Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 162 of 167
Found at i:53754063 original size:24 final size:24
Alignment explanation
Indices: 53754032--53754083 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53754022 TACAATTTTA
* *
53754032 AAAATTTTTAATT-TTTATTATTT
1 AAAATTTTTTATTATTTATGATTT
53754055 AAAATTTTTTATTATTTATGATTT
1 AAAATTTTTTATTATTTATGATTT
*
53754079 TAAAT
1 AAAAT
53754084 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
AAAATTTTTTATTATTTATGATTT
Found at i:53754097 original size:19 final size:19
Alignment explanation
Indices: 53754075--53754111 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
53754065 ATTATTTATG
53754075 ATTTT-AAATAAATTTTAAA
1 ATTTTAAAAT-AATTTTAAA
53754094 ATTTTAAAATAATTTTAA
1 ATTTTAAAATAATTTTAA
53754112 TCTATTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTAAAATAATTTTAAA
Found at i:53754693 original size:21 final size:21
Alignment explanation
Indices: 53754668--53754707 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53754658 GCTTCTTTGC
53754668 CTTTACTCTTTCTTCTCTGAA
1 CTTTACTCTTTCTTCTCTGAA
53754689 CTTTACTCTTTCTTCTCTG
1 CTTTACTCTTTCTTCTCTG
53754708 CTTTGTTCCT
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:0.10, C:0.30, G:0.05, T:0.55
Consensus pattern (21 bp):
CTTTACTCTTTCTTCTCTGAA
Found at i:53756798 original size:22 final size:23
Alignment explanation
Indices: 53756761--53756827 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
53756751 GTTTAGACTA
53756761 TGACCATATATA--TTTATATAT
1 TGACCATATATATTTTTATATAT
**
53756782 TGACTGTA-ATATTTTTATACTA-
1 TGACCATATATATTTTTATA-TAT
*
53756804 TGACCATATATATTTATATATAT
1 TGACCATATATATTTTTATATAT
53756827 T
1 T
53756828 ATCTTATGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 3 0.08
21 6 0.17
22 14 0.39
23 13 0.36
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (23 bp):
TGACCATATATATTTTTATATAT
Found at i:53756820 original size:21 final size:21
Alignment explanation
Indices: 53756752--53756821 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
53756742 TCTCCATTGG
*
53756752 TTTAGACTATGACCATATATA
1 TTTATACTATGACCATATATA
** *
53756773 TTTATA-TATTGACTGTAATATT
1 TTTATACTA-TGACCAT-ATATA
53756795 TTTATACTATGACCATATATA
1 TTTATACTATGACCATATATA
53756816 TTTATA
1 TTTATA
53756822 TATATTATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.05
21 20 0.51
22 15 0.38
23 2 0.05
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTATACTATGACCATATATA
Found at i:53757772 original size:18 final size:18
Alignment explanation
Indices: 53757751--53757834 Score: 150
Period size: 18 Copynumber: 4.7 Consensus size: 18
53757741 AAAATGTGAG
53757751 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
53757769 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
* *
53757787 AAATAATGTTCACATTTC
1 AAATGATGTTCACATTTT
53757805 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
53757823 AAATGATGTTCA
1 AAATGATGTTCA
53757835 AATTGATGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTT
Found at i:53758358 original size:72 final size:72
Alignment explanation
Indices: 53758263--53758717 Score: 752
Period size: 72 Copynumber: 6.3 Consensus size: 72
53758253 AAATGCTAAA
*
53758263 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
53758328 GTGTAAT
66 GTGTAAT
* *
53758335 CTAGTTTTACCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
53758400 GTGTAAT
66 GTGTAAT
* *
53758407 CTAGTTTTACCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
53758472 GTGTAAT
66 GTGTAAT
* *
53758479 CTAGTTTTACCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
53758544 GTGTAAT
66 GTGTAAT
*
53758551 CTAGTTTTATTAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
53758616 GTTTAAT
66 GTGTAAT
* * * *
53758623 TTAGTTTTATTAATAGTTGTTTATGTTTGGTATTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
53758688 ACT-AAAT
66 -GTGTAAT
53758695 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
53758718 ATATGATTTT
Statistics
Matches: 369, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
71 22 0.06
72 346 0.94
73 1 0.00
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:53758671 original size:26 final size:26
Alignment explanation
Indices: 53758570--53758675 Score: 70
Period size: 26 Copynumber: 4.3 Consensus size: 26
53758560 TTAATAGTTG
* *
53758570 TTTATGTTTGGTTTTTGGATATTGAA
1 TTTATGTTTGGTATTTAGATATTGAA
**
53758596 TTTATGTTCTACTTATTTATG-T-TT-AA
1 TTTATGTT-T-GGTATTTA-GATATTGAA
53758622 TTTA-GTTT--TA-TTA-ATAGTTG--
1 TTTATGTTTGGTATTTAGATA-TTGAA
53758642 TTTATGTTTGGTATTTAGATATTGAA
1 TTTATGTTTGGTATTTAGATATTGAA
53758668 TTTATGTT
1 TTTATGTT
53758676 CTACTTATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 28
0.66 0.04 0.30
Matches are distributed among these distances:
19 1 0.02
20 7 0.11
21 8 0.13
23 2 0.03
24 7 0.11
25 6 0.10
26 22 0.35
27 3 0.05
28 5 0.08
29 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.59
Consensus pattern (26 bp):
TTTATGTTTGGTATTTAGATATTGAA
Found at i:53760362 original size:19 final size:19
Alignment explanation
Indices: 53760294--53760352 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
53760284 TTACTTAGAA
*
53760294 ATATTTAAA-ATTAATATTAT
1 ATATTAAAATATTAATA--AT
53760314 ATATTAAAATATTAATAAT
1 ATATTAAAATATTAATAAT
53760333 ATATTAAAATATTAATAAT
1 ATATTAAAATATTAATAAT
53760352 A
1 A
53760353 AGTTATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 22 0.59
20 8 0.22
21 7 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAAATATTAATAAT
Found at i:53760551 original size:13 final size:13
Alignment explanation
Indices: 53760513--53760563 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
53760503 ACACTTAAAT
*
53760513 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
* **
53760526 TTTTCCACCGCAC
1 TTTTCAAAAGCAC
*
53760539 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
53760552 TTTTCAAAAGCA
1 TTTTCAAAAGCA
53760564 TTGCCAAATT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:53777256 original size:38 final size:36
Alignment explanation
Indices: 53777190--53777265 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
53777180 AAACATTTTC
* *
53777190 TTATAAAGATTATATATTGTAAAGTTTATATTAATTT
1 TTATAAAGATTATATATTATAAAATTTATATT-ATTT
53777227 TTATAAAG-TTATATATTATAAAAAATTTATATTATTT
1 TTATAAAGATTATATATTAT--AAAATTTATATTATTT
53777264 TT
1 TT
53777266 GTTACCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 10 0.29
37 14 0.40
38 11 0.31
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (36 bp):
TTATAAAGATTATATATTATAAAATTTATATTATTT
Found at i:53778310 original size:13 final size:13
Alignment explanation
Indices: 53778292--53778325 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
53778282 CATTTAATTG
53778292 CATGCCAGTGTAA
1 CATGCCAGTGTAA
53778305 CATGCCAGTGTAA
1 CATGCCAGTGTAA
*
53778318 CATACCAG
1 CATGCCAG
53778326 GATTTGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (13 bp):
CATGCCAGTGTAA
Found at i:53789288 original size:18 final size:19
Alignment explanation
Indices: 53789265--53789302 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53789255 GGAAGCAAGC
*
53789265 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
53789283 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
53789302 A
1 A
53789303 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:53794626 original size:76 final size:76
Alignment explanation
Indices: 53794500--53794652 Score: 261
Period size: 76 Copynumber: 2.0 Consensus size: 76
53794490 AAGAGACCAT
* * *
53794500 TATGGATAATTTTTGCCCCTGATATGAACATTAAGTTATCGCAAGAGCTAATGGTTAAAAGCCAT
1 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAATGGTTAAAAGCCAT
*
53794565 AAAGCAATTGA
66 AAAACAATTGA
*
53794576 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAATGGTTCAAAGCCAT
1 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAATGGTTAAAAGCCAT
53794641 AAAACAATTGA
66 AAAACAATTGA
53794652 T
1 T
53794653 TGTGGTGGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (76 bp):
TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAATGGTTAAAAGCCAT
AAAACAATTGA
Found at i:53795149 original size:31 final size:31
Alignment explanation
Indices: 53795111--53795174 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
53795101 TTGCATTCAA
53795111 CCATTTTGGAAAAGAATTGATACAAAAAATG
1 CCATTTTGGAAAAGAATTGATACAAAAAATG
53795142 CCATTTTGGAAAAGAATTGATACAAAAAATG
1 CCATTTTGGAAAAGAATTGATACAAAAAATG
53795173 CC
1 CC
53795175 TAGATGCCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (31 bp):
CCATTTTGGAAAAGAATTGATACAAAAAATG
Found at i:53795595 original size:23 final size:23
Alignment explanation
Indices: 53795534--53795597 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
53795524 ATGTGTGTAT
*
53795534 CCTTTCATATTCAAGCCTCTTAA
1 CCTTTCATATTCAAGTCTCTTAA
* *
53795557 CCTTTCATTTTCAAGTCTCTTCA
1 CCTTTCATATTCAAGTCTCTTAA
53795580 -CTATTCATATTCAAGTCT
1 CCT-TTCATATTCAAGTCT
53795598 TTTCTAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.44
Consensus pattern (23 bp):
CCTTTCATATTCAAGTCTCTTAA
Found at i:53799271 original size:23 final size:23
Alignment explanation
Indices: 53799228--53799288 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
53799218 ATGTGTGTAT
*
53799228 CCTTTCATATTCAAGCCTCTTAA
1 CCTTTCATATTCAAGCATCTTAA
* * *
53799251 CCTTTCATCTTCAAGTATCTTCA
1 CCTTTCATATTCAAGCATCTTAA
*
53799274 -CTATTCTTATTCAAG
1 CCT-TTCATATTCAAG
53799289 TCTTTTCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 2 0.06
23 29 0.94
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.43
Consensus pattern (23 bp):
CCTTTCATATTCAAGCATCTTAA
Found at i:53802172 original size:20 final size:20
Alignment explanation
Indices: 53802133--53802172 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53802123 TTGTTAGAGT
*
53802133 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
53802153 TAATATAGTCAAAACCGTTG
1 TAATATAGTCAAAACAGTTG
53802173 AACAGAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:53810566 original size:21 final size:21
Alignment explanation
Indices: 53810541--53810584 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53810531 TTTTGTTACA
53810541 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
53810562 ATGGCTTCTACAGATTCATCC
1 ATGGCTTCTACAGATTCATCC
53810583 AT
1 AT
53810585 TCTTTGTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (21 bp):
ATGGCTTCTACAGATTCATCC
Found at i:53815750 original size:20 final size:20
Alignment explanation
Indices: 53815711--53815752 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
53815701 ATGTTAGAGT
*
53815711 TAATATAGTCAAAGCAGTTG
1 TAATATAGTCAAAACAGTTG
*
53815731 TAATATAGTCAAAACCGTTG
1 TAATATAGTCAAAACAGTTG
53815751 TA
1 TA
53815753 CCGTTGCAAG
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:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
TAATATAGTCAAAACAGTTG
Found at i:53815781 original size:15 final size:15
Alignment explanation
Indices: 53815761--53815791 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53815751 TACCGTTGCA
*
53815761 AGTCTGTTAGTAGTT
1 AGTCTGTTAGCAGTT
53815776 AGTCTGTTAGCAGTT
1 AGTCTGTTAGCAGTT
53815791 A
1 A
53815792 AAGATGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42
Consensus pattern (15 bp):
AGTCTGTTAGCAGTT
Found at i:53816001 original size:23 final size:23
Alignment explanation
Indices: 53815966--53816011 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53815956 CGCTTATCTT
* *
53815966 CATGTTGAGCTGCTGCTGGTCTC
1 CATGCTGAACTGCTGCTGGTCTC
53815989 CATGCTGAACTGCTGCTGGTCTC
1 CATGCTGAACTGCTGCTGGTCTC
53816012 TTCTTGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.28, G:0.28, T:0.33
Consensus pattern (23 bp):
CATGCTGAACTGCTGCTGGTCTC
Found at i:53818791 original size:41 final size:41
Alignment explanation
Indices: 53818731--53818812 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
53818721 TCTTCCGAAG
*
53818731 TTAAGCAGGGCATTCTATGATCCACGAACGCTCTTCAATTT
1 TTAAGCAGGACATTCTATGATCCACGAACGCTCTTCAATTT
* * * *
53818772 TTAAGCCGGACATTGTATGATCCACGACCGCTCTTCCATTT
1 TTAAGCAGGACATTCTATGATCCACGAACGCTCTTCAATTT
53818813 AGTGCTCGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (41 bp):
TTAAGCAGGACATTCTATGATCCACGAACGCTCTTCAATTT
Found at i:53819428 original size:20 final size:21
Alignment explanation
Indices: 53819403--53819442 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53819393 ATTTAAATAA
53819403 AATAAATA-TAATTAATTTAT
1 AATAAATACTAATTAATTTAT
*
53819423 AATAAATACTATTTAATTTA
1 AATAAATACTAATTAATTTA
53819443 GTAGGTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAATACTAATTAATTTAT
Found at i:53820546 original size:212 final size:212
Alignment explanation
Indices: 53820179--53820565 Score: 641
Period size: 212 Copynumber: 1.8 Consensus size: 212
53820169 TTATGATTAT
* * *
53820179 CACTCCATTTTCGAAATATTAAATTATATAATTGTAAAATTTTTAGTTTCAGATCTCAAATGTAA
1 CACTCCATTTTCAAAATATTAAATTATATAATTATAAAATTTTTAGTTTCAGATCTCAAAGGTAA
*
53820244 TCAATTCCTAAAAAAATAAACCATATAAATAGGTTATGATTATCAACATTTTGTCATATCTTAAA
66 TCAATTCCTAAAAAAATAAACCATATAAATAGGTTATGATTATCAACATTTTGTCAAATCTTAAA
*
53820309 TCCGAACATTTTACCGATACTCAAGCATA-AGTATCAATATATTTATCCCGAGTATCGATAATTG
131 TCCAAACATTTTACCGATACTCAAGCATAGA-TATCAATATATTTATCCCGAGTATCGATAATTG
53820373 TAAAAAGTGATTTCGACA
195 TAAAAAGTGATTTCGACA
* *
53820391 CACTCCATTTTCAAAATATTAAATTATATAATTATAAATTTTTTAGTTTCATATCTCAAAGGTAA
1 CACTCCATTTTCAAAATATTAAATTATATAATTATAAAATTTTTAGTTTCAGATCTCAAAGGTAA
* * * *
53820456 TCAATTTCTCAAAAAATAAACCATATAAATAGGTTATGATTATCAACATTTTGTCAAATTTTGAA
66 TCAATTCCTAAAAAAATAAACCATATAAATAGGTTATGATTATCAACATTTTGTCAAATCTTAAA
* *
53820521 TCTAAACATTTTATCGATACTCAAGCATAGATATCAATATATTTA
131 TCCAAACATTTTACCGATACTCAAGCATAGATATCAATATATTTA
53820566 ATTATTTCAA
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
212 160 0.99
213 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.37
Consensus pattern (212 bp):
CACTCCATTTTCAAAATATTAAATTATATAATTATAAAATTTTTAGTTTCAGATCTCAAAGGTAA
TCAATTCCTAAAAAAATAAACCATATAAATAGGTTATGATTATCAACATTTTGTCAAATCTTAAA
TCCAAACATTTTACCGATACTCAAGCATAGATATCAATATATTTATCCCGAGTATCGATAATTGT
AAAAAGTGATTTCGACA
Found at i:53826975 original size:25 final size:25
Alignment explanation
Indices: 53826925--53826978 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
53826915 TTAAATAACC
* *
53826925 AATATTATTAATATTAGAAAATTTT
1 AATATCATTAATAGTAGAAAATTTT
*
53826950 AATATCATTAATAGTA-ACAATATTT
1 AATATCATTAATAGTAGAAAAT-TTT
53826975 AATA
1 AATA
53826979 ACATAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
AATATCATTAATAGTAGAAAATTTT
Found at i:53827088 original size:57 final size:57
Alignment explanation
Indices: 53827024--53827137 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
53827014 ATTAAAATAA
53827024 TTTTATCTATACTTTAAAAAGCATAAGGCATAATCATAAATTTAACTACTAACATTT
1 TTTTATCTATACTTTAAAAAGCATAAGGCATAATCATAAATTTAACTACTAACATTT
*
53827081 TTTTATCTATACTTTAAAAAGCATAAGGCATAATCTTAAATTTAACTACTAACATTT
1 TTTTATCTATACTTTAAAAAGCATAAGGCATAATCATAAATTTAACTACTAACATTT
53827138 ACTCATTTTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.39
Consensus pattern (57 bp):
TTTTATCTATACTTTAAAAAGCATAAGGCATAATCATAAATTTAACTACTAACATTT
Found at i:53830879 original size:49 final size:49
Alignment explanation
Indices: 53830819--53831055 Score: 183
Period size: 49 Copynumber: 4.7 Consensus size: 49
53830809 GATAATAACA
* * * *
53830819 TGCCAAAGCCATGCCCCAGACATGGTCTTACATAGGATGTT-TCTTGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGA-GTTCTCATAT-CG
* * * *
53830868 TGCCAATGCCATATCCCAGATATGGTCTTATATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGAGTTCTCATATC-G
* ** ** * *
53830918 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGAGTTCTCAT-ATCG
* *
53830967 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGACTTCTCATAATCTCAATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGAGTTCTCAT-A--TC---G
* *
53831022 ATGCCAATGTCATGTCTCAGACATGGTCTTACAT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAT
53831056 GAGATCTCTT
Statistics
Matches: 149, Mismatches: 28, Indels: 15
0.78 0.15 0.08
Matches are distributed among these distances:
48 4 0.03
49 75 0.50
50 38 0.26
52 1 0.01
55 1 0.01
56 30 0.20
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGAGTTCTCATATCG
Found at i:53832765 original size:8 final size:8
Alignment explanation
Indices: 53832754--53832784 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
53832744 AATTAATTTA
53832754 AAATTTTG
1 AAATTTTG
*
53832762 AAATTTTA
1 AAATTTTG
53832770 AAATTTTG
1 AAATTTTG
53832778 AAATTTT
1 AAATTTT
53832785 AAAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (8 bp):
AAATTTTG
Found at i:53832771 original size:16 final size:16
Alignment explanation
Indices: 53832750--53832788 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
53832740 AATTAATTAA
53832750 TTTAAAATTTTGAAAT
1 TTTAAAATTTTGAAAT
53832766 TTTAAAATTTTGAAAT
1 TTTAAAATTTTGAAAT
53832782 TTTAAAA
1 TTTAAAA
53832789 AATATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TTTAAAATTTTGAAAT
Found at i:53833113 original size:14 final size:14
Alignment explanation
Indices: 53833080--53833126 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
53833070 AATTTTCAAG
*
53833080 AAATAAAAAATATAT
1 AAATTAAAAATAT-T
*
53833095 AAAATTATAAATATT
1 -AAATTAAAAATATT
53833110 AAATTAAAAATA-T
1 AAATTAAAAATATT
53833123 AAAT
1 AAAT
53833127 ATTTAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 5 0.18
14 11 0.39
15 1 0.04
16 11 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATTAAAAATATT
Found at i:53834604 original size:22 final size:22
Alignment explanation
Indices: 53834579--53834620 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53834569 ATTACTGAAT
*
53834579 TAATTAATACATTTATAATAAA
1 TAATCAATACATTTATAATAAA
53834601 TAATCAATACATTTATAATA
1 TAATCAATACATTTATAATA
53834621 TCAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATCAATACATTTATAATAAA
Found at i:53834685 original size:233 final size:234
Alignment explanation
Indices: 53834351--53834781 Score: 733
Period size: 233 Copynumber: 1.8 Consensus size: 234
53834341 AATTTTGAAG
* *
53834351 ATACATATTTTAATAAATAATCAATACATTTATAATATCAAAATAAAAAATAAAATAATTAATAT
1 ATACATATTATAATAAATAATCAATACATTTATAATATCAAAATAAAAAATAAAATAATTAATAC
* * * *
53834416 AAATTTAAACTTAAACTTAAAAATATTAATAAATAAGTAATAAATTCTAGTCTTGAACAAAAAAA
66 AAATCTAAACTTAAACATAAAAATAATAAAAAATAAGTAATAAATTCTAGTCTTGAACAAAAAAA
* *
53834481 TAATGTATATAACTCAAATCCATTGAATAAAATTAATTTATTGCTAAGTTATGGCATTAAAACAC
131 TAATGTATATAACTCAAATCCATTGAATAAAATTAAATTATTGCTAACTTATGGCATTAAAACAC
53834546 AAATACACAATTAAATAGTCATAATTACTGAATTAATTA
196 AAATACACAATTAAATAGTCATAATTACTGAATTAATTA
53834585 ATACAT-TTATAATAAATAATCAATACATTTATAATATCAAAATAAAAAAAATAAAATAATTAAT
1 ATACATATTATAATAAATAATCAATACATTTATAATATCAAAAT--AAAAAATAAAATAATTAAT
* *
53834649 ACAAATCTAAACTTAAA-ATAAAAA-AATAAAAAATAAGTAATAAATTCTAGTCTTTAACTAAAA
64 ACAAATCTAAACTTAAACATAAAAATAATAAAAAATAAGTAATAAATTCTAGTCTTGAACAAAAA
53834712 AATAATGTATATAACTCAAATCCATTGAATAAAATTAAATTATTGCTAACTTATGGCATTAAAAC
129 AATAATGTATATAACTCAAATCCATTGAATAAAATTAAATTATTGCTAACTTATGGCATTAAAAC
53834777 ACAAA
194 ACAAA
53834782 AACTTGTATG
Statistics
Matches: 185, Mismatches: 10, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
233 139 0.75
234 12 0.06
235 34 0.18
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (234 bp):
ATACATATTATAATAAATAATCAATACATTTATAATATCAAAATAAAAAATAAAATAATTAATAC
AAATCTAAACTTAAACATAAAAATAATAAAAAATAAGTAATAAATTCTAGTCTTGAACAAAAAAA
TAATGTATATAACTCAAATCCATTGAATAAAATTAAATTATTGCTAACTTATGGCATTAAAACAC
AAATACACAATTAAATAGTCATAATTACTGAATTAATTA
Found at i:53834864 original size:24 final size:24
Alignment explanation
Indices: 53834832--53834878 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
53834822 TTACTGACAC
53834832 CATGTTTGGTTGGGTGTATTGGCT
1 CATGTTTGGTTGGGTGTATTGGCT
53834856 CATGTTTGGTTGGGTGTATTGGC
1 CATGTTTGGTTGGGTGTATTGGC
53834879 ATAGCCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.45
Consensus pattern (24 bp):
CATGTTTGGTTGGGTGTATTGGCT
Found at i:53844845 original size:162 final size:162
Alignment explanation
Indices: 53844578--53844903 Score: 600
Period size: 162 Copynumber: 2.0 Consensus size: 162
53844568 TGGAAATTGG
53844578 TAATTGTCGAAGCTTGGTTTCTTTTGCAAAGAATAACTTACCTCCTAATTTAAAAAAGCTGACAA
1 TAATTGTCGAAGCTTGGTTTCTTTTGCAAAGAATAACTTACCTCCTAATTTAAAAAAGCTGACAA
*
53844643 TTGATACCTGTGAGAATTTGGAGTATTTGGTTGATGAAAAAGAAGATAATAAGAGTATGAGTAGT
66 TTGATAACTGTGAGAATTTGGAGTATTTGGTTGATGAAAAAGAAGATAATAAGAGTATGAGTAGT
53844708 ACCCTCTGTCTTCTTGAGGAGTTGTCTATCTA
131 ACCCTCTGTCTTCTTGAGGAGTTGTCTATCTA
* *
53844740 TAATTGTCGAAGCTTGGTTTCTTTTGCAGAGAATAACTTACCTCCTAATTTAAAAAAGCTGAGAA
1 TAATTGTCGAAGCTTGGTTTCTTTTGCAAAGAATAACTTACCTCCTAATTTAAAAAAGCTGACAA
53844805 TTAGA-AACTGTGAGAATTTGGAGTATTTGGTTGATGAAAAAGAAGATAATAAGAGTATGAGTAG
66 TT-GATAACTGTGAGAATTTGGAGTATTTGGTTGATGAAAAAGAAGATAATAAGAGTATGAGTAG
*
53844869 TACCCTCTGTCTTCTTGAGGAGTTGTTTATCTA
130 TACCCTCTGTCTTCTTGAGGAGTTGTCTATCTA
53844902 TA
1 TA
53844904 TGTGTCCGTC
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
162 157 0.99
163 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (162 bp):
TAATTGTCGAAGCTTGGTTTCTTTTGCAAAGAATAACTTACCTCCTAATTTAAAAAAGCTGACAA
TTGATAACTGTGAGAATTTGGAGTATTTGGTTGATGAAAAAGAAGATAATAAGAGTATGAGTAGT
ACCCTCTGTCTTCTTGAGGAGTTGTCTATCTA
Found at i:53846362 original size:18 final size:21
Alignment explanation
Indices: 53846322--53846364 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
53846312 TTCTATTTCA
*
53846322 CTTTCTTGTTTTTCCCTATTT
1 CTTTCTTGTTCTTCCCTATTT
53846343 CTTTCTT-TTCTT-CCTA-TT
1 CTTTCTTGTTCTTCCCTATTT
53846361 CTTT
1 CTTT
53846365 TCCTCTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 4 0.19
21 7 0.33
ACGTcount: A:0.05, C:0.26, G:0.02, T:0.67
Consensus pattern (21 bp):
CTTTCTTGTTCTTCCCTATTT
Found at i:53846656 original size:14 final size:14
Alignment explanation
Indices: 53846622--53846669 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
53846612 AAAATTTCAA
*
53846622 TAAATAAAAAATAT
1 TAAATTAAAAATAT
*
53846636 ATAAAATTATAAATAT
1 -T-AAATTAAAAATAT
53846652 TAAATTAAAAATA-
1 TAAATTAAAAATAT
53846665 TAAAT
1 TAAAT
53846670 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 2 0.07
16 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:53846749 original size:17 final size:17
Alignment explanation
Indices: 53846727--53846760 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53846717 GGTTAATTTT
53846727 TTTGCAAATATAAACAA
1 TTTGCAAATATAAACAA
53846744 TTTGCAAATATAAACAA
1 TTTGCAAATATAAACAA
53846761 ACTTGGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (17 bp):
TTTGCAAATATAAACAA
Found at i:53848470 original size:12 final size:12
Alignment explanation
Indices: 53848448--53848480 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
53848438 GTAAATAAAA
53848448 ATAAAAATAACT
1 ATAAAAATAACT
53848460 ATAAAAATAACT
1 ATAAAAATAACT
*
53848472 ATAATAATA
1 ATAAAAATA
53848481 GTAAAGATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAAATAACT
Found at i:53848518 original size:18 final size:17
Alignment explanation
Indices: 53848471--53848520 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
53848461 TAAAAATAAC
*
53848471 TATAATAATAGTAAAGA
1 TATAATAATAATAAAGA
*
53848488 TGATAATAGTAATAATAGA
1 T-ATAATAATAATAA-AGA
53848507 TATAATAATAATAA
1 TATAATAATAATAA
53848521 CTAAATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 23 0.82
19 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (17 bp):
TATAATAATAATAAAGA
Found at i:53856319 original size:103 final size:104
Alignment explanation
Indices: 53855978--53856348 Score: 602
Period size: 105 Copynumber: 3.6 Consensus size: 104
53855968 TGTATATAAA
** * * *
53855978 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
**
53856042 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
53856082 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
53856147 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
53856187 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
53856252 TGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
53856290 AGGGGTTGCTAAGTGCTGATTCCCTGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
53856349 ATAACGGCTA
Statistics
Matches: 252, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
103 86 0.34
104 69 0.27
105 96 0.38
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:53858136 original size:41 final size:41
Alignment explanation
Indices: 53858078--53858159 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
53858068 TATTTTGGAA
53858078 CATTAACTCATAATGTTATTGAGTTGTAATAATCATAGGCC
1 CATTAACTCATAATGTTATTGAGTTGTAATAATCATAGGCC
*
53858119 CATTAACTCATAGTGTTATTGAGTTGTAATAATCATAGGCC
1 CATTAACTCATAATGTTATTGAGTTGTAATAATCATAGGCC
53858160 TTTAGCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (41 bp):
CATTAACTCATAATGTTATTGAGTTGTAATAATCATAGGCC
Found at i:53858707 original size:76 final size:76
Alignment explanation
Indices: 53858625--53858854 Score: 442
Period size: 76 Copynumber: 3.0 Consensus size: 76
53858615 AAGAGACCAT
53858625 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
1 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
53858690 AAAACAATTGA
66 AAAACAATTGA
53858701 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
1 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
53858766 AAAACAATTGA
66 AAAACAATTGA
* *
53858777 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAATGGTTGAAAGCCAT
1 TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
53858842 AAAACAATTGA
66 AAAACAATTGA
53858853 TA
1 TA
53858855 GTCGTGGATC
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 152 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (76 bp):
TATGGATAATTTTTGCCCATGATATGAACATTAAATTATCACAAGAGCTAGTGGTTAAAAGCCAT
AAAACAATTGA
Found at i:53859231 original size:23 final size:23
Alignment explanation
Indices: 53859201--53859247 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
53859191 ACACATTTTG
53859201 TAATCTAGTTTTCAACTAAACAT
1 TAATCTAGTTTTCAACTAAACAT
*
53859224 TAATCTAGTTTTTAACTAAACAT
1 TAATCTAGTTTTCAACTAAACAT
53859247 T
1 T
53859248 CTTGGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.43
Consensus pattern (23 bp):
TAATCTAGTTTTCAACTAAACAT
Found at i:53860909 original size:2 final size:2
Alignment explanation
Indices: 53860902--53860932 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53860892 TGAAATTCAA
53860902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53860933 ATTAAAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53883274 original size:23 final size:23
Alignment explanation
Indices: 53883247--53883322 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
53883237 AGTGTTATTG
*
53883247 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
53883270 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53883293 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
53883316 ATCAGTG
1 ATCAGTG
53883323 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:53887463 original size:50 final size:50
Alignment explanation
Indices: 53887291--53887523 Score: 290
Period size: 50 Copynumber: 4.6 Consensus size: 50
53887281 TATCGATGAA
* * * * *
53887291 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGAT
* * * * * * *
53887342 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
*
53887393 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
53887443 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
53887493 CACGTGTGTAGTACTATGTGAAGGCTACTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTAC
53887524 ATGTATCGAA
Statistics
Matches: 160, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 85 0.53
51 73 0.46
52 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:53897104 original size:70 final size:70
Alignment explanation
Indices: 53896991--53897131 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
53896981 AACAAAAGAG
53896991 AGCAGAAGCAAAATCGAGAGGAAAGAGTTTGAACAGGAAGATAACTGAAAATTCTCATTGATTTC
1 AGCAGAAGCAAAATCGAGAGGAAAGAGTTTGAACAGGAAGATAACTGAAAATTCTCATTGATTTC
53897056 ATTAA
66 ATTAA
*
53897061 AGCAGAAGCAAAATCGAGAGGAAAGAGTTTGAACGGGAAGATAACTGAAAATTCTCATTGATTTC
1 AGCAGAAGCAAAATCGAGAGGAAAGAGTTTGAACAGGAAGATAACTGAAAATTCTCATTGATTTC
53897126 ATTAA
66 ATTAA
53897131 A
1 A
53897132 AAATATAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (70 bp):
AGCAGAAGCAAAATCGAGAGGAAAGAGTTTGAACAGGAAGATAACTGAAAATTCTCATTGATTTC
ATTAA
Found at i:53898381 original size:76 final size:76
Alignment explanation
Indices: 53898253--53898406 Score: 256
Period size: 76 Copynumber: 2.0 Consensus size: 76
53898243 AAGAGACCAT
* * *
53898253 TATGGATAATTTTTGCTCCTGATATGAACTTTAAGTTATCACAAGAGCTAATGGTTAAAAGCCAT
1 TATGGATAATTTTTGCTCCTGATATGAACATTAAATTATCACAAGAGATAATGGTTAAAAGCCAT
53898318 AAAACAATTGA
66 AAAACAATTGA
*
53898329 TATGGATAATTTTTGC-CCATGATATGAACATTAAATTATCACAAGAGATAATGGTTCAAAGCCA
1 TATGGATAATTTTTGCTCC-TGATATGAACATTAAATTATCACAAGAGATAATGGTTAAAAGCCA
53898393 TAAAACAATTGA
65 TAAAACAATTGA
53898405 TA
1 TA
53898407 GTCGTGGATC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 2 0.03
76 71 0.97
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (76 bp):
TATGGATAATTTTTGCTCCTGATATGAACATTAAATTATCACAAGAGATAATGGTTAAAAGCCAT
AAAACAATTGA
Found at i:53898905 original size:31 final size:31
Alignment explanation
Indices: 53898867--53898927 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
53898857 CATTCAACCT
53898867 TTTTGGAAAAGAATTAATACAAAAAATGCCA
1 TTTTGGAAAAGAATTAATACAAAAAATGCCA
*
53898898 TTTTGGAAAAGAATTGATACAAAAAATGCC
1 TTTTGGAAAAGAATTAATACAAAAAATGCC
53898928 TAGATGCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (31 bp):
TTTTGGAAAAGAATTAATACAAAAAATGCCA
Found at i:53910591 original size:20 final size:21
Alignment explanation
Indices: 53910568--53910607 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
53910558 AAAAATTACA
53910568 AAAAATTC-AAAATAATTTTC
1 AAAAATTCAAAAATAATTTTC
53910588 AAAAATTCAAAAATAATTTT
1 AAAAATTCAAAAATAATTTT
53910608 TAAACTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATTCAAAAATAATTTTC
Found at i:53910639 original size:20 final size:19
Alignment explanation
Indices: 53910568--53910639 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
53910558 AAAAATTACA
53910568 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
53910587 CAAAAATTCAAAAATAATTTT
1 -AAAAATTC-AAAATAATTTT
* *
53910608 -TAAACTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
53910626 AAAAATTCCAAAAT
1 AAAAATT-CAAAAT
53910640 TTATATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.09
18 6 0.14
19 9 0.20
20 14 0.32
21 11 0.25
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:53910685 original size:11 final size:9
Alignment explanation
Indices: 53910683--53910723 Score: 57
Period size: 9 Copynumber: 4.4 Consensus size: 9
53910673 AAAAGTTCTA
53910683 AAAAAATTAT
1 AAAAAATT-T
53910693 AAAGAAATTT
1 AAA-AAATTT
53910703 AAAAAA-TT
1 AAAAAATTT
53910711 AAAAAATTT
1 AAAAAATTT
53910720 AAAA
1 AAAA
53910724 TAATGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.28
9 9 0.31
10 7 0.24
11 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAAAATTT
Found at i:53910685 original size:12 final size:10
Alignment explanation
Indices: 53910651--53910723 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 10
53910641 TATATTTTTC
53910651 AAAAAA-TTA
1 AAAAAATTTA
* *
53910660 TAAAATTTTAA
1 AAAAAATTT-A
53910671 AAAAAAGTTCTA
1 AAAAAA-TT-TA
53910683 AAAAAATTATA
1 AAAAAATT-TA
*
53910694 AAGAAATTT-
1 AAAAAATTTA
53910703 AAAAAA-TT-
1 AAAAAATTTA
53910711 AAAAAATTTA
1 AAAAAATTTA
53910721 AAA
1 AAA
53910724 TAATGTATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
8 8 0.16
9 11 0.22
10 6 0.12
11 16 0.31
12 9 0.18
13 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:53923035 original size:3 final size:3
Alignment explanation
Indices: 53923027--53923057 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53923017 TATCTTTCCT
53923027 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53923058 AATTTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53923313 original size:21 final size:21
Alignment explanation
Indices: 53923289--53923328 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53923279 TTGGATTTAA
**
53923289 ATAAATATTTTTAAAAAATAC
1 ATAAATAAATTTAAAAAATAC
53923310 ATAAATAAATTTAAAAAAT
1 ATAAATAAATTTAAAAAAT
53923329 TTAATGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAAATTTAAAAAATAC
Found at i:53936669 original size:31 final size:30
Alignment explanation
Indices: 53936633--53936693 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
53936623 AACGTCAATT
*
53936633 GATGTCTTTGAGTGATTGTGATATTATTGG
1 GATGTCTTTGAGTGATTGTGATAGTATTGG
*
53936663 NGATGTCTTTGAGTGATTGTTATAGTATTGG
1 -GATGTCTTTGAGTGATTGTGATAGTATTGG
53936694 TTTCAAGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.46
Consensus pattern (30 bp):
GATGTCTTTGAGTGATTGTGATAGTATTGG
Found at i:53947965 original size:21 final size:21
Alignment explanation
Indices: 53947936--53947987 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
53947926 TGAACCCCCG
*
53947936 AACCTTAAACATCAAATCCTA
1 AACCATAAACATCAAATCCTA
* *
53947957 AACCATAAACATCAAATTCTG
1 AACCATAAACATCAAATCCTA
*
53947978 AACCCTAAAC
1 AACCATAAAC
53947988 CTTTAACCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (21 bp):
AACCATAAACATCAAATCCTA
Found at i:53948056 original size:20 final size:20
Alignment explanation
Indices: 53948031--53948076 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
53948021 CCCCTCGAAC
53948031 CTTGAACC-CGGAA-CCTAAAT
1 CTTGAACCTC-GAATCCT-AAT
53948051 CTTGAACCTCGAATCCTAAT
1 CTTGAACCTCGAATCCTAAT
53948071 CTTGAA
1 CTTGAA
53948077 TTTAGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
CTTGAACCTCGAATCCTAAT
Found at i:53949002 original size:25 final size:25
Alignment explanation
Indices: 53948965--53949014 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
53948955 GACTCCGTTA
* *
53948965 ATGGAGTTCTAGTGGAATCGGATGG
1 ATGGAGCTCTAGTGGAATCAGATGG
*
53948990 ATGGAGCTGTAGTGGAATCAGATGG
1 ATGGAGCTCTAGTGGAATCAGATGG
53949015 CAATTGCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.40, T:0.26
Consensus pattern (25 bp):
ATGGAGCTCTAGTGGAATCAGATGG
Found at i:53949421 original size:228 final size:228
Alignment explanation
Indices: 53948990--53949722 Score: 1127
Period size: 228 Copynumber: 3.2 Consensus size: 228
53948980 AATCGGATGG
* *
53948990 ATGGAGCTGTAGTGGAATCAGATGGCAATTGCATTGTCGAAGAAGACCATGAAGTGAAATCCGAA
1 ATGGAGCTGTAGTGGAATCAGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
53949055 TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
66 TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
53949120 AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATG
131 AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATG
53949185 TTTATGTTAACGTAAATGGAAGCGACTCCGTTA
196 TTTATGTTAACGTAAATGGAAGCGACTCCGTTA
* * * *
53949218 ATGGAGTTGTTGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
1 ATGGAGCTGTAGTGGAATCAGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
53949283 TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
66 TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
* * * * * * * * *
53949348 AACGAGATATCTTCTCATTGGCGCCAACGCGATTTGCGTTAAGGTTAGCTCTGGCAGCTCAGATG
131 AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATG
* *
53949413 TCTATG-T----T-AATGGAAACGACTCCGTTA
196 TTTATGTTAACGTAAATGGAAGCGACTCCGTTA
* *
53949440 ATGGAGCTGTAGTGGAATCAGATGGCAATTGCATTGTCGAAGAAGACCATGAAGTGAAATCCGAA
1 ATGGAGCTGTAGTGGAATCAGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
* * * * * *
53949505 TCTGATTCGGTCACTATTACTATGAATCAGCAGGAGGCGGATATAGTAGATGAGAAAGAGAATGA
66 TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
*
53949570 AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGAGTTAAGGTTGGCACCGGCAGCACGGATG
131 AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATG
* *
53949635 TTTATGTTAACGTAAATAGAAGCGACCCCGTTA
196 TTTATGTTAACGTAAATGGAAGCGACTCCGTTA
* * * * *
53949668 ATGGAGTTGTAGTGGAATCGGGTGACAATTGTATTGTCGAAGAAGACCACAAAGT
1 ATGGAGCTGTAGTGGAATCAGATGACAATTGCATTGTCGAAGAAGACCACGAAGT
53949723 TACTATCAGT
Statistics
Matches: 449, Mismatches: 50, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
222 196 0.44
223 2 0.00
227 2 0.00
228 249 0.55
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.25
Consensus pattern (228 bp):
ATGGAGCTGTAGTGGAATCAGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
TCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAAAGAGAATGA
AACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATG
TTTATGTTAACGTAAATGGAAGCGACTCCGTTA
Found at i:53949798 original size:21 final size:21
Alignment explanation
Indices: 53949759--53949798 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53949749 GGGAGAAACC
* *
53949759 TGTTGAAGAAAAGGGAGGGTA
1 TGTTGAAGAAAAAGCAGGGTA
*
53949780 TGTTGAAGAAAAATCAGGG
1 TGTTGAAGAAAAAGCAGGG
53949799 GATGGAGATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.38, T:0.20
Consensus pattern (21 bp):
TGTTGAAGAAAAAGCAGGGTA
Found at i:53952140 original size:33 final size:33
Alignment explanation
Indices: 53952098--53952174 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
53952088 CCTTAAGTAT
*
53952098 CAACATTTTTTGGTTGTTTCCTTGTTGATCAAG
1 CAACATTTTTCGGTTGTTTCCTTGTTGATCAAG
53952131 CAACATTTTTCGGTTGTTTCCTTGTTGATCAAG
1 CAACATTTTTCGGTTGTTTCCTTGTTGATCAAG
53952164 CAACATTTTTC
1 CAACATTTTTC
53952175 TTTCTTCAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.19, C:0.18, G:0.16, T:0.47
Consensus pattern (33 bp):
CAACATTTTTCGGTTGTTTCCTTGTTGATCAAG
Found at i:53960950 original size:27 final size:29
Alignment explanation
Indices: 53960900--53960969 Score: 110
Period size: 27 Copynumber: 2.5 Consensus size: 29
53960890 ATAATAAAAA
*
53960900 TTACCAAAATGT-TATACATTTTTTTTAT
1 TTACCAAAATATATATACATTTTTTTTAT
53960928 TTACCAAAATATATATA-A-TTTTTTTAT
1 TTACCAAAATATATATACATTTTTTTTAT
53960955 TTACCAAAATATATA
1 TTACCAAAATATATA
53960970 AAAAAAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 24 0.60
28 12 0.30
29 4 0.10
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (29 bp):
TTACCAAAATATATATACATTTTTTTTAT
Found at i:53961010 original size:9 final size:8
Alignment explanation
Indices: 53960972--53961017 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
53960962 AATATATAAA
53960972 AAAAAAAC
1 AAAAAAAC
53960980 TAAAAAAAC
1 -AAAAAAAC
53960989 AAAAAAA-
1 AAAAAAAC
53960996 ATAAAAAAC
1 A-AAAAAAC
*
53961005 AGAAAAA-
1 AAAAAAAC
53961012 AAAAAA
1 AAAAAA
53961018 CCTGGACCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 6 0.18
8 18 0.55
9 9 0.27
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.04
Consensus pattern (8 bp):
AAAAAAAC
Found at i:53961014 original size:18 final size:18
Alignment explanation
Indices: 53960971--53961013 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 18
53960961 AAATATATAA
53960971 AAAAAAAACTAAAAAAAC
1 AAAAAAAACTAAAAAAAC
53960989 AAAAAAAA-T-AAAAAAC
1 AAAAAAAACTAAAAAAAC
53961005 AGAAAAAAA
1 A-AAAAAAA
53961014 AAAACCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 8 0.33
18 8 0.33
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAAAAAACTAAAAAAAC
Found at i:53961086 original size:27 final size:27
Alignment explanation
Indices: 53961046--53961151 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
53961036 TTCCCTGGGT
*
53961046 CAAGGGAACACTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
* *
53961073 GAAGGGAACCCTGTTGGTGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
53961100 CAAGGGTTCCCTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
53961127 CAAGGGTTCCCTGTTGGCGGCACCA
1 CAAGGGAACCCTGTTGGCGGCACCA
53961152 CTCGTGTTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.16
Consensus pattern (27 bp):
CAAGGGAACCCTGTTGGCGGCACCAAA
Found at i:53961446 original size:3 final size:3
Alignment explanation
Indices: 53961438--53961565 Score: 256
Period size: 3 Copynumber: 42.7 Consensus size: 3
53961428 AATTTTATAG
53961438 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53961486 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
53961534 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53961566 AGATGTTAGT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 125 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:53961624 original size:63 final size:62
Alignment explanation
Indices: 53961538--53961688 Score: 159
Period size: 63 Copynumber: 2.5 Consensus size: 62
53961528 TATTATTATT
* * * *
53961538 ATTATTATTATTATTATTATTA-TTATTAA-GATGTTAGTTAGTATTA-TTGT-TAGTAAAA-A
1 ATTAATATTATTATT-GTGTTAGTTATTAATAATGTTAGTTAGTATTATTTGTATA-TAAAATA
* * * *
53961597 ATTAGTATTATTTTTGTAGTTAGTTATTAATAATTTTAGTTAGTATTATTTTGTATATAAAATT
1 ATTAATATTATTATTGT-GTTAGTTATTAATAATGTTAGTTAGTATTA-TTTGTATATAAAATA
53961661 ATTAATATTATTATTGTGTTAGTTATTA
1 ATTAATATTATTATTGTGTTAGTTATTA
53961689 GGATTAGTGG
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
58 1 0.01
59 16 0.21
60 7 0.09
61 15 0.20
63 20 0.26
64 17 0.22
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (62 bp):
ATTAATATTATTATTGTGTTAGTTATTAATAATGTTAGTTAGTATTATTTGTATATAAAATA
Found at i:53961645 original size:61 final size:62
Alignment explanation
Indices: 53961571--53961688 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 62
53961561 TATTAAGATG
* *
53961571 TTAGTTAGTATTA-TTGT-TAGTAAAA-AATTAGTATTATTTTTGTAGTTAGTTATTAATAATT
1 TTAGTTAGTATTATTTGTATA-TAAAATAATTAATATTATTATTGT-GTTAGTTATTAATAATT
*
53961632 TTAGTTAGTATTATTTTGTATATAAAATTATTAATATTATTATTGTGTTAGTTATTA
1 TTAGTTAGTATTA-TTTGTATATAAAATAATTAATATTATTATTGTGTTAGTTATTA
53961689 GGATTAGTGG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 13 0.26
63 20 0.40
64 17 0.34
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (62 bp):
TTAGTTAGTATTATTTGTATATAAAATAATTAATATTATTATTGTGTTAGTTATTAATAATT
Found at i:53962331 original size:18 final size:18
Alignment explanation
Indices: 53962303--53962347 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
53962293 TTGATATGGT
*
53962303 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
*
53962321 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
53962339 TGGTGGCGA
1 TGGTGGCGA
53962348 TCATTGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.49, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:53965246 original size:27 final size:27
Alignment explanation
Indices: 53965208--53965275 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
53965198 ATATTTAAGG
53965208 TGGTGCCGCCAACAAGGAATCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
**
53965235 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
53965262 TGGTGCCGCCAACA
1 TGGTGCCGCCAACA
53965276 GTGTTCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAATCCTTGTT
Found at i:53965285 original size:27 final size:27
Alignment explanation
Indices: 53965208--53965286 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 27
53965198 ATATTTAAGG
*
53965208 TGGTGCCGCCAACAAGGAAT-CCTTGTT
1 TGGTGCCGCCAACAAGG-TTCCCTTGTT
*
53965235 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
53965262 TGGTGCCGCCAAC-AGTGTTCCCTTG
1 TGGTGCCGCCAACAAG-GTTCCCTTG
53965287 ACCAAGGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.06
27 45 0.94
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGTTCCCTTGTT
Found at i:53965397 original size:26 final size:25
Alignment explanation
Indices: 53965341--53965397 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
53965331 TTGGTTTTTT
*
53965341 TTATATATTTTGGTAAATAAAAAAT
1 TTATATATTTTGGTAAATAAAAAAA
53965366 TATATATATTTTGGTAAATAAAAAAAA
1 T-TATATATTTTGGTAAAT-AAAAAAA
53965393 TTATA
1 TTATA
53965398 ACATTTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 21 0.72
27 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (25 bp):
TTATATATTTTGGTAAATAAAAAAA
Found at i:53973242 original size:33 final size:33
Alignment explanation
Indices: 53973200--53973264 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
53973190 ATCCACATCG
*
53973200 TAAGCTAAGTCTTGGAGATCGTCCAACCAATTA
1 TAAGCTAAGTCTTGGAGATCGCCCAACCAATTA
53973233 TAAGCTAAGTCTTGGAGATCGCCCAACCAATT
1 TAAGCTAAGTCTTGGAGATCGCCCAACCAATT
53973265 CTTGACACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (33 bp):
TAAGCTAAGTCTTGGAGATCGCCCAACCAATTA
Found at i:53976164 original size:223 final size:223
Alignment explanation
Indices: 53975776--53976228 Score: 897
Period size: 223 Copynumber: 2.0 Consensus size: 223
53975766 TCAACTTTTA
53975776 CTTTTTATGCGTTTTATTTATTTATTTCAGGTTCCAGGTTTTTGATTTTATCCTCCCCCCTAATA
1 CTTTTTATGCGTTTTATTTATTTATTTCAGGTTCCAGGTTTTTGATTTTATCCTCCCCCCTAATA
53975841 TCTTGGGCACGACAACTGCCCCGACATAAATCTGGTCAAGAGAGCAACAATTTGCAGTAAACCCA
66 TCTTGGGCACGACAACTGCCCCGACATAAATCTGGTCAAGAGAGCAACAATTTGCAGTAAACCCA
53975906 GTTTCTGAGGGATCGGCCCTACTCCCTATACTGCTTAAATTTTCAAAATTAGGTGTAGGTTTATA
131 GTTTCTGAGGGATCGGCCCTACTCCCTATACTGCTTAAATTTTCAAAATTAGGTGTAGGTTTATA
53975971 TTGGTGGATTCAACACCTATCAATATAT
196 TTGGTGGATTCAACACCTATCAATATAT
53975999 CTTTTTATGCGTTTTATTTATTTATTTCAGGTTCCAGGTTTTTGATTTTATCCTCCCCCCTAATA
1 CTTTTTATGCGTTTTATTTATTTATTTCAGGTTCCAGGTTTTTGATTTTATCCTCCCCCCTAATA
53976064 TCTTGGGCACGACAACTGCCCCGACATAAATCTGGTCAAGAGAGCAACAATTTGCAGTAAACCCA
66 TCTTGGGCACGACAACTGCCCCGACATAAATCTGGTCAAGAGAGCAACAATTTGCAGTAAACCCA
53976129 GTTTCTGAGGGATCGGCCCTACTCCCTATACTGCTTAAATTTTCAAAATTAGGTGTAGGTTTATA
131 GTTTCTGAGGGATCGGCCCTACTCCCTATACTGCTTAAATTTTCAAAATTAGGTGTAGGTTTATA
53976194 TTGGTGGATTCAACACCTATCAATATAT
196 TTGGTGGATTCAACACCTATCAATATAT
*
53976222 TTTTTTA
1 CTTTTTA
53976229 GAATTTTTTT
Statistics
Matches: 229, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
223 229 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (223 bp):
CTTTTTATGCGTTTTATTTATTTATTTCAGGTTCCAGGTTTTTGATTTTATCCTCCCCCCTAATA
TCTTGGGCACGACAACTGCCCCGACATAAATCTGGTCAAGAGAGCAACAATTTGCAGTAAACCCA
GTTTCTGAGGGATCGGCCCTACTCCCTATACTGCTTAAATTTTCAAAATTAGGTGTAGGTTTATA
TTGGTGGATTCAACACCTATCAATATAT
Found at i:53982060 original size:15 final size:16
Alignment explanation
Indices: 53982024--53982055 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53982014 TTTTCACTAC
53982024 AAAACCAGAAAAATTT
1 AAAACCAGAAAAATTT
53982040 AAAACCAGAAAAATTT
1 AAAACCAGAAAAATTT
53982056 TAACCCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAACCAGAAAAATTT
Found at i:53982127 original size:23 final size:23
Alignment explanation
Indices: 53982100--53982145 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53982090 AATGCAACAA
*
53982100 GAGACCAGCAGCAGTTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
*
53982123 GAGACTAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
53982146 AAGATAAGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.13
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:53983065 original size:39 final size:39
Alignment explanation
Indices: 53983022--53983099 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
53983012 CTTTGCTAAT
53983022 ATTCAGTCAATCAATCAACAAAAACATCATAAGGTTTAC
1 ATTCAGTCAATCAATCAACAAAAACATCATAAGGTTTAC
*
53983061 ATTCAGTCAATCAATCGACAAAAACATCATAAGGTTTAC
1 ATTCAGTCAATCAATCAACAAAAACATCATAAGGTTTAC
53983100 CAACTTAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.26
Consensus pattern (39 bp):
ATTCAGTCAATCAATCAACAAAAACATCATAAGGTTTAC
Found at i:53988782 original size:16 final size:16
Alignment explanation
Indices: 53988761--53988792 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53988751 ATTCGTCGAG
53988761 CAGTAAATGGAAGAGC
1 CAGTAAATGGAAGAGC
53988777 CAGTAAATGGAAGAGC
1 CAGTAAATGGAAGAGC
53988793 GTTCGTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (16 bp):
CAGTAAATGGAAGAGC
Found at i:53991700 original size:21 final size:20
Alignment explanation
Indices: 53991646--53991703 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
53991636 AAACCTTGAA
*
53991646 CCTGAACACTAAACATCGAAT
1 CCTGAAC-CTAAACATCAAAT
* *
53991667 CCTAAACCATAAATATCAAAT
1 CCTGAACC-TAAACATCAAAT
53991688 CCTGAACTCTAAACAT
1 CCTGAAC-CTAAACAT
53991704 TGAACCTCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.22
Consensus pattern (20 bp):
CCTGAACCTAAACATCAAAT
Found at i:53991752 original size:23 final size:20
Alignment explanation
Indices: 53991720--53991770 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 20
53991710 TCGAATCTCA
53991720 AACTTGAACCCTAAACCCTTCG
1 AACTTGAACCCTAAA-CC-TCG
53991742 AACCTTGAACCCTAAACCTCG
1 AA-CTTGAACCCTAAACCTCG
53991763 AACTTGAA
1 AACTTGAA
53991771 TTTTGAACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.21
21 5 0.18
22 4 0.14
23 13 0.46
ACGTcount: A:0.35, C:0.33, G:0.10, T:0.22
Consensus pattern (20 bp):
AACTTGAACCCTAAACCTCG
Found at i:53993729 original size:29 final size:29
Alignment explanation
Indices: 53993692--53993748 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
53993682 AGAAGAAGTA
* *
53993692 TAAACATATTGGGCCATTTATGCAAAAAG
1 TAAACATATTGGGACATTTATGAAAAAAG
*
53993721 TAAAGATATTGGGACATTTATGAAAAAA
1 TAAACATATTGGGACATTTATGAAAAAA
53993749 TGAAAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.28
Consensus pattern (29 bp):
TAAACATATTGGGACATTTATGAAAAAAG
Found at i:53995114 original size:228 final size:226
Alignment explanation
Indices: 53994664--53995890 Score: 1621
Period size: 228 Copynumber: 5.5 Consensus size: 226
53994654 ATGTAGCCGC
* * *
53994664 GGAGGTGGATATTGTAGCTGAGAAAGGGAATGAAAAGAAATATCTTCTCAA---CG------CGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* * * *
53994720 GTTGCGTTAAGGTTGGTTCCGGGAGCTCGGATGTTTATG-T---TAATGGAAACGACTCCGATAA
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAACTAATGGAAACGACTCCGTTAA
* * *
53994781 TGGAGTTGTAATGGAATC-GGATGGCAATTGCATTGTCGAAGAAGACCACGAAGTGCCAA-CCGA
131 TGGAGTTGTAGTGGAATCGGGA-GACAATTGCATTGTCGAAGAAGACCACGAAGTG-AAATCCGA
53994844 ATCTGATTCGGTTACTATTACTATGAATCAGCA
194 ATCTGATTCGGTTACTATTACTATGAATCAGCA
*
53994877 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACATGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* * *
53994942 GCAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAACCTAGATGGGAACGACTCTGTT
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAA-CTA-ATGGAAACGACTCCGTT
* * *
53995007 AATGGAGTTGTAGTGGAACCGGGAGACAATTGCATTGTCGAAGAAGACCATGAAGTGCAATCCGA
129 AATGGAGTTGTAGTGGAATCGGGAGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGA
53995072 ATCTGATTCGGTTACTATTACTATGAATCAGCA
194 ATCTGATTCGGTTACTATTACTATGAATCAGCA
*
53995105 GGAGGTGGATATTGTAGCTGAGAAACAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* *** * * *
53995170 GTAGCGTTAACGTTGGCTCCGATGGCTCGGATGCTTATGCTAACCTAGATGGCAACGACTCCGTT
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAA-CTA-ATGGAAACGACTCCGTT
* *
53995235 AATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGAACACGAAGTGAAATCCGA
129 AATGGAGTTGTAGTGGAATCGGGAGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGA
* * *
53995300 ATCTGATTCGGTTACAATTACTATGACTCAACA
194 ATCTGATTCGGTTACTATTACTATGAATCAGCA
* * *
53995333 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTTATTGGCGCCAACGCGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* * * * *
53995398 TTTGCGTTAAGGTTGGCTCTGGCAGCTCAGATGTCTATG-T---TAATGGAAACGACTCCGTTAA
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAACTAATGGAAACGACTCCGTTAA
* * * *
53995459 TGGAGCTGTAGTGGAATC-AGATGGCAATTGCATTGTCGAAGAAAACCACGAAGTGAAATCCGAA
131 TGGAGTTGTAGTGGAATCGGGA-GACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAA
*
53995523 TCTGATTCGGTCACTATTACTATGAATCAGCA
195 TCTGATTCGGTTACTATTACTATGAATCAGCA
* * * *
53995555 GGAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGACATCTTCTCAATGGCGCCAACACGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* * * * *
53995620 GTAGAGTTAAGGTTGGCACCGGCAGCACGGATATTTATGTTAACGTAAATGGAAGCGACTCCGTT
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAAC-T-AATGGAAACGACTCCGTT
* * * *
53995685 AATGGAGTTGTTGTGGAATCGGGTGACAATTGCATTGTCGAAGAGGACCAGGAAGTGAAATCCGA
129 AATGGAGTTGTAGTGGAATCGGGAGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGA
* * *
53995750 ACCTGATTCGGTTACAATTACTATGACTCAGCA
194 ATCTGATTCGGTTACTATTACTATGAATCAGCA
* * **
53995783 GGAGGTGGATATTGTAACTGAGAAAGAGAATGAAACGAGATATCTTCTCATTGGCGCCAATGCGA
1 GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
* * * **
53995848 TTTGCGTTAAGGTTGGCTCCGGTAGCTTAGATGTTTATGTTAA
66 GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAA
53995891 TGGAGCAGTA
Statistics
Matches: 884, Mismatches: 105, Indels: 35
0.86 0.10 0.03
Matches are distributed among these distances:
213 48 0.05
216 2 0.00
221 1 0.00
222 227 0.26
223 4 0.00
227 7 0.01
228 591 0.67
229 4 0.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (226 bp):
GGAGGTGGATATTGTAGCTGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACACGA
GTAGCGTTAAGGTTGGCTCCGGCAGCTCGGATGTTTATGTTAACTAATGGAAACGACTCCGTTAA
TGGAGTTGTAGTGGAATCGGGAGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAAT
CTGATTCGGTTACTATTACTATGAATCAGCA
Found at i:53995703 original size:450 final size:446
Alignment explanation
Indices: 53994712--53996172 Score: 2014
Period size: 450 Copynumber: 3.3 Consensus size: 446
53994702 AATATCTTCT
* * ** * * *
53994712 CAACGCGAGTTGCGTTAAGGTTGGTTCCGGGAGCTCGGATGTTTATG-T----T-AATGGAAACG
1 CAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGGAAGCG
* * * *
53994771 ACTCCGATAATGGAGTTGTAATGGAATCGGATGGCAATTGCATTGTCGAAGAAGACCACGAAGTG
66 ACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGTG
* * *
53994836 CCAA-CCGAATCTGATTCGGTTACTATTACTATGAATCAGCAGGAGGTGGATATTGTAGCTGAGA
131 -AAATCCGAATCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGA
* ** ***
53994900 AAGAGAATGAAACGAGATATCTTCTCAATGGCGCCAACATGAGCAGCGTTAAGGTTGGCTCCGGC
195 AAGAGAATGAAACGAGATATCTTCTCATTGGCGCCAACGCGATTTGCGTTAAGGTTGGCTCCGGC
* *
53994965 AGCTCGGATGTTTATGTTAACCTAGATGGGAACGACTCTGTTAATGGAGTTGTAGTGGAACCGGG
260 AGCTC-GATG-TTATG-T----TA-AT-GGAACGACTC-GTTAATGGAGCTGTAGTGGAATC-GG
* * * *
53995030 A-GACAATTGCATTGTCGAAGAAGACCATGAAGTGCAATCCGAATCTGATTCGGTTACTATTACT
314 ATGGCAATTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAATCTGATTCGGTCACTATTACT
* * * *
53995094 ATGAATCAGCAGGAGGTGGATATTGTAGCTGAGAAACAGAATGAAACGAGATATCTTCTCAATGG
379 ATGAATCAGCAGGAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGATATCTTCTCAATGG
53995159 CGC
444 CGC
* * *** * * * * *
53995162 CAACACGAGTAGCGTTAACGTTGGCTCCGATGGCTCGGATGCTTATGCTAACCTAGATGGCAA-C
1 CAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGG-AAGC
*
53995226 GACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGAACACGAAGT
65 GACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGT
*
53995291 GAAATCCGAATCTGATTCGGTTACAATTACTATGACTCAACAGGAGGTGGATATTGTAGCTGAGA
130 GAAATCCGAATCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGA
* *
53995356 AAGAGAATGAAACGAGATATCTTCTTATTGGCGCCAACGCGATTTGCGTTAAGGTTGGCTCTGGC
195 AAGAGAATGAAACGAGATATCTTCTCATTGGCGCCAACGCGATTTGCGTTAAGGTTGGCTCCGGC
*
53995421 AGCTCAGATGTCTATGTTAATGGAAACGACTCCGTTAATGGAGCTGTAGTGGAATCAGATGGCAA
260 AGCTC-GATGT-TATGTTAATGG-AACGACT-CGTTAATGGAGCTGTAGTGGAATCGGATGGCAA
*
53995486 TTGCATTGTCGAAGAAAACCACGAAGTGAAATCCGAATCTGATTCGGTCACTATTACTATGAATC
321 TTGCATTGTCGAAGAAGACCACGAAGTGAAATCCGAATCTGATTCGGTCACTATTACTATGAATC
*
53995551 AGCAGGAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGACATCTTCTCAATGGCGC
386 AGCAGGAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGC
* *
53995612 CAACACGAGTAGAGTTAAGGTTGGCACCGGCAGCACGGATATTTATGTTAACGTAAATGGAAGCG
1 CAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGGAAGCG
* * *
53995677 ACTCCGTTAATGGAGTTGTTGTGGAATCGGGTGACAATTGCATTGTCGAAGAGGACCAGGAAGTG
66 ACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGTG
* *
53995742 AAATCCGAACCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAACTGAGAA
131 AAATCCGAATCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAA
* *
53995807 AGAGAATGAAACGAGATATCTTCTCATTGGCGCCAATGCGATTTGCGTTAAGGTTGGCTCCGGTA
196 AGAGAATGAAACGAGATATCTTCTCATTGGCGCCAACGCGATTTGCGTTAAGGTTGGCTCCGGCA
* *
53995872 GCT-TA-G--ATGTT--T------A-T-GTTAATGGAGCAGTAGTGGAATCGGATGGCAATTGCA
261 GCTCGATGTTATGTTAATGGAACGACTCGTTAATGGAGCTGTAGTGGAATCGGATGGCAATTGCA
*
53995923 TTGTCGAAGAAGACCACGAAGTGAAATCTGAATCTGATTCGGTCACTATTACTATGAATCAGCAG
326 TTGTCGAAGAAGACCACGAAGTGAAATCCGAATCTGATTCGGTCACTATTACTATGAATCAGCAG
* *
53995988 GAGGCGGATATAGTAGATGAGAAAGAGAATGAAAGGATATATCTTCTCAATGGCGC
391 GAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGC
*
53996044 CAACATGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGGAAGCG
1 CAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGGAAGCG
* * * *
53996109 ACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGGCAATTGTATTATCGAAGAAGACCACAAAGT
66 ACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGT
53996173 TACTATCAGT
Statistics
Matches: 917, Mismatches: 81, Indels: 44
0.88 0.08 0.04
Matches are distributed among these distances:
432 270 0.29
434 1 0.00
435 1 0.00
442 1 0.00
444 5 0.01
447 1 0.00
448 1 0.00
449 6 0.01
450 427 0.47
451 4 0.00
455 5 0.01
456 193 0.21
457 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (446 bp):
CAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACGGATGTTTATGTTAACGTAAATGGAAGCG
ACTCCGTTAATGGAGTTGTAGTGGAATCGGGTGACAATTGCATTGTCGAAGAAGACCACGAAGTG
AAATCCGAATCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAGCTGAGAA
AGAGAATGAAACGAGATATCTTCTCATTGGCGCCAACGCGATTTGCGTTAAGGTTGGCTCCGGCA
GCTCGATGTTATGTTAATGGAACGACTCGTTAATGGAGCTGTAGTGGAATCGGATGGCAATTGCA
TTGTCGAAGAAGACCACGAAGTGAAATCCGAATCTGATTCGGTCACTATTACTATGAATCAGCAG
GAGGCGGATATAGTAGATGAGAAAGAGAATGAAACGAGATATCTTCTCAATGGCGC
Found at i:53996032 original size:204 final size:204
Alignment explanation
Indices: 53995682--53996094 Score: 567
Period size: 204 Copynumber: 2.0 Consensus size: 204
53995672 AAGCGACTCC
** * * * *
53995682 GTTAATGGAGTTGTTGTGGAATCGGGTGACAATTGCATTGTCGAAGAGGACCAGGAAGTGAAATC
1 GTTAATGGAGCAGTAGTGGAATCGGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATC
* * * *
53995747 CGAACCTGATTCGGTTACAATTACTATGACTCAGCAGGAGGTGGATATTGTAACTGAGAAAGAGA
66 CGAACCTGATTCGGTCACAATTACTATGAATCAGCAGGAGGCGGATATAGTAACTGAGAAAGAGA
* ** * * * * **
53995812 ATGAAACGAGATATCTTCTCATTGGCGCCAATGCGATTTGCGTTAAGGTTGGCTCCGGTAGCTTA
131 ATGAAACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACA
53995877 GATGTTTAT
196 GATGTTTAT
*
53995886 GTTAATGGAGCAGTAGTGGAATCGGATGGCAATTGCATTGTCGAAGAAGACCACGAAGTGAAATC
1 GTTAATGGAGCAGTAGTGGAATCGGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATC
* * *
53995951 TGAATCTGATTCGGTCACTATTACTATGAATCAGCAGGAGGCGGATATAGTAGA-TGAGAAAGAG
66 CGAACCTGATTCGGTCACAATTACTATGAATCAGCAGGAGGCGGATATAGTA-ACTGAGAAAGAG
* * *
53996015 AATGAAAGGATATATCTTCTCAATGGCGCCAACATGAGTAGCGTTAAGGTTGGCACCGGCAGCAC
130 AATGAAACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCAC
*
53996080 GGATGTTTAT
195 AGATGTTTAT
53996090 GTTAA
1 GTTAA
53996095 CGTAAATGGA
Statistics
Matches: 181, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
204 180 0.99
205 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (204 bp):
GTTAATGGAGCAGTAGTGGAATCGGATGACAATTGCATTGTCGAAGAAGACCACGAAGTGAAATC
CGAACCTGATTCGGTCACAATTACTATGAATCAGCAGGAGGCGGATATAGTAACTGAGAAAGAGA
ATGAAACGAGATATCTTCTCAATGGCGCCAACACGAGTAGCGTTAAGGTTGGCACCGGCAGCACA
GATGTTTAT
Found at i:53998258 original size:278 final size:278
Alignment explanation
Indices: 53997761--53998315 Score: 984
Period size: 278 Copynumber: 2.0 Consensus size: 278
53997751 TTGGCAGTAC
* *
53997761 AAGGATGATTTAAATAAAGCGAATGAGTTGGCTTCGAAAGGGTATAAAGTGGCACTCCAAAATTT
1 AAGGATGATTTAAATAAAGCGAATGAGTTGGCTTCGAAAGGGGATAAAGTAGCACTCCAAAATTT
* * * *
53997826 TTGTATTAACCAGGTGAGGTCGTGCATTTGTTTTATTCCTTCCAAATCAAGAATTTTGTACAATA
66 TTGTATTAACCAGGTGAGGTCATGCATTTGTCTTATTCCTTCCAAATAAAAAATTTTGTACAATA
53997891 TTTGATCTAAACAGTTGATGGCTCAGGTGGAGAAATTTATGGACTAATGGAATAACAACGATGAA
131 TTTGATCTAAACAGTTGATGGCTCAGGTGGAGAAATTTATGGACTAATGGAATAACAACGATGAA
*
53997956 TTCCGAAAAGAATATGTTAGATGCAATGAAAGGAGCACACTGTGGAGACTGAGGACATTAGATGG
196 TTCCGAAAAGAATACGTTAGATGCAATGAAAGGAGCACACTGTGGAGACTGAGGACATTAGATGG
53998021 CCGTGCACTTGGTCCTGA
261 CCGTGCACTTGGTCCTGA
53998039 AAGGATGATTTAAATAAAGCGAATGAGTTGGCTTCGAAAGGGGATAAAGTAGCACTCCAAAATTT
1 AAGGATGATTTAAATAAAGCGAATGAGTTGGCTTCGAAAGGGGATAAAGTAGCACTCCAAAATTT
* *
53998104 TTGTATTAACCAGGTGAGGTCATGCATTTGTCTTATTTCTTCGAAATAAAAAATTTTGTACAATA
66 TTGTATTAACCAGGTGAGGTCATGCATTTGTCTTATTCCTTCCAAATAAAAAATTTTGTACAATA
* * * *
53998169 TTTTATCTAAACAGTTGATGGTTCAGGTGGAGAAATTTATGGACTTATGGAATAACAATGATGAA
131 TTTGATCTAAACAGTTGATGGCTCAGGTGGAGAAATTTATGGACTAATGGAATAACAACGATGAA
*
53998234 TTCCGAAAAGAATACGTTAGATGCAATGAAAGGAGCACACTTTGGAGACTGAGGACATTAGATGG
196 TTCCGAAAAGAATACGTTAGATGCAATGAAAGGAGCACACTGTGGAGACTGAGGACATTAGATGG
53998299 CCGTGCACTTGGTCCTG
261 CCGTGCACTTGGTCCTG
53998316 GTGAAGTGCC
Statistics
Matches: 263, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
278 263 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (278 bp):
AAGGATGATTTAAATAAAGCGAATGAGTTGGCTTCGAAAGGGGATAAAGTAGCACTCCAAAATTT
TTGTATTAACCAGGTGAGGTCATGCATTTGTCTTATTCCTTCCAAATAAAAAATTTTGTACAATA
TTTGATCTAAACAGTTGATGGCTCAGGTGGAGAAATTTATGGACTAATGGAATAACAACGATGAA
TTCCGAAAAGAATACGTTAGATGCAATGAAAGGAGCACACTGTGGAGACTGAGGACATTAGATGG
CCGTGCACTTGGTCCTGA
Found at i:54003150 original size:200 final size:200
Alignment explanation
Indices: 54002849--54003251 Score: 788
Period size: 200 Copynumber: 2.0 Consensus size: 200
54002839 GTCACTTTAT
54002849 TCAGTTGACGATAGTCAATGCACAACCTCATGGTTCCGTCCTTCTTTTTCACGAACAATACTGGT
1 TCAGTTGACGATAGTCAATGCACAACCTCATGGTTCCGTCCTTCTTTTTCACGAACAATACTGGT
54002914 GCACCCCAAGGTGAGAAACTTGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTT
66 GCACCCCAAGGTGAGAAACTTGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTT
*
54002979 CAACTCTTTTAACTCGGTTGGTGCCATACGATACGGAGCTATCGAAATCGGCGTAGTCCCAGGTA
131 CAACTCTTTTAACTCGGTTGGTGCCATACGATACGGAGCTATCGAAATCAGCGTAGTCCCAGGTA
54003044 CAAGC
196 CAAGC
54003049 TCAGTTGACGATAGTCAATGCACAACCTCATGGTTCCGTCCTTCTTTTTCACGAACAATACTGGT
1 TCAGTTGACGATAGTCAATGCACAACCTCATGGTTCCGTCCTTCTTTTTCACGAACAATACTGGT
54003114 GCACCCCAAGGTGAGAAACTTGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTT
66 GCACCCCAAGGTGAGAAACTTGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTT
*
54003179 CAACTCTTTTAACTCGGTTGGTGCCATATGATACGGAGCTATCGAAATCAGCGTAGTCCCAGGTA
131 CAACTCTTTTAACTCGGTTGGTGCCATACGATACGGAGCTATCGAAATCAGCGTAGTCCCAGGTA
54003244 CAAGC
196 CAAGC
54003249 TCA
1 TCA
54003252 ATACCAAACT
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.27
Consensus pattern (200 bp):
TCAGTTGACGATAGTCAATGCACAACCTCATGGTTCCGTCCTTCTTTTTCACGAACAATACTGGT
GCACCCCAAGGTGAGAAACTTGGTCGAGCAAAACCTCTATCCGTCAATTCTTGCAACTGAGCTTT
CAACTCTTTTAACTCGGTTGGTGCCATACGATACGGAGCTATCGAAATCAGCGTAGTCCCAGGTA
CAAGC
Found at i:54006871 original size:39 final size:41
Alignment explanation
Indices: 54006750--54006933 Score: 190
Period size: 40 Copynumber: 4.6 Consensus size: 41
54006740 GCTCCTCGTT
* *
54006750 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* * *
54006790 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAA-CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
54006830 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
54006869 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
54006910 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54006934 CATCATTCAA
Statistics
Matches: 126, Mismatches: 9, Indels: 19
0.82 0.06 0.12
Matches are distributed among these distances:
38 3 0.02
39 47 0.37
40 65 0.52
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:54006927 original size:79 final size:81
Alignment explanation
Indices: 54006750--54006933 Score: 215
Period size: 79 Copynumber: 2.3 Consensus size: 81
54006740 GCTCCTCGTT
* *
54006750 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTG
*
54006814 GATTTAGTAACTCGCA
66 GATTTAGTAACTAGCA
*
54006830 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTA-AC
*
54006891 C-GGATATT-GTCACTTAGCA
63 CTGGAT-TTAGTAAC-TAGCA
54006910 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54006934 CATCATTCAA
Statistics
Matches: 92, Mismatches: 5, Indels: 15
0.82 0.04 0.13
Matches are distributed among these distances:
78 14 0.15
79 54 0.59
80 24 0.26
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTG
GATTTAGTAACTAGCA
Found at i:54011353 original size:39 final size:39
Alignment explanation
Indices: 54011310--54011388 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
54011300 TATGATACGG
54011310 AGCTATCGAAATCAGCGTAGTCCCAGGTACAAGCTCAAT
1 AGCTATCGAAATCAGCGTAGTCCCAGGTACAAGCTCAAT
54011349 AGCTATCGAAATCAGCGTAGTCCCAGGTACAAGCTCAAT
1 AGCTATCGAAATCAGCGTAGTCCCAGGTACAAGCTCAAT
54011388 A
1 A
54011389 CCAAACTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.20
Consensus pattern (39 bp):
AGCTATCGAAATCAGCGTAGTCCCAGGTACAAGCTCAAT
Found at i:54014836 original size:79 final size:78
Alignment explanation
Indices: 54014736--54014958 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
54014726 GCTCCTCGTT
* *
54014736 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
*
54014801 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
54014816 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCGG
*
54014879 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * * * *
54014894 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAACCCG
54014957 GA
63 GA
54014959 CATCATTCAA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 46 0.37
79 57 0.46
80 20 0.16
81 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGAA
TTAGTAACTCGCA
Found at i:54014857 original size:39 final size:40
Alignment explanation
Indices: 54014736--54014958 Score: 257
Period size: 39 Copynumber: 5.7 Consensus size: 40
54014726 GCTCCTCGTT
* *
54014736 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
54014776 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54014816 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
54014855 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
54014894 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
54014935 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54014959 CATCATTCAA
Statistics
Matches: 164, Mismatches: 11, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 63 0.38
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:54022841 original size:39 final size:39
Alignment explanation
Indices: 54022724--54022922 Score: 267
Period size: 39 Copynumber: 5.1 Consensus size: 39
54022714 GCTTCTCGTT
* *
54022724 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * *
54022764 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
54022804 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* *
54022843 CAAATACCTTCGGGCTTAGCCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
54022882 CAAATGCCTTCGGGCTTAGCCTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
54022921 CA
1 CA
54022923 GATCTTAGTC
Statistics
Matches: 144, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 97 0.67
40 45 0.31
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:54030854 original size:41 final size:41
Alignment explanation
Indices: 54030797--54030879 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
54030787 TTTTAAGTCG
54030797 TAACTCGATCTACCTATTTCTGGCACTAATTTGAGGTATGA
1 TAACTCGATCTACCTATTTCTGGCACTAATTTGAGGTATGA
*
54030838 TAACTCGATCTACCTATTTTTGGCACTAATTTGAGGTATGA
1 TAACTCGATCTACCTATTTCTGGCACTAATTTGAGGTATGA
54030879 T
1 T
54030880 TCAGTTATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (41 bp):
TAACTCGATCTACCTATTTCTGGCACTAATTTGAGGTATGA
Found at i:54043314 original size:21 final size:21
Alignment explanation
Indices: 54043270--54043346 Score: 102
Period size: 21 Copynumber: 3.6 Consensus size: 21
54043260 GTAGGGGTCA
*
54043270 ACACACCCGTGTGG-GAGGAGGC
1 ACACACCCGTGTGGCTA--AGGC
*
54043292 ACACAGCCGTGTGGCTAAGGC
1 ACACACCCGTGTGGCTAAGGC
*
54043313 ACACATCCGTGTGGCTAAGGC
1 ACACACCCGTGTGGCTAAGGC
54043334 ACACACCCGTGTG
1 ACACACCCGTGTG
54043347 AGCCAGAGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
21 36 0.72
22 13 0.26
23 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.14
Consensus pattern (21 bp):
ACACACCCGTGTGGCTAAGGC
Found at i:54044525 original size:20 final size:21
Alignment explanation
Indices: 54044502--54044540 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
54044492 AATTACTTTC
54044502 GAAACATCTAA-TAATATAAA
1 GAAACATCTAATTAATATAAA
* *
54044522 GAAACTTGTAATTAATATA
1 GAAACATCTAATTAATATA
54044541 TATTCCCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
GAAACATCTAATTAATATAAA
Found at i:54057833 original size:22 final size:22
Alignment explanation
Indices: 54057808--54057851 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
54057798 ATCAAAGTCT
54057808 CTATTTATAGGTATAAGAAGTA
1 CTATTTATAGGTATAAGAAGTA
54057830 CTATTTATAGGTATAAGAAGTA
1 CTATTTATAGGTATAAGAAGTA
54057852 TAAAAGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (22 bp):
CTATTTATAGGTATAAGAAGTA
Found at i:54060391 original size:46 final size:46
Alignment explanation
Indices: 54060319--54060814 Score: 861
Period size: 46 Copynumber: 10.8 Consensus size: 46
54060309 TGTAACCCGC
*
54060319 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060365 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060411 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060457 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060503 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060549 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060595 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
54060641 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
* *** * * **
54060687 CCATGAGTGAACTCGGACTCAACTCAACGA-CTAC-CATGTAACCCGC
1 CCATGAGTGAACTCGGACTCAACTCAACGAGAT-CGGGCGT-TCGCAT
*
54060733 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
*
54060779 CCATGAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATGAGTGAACTCGGACTCAACTCAACGAGATCGG
54060815 ATGCCTAGTT
Statistics
Matches: 426, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
45 3 0.01
46 420 0.99
47 3 0.01
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (46 bp):
CCATGAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
Found at i:54060883 original size:92 final size:94
Alignment explanation
Indices: 54060787--54060957 Score: 310
Period size: 92 Copynumber: 1.8 Consensus size: 94
54060777 ATCCATGAGT
54060787 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAA-T-A
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAACTCA
54060850 ACGAGTTCGGATGCCTAGTTACATCTCAC
66 ACGAGTTCGGATGCCTAGTTACATCTCAC
* *
54060879 GAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAACTCA
54060944 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
54060958 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 59 0.79
93 1 0.01
94 15 0.20
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (94 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54060918 original size:47 final size:47
Alignment explanation
Indices: 54060787--54060957 Score: 310
Period size: 47 Copynumber: 3.7 Consensus size: 47
54060777 ATCCATGAGT
54060787 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
54060834 GAACTCGGACTCAA-T-AACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
*
54060879 GAACTTGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
*
54060926 GAACTTGGACTCAACTCAACGAGTTCGGATGC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC
54060958 TCAACCATCC
Statistics
Matches: 121, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
45 43 0.36
46 2 0.02
47 76 0.63
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54063380 original size:30 final size:30
Alignment explanation
Indices: 54063336--54063424 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
54063326 CAAAGATAAC
54063336 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
54063365 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * *
54063395 AAGAGATCCAGGATAAAGAAA-CTCAAGATA
1 AAGAAAACCAGAATAAAGAAATC-CAAGATA
54063425 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 10 0.20
30 38 0.76
31 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:54063384 original size:15 final size:15
Alignment explanation
Indices: 54063336--54063415 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
54063326 CAAAGATAAC
*
54063336 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
54063350 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
54063365 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
54063380 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
54063395 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
54063410 AAGAAA
1 AAGAAA
54063416 CTCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:54063424 original size:15 final size:14
Alignment explanation
Indices: 54063347--54063424 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 14
54063337 AGAAAACCGA
54063347 ATAAAGAAATCCAAG
1 ATAAAGAAAT-CAAG
* * *
54063362 ATAGAGAAACCCAG
1 ATAAAGAAATCAAG
*
54063376 AATAAAGAAATCCAG
1 -ATAAAGAAATCAAG
* *
54063391 AATAAAGAGATCCAGG
1 -ATAAAGAAAT-CAAG
54063407 ATAAAGAAACTCAAG
1 ATAAAGAAA-TCAAG
54063422 ATA
1 ATA
54063425 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.13
Consensus pattern (14 bp):
ATAAAGAAATCAAG
Found at i:54065653 original size:77 final size:77
Alignment explanation
Indices: 54065525--54065678 Score: 263
Period size: 77 Copynumber: 2.0 Consensus size: 77
54065515 GCCCTATTTC
*
54065525 ACAAAAATTTAAACATCTCATAAAATATAGCTCATATACCTGTTTCACTTCTTCCATATGAAAAT
1 ACAAAAATTTAAACATCTCATAAAATATAGCTCATATACCTATTTCACTTCTTCCATATGAAAAT
54065590 AGACTCATCAAG
66 AGACTCATCAAG
* * *
54065602 ACAAAAATTTAAACATCTCCTAAAATATAGCTCATATACGTATTTCGCTTCTTCCATATGAAAAT
1 ACAAAAATTTAAACATCTCATAAAATATAGCTCATATACCTATTTCACTTCTTCCATATGAAAAT
*
54065667 AGGCTCATCAAG
66 AGACTCATCAAG
54065679 CTTCGATTCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (77 bp):
ACAAAAATTTAAACATCTCATAAAATATAGCTCATATACCTATTTCACTTCTTCCATATGAAAAT
AGACTCATCAAG
Found at i:54066133 original size:46 final size:46
Alignment explanation
Indices: 54066066--54066536 Score: 802
Period size: 46 Copynumber: 10.2 Consensus size: 46
54066056 AATGAAAAGA
54066066 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066112 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066158 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066204 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066250 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066296 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066342 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
54066388 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
* *** * * ** *
54066434 AACGA-CTAC-CATGTAACCCGCCCATAAGTGAACTCGGACTCAACTC
1 AACGAGAT-CGGGCGT-TCGCATCCATGAGTGAACTCGGACTCAACTC
* *
54066480 AACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCAGACTCAACTC
1 AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
*
54066526 AACGAGTTCGG
1 AACGAGATCGG
54066537 ATGCCTAGTT
Statistics
Matches: 402, Mismatches: 19, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
45 3 0.01
46 395 0.98
47 4 0.01
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (46 bp):
AACGAGATCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTC
Found at i:54066573 original size:47 final size:47
Alignment explanation
Indices: 54066516--54066681 Score: 332
Period size: 47 Copynumber: 3.5 Consensus size: 47
54066506 AGTGAACTCA
54066516 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
1 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
54066563 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
1 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
54066610 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
1 GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
54066657 GACTCAACTCAACGAGTTCGGATGC
1 GACTCAACTCAACGAGTTCGGATGC
54066682 TCAACCATCC
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 119 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (47 bp):
GACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACGAACTTG
Found at i:54069356 original size:34 final size:33
Alignment explanation
Indices: 54069301--54069404 Score: 109
Period size: 34 Copynumber: 3.1 Consensus size: 33
54069291 GTATGCATTT
54069301 CTGATACTGTACTGAAATGGGCTAAGGCCCAAA
1 CTGATACTGTACTGAAATGGGCTAAGGCCCAAA
* * *
54069334 CTGATACTGTTACTGTATTGGGCTAAGGCCCACA
1 CTGATACTG-TACTGAAATGGGCTAAGGCCCAAA
* * * * * *
54069368 TTGATATTGCGACTAAAATGGGCTTAGGCCCAGA
1 CTGATACTG-TACTGAAATGGGCTAAGGCCCAAA
54069402 CTG
1 CTG
54069405 TTCAACACTG
Statistics
Matches: 57, Mismatches: 13, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
33 9 0.16
34 48 0.84
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (33 bp):
CTGATACTGTACTGAAATGGGCTAAGGCCCAAA
Found at i:54078839 original size:9 final size:9
Alignment explanation
Indices: 54078825--54078861 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54078815 ATCAATTTCC
*
54078825 AACACATAG
1 AACACATTG
54078834 AACACATTG
1 AACACATTG
*
54078843 CACACATTG
1 AACACATTG
54078852 AACACATTG
1 AACACATTG
54078861 A
1 A
54078862 GAATTGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (9 bp):
AACACATTG
Found at i:54086623 original size:18 final size:18
Alignment explanation
Indices: 54086600--54086635 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54086590 ATTTATATTA
54086600 AATAAAAATTAAAATAAT
1 AATAAAAATTAAAATAAT
**
54086618 AATAAAGGTTAAAATAAT
1 AATAAAAATTAAAATAAT
54086636 TACATTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AATAAAAATTAAAATAAT
Found at i:54089429 original size:12 final size:12
Alignment explanation
Indices: 54089407--54089439 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
54089397 AACTTATTTT
54089407 TTTCTTTTAAAAG
1 TTTC-TTTAAAAG
54089420 TTTCTTT-AAAG
1 TTTCTTTAAAAG
54089431 TTTCTTTAA
1 TTTCTTTAA
54089440 TCGTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 4 0.21
13 4 0.21
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (12 bp):
TTTCTTTAAAAG
Found at i:54103589 original size:49 final size:49
Alignment explanation
Indices: 54103517--54103909 Score: 650
Period size: 49 Copynumber: 8.1 Consensus size: 49
54103507 TATGAAATGA
*
54103517 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54103566 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54103615 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54103664 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54103713 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
** *
54103760 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAAAGTGTATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
* *
54103809 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
* * * * * *
54103858 TGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATG
1 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54103905 TGATA
1 TGATA
54103910 AGTCCCGAAG
Statistics
Matches: 325, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 52 0.16
48 1 0.00
49 272 0.84
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (49 bp):
TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
Found at i:54103821 original size:145 final size:145
Alignment explanation
Indices: 54103517--54103909 Score: 660
Period size: 145 Copynumber: 2.7 Consensus size: 145
54103507 TATGAAATGA
54103517 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
54103582 CCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGT
66 CCGATGTGATGAATGTGAAAGTG--TATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGT
**
54103647 GAAAGTGTATATATATG
129 GAAAAAGTATATATATG
*
54103664 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
54103729 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
66 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
*
54103794 AAAAGTGTATATATG
131 AAAAGTATATATATG
* * * *
54103809 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGACAGGGCCGAGTGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
* * * *
54103874 CCAACGTGATGGATGTGAAAGTGTATAAATGTGATA
66 CCGATGTGATGAATGTGAAAGTGTATATATGTGATA
54103910 AGTCCCGAAG
Statistics
Matches: 233, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
145 146 0.63
147 87 0.37
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (145 bp):
TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGA
AAAAGTATATATATG
Found at i:54104086 original size:37 final size:37
Alignment explanation
Indices: 54104030--54104108 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
54104020 CCGAGCTCTA
* * * *
54104030 AAGACCTGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54104067 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54104104 AAGAC
1 AAGAC
54104109 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54115866 original size:30 final size:30
Alignment explanation
Indices: 54115832--54115891 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
54115822 ATTTAATACG
54115832 AACTTTTGAAAAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
* *
54115862 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTGAAAAATTACACTTTTGCCCCTA
54115892 GGCTCAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTTGAAAAATTACACTTTTGCCCCTA
Found at i:54121221 original size:60 final size:60
Alignment explanation
Indices: 54121146--54121279 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 60
54121136 ATAACTTTCA
* ** **
54121146 AAAAAATTAAAAGATATAAAGAAATTTTTTAAAAATTTTGAAGGGTC-AATTACAATTT-TTT
1 AAAAAATT-TAAGATA-AAAGAAATCATTTAAAAATTTTGAAGGACCTAATTA-AATTTGTTT
* *
54121207 AAAAAATTTAAGATAAATGAAATCATTTCAAAATTTTGAAGGACCTAATTAAATTTGTTT
1 AAAAAATTTAAGATAAAAGAAATCATTTAAAAATTTTGAAGGACCTAATTAAATTTGTTT
54121267 -AAAAATTTCAAGA
1 AAAAAATTT-AAGA
54121280 GAACTAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 37 0.59
60 18 0.29
61 8 0.13
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (60 bp):
AAAAAATTTAAGATAAAAGAAATCATTTAAAAATTTTGAAGGACCTAATTAAATTTGTTT
Found at i:54121297 original size:60 final size:59
Alignment explanation
Indices: 54121167--54121299 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
54121157 AGATATAAAG
* ** * *
54121167 AAATTTTTTAAAAATTTTGAAGGGTCAATTACAATTTTTTAAAAAATTTAAGATAAATG
1 AAATTTTTTCAAAATTTTGAAGGACCAATTACAATTTTTTAAAAAATTTAAGAGAAATA
** *
54121226 AAATCATTTCAAAATTTTGAAGGACCTAATTA-AATTTGTTT-AAAAATTTCAAGAGAACTA
1 AAATTTTTTCAAAATTTTGAAGGACC-AATTACAATTT-TTTAAAAAATTT-AAGAGAAATA
54121286 AAATTTTTTCAAAA
1 AAATTTTTTCAAAA
54121300 AATTGAGAGG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 34 0.56
60 27 0.44
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (59 bp):
AAATTTTTTCAAAATTTTGAAGGACCAATTACAATTTTTTAAAAAATTTAAGAGAAATA
Found at i:54125216 original size:3 final size:3
Alignment explanation
Indices: 54125208--54125248 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
54125198 TATGTTTTCT
54125208 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54125249 TAAACTCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54132974 original size:22 final size:24
Alignment explanation
Indices: 54132928--54132979 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
54132918 ATTTTTTAAA
*
54132928 TATTTTTAATTTTGAAACTTTTATG
1 TATTTTTAA-TTTGAAAATTTTATG
54132953 TATTTTTAA-TT-AAAATTTTATG
1 TATTTTTAATTTGAAAATTTTATG
54132975 -ATTTT
1 TATTTT
54132980 CTAAAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 2 0.08
25 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (24 bp):
TATTTTTAATTTGAAAATTTTATG
Found at i:54134228 original size:6 final size:6
Alignment explanation
Indices: 54134217--54134244 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
54134207 TTTTGCTCTT
54134217 CCTTTC CCTTTC CCTTTC CCTTTC CCTT
1 CCTTTC CCTTTC CCTTTC CCTTTC CCTT
54134245 CATCTCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CCTTTC
Done.