Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 54 of 145
Found at i:18825184 original size:2 final size:2
Alignment explanation
Indices: 18825177--18825203 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18825167 CTTTTCCGAT
18825177 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
18825204 TAGAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18832390 original size:14 final size:14
Alignment explanation
Indices: 18832371--18832422 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
18832361 TATGCTATTA
18832371 TTTTTTATAACATT
1 TTTTTTATAACATT
*
18832385 TTTTTTATAATATT
1 TTTTTTATAACATT
*
18832399 ATTTTTATAA-ATT
1 TTTTTTATAACATT
18832412 TTTTTTATAAC
1 TTTTTTATAAC
18832423 CTTAATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 12 0.35
14 22 0.65
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTATAACATT
Found at i:18832412 original size:27 final size:29
Alignment explanation
Indices: 18832366--18832421 Score: 98
Period size: 27 Copynumber: 2.0 Consensus size: 29
18832356 CATAATATGC
18832366 TATTATTTTTTATAACATTTTTTTTATAA
1 TATTATTTTTTATAACATTTTTTTTATAA
18832395 TATTA-TTTTTATAA-ATTTTTTTTATAA
1 TATTATTTTTTATAACATTTTTTTTATAA
18832422 CCTTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 13 0.48
28 9 0.33
29 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTATTTTTTATAACATTTTTTTTATAA
Found at i:18832430 original size:28 final size:28
Alignment explanation
Indices: 18832367--18832431 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
18832357 ATAATATGCT
*
18832367 ATTATTTTTTATAACATTTTTTTTATAAT
1 ATTA-TTTTTATAACATTTTTTTTATAAC
18832396 ATTATTTTTATAA-ATTTTTTTTATAAC
1 ATTATTTTTATAACATTTTTTTTATAAC
* *
18832423 CTTAATTTT
1 ATTATTTTT
18832432 CTTTTTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 20 0.61
28 9 0.27
29 4 0.12
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTATTTTTATAACATTTTTTTTATAAC
Found at i:18834041 original size:19 final size:19
Alignment explanation
Indices: 18833967--18834038 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
18833957 AATCTTCAAG
*
18833967 GATATCCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18833986 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
18834005 GATATATGCAATCTTGGATAT
1 G--ATATGCAATCTTAGATAT
18834026 GATATGCAATCTT
1 GATATGCAATCTT
18834039 GGAAGATATG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 31 0.63
21 18 0.37
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:18834785 original size:12 final size:12
Alignment explanation
Indices: 18834764--18834795 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18834754 AACAAGGAAG
18834764 AAAA-TAAAAAA
1 AAAAGTAAAAAA
18834775 AAAAGTAAAAAA
1 AAAAGTAAAAAA
18834787 AAAAG-AAAA
1 AAAAGTAAAA
18834796 GGAAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (12 bp):
AAAAGTAAAAAA
Found at i:18834789 original size:17 final size:17
Alignment explanation
Indices: 18834763--18834804 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
18834753 AAACAAGGAA
*
18834763 GAAAATAAAAAAAAAAG
1 GAAAAAAAAAAAAAAAG
* *
18834780 TAAAAAAAAAAGAAAAG
1 GAAAAAAAAAAAAAAAG
18834797 GAAAAAAA
1 GAAAAAAA
18834805 CAAACTAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
GAAAAAAAAAAAAAAAG
Found at i:18849226 original size:12 final size:12
Alignment explanation
Indices: 18849204--18849246 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
18849194 GTTAGGTTCT
*
18849204 CACACGTCCTAG
1 CACACGGCCTAG
*
18849216 CACATGGCCTAG
1 CACACGGCCTAG
* *
18849228 CATACGGCCTGG
1 CACACGGCCTAG
18849240 CACACGG
1 CACACGG
18849247 GCGTGTGAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.37, G:0.26, T:0.14
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:18859090 original size:20 final size:22
Alignment explanation
Indices: 18859065--18859112 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
18859055 CGAATCTGTC
18859065 AAAAATAA-T-AAAAATTCACT
1 AAAAATAATTGAAAAATTCACT
* *
18859085 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGAAAAATTCACT
18859107 AAAAAT
1 AAAAAT
18859113 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGAAAAATTCACT
Found at i:18871298 original size:13 final size:13
Alignment explanation
Indices: 18871280--18871304 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18871270 TCTCCCTGAA
18871280 GTTACAGTGGAGC
1 GTTACAGTGGAGC
18871293 GTTACAGTGGAG
1 GTTACAGTGGAG
18871305 TAGATTAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.40, T:0.24
Consensus pattern (13 bp):
GTTACAGTGGAGC
Found at i:18871388 original size:44 final size:44
Alignment explanation
Indices: 18871317--18871770 Score: 372
Period size: 44 Copynumber: 10.0 Consensus size: 44
18871307 GATTAAAGAC
* * *
18871317 AAGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCATATTA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * * * * *
18871361 AAGCCACAAACCTTATCTCCCTGAAGTTGTAGTGGAACAGGTGA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
** *
18871405 AAAATAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
1 AAGCT--ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--A
* *
18871453 GACAGACTACAAATCTTATC-CCCTTGAAGTTGCTGTGGAGCAGATTG
1 -A-AG-CTACAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTA
* * ** * *
18871500 AAGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGATTAGGTTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * * *
18871544 AAGATTCCAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--A
* *
18871590 GACAGACTACAAATCTTAT-TCCCTTGAAGTTGCAGTGGAGCATATTG
1 -A-AG-CTACAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTA
* * * * *
18871637 AAGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * * * * *
18871681 AAGATTCTAATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* ** * * * *
18871725 AAGATACTGATCCTATCTCCCTGAAGTTGTAGTTGAGCGGATTA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
18871769 AA
1 AA
18871771 ATGATGAATC
Statistics
Matches: 326, Mismatches: 68, Indels: 32
0.77 0.16 0.08
Matches are distributed among these distances:
44 205 0.63
45 11 0.03
46 34 0.10
47 1 0.00
48 10 0.03
49 63 0.19
50 1 0.00
51 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
Found at i:18871534 original size:93 final size:92
Alignment explanation
Indices: 18871317--18871728 Score: 318
Period size: 93 Copynumber: 4.5 Consensus size: 92
18871307 GATTAAAGAC
* * * * ** *
18871317 AAGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCATATT--A-A-AGCCACAAACCTTATC
1 AAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGATACAAATCTTATC
* *
18871378 TCCCTGAAGTTG-TAGTGGAACAG-GTG
66 TCCCTGAAGTTGCT-GTGGAGCAGATTG
*** *
18871404 AAAAATAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGACTACAAATCT
1 ---AAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGA-TACAAATCT
18871469 TATC-CCCTTGAAGTTGCTGTGGAGCAGATTG
62 TATCTCCC-TGAAGTTGCTGTGGAGCAGATTG
* ** * * *
18871500 AAGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGATTAGGTT---GA-AGATTCCAATCTTATC
1 AAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGATACAAATCTTATC
18871561 TCCCTGAAGTTG-TAGTGGAGCAGATTG
66 TCCCTGAAGTTGCT-GTGGAGCAGATTG
* *
18871588 AAGACAGACTACAAATCTTAT-TCCCTTGAAGTTGCAGTGGAGCATATTGAAG-C-G--ACAAAC
1 AAG-C-G---ACAAATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTGAAGACAGATACAAAT
* * *
18871648 CTTATCTCCCTGAAGTTGCAGTGGAACAGGTTG
60 CTTATCTCCCTGAAGTTGCTGTGGAGCAGATTG
*** * * *
18871681 AAGATTCTAATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGA
1 AAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA
18871729 TACTGATCCT
Statistics
Matches: 259, Mismatches: 40, Indels: 47
0.75 0.12 0.14
Matches are distributed among these distances:
87 1 0.00
88 68 0.26
89 10 0.04
90 39 0.15
92 5 0.02
93 99 0.38
94 5 0.02
95 28 0.11
96 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (92 bp):
AAGCGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGACAGATACAAATCTTATC
TCCCTGAAGTTGCTGTGGAGCAGATTG
Found at i:18871607 original size:137 final size:137
Alignment explanation
Indices: 18871297--18871728 Score: 636
Period size: 137 Copynumber: 3.1 Consensus size: 137
18871287 TGGAGCGTTA
* * * *
18871297 CAGTGGAGTAGATTAAAGACA-AGCTACAAATCTTATCTCCC-TAAAGTTACAGTGGAGCATATT
1 CAGTGGAGCAGATTGAAGACAGA-CTACAAATCTTATC-CCCTTGAAGTTGCAGTGGAGCATATT
* * * * *
18871360 AAAGCCACAAACCTTATCTCCCTGAAGTTGTAGTGGAACAGG-TGAAAAATAAACCAATCTTATC
64 GAAGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTG-AAGAT--TCCAATCTTATC
18871424 TCCCTGAAGTTG
126 TCCCTGAAGTTG
* *
18871436 CAGTGGAGCAGATTGAAGACAGACTACAAATCTTATCCCCTTGAAGTTGCTGTGGAGCAGATTGA
1 CAGTGGAGCAGATTGAAGACAGACTACAAATCTTATCCCCTTGAAGTTGCAGTGGAGCATATTGA
**
18871501 AGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGATTAGGTTGAAGATTCCAATCTTATCTCCCT
66 AGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGATTCCAATCTTATCTCCCT
18871566 GAAGTTG
131 GAAGTTG
* *
18871573 TAGTGGAGCAGATTGAAGACAGACTACAAATCTTATTCCCTTGAAGTTGCAGTGGAGCATATTGA
1 CAGTGGAGCAGATTGAAGACAGACTACAAATCTTATCCCCTTGAAGTTGCAGTGGAGCATATTGA
* *
18871638 AGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGATTCTAATCTTATCTCTCT
66 AGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGATTCCAATCTTATCTCCCT
18871703 GAAGTTG
131 GAAGTTG
*
18871710 CAGTGGAGTAGATTGAAGA
1 CAGTGGAGCAGATTGAAGA
18871729 TACTGATCCT
Statistics
Matches: 267, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
137 169 0.63
138 3 0.01
139 92 0.34
140 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (137 bp):
CAGTGGAGCAGATTGAAGACAGACTACAAATCTTATCCCCTTGAAGTTGCAGTGGAGCATATTGA
AGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTGAAGATTCCAATCTTATCTCCCT
GAAGTTG
Found at i:18881659 original size:39 final size:38
Alignment explanation
Indices: 18881605--18881716 Score: 118
Period size: 37 Copynumber: 2.9 Consensus size: 38
18881595 AAAAGATCTT
* * *
18881605 ATTCAATATGATCAATGGATAATGCTCGTTTGAGCAAAC
1 ATTCAATATAATCAATAGATATTGCTCGTTTGAGC-AAC
* * * * *
18881644 ATTCAGTATAATCAATTGACATTGCTCTTTTGAGC-TC
1 ATTCAATATAATCAATAGATATTGCTCGTTTGAGCAAC
* *
18881681 ATTCAATATATTCAGTAGATATTGCTCGTTTGAGCA
1 ATTCAATATAATCAATAGATATTGCTCGTTTGAGCA
18881717 TACTTTCAGT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
37 30 0.51
39 29 0.49
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (38 bp):
ATTCAATATAATCAATAGATATTGCTCGTTTGAGCAAC
Found at i:18881747 original size:39 final size:39
Alignment explanation
Indices: 18881704--18881813 Score: 168
Period size: 39 Copynumber: 2.8 Consensus size: 39
18881694 AGTAGATATT
*
18881704 GCTCGTTTGAGCATACTTTCAGTAGAATCAGTGGGTATG
1 GCTCGATTGAGCATACTTTCAGTAGAATCAGTGGGTATG
* * *
18881743 GCTCGACTGAACATACCTTT-AGTACAATCAGTGGGTATG
1 GCTCGATTGAGCATA-CTTTCAGTAGAATCAGTGGGTATG
18881782 GCTCGATTGAGCATACTTTCAGTAGAATCAGT
1 GCTCGATTGAGCATACTTTCAGTAGAATCAGT
18881814 ATCCCATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 4 0.06
39 54 0.87
40 4 0.06
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (39 bp):
GCTCGATTGAGCATACTTTCAGTAGAATCAGTGGGTATG
Found at i:18885720 original size:16 final size:18
Alignment explanation
Indices: 18885701--18885733 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
18885691 TTAAATAAAA
18885701 AATTAAA-C-AAATTTAC
1 AATTAAATCTAAATTTAC
18885717 AATTAAATCTAAATTTA
1 AATTAAATCTAAATTTA
18885734 TTCTATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAATCTAAATTTAC
Found at i:18889470 original size:23 final size:23
Alignment explanation
Indices: 18889444--18889496 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
18889434 AAACTAAGCA
*
18889444 TTATTTAAAAAAAATACTCATAT
1 TTATATAAAAAAAATACTCATAT
** *
18889467 TTATATAATTAAAATATTCATAT
1 TTATATAAAAAAAATACTCATAT
*
18889490 TTTTATA
1 TTATATA
18889497 TTAGGTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATATAAAAAAAATACTCATAT
Found at i:18889730 original size:21 final size:22
Alignment explanation
Indices: 18889687--18889730 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
18889677 ATGTTTAATA
*
18889687 ATATTGAAAATTATAATATTTT
1 ATATTGAAAATTATAATACTTT
18889709 ATATT-AAAATTA-AATACCTTT
1 ATATTGAAAATTATAATA-CTTT
18889730 A
1 A
18889731 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTGAAAATTATAATACTTT
Found at i:18894097 original size:8 final size:8
Alignment explanation
Indices: 18894080--18894120 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
18894070 TTGTATAAGC
18894080 ATATAT-T
1 ATATATGT
18894087 ATATATGT
1 ATATATGT
18894095 ATATATGT
1 ATATATGT
18894103 ATATATGT
1 ATATATGT
*
18894111 ATATCTGT
1 ATATATGT
18894119 AT
1 AT
18894121 TTTGTATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (8 bp):
ATATATGT
Found at i:18897795 original size:16 final size:16
Alignment explanation
Indices: 18897776--18897806 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18897766 AAAAGAAGTT
18897776 GTTAAGGTTGTTAGCA
1 GTTAAGGTTGTTAGCA
*
18897792 GTTAGGGTTGTTAGC
1 GTTAAGGTTGTTAGC
18897807 TGCAGCTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.39
Consensus pattern (16 bp):
GTTAAGGTTGTTAGCA
Found at i:18898022 original size:6 final size:6
Alignment explanation
Indices: 18898011--18898047 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
18898001 TCTTTTACTC
*
18898011 ATATTT ATATTT TTATTT CATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT
18898048 TTTTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (6 bp):
ATATTT
Found at i:18898033 original size:19 final size:19
Alignment explanation
Indices: 18898009--18898047 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
18897999 CCTCTTTTAC
*
18898009 TCATATTTATATTTTTATT
1 TCATATTTATATTTATATT
18898028 TCATATTTATATTTATATT
1 TCATATTTATATTTATATT
18898047 T
1 T
18898048 TTTTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TCATATTTATATTTATATT
Found at i:18898058 original size:27 final size:25
Alignment explanation
Indices: 18898011--18898061 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
18898001 TCTTTTACTC
18898011 ATATTTATATTTTTATTTCATATTT
1 ATATTTATATTTTTATTTCATATTT
18898036 ATATTTATATTTTTTTATTTCATATT
1 ATATTTATA--TTTTTATTTCATATT
18898062 GTTTTAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
ATATTTATATTTTTATTTCATATTT
Found at i:18900017 original size:24 final size:24
Alignment explanation
Indices: 18899985--18900046 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
18899975 GCAACATTTA
* *
18899985 ATTACAAGCCTAAACTCATCGTTTC
1 ATTA-AAGCATAAACTCACCGTTTC
* *
18900010 ATTTAAGCATAAACTCACCGTTTT
1 ATTAAAGCATAAACTCACCGTTTC
*
18900034 ATTAAAGCTTAAA
1 ATTAAAGCATAAA
18900047 ACCAATTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (24 bp):
ATTAAAGCATAAACTCACCGTTTC
Found at i:18906072 original size:27 final size:25
Alignment explanation
Indices: 18906027--18906078 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
18906017 GTAACCAAAA
18906027 CTCTCTCCTCTCCTTCTTTTCTTTT
1 CTCTCTCCTCTCCTTCTTTTCTTTT
*
18906052 CTCTCTCGTTCTCCTTACTTTTCTTTT
1 CTCTCTC-CTCTCCTT-CTTTTCTTTT
18906079 TTGTAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (25 bp):
CTCTCTCCTCTCCTTCTTTTCTTTT
Found at i:18906330 original size:21 final size:21
Alignment explanation
Indices: 18906299--18906363 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
18906289 AAGAGAAGCG
18906299 GAAAAAGGAAAGAAAAAAAATA
1 GAAAAA-GAAAGAAAAAAAATA
**
18906321 GAAAAAGAAAGGAAAAAGCATA
1 GAAAAAGAAA-GAAAAAAAATA
* * *
18906343 -AATATGAAAGAATAAAAATA
1 GAAAAAGAAAGAAAAAAAATA
18906363 G
1 G
18906364 GTTAAAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 8 0.24
21 11 0.32
22 15 0.44
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (21 bp):
GAAAAAGAAAGAAAAAAAATA
Found at i:18910595 original size:12 final size:12
Alignment explanation
Indices: 18910578--18910602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18910568 ATTGATTTTC
18910578 TCATAATCATAG
1 TCATAATCATAG
18910590 TCATAATCATAG
1 TCATAATCATAG
18910602 T
1 T
18910603 AATGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATAATCATAG
Found at i:18916920 original size:12 final size:12
Alignment explanation
Indices: 18916903--18916927 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18916893 ATTGATTTAC
18916903 TCATAATCATAG
1 TCATAATCATAG
18916915 TCATAATCATAG
1 TCATAATCATAG
18916927 T
1 T
18916928 AATGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATAATCATAG
Found at i:18917264 original size:13 final size:13
Alignment explanation
Indices: 18917246--18917272 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18917236 TTATTATTTC
18917246 ATTATTTATTCTA
1 ATTATTTATTCTA
18917259 ATTATTTATTCTA
1 ATTATTTATTCTA
18917272 A
1 A
18917273 CATGATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTTATTCTA
Found at i:18933054 original size:14 final size:14
Alignment explanation
Indices: 18933035--18933068 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
18933025 ACAAGTTCCC
18933035 AGAAGAGTCACTAA
1 AGAAGAGTCACTAA
18933049 AGAAGAGTCACTAA
1 AGAAGAGTCACTAA
18933063 AGAAGA
1 AGAAGA
18933069 ACCACTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.12
Consensus pattern (14 bp):
AGAAGAGTCACTAA
Found at i:18940460 original size:21 final size:20
Alignment explanation
Indices: 18940432--18940475 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
18940422 GATGAAAAAA
*
18940432 AAATTTAAA-AGTTGTATTAT
1 AAATTTAAACA-TTATATTAT
18940452 AAATCTTAAACATTATATTAT
1 AAAT-TTAAACATTATATTAT
18940473 AAA
1 AAA
18940476 AATAATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 16 0.76
22 1 0.05
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATTTAAACATTATATTAT
Found at i:18942100 original size:24 final size:24
Alignment explanation
Indices: 18942046--18942096 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
18942036 AATCATGGTG
*
18942046 TATTATTATTTCAAAGTTACTATG
1 TATTATTATTTCAAAGTTACTATA
18942070 TATTATTATTT-AAAGTTATCT-TA
1 TATTATTATTTCAAAGTTA-CTATA
18942093 TATT
1 TATT
18942097 TATTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TATTATTATTTCAAAGTTACTATA
Found at i:18945726 original size:27 final size:27
Alignment explanation
Indices: 18945696--18945764 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
18945686 AACAAGTCGA
*
18945696 GAAAGAAAAGCCTTTCTGGCGAAATGT
1 GAAAGAAAAGCCTTTCTGGCGAAATAT
* * *
18945723 GAAAGAAAATCCTTTTTGGTGAAATAT
1 GAAAGAAAAGCCTTTCTGGCGAAATAT
* *
18945750 GAAAGGAATGCCTTT
1 GAAAGAAAAGCCTTT
18945765 GTGTCAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTCTGGCGAAATAT
Found at i:18946780 original size:19 final size:19
Alignment explanation
Indices: 18946756--18946793 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18946746 TATCAGATGT
18946756 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
18946775 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
18946794 CATATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
GTGGTAATAAGTTGTTTAA
Found at i:18948001 original size:23 final size:22
Alignment explanation
Indices: 18947975--18948054 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
18947965 AACACTCCAC
*
18947975 GCTAGAATGAAATGCACATAAGT
1 GCTAGAATGAATTGCACA-AAGT
*
18947998 GCTA-AAGTGATTTGCATCAAAGT
1 GCTAGAA-TGAATTGCA-CAAAGT
* *
18948021 GCCTAGAATTAATTGCAAACAAGT
1 G-CTAGAATGAATTGCACA-AAGT
18948045 GCTAGAATGA
1 GCTAGAATGA
18948055 TTTGTATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 2 0.04
23 25 0.54
24 17 0.37
25 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (22 bp):
GCTAGAATGAATTGCACAAAGT
Found at i:18954392 original size:13 final size:13
Alignment explanation
Indices: 18954374--18954403 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18954364 AAACTAGATT
*
18954374 TTAACTAAGTAAA
1 TTAACTAAGAAAA
18954387 TTAACTAAGAAAA
1 TTAACTAAGAAAA
18954400 TTAA
1 TTAA
18954404 AAGATAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:18956240 original size:16 final size:16
Alignment explanation
Indices: 18956219--18956252 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18956209 TTACCAATGA
* *
18956219 AATTCTTTTATTTCTC
1 AATTCTTTCACTTCTC
18956235 AATTCTTTCACTTCTC
1 AATTCTTTCACTTCTC
18956251 AA
1 AA
18956253 GCTAAGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTCTTTCACTTCTC
Found at i:18958639 original size:29 final size:29
Alignment explanation
Indices: 18958606--18958740 Score: 144
Period size: 29 Copynumber: 4.7 Consensus size: 29
18958596 CAGAGTCTCA
* *
18958606 CCACAAAGGCATCTTTTTAACAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * **
18958635 CCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
** * *
18958664 CCACAAATTCTTCCTTTTAATAGAGAAAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * *
18958693 CTACAAAGGCTTCCTTGTAACAAAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
*
18958722 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCTTCCTTTTA
18958741 TGAAATTTGG
Statistics
Matches: 83, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTTAACAGAGATAG
Found at i:18958737 original size:58 final size:58
Alignment explanation
Indices: 18958606--18958740 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 58
18958596 CAGAGTCTCA
* * * * * *
18958606 CCACAAAGGCATCTTTTTAACAGAGATAGCCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
** * * * *
18958664 CCACAAATTCTTCCTTTTAATAGAGAAAGCTACAAAGGCTTCCTTGTAACAAAGATAG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
18958722 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCATCCTTTTA
18958741 TGAAATTTGG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (58 bp):
CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
Found at i:18961776 original size:31 final size:30
Alignment explanation
Indices: 18961739--18961888 Score: 99
Period size: 31 Copynumber: 4.8 Consensus size: 30
18961729 TATATGGTTG
18961739 AACATTGCTGAAAATAATTTTTATGTAGTT
1 AACATTGCTGAAAATAATTTTTATGTAGTT
* * * *
18961769 ATTCATTGTTGAAATTGAATTGTATATGTA-TAT
1 A-ACATTGCTGAAAAT-AATT-TTTATGTAGT-T
* * * * *
18961802 AA-GTTGCTG-AAATGATTTGTATATGGTT
1 AACATTGCTGAAAATAATTTTTATGTAGTT
*
18961830 GAACATTGCTGAAAATAATTTTTATATAGTT
1 -AACATTGCTGAAAATAATTTTTATGTAGTT
* *
18961861 ATACATTGTTGAAATTAAATTGTTTATG
1 A-ACATTGCTGAAAAT-AATT-TTTATG
18961889 AATATAGGAT
Statistics
Matches: 90, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
28 6 0.07
29 6 0.07
30 11 0.12
31 44 0.49
32 9 0.10
33 14 0.16
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.45
Consensus pattern (30 bp):
AACATTGCTGAAAATAATTTTTATGTAGTT
Found at i:18961831 original size:92 final size:92
Alignment explanation
Indices: 18961675--18961894 Score: 343
Period size: 92 Copynumber: 2.4 Consensus size: 92
18961665 ATTGTTTTTG
* * *
18961675 GTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGTTG
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
*
18961739 AACATTGCTGAAAATAATTTTTATGTA
66 AACATTGCTGAAAATAATTTTTATATA
* * *
18961766 GTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTTGTATATGGTTG
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
18961831 AACATTGCTGAAAATAATTTTTATATA
66 AACATTGCTGAAAATAATTTTTATATA
* * *
18961858 GTTATACATTGTTGAAATTAAATTGTTTATGAATATA
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATA
18961895 GGATGTCGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
91 27 0.23
92 90 0.77
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
AACATTGCTGAAAATAATTTTTATATA
Found at i:18961938 original size:31 final size:31
Alignment explanation
Indices: 18961903--18961968 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
18961893 TAGGATGTCG
18961903 AATTTGATT-TGTATATGATTATACATTGCCA
1 AATTTGATTCT-TATATGATTATACATTGCCA
* * *
18961934 AATTTGATTCTTATATGGTTATATATTGCCG
1 AATTTGATTCTTATATGATTATACATTGCCA
18961965 AATT
1 AATT
18961969 GCTTGGCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (31 bp):
AATTTGATTCTTATATGATTATACATTGCCA
Found at i:18961955 original size:93 final size:92
Alignment explanation
Indices: 18961675--18961961 Score: 276
Period size: 92 Copynumber: 3.1 Consensus size: 92
18961665 ATTGTTTTTG
* * * * * * * * *
18961675 GTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGTTG
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
* * *
18961739 AACATTGCTGAAAATAATTTTTATGTA
66 AACATTGCTCAAAATAATTCTTATATA
* * * * *
18961766 GTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTTGTATATGGTTG
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
* *
18961831 AACATTGCTGAAAATAATTTTTATATA
66 AACATTGCTCAAAATAATTCTTATATA
* * *
18961858 GTTATACATTGTTGAAATTAAATTGTTTATGAATATAGGATG-TCGAATTTGATTTGTATATGAT
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCT-GAA-ATGATTTGTATATGAT
* * *
18961922 T-ATACATTGC-CAAATTTGATTCTTATATG
64 TGA-ACATTGCTCAAA-ATAATTCTTATATA
*
18961951 GTTATATATTG
1 GTTATACATTG
18961962 CCGAATTGCT
Statistics
Matches: 170, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
91 28 0.16
92 100 0.59
93 42 0.25
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
AACATTGCTCAAAATAATTCTTATATA
Found at i:18966126 original size:20 final size:21
Alignment explanation
Indices: 18966101--18966150 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
18966091 AAGCTTACGC
18966101 TAAGTAAATGA-AATGGA-AAG
1 TAAGTAAATGAGAAT-GATAAG
18966121 TAAGTAAAT-AGAATGATAAG
1 TAAGTAAATGAGAATGATAAG
18966141 TAAGTAAATG
1 TAAGTAAATG
18966151 GAGTGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
TAAGTAAATGAGAATGATAAG
Found at i:18970068 original size:31 final size:32
Alignment explanation
Indices: 18970030--18970092 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
18970020 AGGCAAATTA
18970030 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
18970061 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
18970093 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:18976369 original size:12 final size:12
Alignment explanation
Indices: 18976351--18976380 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18976341 AGGTAGGCAA
18976351 CTTTTTTTTGCG
1 CTTTTTTTTGCG
*
18976363 GTTTTTTTTGCG
1 CTTTTTTTTGCG
18976375 CTTTTT
1 CTTTTT
18976381 GCTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.70
Consensus pattern (12 bp):
CTTTTTTTTGCG
Found at i:18986344 original size:27 final size:30
Alignment explanation
Indices: 18986314--18986371 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 30
18986304 GTTTCTCTTC
18986314 TCTCAC-CACTTTT-TTCTT-TTGGCCGAA
1 TCTCACTCACTTTTCTTCTTGTTGGCCGAA
* *
18986341 TCTCTCTTCCCTTTTCTTCTTGTTGGCCGAA
1 TCTCAC-TCACTTTTCTTCTTGTTGGCCGAA
18986372 CCTTTTCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.20
29 6 0.24
30 5 0.20
31 9 0.36
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.47
Consensus pattern (30 bp):
TCTCACTCACTTTTCTTCTTGTTGGCCGAA
Found at i:18987098 original size:27 final size:27
Alignment explanation
Indices: 18987059--18987392 Score: 323
Period size: 27 Copynumber: 12.4 Consensus size: 27
18987049 AAATTGTGGG
* * *
18987059 AAAATGTCTGAAATACTCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
18987086 AAAATGACCGAAATATCCC-CGAATGGT
1 AAAATGACCGAAATA-CCCTCGAAGGGT
* * *
18987113 AAAATAACTGAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
18987140 AAAATGACCGAAATACTCC-CGAAAGGT
1 AAAATGACCGAAATAC-CCTCGAAGGGT
** *
18987167 AAAATGACTAAAATA-CCTCCGAAGTGT
1 AAAATGACCGAAATACCCT-CGAAGGGT
* **
18987194 AAAATAACTAAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
18987221 AAAATGACCGAAATACCCTCGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
18987248 AAAATGACCAAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* ** * *
18987275 AAAATAATTGAAATACCCTAGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * *
18987302 CAAATAACTGAAATACCCTAGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
18987329 AAAATGATCGAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * * *
18987356 AAAATGACCAAAATAACTTCGAAAGTT
1 AAAATGACCGAAATACCCTCGAAGGGT
18987383 AAAATGACCG
1 AAAATGACCG
18987393 TTATACCCCT
Statistics
Matches: 254, Mismatches: 47, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
25 2 0.01
26 3 0.01
27 242 0.95
28 7 0.03
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCGAAGGGT
Found at i:18987400 original size:81 final size:81
Alignment explanation
Indices: 18987059--18987392 Score: 391
Period size: 81 Copynumber: 4.1 Consensus size: 81
18987049 AAATTGTGGG
* * * * * * * *
18987059 AAAATGTCTGAAATACTCTCGAAGGGTAAAATGACCGAAATATCCCCGAATGGTAAAATAACTGA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
* *
18987124 AATACCCCCGAAGGGT
66 AATACCCTCGAAAGGT
* * *
18987140 AAAATGACCGAAATACTCC-CGAAAGGTAAAATGACTAAAATACCTCCGAAGTGTAAAATAACTA
1 AAAATGACCGAAATAC-CCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTA
*
18987204 AAATACCCTCGAAGGGT
65 AAATACCCTCGAAAGGT
* *
18987221 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAATTGA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
*
18987286 AATACCCTAGAAAGGT
66 AATACCCTCGAAAGGT
* * * * * * * * *
18987302 CAAATAACTGAAATACCCTAGAAGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACCAA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
* * *
18987367 AATAACTTCGAAAGTT
66 AATACCCTCGAAAGGT
18987383 AAAATGACCG
1 AAAATGACCG
18987393 TTATACCCCT
Statistics
Matches: 214, Mismatches: 37, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
80 2 0.01
81 211 0.99
82 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (81 bp):
AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
AATACCCTCGAAAGGT
Found at i:18987788 original size:28 final size:28
Alignment explanation
Indices: 18987748--18987832 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
18987738 ATTGTACTAA
* * *
18987748 TTACTGTATTGGGCTAAGGGCCATATTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
18987776 TTACTTTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
* *
18987804 TTACTGTAATGGGCTAAGACCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
18987832 T
1 T
18987833 ACTTTTACTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:19004617 original size:35 final size:35
Alignment explanation
Indices: 19004558--19004674 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
19004548 ACTCTCTGTT
* ** *
19004558 TTGGTGTATTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* *
19004593 TTAGTGTGTTTTGGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * **
19004628 TTGGTGTGTTTCGGATGGATTTGCTCTTACAAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
19004663 TCTGGTGTGTTT
1 T-TGGTGTGTTT
19004675 GGGTGGTTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 59 0.86
36 10 0.14
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:19007198 original size:109 final size:110
Alignment explanation
Indices: 19007029--19007226 Score: 344
Period size: 109 Copynumber: 1.8 Consensus size: 110
19007019 AGACATATTT
*
19007029 ATGAAAATGTTGTGTGTAAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
1 ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
*
19007094 AATACGTTATTTTGTCTTAATGAAATATCATTAATAGATTAATAC
66 AATACGTTATTTTGGCTTAATGAAATATCATTAATAGATTAATAC
*
19007139 ATGAAAATGTTGTGTGT-AAATCCATATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
1 ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
* *
19007203 AATACGTTGTTTTGGCTTGATGAA
66 AATACGTTATTTTGGCTTAATGAA
19007227 TTATTGTTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
109 66 0.80
110 17 0.20
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (110 bp):
ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
AATACGTTATTTTGGCTTAATGAAATATCATTAATAGATTAATAC
Found at i:19009179 original size:15 final size:15
Alignment explanation
Indices: 19009159--19009195 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19009149 TACCTACGCA
19009159 TTAAAATTAAACGTG
1 TTAAAATTAAACGTG
19009174 TTAAAATTAAACGTG
1 TTAAAATTAAACGTG
*
19009189 TCAAAAT
1 TTAAAAT
19009196 ATGGTACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (15 bp):
TTAAAATTAAACGTG
Found at i:19009495 original size:22 final size:23
Alignment explanation
Indices: 19009463--19009519 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
19009453 TGCACTAATG
*
19009463 AACAGATAGCACTA-AAGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
* *
19009485 CACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
19009507 AACAGAGAGCACT
1 AACAGAGAGCACT
19009520 GACATGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (23 bp):
AACAGAGAGCACTAGAAGTGCTA
Found at i:19009527 original size:22 final size:22
Alignment explanation
Indices: 19009463--19009530 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
19009453 TGCACTAATG
*
19009463 AACAGATAGCACT-AAAGTGCTA
1 AACAGAGAGCACTGAAA-TGCTA
* * **
19009485 CACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACTGAAATGCTA
*
19009507 AACAGAGAGCACTGACATGCTA
1 AACAGAGAGCACTGAAATGCTA
19009529 AA
1 AA
19009531 TATCAGAGAG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAAATGCTA
Found at i:19009540 original size:25 final size:25
Alignment explanation
Indices: 19009509--19009591 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
19009499 ATGTGCTAAA
**
19009509 CAGAGAGCACTGACATGCTAA-ATAT
1 CAGAGAGCACCAACATGCTAATA-AT
*
19009534 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
**
19009559 CAGAGAGCACCAATGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
19009584 CAGAGAGC
1 CAGAGAGC
19009592 GCGCTAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 52 0.98
26 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACCAACATGCTAATAAT
Found at i:19009885 original size:41 final size:40
Alignment explanation
Indices: 19009810--19009895 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
19009800 TAAAAAATTT
*
19009810 TAAAACAAATATTAAAACAAAAAACAAATAAAAAATAATAC
1 TAAAACAAATATTAAAACAAAAAACAAATAAAAAAT-ATAA
* * * * * *
19009851 TAAAACAATTCTTAAAACAATACATAAATTAAAAATATAA
1 TAAAACAAATATTAAAACAAAAAACAAATAAAAAATATAA
19009891 TAAAA
1 TAAAA
19009896 AGTAATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (40 bp):
TAAAACAAATATTAAAACAAAAAACAAATAAAAAATATAA
Found at i:19009992 original size:25 final size:27
Alignment explanation
Indices: 19009944--19009994 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
19009934 TAATAGTCAA
*
19009944 ATTAATAATAAAACAAAAGTATATTTG
1 ATTAAAAATAAAACAAAAGTATATTTG
19009971 ATTAAAAATAAAA-AAAA-TATATTT
1 ATTAAAAATAAAACAAAAGTATATTT
19009995 AATATATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
ATTAAAAATAAAACAAAAGTATATTTG
Found at i:19010485 original size:14 final size:14
Alignment explanation
Indices: 19010466--19010495 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19010456 ATAATATAGC
*
19010466 ATTTAAATAAAATA
1 ATTTAAAAAAAATA
19010480 ATTTAAAAAAAATA
1 ATTTAAAAAAAATA
19010494 AT
1 AT
19010496 CTTGTAGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTTAAAAAAAATA
Found at i:19010858 original size:23 final size:23
Alignment explanation
Indices: 19010831--19010876 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19010821 ACTCTCAAAT
19010831 TTTCACTAATAAACCCTAATTTC
1 TTTCACTAATAAACCCTAATTTC
*
19010854 TTTCACTAATAAACCTTAATTTC
1 TTTCACTAATAAACCCTAATTTC
19010877 GAATTTCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTCACTAATAAACCCTAATTTC
Found at i:19011223 original size:5 final size:5
Alignment explanation
Indices: 19011199--19011270 Score: 117
Period size: 5 Copynumber: 14.0 Consensus size: 5
19011189 TTCTTTTGTT
*
19011199 TTATA TATATAA TAATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA T-TAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
19011251 TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA
19011271 AAATTATCTT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 56 0.89
6 5 0.08
7 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:19013806 original size:21 final size:22
Alignment explanation
Indices: 19013782--19013823 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19013772 TTATTAAATA
*
19013782 AAAATAAAAAAAT-ATTTTTCG
1 AAAACAAAAAAATAATTTTTCG
*
19013803 AAAACAAAATAATAATTTTTC
1 AAAACAAAAAAATAATTTTTC
19013824 AAAGTGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAACAAAAAAATAATTTTTCG
Found at i:19014770 original size:19 final size:19
Alignment explanation
Indices: 19014733--19014819 Score: 99
Period size: 19 Copynumber: 4.5 Consensus size: 19
19014723 NNNNNNTTAA
*
19014733 TTTT-TAATTTATTTCTA-
1 TTTTATAATTTATTTATAT
19014750 TTTTATAATTTAATTTATATT
1 TTTTATAATTT-ATTTATA-T
*
19014771 TTTTATATATTT-TTTAGAT
1 TTTTATA-ATTTATTTATAT
19014790 TTTTATACATTTATTTATAT
1 TTTTATA-ATTTATTTATAT
19014810 TTTTATAATT
1 TTTTATAATT
19014820 CTTTAAAGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.07
18 6 0.10
19 21 0.35
20 18 0.30
21 7 0.12
22 4 0.07
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTATTTATAT
Found at i:19015654 original size:14 final size:13
Alignment explanation
Indices: 19015623--19015661 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
19015613 TTCAACTAGT
19015623 ATAATA-ATAATC
1 ATAATATATAATC
19015635 ATTAATATATAATAC
1 A-TAATATATAAT-C
19015650 ATAATATATAAT
1 ATAATATATAAT
19015662 GTACTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 5 0.21
14 16 0.67
15 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATATAATC
Found at i:19015678 original size:20 final size:20
Alignment explanation
Indices: 19015653--19015693 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19015643 ATAATACATA
19015653 ATATATA-ATGTACTACTATT
1 ATATATATATG-ACTACTATT
*
19015673 ATATATATATGACTATTATT
1 ATATATATATGACTACTATT
19015693 A
1 A
19015694 CAATATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATATATGACTACTATT
Found at i:19023080 original size:21 final size:21
Alignment explanation
Indices: 19023056--19023205 Score: 110
Period size: 21 Copynumber: 7.2 Consensus size: 21
19023046 TTACTTTTCA
* *
19023056 TTTAGCTCTTACGAGCTTCTG
1 TTTAACTCTTATGAGCTTCTG
* * *
19023077 TTTAACTCATATGAGTTTCCG
1 TTTAACTCTTATGAGCTTCTG
* *
19023098 TTCAACTC-TATTGAGCTTCTA
1 TTTAACTCTTA-TGAGCTTCTG
* *
19023119 TTTAACTCTTATG-GGTTTTCG
1 TTTAACTCTTATGAGCTTCT-G
* *
19023140 TTTAGCTCTTATGAGCTTCCG
1 TTTAACTCTTATGAGCTTCTG
* *
19023161 TTCAAAC-CTTATGGGCTTCTG
1 TT-TAACTCTTATGAGCTTCTG
* *
19023182 TTTAGCTC-AATGAGCTTCTG
1 TTTAACTCTTATGAGCTTCTG
19023202 TTTA
1 TTTA
19023206 GCCTTCGAGC
Statistics
Matches: 98, Mismatches: 25, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
20 22 0.22
21 69 0.70
22 7 0.07
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (21 bp):
TTTAACTCTTATGAGCTTCTG
Found at i:19023155 original size:42 final size:41
Alignment explanation
Indices: 19023050--19023205 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 41
19023040 TTGTGTTTAC
* * * *
19023050 TTTTCATTTAGCTCTTACGAGCTTCTGTTTAACTCATATGAG
1 TTTTCGTTTAGCTC-TATGAGCTTCTGTTTAACTCTTATGGG
* * * *
19023092 TTTCCGTTCAACTCTATTGAGCTTCTATTTAACTCTTATGGG
1 TTTTCGTTTAGCTCTA-TGAGCTTCTGTTTAACTCTTATGGG
* *
19023134 TTTTCGTTTAGCTCTTATGAGCTTCCGTTCAAAC-CTTATGGG
1 TTTTCGTTTAGCTC-TATGAGCTTCTGTT-TAACTCTTATGGG
* *
19023176 -CTTCTGTTTAGCTCAATGAGCTTCTGTTTA
1 TTTTC-GTTTAGCTCTATGAGCTTCTGTTTA
19023206 GCCTTCGAGC
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 17 0.18
42 69 0.75
43 5 0.05
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45
Consensus pattern (41 bp):
TTTTCGTTTAGCTCTATGAGCTTCTGTTTAACTCTTATGGG
Found at i:19026838 original size:51 final size:49
Alignment explanation
Indices: 19026706--19026901 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 49
19026696 GTGAAAGTGA
* *
19026706 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-G-T
* * * * *
19026756 AGGTCGCATGTGTAATACTATGTGCAAGCTACTATGTGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* * * * *
19026806 TCGATCACATGTGTAGTACTATATGTAGGCTACGACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
* * *
19026856 GATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCGG
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
19026902 TATCATTAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.35
51 76 0.64
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
Found at i:19026988 original size:46 final size:43
Alignment explanation
Indices: 19026897--19026995 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
19026887 TACTATGTGA
* *
19026897 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
* *
19026940 ACCGGATATCATTGATTAGAAAGGGTGGTTGCTGTGTGCTAAAT-CC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCT-AATCCC
19026986 ACCGTGTATC
1 ACCG-GTATC
19026996 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
Found at i:19030753 original size:19 final size:18
Alignment explanation
Indices: 19030714--19030755 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19030704 ACACTTGCCG
* *
19030714 ATCA-CAACAATCTCCAC
1 ATCATCAACAATCTCAAA
19030731 ATCATCAACAATTCTCAAA
1 ATCATCAACAA-TCTCAAA
19030750 ATCATC
1 ATCATC
19030756 CTCTTAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (18 bp):
ATCATCAACAATCTCAAA
Found at i:19032367 original size:37 final size:37
Alignment explanation
Indices: 19032317--19032387 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
19032307 GTTTACAGAT
19032317 CAAATATAATTAAATCGTATCATTTACTATTCATATC
1 CAAATATAATTAAATCGTATCATTTACTATTCATATC
*
19032354 CAAATATAATTAAATTGTATCATTTACTATTCAT
1 CAAATATAATTAAATCGTATCATTTACTATTCAT
19032388 GCATATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (37 bp):
CAAATATAATTAAATCGTATCATTTACTATTCATATC
Found at i:19033666 original size:27 final size:25
Alignment explanation
Indices: 19033636--19033691 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
19033626 CATAATTGGA
19033636 AAGCACACTCTCGAGCCATATAACAAG
1 AAGCACA-TCT-GAGCCATATAACAAG
* * * *
19033663 AAGCTCATGTGAGCCATGTAACAGG
1 AAGCACATCTGAGCCATATAACAAG
19033688 AAGC
1 AAGC
19033692 TTATCCAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 17 0.68
26 2 0.08
27 6 0.24
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (25 bp):
AAGCACATCTGAGCCATATAACAAG
Found at i:19033766 original size:25 final size:25
Alignment explanation
Indices: 19033704--19033768 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
19033694 ATCCAGGTCA
*
19033704 TATAACGGGAAGCT-CATGCGAGCC
1 TATAACGGGAAGCTCCATGAGAGCC
*
19033728 TATAACGGGTAGCTCCAT-AGAGCC
1 TATAACGGGAAGCTCCATGAGAGCC
19033752 -ATCAATCGGGAAGCTCC
1 TAT-AA-CGGGAAGCTCC
19033769 GGATAGCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 20 0.57
25 13 0.37
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (25 bp):
TATAACGGGAAGCTCCATGAGAGCC
Found at i:19037484 original size:45 final size:45
Alignment explanation
Indices: 19037420--19037510 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
19037410 TTCTGAACTT
19037420 GAGCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAA
1 GAGCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAA
19037465 GAGCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAA
1 GAGCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAA
19037510 G
1 G
19037511 TCCCCAATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.26
Consensus pattern (45 bp):
GAGCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAA
Found at i:19043305 original size:20 final size:20
Alignment explanation
Indices: 19043268--19043305 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19043258 ATAGTGACTG
*
19043268 ATTAAATTAGTCACTTTACT
1 ATTAAATTAGTCAATTTACT
19043288 ATTAAA-TAGATCAATTTA
1 ATTAAATTAG-TCAATTTA
19043306 GTTTTTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTAAATTAGTCAATTTACT
Found at i:19044661 original size:21 final size:20
Alignment explanation
Indices: 19044628--19044667 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19044618 CCTTTTTAAT
19044628 ATAAAACCAAATAGAAACCA
1 ATAAAACCAAATAGAAACCA
* *
19044648 ATAAATCCTAAATATAAACC
1 ATAAAACC-AAATAGAAACC
19044668 CACAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (20 bp):
ATAAAACCAAATAGAAACCA
Found at i:19051632 original size:221 final size:219
Alignment explanation
Indices: 19051224--19051667 Score: 601
Period size: 218 Copynumber: 2.0 Consensus size: 219
19051214 AGTGTAAATC
* * **
19051224 CCTTAGGACTCTCATCTTGCAGATAGGCACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
1 CCTTAGGAATCTCATATTGCAGATAAACACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
* * * * *
19051289 TTGGATTTGGGGGAGCTCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTTAGTTATTCC
66 TTGGATCTGGGAGAGATCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAGTTAATCC
* * *
19051354 TTCTAAGTAATAGAATATTTTTTAGAACATTTACTCAAACACTTGGTGTGTTATTATTCTCTTTT
131 TTCTAAGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATTCTCTTTT
19051419 GGC-TTTTCTGTTCAATACAAGTT
196 GGCTTTTTCTGTTCAATACAAGTT
* * * *
19051442 CCTTAGGAATCTCATATTGTAGATAAACACTAATC-CTAGTCATTGATGTAATTCAATTTGTACC
1 CCTTAGGAATCTCATATTGCAGATAAACACTAATCTC-AGCCACTGATGTAATTCAATCTGTACC
19051506 GTTGGATCT-GGAGAGATCAACTATAAATAGA-GTCATTCCCCCTCATTTGTAATCACTCAGTTG
65 GTTGGATCTGGGAGAGATCAAC--TAAATAGAGGTC-TTCCCCCTCATTTGTAATCACTCAG-T-
**
19051569 TAATCCTTC-ATAGTAATAGAACATCTTTTAGAGTATTTACTCAAACACTTGGTGTGATATTATT
125 TAATCCTTCTA-AGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATT
* * *
19051633 TTCTTTTGGCTTTTTTTGTTCAATATAAGTT
189 CTCTTTTGGCTTTTTCTGTTCAATACAAGTT
19051664 CCTT
1 CCTT
19051668 TGTATTTTCG
Statistics
Matches: 197, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
217 11 0.06
218 65 0.33
219 32 0.16
220 2 0.01
221 65 0.33
222 22 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (219 bp):
CCTTAGGAATCTCATATTGCAGATAAACACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
TTGGATCTGGGAGAGATCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAGTTAATCC
TTCTAAGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATTCTCTTTT
GGCTTTTTCTGTTCAATACAAGTT
Found at i:19059947 original size:32 final size:32
Alignment explanation
Indices: 19059893--19059953 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
19059883 AAATTAACAC
19059893 ATAATTATTCATTTAATATTATAACTATTGAA
1 ATAATTATTCATTTAATATTATAACTATTGAA
*
19059925 ATAA-TATT-ATTTAAATAGTTATAATTATT
1 ATAATTATTCATTT-AATA-TTATAACTATT
19059954 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATTATTCATTTAATATTATAACTATTGAA
Found at i:19082386 original size:27 final size:27
Alignment explanation
Indices: 19082346--19082411 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
19082336 CAGCAGAGCT
19082346 ACCAGT-ACAGTATATGTGGCAAAGCC
1 ACCAGTAACAGTATATGTGGCAAAGCC
* *
19082372 ACGAGTAACAGTATATGTGGCAGAGCC
1 ACCAGTAACAGTATATGTGGCAAAGCC
*
19082399 ACCCGTAACAGTA
1 ACCAGTAACAGTA
19082412 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 5 0.14
27 30 0.86
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
ACCAGTAACAGTATATGTGGCAAAGCC
Found at i:19082664 original size:27 final size:27
Alignment explanation
Indices: 19082613--19082664 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19082603 ATGGTCATTT
* * **
19082613 TACCCTATAAGGGTATTTCGGTAATCC
1 TACCCTACAAAGGTATTTCAATAATCC
19082640 TACCCTACAAAGGTATTTCAATAAT
1 TACCCTACAAAGGTATTTCAATAAT
19082665 TTCACAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (27 bp):
TACCCTACAAAGGTATTTCAATAATCC
Found at i:19082681 original size:27 final size:27
Alignment explanation
Indices: 19082651--19082780 Score: 102
Period size: 27 Copynumber: 4.8 Consensus size: 27
19082641 ACCCTACAAA
*
19082651 GGTATTTCAATAATTTCACAAACCAAG
1 GGTATTTCGATAATTTCACAAACCAAG
**
19082678 GGTATTTCGATAATTTCACAAATTAAG
1 GGTATTTCGATAATTTCACAAACCAAG
* * * * ** *
19082705 GGTGTTTTGGTAATTTTACAAATTAGG
1 GGTATTTCGATAATTTCACAAACCAAG
* * *
19082732 GGTATTTC-AGTAATTTTACACACC-GG
1 GGTATTTCGA-TAATTTCACAAACCAAG
*
19082758 AGGTATTTTGATAATTTCACAAA
1 -GGTATTTCGATAATTTCACAAA
19082781 TCGGGGGTCT
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.96
28 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (27 bp):
GGTATTTCGATAATTTCACAAACCAAG
Found at i:19091051 original size:14 final size:14
Alignment explanation
Indices: 19091032--19091067 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
19091022 ATTACGTTAG
19091032 AAATTAAAGTATAT
1 AAATTAAAGTATAT
19091046 AAATTAAAGTATAT
1 AAATTAAAGTATAT
19091060 AAATTAAA
1 AAATTAAA
19091068 TCAGAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
AAATTAAAGTATAT
Found at i:19092864 original size:18 final size:17
Alignment explanation
Indices: 19092832--19092930 Score: 67
Period size: 17 Copynumber: 5.7 Consensus size: 17
19092822 AGGCCAGATC
19092832 GGGCATGTGGGCCACAA
1 GGGCATGTGGGCCACAA
*
19092849 GGGCGTGTGGGCCCACACA
1 GGGCATGTGGG-CCACA-A
* * * *
19092868 -AGCATATGGGCCAGAC
1 GGGCATGTGGGCCACAA
* *
19092884 GGGCATGTGAGCCAGACA
1 GGGCATGTGGGCCACA-A
* *
19092902 -GGCGTGTGGGCCCACAC
1 GGGCATGTGGG-CCACAA
19092919 GGGCATGTGGGC
1 GGGCATGTGGGC
19092931 TCATAATTCT
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
17 35 0.57
18 25 0.41
19 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.41, T:0.12
Consensus pattern (17 bp):
GGGCATGTGGGCCACAA
Found at i:19092930 original size:52 final size:53
Alignment explanation
Indices: 19092803--19092918 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 53
19092793 TGAGTGTGGT
* *
19092803 CGTGTGGG-CCACACGAGC-TA--GGCCAGATCGGGCATGTGGGCCACAAGGG
1 CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACAAGGG
*
19092852 CGTGTGGGCCCACACAAGCATATGGGCCAGA-CGGGCATGTGAGCCAGACA-GG
1 CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACA-AGGG
19092904 CGTGTGGGCCCACAC
1 CGTGTGGGCCCACAC
19092919 GGGCATGTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 8 0.14
50 9 0.15
51 2 0.03
52 32 0.54
53 8 0.14
ACGTcount: A:0.22, C:0.28, G:0.38, T:0.12
Consensus pattern (53 bp):
CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACAAGGG
Found at i:19098913 original size:16 final size:16
Alignment explanation
Indices: 19098892--19098922 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19098882 TAGTAGGTAA
*
19098892 TCTAAAAGGTCTATTG
1 TCTAAAAGGACTATTG
19098908 TCTAAAAGGACTATT
1 TCTAAAAGGACTATT
19098923 ATGTCGTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (16 bp):
TCTAAAAGGACTATTG
Found at i:19099276 original size:296 final size:296
Alignment explanation
Indices: 19098742--19099332 Score: 1094
Period size: 296 Copynumber: 2.0 Consensus size: 296
19098732 ATTCACATTA
19098742 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
1 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
19098807 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
66 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
*
19098872 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATTGTCTAAAAGGACTATTATGTCGTCTATCAA
131 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
*
19098937 GTCCAAATAGGGGGATACCTTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
196 GTCCAAATAGGGGGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
19099002 AATATTATTTTCTAGACTAACAATACATTAGACATG
261 AATATTATTTTCTAGACTAACAATACATTAGACATG
* *
19099038 ATATCATTTGTATTTGTCCTTGATGGTTTTTGCACTCAAAACAAAATTTAAGCAAATATTTGCTC
1 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
* * *
19099103 ATTGATTACCTAAATTTTAACTAATATTAAGTTGTATTACGTTGTCTGATCGGAATGTAAGAAGA
66 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
19099168 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
131 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
19099233 GTCCAAAT-GGGGAGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACAT
196 GTCCAAATAGGGG-GATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACAT
*
19099297 AAATGTTATTTTCTAGACTAACAATACATTAGACAT
260 AAATATTATTTTCTAGACTAACAATACATTAGACAT
19099333 AACCCAAGTT
Statistics
Matches: 286, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
295 4 0.01
296 282 0.99
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (296 bp):
ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
GTCCAAATAGGGGGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
AATATTATTTTCTAGACTAACAATACATTAGACATG
Found at i:19100027 original size:13 final size:13
Alignment explanation
Indices: 19099995--19100027 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19099985 CTGGGCATTT
*
19099995 CCACACAGGATGG
1 CCACACGGGATGG
19100008 CCACACGGGATGG
1 CCACACGGGATGG
19100021 CCACACG
1 CCACACG
19100028 CCCATGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.36, G:0.30, T:0.06
Consensus pattern (13 bp):
CCACACGGGATGG
Found at i:19105109 original size:20 final size:20
Alignment explanation
Indices: 19105067--19105109 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19105057 ATTTTCTTTG
* * *
19105067 TTTTTATTTTATTTATTTAT
1 TTTTTAATTTAGTTACTTAT
*
19105087 TTTTTAATTTAGTTACTTCT
1 TTTTTAATTTAGTTACTTAT
19105107 TTT
1 TTT
19105110 CTTGGTGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTAATTTAGTTACTTAT
Found at i:19106852 original size:19 final size:19
Alignment explanation
Indices: 19106825--19106884 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
19106815 ATGAGGACCA
*
19106825 TTAAGTTTATTTCTTTATT
1 TTAATTTTATTTCTTTATT
*
19106844 TTAATTTTAATT-TTTATGT
1 TTAATTTTATTTCTTTAT-T
19106863 TT-ATTGTTATTTTCTTATATT
1 TTAATT-TTA-TTTCTT-TATT
19106884 T
1 T
19106885 ATTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 16 0.48
20 2 0.06
21 4 0.12
22 3 0.09
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (19 bp):
TTAATTTTATTTCTTTATT
Found at i:19109616 original size:14 final size:14
Alignment explanation
Indices: 19109593--19109623 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19109583 TATTGCGTTC
*
19109593 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
19109607 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
19109621 TTA
1 TTA
19109624 AAAATAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:19110580 original size:29 final size:29
Alignment explanation
Indices: 19110539--19110600 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
19110529 TTTAACAAAA
*
19110539 TTGT-CAATATGGTACATGTACTTTAATT
1 TTGTCCAATATGGTACATGAACTTTAATT
* * *
19110567 TTGTCCAATGTGGTACCTGAACTTTTATT
1 TTGTCCAATATGGTACATGAACTTTAATT
19110596 TTGTC
1 TTGTC
19110601 TACCGATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (29 bp):
TTGTCCAATATGGTACATGAACTTTAATT
Found at i:19128820 original size:195 final size:196
Alignment explanation
Indices: 19128478--19128866 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 196
19128468 TGGATTTTCT
19128478 TCCAAATCATTCATTCATTTAATTCATAATCATATTGTACAAATAGTTCTTCATAAATTTTTACA
1 TCCAAATCATTCATTCATTTAATTCATAATCATATTGTACAAATAGTTCTTCATAAATTTTTACA
19128543 TTCTTTTGTACATTCTTTGGTATTTATTATGGGCCCCCAGATATCAATGACATGAATGGCACTGC
66 TTCTTTTGTACATTCTTTGGTATTTATTATGGGCCCCCAGATATCAATGACATGAATGGCACTGC
19128608 TACAGATTTAGAATATCCTTTTGAGCAAGACATGTGTTTAGAAGGATCTCATGACTTTAAAGATG
131 TACAGATTTAGAATATCCTTTTGAGCAAGACATGTGTTTAGAAGGATCTCATGACTTTAAAGATG
19128673 A
196 A
19128674 TCCAAATCA-TCATTCATTTAATTCATAATCATATTGTACAAATAGTTCTTCATAAATTTTTACA
1 TCCAAATCATTCATTCATTTAATTCATAATCATATTGTACAAATAGTTCTTCATAAATTTTTACA
19128738 TTCTTTTGTACATTCTTTGGTATTTATTATGGGCCCCCAGATATCAATGACATGAATGGCACTGC
66 TTCTTTTGTACATTCTTTGGTATTTATTATGGGCCCCCAGATATCAATGACATGAATGGCACTGC
19128803 TACAGATTTAGAATATCCTTTTGAGCAAGACATGTGTTTAGAAGGATCTCATGACTTTAAAGAT
131 TACAGATTTAGAATATCCTTTTGAGCAAGACATGTGTTTAGAAGGATCTCATGACTTTAAAGAT
19128867 TACATAGATT
Statistics
Matches: 193, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
195 184 0.95
196 9 0.05
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (196 bp):
TCCAAATCATTCATTCATTTAATTCATAATCATATTGTACAAATAGTTCTTCATAAATTTTTACA
TTCTTTTGTACATTCTTTGGTATTTATTATGGGCCCCCAGATATCAATGACATGAATGGCACTGC
TACAGATTTAGAATATCCTTTTGAGCAAGACATGTGTTTAGAAGGATCTCATGACTTTAAAGATG
A
Found at i:19129454 original size:1 final size:1
Alignment explanation
Indices: 19129448--19129540 Score: 60
Period size: 1 Copynumber: 93.0 Consensus size: 1
19129438 GATTTAATGC
* * * * * * * * * * *
19129448 AAAAAAACAAAATAAAAAACAAAAAACAAAAACAAAAAAAAAGAGAAAAGAAAGAGAAAAAAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
19129513 AAAAACAAAAACAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
19129541 CCTCTACCGG
Statistics
Matches: 64, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:19129466 original size:13 final size:12
Alignment explanation
Indices: 19129448--19129541 Score: 84
Period size: 12 Copynumber: 7.7 Consensus size: 12
19129438 GATTTAATGC
19129448 AAAAAAACAAAA
1 AAAAAAACAAAA
*
19129460 TAAAAAACAAAA
1 AAAAAAACAAAA
19129472 AACAAAAACAAAA
1 AA-AAAAACAAAA
* *
19129485 AAAAAGAGAAAA
1 AAAAAAACAAAA
19129497 GAAAGAGAAA-AAAA
1 -AAA-A-AAACAAAA
*
19129511 CAAAAAACAAAA
1 AAAAAAACAAAA
* *
19129523 ACAAAAA-AATA
1 AAAAAAACAAAA
19129534 AAAAAAAC
1 AAAAAAAC
19129542 CTCTACCGGG
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
11 12 0.18
12 30 0.45
13 17 0.26
14 5 0.08
15 2 0.03
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:19130055 original size:15 final size:16
Alignment explanation
Indices: 19130037--19130075 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
19130027 AAAAAGATGT
19130037 GAAAAAAT-AAAAATG
1 GAAAAAATGAAAAATG
19130052 G-AAAAATGAAAAATG
1 GAAAAAATGAAAAATG
19130067 GAAAAAATG
1 GAAAAAATG
19130076 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (16 bp):
GAAAAAATGAAAAATG
Found at i:19130072 original size:9 final size:8
Alignment explanation
Indices: 19130045--19130077 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
19130035 GTGAAAAAAT
19130045 AAAAATGG
1 AAAAATGG
19130053 AAAAAT-G
1 AAAAATGG
19130060 AAAAATGG
1 AAAAATGG
19130068 AAAAAATGG
1 -AAAAATGG
19130077 A
1 A
19130078 GAGGCTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
8 8 0.35
9 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (8 bp):
AAAAATGG
Found at i:19131574 original size:99 final size:99
Alignment explanation
Indices: 19131391--19132367 Score: 1564
Period size: 99 Copynumber: 9.9 Consensus size: 99
19131381 TTAACGTTGT
* * *
19131391 AGCGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTGAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
* * *
19131456 GCCACAATGGCAGATCTTACTTCCCTGGCGATGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
* * ** * * *
19131490 AGTGGAA-CAGATTGAAGTCACAACGGTAGATCTGGTTTCCCCGACAGCGTAATTAAAAGATTGA
1 AG-CGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAA
* * *
19131554 AGCCACAACGGCGGAGCTTACTTCCCAGGCGGTGC
65 AGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19131589 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
19131654 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19131688 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
19131753 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19131787 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
19131852 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19131886 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
19131951 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19131985 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
19132050 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
19132084 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
* *
19132149 GCCACAACGGCGGATCTTACTTCCCTGGCGATGC
66 GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
* * * ** ** *
19132183 AGTGGAGTAGATTGAAGTCACAATGGTAGATCTGGTTTC-CCTGACAGCGCAATTAAAAGATTGA
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAAAGATTAA
** *
19132247 AGCCACAACAGCGGATCTTACTTCCCTGGCAGTGC
65 AGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
* * * * * *
19132282 AGCGGAGTAGATTGAAGTCACAACGGCAGATCTGGTTTC-CTCGACAACGCAATTAAAAAGATTG
1 AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTC-CGACAGCGCAATT-AAAAGATTA
* *
19132346 AAGCCACAACGGCAGATCTTAC
64 AAGCCACAAGGGCGGATCTTAC
19132368 CTCCTTAGCA
Statistics
Matches: 833, Mismatches: 40, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
98 5 0.01
99 796 0.96
100 32 0.04
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (99 bp):
AGCGAAGCAGATTGAAGTCACAGCGGCGGATCTGGTTTCTCCGACAGCGCAATTAAAAGATTAAA
GCCACAAGGGCGGATCTTACTTCCCTGGCGGTGC
Found at i:19132344 original size:50 final size:49
Alignment explanation
Indices: 19131399--19132364 Score: 431
Period size: 50 Copynumber: 19.5 Consensus size: 49
19131389 GTAGCGGAGC
* *
19131399 AGATTGAAGTCACAACGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* *** * * * * *
19131448 AGATTGAAGCCACAATGGCAGATCTTACTTCCCTGGC-GATGCAGTGGAAC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAG-CGCAAT-TAAA
* * * *
19131498 AGATTGAAGTCACAACGGTAGATCTGGTTTCCCCGACAGCGTAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAAA
* * *** * * * * *** *
19131547 AGATTGAAGCCACAACGGCGGAGCTTACTTCCCAGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19131597 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * * *** * * * *** *
19131646 AGATTAAAGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19131696 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * * *** * * * *** *
19131745 AGATTAAAGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19131795 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * * *** * * * *** *
19131844 AGATTAAAGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19131894 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * * *** * * * *** *
19131943 AGATTAAAGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19131993 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * * *** * * * *** *
19132042 AGATTAAAGCCACAAGGGCGGATCTTACTTCCCTGGCGGTGCAGCGAAGC
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAA-A
* * *
19132092 AGATTGAAGTCACAGCGGCGGATCTGGTTTCTCC-GACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTC-CCTGACAGCGCAATTAAA
* * *** * * * * **
19132141 AGATTAAAGCCACAACGGCGGATCTTACTTCCCTGGC-GATGCAGTGGAGT
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAG-CGCAAT-TAAA
* * *
19132191 AGATTGAAGTCACAATGGTAGATCTGGTTTCCCTGACAGCGCAATTAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAAA
* * *** * * *** **
19132240 AGATTGAAGCCACAACAGCGGATCTTACTTCCCTGGCAGTGCAGCGGAGT
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCA-ATTAAA
* *
19132290 AGATTGAAGTCACAACGGCAGATCTGGTTT-CCTCGACAACGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTGGTTTCCCT-GACAGCGCAATT-AAA
19132340 AGATTGAAGCCACAACGGCAGATCT
1 AGATTGAAGCCACAACGGCAGATCT
19132365 TACCTCCTTA
Statistics
Matches: 640, Mismatches: 249, Indels: 55
0.68 0.26 0.06
Matches are distributed among these distances:
48 16 0.03
49 294 0.46
50 316 0.49
51 14 0.02
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.21
Consensus pattern (49 bp):
AGATTGAAGCCACAACGGCAGATCTGGTTTCCCTGACAGCGCAATTAAA
Found at i:19132394 original size:50 final size:49
Alignment explanation
Indices: 19132141--19132415 Score: 160
Period size: 50 Copynumber: 5.5 Consensus size: 49
19132131 CGCAATTAAA
* * * * *
19132141 AGATTAAAGCCACAACGGCGGATCTTACTTCCCTGGC-GATGCAGTGGAGT
1 AGATTGAAGCCACAACGGCAGATCTTACTT-CCTAGCAG-TGCAGTTGAAT
* * * *** * * *
19132191 AGATTGAAGTCACAATGGTAGATCTGGTTTCCCT-GACAGCGCAATT-AAA
1 AGATTGAAGCCACAACGGCAGATCTTACTT-CCTAG-CAGTGCAGTTGAAT
* * * ** *
19132240 AGATTGAAGCCACAACAGCGGATCTTACTTCCCTGGCAGTGCAGCGGAGT
1 AGATTGAAGCCACAACGGCAGATCTTACTT-CCTAGCAGTGCAGTTGAAT
* *** * ** * * *
19132290 AGATTGAAGTCACAACGGCAGATCTGGTTTCCTCGACAACGCAATTAAAA
1 AGATTGAAGCCACAACGGCAGATCTTACTTCCTAG-CAGTGCAGTTGAAT
*
19132340 AGATTGAAGCCACAACGGCAGATCTTACCTCCTTAGCAGTGCAGTTGAAT
1 AGATTGAAGCCACAACGGCAGATCTTACTTCC-TAGCAGTGCAGTTGAAT
** *
19132390 AGATTGAAGTTACGACGGCAGATCTT
1 AGATTGAAGCCACAACGGCAGATCTT
19132416 GTTTCCTCGA
Statistics
Matches: 163, Mismatches: 56, Indels: 12
0.71 0.24 0.05
Matches are distributed among these distances:
49 38 0.23
50 122 0.75
51 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23
Consensus pattern (49 bp):
AGATTGAAGCCACAACGGCAGATCTTACTTCCTAGCAGTGCAGTTGAAT
Found at i:19133749 original size:18 final size:19
Alignment explanation
Indices: 19133728--19133770 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
19133718 ATATACGTAC
19133728 ATATATTTATA-TTTTATA
1 ATATATTTATAGTTTTATA
*
19133746 ATATTTTTATAGTTTT-T-
1 ATATATTTATAGTTTTATA
19133763 ATATATTT
1 ATATATTT
19133771 TATAATCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATATATTTATAGTTTTATA
Found at i:19136156 original size:3 final size:3
Alignment explanation
Indices: 19136150--19136178 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19136140 TTCCTCTTCT
19136150 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
19136179 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:19139310 original size:133 final size:134
Alignment explanation
Indices: 19139071--19139332 Score: 314
Period size: 133 Copynumber: 2.0 Consensus size: 134
19139061 GTGTTTACTT
* ** ** *
19139071 CTTGTCTTACTACACCTATCAAAATGGCATTGAGATGGTAAAACTTTTAGCCATATATTTAGGAT
1 CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
* * * * ** * *
19139136 GACTTGTATTTTTCATTTGGGAAATGTTCTCCTTTTTGGTATCCATGCTGTATATAAATCATGAC
66 CACTTGTATTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATGAC
19139201 ATGA
131 ATGA
* * * *
19139205 CTTGTCTTACTA-ACCTATCAAGATGACATCAAGGTGGTAAAACTTCAAGCCTTGTAATTAGGAT
1 CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
*
19139269 CA-TGTGTAGTTTTT-ATTTGGGAAATATTGGCCTTCTTGGTATCCACACTCTAGATAAATCATG
66 CACT-TGTA-TTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATG
19139332 A
129 A
19139333 GAATGCATCT
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
132 1 0.01
133 89 0.83
134 17 0.16
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (134 bp):
CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
CACTTGTATTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATGAC
ATGA
Found at i:19144689 original size:11 final size:12
Alignment explanation
Indices: 19144672--19144700 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
19144662 ATGGTGGTGG
19144672 GTTTTTTTTTCT
1 GTTTTTTTTTCT
19144684 -TTTTTTTTTCT
1 GTTTTTTTTTCT
19144695 GTTTTT
1 GTTTTT
19144701 GTAAAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
GTTTTTTTTTCT
Found at i:19150296 original size:85 final size:85
Alignment explanation
Indices: 19150151--19150321 Score: 218
Period size: 85 Copynumber: 2.0 Consensus size: 85
19150141 AACGCTCCAC
* * * * * *
19150151 ATACTTGTGTTGTTGCAAGTATGTTACAGGATCATCTGGAATTGGATTTTGACCTAATCTCTAAC
1 ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCTGAAATTGGATTCTAACATAATCTCTAAC
* * *
19150216 ATTGTCTTACTTATTTTGAA
66 ATTATCTTACCTATGTTGAA
* * *
19150236 ATACTTGTGTTGTTGCAGGTATGTCACAAGATCA-CTCGAAATTGGATTCTAAGATGATCTCTAA
1 ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCT-GAAATTGGATTCTAACATAATCTCTAA
19150300 CATTATCTTACCTATGTTGAA
65 CATTATCTTACCTATGTTGAA
19150321 A
1 A
19150322 GCGAGTCCTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.03
85 71 0.97
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (85 bp):
ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCTGAAATTGGATTCTAACATAATCTCTAAC
ATTATCTTACCTATGTTGAA
Found at i:19151465 original size:5 final size:5
Alignment explanation
Indices: 19151457--19151507 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
19151447 CCTAATCTAA
* *
19151457 AAAAG AAAAG AAAAAG AAAAAG AGAAG AGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
19151508 AAGCCCTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 32 0.74
6 11 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19155855 original size:25 final size:26
Alignment explanation
Indices: 19155827--19155875 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19155817 CAACAAAACT
*
19155827 AAAATCTAACCT-AAAAAGAAAAGAG
1 AAAACCTAACCTAAAAAAGAAAAGAG
*
19155852 AAAACCTAATCTAAAAAAGAAAAG
1 AAAACCTAACCTAAAAAAGAAAAG
19155876 TAAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (26 bp):
AAAACCTAACCTAAAAAAGAAAAGAG
Found at i:19155880 original size:25 final size:24
Alignment explanation
Indices: 19155821--19155880 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
19155811 AGGAAACAAC
* *
19155821 AAAACTAAAATCTAACCTAAAAAG
1 AAAAGTAAAACCTAACCTAAAAAG
* *
19155845 AAAAGAGAAAACCTAATCTAAAAAAG
1 AAAAG-TAAAACCTAACCT-AAAAAG
19155871 AAAAGTAAAA
1 AAAAGTAAAA
19155881 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 14 0.48
26 11 0.38
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.13
Consensus pattern (24 bp):
AAAAGTAAAACCTAACCTAAAAAG
Found at i:19158041 original size:79 final size:76
Alignment explanation
Indices: 19157942--19158226 Score: 355
Period size: 75 Copynumber: 3.8 Consensus size: 76
19157932 TTTTCATTGC
* * * * * *
19157942 TTTTA-TTTTTTGGTAAATTGTAAATAAGTATATATTATTGATGTAAAATATAGTAGAATATAAT
1 TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
* *
19158006 ATAAACAATTTTT
66 ACAAATAA--TTT
* *
19158019 TTTTCATTTTTTTCGTATATTGTAAATAAGTATATATTATTGATATAAAATACAATAAAATACAA
1 TTTT-ATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAA
*
19158084 GACAAATAA-TT
65 TACAAATAATTT
** *
19158095 TTTTAAATTTTTCGTAGATTGTAAATAAATATATATTATTGATATAAAATACAATAGAATACAAT
1 TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
19158160 ACAAATAATTT
66 ACAAATAATTT
* *
19158171 TTCTATTGTTTTT-GTAGATTGTAAATAA--ATATATTATTGATGTAAAATACAATAGA
1 TTTTATT-TTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGA
19158227 TAAACTTTTT
Statistics
Matches: 184, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
74 27 0.15
75 63 0.34
76 27 0.15
77 9 0.05
78 1 0.01
79 57 0.31
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (76 bp):
TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
ACAAATAATTT
Found at i:19163065 original size:16 final size:16
Alignment explanation
Indices: 19163044--19163074 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19163034 TGGCAGTTTG
19163044 ATAGTTAATTGAAATT
1 ATAGTTAATTGAAATT
*
19163060 ATAGTTGATTGAAAT
1 ATAGTTAATTGAAAT
19163075 GGATTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
ATAGTTAATTGAAATT
Found at i:19163151 original size:16 final size:16
Alignment explanation
Indices: 19163132--19163165 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19163122 AAATGAATAT
* *
19163132 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
19163148 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
19163164 AT
1 AT
19163166 TGGATATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:19168819 original size:18 final size:17
Alignment explanation
Indices: 19168806--19168842 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
19168796 GAATTATTAT
19168806 TATTAGTATTATTATTTA
1 TATTAGT-TTATTATTTA
19168824 TATTAGTTTATATATTTA
1 TATTAGTTTAT-TATTTA
19168842 T
1 T
19168843 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTAGTTTATTATTTA
Found at i:19169047 original size:12 final size:13
Alignment explanation
Indices: 19169015--19169056 Score: 68
Period size: 14 Copynumber: 3.2 Consensus size: 13
19169005 AACATAGGAT
19169015 TTATATATTATTA
1 TTATATATTATTA
19169028 TGTATATATTATTA
1 T-TATATATTATTA
19169042 TT-TATATTATTA
1 TTATATATTATTA
19169054 TTA
1 TTA
19169057 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.44
13 2 0.07
14 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:19173628 original size:19 final size:19
Alignment explanation
Indices: 19173606--19173648 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
19173596 AATCCAAATC
19173606 AAAAACAAAAAAAAAAGAA
1 AAAAACAAAAAAAAAAGAA
* ***
19173625 AAAATCAAAGTCAAAAGAA
1 AAAAACAAAAAAAAAAGAA
19173644 AAAAA
1 AAAAA
19173649 AAGAGAAATC
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.81, C:0.07, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAAACAAAAAAAAAAGAA
Found at i:19173630 original size:31 final size:31
Alignment explanation
Indices: 19173592--19173694 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
19173582 TCAGATTAAA
19173592 AAAAAATCCAAA-TCAAAA-ACAAAAAAAAAAG
1 AAAAAAT-CAAAGTCAAAAGA-AAAAAAAAAAG
*
19173623 AAAAAATCAAAGTCAAAAGAAAAAAAAAGAG
1 AAAAAATCAAAGTCAAAAGAAAAAAAAAAAG
* * *
19173654 AAATCAATTAAAGTCAAAATAAAAATATGAAAAAG
1 AAA-AAATCAAAGTCAAAAGAAAAA-A--AAAAAG
19173689 AAAAAA
1 AAAAAA
19173695 GGAAAAAGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.07
31 26 0.43
32 19 0.32
33 1 0.02
34 2 0.03
35 8 0.13
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.11
Consensus pattern (31 bp):
AAAAAATCAAAGTCAAAAGAAAAAAAAAAAG
Found at i:19175725 original size:50 final size:50
Alignment explanation
Indices: 19175667--19176225 Score: 343
Period size: 50 Copynumber: 11.2 Consensus size: 50
19175657 GTGGTGGAAC
* *
19175667 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * ** ** **
19175717 AGATTAAAGCTACAATAGCGAATCTTAC-TCCCC-AGGTGATGCAGCGGAGCA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACAT--TGCAG-TTAAAA
19175768 A-ATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * * * *** *
19175817 AGATTAAAGCTACAGCAGCGAATCTTACCTCTCAGGCAGTGCAGCGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * **
19175867 AGATTAAAGCCACAACGTTGAATCTTGCCTCCATGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * * * *** *
19175917 AGATTAAAGCTACAATAGTGAATCTTACTTCCCAGGCGA-TGTAGCGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
*
19175967 AGATTAAAGCCACAACGGTGAAACTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * *** * **
19176017 AGACTAAAGCCACATCGGCGAGTGTTACTTCCCTGGCAACACAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * *
19176067 AGACTAAAGCCACAACGTTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * * ** * **
19176117 ATACTAAAGCCACAGCGGCGAGTGTTACTTCCCTGGCAACGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * *
19176167 AGACTAAAGCCACAACGGTGAATTTTGCTTTCTCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
19176217 GGATTAAAG
1 AGATTAAAG
19176226 TCAAAATGAT
Statistics
Matches: 360, Mismatches: 141, Indels: 16
0.70 0.27 0.03
Matches are distributed among these distances:
48 2 0.01
49 9 0.03
50 338 0.94
51 9 0.03
52 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:19175813 original size:100 final size:100
Alignment explanation
Indices: 19175666--19176326 Score: 646
Period size: 100 Copynumber: 6.6 Consensus size: 100
19175656 TGTGGTGGAA
* *
19175666 CAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAAGCTACA
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* **
19175731 ATAGCGAATCTTACTCCCCAGGTGATGCAGCGGAG
66 ATAGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
*
19175766 CAAATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
** * * * *
19175831 GCAGCGAATCTTACCTCTCAGGCAGTGCAGCGGAA
66 ATAGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
* * **
19175866 CAGATTAAAGCCACAACGTTGAATCTTGCCTCCATGACATTGCAGTTAAAAAGATTAAAGCTACA
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * *
19175931 ATAGTGAATCTTACTTCCCAGGCGATGTAGCGGAA
66 ATAGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
* * *
19175966 CAGATTAAAGCCACAACGGTGAAACTTGCTTCCCCGACATTGCAGTTAAAAAGACTAAAGCCAC-
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * * ** * *
19176030 ATCGGCGAGTGTTACTTCCCTGGCAACACAGTGAAG
66 AT-AGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
* * * * * *
19176066 CAGACTAAAGCCACAACGTTGAATCTTGCTTCCCCGACATTGTAGTTAAAAATACTAAAGCCACA
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
*** * * * * * *
19176131 GCGGCGAGTGTTACTTCCCTGGCAACGCAGTGAAG
66 ATAGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
* * * * *
19176166 CAGACTAAAGCCACAACGGTGAATTTTGCTTTCTCGACATTGCAGTTAAAAGGATTAAAG-T-CA
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
* * * * ***
19176229 AAATGATGAATCTTACTCTCTCA-GCTAGTGCATTAGAG
66 ATA-G-CGAATCTTACT-TCCCAGGC-AATGCAGCGGAG
* * * ** * ** *
19176267 CAGATTGAAGCTACAATGGTGAATCTTAATTCCTCGACATCACAGTTAAACAGATTAAAG
1 CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
19176327 TAACGTGTTA
Statistics
Matches: 469, Mismatches: 86, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
98 2 0.00
99 3 0.01
100 406 0.87
101 58 0.12
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
ATAGCGAATCTTACTTCCCAGGCAATGCAGCGGAG
Found at i:19179061 original size:5 final size:6
Alignment explanation
Indices: 19179010--19179066 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
19179000 ACCAATTTAG
* ** * *
19179010 TTTATC TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT
19179060 TTTATT T
1 TTTATT T
19179067 GAATTCCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 35 0.85
7 2 0.05
8 4 0.10
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:19179100 original size:3 final size:3
Alignment explanation
Indices: 19179092--19179145 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
19179082 TTTTAATCCC
19179092 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19179140 ATT ATT
1 ATT ATT
19179146 TCTTCTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19183614 original size:6 final size:6
Alignment explanation
Indices: 19183605--19183663 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
19183595 AACAAAAAAG
* * *
19183605 AAGAAA AAGAAA AAGAAA AAGAAA AATCAAA ATGAAA AAGAAAA AAGAGAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AAGAAA AAG-AAA AAGA-AA
19183656 AAGAAA AA
1 AAGAAA AA
19183664 AGGAGAGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 29 0.66
7 15 0.34
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:19183622 original size:12 final size:12
Alignment explanation
Indices: 19183605--19183663 Score: 64
Period size: 13 Copynumber: 4.7 Consensus size: 12
19183595 AACAAAAAAG
19183605 AAGAAAAAGAAA
1 AAGAAAAAGAAA
19183617 AAGAAAAAGAAA
1 AAGAAAAAGAAA
* *
19183629 AATCAAAATGAAA
1 AA-GAAAAAGAAA
*
19183642 AAGAAAAAAGAGAG
1 AAG-AAAAAGA-AA
19183656 AAGAAAAA
1 AAGAAAAA
19183664 AGGAGAGGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 14 0.36
13 21 0.54
14 4 0.10
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (12 bp):
AAGAAAAAGAAA
Done.