TTTTTATTTCCATATTGAT-A-TAATTATAATTATAATTA
1 TTTTTAATTCCATATTGATGACTAATTATAATTATAATTA
5413276 TAATTCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 18 0.50
43 1 0.03
44 17 0.47
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (44 bp):
TTTTTAATTCCATATTGATGACTAATTATAATTATAATTACATA
Found at i:5413288 original size:42 final size:44
Alignment explanation
Indices: 5413201--5413288 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 44
5413191 CAGTTTTTAA
* *
5413201 TTCCATATTTATGACTAATTATAATTATAATTACATATTTTTAT
1 TTCCATATTGATGACTAATTATAATTATAATTACATATTTATAT
*
5413245 TTCCATATTGAT-A-TAATTATAATTATAATTATA-ATTCTATAT
1 TTCCATATTGATGACTAATTATAATTATAATTACATATT-TATAT
5413287 TT
1 TT
5413289 ACCTATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 3 0.08
42 25 0.62
43 1 0.03
44 11 0.28
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (44 bp):
TTCCATATTGATGACTAATTATAATTATAATTACATATTTATAT
Found at i:5413716 original size:2 final size:2
Alignment explanation
Indices: 5413711--5413735 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5413701 ATAAACGCGC
5413711 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 A
5413736 ACTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5413863 original size:5 final size:5
Alignment explanation
Indices: 5413853--5413877 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5413843 TAAGGGTGTA
5413853 TTCGG TTCGG TTCGG TTCGG TTCGG
1 TTCGG TTCGG TTCGG TTCGG TTCGG
5413878 GTTTTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
TTCGG
Found at i:5414035 original size:18 final size:19
Alignment explanation
Indices: 5414006--5414042 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5413996 ATTTTTTTAA
*
5414006 CGGTTCGAGTTTTTCGGTT
1 CGGTTCGAGTTTATCGGTT
5414025 CGGTTCG-GTTTATCGGTT
1 CGGTTCGAGTTTATCGGTT
5414043 TTTCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.05, C:0.16, G:0.32, T:0.46
Consensus pattern (19 bp):
CGGTTCGAGTTTATCGGTT
Found at i:5415628 original size:21 final size:21
Alignment explanation
Indices: 5415604--5415644 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5415594 ATTAATAATA
5415604 TGATATTATAATCTATATATT
1 TGATATTATAATCTATATATT
5415625 TGATATTATAATCTATATAT
1 TGATATTATAATCTATATAT
5415645 AATATTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
TGATATTATAATCTATATATT
Found at i:5415649 original size:19 final size:19
Alignment explanation
Indices: 5415601--5415655 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
5415591 CATATTAATA
5415601 ATATGATATTATAATCTAT
1 ATATGATATTATAATCTAT
5415620 ATATTTGATATTATAATCTAT
1 ATA--TGATATTATAATCTAT
* *
5415641 ATATAATATTGTAAT
1 ATATGATATTATAAT
5415656 ATATTGTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 13 0.41
21 19 0.59
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATGATATTATAATCTAT
Found at i:5416381 original size:25 final size:25
Alignment explanation
Indices: 5416331--5416402 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
5416321 CATTTAAGTT
*
5416331 TATAAAAACATAATAAAAAAAACTTAA
1 TATAAAAACGTAAT--AAAAAACTTAA
* *
5416358 TATAAAGATGTAATAAAAAACTTAA
1 TATAAAAACGTAATAAAAAACTTAA
5416383 TATAAAAACGTAATAAAAAA
1 TATAAAAACGTAATAAAAAA
5416403 TAAAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 29 0.73
27 11 0.28
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (25 bp):
TATAAAAACGTAATAAAAAACTTAA
Found at i:5416389 original size:13 final size:13
Alignment explanation
Indices: 5416331--5416402 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 13
5416321 CATTTAAGTT
*
5416331 TATAAAAACATAA
1 TATAAAAACTTAA
*
5416344 TAAAAAAAACTTAA
1 T-ATAAAAACTTAA
*
5416358 TATAAAGA-TGTAA
1 TATAAAAACT-TAA
5416371 TA-AAAAACTTAA
1 TATAAAAACTTAA
*
5416383 TATAAAAACGTAA
1 TATAAAAACTTAA
5416396 TA-AAAAA
1 TATAAAAA
5416403 TAAAAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
12 15 0.31
13 23 0.47
14 11 0.22
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (13 bp):
TATAAAAACTTAA
Found at i:5424884 original size:20 final size:20
Alignment explanation
Indices: 5424856--5424913 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
5424846 TTCTAAAACT
*
5424856 TCATGGAAGGTT-TTGAGACA
1 TCATGGAAGGTTCTGGA-ACA
*
5424876 TCATAGAAGGTTCTGGAACA
1 TCATGGAAGGTTCTGGAACA
5424896 TCATGGAAGGTTCTGGAA
1 TCATGGAAGGTTCTGGAA
5424914 TATTATAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.28
Consensus pattern (20 bp):
TCATGGAAGGTTCTGGAACA
Found at i:5424924 original size:20 final size:20
Alignment explanation
Indices: 5424873--5424924 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
5424863 AGGTTTTGAG
5424873 ACATCATAGAAGGTTCTGGA
1 ACATCATAGAAGGTTCTGGA
*
5424893 ACATCATGGAAGGTTCTGGA
1 ACATCATAGAAGGTTCTGGA
* *
5424913 ATATTATAGAAG
1 ACATCATAGAAG
5424925 CTCATGGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (20 bp):
ACATCATAGAAGGTTCTGGA
Found at i:5424951 original size:20 final size:20
Alignment explanation
Indices: 5424909--5424952 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5424899 TGGAAGGTTC
* *
5424909 TGGAATATTATAGAAGCTCA
1 TGGAAGATTATAGAAACTCA
* *
5424929 TGGAAGATTCTAGAAACTTA
1 TGGAAGATTATAGAAACTCA
5424949 TGGA
1 TGGA
5424953 GAATTTTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (20 bp):
TGGAAGATTATAGAAACTCA
Found at i:5427394 original size:31 final size:31
Alignment explanation
Indices: 5427353--5427427 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
5427343 TAACTCGTAA
*
5427353 TGACTATATCTTAATTAAATAAAAATGAAAG
1 TGACTATATCTTAATTAAATAAAAACGAAAG
*
5427384 TGACTGTATCTTAATTAAATAAAAACGAAAG
1 TGACTATATCTTAATTAAATAAAAACGAAAG
5427415 TGAAC-ATATCTTA
1 TG-ACTATATCTTA
5427428 TGTTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (31 bp):
TGACTATATCTTAATTAAATAAAAACGAAAG
Found at i:5428472 original size:36 final size:36
Alignment explanation
Indices: 5428405--5428638 Score: 192
Period size: 36 Copynumber: 6.6 Consensus size: 36
5428395 TGGGTAAAAG
* * *
5428405 ATCATGCATATAATCATTAGTAACCAA-CACATGTAT
1 ATCATGCTTATAATCATCAGT-AGCAAGCACATGTAT
* * * *
5428441 ATTATGCTTATAATAATCAGTAGC--GCGCA--CAT
1 ATCATGCTTATAATCATCAGTAGCAAGCACATGTAT
* * * * *
5428473 ATCATGCATATAATCATTAGCAGTAAGCACATATAT
1 ATCATGCTTATAATCATCAGTAGCAAGCACATGTAT
* ***
5428509 ATCATG-TATATAATCATCATTAGCAAGCGTGTGTAT
1 ATCATGCT-TATAATCATCAGTAGCAAGCACATGTAT
* * **
5428545 ATCATGCATATAATCATCAGTACCAAATACATGTAT
1 ATCATGCTTATAATCATCAGTAGCAAGCACATGTAT
* * *
5428581 ATAATGCTCATAATAATCAGTAGCAAGCACATGTAT
1 ATCATGCTTATAATCATCAGTAGCAAGCACATGTAT
*
5428617 ATCATGCTTATAATCATTAGTA
1 ATCATGCTTATAATCATCAGTA
5428639 ATCAATGCAT
Statistics
Matches: 148, Mismatches: 43, Indels: 14
0.72 0.21 0.07
Matches are distributed among these distances:
32 20 0.14
34 7 0.05
35 2 0.01
36 119 0.80
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (36 bp):
ATCATGCTTATAATCATCAGTAGCAAGCACATGTAT
Found at i:5428654 original size:72 final size:72
Alignment explanation
Indices: 5428405--5428654 Score: 244
Period size: 72 Copynumber: 3.5 Consensus size: 72
5428395 TGGGTAAAAG
* * *
5428405 ATCATGCATATAATCATTAGTAACCAACACATGTATATTATGCTTATAATAATCAGTAGC--GCG
1 ATCATGCATATAATCATTAGTAACCAATACATATATATAATGCTTATAATAATCAGTAGCAAGCG
*
5428468 CA--CAT
66 CATGTAT
* ** * * * *
5428473 ATCATGCATATAATCATTAG-CAGTAAGCACATATATATCATG-TATATAATCATCATTAGCAAG
1 ATCATGCATATAATCATTAGTAACCAA-TACATATATATAATGCT-TATAATAATCAGTAGCAAG
**
5428536 CGTGTGTAT
64 CGCATGTAT
* * *
5428545 ATCATGCATATAATCATCAGT-ACCAAATACATGTATATAATGCTCATAATAATCAGTAGCAAGC
1 ATCATGCATATAATCATTAGTAACC-AATACATATATATAATGCTTATAATAATCAGTAGCAAGC
*
5428609 ACATGTAT
65 GCATGTAT
* * *
5428617 ATCATGCTTATAATCATTAGTAATCAATGCATATATAT
1 ATCATGCATATAATCATTAGTAACCAATACATATATAT
5428655 CATACATAGA
Statistics
Matches: 145, Mismatches: 27, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
67 4 0.03
68 47 0.32
70 3 0.02
72 86 0.59
73 5 0.03
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (72 bp):
ATCATGCATATAATCATTAGTAACCAATACATATATATAATGCTTATAATAATCAGTAGCAAGCG
CATGTAT
Found at i:5429564 original size:38 final size:38
Alignment explanation
Indices: 5429522--5429614 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 38
5429512 GTTGCAATCC
* *
5429522 AAAATCTGACTTGCAACCTAAAATCTAGGTAGTAAAAT
1 AAAATCTGACTTGCAACCTAAAATCTAGCTAGCAAAAT
* * * * * **
5429560 AAAATATGAATTACAACCTAAAGTCTAGCTTGCAACCT
1 AAAATCTGACTTGCAACCTAAAATCTAGCTAGCAAAAT
5429598 AAAATCTGACTTGCAAC
1 AAAATCTGACTTGCAAC
5429615 ACTTAATTTC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (38 bp):
AAAATCTGACTTGCAACCTAAAATCTAGCTAGCAAAAT
Found at i:5429595 original size:19 final size:19
Alignment explanation
Indices: 5429559--5429614 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
5429549 GGTAGTAAAA
* * *
5429559 TAAAATATGAATTACAACC
1 TAAAATCTGACTTGCAACC
*
5429578 TAAAGTCT-AGCTTGCAACC
1 TAAAATCTGA-CTTGCAACC
5429597 TAAAATCTGACTTGCAAC
1 TAAAATCTGACTTGCAAC
5429615 ACTTAATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAATCTGACTTGCAACC
Found at i:5429930 original size:35 final size:35
Alignment explanation
Indices: 5429890--5429961 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5429880 TAATTCAAAG
5429890 TCCATTAAACTAGAATTTGAGCAAAAAACAGTTTT
1 TCCATTAAACTAGAATTTGAGCAAAAAACAGTTTT
*
5429925 TCCATTAAACTAGAATTTGAGCAAAAAATAGTTTT
1 TCCATTAAACTAGAATTTGAGCAAAAAACAGTTTT
5429960 TC
1 TC
5429962 TGGGTATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (35 bp):
TCCATTAAACTAGAATTTGAGCAAAAAACAGTTTT
Found at i:5441198 original size:42 final size:41
Alignment explanation
Indices: 5441151--5441247 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
5441141 ATAATTTAAG
* * *
5441151 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * * *
5441193 TCCTTCGGGTCATCTGTAAGCCTTTAGATCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
5441234 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
5441248 CATAAGACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:5441510 original size:22 final size:21
Alignment explanation
Indices: 5441484--5441558 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
5441474 AACCCATCAG
5441484 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
5441505 TGAAGTCTTTTGGGCCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
*
5441526 TAAGTCTTTCAAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
*
5441547 TTAAATCTTTCG
1 -TAAGTCTTTCG
5441559 GGTAATTTGT
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
19 4 0.10
20 10 0.25
21 2 0.05
22 20 0.50
23 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:5441577 original size:122 final size:122
Alignment explanation
Indices: 5441360--5441610 Score: 376
Period size: 122 Copynumber: 2.1 Consensus size: 122
5441350 TTTTGCACTT
* * * *
5441360 AGTAAGTCTTTCGAGCATGCTGATGAAATCCTTTGATCCATCAGTAAGGCTTTCGAGGATGATGA
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGAGCCATCAGTAAGGCTTTCAAGCATGATGA
*
5441425 TTAAGTCTTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATC
66 TTAAATCTTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATC
* * * *
5441482 AGTAAGTCTTTCGAGCATGATGATGAAGTCTTTTGGGCCATCAGTAAGTCTTTCAAGCATGATGA
1 AGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGAGCCATCAGTAAGGCTTTCAAGCATGATGA
* * * *
5441547 TTAAATCTTTCGGGTAATTTGTAAGCCTTCACCGAATAGTAGTGAAGCAAATCCATC
66 TTAAATCTTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATC
*
5441604 AATAAGT
1 AGTAAGT
5441611 GCCATCAGTA
Statistics
Matches: 115, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
122 115 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (122 bp):
AGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGAGCCATCAGTAAGGCTTTCAAGCATGATGA
TTAAATCTTTCAGGTAATTTGTAAGCCTTCACCAAAGAGTAGTGAAGCAAACCCATC
Found at i:5441783 original size:42 final size:42
Alignment explanation
Indices: 5441477--5441783 Score: 267
Period size: 42 Copynumber: 7.1 Consensus size: 42
5441467 TGAAGCAAAC
* * *
5441477 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTTGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
5441519 CCATCAGTAAGTCTTTCAAGCATGATGATTAAATCTTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
** ** * * * * *
5441561 TAATTTGTAAG-CCTTC-ACCGAATAGTAGTGAAGCAAATCCATCAATAAGTG
1 CCATCAGTAAGTCTTTCGA--GCAT-G-A-TGATG-AAATCC-T---T-CGGG
* * *
5441612 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTTGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * * *
5441654 TCATCACTAAGTCTTTCGAGCATGACGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
*
5441696 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
* * *
5441738 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
5441780 CCAT
1 CCAT
5441784 TTTAAGCCTT
Statistics
Matches: 212, Mismatches: 40, Indels: 26
0.76 0.14 0.09
Matches are distributed among these distances:
40 1 0.00
41 4 0.02
42 166 0.78
43 2 0.01
44 1 0.00
45 3 0.01
46 6 0.03
47 6 0.03
48 3 0.01
49 1 0.00
50 2 0.01
51 12 0.06
52 4 0.02
53 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGG
Found at i:5442281 original size:53 final size:53
Alignment explanation
Indices: 5442164--5442508 Score: 446
Period size: 53 Copynumber: 6.6 Consensus size: 53
5442154 ATCACACCAA
* * * *
5442164 AAGATTATTCGAGTTTTACTCTCTGAAGCAAGAGGGAG-G-A-CTGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* *
5442214 AAGATTG-TCTGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCTGTAGGCAG
1 AAGATTGTTC-GAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* * * * *
5442267 AATATTGTTCGAGTTCTACTCCGTGAAGCAAGAGGGAGCGAACCCATAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* *
5442320 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* *
5442373 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAGTGAACCCGTAGGCAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* * *** *
5442426 AAGATTGTTCGAGTTCTACCCCCTAAAGCAAGAGGGAGCCCACCCGTAAGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
* *
5442479 AAGATTATTCGGGTTCTACTCCCTGAAGCA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCA
5442509 TTAGGGAGCA
Statistics
Matches: 256, Mismatches: 34, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
49 2 0.01
50 31 0.12
51 1 0.00
52 1 0.00
53 219 0.86
54 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGCAG
Found at i:5442516 original size:159 final size:159
Alignment explanation
Indices: 5442164--5442508 Score: 491
Period size: 159 Copynumber: 2.2 Consensus size: 159
5442154 ATCACACCAA
* * * *
5442164 AAGATTATTCGAGTTTTACTCTCTGAAGCAAGAGGGAG-G-A-CTGTAGGCAGAAGATTG-TCTG
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAAGCAGAAGATTGTTC-G
* * * * * * *
5442225 AGTTCTACTCCCTGAAGCAAGAGGGAATGAACCTGTAGGCAGAATATTGTTCGAGTTCTACTCCG
65 AGTTCTACTCCCTGAAGCAAGAAGGAGTGAACCCGTAGGCAAAAGATTGTTCGAGTTCTACCCCC
* * * *
5442290 TGAAGCAAGAGGGAGCGAACCCATAGGTAG
130 TAAAGCAAGAGGGAGCCAACCCATAAGCAG
5442320 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAAGCAGAAGATTGTTCGA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAAGCAGAAGATTGTTCGA
5442385 GTTCTACTCCCTGAAGCAAGAAGGAGTGAACCCGTAGGCAAAAGATTGTTCGAGTTCTACCCCCT
66 GTTCTACTCCCTGAAGCAAGAAGGAGTGAACCCGTAGGCAAAAGATTGTTCGAGTTCTACCCCCT
* *
5442450 AAAGCAAGAGGGAGCCCACCCGTAAGCAG
131 AAAGCAAGAGGGAGCCAACCCATAAGCAG
*
5442479 AAGATTATTCGGGTTCTACTCCCTGAAGCA
1 AAGATTATTCGAGTTCTACTCCCTGAAGCA
5442509 TTAGGGAGCA
Statistics
Matches: 167, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
156 36 0.22
157 1 0.01
158 1 0.01
159 127 0.76
160 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (159 bp):
AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAAGCAGAAGATTGTTCGA
GTTCTACTCCCTGAAGCAAGAAGGAGTGAACCCGTAGGCAAAAGATTGTTCGAGTTCTACCCCCT
AAAGCAAGAGGGAGCCAACCCATAAGCAG
Found at i:5445037 original size:19 final size:19
Alignment explanation
Indices: 5445013--5445059 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
5445003 AATGATTTTC
*
5445013 TTTTGAAAGCAAAATTG-AA
1 TTTTGAAAACAAAA-TGAAA
5445032 TTTTGAAAACAAAATGAAA
1 TTTTGAAAACAAAATGAAA
5445051 TTTTGAAAA
1 TTTTGAAAA
5445060 ATTATTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.08
19 24 0.92
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:5453292 original size:32 final size:32
Alignment explanation
Indices: 5453231--5453293 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
5453221 AATTAATGAA
* **
5453231 AATAAATAAATAAATATTGAATAAAAATTAAT
1 AATAAAAAAATAAATAAAGAATAAAAATTAAT
* *
5453263 AATAAAAAAATAAATAAAGTATAATAATTAA
1 AATAAAAAAATAAATAAAGAATAAAAATTAA
5453294 ATAAAGATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (32 bp):
AATAAAAAAATAAATAAAGAATAAAAATTAAT
Found at i:5454113 original size:20 final size:21
Alignment explanation
Indices: 5454062--5454109 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
5454052 AATAAGAGTT
*
5454062 ATAATAAAATAACTAATTTTA
1 ATAATAAAATAACTAATTTAA
5454083 A-AATAAAATAA-TAA-TTAA
1 ATAATAAAATAACTAATTTAA
5454101 ATAATAAAA
1 ATAATAAAA
5454110 ATAAAAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 10 0.40
21 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAAAATAACTAATTTAA
Found at i:5458374 original size:16 final size:17
Alignment explanation
Indices: 5458353--5458384 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5458343 TTACTATTAA
5458353 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
5458369 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
5458385 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:5463725 original size:12 final size:12
Alignment explanation
Indices: 5463708--5463737 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5463698 TTGCTAAGTA
*
5463708 TTATATCTTCTC
1 TTATATATTCTC
5463720 TTATATATTCTC
1 TTATATATTCTC
5463732 TTATAT
1 TTATAT
5463738 GTGAATGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATATTCTC
Found at i:5468422 original size:2 final size:2
Alignment explanation
Indices: 5468415--5468513 Score: 198
Period size: 2 Copynumber: 49.5 Consensus size: 2
5468405 TTATTTAACT
5468415 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5468457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5468499 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5468514 GAACTTAACA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 97 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5470696 original size:20 final size:20
Alignment explanation
Indices: 5470671--5470712 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5470661 CAAATTCCAC
*
5470671 CAAATTCCACTAATCCATAT
1 CAAATTCCACTAATCCAAAT
*
5470691 CAAATTCCACTGATCCAAAT
1 CAAATTCCACTAATCCAAAT
5470711 CA
1 CA
5470713 TCATTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.31, G:0.02, T:0.26
Consensus pattern (20 bp):
CAAATTCCACTAATCCAAAT
Found at i:5473506 original size:20 final size:20
Alignment explanation
Indices: 5473481--5473523 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5473471 TTGTCTCTTG
*
5473481 AAAGCAAAATTG-GATTTTGA
1 AAAGCAAAA-TGAAATTTTGA
5473501 AAAGCAAAATGAAATTTTGA
1 AAAGCAAAATGAAATTTTGA
5473521 AAA
1 AAA
5473524 ATGATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (20 bp):
AAAGCAAAATGAAATTTTGA
Found at i:5475001 original size:20 final size:20
Alignment explanation
Indices: 5474976--5475023 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
5474966 TACATAGTAG
5474976 TATCGATACCATGATCATAA
1 TATCGATACCATGATCATAA
5474996 TATCGATACCATGATCATAA
1 TATCGATACCATGATCATAA
5475016 TATCGATA
1 TATCGATA
5475024 ATGGTCAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCGATACCATGATCATAA
Found at i:5481392 original size:3 final size:3
Alignment explanation
Indices: 5481384--5481449 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
5481374 ATGTAAATTA
5481384 AAT AAT AAT 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 AAT AAT AAT
5481432 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
5481450 TACAATTAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5481766 original size:47 final size:47
Alignment explanation
Indices: 5481626--5481772 Score: 187
Period size: 47 Copynumber: 3.2 Consensus size: 47
5481616 ACACTGCTCA
5481626 TACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
1 TACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
* * ** * * *
5481673 TACGTGATGAGGACG-GC-TGGTTATC-TATGGT--TGACACGGCTCC
1 TACGTGATGAAGA-GTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
5481716 TACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
1 TACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
5481763 TACGTGATGA
1 TACGTGATGA
5481773 GGACGGCTGG
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
42 1 0.01
43 23 0.29
44 6 0.08
45 10 0.12
46 6 0.08
47 33 0.41
48 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (47 bp):
TACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCC
Found at i:5481768 original size:90 final size:90
Alignment explanation
Indices: 5481615--5481865 Score: 390
Period size: 90 Copynumber: 2.9 Consensus size: 90
5481605 TGTTGGGGAC
*
5481615 GACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
1 GACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
5481680 TGAGGACGGCTGGTTATCTATGGTT
66 TGAGGACGGCTGGTTATCTATGGTT
*
5481705 GACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
1 GACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
5481770 TGAGGACGGCTGGTTATCTATGGTT
66 TGAGGACGGCTGGTTATCTATGGTT
* * * * *
5481795 GACACGGCTCATAAGTGATGAAGAGATC-TGG---TC-T--GGGGATGACACGGTTCCTACATGA
1 GACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
5481853 TGAGGACGGCTGG
66 TGAGGACGGCTGG
5481866 CCATCTAAAG
Statistics
Matches: 153, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
83 34 0.22
85 1 0.01
86 2 0.01
89 3 0.02
90 113 0.74
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (90 bp):
GACACGGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCTATGGTT
Found at i:5481883 original size:129 final size:129
Alignment explanation
Indices: 5481734--5482000 Score: 507
Period size: 129 Copynumber: 2.1 Consensus size: 129
5481724 GAAGAGTTCT
*
5481734 TGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
1 TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
5481799 CGGCTCATAAGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGC
66 CGGCTCATAAGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGC
*
5481863 TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGAGA
1 TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
*
5481928 CGGCTCATATGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGC
66 CGGCTCATAAGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGC
5481992 TGGCCATCT
1 TGGCCATCT
5482001 TTAGGAGTTA
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 135 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (129 bp):
TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACA
CGGCTCATAAGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGACGGC
Found at i:5482053 original size:28 final size:28
Alignment explanation
Indices: 5482033--5482094 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
5482023 AAACCAAATT
5482033 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
5482061 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
5482089 AAAGAT
1 AAAGAT
5482095 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:5483027 original size:64 final size:64
Alignment explanation
Indices: 5482948--5483117 Score: 157
Period size: 64 Copynumber: 2.6 Consensus size: 64
5482938 TTTCAAAATG
* * * *
5482948 AACATATTCAAAGATTTACTT-CAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGA
1 AACAGATTCAAAGATTT-CTTCCAAAAGAAACTATCTCAAGAGAGACAAAATT-ATGTTTCAA-A
5483010 GA
63 GA
* * * *
5483012 AACAGATTCAAAGATTTTTTCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGA
1 AACAGATTCAAAGATTTCTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTT-CAAAGA
* * * *
5483077 AACAGACTCAAAGATTTTTGTTTCAAAAGAAACAATCTCAA
1 AACAGATTCAAAGA--TTTCTTCCAAAAGAAACTATCTCAA
5483118 AGATTTTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
63 3 0.03
64 45 0.52
65 16 0.19
66 2 0.02
67 20 0.23
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (64 bp):
AACAGATTCAAAGATTTCTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTTCAAAGA
Found at i:5483132 original size:31 final size:30
Alignment explanation
Indices: 5483062--5483125 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
5483052 AGAGACAAAA
*
5483062 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
5483092 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
5483122 TTTT
1 TTTT
5483126 TTTTTCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:5483298 original size:29 final size:29
Alignment explanation
Indices: 5483230--5483483 Score: 349
Period size: 29 Copynumber: 8.8 Consensus size: 29
5483220 AACGAAATAG
*
5483230 ACTCAAAGATTTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
5483257 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
5483286 ACTCAAAG-TTTTTATTCAAAATGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
5483314 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
5483343 ACTCAAAGATTTTTATTCAAAATGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
5483372 ATTCAAAGATTTTTTTTTTCTCAAAA-GAACAA
1 ACTCAAAGA---TTTTTAT-TCAAAAGGAACAA
*
5483404 ACTCAAAGA-TTTT-TTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
5483431 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
5483460 ACTCAAAGATTTTTTTCTCAAAAG
1 ACTCAAAGATTTTTAT-TCAAAAG
5483484 AAATTGTCTT
Statistics
Matches: 204, Mismatches: 12, Indels: 19
0.87 0.05 0.08
Matches are distributed among these distances:
26 5 0.02
27 29 0.14
28 46 0.23
29 91 0.45
30 7 0.03
32 20 0.10
33 6 0.03
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:5483333 original size:57 final size:57
Alignment explanation
Indices: 5483230--5483476 Score: 351
Period size: 57 Copynumber: 4.3 Consensus size: 57
5483220 AACGAAATAG
5483230 ACTCAAAGATTTTTTTCAAAA-GAA-ACAACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAATGAACA-AACTCAAAGATTTTTATTCAAAAGGAACAA
5483286 ACTCAAAG-TTTTTATTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
* *
5483343 ACTCAAAGATTTTTATTCAAAATGAACAAATTCAAAGATTTTTTTTTTCTCAAAA-GAACAA
1 ACTCAAAGATTTTT-TTCAAAATGAACAAACTCAAAGA---TTTTTAT-TCAAAAGGAACAA
* * *
5483404 ACTCAAAGA-TTTTTTCAAGAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
5483460 ACTCAAAGATTTTTTTC
1 ACTCAAAGATTTTTTTC
5483477 TCAAAAGAAA
Statistics
Matches: 174, Mismatches: 7, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
55 11 0.06
56 36 0.21
57 48 0.28
58 29 0.17
59 19 0.11
60 4 0.02
61 21 0.12
62 6 0.03
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.32
Consensus pattern (57 bp):
ACTCAAAGATTTTTTTCAAAATGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:5483812 original size:36 final size:35
Alignment explanation
Indices: 5483728--5483825 Score: 110
Period size: 36 Copynumber: 2.8 Consensus size: 35
5483718 GAGAAAATGA
* *
5483728 TGTCTCAAGCGAGACGAAATTTG-CTTTAAGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGATAT
* **
5483762 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGCA-AT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTA-AG-ATAT
*
5483798 TGTCTCAAGCGAGACAAAGTTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT
5483826 TGAGAAAACA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
34 19 0.37
35 4 0.08
36 28 0.54
37 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAAGATAT
Found at i:5483924 original size:103 final size:105
Alignment explanation
Indices: 5483799--5484035 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 105
5483789 TAGAGCAATT
** * *
5483799 GTCTCAAGCGAGAC-AAAGTTTGTTTTTTGA-GAA-AACAATCTCAAGTGAGATCAACTTTGTTT
1 GTCTCAAGCGAGACGAAA-TTTGTTTTTAAATAAACAACAATCTCAAGTAAGATCAACTTTGTTT
* **
5483861 -AATGTGAAACAAATTCGAAATTTAG-ATCTCAAAGGGAAAAG
65 CAA-GTGAAACAAATTCAAAATTT-GTATCTCAAAGAAAAAAG
* * *
5483902 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAATCTCAAGTAAGATTAATTTTGTTTC
1 GTCTCAAGCGAGACGAAATTTGTTTTTAAATAAACAACAATCTCAAGTAAGATCAACTTTGTTTC
* *
5483967 AAGTGAAGCAAATTCAAAATTTGTATCTCAAAGAAAAAAT
66 AAGTGAAACAAATTCAAAATTTGTATCTCAAAGAAAAAAG
*
5484007 GTCTCAAACGAGACGAAATTT-TTTTTAAA
1 GTCTCAAGCGAGACGAAATTTGTTTTTAAA
5484036 GAGAAAGTTG
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
103 23 0.20
104 13 0.11
105 77 0.67
106 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (105 bp):
GTCTCAAGCGAGACGAAATTTGTTTTTAAATAAACAACAATCTCAAGTAAGATCAACTTTGTTTC
AAGTGAAACAAATTCAAAATTTGTATCTCAAAGAAAAAAG
Found at i:5484511 original size:4 final size:4
Alignment explanation
Indices: 5484454--5484499 Score: 78
Period size: 4 Copynumber: 12.0 Consensus size: 4
5484444 TTTATGTATC
5484454 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5484500 GTTGATGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 38 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5485697 original size:11 final size:11
Alignment explanation
Indices: 5485681--5485720 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
5485671 TTCTTTGCTC
5485681 TTTTTCTTTGA
1 TTTTTCTTTGA
5485692 TTTTTCTTTG-
1 TTTTTCTTTGA
5485702 TTTTTGCTTTGA
1 TTTTT-CTTTGA
5485714 TTTTTCT
1 TTTTTCT
5485721 CTCTGCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 17 0.63
12 5 0.19
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.75
Consensus pattern (11 bp):
TTTTTCTTTGA
Found at i:5485711 original size:22 final size:24
Alignment explanation
Indices: 5485669--5485731 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 24
5485659 TGTTCTTTGC
*
5485669 TTTTCTTTGCTCTTTTTCTTTGAT
1 TTTTCTTTGCTCTTTTGCTTTGAT
5485693 TTTTCTTTG-T-TTTTGCTTTGAT
1 TTTTCTTTGCTCTTTTGCTTTGAT
5485715 TTTTCTCTCTGCTCTTT
1 TTTTCT-T-TGCTCTTT
5485732 GTTTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 17 0.50
23 2 0.06
24 11 0.32
25 1 0.03
26 3 0.09
ACGTcount: A:0.03, C:0.17, G:0.10, T:0.70
Consensus pattern (24 bp):
TTTTCTTTGCTCTTTTGCTTTGAT
Found at i:5485742 original size:25 final size:25
Alignment explanation
Indices: 5485714--5485761 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5485704 TTTGCTTTGA
5485714 TTTTT-CTCTCTGCTCTTTGTTTTT
1 TTTTTGCTCTCTGCTCTTTGTTTTT
* *
5485738 TTTTTGCTCTTTTCTCTTTGTTTT
1 TTTTTGCTCTCTGCTCTTTGTTTT
5485762 GATTGGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.00, C:0.19, G:0.08, T:0.73
Consensus pattern (25 bp):
TTTTTGCTCTCTGCTCTTTGTTTTT
Found at i:5488655 original size:31 final size:31
Alignment explanation
Indices: 5488599--5488691 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
5488589 TGACAAAATG
5488599 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAA-AAATAAGTTAGTAT
5488631 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
5488662 ACACAAACAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGAAAAATAAGTTAGTA
5488692 CATGTAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 44 0.72
32 17 0.28
ACGTcount: A:0.61, C:0.10, G:0.14, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGTAT
Found at i:5492389 original size:3 final size:3
Alignment explanation
Indices: 5492381--5492431 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
5492371 ATGTAAATTA
* *
5492381 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5492429 AAT
1 AAT
5492432 TACAATTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:5493414 original size:21 final size:21
Alignment explanation
Indices: 5493389--5493428 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5493379 TCCAAGTTCA
5493389 ATAATTGAAACAAAGTTTACG
1 ATAATTGAAACAAAGTTTACG
5493410 ATAATTGAAACAAAGTTTA
1 ATAATTGAAACAAAGTTTA
5493429 AAAATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTTACG
Found at i:5494515 original size:12 final size:13
Alignment explanation
Indices: 5494491--5494519 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5494481 TTTTAAAAAT
5494491 AAAATATTATTTA
1 AAAATATTATTTA
5494504 AAAATATT-TTTA
1 AAAATATTATTTA
5494516 AAAA
1 AAAA
5494520 GTTAACCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:5496291 original size:52 final size:51
Alignment explanation
Indices: 5496214--5496313 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
5496204 TTGAAAACTT
* * *
5496214 AACAAAATAGGGGTTCATCTATTTTATCTCGTCTCGGGCCAAAAAATAAAA
1 AACAAAATAGGGGCTCATCTATTTTATCTCGTCACAGGCCAAAAAATAAAA
* * *
5496265 AACATAAATAGGGGCTCATTTCTTTTATTTCGTCACAGGCCAAAAAATA
1 AACA-AAATAGGGGCTCATCTATTTTATCTCGTCACAGGCCAAAAAATA
5496314 CATAGAGCCG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 4 0.10
52 38 0.90
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (51 bp):
AACAAAATAGGGGCTCATCTATTTTATCTCGTCACAGGCCAAAAAATAAAA
Found at i:5496711 original size:2 final size:2
Alignment explanation
Indices: 5496695--5496757 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
5496685 TATTCGAATT
5496695 TA TA T- TA TA TA -A TA TA TA TA TA TA T- TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5496733 TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5496758 AATTCAGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 5 0.09
2 51 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5497548 original size:14 final size:15
Alignment explanation
Indices: 5497507--5497552 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5497497 AATTACTGGA
5497507 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
5497522 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
5497537 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
5497551 AC
1 AC
5497553 ATTCCGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:5505939 original size:20 final size:20
Alignment explanation
Indices: 5505914--5505965 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5505904 TTAAGCTTAT
5505914 AGTATCGATACTGTTCAACC
1 AGTATCGATACTGTTCAACC
* *
5505934 AGTATCGATATTGTTCAATC
1 AGTATCGATACTGTTCAACC
5505954 AGTATCGATACT
1 AGTATCGATACT
5505966 CATACCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTGTTCAACC
Found at i:5509032 original size:21 final size:21
Alignment explanation
Indices: 5509008--5509066 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
5508998 ATTGTCCAAT
* * *
5509008 AAACTTGACATCTATAGCAAC
1 AAACTTGAAATCCATAACAAC
*
5509029 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
5509050 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
5509067 TAATAAATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.20, G:0.08, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:5511765 original size:35 final size:35
Alignment explanation
Indices: 5511716--5511964 Score: 291
Period size: 35 Copynumber: 7.1 Consensus size: 35
5511706 ATTTAGAGTT
* * *
5511716 TGAACGGAAAGAAGCATCGGTACTTTTGATTCAAG
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
* * * * *
5511751 TGAACGGAATGAAGCATCGGTAATTTTGATTCAAT
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
* *
5511786 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAG
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
*
5511821 TCAAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
1 T-GAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
* ** *
5511857 TGAACAGAAGGAAGCATATGCACTTTTGATTCAAG
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
* * * **
5511892 AAGAACGAAATGAAGCATCAACACTTTCGATTCAAG
1 -TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
*
5511928 TGAACGGAAGGAAGCATCAGCACTTTCGATTCAAG
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
5511963 TG
1 TG
5511965 TTCATCTTTT
Statistics
Matches: 183, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
35 124 0.68
36 59 0.32
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (35 bp):
TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAG
Found at i:5511861 original size:71 final size:70
Alignment explanation
Indices: 5511716--5511963 Score: 298
Period size: 71 Copynumber: 3.5 Consensus size: 70
5511706 ATTTAGAGTT
* * * * * * *
5511716 TGAACGGAAAGAAGCATCGGTACTTTTGATTCAAGTGAACGGAATGAAGCATCGGTAATTTTGAT
1 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGTAAACGGAATGAAGCATCGGCACTTTCGAT
*
5511781 TCAAT
66 TCAAG
*
5511786 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGTCAAACGGAAGGAAGCATCGGCACTTTCGA
1 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGT-AAACGGAATGAAGCATCGGCACTTTCGA
5511851 TTCAAG
65 TTCAAG
* ** * * * **
5511857 TGAACAGAAGGAAGCATATGCACTTTTGATTCAAGAAGAACGAAATGAAGCATCAACACTTTCGA
1 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGTA-AACGGAATGAAGCATCGGCACTTTCGA
5511922 TTCAAG
65 TTCAAG
* * *
5511928 TGAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
1 TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGT
5511964 GTTCATCTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
70 34 0.22
71 119 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (70 bp):
TGAACAGAAAGAAGCATCGGCACTTTCGATTCAAGTAAACGGAATGAAGCATCGGCACTTTCGAT
TCAAG
Found at i:5511934 original size:106 final size:105
Alignment explanation
Indices: 5511716--5511964 Score: 329
Period size: 106 Copynumber: 2.4 Consensus size: 105
5511706 ATTTAGAGTT
* * * * * * *
5511716 TGAACGGAAAGAAGCATCGGTACTTTTGATTCAAGTGAACGGAATGAAGCATCGGTAATTTTGAT
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAGGCAATTTTGAT
** **
5511781 TCAATTGAACAGAAAGAAGCATCGGCACTTTCGATTCAAG
66 TCAAAAGAACAGAAAGAAGCATCAACACTTTCGATTCAAG
* * *
5511821 TCAAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATATGCACTTTTGA
1 T-GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAGGCAATTTTGA
5511886 TTCAAGAAGAAC-GAAATGAAGCATCAACACTTTCGATTCAAG
65 TTCAA-AAGAACAGAAA-GAAGCATCAACACTTTCGATTCAAG
*
5511928 TGAACGGAAGGAAGCATCAGCACTTTCGATTCAAGTG
1 TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTG
5511965 TTCATCTTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 96 0.77
107 28 0.22
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (105 bp):
TGAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAGGCAATTTTGAT
TCAAAAGAACAGAAAGAAGCATCAACACTTTCGATTCAAG
Found at i:5512044 original size:52 final size:52
Alignment explanation
Indices: 5511982--5512081 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
5511972 TTTCATCAAG
5511982 AAGGTTGAGAAAGCAGAGAGAATGTTGAGAGTTACTGCACAGCAGATCCAAA
1 AAGGTTGAGAAAGCAGAGAGAATGTTGAGAGTTACTGCACAGCAGATCCAAA
* * *
5512034 AAGGTTGAGAAAGCAGGGAGAATGTTGAGAGTTACTGTACAGTAGATC
1 AAGGTTGAGAAAGCAGAGAGAATGTTGAGAGTTACTGCACAGCAGATC
5512082 TATGCATGCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.31, T:0.20
Consensus pattern (52 bp):
AAGGTTGAGAAAGCAGAGAGAATGTTGAGAGTTACTGCACAGCAGATCCAAA
Found at i:5512725 original size:68 final size:68
Alignment explanation
Indices: 5512653--5512811 Score: 151
Period size: 68 Copynumber: 2.3 Consensus size: 68
5512643 TTTCTATGTG
* ** * *
5512653 AGTCACTCAGAATAATATGATTAGGTGCTCCCGTGAAAGTTACTCTAATCTTTCAG-GGCTCCCG
1 AGTCACTCAGAATAATATGATTAGATGCTCCAATGAAAGTCACTCTAATC-TTCAGAGGCTCCCA
5512717 TGCA
65 TGCA
* ** ** * *
5512721 AGTCAC-CCGAAATAGCATGATTAGATGCTCCAATGCGAGTCACTCTAATCTTCTGAGGCTTCCA
1 AGTCACTCAG-AATAATATGATTAGATGCTCCAATGAAAGTCACTCTAATCTTCAGAGGCTCCCA
**
5512785 TGTG
65 TGCA
*
5512789 AGTCACTCAAAATAATATGATTA
1 AGTCACTCAGAATAATATGATTA
5512812 AGTACTCTAT
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
67 6 0.09
68 63 0.90
69 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (68 bp):
AGTCACTCAGAATAATATGATTAGATGCTCCAATGAAAGTCACTCTAATCTTCAGAGGCTCCCAT
GCA
Found at i:5516410 original size:15 final size:15
Alignment explanation
Indices: 5516390--5516419 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5516380 AAGATTCAGG
*
5516390 TTCTTCATCTTCGTC
1 TTCTTCATCGTCGTC
5516405 TTCTTCATCGTCGTC
1 TTCTTCATCGTCGTC
5516420 ATCGGCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.33, G:0.10, T:0.50
Consensus pattern (15 bp):
TTCTTCATCGTCGTC
Found at i:5530768 original size:14 final size:14
Alignment explanation
Indices: 5530749--5530802 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
5530739 TTAATAAGAA
5530749 AATGCAAAAATAAG
1 AATGCAAAAATAAG
**
5530763 AATGCAAATGTAGATG
1 AATGCAAAAATA-A-G
5530779 CAAATGCAAAAATAAG
1 --AATGCAAAAATAAG
5530795 AATGCAAA
1 AATGCAAA
5530803 TGTAGATGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 18 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 10 0.31
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (14 bp):
AATGCAAAAATAAG
Found at i:5530771 original size:20 final size:20
Alignment explanation
Indices: 5530748--5530804 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
5530738 ATTAATAAGA
5530748 AAATGCAAAAATAAGAATGC
1 AAATGCAAAAATAAGAATGC
5530768 AAATG------T-AGA-TGC
1 AAATGCAAAAATAAGAATGC
5530780 AAATGCAAAAATAAGAATGC
1 AAATGCAAAAATAAGAATGC
5530800 AAATG
1 AAATG
5530805 TAGATGCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 1 0.03
18 1 0.03
19 3 0.10
20 13 0.45
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATGCAAAAATAAGAATGC
Found at i:5530784 original size:32 final size:32
Alignment explanation
Indices: 5530748--5530820 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
5530738 ATTAATAAGA
5530748 AAATGCAAAAATAAGAATGCAAATGTAGATGC
1 AAATGCAAAAATAAGAATGCAAATGTAGATGC
5530780 AAATGCAAAAATAAGAATGCAAATGTAGATGC
1 AAATGCAAAAATAAGAATGCAAATGTAGATGC
5530812 AAATGCAAA
1 AAATGCAAA
5530821 TGCAAATGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.55, C:0.10, G:0.18, T:0.18
Consensus pattern (32 bp):
AAATGCAAAAATAAGAATGCAAATGTAGATGC
Found at i:5530785 original size:6 final size:6
Alignment explanation
Indices: 5530763--5530830 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
5530753 CAAAAATAAG
* * * * *
5530763 AATGCA AATGTA GATGCA AATGCAAA AAT-AA GAATGCA AATGTA GATGCA
1 AATGCA AATGCA AATGCA AATGC--A AATGCA -AATGCA AATGCA AATGCA
5530813 AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA
5530831 CGAGGTGTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
5 1 0.02
6 42 0.88
7 1 0.02
8 4 0.08
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (6 bp):
AATGCA
Found at i:5536662 original size:36 final size:36
Alignment explanation
Indices: 5536615--5536735 Score: 129
Period size: 36 Copynumber: 3.3 Consensus size: 36
5536605 GGGCAAGTCA
5536615 ATCTTAAGCCTTCACC-AGAGAGTAGTGAAACAAACC
1 ATCTTAAGCCTTCACCGA-AGAGTAGTGAAACAAACC
* * * *
5536651 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAACC
* * * *
5536687 ATCTTAAACATTCACCGAAGAGGAGT-AAAGCAAATC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAA-CAAACC
5536723 ATCTGTAAGCCTT
1 ATCT-TAAGCCTT
5536736 TAGAGCAAGA
Statistics
Matches: 68, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
35 2 0.03
36 59 0.87
37 7 0.10
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAACC
Found at i:5537102 original size:216 final size:216
Alignment explanation
Indices: 5536721--5537600 Score: 1485
Period size: 216 Copynumber: 4.1 Consensus size: 216
5536711 GTAAAGCAAA
* *
5536721 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* *
5536786 ATGTTTTCAAATGAATTTGAGAATGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
66 ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
*
5536851 AAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
131 AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
5536916 ATGATGCTTAAAATCCTTCGGG
196 ATGATGCTT-AAATCCTTCGGG
* *
5536938 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCTGGCCATCCATAAAACCTTTGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
5537003 ATGTTTTCACATGAATTTGAAAATG-AAGAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
66 ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
** *
5537067 AAGAATATGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGC
131 AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
**
5537132 ATGATGCTTAAATCCTTTTGG
196 ATGATGCTTAAATCCTTCGGG
* *
5537153 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATTCATAAAACCTACGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* * *
5537218 ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAAATGGAATTTTTAAAAATG
66 ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
*
5537283 AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGC
131 AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
*
5537348 ATGATGTTTAAATCCTTCGGG
196 ATGATGCTTAAATCCTTCGGG
* *
5537369 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCATTCAGGCCATCCATAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
5537434 ATGTTTTCACATGAATTTGAAAATG-AAAAAATGATGTTTTAAGAAGATGAAATTTTTTGAAAAC
66 ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGGAA-TTTTTGAAAAC
*
5537498 GAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGACCATCAGTAAGTCTTTCGAG
130 GAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG
5537563 CATGATGCTTAAATCCTTCGGG
195 CATGATGCTTAAATCCTTCGGG
* * *
5537585 GCATCTATAAGACTTT
1 TCATCTGTAAGCCTTT
5537601 CAGGTATGAT
Statistics
Matches: 621, Mismatches: 40, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
215 121 0.19
216 416 0.67
217 84 0.14
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (216 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACG
AAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
ATGATGCTTAAATCCTTCGGG
Found at i:5537640 original size:57 final size:56
Alignment explanation
Indices: 5537572--5537716 Score: 143
Period size: 57 Copynumber: 2.6 Consensus size: 56
5537562 GCATGATGCT
* * * *
5537572 TAAATCCTTCGGGGCATCTATAAGACTTTCAGGTATGATGTTTT-CACTGCAAGATGA
1 TAAATCATTCGGGCCATCTATAAGACTTTCAGGCAGGATGTTTTGCAC--CAAGATGA
* * *
5537629 TAAATCATTCGGGTCATCCATAAGACCTTT-GGGCAGGATGTTTTGCACCAAGATGA
1 TAAATCATTCGGGCCATCTATAAGA-CTTTCAGGCAGGATGTTTTGCACCAAGATGA
* * *
5537685 TAAGTCATCCGGGCCAT-TTTAAGACTTCTCAG
1 TAAATCATTCGGGCCATCTATAAGACTT-TCAG
5537717 AAGAATAGGG
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
54 3 0.04
55 6 0.08
56 23 0.32
57 33 0.46
58 7 0.10
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (56 bp):
TAAATCATTCGGGCCATCTATAAGACTTTCAGGCAGGATGTTTTGCACCAAGATGA
Found at i:5541292 original size:21 final size:20
Alignment explanation
Indices: 5541249--5541292 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
5541239 GTGTAAATAC
* * *
5541249 AATTTAAATATTATATTTTT
1 AATTTAAATATAATATATAT
5541269 AATTTACAATATAATATATAT
1 AATTTA-AATATAATATATAT
5541290 AAT
1 AAT
5541293 AATTATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAAATATAATATATAT
Found at i:5542816 original size:16 final size:16
Alignment explanation
Indices: 5542791--5542821 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5542781 AACATATGAA
5542791 ATTTCATAGATTTTGT
1 ATTTCATAGATTTTGT
*
5542807 ATTTCCTAGATTTTG
1 ATTTCATAGATTTTG
5542822 GATTCAGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.55
Consensus pattern (16 bp):
ATTTCATAGATTTTGT
Found at i:5546389 original size:2 final size:2
Alignment explanation
Indices: 5546384--5546443 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
5546374 TAAAAAAAAC
5546384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5546426 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
5546444 TCACATAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5552553 original size:17 final size:17
Alignment explanation
Indices: 5552531--5552566 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5552521 GATTTTGAGT
5552531 TCGATTCAAGCTCGAAC
1 TCGATTCAAGCTCGAAC
5552548 TCGATTCAAGCTCGAAC
1 TCGATTCAAGCTCGAAC
5552565 TC
1 TC
5552567 AAACTCGAAT
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:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (17 bp):
TCGATTCAAGCTCGAAC
Found at i:5552561 original size:11 final size:11
Alignment explanation
Indices: 5552481--5552597 Score: 57
Period size: 11 Copynumber: 10.6 Consensus size: 11
5552471 AAAATTCAGG
*
5552481 AGCTCGATTAA
1 AGCTCGATTCA
* *
5552492 AGCTCGAGACTCG
1 AGCTC--GATTCA
*
5552505 AGCTCGATTGA
1 AGCTCGATTCA
**
5552516 AGCTCGATTTTG
1 AGCTCGA-TTCA
*
5552528 AGTTCGATTCA
1 AGCTCGATTCA
5552539 AGCTCG----A
1 AGCTCGATTCA
5552546 A-CTCGATTCA
1 AGCTCGATTCA
*
5552556 AGCTCGAACTCA
1 AGCTCG-ATTCA
*
5552568 AACTCGAATT-A
1 AGCTCG-ATTCA
5552579 GAGCTCGATTCA
1 -AGCTCGATTCA
5552591 AGCTCGA
1 AGCTCGA
5552598 ACTCAAACTC
Statistics
Matches: 79, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
10 2 0.03
11 37 0.47
12 26 0.33
13 8 0.10
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:5552573 original size:12 final size:12
Alignment explanation
Indices: 5552553--5552610 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
5552543 CGAACTCGAT
5552553 TCAAGCTCGAAC
1 TCAAGCTCGAAC
*
5552565 TCAAACTCGAA-
1 TCAAGCTCGAAC
* *
5552576 TTAGAGCTCG-AT
1 TCA-AGCTCGAAC
5552588 TCAAGCTCGAAC
1 TCAAGCTCGAAC
*
5552600 TCAAACTCGAA
1 TCAAGCTCGAA
5552611 TTTGAACCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (12 bp):
TCAAGCTCGAAC
Found at i:5554302 original size:11 final size:11
Alignment explanation
Indices: 5554286--5554359 Score: 85
Period size: 11 Copynumber: 7.5 Consensus size: 11
5554276 GTAAAATGTT
5554286 ATCATGACTCG
1 ATCATGACTCG
5554297 ATCATG-C-C-
1 ATCATGACTCG
5554305 ATCATGACTCG
1 ATCATGACTCG
5554316 ATCATG-C-C-
1 ATCATGACTCG
5554324 ATCATGACTCG
1 ATCATGACTCG
5554335 ATCATG-C-C-
1 ATCATGACTCG
5554343 ATCATGACTCG
1 ATCATGACTCG
5554354 ATCATG
1 ATCATG
5554360 CCATTCATGC
Statistics
Matches: 54, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
8 18 0.33
9 6 0.11
10 6 0.11
11 24 0.44
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (11 bp):
ATCATGACTCG
Found at i:5554310 original size:8 final size:8
Alignment explanation
Indices: 5554297--5554369 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
5554287 TCATGACTCG
5554297 ATCATGCC
1 ATCATGCC
5554305 ATCATGACTC
1 ATCATG-C-C
5554315 GATCATGCC
1 -ATCATGCC
5554324 ATCATGACTC
1 ATCATG-C-C
5554334 GATCATGCC
1 -ATCATGCC
5554343 ATCATGACTC
1 ATCATG-C-C
5554353 GATCATGCC
1 -ATCATGCC
5554362 ATTCATGC
1 A-TCATGC
5554370 AATTCAAGAG
Statistics
Matches: 55, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
8 19 0.35
9 12 0.22
10 6 0.11
11 18 0.33
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (8 bp):
ATCATGCC
Found at i:5554310 original size:19 final size:19
Alignment explanation
Indices: 5554286--5554368 Score: 157
Period size: 19 Copynumber: 4.3 Consensus size: 19
5554276 GTAAAATGTT
5554286 ATCATGACTCGATCATGCC
1 ATCATGACTCGATCATGCC
5554305 ATCATGACTCGATCATGCC
1 ATCATGACTCGATCATGCC
5554324 ATCATGACTCGATCATGCC
1 ATCATGACTCGATCATGCC
5554343 ATCATGACTCGATCATGCC
1 ATCATGACTCGATCATGCC
5554362 ATTCATG
1 A-TCATG
5554369 CAATTCAAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 58 0.92
20 5 0.08
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (19 bp):
ATCATGACTCGATCATGCC
Found at i:5555440 original size:17 final size:18
Alignment explanation
Indices: 5555418--5555460 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
5555408 TTAGTGTTCC
5555418 TTTAATT-TGTACTTGT-T
1 TTTAATTGTGT-CTTGTAT
5555435 TTTAATTGTGTCTTGTAAT
1 TTTAATTGTGTCTTGT-AT
5555454 TTTAATT
1 TTTAATT
5555461 ATTTTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.21, C:0.05, G:0.12, T:0.63
Consensus pattern (18 bp):
TTTAATTGTGTCTTGTAT
Found at i:5555914 original size:7 final size:7
Alignment explanation
Indices: 5555844--5555929 Score: 61
Period size: 7 Copynumber: 11.7 Consensus size: 7
5555834 GTGTATAACT
*
5555844 TAAACCC
1 TAAACCA
5555851 TAAATCC-
1 TAAA-CCA
5555858 TAACACC-
1 TAA-ACCA
5555865 TAAACCA
1 TAAACCA
*
5555872 TAAACTA
1 TAAACCA
5555879 TAAACTCA
1 TAAAC-CA
*
5555887 -AAACCC
1 TAAACCA
5555893 TAAACCCTA
1 TAAA-CC-A
5555902 TTTAAACCA
1 --TAAACCA
5555911 TAAACCA
1 TAAACCA
5555918 TAAACCA
1 TAAACCA
5555925 TAAAC
1 TAAAC
5555930 TCTATCACAC
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
6 4 0.06
7 49 0.74
8 6 0.09
9 1 0.02
10 2 0.03
11 4 0.06
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCA
Found at i:5555914 original size:32 final size:32
Alignment explanation
Indices: 5555872--5555934 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
5555862 ACCTAAACCA
* *
5555872 TAAACTATAAACTCA-AAACCCTAAACCCTATT
1 TAAACCATAAAC-CATAAACCATAAACCCTATT
*
5555904 TAAACCATAAACCATAAACCATAAACTCTAT
1 TAAACCATAAACCATAAACCATAAACCCTAT
5555935 CACACAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (32 bp):
TAAACCATAAACCATAAACCATAAACCCTATT
Found at i:5556030 original size:14 final size:14
Alignment explanation
Indices: 5556011--5556040 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5556001 TATAATTATC
*
5556011 AATAATGTATTTTT
1 AATAATGTAATTTT
5556025 AATAATGTAATTTT
1 AATAATGTAATTTT
5556039 AA
1 AA
5556041 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:5556185 original size:37 final size:37
Alignment explanation
Indices: 5556144--5556262 Score: 95
Period size: 37 Copynumber: 3.2 Consensus size: 37
5556134 CGAGTCGAGC
5556144 TCGAG-CTCGAGTCGAGTCCATTCGATCCGAGTATTTA
1 TCGAGCCTCGAGTCGAGTCCATTC-ATCCGAGTATTTA
* * ** *
5556181 TCGAGCCTTGA-TCGAGTCGA-TC-T-CGAGTAGCTC
1 TCGAGCCTCGAGTCGAGTCCATTCATCCGAGTATTTA
* *
5556214 GCGATCTGTCTCGAGTCGAGTCCATTCAATCCGAGTATTTA
1 TCGA---GCCTCGAGTCGAGTCCATTC-ATCCGAGTATTTA
5556255 TCGAGCCT
1 TCGAGCCT
5556263 TCTGCATCAT
Statistics
Matches: 59, Mismatches: 14, Indels: 17
0.66 0.16 0.19
Matches are distributed among these distances:
33 10 0.17
34 1 0.02
36 7 0.12
37 21 0.36
38 9 0.15
40 1 0.02
41 10 0.17
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.29
Consensus pattern (37 bp):
TCGAGCCTCGAGTCGAGTCCATTCATCCGAGTATTTA
Found at i:5556674 original size:20 final size:20
Alignment explanation
Indices: 5556649--5556761 Score: 208
Period size: 20 Copynumber: 5.7 Consensus size: 20
5556639 TTTTCCTAAT
5556649 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
5556669 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
5556689 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5556709 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
5556729 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
5556749 TCGCAACGCGAAT
1 TCGCAATGCGAAT
5556762 CTGACTATCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:5556771 original size:20 final size:20
Alignment explanation
Indices: 5556748--5556794 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5556738 GAATACGTAA
**
5556748 ATCGCAACGCGAATCTGACT
1 ATCGCAACAAGAATCTGACT
*
5556768 ATCGCAACAAGATTCTGACT
1 ATCGCAACAAGAATCTGACT
5556788 ATCGCAA
1 ATCGCAA
5556795 TACTGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACAAGAATCTGACT
Found at i:5557435 original size:20 final size:21
Alignment explanation
Indices: 5557410--5557488 Score: 103
Period size: 20 Copynumber: 4.0 Consensus size: 21
5557400 CAACGTGGAA
5557410 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCAGAATATGACT
* *
5557430 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCAGAATATGACT
5557450 ATCGCAACGCAGAAT-TGACT
1 ATCGCAACGCAGAATATGACT
*
5557470 ATCGCAACGC-GAAAATGAC
1 ATCGCAACGCAGAATATGAC
5557489 AATCACAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.06
20 46 0.88
21 3 0.06
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCAGAATATGACT
Found at i:5557469 original size:40 final size:40
Alignment explanation
Indices: 5557410--5557488 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
5557400 CAACGTGGAA
*
5557410 ATCGCAACGCGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGAAAATGACT
*
5557450 ATCGCAACGCAGAAT-TGACTATCGCAACGCGAAAATGAC
1 ATCGCAACGC-GAATATGACTATCGCAACACGAAAATGAC
5557489 AATCACAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.16
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGAAAATGACT
Found at i:5557560 original size:34 final size:34
Alignment explanation
Indices: 5557470--5557565 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
5557460 AGAATTGACT
* * * *
5557470 ATCGCAACGCGAAAATGACAATCACAATGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
5557504 ATCGCAATGCG-AAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
5557537 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
5557566 CGAATTTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGAGA
Found at i:5557561 original size:20 final size:19
Alignment explanation
Indices: 5557503--5557569 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
5557493 ACAATGAGAG
5557503 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5557522 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
5557536 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
5557556 AATCGCAACGCGAA
1 AATCGCAATGCGAA
5557570 TTTAGTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
19 11 0.28
20 13 0.33
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5557621 original size:14 final size:14
Alignment explanation
Indices: 5557602--5557669 Score: 73
Period size: 14 Copynumber: 4.5 Consensus size: 14
5557592 CATTTTCGCA
5557602 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
5557616 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
5557630 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
5557647 CATTGCGATTCTCTCA
1 --TTGCGATTCTCTCG
5557663 TTGCGAT
1 TTGCGAT
5557670 AGTCATTTCC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
14 27 0.59
16 6 0.13
17 7 0.15
19 6 0.13
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:5557658 original size:33 final size:34
Alignment explanation
Indices: 5557616--5557689 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
5557606 GATTCTCTCG
* **
5557616 TTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
1 TTGCGATTCTCTCATTGCGATAGTCATTTCCGCA
5557649 TTGCGATTCTCTCATTGCGATAGTCATTTCCGCA
1 TTGCGATTCTCTCATTGCGATAGTCATTTCCGCA
5557683 TTGCGAT
1 TTGCGAT
5557690 AGTCTGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 26 0.70
34 11 0.30
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (34 bp):
TTGCGATTCTCTCATTGCGATAGTCATTTCCGCA
Found at i:5557816 original size:14 final size:14
Alignment explanation
Indices: 5557797--5557831 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5557787 TCAATTAAAT
5557797 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
5557811 AAATCATCTTTTAC
1 AAATCAACATTTAC
5557825 AAATCAA
1 AAATCAA
5557832 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:5559310 original size:42 final size:42
Alignment explanation
Indices: 5559231--5559323 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
5559221 CCTCTTCAAC
* * *
5559231 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
5559273 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
5559315 GATGACAGG
1 GATGACAGG
5559324 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:5559830 original size:20 final size:20
Alignment explanation
Indices: 5559807--5559911 Score: 156
Period size: 20 Copynumber: 5.2 Consensus size: 20
5559797 CTTAAAATCA
5559807 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
5559827 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
5559847 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
* **
5559867 CAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
* **
5559887 CAATGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
5559907 CAACG
1 CAACG
5559912 AGAGAATCGC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:5559981 original size:20 final size:20
Alignment explanation
Indices: 5559956--5560132 Score: 166
Period size: 20 Copynumber: 9.5 Consensus size: 20
5559946 GATTCTTTCG
**
5559956 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
5559976 TTGCGATAGACATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
5559996 TTGTGATAGTCATTTTCTCA
1 TTGCGATAGTCATTTTCGCA
*
5560016 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
5560036 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
5560050 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
5560069 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
5560083 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
5560103 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
5560123 TTGCGATAGT
1 TTGCGATAGT
5560133 AAACTATTAT
Statistics
Matches: 132, Mismatches: 11, Indels: 28
0.77 0.06 0.16
Matches are distributed among these distances:
14 14 0.11
16 12 0.09
17 6 0.05
18 5 0.04
19 7 0.05
20 88 0.67
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:5560073 original size:33 final size:34
Alignment explanation
Indices: 5560011--5560109 Score: 128
Period size: 33 Copynumber: 2.9 Consensus size: 34
5560001 ATAGTCATTT
* * *
5560011 TCTCATTGCGATAGTCATTTTCGCGTTGCGATTT
1 TCTCGTTGCGATAGTCATTTTCGCATTGCGATTC
* * **
5560045 TGTTGTTGCGATTTTCA-TTTCGCATTGCGATTC
1 TCTCGTTGCGATAGTCATTTTCGCATTGCGATTC
5560078 TCTCGTTGCGATAGTCATTTTCGCATTGCGAT
1 TCTCGTTGCGATAGTCATTTTCGCATTGCGAT
5560110 AGTCATTTTC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.44
Consensus pattern (34 bp):
TCTCGTTGCGATAGTCATTTTCGCATTGCGATTC
Found at i:5561890 original size:20 final size:20
Alignment explanation
Indices: 5561867--5561916 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5561857 TTGAAACTTT
5561867 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
5561887 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
5561907 CTATCGCAAC
1 AAATCGCAAC
5561917 GCTAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.24, G:0.14, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:5562363 original size:22 final size:22
Alignment explanation
Indices: 5562301--5562366 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
5562291 TGACCGTGAA
*
5562301 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
5562323 TGATATCGTCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAC
5562345 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
5562367 GGATGTCGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.21, C:0.12, G:0.39, T:0.27
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:5562593 original size:20 final size:20
Alignment explanation
Indices: 5562570--5562675 Score: 194
Period size: 20 Copynumber: 5.3 Consensus size: 20
5562560 CAGATTTGCG
*
5562570 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
5562590 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
5562610 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
5562630 TTGCGATTTACGTATTCACA
1 TTGCGATTTACGTATTCGCA
5562650 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
5562670 TTGCGA
1 TTGCGA
5562676 ATTAGGAAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:5562738 original size:21 final size:21
Alignment explanation
Indices: 5562665--5562738 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
5562655 ATTTACGTAT
*
5562665 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
5562686 TCACATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* *
5562707 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
5562728 TCGTAATGCGA
1 TCGCAATGCGA
5562739 TAGTCAGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:5563344 original size:22 final size:18
Alignment explanation
Indices: 5563299--5563341 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
5563289 GTTGTTTTTA
5563299 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
5563317 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
5563335 AAATAAA
1 AAATAAA
5563342 TAATTTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:5565122 original size:12 final size:12
Alignment explanation
Indices: 5565094--5565136 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5565084 ATTGTCTCTT
5565094 TTTTTCCTTTTC
1 TTTTTCCTTTTC
*
5565106 CTTTTCCTTTTC
1 TTTTTCCTTTTC
*
5565118 TTTTTTTCTTTTTC
1 --TTTTTCCTTTTC
5565132 TTTTT
1 TTTTT
5565137 TCGTTCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTCCTTTTC
Found at i:5565124 original size:14 final size:14
Alignment explanation
Indices: 5565090--5565137 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
5565080 ACAAATTGTC
5565090 TCTTTTTTTCCTTT
1 TCTTTTTTTCCTTT
*
5565104 TC--CTTTTCCTTT
1 TCTTTTTTTCCTTT
*
5565116 TCTTTTTTTCTTTT
1 TCTTTTTTTCCTTT
5565130 TCTTTTTT
1 TCTTTTTT
5565138 CGTTCGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.38
14 18 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TCTTTTTTTCCTTT
Found at i:5566424 original size:40 final size:40
Alignment explanation
Indices: 5566380--5566608 Score: 141
Period size: 40 Copynumber: 5.8 Consensus size: 40
5566370 CAACGCGATT
* **
5566380 TTGCGATAGTCCAAGTTCGCGTTGAGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCACGTTGAGATAGTCCAAATTCG
** * * *
5566420 TTGCGATTTTTCAAATTTACG-T----TAGTCCAAATTCG
1 TTGCGATAGTCCAAGTTCACGTTGAGATAGTCCAAATTCG
* * * *
5566455 TTGCGATAGTCAAAGTTCACGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCACGTTGAGATAGTCCAAATT--CG
** * * *
5566497 TTGCGATTTTCCAAATTCA--TTGCTG-TAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTCACGTTG-AGATAGTCCAAATT--CG
* * * * **
5566537 TTGTGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCG
1 TTGCGATAGTCCAAGTTCACGTTGAGATAGTCCAAATTCG
*
5566577 TTGCGATAGTCCAAGTTCACGTTGCGATAGTC
1 TTGCGATAGTCCAAGTTCACGTTGAGATAGTC
5566609 GAAGTTCGCG
Statistics
Matches: 140, Mismatches: 38, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
35 26 0.19
36 1 0.01
39 1 0.01
40 82 0.59
41 2 0.01
42 28 0.20
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (40 bp):
TTGCGATAGTCCAAGTTCACGTTGAGATAGTCCAAATTCG
Found at i:5566477 original size:35 final size:35
Alignment explanation
Indices: 5566410--5566477 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
5566400 GTTGAGATTT
** *
5566410 TCCAAATTCGTTGCGATTTTTCAAATTTACGTTAG
1 TCCAAATTCGTTGCGATTAGTCAAATTCACGTTAG
5566445 TCCAAATTCGTTGCGA-TAGTCAAAGTTCACGTT
1 TCCAAATTCGTTGCGATTAGTCAAA-TTCACGTT
5566478 GCGATAGTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 6 0.21
35 23 0.79
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.38
Consensus pattern (35 bp):
TCCAAATTCGTTGCGATTAGTCAAATTCACGTTAG
Found at i:5566478 original size:21 final size:21
Alignment explanation
Indices: 5566453--5566625 Score: 153
Period size: 21 Copynumber: 8.4 Consensus size: 21
5566443 AGTCCAAATT
5566453 CGTTGCGATAGTCAAAGTTCA
1 CGTTGCGATAGTCAAAGTTCA
* *
5566474 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCAAAGTTCA
**
5566495 CGTTGCGATTTTCCAAA-TTCA
1 CGTTGCGATAGT-CAAAGTTCA
*
5566516 --TTGCTG-TAGTCCAAGTTCA
1 CGTTGC-GATAGTCAAAGTTCA
* * *
5566535 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCAAAGTTCA
**
5566556 CGTTGCGATTTTCCAAA-TT--
1 CGTTGCGATAGT-CAAAGTTCA
*
5566575 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCAAAGTTCA
* *
5566596 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCAAAGTTCA
5566617 CGTTGCGAT
1 CGTTGCGAT
5566626 TTTCCAAAAT
Statistics
Matches: 121, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
18 6 0.05
19 22 0.18
20 2 0.02
21 85 0.70
22 6 0.05
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCAAAGTTCA
Found at i:5566526 original size:61 final size:61
Alignment explanation
Indices: 5566445--5566633 Score: 335
Period size: 61 Copynumber: 3.1 Consensus size: 61
5566435 TTTACGTTAG
*
5566445 TCCAAATTCGTTGCGATAGTCAAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
* *
5566506 TCCAAATTCATTGCTG-TAGTCCAAGTTCACGTTGTGATAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGTTGC-GATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
5566567 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
5566628 TCCAAA
1 TCCAAA
5566634 ATCACAACGA
Statistics
Matches: 121, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
60 1 0.01
61 119 0.98
62 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (61 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTT
Found at i:5567069 original size:19 final size:20
Alignment explanation
Indices: 5567044--5567134 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
5567034 CTTATTTTGG
5567044 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
5567064 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
5567084 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
5567108 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
5567127 ATTTTTCA
1 ATTTTTCA
5567135 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:5567106 original size:44 final size:41
Alignment explanation
Indices: 5567055--5567136 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
5567045 TTTTTCACTA
* *
5567055 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
5567099 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
5567137 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:5567568 original size:5 final size:5
Alignment explanation
Indices: 5567558--5567623 Score: 69
Period size: 5 Copynumber: 12.0 Consensus size: 5
5567548 TGTTTGGAGA
*
5567558 AAAAT AAAAT AAAATT AAACAT CAAAT AAAAT AAAAT AAAGAGTT AAAAAT
1 AAAAT AAAAT AAAA-T AAA-AT AAAAT AAAAT AAAAT AAA-A--T -AAAAT
5567609 AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT
5567624 GGGTTGTCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
5 38 0.72
6 9 0.17
7 1 0.02
8 2 0.04
9 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:5567614 original size:29 final size:27
Alignment explanation
Indices: 5567558--5567623 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 27
5567548 TGTTTGGAGA
* *
5567558 AAAATAAAATAAAATTAAACATCAAAT
1 AAAATAAAATAAAATTAAAAATAAAAT
5567585 AAAATAAAATAAAGAGTTAAAAATAAAAT
1 AAAATAAAATAAA-A-TTAAAAATAAAAT
5567614 AAAATAAAAT
1 AAAATAAAAT
5567624 GGGTTGTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
29 21 0.60
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (27 bp):
AAAATAAAATAAAATTAAAAATAAAAT
Found at i:5571133 original size:24 final size:24
Alignment explanation
Indices: 5571065--5571142 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
5571055 GATATCAGAA
* * *
5571065 ATCAAAACATAATTCAAATCATAT
1 ATCAGAACAGAATTCAAGTCATAT
* * *
5571089 ATCAGAACAGAATCCAGGTCATGT
1 ATCAGAACAGAATTCAAGTCATAT
* * * *
5571113 ATCATAATAGAATTCAAGTCAGAA
1 ATCAGAACAGAATTCAAGTCATAT
5571137 ATCAGA
1 ATCAGA
5571143 TAAAATCTTT
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCATAT
Found at i:5582587 original size:20 final size:20
Alignment explanation
Indices: 5582559--5582596 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5582549 TTTATATGTA
5582559 TTAAATTTTAAATTATTTGC
1 TTAAATTTTAAATTATTTGC
* *
5582579 TTAATTTTTTAATTATTT
1 TTAAATTTTAAATTATTT
5582597 ATTCTTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
TTAAATTTTAAATTATTTGC
Found at i:5589255 original size:3 final size:3
Alignment explanation
Indices: 5589247--5589273 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5589237 AGAGAGAATT
5589247 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
5589274 AAGGGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5597901 original size:40 final size:40
Alignment explanation
Indices: 5597857--5598174 Score: 483
Period size: 40 Copynumber: 8.0 Consensus size: 40
5597847 TTCATTTGAC
* * *
5597857 TCAAGACTGTTTTTCCTTGAAACACAAGATTTTATCTTAT
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
* *
5597897 TCAAGATTGTTTTTCCTTGAAACAAAATATTTTATCTCAC
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
*
5597937 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAC
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
* *
5597977 TCAAGATTGTTTTTCCTTGAAACAGAAGATTTAATCTCAT
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
* *
5598017 TCAAGATTGTTTCTCCTTGAAACAGAAGATTTTATCTCAT
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
* * *
5598057 TCAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCAC
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
* * *
5598097 TCAAGATTGTTTTTCCTTGAAACATAAGTTTTTATCTCGT
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
*
5598137 TCAAGATTGTTTTTCCTTGAAACAAAAAATTTTATCTC
1 TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTC
5598175 CCTTGAGATA
Statistics
Matches: 256, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 256 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (40 bp):
TCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCAT
Found at i:5597939 original size:80 final size:80
Alignment explanation
Indices: 5597855--5598213 Score: 506
Period size: 80 Copynumber: 4.5 Consensus size: 80
5597845 ATTTCATTTG
* *
5597855 ACTCAAGACTGTTTTTCCTTGAAACACAAGATTTTATCTTATTCAAGATTGTTTTTCCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACACAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
5597920 AAAATATTTTATCTC
66 AAAAGATTTTATCTC
* *
5597935 ACTCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACACAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* *
5598000 AGAAGATTTAATCTC
66 AAAAGATTTTATCTC
* * * *
5598015 ATTCAAGATTGTTTCTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTATTTTTCCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACACAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
5598080 AGAAGATTTTATCTC
66 AAAAGATTTTATCTC
* * *
5598095 ACTCAAGATTGTTTTTCCTTGAAACATAAGTTTTTATCTCGTTCAAGATTGTTTTTCCTTGAAAC
1 ACTCAAGATTGTTTTTCCTTGAAACACAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
5598160 AAAAAATTTTATCTC
66 AAAAGATTTTATCTC
* ** * *
5598175 CCTTGAGATAG-TTTTCCTTGAAACGACAA-ATTTTGTCTC
1 ACTCAAGATTGTTTTTCCTTGAAAC-ACAAGATTTTATCTC
5598214 CCTTGAGATA
Statistics
Matches: 250, Mismatches: 28, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
79 21 0.08
80 229 0.92
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (80 bp):
ACTCAAGATTGTTTTTCCTTGAAACACAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
AAAAGATTTTATCTC
Found at i:5598054 original size:23 final size:23
Alignment explanation
Indices: 5598019--5598087 Score: 53
Period size: 23 Copynumber: 3.3 Consensus size: 23
5598009 AATCTCATTC
*
5598019 AAGATTGTTTCTCCTTGAAACAG
1 AAGATTATTTCTCCTTGAAACAG
*
5598042 AAGATT-TTATCTCATT----C--
1 AAGATTATT-TCTCCTTGAAACAG
*
5598059 AAGATTATTTTTCCTTGAAACAG
1 AAGATTATTTCTCCTTGAAACAG
5598082 AAGATT
1 AAGATT
5598088 TTATCTCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 18 0.51
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (23 bp):
AAGATTATTTCTCCTTGAAACAG
Found at i:5598189 original size:40 final size:40
Alignment explanation
Indices: 5597859--5598238 Score: 396
Period size: 40 Copynumber: 9.6 Consensus size: 40
5597849 CATTTGACTC
* * **
5597859 AAGACTGTTTTTCCTTGAAACACAAGATTTTATCT-TATT
1 AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * *
5597898 CAAGATTGTTTTTCCTTGAAACAAAATATTTTATCTCACTC
1 -AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* *
5597939 AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * *
5597979 AAGATTGTTTTTCCTTGAAACAGAAGATTTAATCT-CATT
1 AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * *
5598018 CAAGATTGTTTCTCCTTGAAACAGAAGATTTTATCT-CATT
1 -AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * * *
5598058 CAAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 -AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * *
5598099 AAGATTGTTTTTCCTTGAAACATAAGTTTTTATCT-CGTT
1 AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
*
5598138 CAAGATTGTTTTTCCTTGAAACAAAAAATTTTATCTCCCTT
1 -AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
* * * *
5598179 GAGATAG-TTTTCCTTGAAACGACAA-ATTTTGTCTCCCTT
1 AAGATTGTTTTTCCTTGAAAC-AAAAGATTTTATCTCCCTT
* * *
5598218 GAGATAGTTTCT-CTTGAAACA
1 AAGATTGTTTTTCCTTGAAACA
5598239 CAGAACTTTG
Statistics
Matches: 299, Mismatches: 34, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
38 1 0.00
39 43 0.14
40 250 0.84
41 5 0.02
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (40 bp):
AAGATTGTTTTTCCTTGAAACAAAAGATTTTATCTCCCTT
Found at i:5598329 original size:65 final size:66
Alignment explanation
Indices: 5598177--5598334 Score: 169
Period size: 66 Copynumber: 2.4 Consensus size: 66
5598167 TTTATCTCCC
* * * *
5598177 TTGAGATAGTTTTCCTTGAAACGACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAG
1 TTGAGATAGTTTCCCTTG-AA--ACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAACACAG
5598242 AACT
63 AACT
* * *
5598246 TTGA-AAACGTTTCCCTTGAAACAAATTTTGTTTCTCTTAAGACAGTTTTCCCTTGAAACA-AG-
1 TTGAGATA-GTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAG-TTTCCCTTGAAACACAGA
**
5598308 TTT
64 ACT
5598311 TTGAGATAGTTTCCCTTGAAACAA
1 TTGAGATAGTTTCCCTTGAAACAA
5598335 GAAATTGAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
65 21 0.28
66 25 0.33
67 13 0.17
68 4 0.05
69 13 0.17
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (66 bp):
TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTAAGACAGTTTCCCTTGAAACACAGAAC
T
Done.