Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 71 of 199
Found at i:19974539 original size:33 final size:34
Alignment explanation
Indices: 19974480--19974549 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
19974470 TAAGGCCCAC
* *
19974480 ACTGTTACTGTATCGATCTAAGGCCTACACTG-T
1 ACTGTTACTGTATAGAGCTAAGGCCTACACTGAT
* *
19974513 ACTGTTACTGTATAGGGCTCAA-GCCTAGACTGAT
1 ACTGTTACTGTATAGAGCT-AAGGCCTACACTGAT
19974547 ACT
1 ACT
19974550 ACATGTTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (34 bp):
ACTGTTACTGTATAGAGCTAAGGCCTACACTGAT
Found at i:19978621 original size:7 final size:7
Alignment explanation
Indices: 19978609--19978646 Score: 55
Period size: 6 Copynumber: 5.9 Consensus size: 7
19978599 TTCAAATGGA
19978609 TCATTTC
1 TCATTTC
19978616 TCATTTC
1 TCATTTC
19978623 TCATTT-
1 TCATTTC
19978629 TCATTTC
1 TCATTTC
19978636 -CATTTC
1 TCATTTC
19978642 -CATTT
1 TCATTT
19978647 TTTTTATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (7 bp):
TCATTTC
Found at i:19978649 original size:20 final size:20
Alignment explanation
Indices: 19978609--19978647 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19978599 TTCAAATGGA
19978609 TCATTTCTCATTTCTCATTT
1 TCATTTCTCATTTCTCATTT
19978629 TCATTTC-CATTTC-CATTT
1 TCATTTCTCATTTCTCATTT
19978647 T
1 T
19978648 TTTTATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (20 bp):
TCATTTCTCATTTCTCATTT
Found at i:19979973 original size:27 final size:27
Alignment explanation
Indices: 19979942--19980002 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
19979932 CATATTAGCT
19979942 AGATAGTTCC-GACGGACTTCCCACATA
1 AGATAGTTCCTG-CGGACTTCCCACATA
*
19979969 AGATAG-TCCTTGCGGACTTCCCACATT
1 AGATAGTTCC-TGCGGACTTCCCACATA
19979996 AGATAGT
1 AGATAGT
19980003 CTTGATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 26 0.87
28 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (27 bp):
AGATAGTTCCTGCGGACTTCCCACATA
Found at i:19980000 original size:54 final size:53
Alignment explanation
Indices: 19979941--19980044 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 53
19979931 TCATATTAGC
19979941 TAGATAGT-TCCGACGG-ACTTCCCACATAAGATAGTCCTTGCGGACTTCCCACAT
1 TAGATAGTCT-CGACGGAACTTCCC-CATAAGATAGTCCTTGCGGAC-TCCCACAT
* * * * *
19979995 TAGATAGTCTTGATGGAATTTCCCCATTAGATAGTCCTTGTGGACTCCCA
1 TAGATAGTCTCGACGGAACTTCCCCATAAGATAGTCCTTGCGGACTCCCA
19980045 TAATAGATGG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
53 5 0.12
54 31 0.72
55 7 0.16
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (53 bp):
TAGATAGTCTCGACGGAACTTCCCCATAAGATAGTCCTTGCGGACTCCCACAT
Found at i:19980003 original size:27 final size:27
Alignment explanation
Indices: 19979954--19980229 Score: 154
Period size: 27 Copynumber: 10.3 Consensus size: 27
19979944 ATAGTTCCGA
*
19979954 CGGACTTCCCACATAAGATAGTCCTTG
1 CGGACTTCCCACATTAGATAGTCCTTG
19979981 CGGACTTCCCACATTAGATAGT-CTTG
1 CGGACTTCCCACATTAGATAGTCCTTG
* *
19980007 ATGGAATTTCCC-CATTAGATAGTCCTTG
1 -CGG-ACTTCCCACATTAGATAGTCCTTG
* * * * *
19980035 TGGAC-TCCCATAATAGATGGTCATT-
1 CGGACTTCCCACATTAGATAGTCCTTG
** * * * *
19980060 ATGAATTTCCACAATAGATAGTTCTTG
1 CGGACTTCCCACATTAGATAGTCCTTG
* * * *
19980087 CAGA-TTTCCACAATAGATAGTCCCTG
1 CGGACTTCCCACATTAGATAGTCCTTG
*
19980113 TGGACTTCCCACATAATAGAT-GATCCTTG
1 CGGACTTCCCACAT--TAGATAG-TCCTTG
* *
19980142 CAGACTTCCCACATAAGATAGT-CTTG
1 CGGACTTCCCACATTAGATAGTCCTTG
* * ** * *
19980168 ACAGACTTTCTTCAATGGATAGTCCTTG
1 -CGGACTTCCCACATTAGATAGTCCTTG
* * * *
19980196 CGGGCTTCTCATATAAGATAGTCC-TG
1 CGGACTTCCCACATTAGATAGTCCTTG
19980222 ACGGACTT
1 -CGGACTT
19980230 TCCATATATA
Statistics
Matches: 190, Mismatches: 45, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
25 6 0.03
26 59 0.31
27 87 0.46
28 16 0.08
29 22 0.12
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (27 bp):
CGGACTTCCCACATTAGATAGTCCTTG
Found at i:19980034 original size:28 final size:28
Alignment explanation
Indices: 19979957--19980164 Score: 125
Period size: 26 Copynumber: 7.7 Consensus size: 28
19979947 GTTCCGACGG
* *
19979957 ACTTCCCACATAAGATAGTCCTTGCGG-
1 ACTTCCCACATTAGATAGTCCTTGTGGA
19979984 ACTTCCCACATTAGATAGT-CTTGATGGA
1 ACTTCCCACATTAGATAGTCCTTG-TGGA
*
19980012 ATTTCCC-CATTAGATAGTCCTTGTGG-
1 ACTTCCCACATTAGATAGTCCTTGTGGA
* * * * *
19980038 AC-TCCCATAATAGATGGTCATTAT-GA
1 ACTTCCCACATTAGATAGTCCTTGTGGA
* * * **
19980064 A-TTTCCACAATAGATAGTTCTTGCAG-
1 ACTTCCCACATTAGATAGTCCTTGTGGA
* * *
19980090 A-TTTCCACAATAGATAGTCCCTGTGG-
1 ACTTCCCACATTAGATAGTCCTTGTGGA
**
19980116 ACTTCCCACATAATAGAT-GATCCTTGCAG-
1 ACTTCCCACAT--TAGATAG-TCCTTGTGGA
*
19980145 ACTTCCCACATAAGATAGTC
1 ACTTCCCACATTAGATAGTC
19980165 TTGACAGACT
Statistics
Matches: 143, Mismatches: 26, Indels: 24
0.74 0.13 0.12
Matches are distributed among these distances:
25 5 0.03
26 56 0.39
27 48 0.34
28 12 0.08
29 22 0.15
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (28 bp):
ACTTCCCACATTAGATAGTCCTTGTGGA
Found at i:19980102 original size:52 final size:53
Alignment explanation
Indices: 19979969--19980198 Score: 173
Period size: 52 Copynumber: 4.3 Consensus size: 53
19979959 TTCCCACATA
* * *
19979969 AGATAGTCCTTGCGGACTTCCCACATTAGATAGTCTTGATGGAATTTCCCCATT
1 AGATAGTCCTTGCGGA-TTCCCACAATAGATAGTCTTGATGGAATTTCCACAAT
* * * *
19980023 AGATAGTCCTTGTGGACTCCCATAATAGATGGTCATT-AT-GAATTTCCACAAT
1 AGATAGTCCTTGCGGATTCCCACAATAGATAGTC-TTGATGGAATTTCCACAAT
* * * * * *
19980075 AGATAGTTCTTGCAGATTTCCACAATAGATAGTCCCTG-TGGACTTCCCACATAAT
1 AGATAGTCCTTGCGGATTCCCACAATAGATAGT-CTTGATGGAATTTCCAC--AAT
* ** * **
19980130 AGAT-GATCCTTGCAGACTTCCCAC-ATAAGATAGTCTTGACAGACTTTCTTCAAT
1 AGATAG-TCCTTGCGGA-TTCCCACAAT-AGATAGTCTTGATGGAATTTCCACAAT
*
19980184 GGATAGTCCTTGCGG
1 AGATAGTCCTTGCGG
19980199 GCTTCTCATA
Statistics
Matches: 138, Mismatches: 27, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
52 39 0.28
53 25 0.18
54 32 0.23
55 22 0.16
56 20 0.14
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (53 bp):
AGATAGTCCTTGCGGATTCCCACAATAGATAGTCTTGATGGAATTTCCACAAT
Found at i:19990250 original size:17 final size:17
Alignment explanation
Indices: 19990223--19990262 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
19990213 TAAGTTACTC
19990223 TTTTAAGAATACAATATA
1 TTTT-AGAATACAATATA
19990241 TTTTAGAATACAATATA
1 TTTTAGAATACAATATA
19990258 TTTTA
1 TTTTA
19990263 CCATTGTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
TTTTAGAATACAATATA
Found at i:19995732 original size:40 final size:41
Alignment explanation
Indices: 19995659--19995750 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 41
19995649 ACCTGAACAT
* *
19995659 CAGGCTTTGTGCCGGTGTTATTTATCAGGCTTTGTGCCTAG
1 CAGGCTTTGTGCCAGTGTTATTTATCAAGCTTTGTGCCTAG
* *
19995700 CAGGCTTTGTGCCATTG-TGTTTATCAAGCTTTGTGCCTAG
1 CAGGCTTTGTGCCAGTGTTATTTATCAAGCTTTGTGCCTAG
* *
19995740 CATGCCTTGTG
1 CAGGCTTTGTG
19995751 TCGATGTTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 30 0.67
41 15 0.33
ACGTcount: A:0.13, C:0.21, G:0.27, T:0.39
Consensus pattern (41 bp):
CAGGCTTTGTGCCAGTGTTATTTATCAAGCTTTGTGCCTAG
Found at i:19995984 original size:110 final size:109
Alignment explanation
Indices: 19995786--19995996 Score: 280
Period size: 110 Copynumber: 1.9 Consensus size: 109
19995776 CTGGTGATCA
* * * * *
19995786 TTTATCAGGTACTACGTATCGGTGATATAGACCGTAGCGATGGCTGAGATCCTGCATCTGTTGCA
1 TTTAACAGGTACTACGTATCGGTGATACAGACCGTAACGATGGCTAAGATCCTACATCTGTTGCA
19995851 GATTCTCTACAGCCTGTGTGAGCAACA-CTGTGAGCCAATGGTTT
66 GATTCTCTACAGCCTGTGTGAGCAACATC-GTGAGCCAATGGTTT
** * *
19995895 TTTAACAGGTACTGTGTATCGGTGATACAGGCCGTAACGATGGCTTAAGATCTTACATCTGTTGC
1 TTTAACAGGTACTACGTATCGGTGATACAGACCGTAACGATGGC-TAAGATCCTACATCTGTTGC
* ** *
19995960 GGATTCTCTGTAGCTTGTGTGAGCAACATCGTGAGCC
65 AGATTCTCTACAGCCTGTGTGAGCAACATCGTGAGCC
19995997 GATCAAAGTT
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
109 38 0.44
110 48 0.55
111 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (109 bp):
TTTAACAGGTACTACGTATCGGTGATACAGACCGTAACGATGGCTAAGATCCTACATCTGTTGCA
GATTCTCTACAGCCTGTGTGAGCAACATCGTGAGCCAATGGTTT
Found at i:19998775 original size:13 final size:14
Alignment explanation
Indices: 19998737--19998778 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
19998727 TATGTGAAGA
19998737 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
19998752 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
19998767 -TATTATTAAAAT
1 ATATTATTAAAAT
19998779 AAAATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:19998876 original size:10 final size:10
Alignment explanation
Indices: 19998863--19998888 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19998853 AAATATAATA
19998863 TTTAAATATT
1 TTTAAATATT
19998873 TTTAAATATT
1 TTTAAATATT
19998883 TTTAAA
1 TTTAAA
19998889 AATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTAAATATT
Found at i:19999129 original size:14 final size:14
Alignment explanation
Indices: 19999110--19999136 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19999100 CAGAAAAATA
19999110 CATAAAACCTTTTC
1 CATAAAACCTTTTC
19999124 CATAAAACCTTTT
1 CATAAAACCTTTT
19999137 ACATGTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.37
Consensus pattern (14 bp):
CATAAAACCTTTTC
Found at i:20002009 original size:9 final size:9
Alignment explanation
Indices: 20001985--20002028 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
20001975 CGAACAAGAC
*
20001985 TTGAGAAAA
1 TTGAGAGAA
20001994 TTGAGAGAA
1 TTGAGAGAA
*
20002003 TTGAGAG-T
1 TTGAGAGAA
20002011 TTAGAGAGAA
1 TT-GAGAGAA
20002021 TTGAGAGA
1 TTGAGAGA
20002029 GTTGGATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 2 0.07
9 26 0.87
10 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:20006516 original size:11 final size:11
Alignment explanation
Indices: 20006496--20006617 Score: 75
Period size: 11 Copynumber: 11.6 Consensus size: 11
20006486 ACAAAAATTA
20006496 AAAAAGTATTTT
1 AAAAA-TATTTT
20006508 AAAAATATTTT
1 AAAAATATTTT
20006519 --AAA-A--TT
1 AAAAATATTTT
* *
20006525 AAAAAAAATTT
1 AAAAATATTTT
*
20006536 AAAAAGCATTTT
1 AAAAA-TATTTT
* *
20006548 AAAAAAAATTT
1 AAAAATATTTT
20006559 AAAAATATTTT
1 AAAAATATTTT
20006570 --AAA-A-TTT
1 AAAAATATTTT
*
20006577 AAAAA-ATTTCA
1 AAAAATATTT-T
20006588 AAAAAGTATTTT
1 AAAAA-TATTTT
*
20006600 AAAAGTATTTT
1 AAAAATATTTT
20006611 AAAAATA
1 AAAAATA
20006618 AAAAAATAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 5 0.06
9 11 0.12
10 2 0.02
11 43 0.49
12 18 0.20
13 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:20006528 original size:17 final size:17
Alignment explanation
Indices: 20006506--20006539 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20006496 AAAAAGTATT
* *
20006506 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
20006523 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
20006540 AGCATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:20006534 original size:52 final size:51
Alignment explanation
Indices: 20006476--20006617 Score: 153
Period size: 51 Copynumber: 2.7 Consensus size: 51
20006466 AATTTATTTT
*
20006476 AAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAA-AAATATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* * * *
20006528 AAAAATTTAAAAAGCATTTTAAAAAA--AATTTAAAAATATTTTAAAATTTAA
1 AAAAA-TTAAAAA-AATATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* * **
20006579 AAAATTTCAAAAAAGTATTTTAAAAGTATTTTAAAAATA
1 AAAAATT-AAAAAAATATTAAAAAAGTATTTTAAAAATA
20006618 AAAAAATAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
50 9 0.12
51 32 0.44
52 17 0.23
53 15 0.21
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (51 bp):
AAAAATTAAAAAAATATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:20006553 original size:23 final size:22
Alignment explanation
Indices: 20006523--20006573 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
20006513 TATTTTAAAA
20006523 TTAAAAAAAATTTAAAAAGCATT
1 TTAAAAAAAATTTAAAAA-CATT
*
20006546 TTAAAAAAAATTTAAAAATATT
1 TTAAAAAAAATTTAAAAACATT
20006568 TTAAAA
1 TTAAAA
20006574 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAAAAAATTTAAAAACATT
Found at i:20006553 original size:41 final size:40
Alignment explanation
Indices: 20006470--20006603 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 40
20006460 ACCAAAAATT
*
20006470 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTT-AAAAA
1 TATTTT-AAAATT-AAA-AAAAATTTAAAAAG-ATTTTAAAAAA
20006513 TATTTTAAAATTAAAAAAAATTTAAAAAGCATTTTAAAAAA
1 TATTTTAAAATTAAAAAAAATTTAAAAAG-ATTTTAAAAAA
* * *** *
20006554 -AATTTAAAAATATTTTAAAATTTAAAAA-ATTTCAAAAAA
1 TATTTTAAAATTA-AAAAAAATTTAAAAAGATTTTAAAAAA
20006593 GTATTTTAAAA
1 -TATTTTAAAA
20006604 GTATTTTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
39 10 0.13
40 28 0.36
41 28 0.36
42 6 0.08
43 6 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTTAAAAAGATTTTAAAAAA
Found at i:20006564 original size:51 final size:51
Alignment explanation
Indices: 20006505--20006617 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 51
20006495 AAAAAAGTAT
20006505 TTTAAAAATATTTTAAAATTAAAAAAAATTT-AAAAAGCATTTTAAAAAAAA
1 TTTAAAAATATTTTAAAATT-AAAAAAATTTAAAAAAGCATTTTAAAAAAAA
* * ** *
20006556 TTTAAAAATATTTTAAAATTTAAAAAATTTCAAAAAAGTATTTTAAAAGTAT
1 TTTAAAAATATTTTAAAATTAAAAAAATTT-AAAAAAGCATTTTAAAAAAAA
20006608 TTTAAAAATA
1 TTTAAAAATA
20006618 AAAAAATAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 9 0.16
51 20 0.36
52 26 0.47
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (51 bp):
TTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAGCATTTTAAAAAAAA
Found at i:20006575 original size:18 final size:17
Alignment explanation
Indices: 20006552--20006590 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
20006542 CATTTTAAAA
*
20006552 AAAATTTAAAAATATTTT
1 AAAATTTAAAAA-ATTTC
20006570 AAAATTTAAAAAATTTC
1 AAAATTTAAAAAATTTC
20006587 AAAA
1 AAAA
20006591 AAGTATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTTAAAAAATTTC
Found at i:20006931 original size:27 final size:26
Alignment explanation
Indices: 20006829--20006977 Score: 88
Period size: 28 Copynumber: 5.5 Consensus size: 26
20006819 ACATGTGGAA
* *
20006829 AAAAATGATAAAAA-ATAAAAATCAAT
1 AAAAATTATAAAAATATAAAAAT-TAT
* * * **
20006855 AAAATTTATAAAATTATTATATTTTAAT
1 AAAAATTATAAAAATA-TAAAAATT-AT
** *
20006883 AAAAAACATAAAAATATTTAAAAACTAT
1 AAAAATTATAAAAATA--TAAAAATTAT
20006911 AAAAATTATAAAAATCATAAAAAAATTAT
1 AAAAATTATAAAAAT-AT--AAAAATTAT
*
20006940 AAAAATGTA-AAGAAATATAAAATTTAT
1 AAAAAT-TATAA-AAATATAAAAATTAT
20006967 AAAAA-TATAAA
1 AAAAATTATAAA
20006978 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 19, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
25 3 0.03
26 13 0.14
27 15 0.16
28 33 0.35
29 24 0.26
30 6 0.06
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAATTATAAAAATATAAAAATTAT
Found at i:20006943 original size:9 final size:9
Alignment explanation
Indices: 20006829--20006977 Score: 76
Period size: 9 Copynumber: 16.3 Consensus size: 9
20006819 ACATGTGGAA
*
20006829 AAAAATGAT
1 AAAAATTAT
20006838 AAAAA--AT
1 AAAAATTAT
*
20006845 AAAAATCAAT
1 AAAAAT-TAT
*
20006855 AAAATTTAT
1 AAAAATTAT
20006864 -AAAATTATT
1 AAAAATTA-T
* **
20006873 ATATTTTAAT
1 AAAAATT-AT
**
20006883 AAAAAACAT
1 AAAAATTAT
*
20006892 AAAAATATTT
1 AAAAAT-TAT
*
20006902 AAAAACTAT
1 AAAAATTAT
20006911 AAAAATTAT
1 AAAAATTAT
*
20006920 AAAAATCATAA
1 AAAAAT--TAT
20006931 AAAAATTAT
1 AAAAATTAT
20006940 AAAAATGTA-
1 AAAAAT-TAT
20006949 AAGAAA-TAT
1 AA-AAATTAT
*
20006958 AAAATTTAT
1 AAAAATTAT
20006967 AAAAA-TAT
1 AAAAATTAT
20006975 AAA
1 AAA
20006978 TTTATTGTAC
Statistics
Matches: 106, Mismatches: 21, Indels: 27
0.69 0.14 0.18
Matches are distributed among these distances:
7 7 0.07
8 16 0.15
9 50 0.47
10 24 0.23
11 9 0.08
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20006962 original size:37 final size:36
Alignment explanation
Indices: 20006880--20006971 Score: 89
Period size: 37 Copynumber: 2.5 Consensus size: 36
20006870 ATTATATTTT
* *
20006880 AATA-AAAAACATAAAAATATTTAAAAACTATAAAA
1 AATATAAAATCATAAAAAAATTTAAAAACTATAAAA
* *
20006915 ATTATAAAAATCATAAAAAAATTATAAAAA-TGTAAAGA
1 AATAT-AAAATCATAAAAAAATT-TAAAAACTATAAA-A
*
20006953 AATATAAAATTTATAAAAA
1 AATATAAAA-TCATAAAAA
20006972 TATAAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
35 3 0.07
37 24 0.52
38 19 0.41
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.26
Consensus pattern (36 bp):
AATATAAAATCATAAAAAAATTTAAAAACTATAAAA
Found at i:20018155 original size:15 final size:15
Alignment explanation
Indices: 20018135--20018166 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20018125 TATTCATACA
*
20018135 AAATATGAAAGACAT
1 AAATATAAAAGACAT
20018150 AAATATAAAAGACAT
1 AAATATAAAAGACAT
20018165 AA
1 AA
20018167 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:20022386 original size:5 final size:5
Alignment explanation
Indices: 20022374--20022411 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
20022364 AAAAGTTAAG
*
20022374 TATA- TATAT TATA- TATAT TATAT TATAT AATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
20022412 AATAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:20022453 original size:13 final size:13
Alignment explanation
Indices: 20022437--20022461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20022427 GAAATAAAAG
20022437 ATAGAAACAGAGA
1 ATAGAAACAGAGA
20022450 ATAGAAACAGAG
1 ATAGAAACAGAG
20022462 GGCAAAACAA
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:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (13 bp):
ATAGAAACAGAGA
Found at i:20033297 original size:16 final size:16
Alignment explanation
Indices: 20033278--20033321 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
20033268 TATAAATATC
20033278 AAATAATTCAAACTTA
1 AAATAATTCAAACTTA
* * *
20033294 AAATAAGTAAAACTTG
1 AAATAATTCAAACTTA
*
20033310 AAATGATTCAAA
1 AAATAATTCAAA
20033322 TTCTTAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (16 bp):
AAATAATTCAAACTTA
Found at i:20036255 original size:18 final size:19
Alignment explanation
Indices: 20036222--20036259 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
20036212 AGACTCCAGG
*
20036222 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
20036241 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
20036259 T
1 T
20036260 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:20045236 original size:34 final size:34
Alignment explanation
Indices: 20045193--20045261 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20045183 GATTTGACTT
20045193 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
1 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
20045227 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
1 TTCACTAAATGAGTAAACAAACAAGAGTACAATA
20045261 T
1 T
20045262 GAAGAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.22
Consensus pattern (34 bp):
TTCACTAAATGAGTAAACAAACAAGAGTACAATA
Found at i:20048618 original size:11 final size:11
Alignment explanation
Indices: 20048602--20048632 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20048592 AAGTATGGGT
20048602 AGGTATGGGAA
1 AGGTATGGGAA
*
20048613 AGGTATGGGCA
1 AGGTATGGGAA
20048624 AGGTATGGG
1 AGGTATGGG
20048633 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:20052709 original size:18 final size:18
Alignment explanation
Indices: 20052686--20052778 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
20052676 CCCAACTACT
*
20052686 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
20052704 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
20052722 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
20052740 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
20052758 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
20052776 GTA
1 GTA
20052779 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:20052738 original size:36 final size:36
Alignment explanation
Indices: 20052686--20052778 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
20052676 CCCAACTACT
*
20052686 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
20052722 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
20052758 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
20052779 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:20065967 original size:10 final size:9
Alignment explanation
Indices: 20065954--20066072 Score: 89
Period size: 10 Copynumber: 12.6 Consensus size: 9
20065944 TTTTTAATAC
20065954 TTTATAATAT
1 TTTATAAT-T
*
20065964 TTTAAAATT
1 TTTATAATT
*
20065973 TTAATAATT
1 TTTATAATT
*
20065982 TATTAGAATT
1 T-TTATAATT
20065992 TTTATAAGTT
1 TTTATAA-TT
20066002 TTTATGAATT
1 TTTAT-AATT
*
20066012 TTTATATTTT
1 TTTATA-ATT
20066022 TTTATAA-T
1 TTTATAATT
**
20066030 TTTATTGTT
1 TTTATAATT
*
20066039 CTTATAATTTT
1 TTTATAA--TT
20066050 TTTATAATT
1 TTTATAATT
20066059 TATTAT-ATT
1 T-TTATAATT
20066068 TTTAT
1 TTTAT
20066073 GAGTTTCTAT
Statistics
Matches: 87, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
8 10 0.11
9 27 0.31
10 40 0.46
11 10 0.11
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:20066013 original size:19 final size:19
Alignment explanation
Indices: 20065954--20066032 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
20065944 TTTTTAATAC
*
20065954 TTTATAATATTTTA-AAATT
1 TTTATAAT-TTTTATGAATT
*
20065973 TTAATAATTTATTA-GAATT
1 TTTATAATTT-TTATGAATT
20065992 TTTATAAGTTTTTATGAATT
1 TTTATAA-TTTTTATGAATT
*
20066012 TTTATATTTTTTTAT-AATT
1 TTTATA-ATTTTTATGAATT
20066031 TT
1 TT
20066033 ATTGTTCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.04
19 29 0.56
20 21 0.40
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTATAATTTTTATGAATT
Found at i:20066031 original size:39 final size:39
Alignment explanation
Indices: 20065954--20066127 Score: 139
Period size: 39 Copynumber: 4.5 Consensus size: 39
20065944 TTTTTAATAC
* *
20065954 TTTATAA-TATTTTA-AAATTTTAATAATTTATTAGAATT
1 TTTATAAGT-TTTTATAAATTTTTATAATTTATTATAATT
* * *
20065992 TTTATAAGTTTTTATGAATTTTTATATTTTTTTATAA-T
1 TTTATAAGTTTTTATAAATTTTTATAATTTATTATAATT
* * *
20066030 TTTAT-TGTTCTTATAATTTTTTTATAATTTATTAT-ATT
1 TTTATAAGTTTTTATAA-ATTTTTATAATTTATTATAATT
* * *
20066068 TTTATGAGTTTCTATAAAATTTTGT-TAATATT-TT-TAAGT
1 TTTATAAGTTTTTAT-AAATTTT-TATAAT-TTATTATAATT
*
20066107 TTTATAAGTTTATATAAATTT
1 TTTATAAGTTTTTATAAATTT
20066128 GAAAATTTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
37 9 0.08
38 46 0.42
39 49 0.45
40 5 0.05
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (39 bp):
TTTATAAGTTTTTATAAATTTTTATAATTTATTATAATT
Found at i:20066311 original size:15 final size:16
Alignment explanation
Indices: 20066291--20066323 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20066281 ATATTTAATT
20066291 ATTCAAATATT-GATA
1 ATTCAAATATTGGATA
*
20066306 ATTCAATTATTGGATA
1 ATTCAAATATTGGATA
20066322 AT
1 AT
20066324 AAAGATAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTCAAATATTGGATA
Found at i:20079597 original size:51 final size:51
Alignment explanation
Indices: 20079541--20079677 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 51
20079531 TATGGTAACT
* *
20079541 AATCTTAGAGGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * *** * * **
20079592 AATCTTATAAGATATTATTTTATAAGAATACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
*
20079643 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
20079678 TTGATGGTAG
Statistics
Matches: 65, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:20082617 original size:51 final size:51
Alignment explanation
Indices: 20082561--20082697 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 51
20082551 TATGGTAACT
* *
20082561 AATCTTAGAGGATATGATATTATAATCTTAGAGATCTTAGATATGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
* * * *** * * **
20082612 AATCTTATAAGATATTATTTTATAAGAATACATATCTTATCTAAGATATGG
1 AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
*
20082663 AATCTTAGAAGATATGATATTATATTCTTAGAGAT
1 AATCTTAGAAGATATGATATTATAATCTTAGAGAT
20082698 TTGATGGTAG
Statistics
Matches: 65, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (51 bp):
AATCTTAGAAGATATGATATTATAATCTTAGAGATCTTAGATAAGATATGG
Found at i:20084329 original size:13 final size:13
Alignment explanation
Indices: 20084313--20084377 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
20084303 TTTAAACTAA
20084313 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
20084326 ACTTTTCCACAG-
1 ACTTTTCAAAAGC
* *
20084338 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
20084351 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
20084364 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
20084377 A
1 A
20084378 TTGCCAAACT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
12 12 0.26
13 35 0.74
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:20084341 original size:25 final size:26
Alignment explanation
Indices: 20084313--20084377 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
20084303 TTTAAACTAA
* *
20084313 ACTTTTCAAAAGCACTTTTCCACAG-
1 ACTTTTCAAAAGCACTTTTCAAAAGC
* *
20084338 ACTTTTCCACAGCACTTTTCAAAAGC
1 ACTTTTCAAAAGCACTTTTCAAAAGC
20084364 ACTTTTCAAAAGCA
1 ACTTTTCAAAAGCA
20084378 TTGCCAAACT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 21 0.64
26 12 0.36
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTTTCAAAAGC
Found at i:20092519 original size:64 final size:64
Alignment explanation
Indices: 20092418--20092567 Score: 282
Period size: 64 Copynumber: 2.3 Consensus size: 64
20092408 GGACTGGCAC
*
20092418 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGATTAAGAAA
1 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
*
20092482 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAC
1 CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
20092546 CATTGGATCATCACTTATTCAA
1 CATTGGATCATCACTTATTCAA
20092568 CCAATAGAAC
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 84 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (64 bp):
CATTGGATCATCACTTATTCAATAAAACCTTGAAACTAAGTCCAAAGATTCTTTGAGTAAGAAA
Found at i:20092987 original size:28 final size:28
Alignment explanation
Indices: 20092943--20093016 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
20092933 GTGGTCCAAA
*
20092943 AAATT-CAACGGCCATATTGCAA-TAGTC
1 AAATTACAACGGTCATATTGCAACT-GTC
* * * *
20092970 ATATTCCAACGGTTATATTGTAACTGTC
1 AAATTACAACGGTCATATTGCAACTGTC
20092998 AAATTACAACGGTCATATT
1 AAATTACAACGGTCATATT
20093017 TTTGCATTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 4 0.11
28 33 0.87
29 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (28 bp):
AAATTACAACGGTCATATTGCAACTGTC
Found at i:20098329 original size:18 final size:18
Alignment explanation
Indices: 20098306--20098341 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20098296 ACCGTAAAAG
20098306 AATCTATGAGAAAATATA
1 AATCTATGAGAAAATATA
20098324 AATCTATGAGAAAATATA
1 AATCTATGAGAAAATATA
20098342 TTTAATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
AATCTATGAGAAAATATA
Found at i:20102671 original size:21 final size:20
Alignment explanation
Indices: 20102634--20102677 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
20102624 TCTCACGAGC
*
20102634 TTCTGTTAACTCATATGAGT
1 TTCTGTTAACCCATATGAGT
* *
20102654 TTCTGTTTAACCCTTATGGGT
1 TTCTG-TTAACCCATATGAGT
20102675 TTC
1 TTC
20102678 CGTTCAGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (20 bp):
TTCTGTTAACCCATATGAGT
Found at i:20105708 original size:19 final size:19
Alignment explanation
Indices: 20105684--20105723 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20105674 CATGGTGTGC
*
20105684 TTAGTTTTCTTATGACTTT
1 TTAGTTTGCTTATGACTTT
* *
20105703 TTAGTTTGCTTTTTACTTT
1 TTAGTTTGCTTATGACTTT
20105722 TT
1 TT
20105724 CGCCTTTCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (19 bp):
TTAGTTTGCTTATGACTTT
Found at i:20106500 original size:24 final size:24
Alignment explanation
Indices: 20106473--20106518 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20106463 GTCACTGCAT
* *
20106473 TATTAAAATTTAATTAAATAAAAA
1 TATTAAAATTAAATAAAATAAAAA
*
20106497 TATTAATATTAAATAAAATAAA
1 TATTAAAATTAAATAAAATAAA
20106519 TAAATATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TATTAAAATTAAATAAAATAAAAA
Found at i:20107262 original size:31 final size:31
Alignment explanation
Indices: 20107159--20107267 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
20107149 ATTGGTAATG
* *
20107159 AAGT-TTGAGTATTAAATTAATAGAATTTGT
1 AAGTATTGAGGATTAAATTAATAGAATATGT
* *
20107189 AA--ATGTGAAGGGTTAGATTTAAT-GAATTAT-T
1 AAGTAT-TG-AGGATTA-AATTAATAGAA-TATGT
* *
20107220 TAGAATT-AGGATTAAATTAATAGAATATGT
1 AAGTATTGAGGATTAAATTAATAGAATATGT
20107250 AAGTATTGAGGATTAAAT
1 AAGTATTGAGGATTAAAT
20107268 ATGTTTTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
29 10 0.17
30 19 0.32
31 20 0.33
32 9 0.15
33 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (31 bp):
AAGTATTGAGGATTAAATTAATAGAATATGT
Found at i:20107978 original size:19 final size:21
Alignment explanation
Indices: 20107954--20107992 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20107944 AAAATATATT
20107954 TTTTAT-TATTTTT-TAAATA
1 TTTTATATATTTTTATAAATA
20107973 TTTTATATATTTTTATAAAT
1 TTTTATATATTTTTATAAAT
20107993 TTAATACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATATTTTTATAAATA
Found at i:20108031 original size:19 final size:19
Alignment explanation
Indices: 20107951--20108031 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 19
20107941 GTGAAAATAT
20107951 ATTTTTTAT-TATTTTTTAA
1 ATTTTTTATATATTTTTT-A
*
20107970 ATATTTTATATATTTTTATA
1 ATTTTTTATATATTTTT-TA
* *
20107990 A--ATTTA-ATACTTTTTGA
1 ATTTTTTATATA-TTTTTTA
*
20108007 ATTTTTTTATGTATTTTTTA
1 A-TTTTTTATATATTTTTTA
20108027 ATTTT
1 ATTTT
20108032 AATTTTGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 5 0.10
18 9 0.18
19 12 0.24
20 20 0.41
21 3 0.06
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTTATATATTTTTTA
Found at i:20108040 original size:21 final size:20
Alignment explanation
Indices: 20108000--20108044 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
20107990 AATTTAATAC
20108000 TTTTTGAATTTTTTTATGTA
1 TTTTTGAATTTTTTTATGTA
*
20108020 TTTTTTAATTTTAATTT-TGTA
1 TTTTTGAATTTT--TTTATGTA
20108041 TTTT
1 TTTT
20108045 CTTAGTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 8 0.36
22 3 0.14
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (20 bp):
TTTTTGAATTTTTTTATGTA
Found at i:20108245 original size:31 final size:31
Alignment explanation
Indices: 20108173--20108248 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
20108163 ATTTTAAGGT
* * **
20108173 AGAGTGATTACAATTGACAACTTATCTAACA
1 AGAGTGACTAAAATTGACAACGAATCTAACA
* * *
20108204 AAAGTAACTAAAATTGACAACGAATCTAAGA
1 AGAGTGACTAAAATTGACAACGAATCTAACA
*
20108235 GGAGTGACTAAAAT
1 AGAGTGACTAAAAT
20108249 AACAAATTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (31 bp):
AGAGTGACTAAAATTGACAACGAATCTAACA
Found at i:20112490 original size:26 final size:25
Alignment explanation
Indices: 20112461--20112543 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
20112451 GACTCGAAAT
20112461 CTAAAACCTAAAACTTAATATAAACC
1 CTAAAACCT-AAACTTAATATAAACC
** *
20112487 CTAATTCCTAAACTCAAATCATAAACC
1 CTAAAACCTAAACT-TAAT-ATAAACC
* * *
20112514 TTATAAACCCAAAC-TCATATAAACC
1 CTA-AAACCTAAACTTAATATAAACC
20112539 CTAAA
1 CTAAA
20112544 CTATAATCTT
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
24 2 0.05
25 14 0.32
26 12 0.27
27 9 0.20
28 7 0.16
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (25 bp):
CTAAAACCTAAACTTAATATAAACC
Found at i:20112925 original size:21 final size:21
Alignment explanation
Indices: 20112899--20112938 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20112889 GAGACAGGTG
20112899 ACGTGGCTC-GTTAACTAGCTA
1 ACGTGGC-CGGTTAACTAGCTA
20112920 ACGTGGCCGGTTAACTAGC
1 ACGTGGCCGGTTAACTAGC
20112939 CACGTCGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.25
Consensus pattern (21 bp):
ACGTGGCCGGTTAACTAGCTA
Found at i:20115695 original size:28 final size:28
Alignment explanation
Indices: 20115655--20115719 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
20115645 GAGCAAATTC
20115655 CACAATATGATATGGTAAAATTTAAACT
1 CACAATATGATATGGTAAAATTTAAACT
20115683 CACAATATGATATGGTAAAATTTAAACT
1 CACAATATGATATGGTAAAATTTAAACT
*
20115711 CATAATATG
1 CACAATATG
20115720 GTATAGTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
CACAATATGATATGGTAAAATTTAAACT
Found at i:20116237 original size:23 final size:19
Alignment explanation
Indices: 20116190--20116228 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
20116180 TATTTTTCTT
20116190 AATAAATAATTAAAAAATA
1 AATAAATAATTAAAAAATA
*
20116209 ATTAAATAGATTAATAAAAT
1 AATAAATA-ATTAA-AAAAT
20116229 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AATAAATAATTAAAAAATA
Found at i:20116325 original size:15 final size:15
Alignment explanation
Indices: 20116306--20116360 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
20116296 TATTTGATAA
20116306 ACTGAAATTTTAAGT
1 ACTGAAATTTTAAGT
* **
20116321 GCTGAAAAATTAAGT
1 ACTGAAATTTTAAGT
* *
20116336 ACTG-AATTTTTATT
1 ACTGAAATTTTAAGT
20116350 ACT-AAATTTTA
1 ACTGAAATTTTA
20116361 TAAGTGTTTA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (15 bp):
ACTGAAATTTTAAGT
Found at i:20123505 original size:7 final size:6
Alignment explanation
Indices: 20123475--20123504 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
20123465 GATTTTCTCA
20123475 AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATG-G AAATG
20123505 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:20126852 original size:16 final size:16
Alignment explanation
Indices: 20126828--20126880 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
20126818 AGAGTGGAAA
20126828 AAAAATTGAA-ATGATG
1 AAAAATTGAAGA-GATG
*
20126844 AAAATTTGAAGAGATG
1 AAAAATTGAAGAGATG
*
20126860 AAAAACTAGAAGA-ATG
1 AAAAA-TTGAAGAGATG
20126876 AAAAA
1 AAAAA
20126881 AAAATTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 25 0.78
17 7 0.22
ACGTcount: A:0.60, C:0.02, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAAATTGAAGAGATG
Found at i:20129576 original size:26 final size:26
Alignment explanation
Indices: 20129547--20129605 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
20129537 TATTTTCTTG
20129547 AAATTTTAAT-AGGGGCAAAATCGTCA
1 AAATTTT-ATCAGGGGCAAAATCGTCA
* *
20129573 AAATTTTATCGGGGGTAAAATCGTCA
1 AAATTTTATCAGGGGCAAAATCGTCA
20129599 AAATTTT
1 AAATTTT
20129606 GCTGAGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (26 bp):
AAATTTTATCAGGGGCAAAATCGTCA
Found at i:20134790 original size:40 final size:40
Alignment explanation
Indices: 20134569--20134790 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
20134559 GCTACTCGTT
* *
20134569 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20134609 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20134649 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20134689 TC-AATGCCTTCGGG-CTTAGCCCGAAT-TAGT-ACTCGCA
1 -CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
20134726 CAAATGCCTTC--GATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20134766 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20134791 CATCATTCAA
Statistics
Matches: 162, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 26 0.16
38 7 0.04
39 18 0.11
40 106 0.65
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20142870 original size:119 final size:120
Alignment explanation
Indices: 20142664--20142886 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 120
20142654 CTACTGTTCA
* *
20142664 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
20142729 ATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
20142784 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* * *
20142846 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
20142887 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
118 4 0.04
119 68 0.74
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:20142886 original size:40 final size:40
Alignment explanation
Indices: 20142662--20142886 Score: 305
Period size: 40 Copynumber: 5.7 Consensus size: 40
20142652 AGCTACTGTT
* *
20142662 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20142702 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
20142742 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
20142782 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
20142821 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
20142862 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
20142887 CATCATTCAA
Statistics
Matches: 166, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 120 0.72
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:20163560 original size:119 final size:120
Alignment explanation
Indices: 20163384--20163606 Score: 310
Period size: 119 Copynumber: 1.9 Consensus size: 120
20163374 TACTCGTTCA
* * *
20163384 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
*
20163449 ATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
20163504 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
* * *
20163566 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
20163607 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
118 4 0.04
119 67 0.74
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:20163606 original size:40 final size:40
Alignment explanation
Indices: 20163363--20163606 Score: 300
Period size: 40 Copynumber: 6.1 Consensus size: 40
20163353 CGGAATTTAA
** *
20163363 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20163403 CCGGTTATAGTGACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20163443 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20163483 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
20163522 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
20163562 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
20163602 CCGGA
1 CCGGA
20163607 CATCATTCAA
Statistics
Matches: 180, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.18
40 133 0.74
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:20171687 original size:119 final size:120
Alignment explanation
Indices: 20171511--20171733 Score: 319
Period size: 119 Copynumber: 1.9 Consensus size: 120
20171501 TACTCGTTCA
* * *
20171511 AATGCCTTCGGGACATAGCCCGGTTATAGTGACTCGCACAAATGCCTTCGAGACTTAGCCCGGTT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGAT
20171576 ATAGTAACTT-GCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* *
20171631 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTCG-GATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGAGA-CTTAGCCCGG
* * *
20171693 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
20171734 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
118 3 0.03
119 70 0.76
120 19 0.21
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:20171733 original size:40 final size:40
Alignment explanation
Indices: 20171490--20171733 Score: 282
Period size: 40 Copynumber: 6.1 Consensus size: 40
20171480 CGAAATTTAA
** *
20171490 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
20171530 CCGGTTATAGTGACTCGCACAAATGCCTTCGAGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
20171570 CCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
20171610 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
20171649 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
20171689 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
20171729 CCGGA
1 CCGGA
20171734 CATCATTCAA
Statistics
Matches: 176, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.01
39 33 0.19
40 129 0.73
41 12 0.07
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:20173852 original size:62 final size:63
Alignment explanation
Indices: 20173733--20173856 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
20173723 TCCTTGGCCC
* * * * *
20173733 GTGTGACCCTAAATCCAAAACAGTGAGTTACACGGCTTAGATACACGCCCATGTCCCTAGCCT
1 GTGTGACCCAAAATACAAAACAGTGAGTTACACGACTTAGACACACACCCATGTCCCTAGCCT
* * * * *
20173796 GTGTGACCCAAAATAC-AAACAGTGAGTTACACTACTTGGACATACACCCGTTTCCCTAGCC
1 GTGTGACCCAAAATACAAAACAGTGAGTTACACGACTTAGACACACACCCATGTCCCTAGCC
20173857 CTTGTGTCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
62 37 0.73
63 14 0.27
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (63 bp):
GTGTGACCCAAAATACAAAACAGTGAGTTACACGACTTAGACACACACCCATGTCCCTAGCCT
Found at i:20177549 original size:25 final size:25
Alignment explanation
Indices: 20177520--20177567 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
20177510 TCCATATTGG
* *
20177520 ATGAGATTGAAAAGTAATATTAGCA
1 ATGAGACTGAAAAGTAAAATTAGCA
*
20177545 ATGAGACTGAAGAGTAAAATTAG
1 ATGAGACTGAAAAGTAAAATTAG
20177568 GAATTCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (25 bp):
ATGAGACTGAAAAGTAAAATTAGCA
Found at i:20180250 original size:7 final size:7
Alignment explanation
Indices: 20180238--20180262 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20180228 TATCTTTGTA
20180238 ATACTCC
1 ATACTCC
20180245 ATACTCC
1 ATACTCC
20180252 ATACTCC
1 ATACTCC
20180259 ATAC
1 ATAC
20180263 ATCATCTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTCC
Found at i:20183045 original size:34 final size:33
Alignment explanation
Indices: 20182969--20183051 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 33
20182959 CAATTCAATA
*
20182969 ACAGT-TCAGT-TCAGTTGGGCCTTTGCCCATT
1 ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
20183000 ACAGTATCAGTATCAGTGTGGGCCTTAGCCCATT
1 ACAGTATCAGTATCAGT-TGGGCCTTAGCCCATT
*
20183034 ACAGTGA-CAGTAACAGTT
1 ACAGT-ATCAGTATCAGTT
20183052 CAAACATGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
31 5 0.11
32 5 0.11
33 6 0.13
34 29 0.63
35 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (33 bp):
ACAGTATCAGTATCAGTTGGGCCTTAGCCCATT
Found at i:20183356 original size:27 final size:27
Alignment explanation
Indices: 20183317--20183387 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
20183307 ATAAGGTAAA
*
20183317 GCAT-ACAGTCATTTTATTACATAAGG
1 GCATAACAGTCATTTTATCACATAAGG
* * *
20183343 GCATAACAGTCATTTTACCACGTGAGG
1 GCATAACAGTCATTTTATCACATAAGG
* *
20183370 CCATAACATTCATTTTAT
1 GCATAACAGTCATTTTAT
20183388 ATCAGTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (27 bp):
GCATAACAGTCATTTTATCACATAAGG
Found at i:20193743 original size:10 final size:10
Alignment explanation
Indices: 20193726--20193755 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20193716 AACATAACCT
20193726 AAAAATGAAA
1 AAAAATGAAA
*
20193736 AGAAATGAAA
1 AAAAATGAAA
20193746 AAAAATGAAA
1 AAAAATGAAA
20193756 CCTAACCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:20194616 original size:29 final size:30
Alignment explanation
Indices: 20194561--20194656 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 30
20194551 TTATAATGAT
* *
20194561 AAAGTAAAGAAAAAGAAATAGAAAAGGAATG
1 AAAGAAAAG-AAAAGAAATAGAAAAGGAAAG
* *
20194592 AGAG-AAAGAAACGAAATA-AAGAAGGAAAG
1 AAAGAAAAGAAAAGAAATAGAA-AAGGAAAG
*
20194621 AAAGAAAAGAAAA-AAAAAGAAAA-GAAAG
1 AAAGAAAAGAAAAGAAATAGAAAAGGAAAG
*
20194649 -GAGAAAAG
1 AAAGAAAAG
20194657 TTAAGGTTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 7 0.13
28 7 0.13
29 25 0.45
30 13 0.24
31 3 0.05
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (30 bp):
AAAGAAAAGAAAAGAAATAGAAAAGGAAAG
Found at i:20194622 original size:8 final size:8
Alignment explanation
Indices: 20194594--20194648 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 8
20194584 AAGGAATGAG
20194594 AGAAAGAA
1 AGAAAGAA
*
20194602 ACGAAATAA
1 A-GAAAGAA
*
20194611 AGAAGGAA
1 AGAAAGAA
20194619 AGAAAGAAA
1 AGAAAG-AA
20194628 AGAAA-AA
1 AGAAAGAA
20194635 A-AAAGAAA
1 AGAAAG-AA
20194643 AGAAAG
1 AGAAAG
20194649 GAGAAAAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
8 14 0.37
9 18 0.47
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (8 bp):
AGAAAGAA
Found at i:20194625 original size:4 final size:4
Alignment explanation
Indices: 20194594--20194648 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
20194584 AAGGAATGAG
* *
20194594 AGAA AGAA ACGAA ATAA AGAA GGAA AGAA AGAAA AGAA A-AA A-AA AGAAA
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AG-AA
20194643 AGAA AG
1 AGAA AG
20194649 GAGAAAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
3 6 0.14
4 25 0.58
5 12 0.28
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:20194631 original size:5 final size:5
Alignment explanation
Indices: 20194561--20194647 Score: 52
Period size: 5 Copynumber: 16.4 Consensus size: 5
20194551 TTATAATGAT
* * *
20194561 AAAGT AAAGAA AAAGA AATAGA AAAGGA ATGAGA GAAAGA AACGA AATA-A
1 AAAGA AAAG-A AAAGA AA-AGA AAA-GA A-AAGA -AAAGA AAAGA AA-AGA
* *
20194611 AGAAGG AAAG- AAAGA AAAGA AAAAA AAAGA AAAGA AA
1 A-AAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AA
20194648 GGAGAAAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.06
5 40 0.62
6 19 0.29
7 2 0.03
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:20194655 original size:12 final size:11
Alignment explanation
Indices: 20194561--20194656 Score: 54
Period size: 12 Copynumber: 8.4 Consensus size: 11
20194551 TTATAATGAT
20194561 AAAGTAAAGA-A
1 AAAG-AAAGAGA
*
20194572 AAAGAAATAGA
1 AAAGAAAGAGA
*
20194583 AAAGGAATGAGA
1 AAA-GAAAGAGA
*
20194595 GAAAGAAACGAAA
1 -AAAGAAA-GAGA
* *
20194608 TAAAGAAGGAAA
1 -AAAGAAAGAGA
20194620 GAAAGAAA-AGA
1 -AAAGAAAGAGA
*
20194631 AAA-AAAAAGA
1 AAAGAAAGAGA
20194641 AAAGAAAGGAGA
1 AAAGAAA-GAGA
20194653 AAAG
1 AAAG
20194657 TTAAGGTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
9 3 0.04
10 13 0.19
11 13 0.19
12 26 0.39
13 12 0.18
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (11 bp):
AAAGAAAGAGA
Found at i:20201003 original size:15 final size:15
Alignment explanation
Indices: 20200967--20201016 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
20200957 CATGATTGAT
*
20200967 TTATTTTT-TTTATTA
1 TTATTTTTGTTCA-TA
20200982 TTCATTTTTGTTCATA
1 TT-ATTTTTGTTCATA
*
20200998 TTATTTTTGTTCACA
1 TTATTTTTGTTCATA
20201013 TTAT
1 TTAT
20201017 CATATTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 18 0.58
16 10 0.32
17 3 0.10
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.68
Consensus pattern (15 bp):
TTATTTTTGTTCATA
Found at i:20201276 original size:109 final size:109
Alignment explanation
Indices: 20201071--20201392 Score: 452
Period size: 109 Copynumber: 3.0 Consensus size: 109
20201061 AAGGAAAATT
* * * * *
20201071 TTTCAAAGTAAGGCAATATTTTGCGATTGGAAATTGGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
* *
20201136 CGATTTTTCTCCTTCAACCAAAAAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTTAAAAA
*
20201180 TTTCAAAATAAGGCAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
* * *
20201245 CGATTTTTCTCGTTCGATCAAATAGCCAAATATCCTTTT-AAAA
66 CGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTTAAAAA
* * * * *
20201288 TTTCGAAATAAGACAATATTTTACGTTTAGAAATTCGAGGAAATGTGCCCTAATGTGTTGGGTTT
1 TTTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
* * *
20201353 CGA--TTTCTCCTTTAACCAAATAGTCAAATATCCTCTTAAA
66 CGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTTAAA
20201393 TTTTAATACA
Statistics
Matches: 189, Mismatches: 23, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
106 28 0.15
107 2 0.01
108 66 0.35
109 93 0.49
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTT
CGATTTTTCTCCTTCAACCAAATAGCCAAATATCCTTTTAAAAA
Found at i:20208280 original size:83 final size:83
Alignment explanation
Indices: 20208141--20208301 Score: 304
Period size: 83 Copynumber: 1.9 Consensus size: 83
20208131 AAAATCAATA
20208141 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
1 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
20208206 AGAGGTAGGTTGAATTGT
66 AGAGGTAGGTTGAATTGT
* *
20208224 ACTTCCTTTTCTTCCGAGCCATTGAAAACATCCTTTGAAGAGTGGCCGACGAGCTTATCTCTCCA
1 ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
20208289 AGAGGTAGGTTGA
66 AGAGGTAGGTTGA
20208302 TCTGAGGACA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (83 bp):
ACTTCCTTTTCTTCCGAGCAATTGAAAACATCCTTTGAAGAGTGGCCAACGAGCTTATCTCTCCA
AGAGGTAGGTTGAATTGT
Found at i:20210939 original size:16 final size:17
Alignment explanation
Indices: 20210918--20210958 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
20210908 AACATAAATA
*
20210918 TTTATTATTAATTA-TT
1 TTTATTATTAATAATTT
*
20210934 TTTATTGTTAATAATTT
1 TTTATTATTAATAATTT
20210951 TTTATTAT
1 TTTATTAT
20210959 AATCATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTATTATTAATAATTT
Found at i:20212577 original size:41 final size:41
Alignment explanation
Indices: 20212527--20212613 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
20212517 TCAAACAAAT
* * *
20212527 TACAACACTTGAAATAATGAAAGGAAATTAGACTCGGAGTG
1 TACATCACTTGAAATAATGAAAGAAAATTAAACTCGGAGTG
*
20212568 TACATCACTTGAAATAATGAAAGAAAATTAAACTCTGAGTG
1 TACATCACTTGAAATAATGAAAGAAAATTAAACTCGGAGTG
20212609 TACAT
1 TACAT
20212614 AAGTGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (41 bp):
TACATCACTTGAAATAATGAAAGAAAATTAAACTCGGAGTG
Found at i:20219923 original size:9 final size:8
Alignment explanation
Indices: 20219908--20219933 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20219898 TATTATAACA
20219908 ATTTTTTT
1 ATTTTTTT
20219916 ATTTTTTT
1 ATTTTTTT
20219924 ATTTTTTT
1 ATTTTTTT
20219932 AT
1 AT
20219934 ATGGTATACT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:20222252 original size:20 final size:19
Alignment explanation
Indices: 20222229--20222274 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
20222219 ATCTTAATTC
*
20222229 TAAAAATTTTAAAAATACAT
1 TAAAAATTTCAAAAAT-CAT
*
20222249 TAAAAA-TTCAAAAATTAT
1 TAAAAATTTCAAAAATCAT
20222267 TAAAAATT
1 TAAAAATT
20222275 ATATAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 6 0.26
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATTTCAAAAATCAT
Found at i:20222271 original size:10 final size:10
Alignment explanation
Indices: 20222229--20222282 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 10
20222219 ATCTTAATTC
20222229 TAAAAATT-T
1 TAAAAATTAT
*
20222238 TAAAAATACAT
1 TAAAAAT-TAT
20222249 TAAAAA-T-T
1 TAAAAATTAT
*
20222257 CAAAAATTAT
1 TAAAAATTAT
20222267 TAAAAATTAT
1 TAAAAATTAT
20222277 ATAAAA
1 -TAAAA
20222283 TGATATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.17
9 8 0.22
10 10 0.28
11 12 0.33
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:20231394 original size:23 final size:23
Alignment explanation
Indices: 20231362--20231405 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20231352 TAACATTCTA
*
20231362 TAAAGCCTTTATGGCGTATTAAG
1 TAAAGCCTTTATGGCATATTAAG
*
20231385 TAAAGGCTTTATGGCATATTA
1 TAAAGCCTTTATGGCATATTA
20231406 TGTGATGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (23 bp):
TAAAGCCTTTATGGCATATTAAG
Found at i:20235760 original size:15 final size:15
Alignment explanation
Indices: 20235740--20235774 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
20235730 TTCTTGAGAA
20235740 TGAGTTCATTTAAAC
1 TGAGTTCATTTAAAC
*
20235755 TGAGTTCATTTAAAT
1 TGAGTTCATTTAAAC
20235770 TGAGT
1 TGAGT
20235775 GAGTTCCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (15 bp):
TGAGTTCATTTAAAC
Found at i:20237795 original size:28 final size:29
Alignment explanation
Indices: 20237724--20237806 Score: 123
Period size: 30 Copynumber: 2.9 Consensus size: 29
20237714 AGCAATACAA
*
20237724 TGTGGGCCTTAGCCCATTACAGTAACAGTG
1 TGTGGGCCTTAGCCCAATACAGTAACAG-G
20237754 TGTGGGCCTTAGCCCAATACAGTAACA-G
1 TGTGGGCCTTAGCCCAATACAGTAACAGG
* *
20237782 TGTGAGCCTCAGCCCAATACAGTAA
1 TGTGGGCCTTAGCCCAATACAGTAA
20237807 TAGTATAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
28 24 0.48
30 26 0.52
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (29 bp):
TGTGGGCCTTAGCCCAATACAGTAACAGG
Found at i:20237946 original size:26 final size:26
Alignment explanation
Indices: 20237916--20237992 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 26
20237906 ACACCAATAT
* *
20237916 CGCAGCAAAGCTACCAGTAATAGTGA
1 CGCAGCAAAGCTACCAGTAACAGTAA
* * * *
20237942 TGCAGCAACGCTGCTAGTAACAGTAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
* *
20237968 CGTAGCAAAGCTACCAATAACAGTA
1 CGCAGCAAAGCTACCAGTAACAGTA
20237993 TATGTGGCAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (26 bp):
CGCAGCAAAGCTACCAGTAACAGTAA
Found at i:20238187 original size:27 final size:27
Alignment explanation
Indices: 20238167--20238444 Score: 348
Period size: 27 Copynumber: 10.3 Consensus size: 27
20238157 GGGTATAATA
*
20238167 ATCATTTTACCCTTCGAGGGTATTTCG
1 ATCATTTTACCCTTCAAGGGTATTTCG
*
20238194 ATTATTTTACCCTTCAAGGGTATTTCG
1 ATCATTTTACCCTTCAAGGGTATTTCG
*
20238221 GTCATTTTACCCTTCAAGGGTATTTCTG
1 ATCATTTTACCCTTCAAGGGTATTTC-G
20238249 -TCATTTTACCCTTCAAGGGTATTTCG
1 ATCATTTTACCCTTCAAGGGTATTTCG
20238275 ATCATTTTACCCTTCAAGGGTATTTC-
1 ATCATTTTACCCTTCAAGGGTATTTCG
* * *
20238301 AGTCATTTTACCTTTTAAGGGTATTTTG
1 A-TCATTTTACCCTTCAAGGGTATTTCG
* * *
20238329 ATTATTTTACCCTTCGAGGGTATTTCA
1 ATCATTTTACCCTTCAAGGGTATTTCG
* *
20238356 ATCATTTTACCTTTCGAGGGTATTTCTG
1 ATCATTTTACCCTTCAAGGGTATTTC-G
* * *
20238384 -TCATTTTACCCTTCGAGAGTATTT-T
1 ATCATTTTACCCTTCAAGGGTATTTCG
* * *
20238409 ATCATTTTACCATTCGAGGGTATTTTG
1 ATCATTTTACCCTTCAAGGGTATTTCG
20238436 ATCATTTTA
1 ATCATTTTA
20238445 GGCCCATTAC
Statistics
Matches: 222, Mismatches: 22, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
26 24 0.11
27 196 0.88
28 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (27 bp):
ATCATTTTACCCTTCAAGGGTATTTCG
Found at i:20238292 original size:81 final size:80
Alignment explanation
Indices: 20238168--20238444 Score: 401
Period size: 81 Copynumber: 3.4 Consensus size: 80
20238158 GGTATAATAA
* *
20238168 TCATTTTACCCTTCGAGGGTATTTCGATTATTTTACCCTTCAAGGGTATTTCGGTCATTTTACCC
1 TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCC
20238233 TTCAAGGGTATTTCTG
66 TTCAAGGGTATTT-TG
* *
20238249 TCATTTTACCCTTCAAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCT
1 TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCC
*
20238314 TTTAAGGGTATTTTG
66 TTCAAGGGTATTTTG
* * * * *
20238329 ATTATTTTACCCTTCGAGGGTATTTCAATCATTTTACCTTTCGAGGGTATTTCTGTCATTTTACC
1 -TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACC
* * *
20238394 CTTCGAGAGTATTTTA
65 CTTCAAGGGTATTTTG
* *
20238410 TCATTTTACCATTCGAGGGTATTTTGATCATTTTA
1 TCATTTTACCCTTCGAGGGTATTTCGATCATTTTA
20238445 GGCCCATTAC
Statistics
Matches: 175, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 33 0.19
81 142 0.81
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.45
Consensus pattern (80 bp):
TCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCAGTCATTTTACCC
TTCAAGGGTATTTTG
Found at i:20245492 original size:13 final size:13
Alignment explanation
Indices: 20245474--20245498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20245464 TAATTTATAT
20245474 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20245487 GTGTGAAAATTT
1 GTGTGAAAATTT
20245499 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20246487 original size:34 final size:35
Alignment explanation
Indices: 20246423--20246495 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
20246413 AAGGATTCTA
* **
20246423 AATTGTATGTATTTATTTTTTACATAGCCGAATTG
1 AATTGTATGTATGTATTAATTACATAGCCGAATTG
*
20246458 AATTGTATGTATGTA-TAATTACATTGCCGAATTG
1 AATTGTATGTATGTATTAATTACATAGCCGAATTG
20246492 AATT
1 AATT
20246496 TAGCATGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 20 0.59
35 14 0.41
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (35 bp):
AATTGTATGTATGTATTAATTACATAGCCGAATTG
Found at i:20246732 original size:43 final size:43
Alignment explanation
Indices: 20246604--20246735 Score: 128
Period size: 43 Copynumber: 3.0 Consensus size: 43
20246594 CATAGGATTC
* *
20246604 TGATATGTGATTTCGTGTAAGACCACGTTTGGGACGTTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
* * *
20246647 CG--ATTTGATATTTACGTGTAAGACC-CTGTCTAGGAAAG-TGGCAT
1 TGATATTTG--ATTT-CGTGTAAGACCAC-GTCT-GGGACGTTGGCAT
* *
20246691 TGATATTTGATTTCATCTAAGACCACGTCTGGGACGTTGGCAT
1 TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
20246734 TG
1 TG
20246736 TACGATCTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
41 4 0.06
42 4 0.06
43 27 0.39
44 26 0.37
45 4 0.06
46 5 0.07
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TGATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:20263985 original size:4 final size:4
Alignment explanation
Indices: 20263976--20264016 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
20263966 GAAATTTGAC
20263976 AATA AATA AA-A AATA AATA AAT- -ATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
20264017 GACGAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 29 0.85
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:20264005 original size:14 final size:14
Alignment explanation
Indices: 20263976--20264014 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
20263966 GAAATTTGAC
20263976 AATAAATAAAAAATA
1 AATAAAT-AAAAATA
*
20263991 AATAAATATAAATA
1 AATAAATAAAAATA
20264005 AATAAATAAA
1 AATAAATAAA
20264015 TAGACGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:20264009 original size:18 final size:17
Alignment explanation
Indices: 20263981--20264016 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
20263971 TTGACAATAA
20263981 ATAAAAAATAAATAAAT
1 ATAAAAAATAAATAAAT
20263998 ATAAATAAATAAATAAAT
1 ATAAA-AAATAAATAAAT
20264016 A
1 A
20264017 GACGAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAAATAAATAAAT
Found at i:20265859 original size:31 final size:30
Alignment explanation
Indices: 20265821--20265880 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
20265811 TCTTTTAGGC
*
20265821 ATATATTTAGGAATATATTATATATGTTTTT
1 ATATATTTAGGAACATATTATATAT-TTTTT
20265852 ATATATTTAGGAACATATTATATATTTTT
1 ATATATTTAGGAACATATTATATATTTTT
20265881 CCTATTCCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 24 0.86
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (30 bp):
ATATATTTAGGAACATATTATATATTTTTT
Found at i:20266344 original size:19 final size:19
Alignment explanation
Indices: 20266304--20266345 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20266294 TGGATAATTT
*
20266304 AAAATAAAAATTTTAAAGA
1 AAAATAAAAATTTAAAAGA
*
20266323 AAAATAAAACA-TTAAAATA
1 AAAATAAAA-ATTTAAAAGA
20266342 AAAA
1 AAAA
20266346 AAGTAAGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATTTAAAAGA
Found at i:20276184 original size:15 final size:15
Alignment explanation
Indices: 20276164--20276193 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20276154 CTTTTTTGGC
*
20276164 CGATTTGCTTTCTGT
1 CGATTTGCTCTCTGT
20276179 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
20276194 TTTACCCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.23, G:0.20, T:0.50
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:20280657 original size:18 final size:17
Alignment explanation
Indices: 20280631--20280680 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
20280621 ATTAAGAATT
*
20280631 TTATGAAATTATATATTA
1 TTATTAAATTATAT-TTA
20280649 TTATTAAATTATATTTA
1 TTATTAAATTATATTTA
*
20280666 ATATT-AATTAT-TTTA
1 TTATTAAATTATATTTA
20280681 AATTGTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 4 0.13
16 6 0.20
17 7 0.23
18 13 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATTAAATTATATTTA
Found at i:20280734 original size:91 final size:91
Alignment explanation
Indices: 20280596--20280803 Score: 344
Period size: 91 Copynumber: 2.3 Consensus size: 91
20280586 TTGATTTTAG
* *
20280596 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT
* * *
20280661 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
20280688 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
20280753 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
20280779 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20280804 GTTATAATTA
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 93 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:20280772 original size:26 final size:28
Alignment explanation
Indices: 20280616--20280778 Score: 84
Period size: 28 Copynumber: 5.6 Consensus size: 28
20280606 TAAGAACATT
* *
20280616 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
** *
20280646 TTATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
* *
20280673 TTATT-TTAAATTGTAT-AAATTCATATAAGAAAA
1 TTATTATTAAATTATATGAAA-T-A-AT----ATA
* * *
20280706 TTTATTATCAAGAATTTTATGAAATTATATA
1 -TTATTAT-TA-AATTATATGAAATAATATA
*
20280737 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
20280764 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
20280779 CAAATTCATA
Statistics
Matches: 104, Mismatches: 16, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
25 2 0.02
26 21 0.20
27 13 0.12
28 27 0.26
29 2 0.02
30 15 0.14
31 2 0.02
32 1 0.01
33 1 0.01
34 5 0.05
35 3 0.03
36 1 0.01
37 8 0.08
38 3 0.03
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:20280778 original size:44 final size:43
Alignment explanation
Indices: 20280636--20280778 Score: 130
Period size: 44 Copynumber: 3.2 Consensus size: 43
20280626 GAATTTTATG
*
20280636 AAATTATATATTATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
20280680 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
20280727 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
20280771 AAATTATA
1 AAATTATA
20280779 CAAATTCATA
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.27
45 12 0.16
46 12 0.16
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:20280896 original size:59 final size:57
Alignment explanation
Indices: 20280830--20281018 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
20280820 ATTTTATTAA
20280830 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
20280889 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
20280950 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
20281009 ATCATATATT
1 ATCATATATT
20281019 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:20280927 original size:66 final size:64
Alignment explanation
Indices: 20280857--20281055 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
20280847 AAATATATTT
20280857 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
20280922 G
64 G
* * * * * **
20280923 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
20280977 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
20281042 G
64 G
*
20281043 AATATTGATTATT
1 AATATTAATTATT
20281056 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:20280943 original size:120 final size:120
Alignment explanation
Indices: 20280819--20281116 Score: 517
Period size: 120 Copynumber: 2.5 Consensus size: 120
20280809 AATTATTTTA
* * * *
20280819 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
20280883 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
20280939 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
20281004 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
20281059 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
20281117 ATGATTAAAT
Statistics
Matches: 169, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 162 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:20280959 original size:61 final size:61
Alignment explanation
Indices: 20280892--20281079 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
20280882 TTATAGTATC
20280892 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
20280953 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
20281011 C
61 T
*
20281012 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
20281073 ATATATT
1 ATATATT
20281080 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:20280979 original size:15 final size:15
Alignment explanation
Indices: 20280944--20280995 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
20280934 TTAAGAATTT
*
20280944 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20280958 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20280972 TATTTAATAATAAT-
1 TATTTAATTATAATA
20280986 TATGTTAATT
1 TAT-TTAATT
20280996 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20281094 original size:16 final size:16
Alignment explanation
Indices: 20281073--20281114 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20281063 TTATTAAATT
*
20281073 ATATATTTTAATTATA
1 ATATATTTTAATAATA
20281089 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
20281104 AT-TATGTTTAA
1 ATATAT-TTTAA
20281115 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:20281099 original size:15 final size:15
Alignment explanation
Indices: 20281064--20281105 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20281054 TTAAGAATTT
*
20281064 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20281078 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20281092 TATTTAATAATAAT
1 TATTTAATTATAAT
20281106 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20281348 original size:16 final size:16
Alignment explanation
Indices: 20281327--20281395 Score: 93
Period size: 16 Copynumber: 4.2 Consensus size: 16
20281317 GATTAGTTAT
* *
20281327 TACACCTCTAATCTAA
1 TACACATCTAATCCAA
*
20281343 TACACCTCTAATCCCAA
1 TACACATCTAAT-CCAA
20281360 TACACATCTAATCCAA
1 TACACATCTAATCCAA
*
20281376 TACACATCTAATCTAA
1 TACACATCTAATCCAA
20281392 TACA
1 TACA
20281396 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
16 35 0.71
17 14 0.29
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACATCTAATCCAA
Found at i:20290939 original size:31 final size:31
Alignment explanation
Indices: 20290904--20290963 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20290894 ACCAAAACTA
20290904 TATATATCAACTTTAGTTTAACATGTAATAT
1 TATATATCAACTTTAGTTTAACATGTAATAT
* *
20290935 TATATATCAATTTTGGTTTAACATGTAAT
1 TATATATCAACTTTAGTTTAACATGTAAT
20290964 TCTATAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (31 bp):
TATATATCAACTTTAGTTTAACATGTAATAT
Found at i:20295504 original size:43 final size:44
Alignment explanation
Indices: 20295448--20295631 Score: 270
Period size: 43 Copynumber: 4.3 Consensus size: 44
20295438 TTTGATAAAT
*
20295448 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
* *
20295491 AAACGCCGTTAAAGACCATA-ACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
* *
20295534 AAACACCGCTAAAGACCA-AGACCTTTAGCGGTGCTTTTCACAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
* *
20295577 AAACGCCGCTATAGA--ATTGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
20295619 AAACGCCGCTAAA
1 AAACGCCGCTAAA
20295632 AATATATTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.01
42 36 0.28
43 90 0.70
44 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (44 bp):
AAACGCCGCTAAAGACCATAGACCTTTAGCGGCGCTTTTCACAC
Found at i:20295954 original size:43 final size:43
Alignment explanation
Indices: 20295888--20295978 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
20295878 ACATATGCAA
* * * *
20295888 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
20295931 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
20295974 -GTAAT
1 GGTAAT
20295979 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:20296816 original size:25 final size:26
Alignment explanation
Indices: 20296776--20296869 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 26
20296766 AAGTTATGTA
* *
20296776 TTATGTAAGATATGTAAGT-TGTATT
1 TTATGTAAGTTATGTAAGTATGTATG
* *
20296801 TTATGTAAGTTCTGT-ATTATGTATG
1 TTATGTAAGTTATGTAAGTATGTATG
* * *
20296826 TTATGTAAGTTGTGT-AGAATGTAAG
1 TTATGTAAGTTATGTAAGTATGTATG
* *
20296851 CTATGTAAGTTATATAAGT
1 TTATGTAAGTTATGTAAGT
20296870 TACGTAAGTT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
24 2 0.04
25 51 0.93
26 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (26 bp):
TTATGTAAGTTATGTAAGTATGTATG
Found at i:20296848 original size:41 final size:41
Alignment explanation
Indices: 20296766--20296857 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
20296756 TAGTTCAGAG
***
20296766 AAGTTATGTATTATGTAAGATATGTAAGTTGTATTTTATGT
1 AAGTTATGTATTATGTAAGATATGTAAGTTGTATAGAATGT
* * * *
20296807 AAGTTCTGTATTATGTATGTTATGTAAGTTGTGTAGAATGT
1 AAGTTATGTATTATGTAAGATATGTAAGTTGTATAGAATGT
*
20296848 AAGCTATGTA
1 AAGTTATGTA
20296858 AGTTATATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (41 bp):
AAGTTATGTATTATGTAAGATATGTAAGTTGTATAGAATGT
Found at i:20296894 original size:9 final size:9
Alignment explanation
Indices: 20296766--20296881 Score: 86
Period size: 9 Copynumber: 13.8 Consensus size: 9
20296756 TAGTTCAGAG
20296766 AAGTTATGT
1 AAGTTATGT
20296775 -A-TTATGT
1 AAGTTATGT
*
20296782 AAGATATGT
1 AAGTTATGT
20296791 AAG-T-TGT
1 AAGTTATGT
**
20296798 ATTTTATGT
1 AAGTTATGT
*
20296807 AAGTTCTGT
1 AAGTTATGT
20296816 -A-TTATGT
1 AAGTTATGT
*
20296823 ATGTTATGT
1 AAGTTATGT
*
20296832 AAGTTGTGT
1 AAGTTATGT
*
20296841 -AG-AATGT
1 AAGTTATGT
*
20296848 AAGCTATGT
1 AAGTTATGT
*
20296857 AAGTTATAT
1 AAGTTATGT
*
20296866 AAGTTACGT
1 AAGTTATGT
20296875 AAGTTAT
1 AAGTTAT
20296882 TATGTAAGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
7 18 0.22
8 9 0.11
9 54 0.67
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (9 bp):
AAGTTATGT
Done.