Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 59 of 199
Found at i:17477431 original size:76 final size:76
Alignment explanation
Indices: 17477351--17477492 Score: 207
Period size: 76 Copynumber: 1.9 Consensus size: 76
17477341 ATAGTTTTTT
17477351 ACTAAAAATAATACTAACTAACAATAATAATTAGGG-TTTTACTAGA-AATAATAACTAACAATA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAGGGTTTTTACTA-ATAATAATAACTAACAATA
17477414 ATATAGTATAAAA
64 ATATAGTATAAAA
* * ** *
17477427 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAATAATAATAACTAACAATAAT
17477492 A
66 A
17477493 ATAATATTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
75 15 0.25
76 44 0.75
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAGGGTTTTTACTAATAATAATAACTAACAATAAT
ATAGTATAAAA
Found at i:17477741 original size:13 final size:13
Alignment explanation
Indices: 17477727--17477767 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
17477717 TCTATTTTTT
*
17477727 TCTTCTCTTTCTT
1 TCTTCTCTTTCTC
17477740 TC-TC-CTTTCTC
1 TCTTCTCTTTCTC
*
17477751 TATTCTCTTTCTC
1 TCTTCTCTTTCTC
17477764 TCTT
1 TCTT
17477768 TTTCTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTCTTTCTC
Found at i:17477777 original size:21 final size:20
Alignment explanation
Indices: 17477736--17477783 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
17477726 TTCTTCTCTT
17477736 TCTTTCTCCTTTCTCTATTC
1 TCTTTCTCCTTTCTCTATTC
* *
17477756 TCTTTCTCTCTTTTTCTTTTC
1 TCTTTCTC-CTTTCTCTATTC
*
17477777 TTTTTCT
1 TCTTTCT
17477784 GGCACTGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTCTCCTTTCTCTATTC
Found at i:17477813 original size:9 final size:9
Alignment explanation
Indices: 17477799--17477874 Score: 55
Period size: 9 Copynumber: 8.0 Consensus size: 9
17477789 TGCCCTCTCT
*
17477799 TTCTCCTCC
1 TTCTCCTTC
17477808 TTCTCCTTC
1 TTCTCCTTC
*
17477817 TTCTTCTTC
1 TTCTCCTTC
17477826 TTCTCTTCTTC
1 TTCTC--CTTC
*
17477837 TTTTTCCTT-
1 -TTCTCCTTC
17477846 TTCTCCTTTCC
1 TTCTCC-TT-C
* *
17477857 TTTTCTTTC
1 TTCTCCTTC
17477866 TTCTCCTTC
1 TTCTCCTTC
17477875 GTGCAGCTGA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
8 5 0.10
9 30 0.58
10 5 0.10
11 8 0.15
12 4 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (9 bp):
TTCTCCTTC
Found at i:17477859 original size:20 final size:20
Alignment explanation
Indices: 17477797--17477873 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
17477787 ACTGCCCTCT
*
17477797 CTTTCTCCTCCTTCTCC-TT-
1 CTTT-TCCTTCTTCTCCTTTC
*
17477816 CTTCTT-CTTCTTCTCTTCTTC
1 CTT-TTCCTTCTTCTCCT-TTC
*
17477837 TTTTTCCTT-TTCTCCTTTC
1 CTTTTCCTTCTTCTCCTTTC
*
17477856 CTTTTCTTTCTTCTCCTT
1 CTTTTCCTTCTTCTCCTT
17477874 CGTGCAGCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
18 8 0.17
19 14 0.30
20 19 0.41
21 5 0.11
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTTCCTTCTTCTCCTTTC
Found at i:17485187 original size:16 final size:16
Alignment explanation
Indices: 17485166--17485198 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17485156 AACAACCATA
17485166 ATTGACATTAATAATT
1 ATTGACATTAATAATT
17485182 ATTGACATTAATAATT
1 ATTGACATTAATAATT
17485198 A
1 A
17485199 ATATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTGACATTAATAATT
Found at i:17485402 original size:17 final size:16
Alignment explanation
Indices: 17485382--17485427 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
17485372 TATATATGTA
17485382 TAATAAATATATAAAAT
1 TAATAAATAT-TAAAAT
*
17485399 TAATAATTATTAAAAT
1 TAATAAATATTAAAAT
17485415 CT-ATAAA-ATTAAA
1 -TAATAAATATTAAA
17485428 TTTTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 6 0.23
16 10 0.38
17 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATAAATATTAAAAT
Found at i:17485414 original size:16 final size:17
Alignment explanation
Indices: 17485382--17485414 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17485372 TATATATGTA
17485382 TAATAAATATATAAAAT
1 TAATAAATATATAAAAT
*
17485399 TAATAATTAT-TAAAAT
1 TAATAAATATATAAAAT
17485415 CTATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAAATATATAAAAT
Found at i:17494845 original size:14 final size:15
Alignment explanation
Indices: 17494826--17494865 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
17494816 GGGACTTTTC
17494826 ATGTAATGAAATG-A
1 ATGTAATGAAATGTA
17494840 ATGTAATGAAATGTA
1 ATGTAATGAAATGTA
17494855 ATGCTAATGAA
1 ATG-TAATGAA
17494866 TAGAAAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 13 0.54
15 4 0.17
16 7 0.29
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (15 bp):
ATGTAATGAAATGTA
Found at i:17495291 original size:20 final size:21
Alignment explanation
Indices: 17495254--17495305 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
17495244 ATTTCAACCA
17495254 ATATAATAATAAACAATA-AT
1 ATATAATAATAAACAATATAT
* **
17495274 ATATGATAATAATTAATATAT
1 ATATAATAATAAACAATATAT
17495295 ATATATATAAT
1 ATATA-ATAAT
17495306 GTTCTACTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 15 0.58
21 6 0.23
22 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATATAATAATAAACAATATAT
Found at i:17495387 original size:2 final size:2
Alignment explanation
Indices: 17495380--17495410 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17495370 TTATTAATAC
*
17495380 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17495411 AACTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17495684 original size:14 final size:16
Alignment explanation
Indices: 17495665--17495696 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
17495655 ATAACATCAA
17495665 TAGTAA-TTAGTA-AT
1 TAGTAATTTAGTATAT
17495679 TAGTAATTTAGTATAT
1 TAGTAATTTAGTATAT
17495695 TA
1 TA
17495697 AAATGTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 6 0.38
16 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
TAGTAATTTAGTATAT
Found at i:17496826 original size:9 final size:9
Alignment explanation
Indices: 17496814--17496865 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
17496804 TTTAAAATTA
17496814 AAAAAATAT
1 AAAAAATAT
*
17496823 AAAAATTATT
1 AAAAAATA-T
*
17496833 AAAAATTAT
1 AAAAAATAT
*
17496842 AAAAAAACAT
1 -AAAAAATAT
*
17496852 AAAAAAAAT
1 AAAAAATAT
17496861 AAAAA
1 AAAAA
17496866 TATTTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 21 0.57
10 16 0.43
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAAAATAT
Found at i:17496827 original size:10 final size:10
Alignment explanation
Indices: 17496807--17496865 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 10
17496797 TTTAAACTTT
17496807 AAAAT-TAAA
1 AAAATATAAA
17496816 AAAATAT-AA
1 AAAATATAAA
* *
17496825 AAATTATTAA
1 AAAATATAAA
*
17496835 AAATTATAAA
1 AAAATATAAA
*
17496845 AAAACATAAA
1 AAAATATAAA
17496855 AAAA-ATAAA
1 AAAATATAAA
17496864 AA
1 AA
17496866 TATTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
9 20 0.45
10 24 0.55
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAATATAAA
Found at i:17499503 original size:141 final size:135
Alignment explanation
Indices: 17499320--17499729 Score: 502
Period size: 141 Copynumber: 3.0 Consensus size: 135
17499310 CGGAGGAAAT
* * *
17499320 GCAGAATGTCCGC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTCAAACCACA
1 GCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCAAACCACA
* * ** *
17499383 GATATCTTTTGCAGCAGAGCAGCATAAGAAATCTGAAATGGCGACAGAAAGTTCTCAAATGCCAC
64 GATATCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCAC
17499448 AACTAAC
129 AACTAAC
17499455 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCAAAC
1 GCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCAAAC
* * * * * * * * *
17499520 CGCAGACATCTTTTGAAACAGAACCGCATGAGAAATCAAAAATGGAAATAGGAAGTTCTGAAATG
60 CACAGATATCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATG
*
17499585 CCACAACTAAT
125 CCACAACTAAC
* * *
17499596 GCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCGAACCACAGA
1 GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAGA
* * *
17499661 TGTCTTTTGCAAAAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCACA
66 TATCTTTTGCAACAGAA-CAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACA
17499725 ACTAA
130 ACTAA
17499730 TGCCAATGGA
Statistics
Matches: 233, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
135 112 0.48
136 3 0.01
141 117 0.50
142 1 0.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (135 bp):
GCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCACAGA
TATCTTTTGCAACAGAACAGCATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCACAA
CTAAC
Found at i:17499711 original size:135 final size:135
Alignment explanation
Indices: 17499317--17499732 Score: 507
Period size: 135 Copynumber: 3.0 Consensus size: 135
17499307 TTTCGGAGGA
* * *
17499317 AATGCAGAATGTCCGC-TTCAAAGTTAAG-AGACCTCAAGAACTACGAACTAAAGAGCTCAAACC
1 AATGCAGAATGTCCACATT-GAAGTTAAGCA-ACCTCAAGAACTACGAACCAAAGAGCTCAAACC
** * ** *
17499380 ACAGATATCTTTTGCAGCAG-AGCAGCATAAGAAATCTGAAATGGCGACAGAAAGTTCTCAAATG
64 ACAGATATCTTTTGCAAAAGAACCA-CATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATG
17499444 CCACAACT
128 CCACAACT
*
17499452 AACGCAGAATGTCCACATTGAAGTTAAGCAACCTCAACCTCAAGAACTACGAACCAAAGAGCTCA
1 AATGCAGAATGTCCACATTGAAGTTAAG------CAACCTCAAGAACTACGAACCAAAGAGCTCA
* * * * * * * *
17499517 AACCGCAGACATCTTTTG-AAACAGAACCGCATGAGAAATCAAAAATGGAAATAGGAAGTTCTGA
60 AACCACAGATATCTTTTGCAAA-AGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCA
17499581 AATGCCACAACT
124 AATGCCACAACT
* * *
17499593 AATGCAGAATGTCCACATTGAAGTTAAGCAACCTGAAGATCTACGAACCAAAGAGCTCGAACCAC
1 AATGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCAC
* *
17499658 AGATGTCTTTTGCAAAAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCACATGCCA
66 AGATATCTTTTGCAAAAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCA
17499723 CAACT
131 CAACT
17499728 AATGC
1 AATGC
17499733 CAATGGAATC
Statistics
Matches: 238, Mismatches: 32, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
135 117 0.49
136 5 0.02
140 1 0.00
141 112 0.47
142 3 0.01
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (135 bp):
AATGCAGAATGTCCACATTGAAGTTAAGCAACCTCAAGAACTACGAACCAAAGAGCTCAAACCAC
AGATATCTTTTGCAAAAGAACCACATAAGAAATCAAAAATGGCAACAGAAAGTTCTCAAATGCCA
CAACT
Found at i:17502834 original size:1 final size:1
Alignment explanation
Indices: 17502828--17502852 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17502818 TTCAGAAAGG
17502828 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17502853 CCTTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17505769 original size:2 final size:2
Alignment explanation
Indices: 17505762--17505789 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17505752 AGAGTAAAAG
17505762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17505790 CAGCTGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17516127 original size:12 final size:12
Alignment explanation
Indices: 17516110--17516137 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17516100 AATTTACTAA
17516110 AAAGTTAAAATT
1 AAAGTTAAAATT
17516122 AAAGTTAAAATT
1 AAAGTTAAAATT
17516134 AAAG
1 AAAG
17516138 AAATCAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (12 bp):
AAAGTTAAAATT
Found at i:17517588 original size:21 final size:21
Alignment explanation
Indices: 17517530--17517588 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
17517520 TGCGTTATAC
* **
17517530 CGATAGAAGTCCTGGTTGTAT
1 CGATAGAACTCCCAGTTGTAT
* *
17517551 CGGTAGAAC-CCAGAGTTGTAT
1 CGATAGAACTCC-CAGTTGTAT
17517572 CGATAGAACTCCCAGTT
1 CGATAGAACTCCCAGTT
17517589 CTACTAGTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (21 bp):
CGATAGAACTCCCAGTTGTAT
Found at i:17519440 original size:2 final size:2
Alignment explanation
Indices: 17519433--17519469 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17519423 CTTTTCAACC
17519433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17519470 CATTAAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17520824 original size:45 final size:45
Alignment explanation
Indices: 17520753--17520918 Score: 157
Period size: 45 Copynumber: 3.7 Consensus size: 45
17520743 AAAAACACAC
* * * *
17520753 TATATTGTGGACAAGTCACTAGTAATTGAAGTTAAGCTGTTAGAAA
1 TATA-TGTGGACAAGCCACCAATAATTGAAGTTAAGCTGTCAGAAA
* *
17520799 TATATGTGGACAAGCCACCAATAATTGCA-TTCAAGCTGCCAGAAA
1 TATATGTGGACAAGCCACCAATAATTGAAGTT-AAGCTGTCAGAAA
*
17520844 TATATGTGGACAAGCCACCAGAT-A-TGCAAATATAA--TGTCA-AAA
1 TATATGTGGACAAGCCACCA-ATAATTG-AAGT-TAAGCTGTCAGAAA
* *
17520887 -ATATGTGGACAAGCCACCAGTAATTGTAGTTA
1 TATATGTGGACAAGCCACCAATAATTGAAGTTA
17520919 TACTGCCAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
41 3 0.03
42 22 0.22
43 5 0.05
44 8 0.08
45 54 0.53
46 9 0.09
47 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (45 bp):
TATATGTGGACAAGCCACCAATAATTGAAGTTAAGCTGTCAGAAA
Found at i:17520864 original size:24 final size:24
Alignment explanation
Indices: 17520794--17520865 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
17520784 TTAAGCTGTT
17520794 AGAAATATATGTGGACAAGCCACC
1 AGAAATATATGTGGACAAGCCACC
* **
17520818 ---AATA-AT-TGCATTCAAGCTGCC
1 AGAAATATATGTGGA--CAAGCCACC
17520839 AGAAATATATGTGGACAAGCCACC
1 AGAAATATATGTGGACAAGCCACC
17520863 AGA
1 AGA
17520866 TATGCAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 11 0.31
24 14 0.40
25 2 0.06
26 3 0.09
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (24 bp):
AGAAATATATGTGGACAAGCCACC
Found at i:17521173 original size:39 final size:39
Alignment explanation
Indices: 17521101--17521175 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
17521091 GTTGTATGCG
* * *
17521101 TACATGCAATCAATATACGTTTCAGTCAATGGCATGTTA
1 TACATGCAATCAATATACGATACAATCAATGGCATGTTA
* *
17521140 TACATGCAATCAATATAGGATACAATCAGTGGCATG
1 TACATGCAATCAATATACGATACAATCAATGGCATG
17521176 CTATTTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (39 bp):
TACATGCAATCAATATACGATACAATCAATGGCATGTTA
Found at i:17522070 original size:15 final size:13
Alignment explanation
Indices: 17522041--17522083 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
17522031 ATGGTGAAGT
17522041 GAGAAGAAAAAAA
1 GAGAAGAAAAAAA
17522054 GAGAATGAAATAAAA
1 GAGAA-GAAA-AAAA
*
17522069 GAGGAGAAGAAAAA
1 GAGAAGAA-AAAAA
17522083 G
1 G
17522084 GATGACGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (13 bp):
GAGAAGAAAAAAA
Found at i:17526063 original size:28 final size:28
Alignment explanation
Indices: 17526030--17526097 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
17526020 TCATCCTTTT
* *
17526030 CCACAAGGGCTTCCCTTTCCTTAGATTG
1 CCACAAAGGCTTCCCTTTCCATAGATTG
* *
17526058 CCACAAAGGC-TCTCTTTTCATAGATTG
1 CCACAAAGGCTTCCCTTTCCATAGATTG
*
17526085 GCACAAAGGCTTC
1 CCACAAAGGCTTC
17526098 GATTTCATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (28 bp):
CCACAAAGGCTTCCCTTTCCATAGATTG
Found at i:17526103 original size:27 final size:27
Alignment explanation
Indices: 17526051--17526106 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
17526041 TCCCTTTCCT
*
17526051 TAGATTGCCACAAAGGCTCTCTTTTCA
1 TAGATTGCCACAAAGGCTCTCATTTCA
*
17526078 TAGATTGGCACAAAGGCT-TCGATTTCA
1 TAGATTGCCACAAAGGCTCTC-ATTTCA
17526105 TA
1 TA
17526107 AAAGGCCTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (27 bp):
TAGATTGCCACAAAGGCTCTCATTTCA
Found at i:17532951 original size:30 final size:29
Alignment explanation
Indices: 17532904--17532965 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 29
17532894 ACTTATTTTA
17532904 TTGTTAATTTTTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTTATTATTTTAAAGGCAT
*
17532933 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTT-TTATTATTTTAAAGGCAT
17532963 TTG
1 TTG
17532966 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (29 bp):
TTGTTAATTTTTTATTATTTTAAAGGCAT
Found at i:17538366 original size:26 final size:26
Alignment explanation
Indices: 17538304--17538366 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
17538294 CATTAGGGCG
* ** *
17538304 TAGCAGGCTTCGTGCCGGTGTATATT
1 TAGCAGGCTTCATGCCAATATATATT
* **
17538330 TAACAAACTTCATGCCAATATATATT
1 TAGCAGGCTTCATGCCAATATATATT
17538356 TAGCAGGCTTC
1 TAGCAGGCTTC
17538367 GTGCTGGTGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (26 bp):
TAGCAGGCTTCATGCCAATATATATT
Found at i:17546989 original size:18 final size:18
Alignment explanation
Indices: 17546949--17546995 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
17546939 TGAAGTGAAA
17546949 AAGAAAAT-AA-GAAGAG
1 AAGAAAATAAAGGAAGAG
* *
17546965 AACAAAATAAAGGAGGAG
1 AAGAAAATAAAGGAAGAG
*
17546983 AAGAAAAAAAAGG
1 AAGAAAATAAAGG
17546996 CAGCGGTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 7 0.28
17 2 0.08
18 16 0.64
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (18 bp):
AAGAAAATAAAGGAAGAG
Found at i:17558864 original size:15 final size:15
Alignment explanation
Indices: 17558846--17558889 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
17558836 ATAACCTAAA
17558846 AAATAATAAGAAAGG
1 AAATAATAAGAAAGG
*
17558861 AAATAA-AAGTAAAGT
1 AAATAATAAG-AAAGG
17558876 AAATAAATAAGAAA
1 AAAT-AATAAGAAA
17558890 CGAGAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 14 0.56
16 5 0.20
17 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (15 bp):
AAATAATAAGAAAGG
Found at i:17571459 original size:18 final size:19
Alignment explanation
Indices: 17571418--17571459 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
17571408 AAAATTACAA
*
17571418 AAAAATTTAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
17571437 TAAAATTCAAAAT-ATTTT
1 AAAAATTCAAAATAATTTT
17571455 AAAAA
1 AAAAA
17571460 AATTATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:17571470 original size:29 final size:30
Alignment explanation
Indices: 17571407--17571471 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
17571397 CTCTCACAAC
* *
17571407 AAAAATTACAAAAAAATTTAAAATAATTTT
1 AAAAATTACAAAAAAATTTAAAAAAATTAT
* * *
17571437 TAAAATT-CAAAATATTTTAAAAAAATTAT
1 AAAAATTACAAAAAAATTTAAAAAAATTAT
17571466 AAAAAT
1 AAAAAT
17571472 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAAATTACAAAAAAATTTAAAAAAATTAT
Found at i:17571493 original size:20 final size:21
Alignment explanation
Indices: 17571416--17571482 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 21
17571406 CAAAAATTAC
17571416 AAAAAAATT-TAAAATA-ATT
1 AAAAAAATTATAAAATATATT
*** * *
17571435 TTTAAAATT-CAAAATATTTT
1 AAAAAAATTATAAAATATATT
17571455 AAAAAAATTATAAAA-ATATT
1 AAAAAAATTATAAAATATATT
17571475 AAAAAAAT
1 AAAAAAAT
17571483 AAAGAATATA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
19 12 0.33
20 20 0.56
21 4 0.11
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAAATTATAAAATATATT
Found at i:17591449 original size:19 final size:19
Alignment explanation
Indices: 17591422--17591470 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
17591412 AAATGATAAG
*
17591422 GATGAGAAATGGAAAATGA
1 GATGTGAAATGGAAAATGA
* *
17591441 GATGTGAAATTGAATATGA
1 GATGTGAAATGGAAAATGA
*
17591460 AATGGTGAAAT
1 GAT-GTGAAAT
17591471 TGGTTCTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
GATGTGAAATGGAAAATGA
Found at i:17600509 original size:15 final size:14
Alignment explanation
Indices: 17600491--17600524 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
17600481 GGTATTAGCA
*
17600491 GTTTAGGGATTATGG
1 GTTTAAGGATTAT-G
17600506 GTTTAAGGATTATG
1 GTTTAAGGATTATG
17600520 GTTTA
1 GTTTA
17600525 TTGTTTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (14 bp):
GTTTAAGGATTATG
Found at i:17600551 original size:14 final size:15
Alignment explanation
Indices: 17600534--17600572 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
17600524 ATTGTTTATT
17600534 GTTTAAGGGTT-GGG
1 GTTTAAGGGTTAGGG
17600548 GTTTAAGGGTTAGGG
1 GTTTAAGGGTTAGGG
17600563 GTTT-AGGGTT
1 GTTTAAGGGTT
17600573 TATAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (15 bp):
GTTTAAGGGTTAGGG
Found at i:17600565 original size:57 final size:57
Alignment explanation
Indices: 17600491--17600716 Score: 192
Period size: 57 Copynumber: 3.9 Consensus size: 57
17600481 GGTATTAGCA
* *
17600491 GTTT-AGGGATTATGGGTTTAAGGATTATGGTTTATTGTTTATTG-TTTAAGGGTTGGG
1 GTTTAAGGG-TTAGGGGTTTAAGGATTATGGTTTATGGTTT-TTGATTTAAGGGTTGGG
* * ** **
17600548 GTTTAAGGGTTAGGGGTTTAGGGTTTATAATTTAT-GTTTTATGATTT-AGGGTTTAAAG
1 GTTTAAGGGTTAGGGGTTTAAGGATTATGGTTTATGGTTTT-TGATTTAAGGG-TT-GGG
* * * * *
17600606 G-ATAAGGGTTAGGGGTTTAAGGATTATGGTTTATGGGTTATGTTTTAAGTGTTGGG
1 GTTTAAGGGTTAGGGGTTTAAGGATTATGGTTTATGGTTTTTGATTTAAGGGTTGGG
* * ** * *
17600662 GTGTATGGGTTAAGATGTTTAGGGATTATGGTTTATGGTTTGTGATTTAAGGGTT
1 GTTTAAGGGTT-AGGGGTTTAAGGATTATGGTTTATGGTTTTTGATTTAAGGGTT
17600717 AGGGATTGAG
Statistics
Matches: 133, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
55 1 0.01
56 12 0.09
57 72 0.54
58 48 0.36
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (57 bp):
GTTTAAGGGTTAGGGGTTTAAGGATTATGGTTTATGGTTTTTGATTTAAGGGTTGGG
Found at i:17600581 original size:14 final size:14
Alignment explanation
Indices: 17600564--17600602 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17600554 GGGTTAGGGG
17600564 TTTAGGGTTTATAA
1 TTTAGGGTTTATAA
* * *
17600578 TTTATGTTTTATGA
1 TTTAGGGTTTATAA
17600592 TTTAGGGTTTA
1 TTTAGGGTTTA
17600603 AAGGATAAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTATAA
Found at i:17600643 original size:22 final size:22
Alignment explanation
Indices: 17600586--17600644 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
17600576 AATTTATGTT
*
17600586 TTATGATTTAGGGTTTAAAGGA
1 TTATGGTTTAGGGTTTAAAGGA
* *
17600608 -TAAGGGTTAGGGGTTT-AAGGA
1 TTATGGTTTA-GGGTTTAAAGGA
17600629 TTATGGTTTATGGGTT
1 TTATGGTTTA-GGGTT
17600645 ATGTTTTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (22 bp):
TTATGGTTTAGGGTTTAAAGGA
Found at i:17603764 original size:28 final size:27
Alignment explanation
Indices: 17603733--17603797 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
17603723 ATTATGTTTG
*
17603733 ATTA-GTTTATTCGGTTTAATGTGAATAA
1 ATTATGTTT-TTCGATTTAAT-TGAATAA
*
17603761 ATTATCGATTTTCGATTTAATTGAATAA
1 ATTAT-GTTTTTCGATTTAATTGAATAA
17603789 ATTATGTTT
1 ATTATGTTT
17603798 GATTAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.09
28 16 0.50
29 10 0.31
30 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (27 bp):
ATTATGTTTTTCGATTTAATTGAATAA
Found at i:17603797 original size:66 final size:66
Alignment explanation
Indices: 17603711--17603859 Score: 235
Period size: 66 Copynumber: 2.3 Consensus size: 66
17603701 ATATATTAGA
* *
17603711 TTAATTGAATAAATTATGTTTGATTAGTTTATTCGGTTTAATGTGAATAAATTATCGATTTTCGA
1 TTAATTGAATAAATTATGTTTGATTAGTTTATTCGATTTAATGTGAATAAATTATCAATTTTCGA
17603776 T
66 T
* * **
17603777 TTAATTGAATAAATTATGTTTGATTAGTTTATTTGATTTTATGTGAATAAATTATCAATTTTTTA
1 TTAATTGAATAAATTATGTTTGATTAGTTTATTCGATTTAATGTGAATAAATTATCAATTTTCGA
17603842 T
66 T
*
17603843 TTAATTTAATAAATTAT
1 TTAATTGAATAAATTAT
17603860 CGATTTTATA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 76 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (66 bp):
TTAATTGAATAAATTATGTTTGATTAGTTTATTCGATTTAATGTGAATAAATTATCAATTTTCGA
T
Found at i:17604237 original size:9 final size:9
Alignment explanation
Indices: 17604220--17604477 Score: 125
Period size: 9 Copynumber: 27.9 Consensus size: 9
17604210 AAATTAATAT
*
17604220 ATAATTTAC
1 ATAACTTAC
17604229 ATAACTTAC
1 ATAACTTAC
* *
17604238 ATAA-ATAT
1 ATAACTTAC
* *
17604246 ATATCATATC
1 ATAACTTA-C
* *
17604256 AAAATTTAC
1 ATAACTTAC
*
17604265 ATAACTTAT
1 ATAACTTAC
*
17604274 ATAATTTAC
1 ATAACTTAC
*
17604283 ATAACTCAC
1 ATAACTTAC
17604292 ATAACTTAC
1 ATAACTTAC
17604301 ATAACTTA-
1 ATAACTTAC
*
17604309 ATAACCATATC
1 ATAA-CTTA-C
17604320 ATAACTTAC
1 ATAACTTAC
*
17604329 ATAATTTAC
1 ATAACTTAC
*
17604338 ATAACTTTAA
1 ATAAC-TTAC
* *
17604348 AGAA-TTAAAA
1 ATAACTT--AC
*
17604358 AAAACTTTGGATC
1 ATAAC-TT--A-C
*
17604371 TTAACTTA-
1 ATAACTTAC
*
17604379 ATAACTTAT
1 ATAACTTAC
*
17604388 ATATATCATATC
1 ATA-A-CTTA-C
17604400 ATAACTTAC
1 ATAACTTAC
*
17604409 ATAACTCAC
1 ATAACTTAC
17604418 ATAACTTAC
1 ATAACTTAC
17604427 ATAACTTAC
1 ATAACTTAC
17604436 ATAA--TAC
1 ATAACTTAC
* *
17604443 ATAA-ATAT
1 ATAACTTAC
* *
17604451 ATATCATATC
1 ATAACTTA-C
17604461 ATAACTTAC
1 ATAACTTAC
17604470 ATAACTTA
1 ATAACTTA
17604478 ATTATACTTA
Statistics
Matches: 191, Mismatches: 40, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
7 7 0.04
8 23 0.12
9 113 0.59
10 29 0.15
11 8 0.04
12 8 0.04
13 3 0.02
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:17604444 original size:34 final size:34
Alignment explanation
Indices: 17604406--17604473 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
17604396 TATCATAACT
* *
17604406 TACATAACTCACATAACTTA-CATAACTTACATAA
1 TACATAAAT-ACATAACATATCATAACTTACATAA
* *
17604440 TACATAAATATATATCATATCATAACTTACATAA
1 TACATAAATACATAACATATCATAACTTACATAA
17604474 CTTAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (34 bp):
TACATAAATACATAACATATCATAACTTACATAA
Found at i:17610310 original size:43 final size:43
Alignment explanation
Indices: 17610263--17610344 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
17610253 TCACAAACAC
*
17610263 CGCTAAA-G-AATGGTACTTTTAGCGGCGTTTGTGAAAAAAACGT
1 CGCTAAATGTAAT-GTAC-TTTAGCAGCGTTTGTGAAAAAAACGT
* *
17610306 CGCTAAATGTCATGTTCTTTAGCAGCGTTTGTGAAAAAA
1 CGCTAAATGTAATGTACTTTAGCAGCGTTTGTGAAAAAA
17610345 GGCGCTGCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
43 28 0.82
44 4 0.12
45 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (43 bp):
CGCTAAATGTAATGTACTTTAGCAGCGTTTGTGAAAAAAACGT
Found at i:17610475 original size:86 final size:86
Alignment explanation
Indices: 17610306--17610546 Score: 347
Period size: 86 Copynumber: 2.8 Consensus size: 86
17610296 AAAAAAACGT
* * * * *
17610306 CGCTAAATGTCATGTTCTTTAGCAGCGTTTGTGAAAAAAGGCGCTGCTAAAGGTCATGTTCTTTA
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAA-GCGCCGCTAAAGATCATGTTCTTTA
* * *
17610371 GTGGTGTTTGTGATAAAAGGAC
65 GTGGCGATTGTGATAAAAGCAC
*
17610393 CGCTAAAGGTCATGTTCTTTATCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAG
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAG
17610458 TGGCGATTGTGATAAAAGCAC
66 TGGCGATTGTGATAAAAGCAC
* * * **
17610479 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATGGCCTTTAG
1 CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAG
17610544 TGG
66 TGG
17610547 TGCTTCTCTT
Statistics
Matches: 139, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
86 104 0.75
87 35 0.25
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (86 bp):
CGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTCTTTAG
TGGCGATTGTGATAAAAGCAC
Found at i:17610543 original size:43 final size:43
Alignment explanation
Indices: 17610280--17610535 Score: 309
Period size: 43 Copynumber: 5.9 Consensus size: 43
17610270 GAATGGTACT
* * *
17610280 TTTAGCGGCGTTTGTGAAAAAAACGTCGCTAAATG-TCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAA-GATCATGTTC
* * * *
17610323 TTTAGCAGCGTTTGTGAAAAAAGGCGCTGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAA-GCGCCGCTAAAGATCATGTTC
* * *
17610367 TTTAGTGGTGTTTGTGATAAAAG-GACCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCG-CCGCTAAAGATCATGTTC
*
17610410 TTTATCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* * * *
17610453 TTTAGTGGCGATTGTGATAAAAGCACCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
* * *
17610496 TTTAGCGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATG
1 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATG
17610536 GCCTTTAGTG
Statistics
Matches: 184, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
42 1 0.01
43 148 0.80
44 35 0.19
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGATCATGTTC
Found at i:17616114 original size:21 final size:21
Alignment explanation
Indices: 17616076--17616115 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17616066 CTTCTTTTAT
*
17616076 CCTATTTTTAACCGTAAAACC
1 CCTATTTTAAACCGTAAAACC
17616097 CCTATTTTAAAACC-TAAAA
1 CCTATTTT-AAACCGTAAAA
17616116 ACACCTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.33
Consensus pattern (21 bp):
CCTATTTTAAACCGTAAAACC
Found at i:17628285 original size:22 final size:21
Alignment explanation
Indices: 17628244--17628286 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
17628234 CATGATAGGT
*
17628244 GATTTTAAATTTTGATTATTA
1 GATTTTAAATTCTGATTATTA
17628265 GATTATTAAATTCT-ATATATTA
1 GATT-TTAAATTCTGAT-TATTA
17628287 CACTGTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (21 bp):
GATTTTAAATTCTGATTATTA
Found at i:17630340 original size:8 final size:8
Alignment explanation
Indices: 17630327--17630352 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17630317 TGATTTCTCA
17630327 TTATTTCT
1 TTATTTCT
17630335 TTATTTCT
1 TTATTTCT
17630343 TTATTTCT
1 TTATTTCT
17630351 TT
1 TT
17630353 TTAGTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTTCT
Found at i:17630761 original size:27 final size:27
Alignment explanation
Indices: 17630723--17630823 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
17630713 ATTCTCTTCG
*
17630723 TAGATTGCCACAAAGGCTTCATTTTCA
1 TAGATTGCCACAAAGGCTTCATTATCA
* *
17630750 TAGATTGCCACAAAAGCTTCCTTATCA
1 TAGATTGCCACAAAGGCTTCATTATCA
* * *
17630777 TAGATTTCCACAAAGGCATCCTTATCA
1 TAGATTGCCACAAAGGCTTCATTATCA
*
17630804 TAGACTGCCACAAAGGCTTC
1 TAGATTGCCACAAAGGCTTC
17630824 CATTTTCTTG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (27 bp):
TAGATTGCCACAAAGGCTTCATTATCA
Found at i:17646791 original size:45 final size:44
Alignment explanation
Indices: 17646735--17646880 Score: 143
Period size: 45 Copynumber: 3.2 Consensus size: 44
17646725 AGTACACAAC
* * *
17646735 ACCACCCTTATAGTCAAGAGTACTTGGTGAAATCAGCACATAGCA
1 ACCACCTTTATAATCAAG-GTACTCGGTGAAATCAGCACATAGCA
* *
17646780 ACCACCTTTATACTCAATGGTTC-CGGGTGAAATCAGCACATAGCA
1 ACCACCTTTATAATCAA-GGTACTC-GGTGAAATCAGCACATAGCA
* * * * *
17646825 ACCACCTATATAACCATTGGTA-TCCGGTAAAATCAACACATAGCA
1 ACCACCTTTATAATCA-AGGTACT-CGGTGAAATCAGCACATAGCA
17646870 ACCACCTTTAT
1 ACCACCTTTAT
17646881 TTTCATTAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
45 82 0.98
46 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (44 bp):
ACCACCTTTATAATCAAGGTACTCGGTGAAATCAGCACATAGCA
Found at i:17646939 original size:90 final size:90
Alignment explanation
Indices: 17646764--17646939 Score: 210
Period size: 90 Copynumber: 2.0 Consensus size: 90
17646754 GTACTTGGTG
* ** *
17646764 AAATCAGCACATAGCAACCACCTTTATACTCAATGGTTCCGGGTGAAATCAGCACATAGCAACCA
1 AAATCAACACATAGCAACCACCTTTATACTCAATAATTCAGGGTGAAATCAGCACATAGCAACCA
** *
17646829 CCTATATAACCATTGGTATCCGGTA
66 CCTATATAACCAACGATATCCGGTA
** * * *
17646854 AAATCAACACATAGCAACCACCTTTATTTTCATTAATAT-AGGGTGGAATCAGCACATAGCATCC
1 AAATCAACACATAGCAACCACCTTTATACTCAATAAT-TCAGGGTGAAATCAGCACATAGCAACC
**
17646918 ACCTATATTTCCAACGATATCC
65 ACCTATATAACCAACGATATCC
17646940 AGCCCATTCT
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
90 70 0.99
91 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (90 bp):
AAATCAACACATAGCAACCACCTTTATACTCAATAATTCAGGGTGAAATCAGCACATAGCAACCA
CCTATATAACCAACGATATCCGGTA
Found at i:17651287 original size:40 final size:41
Alignment explanation
Indices: 17651230--17651318 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 41
17651220 TTATACCCTA
* * *
17651230 AATTGCACTTTCGTG-CCCT-TATTGTACTTCGGTACACCTG
1 AATTGCACTTACATGCCCCTGT-TTGTACTTCAGTACACCTG
*
17651270 AATTGCACTTACATGCCCCTGTTTGTACTTCAGTACCCCTG
1 AATTGCACTTACATGCCCCTGTTTGTACTTCAGTACACCTG
17651311 AATTGCAC
1 AATTGCAC
17651319 ATAAGTGCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 13 0.30
41 29 0.67
42 1 0.02
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (41 bp):
AATTGCACTTACATGCCCCTGTTTGTACTTCAGTACACCTG
Found at i:17651290 original size:21 final size:21
Alignment explanation
Indices: 17651250--17651318 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
17651240 TCGTGCCCTT
* * *
17651250 ATTGTACTTCGGTACACCTGA
1 ATTGCACTTCAGTACCCCTGA
*
17651271 ATTGCACTTACA-TGCCCCTG-
1 ATTGCACTT-CAGTACCCCTGA
* *
17651291 TTTGTACTTCAGTACCCCTGA
1 ATTGCACTTCAGTACCCCTGA
17651312 ATTGCAC
1 ATTGCAC
17651319 ATAAGTGCCT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 14 0.39
21 19 0.53
22 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (21 bp):
ATTGCACTTCAGTACCCCTGA
Found at i:17652306 original size:29 final size:29
Alignment explanation
Indices: 17652249--17652307 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
17652239 GTGTGTCCCT
* * *
17652249 ATTTTGAATGCTCGTGTCTTAGTCATGTG
1 ATTTCGAATGCTCGTGTCTCAGCCATGTG
*
17652278 ATTTCGAATGCTCGTGTCTCAGCCGTGTG
1 ATTTCGAATGCTCGTGTCTCAGCCATGTG
17652307 A
1 A
17652308 GGCACACGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (29 bp):
ATTTCGAATGCTCGTGTCTCAGCCATGTG
Found at i:17657764 original size:20 final size:19
Alignment explanation
Indices: 17657730--17657768 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
17657720 TTTAAAAGGT
17657730 TAAAAGTGTAATTAAGTAAA
1 TAAAAGTGTAATTAA-TAAA
17657750 TAAAAGT-TAATTTAATAAA
1 TAAAAGTGTAA-TTAATAAA
17657769 AAAGAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAAAGTGTAATTAATAAA
Found at i:17658579 original size:40 final size:39
Alignment explanation
Indices: 17658520--17658644 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 39
17658510 TTATACATTG
* * *
17658520 AATTGCACTTACGTACCCCTGATGTACTTCGATACCCCTA
1 AATTGCACTTATGTGCCCCT-ATGTACTTCGGTACCCCTA
* **
17658560 AATTGCACTTATATGCCCCTAT-TTTTCTCTGGTACCCCTA
1 AATTGCACTTATGTGCCCCTATGTACT-TC-GGTACCCCTA
* * *
17658600 AATTGCACTTTTGTGCCCCTATATGTACTTTGGTACCCCTG
1 AATTGCACTTATGTGCCCC--TATGTACTTCGGTACCCCTA
17658641 AATT
1 AATT
17658645 ACACATACGT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
38 2 0.03
39 4 0.06
40 43 0.63
41 13 0.19
42 4 0.06
43 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTGCACTTATGTGCCCCTATGTACTTCGGTACCCCTA
Found at i:17658638 original size:20 final size:21
Alignment explanation
Indices: 17658589--17658644 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
17658579 TATTTTTCTC
17658589 TGGTACCCCTAAATTGCACTT
1 TGGTACCCCTAAATTGCACTT
* * * *
17658610 TTGTGCCCCTATA-TGTACTT
1 TGGTACCCCTAAATTGCACTT
*
17658630 TGGTACCCCTGAATT
1 TGGTACCCCTAAATT
17658645 ACACATACGT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.38
Consensus pattern (21 bp):
TGGTACCCCTAAATTGCACTT
Found at i:17671812 original size:76 final size:76
Alignment explanation
Indices: 17671720--17671871 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
17671710 GAAAGACATT
*
17671720 GAGTTTCAAGTTGGCGATAAAGTGTTTTGGAAAGTGTCTCTGTGGAAGAAGATTTTGAGATTTGG
1 GAGTTTCAAGTTGGCGATAAAGTGTTTTGGAAAGTGTCTCCGTGGAAGAAGATTTTGAGATTTGG
17671785 TCGGAAGGGTA
66 TCGGAAGGGTA
17671796 GAGTTTCAAGTTGGCGATAAAGTGTTTTGGAAAGTGTCTCCGTGGAAGAAGATTTTGAGATTTGG
1 GAGTTTCAAGTTGGCGATAAAGTGTTTTGGAAAGTGTCTCCGTGGAAGAAGATTTTGAGATTTGG
17671861 TCGGAAGGGTA
66 TCGGAAGGGTA
17671872 AATTGAGTCC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.26, C:0.07, G:0.34, T:0.32
Consensus pattern (76 bp):
GAGTTTCAAGTTGGCGATAAAGTGTTTTGGAAAGTGTCTCCGTGGAAGAAGATTTTGAGATTTGG
TCGGAAGGGTA
Found at i:17675395 original size:20 final size:19
Alignment explanation
Indices: 17675367--17675420 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 19
17675357 TAAAGGGTGA
17675367 GAAGTAAAAGTTTAGGGGG
1 GAAGTAAAAGTTTAGGGGG
*
17675386 GAAGTAAAAAGTTT--TGGG
1 GAAGT-AAAAGTTTAGGGGG
17675404 GAA-TAAAAGTTTGAGGG
1 GAAGTAAAAGTTT-AGGG
17675421 AAAGTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 8 0.28
17 1 0.03
18 6 0.21
19 6 0.21
20 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (19 bp):
GAAGTAAAAGTTTAGGGGG
Found at i:17677327 original size:23 final size:23
Alignment explanation
Indices: 17677301--17677351 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
17677291 AAATACAAGT
17677301 GATTGGTTAGGAGCATGTACATA
1 GATTGGTTAGGAGCATGTACATA
17677324 GATTGGTTAGGAGCATGTACATA
1 GATTGGTTAGGAGCATGTACATA
17677347 GATTG
1 GATTG
17677352 CTTATGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.31
Consensus pattern (23 bp):
GATTGGTTAGGAGCATGTACATA
Found at i:17679157 original size:30 final size:30
Alignment explanation
Indices: 17679121--17679178 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
17679111 GGACGATGAC
17679121 CACCTGAAGGCTATAAATAGGCTCATTTGT
1 CACCTGAAGGCTATAAATAGGCTCATTTGT
*
17679151 CACCTGAAGGCTATAAATAGGTTCATTT
1 CACCTGAAGGCTATAAATAGGCTCATTT
17679179 CTTTCATTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
CACCTGAAGGCTATAAATAGGCTCATTTGT
Found at i:17683242 original size:18 final size:18
Alignment explanation
Indices: 17683219--17683259 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
17683209 TCATCTTTTG
*
17683219 CAATAACTCTTCTGCCTC
1 CAATAACTCTTCTGCCTA
17683237 CAATAACTCTTCTGCCTA
1 CAATAACTCTTCTGCCTA
17683255 CAATA
1 CAATA
17683260 CCCACGAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (18 bp):
CAATAACTCTTCTGCCTA
Found at i:17688132 original size:33 final size:32
Alignment explanation
Indices: 17688073--17688134 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
17688063 TAAAAAAATA
17688073 TTTAACTATAAAAAATTAAAAATAATTATCAT
1 TTTAACTATAAAAAATTAAAAATAATTATCAT
* * *
17688105 TTTAACTAATAAATAATTTAAATTAATTAT
1 TTTAACT-ATAAAAAATTAAAAATAATTAT
17688135 ATAATTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (32 bp):
TTTAACTATAAAAAATTAAAAATAATTATCAT
Found at i:17688396 original size:21 final size:22
Alignment explanation
Indices: 17688344--17688396 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
17688334 ACCATTGTTT
*
17688344 CTAATCTCA-CTGCTACAGTAT
1 CTAATCTCACCTGCTACAGTAA
*
17688365 CCAATCTCACCT-CTACAGTAA
1 CTAATCTCACCTGCTACAGTAA
17688386 CTAATCTCACC
1 CTAATCTCACC
17688397 GCCATCGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.28
Consensus pattern (22 bp):
CTAATCTCACCTGCTACAGTAA
Found at i:17692014 original size:13 final size:13
Alignment explanation
Indices: 17691996--17692022 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17691986 AAAGTTGCCC
17691996 TTATAAAATTGTT
1 TTATAAAATTGTT
17692009 TTATAAAATTGTT
1 TTATAAAATTGTT
17692022 T
1 T
17692023 GTTTTATGTA
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:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTATAAAATTGTT
Found at i:17693529 original size:18 final size:17
Alignment explanation
Indices: 17693497--17693538 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
17693487 TTTATAGTTT
17693497 TAAA-TAATTTTTTGGG
1 TAAATTAATTTTTTGGG
17693513 TAAATTAATTATTTTGGG
1 TAAATTAATT-TTTTGGG
17693531 TCAAATTA
1 T-AAATTA
17693539 GAATTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 5 0.22
18 8 0.35
19 6 0.26
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (17 bp):
TAAATTAATTTTTTGGG
Found at i:17698947 original size:14 final size:14
Alignment explanation
Indices: 17698925--17698960 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17698915 AATATTTAGC
*
17698925 AATTCGATTGGATA
1 AATTCGATTGAATA
*
17698939 AATTTGATTGAATA
1 AATTCGATTGAATA
17698953 AATTCGAT
1 AATTCGAT
17698961 ACTTTTAGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (14 bp):
AATTCGATTGAATA
Found at i:17699767 original size:22 final size:22
Alignment explanation
Indices: 17699704--17699767 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
17699694 CTATTTGCAT
* *
17699704 GTTTAGTGCCTAGGG-TTTATGG
1 GTTTAGTG-TTAGGGTTTTAAGG
*
17699726 GTTTAGAGTTTTAGGGTTTTAAGG
1 GTTT--AGTGTTAGGGTTTTAAGG
17699750 GTTTAGTGTTAGGGTTTT
1 GTTTAGTGTTAGGGTTTT
17699768 GTTAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 17 0.49
23 5 0.14
24 13 0.37
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (22 bp):
GTTTAGTGTTAGGGTTTTAAGG
Found at i:17699863 original size:27 final size:27
Alignment explanation
Indices: 17699813--17699864 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
17699803 GGGTTATGGA
*
17699813 TTTTTAAAAATAAATCAAGTTTAGGGT
1 TTTTTAAAAATAAATCAAGATTAGGGT
*
17699840 TTTTTAACAAATAAATTAA-ATTAGG
1 TTTTTAA-AAATAAATCAAGATTAGG
17699865 ATTTAGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (27 bp):
TTTTTAAAAATAAATCAAGATTAGGGT
Found at i:17699938 original size:34 final size:34
Alignment explanation
Indices: 17699831--17699938 Score: 166
Period size: 34 Copynumber: 3.2 Consensus size: 34
17699821 AATAAATCAA
*
17699831 GTTTAGG-GTTTTTTAACAAATAAATTAAATTAGG
1 GTTTAGGATTTTTTTAA-AAATAAATTAAATTAGG
* *
17699865 ATTTA-GATTTTTTTAAAAATAAATTAAATTAAG
1 GTTTAGGATTTTTTTAAAAATAAATTAAATTAGG
17699898 GTTTAGGATTTTTTTAAAAATAAATTAAATTAGG
1 GTTTAGGATTTTTTTAAAAATAAATTAAATTAGG
17699932 GTTTAGG
1 GTTTAGG
17699939 GTTTAGGGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
33 21 0.31
34 46 0.69
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.44
Consensus pattern (34 bp):
GTTTAGGATTTTTTTAAAAATAAATTAAATTAGG
Found at i:17700319 original size:125 final size:126
Alignment explanation
Indices: 17700054--17700438 Score: 531
Period size: 126 Copynumber: 3.1 Consensus size: 126
17700044 TTTTTTTGTT
* * *
17700054 CAGTAGTTTCTGAAAAAATAATTTTGAGAAGA-TGGTTATGAAAAAATAGTGTCAAAAACGCTTC
1 CAGTAGTTTCTGAAAAAATAATTTTGAGAAGACT-GTTCTGAAAAAATAATGTCAAAAATGCTTC
* *
17700118 AAGCAGGATGCATTGTCAACAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTG
65 AAGCAGGATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
* *
17700180 CAGTAGTTTTTGAAAAACTAATTTTGAGAAGACTGTTCTGAAAAAATAATGTCAAAAATGCTTCA
1 CAGTAGTTTCTGAAAAAATAATTTTGAGAAGACTGTTCTGAAAAAATAATGTCAAAAATGCTTCA
* * * *
17700245 AGCAGGATGCACTGTCATCAAAAGTACT-AAAAAAGATCCCATGTGGACACTCTTTTTCTA
66 AGCAGGATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
* * * * * *
17700305 CAGTAGTTTCTGAAAAAATAAATTTAAGAAGACGGTTCTAAAAAAATAATGTCAAATATGTTTCA
1 CAGTAGTTTCTGAAAAAATAATTTTGAGAAGACTGTTCTGAAAAAATAATGTCAAAAATGCTTCA
* * * * * **
17700370 AGCAAGATGTACTATCAGCAAAAGTATTGAAAAACTCTCCCACGTGGACGCTCTTTTTCTA
66 AGCAGGATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
17700431 CAGTAGTT
1 CAGTAGTT
17700439 CTTGCTTGGC
Statistics
Matches: 228, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
125 108 0.47
126 119 0.52
127 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
CAGTAGTTTCTGAAAAAATAATTTTGAGAAGACTGTTCTGAAAAAATAATGTCAAAAATGCTTCA
AGCAGGATGCACTGTCAACAAAAGTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
Found at i:17704573 original size:24 final size:25
Alignment explanation
Indices: 17704520--17704567 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17704510 TTTTCCCTCT
* *
17704520 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTATATAGCTCTTG
17704545 CGAGCTTCCCGTTA-ATAGCTCTT
1 CGAGCTTCCCGTTATATAGCTCTT
17704568 CGGAGCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.15, C:0.27, G:0.21, T:0.38
Consensus pattern (25 bp):
CGAGCTTCCCGTTATATAGCTCTTG
Found at i:17704660 original size:26 final size:25
Alignment explanation
Indices: 17704625--17704699 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
17704615 ACAGCTCTTA
*
17704625 TGAGCGTCCCATTATATGGCTCTTTG
1 TGAGCTTCCCATTA-ATGGCTCTTTG
**
17704651 TGAGCTTCCCGATTAAAAGCTCTTTG
1 TGAGCTTCCC-ATTAATGGCTCTTTG
*
17704677 TGAGCTTCCTAATTAATGGCTCT
1 TGAGCTTCC-CATTAATGGCTCT
17704700 CCGGAGCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 37 0.90
27 4 0.10
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (25 bp):
TGAGCTTCCCATTAATGGCTCTTTG
Found at i:17709982 original size:29 final size:29
Alignment explanation
Indices: 17709927--17709983 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
17709917 GTAATTTTAG
** **
17709927 CCCATTTCGGTAAATAAAGTTTAAAATGA
1 CCCATTTCCATAAATAAAGTAGAAAATGA
*
17709956 CCCATTTCCATAAATAAAGTAGGAAATG
1 CCCATTTCCATAAATAAAGTAGAAAATG
17709984 GACCTTTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (29 bp):
CCCATTTCCATAAATAAAGTAGAAAATGA
Found at i:17716049 original size:13 final size:13
Alignment explanation
Indices: 17716031--17716056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17716021 ATACCTCAGA
17716031 ATTCTTTAGCCCT
1 ATTCTTTAGCCCT
17716044 ATTCTTTAGCCCT
1 ATTCTTTAGCCCT
17716057 CTTGTACTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTCTTTAGCCCT
Found at i:17716323 original size:328 final size:328
Alignment explanation
Indices: 17715726--17716378 Score: 1083
Period size: 328 Copynumber: 2.0 Consensus size: 328
17715716 TCATAAATTT
*
17715726 CCTCTTGTACTCATCTACTGACATACATCATTGCTTCAACTCAAGAAACTCTTTGCATTTCTTAT
1 CCTCTTGTACTCAGCTACTGACATACATCATTGCTTCAACTCAAGAAACTCTTTGCATTTCTTAT
* * * *
17715791 TTTGGAACCTTTTACTCACATATTTCTTTTTGAACTCTGTCTGGAAGAATTCCCAATTTACTTGA
66 CTAGGAACCTCTGACTCACATATTTCTTTTTGAACTCTGTCTGGAAGAATTCCCAATTTACTTGA
* *
17715856 TCCCTCGGTACCACCTTGATAAACGTGTTCCACCACTGATAAGCTGAGTCTTTTAATATAGAAAC
131 TCCCTCGGTACCACCGTGATAAACGTGTTCCACCACTGATAAGCTGAGTCTTTTAATAGAGAAAC
* * *
17715921 AACACATTTCAAGCATTCTCCTAGTGTACACGACGATTCATCAAAAACCCTAATTGTGTTTTCTA
196 AACACATTTCAAGCATTCTACTAGTGTACAAGACAATTCATCAAAAACCCTAATTGTGTTTTCTA
* * *
17715986 ACCAGAACTCGACTGTCTCTGGATCATCTTCAGTTATACCTCAGAATTCTTTAGCCCTATTCTTT
261 ACCAGAACTCGAATCTCTCTGGATCATCTTCAGTTATACCTCAGAATTCTTTAGCCCTATACTTT
17716051 AGC
326 AGC
* *
17716054 CCTCTTGTACTCAGCTACTGACATACGTCATTGCTTCAACTCAAGAAACTCTTTGCGTTTCTTAT
1 CCTCTTGTACTCAGCTACTGACATACATCATTGCTTCAACTCAAGAAACTCTTTGCATTTCTTAT
17716119 CTAGGAACCTCTGACTCACATATTTCTTTTTGAACTCTGTCTGGAAGAATTCCCAATTTACTTGA
66 CTAGGAACCTCTGACTCACATATTTCTTTTTGAACTCTGTCTGGAAGAATTCCCAATTTACTTGA
*
17716184 TCCCTCGGTACCACCGTGATCAACGTGTTCCACCACT-AGTAAGCTGAGTCTTTTAATAGAGAAA
131 TCCCTCGGTACCACCGTGATAAACGTGTTCCACCACTGA-TAAGCTGAGTCTTTTAATAGAGAAA
* ** * * *
17716248 CAACACATTTCAAGCATTCTACTGGTGTACAAGACAATTCATTGAAAACTCTATTTGTGTTTTTT
195 CAACACATTTCAAGCATTCTACTAGTGTACAAGACAATTCATCAAAAACCCTAATTGTGTTTTCT
*
17716313 AACCAGAACTCGAATCTCTCTGGATCATCTTTAGTTATACCTCAGAATTCTTTAGCCCTATACTT
260 AACCAGAACTCGAATCTCTCTGGATCATCTTCAGTTATACCTCAGAATTCTTTAGCCCTATACTT
17716378 T
325 T
17716379 CGAATTTTAT
Statistics
Matches: 301, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
327 1 0.00
328 300 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (328 bp):
CCTCTTGTACTCAGCTACTGACATACATCATTGCTTCAACTCAAGAAACTCTTTGCATTTCTTAT
CTAGGAACCTCTGACTCACATATTTCTTTTTGAACTCTGTCTGGAAGAATTCCCAATTTACTTGA
TCCCTCGGTACCACCGTGATAAACGTGTTCCACCACTGATAAGCTGAGTCTTTTAATAGAGAAAC
AACACATTTCAAGCATTCTACTAGTGTACAAGACAATTCATCAAAAACCCTAATTGTGTTTTCTA
ACCAGAACTCGAATCTCTCTGGATCATCTTCAGTTATACCTCAGAATTCTTTAGCCCTATACTTT
AGC
Found at i:17734595 original size:40 final size:40
Alignment explanation
Indices: 17734551--17734671 Score: 90
Period size: 40 Copynumber: 3.1 Consensus size: 40
17734541 TTGTGCATAG
17734551 CACTATTCGGGTAAACCAACGATATCAAATGTGTGCCCAA
1 CACTATTCGGGTAAACCAACGATATCAAATGTGTGCCCAA
* ** * * ** *
17734591 CACTAGTT-GGATTTACCAAC-A-AT-GAGT-TGCACCCAG
1 CACTA-TTCGGGTAAACCAACGATATCAAATGTGTGCCCAA
* * * *
17734627 CGCTAGTCGGGTAAATCGACGATATCAAATGTGTGCCCAA
1 CACTATTCGGGTAAACCAACGATATCAAATGTGTGCCCAA
17734667 CACTA
1 CACTA
17734672 GTTGGATGAA
Statistics
Matches: 54, Mismatches: 21, Indels: 12
0.62 0.24 0.14
Matches are distributed among these distances:
35 1 0.02
36 17 0.31
37 3 0.06
38 4 0.07
39 3 0.06
40 24 0.44
41 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (40 bp):
CACTATTCGGGTAAACCAACGATATCAAATGTGTGCCCAA
Found at i:17734702 original size:76 final size:76
Alignment explanation
Indices: 17734505--17734719 Score: 250
Period size: 76 Copynumber: 2.8 Consensus size: 76
17734495 TCGATGATCG
* * * * * ** * *
17734505 GTGTGCCCTACACTAGCTGGATAAACCGAGAATGAGTTGTGCATAGCACTATTCGGGTAAACCAA
1 GTGTGCCCAACACTAGTTGGATAAACCAAAAATGAGTTGCGCCCAGCGCTAGTCGGGTAAACCAA
17734570 CGATATCAAAT
66 CGATATCAAAT
** * * * *
17734581 GTGTGCCCAACACTAGTTGGATTTACCAACAATGAGTTGCACCCAGCGCTAGTCGGGTAAATCGA
1 GTGTGCCCAACACTAGTTGGATAAACCAAAAATGAGTTGCGCCCAGCGCTAGTCGGGTAAACCAA
17734646 CGATATCAAAT
66 CGATATCAAAT
* * * * *
17734657 GTGTGCCCAACACTAGTTGGATGAACCAAAAATGAATTGCGCCCAGTGCTAGTCTGATAAACC
1 GTGTGCCCAACACTAGTTGGATAAACCAAAAATGAGTTGCGCCCAGCGCTAGTCGGGTAAACC
17734720 GACAAGTAGA
Statistics
Matches: 116, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
76 116 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (76 bp):
GTGTGCCCAACACTAGTTGGATAAACCAAAAATGAGTTGCGCCCAGCGCTAGTCGGGTAAACCAA
CGATATCAAAT
Found at i:17734769 original size:15 final size:16
Alignment explanation
Indices: 17734732--17734769 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17734722 CAAGTAGATA
*
17734732 CATAATTATATCATTT
1 CATAATTATATCAATT
*
17734748 CACAATTAT-TCAATT
1 CATAATTATATCAATT
17734763 CATAATT
1 CATAATT
17734770 CTAATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (16 bp):
CATAATTATATCAATT
Found at i:17734837 original size:2 final size:2
Alignment explanation
Indices: 17734830--17734869 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
17734820 AACCATTTTC
*
17734830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17734870 TTCCATAGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17739455 original size:57 final size:58
Alignment explanation
Indices: 17739388--17739507 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 58
17739378 TCATTTTCTT
* * *
17739388 TTTTCTTTTTCATTTTAGAGAAAATCACATTCATTTCCAAATG-ATTCCATTTTTCCA
1 TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATGTATTCCATTTTTCCA
* * * * *
17739445 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCTAAATGTTTTTCATTTTTCCA
1 TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATGTATTCCATTTTTCCA
17739503 TTTTC
1 TTTTC
17739508 TCCATTTCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
57 37 0.69
58 17 0.31
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (58 bp):
TTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATGTATTCCATTTTTCCA
Found at i:17745000 original size:17 final size:18
Alignment explanation
Indices: 17744969--17745020 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
17744959 AGAAAATCCA
*
17744969 TTAATGTTTTATCTATATT
1 TTAAT-TTTTTTCTATATT
*
17744988 TT-ATTTTTTTCTACATT
1 TTAATTTTTTTCTATATT
17745005 TTAATTATTTTT-TATA
1 TTAATT-TTTTTCTATA
17745021 CCCTGCGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.46
18 8 0.29
19 7 0.25
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TTAATTTTTTTCTATATT
Found at i:17752045 original size:133 final size:133
Alignment explanation
Indices: 17751804--17752063 Score: 450
Period size: 133 Copynumber: 2.0 Consensus size: 133
17751794 CAAACTCTGA
*
17751804 TAACCCTCATGCAAAGCCTTATACTTACAACTTATTGTTCATATACCACATATAGACTCATTCTT
1 TAACCCTCATGCAAAGCCTTATACTTACAACTTATTGTTCATAGACCACATATAGACTCATTCTT
*
17751869 TCAAAACATCTAACATGCAGAGCTATAATACTTACCTAGAGATGGAATGATCACTAATTAAAACC
66 TCAAAACATCTAACATGCAGAGCTATAATACTTACCTAAAGATGGAATGATCACTAATTAAAACC
17751934 TAG
131 TAG
* * *
17751937 TAACCCTCATGCAGAGCCTTATACTTACAACTTGTTGTTCATAGACCACATATAGACTCATTTTT
1 TAACCCTCATGCAAAGCCTTATACTTACAACTTATTGTTCATAGACCACATATAGACTCATTCTT
*
17752002 TCAAAACATCTAACATGCAGAGCTGTAATACTTA-CTCAAAGATGGAATGATCACTAATTAAA
66 TCAAAACATCTAACATGCAGAGCTATAATACTTACCT-AAAGATGGAATGATCACTAATTAAA
17752064 CCAAGAATCC
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
132 2 0.02
133 118 0.98
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (133 bp):
TAACCCTCATGCAAAGCCTTATACTTACAACTTATTGTTCATAGACCACATATAGACTCATTCTT
TCAAAACATCTAACATGCAGAGCTATAATACTTACCTAAAGATGGAATGATCACTAATTAAAACC
TAG
Found at i:17771049 original size:3 final size:3
Alignment explanation
Indices: 17771041--17771085 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
17771031 AGAGTGTGTA
* *
17771041 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAC AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17771086 GTTTAGGGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:17772569 original size:14 final size:14
Alignment explanation
Indices: 17772550--17772579 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17772540 TGCATTCATC
17772550 TATGTCTATAAACA
1 TATGTCTATAAACA
*
17772564 TATGTCTATAGACA
1 TATGTCTATAAACA
17772578 TA
1 TA
17772580 GAGCAACGTT
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:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (14 bp):
TATGTCTATAAACA
Found at i:17776585 original size:39 final size:39
Alignment explanation
Indices: 17776542--17776616 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
17776532 GATGTTTTTC
* *
17776542 AGTATTGGGATATATGCTTG-AGTGTTATGTGATTATTTG
1 AGTATTGAGATATATGCTTGTA-TGTTAGGTGATTATTTG
17776581 AGTATTGAGATATATGCTTGTATGTTAGGTGATTAT
1 AGTATTGAGATATATGCTTGTATGTTAGGTGATTAT
17776617 ATGTGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.45
Consensus pattern (39 bp):
AGTATTGAGATATATGCTTGTATGTTAGGTGATTATTTG
Found at i:17778833 original size:42 final size:41
Alignment explanation
Indices: 17778787--17778897 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 41
17778777 TGTGGCTCAT
* *
17778787 ACACGCCCATGTCCTTGCCCGTGTGGCTCACACGGCTTGGGC
1 ACACGCCCATGTCCTTGCCCGTGTGGC-CACACGACCTGGGC
* * *
17778829 ACACGCCCATGTCCTTTCTCATGTGAGCCACACGACCTGGGC
1 ACACGCCCATGTCCTTGCCCGTGTG-GCCACACGACCTGGGC
* * * *
17778871 ACATGGCCATGTCCTTGGCCGTATGGC
1 ACACGCCCATGTCCTTGCCCGTGTGGC
17778898 ATCGACAGTC
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (41 bp):
ACACGCCCATGTCCTTGCCCGTGTGGCCACACGACCTGGGC
Found at i:17780946 original size:146 final size:146
Alignment explanation
Indices: 17780682--17780965 Score: 514
Period size: 146 Copynumber: 1.9 Consensus size: 146
17780672 CCATTGTAAC
17780682 CAGATTAAAGACATAGATTTAGCCAGACATAGATTATTATGCAGATTTTATTTCATTCTTAGGTT
1 CAGATTAAAGACATAGATTTAGCCAGACATAGATTATTATGCAGATTTTATTTCATTCTTAGGTT
*
17780747 TTACTTAGTTTATTTTATGTTCACTTAACCAGAGATTTCTATTTCGGCAGTAAGACAATTGTGAA
66 TTACTTAGTTTATTTTATGTTCACTTAACCAGAGATTTCTATTTCGACAGTAAGACAATTGTGAA
17780812 CGGAGATTTTATTATG
131 CGGAGATTTTATTATG
* * * *
17780828 CAGATTAAAGACATAGATTTAGCGAGACATGGATTATTATGCAGGTTTTCTTTCATTCTTAGGTT
1 CAGATTAAAGACATAGATTTAGCCAGACATAGATTATTATGCAGATTTTATTTCATTCTTAGGTT
*
17780893 TTACTTAGTTTATTTTATGTTCGCTTAACCAGAGATTTCTATTTCGACAGTAAGACAATTGTGAA
66 TTACTTAGTTTATTTTATGTTCACTTAACCAGAGATTTCTATTTCGACAGTAAGACAATTGTGAA
17780958 CGGAGATT
131 CGGAGATT
17780966 GTTCCAAATC
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 132 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.40
Consensus pattern (146 bp):
CAGATTAAAGACATAGATTTAGCCAGACATAGATTATTATGCAGATTTTATTTCATTCTTAGGTT
TTACTTAGTTTATTTTATGTTCACTTAACCAGAGATTTCTATTTCGACAGTAAGACAATTGTGAA
CGGAGATTTTATTATG
Found at i:17783129 original size:101 final size:102
Alignment explanation
Indices: 17783002--17783186 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
17782992 AAAGTGATGG
* *
17783002 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGAT-GGTCACATGTGTAGT
17783065 ACTATGTGCAAGCTACTATGCGTACCGGATAGCTTCAA
65 ACTATGTGCAAGCTACTATGCGTACCGGATAGCTTCAA
* * *
17783103 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
*
17783168 CTATGTGCAGGCTACTATG
66 CTATGTGCAAGCTACTATG
17783187 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAAGCTACTATGCGTACCGGATAGCTTCAA
Found at i:17783131 original size:51 final size:50
Alignment explanation
Indices: 17783002--17783186 Score: 169
Period size: 51 Copynumber: 3.7 Consensus size: 50
17782992 AAAGTGATGG
* * * * *
17783002 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATA-A
* *
17783052 TCGCATGTGTAGTACTATGTGCAAGCTACTATGCGTACCGGATAGCT-TCAA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-AA
* * *** * **
17783103 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATAA
17783154 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
17783187 TGAACCGGTA
Statistics
Matches: 108, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
50 37 0.34
51 68 0.63
52 2 0.02
53 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATAA
Found at i:17783194 original size:102 final size:101
Alignment explanation
Indices: 17783002--17783194 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
17782992 AAAGTGATGG
* *
17783002 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATGATAGGTCACATGTGTAGTAC
*
17783067 TATGTGCAAGCTACTATGCGTACCGGATAGCTTCAA
66 TATGTGCAAGCTACTATGCGAACCGGATAGCTTCAA
* * *
17783103 TCACGTGTGTAGTACTATGTGTAGGCTACTACATGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGA-A-TGATAGGTCACATGTGTAGT
* *
17783167 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTGCAAGCTACTATGCGAACCGG
17783195 TATCATTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 38 0.46
102 40 0.49
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAAGCTACTATGCGAACCGGATAGCTTCAA
Found at i:17783433 original size:16 final size:16
Alignment explanation
Indices: 17783412--17783443 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17783402 TGATTGAAAG
*
17783412 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
17783428 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
17783444 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:17788905 original size:20 final size:21
Alignment explanation
Indices: 17788871--17788910 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17788861 TAAATCTAAA
*
17788871 TTTTATTTTCCATTTGTTTAT
1 TTTTATTTTCCATTTATTTAT
*
17788892 TTTTATTTT-TATTTATTTA
1 TTTTATTTTCCATTTATTTA
17788911 AAGTCTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTATTTTCCATTTATTTAT
Found at i:17797803 original size:22 final size:21
Alignment explanation
Indices: 17797768--17797863 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 21
17797758 AAAGGGTCTC
* *
17797768 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
17797789 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
17797812 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
17797831 TATATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
17797850 TGCATATCATATCT
1 TACAAATCATATCT
17797864 ATATTATATC
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 34 0.54
21 4 0.06
22 15 0.24
23 10 0.16
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:17797811 original size:23 final size:22
Alignment explanation
Indices: 17797768--17797825 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
17797758 AAAGGGTCTC
* *
17797768 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
17797789 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
17797812 TGCATATCATATCT
1 TACAAATCATATCT
17797826 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:17797828 original size:19 final size:19
Alignment explanation
Indices: 17797804--17797906 Score: 132
Period size: 19 Copynumber: 5.8 Consensus size: 19
17797794 AATCATATCT
17797804 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
17797823 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
17797842 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
17797861 TCT---A-T--AT-T-ATA
1 TCTAAGATTGCATATCATA
17797872 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
17797891 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
17797907 CCTGAAGATT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
11 6 0.08
12 1 0.01
13 2 0.03
14 1 0.01
15 2 0.03
16 1 0.01
17 2 0.03
18 1 0.01
19 56 0.78
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:17797873 original size:30 final size:30
Alignment explanation
Indices: 17797833--17797894 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
17797823 TCTAAGATTA
17797833 TATATCATATCTAAGATTGCATATCATATC
1 TATATCATATCTAAGATTGCATATCATATC
*
17797863 TATATTATATCTAAGATTGCATATCATATC
1 TATATCATATCTAAGATTGCATATCATATC
17797893 TA
1 TA
17797895 AGATTGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (30 bp):
TATATCATATCTAAGATTGCATATCATATC
Found at i:17798456 original size:132 final size:132
Alignment explanation
Indices: 17798234--17799130 Score: 1467
Period size: 132 Copynumber: 6.8 Consensus size: 132
17798224 TAGGACTTAC
* * *
17798234 AATCTTCAACCTATTCCACTGCTGACCAGGG-AGATATG-ATTACTGGCTTCAATGTACTCCACT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAG-TA-GAATTACTGGCTTCAATGTACTCCACT
*
17798297 GTAACCACAGGGAGGTAAAATCCGCCAT-TTCCGATCTGCTCCACTACTTCTTAGGGAGATAAGA
64 GTAACCACAGGGAGGTAAAATCCGCCATCTT-CGATCTGCTCCACTACTGCTTAGGGAGATAAGA
17798361 TCTGA
128 TCTGA
* *
17798366 AATCTTCAATCTATTCCACTGTTATCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
** *
17798431 AACCACAGACAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGACCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
17798496 GA
131 GA
17798498 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
17798563 AACCACAAGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
17798628 GA
131 GA
* * *
17798630 AATCTGCAATCTATTCCATTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
17798695 AACCACAGGCAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTCAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
*
17798760 AA
131 GA
*
17798762 AATCCTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
17798827 AACCACAGGGAGGTAAAATCCTCCATCTTCGATTTGCTCCACTACTGCTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
17798892 GA
131 GA
* * * *
17798894 AATCTTCAATCTATTCCACTATTGCCCAGGGAAGTAGAATTACTGGCTTTAATGTACTCCACTAT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
*
17798959 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCT
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
17799024 GA
131 GA
* * * *
17799026 AATCCTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTTAATGTACTTCACTGT
1 AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
* *
17799091 AACCACATGGAGGTAAAATCTGCCATCTTCGATCTGCTCC
66 AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCC
17799131 GCTATCGATG
Statistics
Matches: 715, Mismatches: 47, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
131 1 0.00
132 710 0.99
133 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (132 bp):
AATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGT
AACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT
GA
Found at i:17798925 original size:44 final size:44
Alignment explanation
Indices: 17798349--17799057 Score: 102
Period size: 44 Copynumber: 16.1 Consensus size: 44
17798339 ACTACTTCTT
* * *
17798349 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTATCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * *
17798393 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTATAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTATTACC-C
** * * * ** * * * * **
17798437 AGACAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * **
17798481 AGGGAGATAAGACCTGAAATCTTCAATCTATTCCACTGTTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * *
17798525 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTATTACC-C
* * * ** * * * * **
17798569 AAGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * * **
17798613 AGGGAGATAAGATCTGAAATCTGCAATCTATTCCATTGTTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * *
17798657 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTATAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTATTACC-C
* * * * ** * * * * *
17798701 AGGCAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * * **
17798745 AGGGAGATAAGATCTAAAATCCTCAATCTATTCCACTGTTGTCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * *
17798789 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTATTACC-C
* * ** * * * * * **
17798833 AGGGAGGTAAAATCCT-CCATCTTCGATTTGCTCCACTACTGCTT
1 AGGGAGATAAGAT-CTGAAATCTTCAATCTACTCCACTATTACCC
* *
17798877 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTATTGCCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * *
17798921 AGGGA-AGT-AGAATTACTG---GCTTTAATGTACTCCACTATAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTATTACC-C
* * * ** * * * **
17798965 AGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTACTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
* * * *
17799009 AGGGAGATAAGATCTGAAATCCTCAATCTATTCCACTGTTGCCC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
17799053 AGGGA
1 AGGGA
17799058 AGTAGAATTA
Statistics
Matches: 443, Mismatches: 171, Indels: 102
0.62 0.24 0.14
Matches are distributed among these distances:
42 9 0.02
43 110 0.25
44 223 0.50
45 87 0.20
46 14 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTATTACCC
Found at i:17800402 original size:6 final size:6
Alignment explanation
Indices: 17800387--17800420 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
17800377 GGCCTCTCCA
17800387 TTTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
17800421 ATCACTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:17804660 original size:22 final size:22
Alignment explanation
Indices: 17804625--17804682 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
17804615 AAAGGGTCTC
* *
17804625 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
17804646 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
17804669 TGCATATCATATCT
1 TACAAATCATATCT
17804683 ATATTATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:17804710 original size:19 final size:19
Alignment explanation
Indices: 17804683--17804725 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
17804673 TATCATATCT
*
17804683 ATATTATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
17804702 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
17804721 ATATC
1 ATATC
17804726 CCTGAAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:17808906 original size:2 final size:2
Alignment explanation
Indices: 17808899--17808934 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
17808889 AGCGTTTTAA
17808899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17808935 TAAGCAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17809603 original size:13 final size:13
Alignment explanation
Indices: 17809585--17809609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17809575 TTTATTTGTC
17809585 ATTTATTTGTTTT
1 ATTTATTTGTTTT
17809598 ATTTATTTGTTT
1 ATTTATTTGTTT
17809610 ATTGTTAGTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
ATTTATTTGTTTT
Found at i:17809711 original size:36 final size:35
Alignment explanation
Indices: 17809650--17809728 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
17809640 ATTTTACATG
**
17809650 TTTTATAATATTATTTTTAAAAATTTTGCATA-TATT
1 TTTTA-AATATTATTTTTAAAAA-TTTAAATATTATT
* *
17809686 TTTTAAATTATTATTTTTTAGAATTTAAATATTATT
1 TTTTAAA-TATTATTTTTAAAAATTTAAATATTATT
17809722 TTTTAAA
1 TTTTAAA
17809729 AATTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
35 8 0.22
36 29 0.78
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (35 bp):
TTTTAAATATTATTTTTAAAAATTTAAATATTATT
Found at i:17809717 original size:57 final size:56
Alignment explanation
Indices: 17809651--17809758 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 56
17809641 TTTTACATGT
** *
17809651 TTTATAATATTA-TTTTTAAAAATTTTGCATATATTTTTTAAATTATTATTTTTTAGAA
1 TTTATAATATTATTTTTTAAAAA-TTTAAATATAATTTTTAAA--ATTATTTTTTAGAA
17809709 TTTA-AATATTATTTTTTAAAAATTTAAATATAATTTTTAAAATTATTTTT
1 TTTATAATATTATTTTTTAAAAATTTAAATATAATTTTTAAAATTATTTTT
17809759 AAAGATATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 9 0.20
57 23 0.50
58 14 0.30
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (56 bp):
TTTATAATATTATTTTTTAAAAATTTAAATATAATTTTTAAAATTATTTTTTAGAA
Found at i:17809720 original size:21 final size:22
Alignment explanation
Indices: 17809687--17809750 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 22
17809677 GCATATATTT
*
17809687 TTTAAATTATTATTTTTT-AGAA
1 TTTAAA-TATTATTTTTTAAAAA
17809709 TTTAAATATTATTTTTTAAAAA
1 TTTAAATATTATTTTTTAAAAA
*
17809731 TTTAAATA-TAATTTTTAAAA
1 TTTAAATATTATTTTTTAAAA
17809751 TTATTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 22 0.56
22 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTAAATATTATTTTTTAAAAA
Found at i:17815404 original size:17 final size:18
Alignment explanation
Indices: 17815367--17815408 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
17815357 ATGCTATAAT
17815367 TTTTTAACAAATAAATCC
1 TTTTTAACAAATAAATCC
* *
17815385 TTTTTAATAAATAAATCT
1 TTTTTAACAAATAAATCC
17815403 TTTTTA
1 TTTTTA
17815409 TTTTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTTAACAAATAAATCC
Found at i:17815764 original size:23 final size:23
Alignment explanation
Indices: 17815724--17815809 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
17815714 CAAATAAATA
* **
17815724 AAATATTATTTTTTAAAAATTTT
1 AAATATAATTTTAAAAAAATTTT
17815747 AAATATAATTTTAAAAAACA-TTT
1 AAATATAATTTTAAAAAA-ATTTT
* * *
17815770 GAATAT--CTTTAAAAAAATTTC
1 AAATATAATTTTAAAAAAATTTT
17815791 AAA-ATAATAATTTAAAAAA
1 AAATATAAT--TTTAAAAAA
17815810 TTATATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
20 3 0.06
21 13 0.27
23 23 0.47
24 10 0.20
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATATAATTTTAAAAAAATTTT
Found at i:17815844 original size:21 final size:21
Alignment explanation
Indices: 17815797--17815845 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
17815787 TTTCAAAATA
*
17815797 ATAATTTAAAAAATTATATTT
1 ATAATTTAAAAAAGTATATTT
* *
17815818 AAAATTTAAAAAAGTATTTTT
1 ATAATTTAAAAAAGTATATTT
*
17815839 TTAATTT
1 ATAATTT
17815846 TTAAAATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAATTTAAAAAAGTATATTT
Found at i:17815983 original size:22 final size:21
Alignment explanation
Indices: 17815938--17816018 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
17815928 TTATAATATT
* *
17815938 AAAAATTAGATTT-AATATTTA
1 AAAAATAATATTTAAAT-TTTA
17815959 AAAAATAATATTTAAATTTTA
1 AAAAATAATATTTAAATTTTA
17815980 AAAAA-ATATATTTAAGATTTTA
1 AAAAATA-ATATTTAA-ATTTTA
*
17816002 AATAATAATATTATAAA
1 AAAAATAATATT-TAAA
17816019 ACATTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.02
21 28 0.54
22 19 0.37
23 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAATAATATTTAAATTTTA
Found at i:17816093 original size:16 final size:16
Alignment explanation
Indices: 17816074--17816104 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17816064 AAAAAGTAAA
*
17816074 TAAAGAAAAACAAAAT
1 TAAAAAAAAACAAAAT
17816090 TAAAAAAAAACAAAA
1 TAAAAAAAAACAAAA
17816105 AAGGACAAAG
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:0.81, C:0.06, G:0.03, T:0.10
Consensus pattern (16 bp):
TAAAAAAAAACAAAAT
Found at i:17820628 original size:19 final size:19
Alignment explanation
Indices: 17820604--17820644 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17820594 TTATTAATAA
*
17820604 ATTTATTGTTACTATTATT
1 ATTTATTATTACTATTATT
**
17820623 ATTTATTATTGGTATTATT
1 ATTTATTATTACTATTATT
17820642 ATT
1 ATT
17820645 ACACTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTTATTATTACTATTATT
Found at i:17820696 original size:9 final size:9
Alignment explanation
Indices: 17820677--17820710 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
17820667 TCTCTTATTA
17820677 TTATGTTTTT
1 TTAT-TTTTT
17820687 TTATTTTTT
1 TTATTTTTT
17820696 TTATTTTTT
1 TTATTTTTT
17820705 TATATT
1 T-TATT
17820711 ATATTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (9 bp):
TTATTTTTT
Found at i:17825618 original size:17 final size:17
Alignment explanation
Indices: 17825596--17825653 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
17825586 GGGTTCAGAT
17825596 TCAAAAAAAAATCAAAA
1 TCAAAAAAAAATCAAAA
*
17825613 TC--AAAATAA--AAAA
1 TCAAAAAAAAATCAAAA
*
17825626 -CAAAAAAAAATCAAAG
1 TCAAAAAAAAATCAAAA
17825642 TCAAAAGAAAAA
1 TCAAAA-AAAAA
17825654 AAGAGAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 11
0.70 0.07 0.24
Matches are distributed among these distances:
12 1 0.03
13 4 0.12
14 6 0.19
15 6 0.19
16 3 0.09
17 7 0.22
18 5 0.16
ACGTcount: A:0.76, C:0.10, G:0.03, T:0.10
Consensus pattern (17 bp):
TCAAAAAAAAATCAAAA
Found at i:17825624 original size:12 final size:12
Alignment explanation
Indices: 17825603--17825640 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17825593 GATTCAAAAA
*
17825603 AAAATCAAAATC
1 AAAATAAAAATC
*
17825615 AAAATAAAAAAC
1 AAAATAAAAATC
17825627 AAAA-AAAAATC
1 AAAATAAAAATC
17825638 AAA
1 AAA
17825641 GTCAAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:17825634 original size:30 final size:29
Alignment explanation
Indices: 17825598--17825681 Score: 105
Period size: 30 Copynumber: 2.9 Consensus size: 29
17825588 GTTCAGATTC
* *
17825598 AAAAAAAAATCAAAATCAAAATAAAAAAC
1 AAAAAAAAATCAAAGTCAAAATAAAAAAG
*
17825627 AAAAAAAAATCAAAGTCAAAAGAAAAAAAG
1 AAAAAAAAATCAAAGTCAAAA-TAAAAAAG
* * *
17825657 AGAAATAAATTAAAGTCAAAATAAA
1 AAAAAAAAATCAAAGTCAAAATAAA
17825682 GATATGAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.49
30 24 0.51
ACGTcount: A:0.75, C:0.07, G:0.06, T:0.12
Consensus pattern (29 bp):
AAAAAAAAATCAAAGTCAAAATAAAAAAG
Found at i:17825639 original size:29 final size:29
Alignment explanation
Indices: 17825597--17825681 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
17825587 GGTTCAGATT
*
17825597 CAAAAAAAAATCAAAATCAAAATAAAAAA
1 CAAAAAAAAATCAAAGTCAAAATAAAAAA
*
17825626 CAAAAAAAAATCAAAGTCAAAAGAAAAAA
1 CAAAAAAAAATCAAAGTCAAAATAAAAAA
* *
17825655 -AGAGAAATAAATTAAAGTCAAAATAAA
1 CA-A-AAAAAAATCAAAGTCAAAATAAA
17825682 GATATGAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 1 0.02
29 28 0.57
30 20 0.41
ACGTcount: A:0.74, C:0.08, G:0.06, T:0.12
Consensus pattern (29 bp):
CAAAAAAAAATCAAAGTCAAAATAAAAAA
Done.