Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold162
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: 1959167
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 205334 characters in sequence are not A, C, G, or T
File 7 of 12
Found at i:985705 original size:19 final size:20
Alignment explanation
Indices: 985681--985734 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
985671 AAGGTAGTTT
985681 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTATA
** *
985700 TGTATCGATACATTTACTATT
1 TGTATCGATACA-AAACTATA
985721 TGTATCGATACAAA
1 TGTATCGATACAAA
985735 TTATAGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTATA
Found at i:985726 original size:21 final size:19
Alignment explanation
Indices: 985678--985734 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
985668 TGCAAGGTAG
985678 TTTTGTATCGATACAAAAC
1 TTTTGTATCGATACAAAAC
* **
985697 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACA-AAAC
985717 TATTTGTATCGATACAAA
1 T-TTTGTATCGATACAAA
985735 TTATAGAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (19 bp):
TTTTGTATCGATACAAAAC
Found at i:988613 original size:31 final size:32
Alignment explanation
Indices: 988551--988613 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
988541 CGATACACTG
988551 TAGAATGTATCGATACATTTGGGTTCAAAACC
1 TAGAATGTATCGATACATTTGGGTTCAAAACC
*
988583 TAGAATGTATTGATACATTTGGG-TCAAAACC
1 TAGAATGTATCGATACATTTGGGTTCAAAACC
988614 CAAAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (32 bp):
TAGAATGTATCGATACATTTGGGTTCAAAACC
Found at i:988630 original size:31 final size:32
Alignment explanation
Indices: 988558--988630 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
988548 CTGTAGAATG
* * *
988558 TATCGATACATTTGGGTTCAAAACCTAGAATG
1 TATCGATACATTTGGGTTCAAAACCCAAAATA
*
988590 TATTGATACATTTGGG-TCAAAACCCAAAATA
1 TATCGATACATTTGGGTTCAAAACCCAAAATA
*
988621 TATCAATACA
1 TATCGATACA
988631 ATGAAAAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
31 20 0.57
32 15 0.43
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (32 bp):
TATCGATACATTTGGGTTCAAAACCCAAAATA
Found at i:990726 original size:20 final size:20
Alignment explanation
Indices: 990701--990770 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
990691 TCACAATTTA
990701 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
990721 TATCGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
*
990741 TATTGATACATTGTTCATTG
1 TATCGATACATTGTTCATTG
990761 TATCGATACA
1 TATCGATACA
990771 ATGTATCGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.44
Consensus pattern (20 bp):
TATCGATACATTGTTCATTG
Found at i:990777 original size:13 final size:13
Alignment explanation
Indices: 990759--990783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
990749 CATTGTTCAT
990759 TGTATCGATACAA
1 TGTATCGATACAA
990772 TGTATCGATACA
1 TGTATCGATACA
990784 TTTTGGGTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:993197 original size:51 final size:49
Alignment explanation
Indices: 993122--993251 Score: 163
Period size: 51 Copynumber: 2.6 Consensus size: 49
993112 AAATTTCTAG
**
993122 ATTTTTCAT-ATCGGGGATACTCCAATCCCGTTTTCATTTCCAAAACATTA
1 ATTTTTCATAATCGGGGATACTCCAA-CCCGTTTT-ATTTCCAAAACACCA
* *
993172 ATTTTTCTTAATCGTGGATACTCCAACTCCGATTTTATTTCCAAAACACCA
1 ATTTTTCATAATCGGGGATACTCCAAC-CCG-TTTTATTTCCAAAACACCA
* *
993223 ATTTCTCACAATCGGGGATACTCCAACCC
1 ATTTTTCATAATCGGGGATACTCCAACCC
993252 CGTTATTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
50 11 0.16
51 54 0.78
52 4 0.06
ACGTcount: A:0.28, C:0.27, G:0.10, T:0.35
Consensus pattern (49 bp):
ATTTTTCATAATCGGGGATACTCCAACCCGTTTTATTTCCAAAACACCA
Found at i:993385 original size:28 final size:27
Alignment explanation
Indices: 993319--993388 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
993309 TTCATAATCA
993319 AGGG-TACTCCAACCCTGTTATTTCAT
1 AGGGATACTCCAACCCTGTTATTTCAT
* *
993345 CGGGATACTCCAATCCTGTTATTTC-T
1 AGGGATACTCCAACCCTGTTATTTCAT
993371 GAGAGGATACTCCAACCC
1 -AG-GGATACTCCAACCC
993389 CGATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.11
27 20 0.54
28 13 0.35
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (27 bp):
AGGGATACTCCAACCCTGTTATTTCAT
Found at i:993434 original size:51 final size:51
Alignment explanation
Indices: 993373--993492 Score: 165
Period size: 51 Copynumber: 2.4 Consensus size: 51
993363 TTATTTCTGA
*
993373 GAGGATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTT-TCCACAATC
1 GAGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTCT-CACAATC
* *
993424 GAGGATACTCCAACTCCAATTTTATTTTCAAAACACCAATTTCTCACAATC
1 GAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
993475 -AGGGATACTCCAACCCCG
1 GA-GGATACTCCAACCCCG
993493 TTATTTTGCG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 1 0.02
51 55 0.90
52 5 0.08
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.28
Consensus pattern (51 bp):
GAGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCTCACAATC
Found at i:993558 original size:78 final size:81
Alignment explanation
Indices: 993455--993655 Score: 198
Period size: 80 Copynumber: 2.5 Consensus size: 81
993445 TTATTTTCAA
* * *
993455 AACACC-AATTTCTCACAATCAGGGATACTCCAACCCCGTTATTTTGCG-GGGAT-ACTCCAACC
1 AACACCGATTTTC-CACAATCGGGGATACTCCAACCCCGTTATTTTCCGAGGGATAACTCCAACC
*
993517 CTGA-CCTTATTTCTA-
65 ATGATCCTTATTTCTAG
** * * * * * *
993532 AAGCATTGATTTTCCACAATTGGGGATACACCAACCCTGTTA-TTTCCGAGGGGTAACTCTAACT
1 AA-CACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTCCGAGGGATAACTCCAACC
**
993596 ATGATTTTTATTTCTAG
65 ATGATCCTTATTTCTAG
* *
993613 AACACCGATTTTCCATAATCGTGGATACTCCAACCCCGTTATT
1 AACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATT
993656 ATCTCCAAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
77 7 0.07
78 30 0.31
79 15 0.16
80 41 0.43
81 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (81 bp):
AACACCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTCCGAGGGATAACTCCAACCA
TGATCCTTATTTCTAG
Found at i:995159 original size:4 final size:4
Alignment explanation
Indices: 995150--995179 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
995140 TTTTGAGGTG
*
995150 TTTA TTTA TTTA TCTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
995180 CGTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1006630 original size:55 final size:55
Alignment explanation
Indices: 1006561--1006744 Score: 212
Period size: 55 Copynumber: 3.3 Consensus size: 55
1006551 CTCCTTTCAC
*
1006561 CCTTT-AGTTCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA
* *
1006615 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA
** * * * * *
1006670 TTTTTTTTAGTCCTCAAATAGTAGAACACCTTT-AAAGCCCACACAAGCTGGTGGCA
1 --CCTTTCAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA
* *
1006726 -CTTCCCAATCCTCAAAGAG
1 CCTT-TCAGTCCTCAAAGAG
1006745 CAAGACGCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.02
54 16 0.15
55 46 0.42
56 21 0.19
57 24 0.22
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTAGTGGCA
Found at i:1006893 original size:61 final size:62
Alignment explanation
Indices: 1006791--1006973 Score: 282
Period size: 61 Copynumber: 3.0 Consensus size: 62
1006781 GAGCAAGACG
* *
1006791 CCTTTT-AAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAACCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
* * *
1006852 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
*
1006913 CTTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCACTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGC-CTTT
1006974 ATTTTCCTCT
Statistics
Matches: 110, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
61 81 0.74
62 29 0.26
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (62 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
Found at i:1006898 original size:155 final size:151
Alignment explanation
Indices: 1006615--1006907 Score: 367
Period size: 155 Copynumber: 1.9 Consensus size: 151
1006605 GTTAGTGGCA
* * *
1006615 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCATTTTTTTTAG
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTAGTGGCATCTTTTCTAG
* **
1006680 TCCTCAAATAGTAGAACACCTTTAAAGCCCACACAAGCTGGTGGCACTTCCCAATCCTCAAAGAG
66 TCCTCAAAAACCAGAACACCTTTAAAGCCCACACAAGCTGGTGGCACTTCCCAATCCTCAAAGAG
1006745 CAAGACGCTCTCTCCTTTTGC
131 CAAGACGCTCTCTCCTTTTGC
* *
1006766 CCTTT-AGTCCTCAAAGAGCAAGACGCCTTT-TAAGCCCACACAAGTTGGTGGCA-CTTTTCTAG
1 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTAGTGGCATCTTTTCTAG
* * * * * *
1006828 TCCTCAAAAACCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
66 TCCTCAAAAACCA-GA--AC---ACC-TTTAAAGCCCACACAAGCTGGTGGCACTTCCCAATCCT
*
1006893 CAAAGAGCAGGACGC
124 CAAAGAGCAAGACGC
1006908 ATTTTCTTTT
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
148 17 0.14
149 23 0.19
150 24 0.20
151 6 0.05
154 2 0.02
155 48 0.40
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (151 bp):
CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTAGTGGCATCTTTTCTAG
TCCTCAAAAACCAGAACACCTTTAAAGCCCACACAAGCTGGTGGCACTTCCCAATCCTCAAAGAG
CAAGACGCTCTCTCCTTTTGC
Found at i:1007099 original size:42 final size:43
Alignment explanation
Indices: 1006944--1007139 Score: 175
Period size: 42 Copynumber: 4.5 Consensus size: 43
1006934 TGGTGGCACT
* *
1006944 TTTTAGTCCTCAAAGAGCAGGATGCACTTTATTTTCC-TCTTTC
1 TTTT-GTCCTCAAAGAGCAGGACGCACTTCATTTTCCTTCTTTC
** * **
1006987 CCTTGTCCTCAAAGAGCAGGACACACTTCA-TGCCCTTCTTTTCCC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTTC-TTT--C
* * * *
1007032 TTTTGTCCTCAAAGAGTAGGGCGCATTTTATTTTCC-TCTTTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTTCTTTC
* * * *
1007074 TTTTATCCTCAAAGAGCAGGACGCATTTCGTTTTCCTTTTTTC
1 TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTTCTTTC
*
1007117 TTTTGTCCTCGAAA-AGTAGGACG
1 TTTTGTCCTC-AAAGAGCAGGACG
1007140 TACTCTTTTT
Statistics
Matches: 122, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
41 3 0.02
42 57 0.47
43 27 0.22
44 6 0.05
45 26 0.21
46 3 0.02
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (43 bp):
TTTTGTCCTCAAAGAGCAGGACGCACTTCATTTTCCTTCTTTC
Found at i:1007116 original size:87 final size:85
Alignment explanation
Indices: 1006944--1007139 Score: 225
Period size: 87 Copynumber: 2.3 Consensus size: 85
1006934 TGGTGGCACT
* * *
1006944 TTTTAGTCCTCAAAGAGCAGGATGCACTTTATTTTCCTCTTTCCCTTGTCCTCAAAGAGCAGGAC
1 TTTT-GTCCTCAAAGAGTAGGACGCACTTTATTTTCCTCTTTCCCTTATCCTCAAAGAGCAGGAC
1007009 ACACTTCATGCCCTTCTTTTCCC
65 ACACTTCATGCCCTTCTTTT--C
* * ** *
1007032 TTTTGTCCTCAAAGAGTAGGGCGCATTTTATTTTCCTCTTTCTTTTATCCTCAAAGAGCAGGACG
1 TTTTGTCCTCAAAGAGTAGGACGCACTTTATTTTCCTCTTTCCCTTATCCTCAAAGAGCAGGACA
* * **
1007097 CATTTCGTTTTCCTT-TTTTC
66 CACTTC-ATGCCCTTCTTTTC
1007117 TTTTGTCCTCGAAA-AGTAGGACG
1 TTTTGTCCTC-AAAGAGTAGGACG
1007140 TACTCTTTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 19 0.20
86 3 0.03
87 62 0.67
88 9 0.10
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.39
Consensus pattern (85 bp):
TTTTGTCCTCAAAGAGTAGGACGCACTTTATTTTCCTCTTTCCCTTATCCTCAAAGAGCAGGACA
CACTTCATGCCCTTCTTTTC
Found at i:1007243 original size:40 final size:41
Alignment explanation
Indices: 1007146--1007244 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
1007136 GACGTACTCT
* * *
1007146 TTTTCACTTTTTCCTCAAGAAGCAAGACACTTTCCTTTTCTT
1 TTTTC-CTTTATCCTCAAGAAGCAAGACACTTTCCTATTCTG
* *
1007188 TTTTCCTTCATCCTCAAGAAGCAAGAC-CTATTTC-ATTCTG
1 TTTTCCTTTATCCTCAAGAAGCAAGACACT-TTCCTATTCTG
*
1007228 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTATCCTCAA
1007245 AAAGTGGGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 21 0.43
41 23 0.47
42 5 0.10
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.43
Consensus pattern (41 bp):
TTTTCCTTTATCCTCAAGAAGCAAGACACTTTCCTATTCTG
Found at i:1010424 original size:28 final size:28
Alignment explanation
Indices: 1010383--1010469 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
1010373 ATTTTTTTCA
1010383 TCATCAGGGG-TACTCCAACCCCGTTATT
1 TCATC-GGGGATACTCCAACCCCGTTATT
**
1010411 TCATCGGGGATACTCCAATTCCGTTATT
1 TCATCGGGGATACTCCAACCCCGTTATT
* * *
1010439 TC-TAAGGGGATACTACAACCCCTTTTATT
1 TCAT-CGGGGATACTCCAACCCC-GTTATT
1010468 TC
1 TC
1010470 TAAAATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
27 5 0.10
28 37 0.76
29 7 0.14
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (28 bp):
TCATCGGGGATACTCCAACCCCGTTATT
Found at i:1010520 original size:51 final size:49
Alignment explanation
Indices: 1010444--1010559 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 49
1010434 TTATTTCTAA
* * * * **
1010444 GGGGATACTACAACCCCTTTTATTTCTAAAATATTAATTT-TCCACAATC
1 GGGGATACTCCAACCCATTTTATTTCCAAAACACCAATTTCT-CACAATC
1010493 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAAC-CC-ATTTTATTTCCAAAACACCAATTTCTCACAATC
1010544 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
1010560 CGTTATTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
49 13 0.22
50 4 0.07
51 40 0.69
52 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (49 bp):
GGGGATACTCCAACCCATTTTATTTCCAAAACACCAATTTCTCACAATC
Found at i:1010598 original size:79 final size:77
Alignment explanation
Indices: 1010492--1010725 Score: 261
Period size: 79 Copynumber: 2.9 Consensus size: 77
1010482 TTTCCACAAT
* *
1010492 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 CGGGAATACTCCAAC-CCGATTTTATTTCTAAAACACCAATTT-TCACAATCGGGGATACTCCAA
**
1010557 CCCCGTTATTTTTG
64 CCCCGTTATTTCCG
** * ** *
1010571 CGGGAATACTCCAACCCTGACCTTATTTCTAAAGCATTGATTTTTCACAATCGGGGATACTCCAA
1 CGGGAATACTCCAACCC-GATTTTATTTCTAAAACA-CCAATTTTCACAATCGGGGATACTCCAA
*
1010636 CCCTGTTATTTCCG
64 CCCCGTTATTTCCG
* * * *
1010650 AGGGAATACTCCAACCGCGATTTTTATTTCTAGAACACCAATTTTCCATAATCAGGGATACTCCA
1 CGGGAATACTCCAACC-CGA-TTTTATTTCTAAAACACCAATTTT-CACAATCGGGGATACTCCA
*
1010715 TCCCCGTTATT
63 ACCCCGTTATT
1010726 ATCTCCAAAA
Statistics
Matches: 127, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
78 2 0.02
79 82 0.65
80 43 0.34
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (77 bp):
CGGGAATACTCCAACCCGATTTTATTTCTAAAACACCAATTTTCACAATCGGGGATACTCCAACC
CCGTTATTTCCG
Found at i:1011799 original size:59 final size:59
Alignment explanation
Indices: 1011693--1011805 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 59
1011683 GTTGCGACAA
* *
1011693 AAGTCATTGTTAGGTTTTTGATTTTATCTAGGCCATTTTGTTGAGTTTTGGTTTAGTTC
1 AAGTCATTGTTAGGTTTTAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTTAGTTC
1011752 AAGTCATTGTTTAGGTTTCTAG-TTTCATCTAGGCCATTTT-TTGAGTTTTGGTTT
1 AAGTCATTG-TTAGGTTT-TAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTT
1011806 CACCCAAGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
59 23 0.46
60 25 0.50
61 2 0.04
ACGTcount: A:0.17, C:0.10, G:0.21, T:0.52
Consensus pattern (59 bp):
AAGTCATTGTTAGGTTTTAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTTAGTTC
Found at i:1011814 original size:59 final size:60
Alignment explanation
Indices: 1011693--1011823 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 60
1011683 GTTGCGACAA
* * **
1011693 AAGTCATTG-TTAGGTTTTTGATTTTATCTAGGCCATTTTGTTGAGTTTTGGTTTAGTTC
1 AAGTCATTGTTTAGGTTTTAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTTAGCCC
1011752 AAGTCATTGTTTAGGTTTCTAG-TTTCATCTAGGCCATTTT-TTGAGTTTTGGTTTCA-CCC
1 AAGTCATTGTTTAGGTTT-TAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTT-AGCCC
1011811 AAGTCATT-TTTAG
1 AAGTCATTGTTTAG
1011824 ATTCTGGTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
58 5 0.08
59 32 0.49
60 26 0.40
61 2 0.03
ACGTcount: A:0.18, C:0.12, G:0.20, T:0.50
Consensus pattern (60 bp):
AAGTCATTGTTTAGGTTTTAGATTTCATCTAGGCCATTTTGTTGAGTTTTGGTTTAGCCC
Found at i:1012326 original size:20 final size:20
Alignment explanation
Indices: 1012298--1012372 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1012288 TTTTACCCTG
1012298 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1012318 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1012338 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1012358 ATGTATCGATACATT
1 ATGTATCGATACATT
1012373 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1012365 original size:40 final size:39
Alignment explanation
Indices: 1012298--1012375 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1012288 TTTTACCCTG
* *
1012298 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
1012338 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
1012376 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1013277 original size:23 final size:23
Alignment explanation
Indices: 1013241--1013292 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1013231 AGCCTTTGAC
1013241 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1013263 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1013286 CATGCAT
1 CATGCAT
1013293 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1026331 original size:9 final size:9
Alignment explanation
Indices: 1026317--1026376 Score: 54
Period size: 9 Copynumber: 7.0 Consensus size: 9
1026307 CTTTACACCC
1026317 ACAAAAAAA
1 ACAAAAAAA
1026326 ACAAAAAAA
1 ACAAAAAAA
*
1026335 ACAAAACAA
1 ACAAAAAAA
*
1026344 A-AAAACAA
1 ACAAAAAAA
*
1026352 A-AAAAAAG
1 ACAAAAAAA
*
1026360 A-AAAAATA
1 ACAAAAAAA
*
1026368 GCAAAAAAA
1 ACAAAAAAA
1026377 TAGAAGGGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
8 19 0.44
9 24 0.56
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (9 bp):
ACAAAAAAA
Found at i:1026333 original size:8 final size:8
Alignment explanation
Indices: 1026320--1026356 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1026310 TACACCCACA
1026320 AAAAAAAC
1 AAAAAAAC
1026328 -AAAAAA-
1 AAAAAAAC
*
1026334 AACAAAAC
1 AAAAAAAC
1026342 AAAAAAAC
1 AAAAAAAC
1026350 AAAAAAA
1 AAAAAAA
1026357 AAGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1026340 original size:18 final size:17
Alignment explanation
Indices: 1026317--1026376 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1026307 CTTTACACCC
1026317 ACAAAAAAAACAAAAAAA
1 ACAAAAAAAA-AAAAAAA
* *
1026335 ACAAAACAAAAAAACAA
1 ACAAAAAAAAAAAAAAA
* *
1026352 A-AAAAAAGAAAAAATA
1 ACAAAAAAAAAAAAAAA
*
1026368 GCAAAAAAA
1 ACAAAAAAA
1026377 TAGAAGGGTC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
16 11 0.33
17 13 0.39
18 9 0.27
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.02
Consensus pattern (17 bp):
ACAAAAAAAAAAAAAAA
Found at i:1026365 original size:20 final size:20
Alignment explanation
Indices: 1026319--1026381 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
1026309 TTACACCCAC
*
1026319 AAAAAAAACAAAAAAAACAAA
1 AAAAAAAACAAAAAAAA-AGA
1026340 ACAAAAAAACAAAAAAAAAGA
1 A-AAAAAAACAAAAAAAAAGA
* * *
1026361 AAAAATAGCAAAAAAATAGA
1 AAAAAAAACAAAAAAAAAGA
1026381 A
1 A
1026382 GGGTCTAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 17 0.46
21 4 0.11
22 16 0.43
ACGTcount: A:0.84, C:0.08, G:0.05, T:0.03
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAGA
Found at i:1027639 original size:29 final size:29
Alignment explanation
Indices: 1027597--1029003 Score: 1814
Period size: 28 Copynumber: 49.0 Consensus size: 29
1027587 AATGTTCATC
1027597 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027626 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027655 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1027683 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1027712 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027740 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1027768 CCTTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1027797 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1027824 CTTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
1027855 CCTTTTAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027883 ACTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027912 TCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1027941 CTTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1027969 CCTTTCAAAGCCCAAAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1027998 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028026 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028055 CCTTTCAAAGCCCACAAGTCAGTGGCGCT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1028084 CTTTTTAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028113 CTTTTCAAAGCCCATAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028141 CCTTTCAAAGCCCATAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028169 CCTTTCAGAGCCCACAAGTCAATGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028197 CCTTTCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1028225 CCTTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028254 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028281 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
1028312 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028341 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028369 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028398 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028427 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1028456 CTTTTCAAAGCCCATAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028484 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028512 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028540 CCTTGCGAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1028568 CCTTGCGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028597 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028624 CCTTTTAAAGCCCACACAAGTCAGTGGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
*
1028655 CCTTTTAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
1028685 CTTTTGAAAGCCCACGAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1028714 -CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028742 -CTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** *
1028769 CCTTTC-AAGCCCATGAGTCAGTGGTAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028796 CTTTTCAAAGCCCACGAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028825 -CTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1028852 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
1028880 TCTTTCAAAGCCCACGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* **
1028910 CCTTTTTAAAGCCCACGCAAGTCAGTAACACT
1 CC-TTTCAAAGCCCA--CAAGTCAGTGGCACT
* * *
1028942 CTTTTCAAAGCTCACATGTGTCAGTGGCAACT
1 CCTTTCAAAGCCCACA--AGTCAGTGGC-ACT
** *
1028974 TTTTTCAAAGCCTACACAAGTTAGTGGCAC
1 CCTTTCAAAGCC--CACAAGTCAGTGGCAC
1029004 ATTTTTTTTA
Statistics
Matches: 1234, Mismatches: 107, Indels: 72
0.87 0.08 0.05
Matches are distributed among these distances:
27 23 0.02
28 634 0.51
29 387 0.31
30 78 0.06
31 86 0.07
32 22 0.02
34 4 0.00
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1028317 original size:343 final size:341
Alignment explanation
Indices: 1027596--1029003 Score: 2013
Period size: 343 Copynumber: 4.1 Consensus size: 341
1027586 GAATGTTCAT
*
1027596 CCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTT
1 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTT
1027659 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
66 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
* * * * * * *
1027724 CACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAATTCA
131 CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCA
* * * *
1027789 GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTTAAAGCCCACACAAGTCAGTGGCAC
196 GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCAC
* * *
1027854 TCCTTTTAAAGCCCACAAGTCAGTGGCACACTTTCAAAGCCCACAAGTCAGTGGCACTTCTTTCA
259 -CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTGCAAAGCCCACAAGTCAGTGGCAC-TCTTTCA
1027919 AAGCCCACAAGTCAGTGGCA
322 AAGCCCACAAGTCAGTGGCA
* * *
1027939 CTCTTTTCAAAG-CC-CACAAGTTAGTGGCA-TCCTTTCAAAGCCCAAAAATCAGTGGCACTCTT
1 CCCTTTT-AAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTT
1028001 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
65 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGC
* * *
1028066 CCACAAGTCAGTGGCGCTCTTTTTAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAG
130 CCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAATCAGTGGCAC-CTTTTCAAAGCCCACAAG
* * *
1028131 TCAGTGGCACCCTTTCAAAGCCCATAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAATGGCA
193 TCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
1028196 CCCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAATTCAGTGGCACTCTTTCAA
258 CCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTGCAAAGCCCACAAGTCAGTGGCACTCTTTCAA
1028261 AGCCCACAAGTCAGTGGCA
323 AGCCCACAAGTCAGTGGCA
1028280 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTT
1 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTT
1028345 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
66 TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
*
1028410 CACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAGT
131 CACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAATCAGTGGCAC-CTTTTCAAAGCCCACAAGT
* *
1028475 TAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAGAGCCCACAAGTCAGTGGCAC
194 CAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1028540 CCTTGCGAAGCCCACAAGTCAGTGGCACCCTTGCGAAGCCCACAATTCAGTGGCACTCTTTCAAA
259 CCTTTCAAAGCCCACAAGTCAGTGGCACCCTTGCAAAGCCCACAAGTCAGTGGCACTCTTTCAAA
1028605 GCCCACAAGTCAGTGGCA
324 GCCCACAAGTCAGTGGCA
* *
1028623 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTCAGTGGCAC-CT
1 CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAATCAGTGGCACTCT
* * *
1028687 TTTGAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAG
64 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG
* * ** * * *
1028751 CCCACAAGTTAGTGGCACCCTTTC-AAGCCCATGAGTCAGTGGTACCTTTTCAAAGCCCACGAGT
129 CCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGT
* * * * *
1028815 CAGTGGCACTCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACGAGTTAGTGGCAT
194 CAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* ** **
1028880 TCTTTCAAAGCCCACGCAAGTCAGTGGCACCCTTTTTAAAGCCCACGCAAGTCAGTAACACTCTT
259 CCTTTCAAAGCCCA--CAAGTCAGTGGCACCC-TTGCAAAGCCCA--CAAGTCAGTGGCACTC-T
* *
1028945 TTCAAAGCTCACATGTGTCAGTGGCAA
318 TTCAAAGCCCACA--AGTCAGTGGC-A
** * *
1028972 CTTTTTTCAAAGCCTACACAAGTTAGTGGCAC
1 CCCTTTT-AAAGCCCACACAAGTCAGTGGCAC
1029004 ATTTTTTTTA
Statistics
Matches: 976, Mismatches: 71, Indels: 29
0.91 0.07 0.03
Matches are distributed among these distances:
340 90 0.09
341 52 0.05
342 85 0.09
343 518 0.53
344 100 0.10
345 81 0.08
346 13 0.01
348 9 0.01
349 6 0.01
350 22 0.02
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (341 bp):
CCCTTTTAAAGCCCACACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTT
TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCC
CACAAGTCAGTGGCACCTTTTCAAAGCCCACAAATCAGTGGCACCTTTTCAAAGCCCACAAGTCA
GTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACAAGTCAGTGGCACCCTTGCAAAGCCCACAAGTCAGTGGCACTCTTTCAAAGC
CCACAAGTCAGTGGCA
Found at i:1029593 original size:20 final size:20
Alignment explanation
Indices: 1029565--1029639 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1029555 TTTTACCCTG
1029565 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1029585 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1029605 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTTTTCA
1029625 ATGTATCGATACATT
1 ATGTATCGATACATT
1029640 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1029632 original size:40 final size:39
Alignment explanation
Indices: 1029565--1029642 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1029555 TTTTACCCTG
* *
1029565 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCGATACAT-TATGA
* *
1029605 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCGATACATTATG
1029643 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCGATACATTATGA
Found at i:1030570 original size:22 final size:22
Alignment explanation
Indices: 1030544--1030594 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1030534 AGCCTTTGAC
1030544 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1030566 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
1030588 CATGCAT
1 CATGCAT
1030595 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:1033786 original size:66 final size:66
Alignment explanation
Indices: 1033447--1033856 Score: 254
Period size: 66 Copynumber: 6.2 Consensus size: 66
1033437 ACTCTTCTCA
** * *** * * *
1033447 CTTAGTTGACTTTATTTGTTTTACCCTAGTCAACTTTTTTTTGACTTAGACTTT-TCCTTGGTCA
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAG-GTTTCGCCCTGGTCA
1033511 CC
65 CC
* * *** * * * * *
1033513 CTTAG-TGACTTTATCGATTTCATTTTAGTCAACCCCTTTTTGACTTAGGTTCCACCCTGTTTAC
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTCGCCCTGGTCAC
1033577 C
66 C
* * * * * * * * ** * * *
1033578 TTTATTTGATTTTCTCAGTTTTGCCCTGATTAACCCCTTTTCAATTTAGGTTTCACCATGGTCAC
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTCGCCCTGGTCAC
*
1033643 T
66 C
*** * * * * *
1033644 CTTAGTTGACTTTATTACTTTTACCCTGGTTAA-CCCTTTTTGACTTAAGTCTCGTCCTAGTCAC
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTCGCCCTGGTCAC
*
1033708 T
66 C
* * * * * *
1033709 CTTTGTTGACTTTATCGGTTTTGCCCTGGTTAATCCTTTTTTGACTTAGGTTTTGCCCTGGTCAC
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTCGCCCTGGTCAC
1033774 C
66 C
** * * ** * *
1033775 CTTAGTTGACTTTATCGGTTTCGCCATGATCAACCCCTTTTCAACATAAG-TTCTG-CCTAGGTC
1 CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTC-GCCCT-GGTC
1033838 ACC
64 ACC
1033841 CTTAGTTGACTTTATC
1 CTTAGTTGACTTTATC
1033857 AAGTTCACCC
Statistics
Matches: 260, Mismatches: 79, Indels: 10
0.74 0.23 0.03
Matches are distributed among these distances:
64 2 0.01
65 100 0.38
66 158 0.61
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (66 bp):
CTTAGTTGACTTTATCGGTTTTACCCTGGTCAACCCCTTTTTGACTTAGGTTTCGCCCTGGTCAC
C
Found at i:1035263 original size:11 final size:12
Alignment explanation
Indices: 1035240--1035268 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1035230 TATGATTATG
1035240 AATTTTAATTTT
1 AATTTTAATTTT
1035252 AATTTT-ATTTT
1 AATTTTAATTTT
1035263 AATTTT
1 AATTTT
1035269 GGATTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
AATTTTAATTTT
Found at i:1035285 original size:6 final size:6
Alignment explanation
Indices: 1035240--1035268 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1035230 TATGATTATG
1035240 AATTTT AATTTT AATTTT -ATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
1035269 GGATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
AATTTT
Found at i:1038628 original size:21 final size:21
Alignment explanation
Indices: 1038603--1038646 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1038593 ATTTTAATCC
1038603 TCTTAAG-AATTCTACCCAAAT
1 TCTTAAGTAATTCT-CCCAAAT
* *
1038624 TCTTATGTAATTCTCTCAAAT
1 TCTTAAGTAATTCTCCCAAAT
1038645 TC
1 TC
1038647 ACACACCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (21 bp):
TCTTAAGTAATTCTCCCAAAT
Found at i:1042640 original size:2 final size:2
Alignment explanation
Indices: 1042633--1042673 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1042623 TTCCTGCCTC
* *
1042633 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TT TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1042674 TTGGATCTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.44, T:0.54
Consensus pattern (2 bp):
TG
Found at i:1046353 original size:6 final size:6
Alignment explanation
Indices: 1046342--1046378 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1046332 AGCTTACATA
*
1046342 TATAGG TATAGG TATTGG TATAGG TATAGG TATAGG T
1 TATAGG TATAGG TATAGG TATAGG TATAGG TATAGG T
1046379 GTAGATATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.38
Consensus pattern (6 bp):
TATAGG
Found at i:1046870 original size:7 final size:7
Alignment explanation
Indices: 1046858--1046882 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1046848 AAAAGGGGAT
1046858 TTGAACC
1 TTGAACC
1046865 TTGAACC
1 TTGAACC
1046872 TTGAACC
1 TTGAACC
1046879 TTGA
1 TTGA
1046883 CTCTCTAAAT
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:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (7 bp):
TTGAACC
Found at i:1047341 original size:30 final size:30
Alignment explanation
Indices: 1047307--1047394 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 30
1047297 AATATTCATA
1047307 TTTCCTATTGTA-TTTCAATTTTGTTGATTT
1 TTTCC-ATTGTACTTTCAATTTTGTTGATTT
* **
1047337 TTTCCATTGCACTTTCGGTTTTGTTGA-TT
1 TTTCCATTGTACTTTCAATTTTGTTGATTT
*
1047366 TTTCCAGTGTACTTTCAATTTTGTTGATT
1 TTTCCATTGTACTTTCAATTTTGTTGATT
1047395 GTTGGTAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 30 0.61
30 19 0.39
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.58
Consensus pattern (30 bp):
TTTCCATTGTACTTTCAATTTTGTTGATTT
Found at i:1052488 original size:2 final size:2
Alignment explanation
Indices: 1052481--1052518 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1052471 TTTTCTTAAA
1052481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1052519 CACAAGCCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1055479 original size:3 final size:3
Alignment explanation
Indices: 1055471--1055505 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1055461 TTAGTCCAAA
1055471 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1055506 CTATAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1056653 original size:249 final size:250
Alignment explanation
Indices: 1056170--1056662 Score: 780
Period size: 249 Copynumber: 2.0 Consensus size: 250
1056160 TTCTTGATTC
*
1056170 ATTTTTTTGTATAATGTGATCATTGTAATTCAGTTTTGAGAAAATTCATATTTATATCATGTTCG
1 ATTTTTTTGAATAATGTGATCATTGTAATTCAGTTTTGAGAAAATTCATA-TTATATCA--TTCG
* * *
1056235 TGTTCTATTTTAATTTATGAATATTTACTTAATTTGTTGCAGTAATTTAACTTAGCAAAAATTGT
63 TATTCTATTTCAATTCATGAATATTTACTTAATTTGTTGCAGTAATTTAACTTAGCAAAAATTGT
* *
1056300 GTGTTAATAACATATTGGTGTTATTTTTTGTATTTAAAATATTATTTTTATATATTTTTTACATA
128 GTATTAATAACATATTGGTGCTATTTTTTGTATTTAAAATATTATTTTTATATATTTTTTACATA
* *
1056365 TTAATAATTTATTTTATGTATCATGTATATGTTTATATGTACGTTTATTTTTTACACA
193 TTAATAATTTATTTTATGTATCATATATATGTTTATATGTACGTATATTTTTTACACA
* *
1056423 ATTTTTTTGAATAATGTGATCATTGTAATTTAGTTTTGAGAAAATTCATA-TCTAT-A-TCGTAT
1 ATTTTTTTGAATAATGTGATCATTGTAATTCAGTTTTGAGAAAATTCATATTATATCATTCGTAT
*
1056485 TCTATTTCAATTCATGAATATTTACTTAATTTGTTGCAGTAATTTTACTTAGCAAAAATTTTGTG
66 TCTATTTCAATTCATGAATATTTACTTAATTTGTTGCAGTAATTTAACTTAGCAAAAA--TTGTG
1056550 TATTAATAACATATTGGTGCTATTTTTTGTATTTAAAATATTATATTTTTATATATTTTTTACAT
129 TATTAATAACATATTGGTGCTATTTTTTGTATTTAAAATA-T-TATTTTTATATATTTTTTACAT
*
1056615 ATTAATAATTTATTTTAT-T-TCATATTTATGTTTATATGTACGTATATT
192 ATTAATAATTTATTTTATGTATCATATATATGTTTATATGTACGTATATT
1056663 CGTATTATGT
Statistics
Matches: 224, Mismatches: 12, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
247 60 0.27
249 69 0.31
250 3 0.01
251 44 0.20
253 48 0.21
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (250 bp):
ATTTTTTTGAATAATGTGATCATTGTAATTCAGTTTTGAGAAAATTCATATTATATCATTCGTAT
TCTATTTCAATTCATGAATATTTACTTAATTTGTTGCAGTAATTTAACTTAGCAAAAATTGTGTA
TTAATAACATATTGGTGCTATTTTTTGTATTTAAAATATTATTTTTATATATTTTTTACATATTA
ATAATTTATTTTATGTATCATATATATGTTTATATGTACGTATATTTTTTACACA
Found at i:1057101 original size:16 final size:17
Alignment explanation
Indices: 1057072--1057112 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1057062 TTTATTAAAT
1057072 AAATTTTA-TCAATT-A
1 AAATTTTATTCAATTAA
* *
1057087 TAATTTTATTTAATTAA
1 AAATTTTATTCAATTAA
1057104 AAATTTTAT
1 AAATTTTAT
1057113 AAATATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 7 0.33
16 5 0.24
17 9 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTTATTCAATTAA
Found at i:1057244 original size:11 final size:9
Alignment explanation
Indices: 1057217--1057258 Score: 66
Period size: 9 Copynumber: 4.4 Consensus size: 9
1057207 TACGTAGTGG
1057217 AAAAAGAAA
1 AAAAAGAAA
1057226 AAAAAGAAGA
1 AAAAAGAA-A
1057236 AAAAGAGAAA
1 AAAA-AGAAA
1057246 AAAAAGAAA
1 AAAAAGAAA
1057255 AAAA
1 AAAA
1057259 TTATAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 17 0.55
10 10 0.32
11 4 0.13
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1057246 original size:20 final size:18
Alignment explanation
Indices: 1057217--1057258 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
1057207 TACGTAGTGG
1057217 AAAAAGAAAAAAAAGAAGA
1 AAAAAGAAAAAAAAGAA-A
1057236 AAAAGAGAAAAAAAAGAAA
1 AAAA-AGAAAAAAAAGAAA
1057255 AAAA
1 AAAA
1057259 TTATAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAGAAA
Found at i:1057311 original size:24 final size:24
Alignment explanation
Indices: 1057284--1057404 Score: 85
Period size: 24 Copynumber: 5.1 Consensus size: 24
1057274 ATGTTTGTTT
1057284 TTATATTTTTTATTATTTAAAATA
1 TTATATTTTTTATTATTTAAAATA
* *
1057308 TTATA---TTT-TTATTT-ATATT
1 TTATATTTTTTATTATTTAAAATA
* * *
1057327 TTTTATTTATTTA-TATTTTAGAGT-
1 TTATATTT-TTTATTA-TTTAAAATA
1057351 TTATATTTTTTATTATTTAAAATA
1 TTATATTTTTTATTATTTAAAATA
*
1057375 TTATAAATTTTTGTAATATTTATAAATA
1 TTAT--ATTTTT-TATTATTTA-AAATA
1057403 TT
1 TT
1057405 TTTATATTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
19 7 0.09
20 6 0.08
21 3 0.04
23 15 0.20
24 21 0.28
25 1 0.01
26 6 0.08
27 8 0.11
28 7 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTATATTTTTTATTATTTAAAATA
Found at i:1057323 original size:12 final size:13
Alignment explanation
Indices: 1057308--1057364 Score: 53
Period size: 13 Copynumber: 4.1 Consensus size: 13
1057298 ATTTAAAATA
1057308 TTATA-TTTTTAT
1 TTATATTTTTTAT
1057320 TTATATTTTTTAT
1 TTATATTTTTTAT
*
1057333 TTATTTATATTTTAGAGT
1 TTA--TAT-TTTT-TA-T
1057351 TTATATTTTTTAT
1 TTATATTTTTTAT
1057364 T
1 T
1057365 ATTTAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
12 5 0.14
13 12 0.32
14 1 0.03
15 7 0.19
16 7 0.19
17 1 0.03
18 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATATTTTTTAT
Found at i:1057331 original size:29 final size:32
Alignment explanation
Indices: 1057294--1057362 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 32
1057284 TTATATTTTT
* *
1057294 TATTATTTAAAATA-TTATATTTT-TA-TTTA
1 TATTTTTTAAAATATTTATATTTTAGAGTTTA
**
1057323 TATTTTTT-ATTTATTTATATTTTAGAGTTTA
1 TATTTTTTAAAATATTTATATTTTAGAGTTTA
1057354 TATTTTTTA
1 TATTTTTTA
1057363 TTATTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.09
29 16 0.50
30 1 0.03
31 12 0.38
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (32 bp):
TATTTTTTAAAATATTTATATTTTAGAGTTTA
Found at i:1057345 original size:17 final size:17
Alignment explanation
Indices: 1057283--1057345 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
1057273 TATGTTTGTT
1057283 TTTATATTTTTTA-TTA
1 TTTATATTTTTTATTTA
*
1057299 TTTAAAATATTATATT-TTTA
1 TTT---ATATT-TTTTATTTA
1057319 TTTATATTTTTTATTTA
1 TTTATATTTTTTATTTA
1057336 TTTATATTTT
1 TTTATATTTT
1057346 AGAGTTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 6 0.15
17 19 0.49
19 5 0.13
20 9 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTTTTTATTTA
Found at i:1057411 original size:18 final size:19
Alignment explanation
Indices: 1057371--1057434 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1057361 TATTATTTAA
1057371 AATA-TTATAAATTTTTGT
1 AATATTTATAAATTTTTGT
1057389 AATATTTATAAATATTTT-T
1 AATATTTATAAAT-TTTTGT
* * *
1057408 -ATATTTGTATATTTATGT
1 AATATTTATAAATTTTTGT
*
1057426 CATATTTAT
1 AATATTTAT
1057435 TTTTATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.08
18 15 0.39
19 16 0.42
20 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
AATATTTATAAATTTTTGT
Found at i:1057639 original size:2 final size:2
Alignment explanation
Indices: 1057632--1057658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1057622 TAATTTAATA
1057632 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1057659 ATGAGTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1061579 original size:22 final size:23
Alignment explanation
Indices: 1061554--1061625 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1061544 TAATAAAATA
*
1061554 TAAATTTAAACTTAAA-CCCATT
1 TAAATTTAAACTAAAAGCCCATT
* *
1061576 TAAATTTAAACTAAAAGCTCATC
1 TAAATTTAAACTAAAAGCCCATT
* *
1061599 TAAATCTAAACTAAAAGCCCAAT
1 TAAATTTAAACTAAAAGCCCATT
1061622 TAAA
1 TAAA
1061626 ACAAAACAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 15 0.36
23 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (23 bp):
TAAATTTAAACTAAAAGCCCATT
Found at i:1061632 original size:23 final size:23
Alignment explanation
Indices: 1061583--1061637 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1061573 ATTTAAATTT
* * *
1061583 AAACTAAAAGCTCATCTAAATCT
1 AAACTAAAAGCCCATCTAAAACA
1061606 AAACTAAAAGCCCAAT-TAAAACA
1 AAACTAAAAGCCC-ATCTAAAACA
*
1061629 AAACAAAAA
1 AAACTAAAA
1061638 AAGCAACAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (23 bp):
AAACTAAAAGCCCATCTAAAACA
Found at i:1061669 original size:21 final size:22
Alignment explanation
Indices: 1061645--1061692 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1061635 AAAAAGCAAC
1061645 AAAATCTA-ATTAAAACAAAA-A
1 AAAATCTAGATT-AAACAAAATA
* *
1061666 AAAATGTAGATTGAACAAAATA
1 AAAATCTAGATTAAACAAAATA
1061688 AAAAT
1 AAAAT
1061693 AACTCAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAATCTAGATTAAACAAAATA
Found at i:1067913 original size:21 final size:22
Alignment explanation
Indices: 1067875--1067920 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1067865 ATATGTTGAA
* **
1067875 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1067896 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1067918 ACT
1 ACT
1067921 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1076253 original size:2 final size:2
Alignment explanation
Indices: 1076246--1076276 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1076236 ACCCAATAAT
1076246 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 T
1076277 TTGGCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1076589 original size:25 final size:25
Alignment explanation
Indices: 1076544--1076614 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 25
1076534 AATATAATTT
1076544 AAATAAA-ATAAT-TGAATA-AAAA
1 AAATAAATATAATATGAATATAAAA
*
1076566 ATA-AAATATAATATG-ATATAAAA
1 AAATAAATATAATATGAATATAAAA
* * *
1076589 ATATGATTATAATATGAATATAAAA
1 AAATAAATATAATATGAATATAAAA
1076614 A
1 A
1076615 TATATTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 3 0.07
22 10 0.24
23 9 0.22
24 10 0.24
25 9 0.22
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (25 bp):
AAATAAATATAATATGAATATAAAA
Found at i:1076621 original size:24 final size:24
Alignment explanation
Indices: 1076551--1076621 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
1076541 TTTAAATAAA
* *
1076551 ATAAT-TGAATA-AAAAATAAAAT
1 ATAATATGAATATAAAAATATATT
1076573 ATAATATG-ATATAAAAATATGATT
1 ATAATATGAATATAAAAATAT-ATT
1076597 ATAATATGAATATAAAAATATATT
1 ATAATATGAATATAAAAATATATT
1076621 A
1 A
1076622 AAATTTATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.19
23 9 0.21
24 14 0.33
25 12 0.28
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.34
Consensus pattern (24 bp):
ATAATATGAATATAAAAATATATT
Found at i:1076644 original size:17 final size:17
Alignment explanation
Indices: 1076620--1076660 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1076610 AAAAATATAT
1076620 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1076636 TAAATATTTATATAAATA
1 TAAA-ATTTATATAAATA
*
1076654 TATAATT
1 TAAAATT
1076661 ATGTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 11 0.50
18 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1076652 original size:27 final size:28
Alignment explanation
Indices: 1076567--1076657 Score: 79
Period size: 27 Copynumber: 3.4 Consensus size: 28
1076557 GAATAAAAAA
1076567 TAAAATATAATATG-ATATAAAAATATGAT
1 TAAAATAT-ATATGAATATAAAAATAT-AT
1076596 T---ATA-ATATGAATATAAAAATATAT
1 TAAAATATATATGAATATAAAAATATAT
* * *
1076620 TAAAATTTATAT-AATATAAATATTTA-
1 TAAAATATATATGAATATAAAAATATAT
1076646 TATAAATATATA
1 TA-AAATATATA
1076658 ATTATGTTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
24 8 0.15
25 12 0.23
26 5 0.10
27 22 0.42
28 4 0.08
29 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAAATATATATGAATATAAAAATATAT
Found at i:1076997 original size:7 final size:7
Alignment explanation
Indices: 1076957--1076995 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
1076947 TGCGCATCCA
1076957 TTGCCAT
1 TTGCCAT
1076964 TTGCCAT
1 TTGCCAT
1076971 TTGCCAT
1 TTGCCAT
1076978 TTGCCAT
1 TTGCCAT
*
1076985 TTGCAAT
1 TTGCCAT
1076992 TTGC
1 TTGC
1076996 AAAACCAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (7 bp):
TTGCCAT
Found at i:1077326 original size:17 final size:17
Alignment explanation
Indices: 1077303--1077349 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 17
1077293 TATTTAATTT
1077303 TTTAAAATATTTTAATA
1 TTTAAAATATTTTAATA
1077320 -TTAAAA-ATTTTAATA
1 TTTAAAATATTTTAATA
1077335 TTTTAAAAATATTTT
1 -TTT-AAAATATTTT
1077350 TAAGTTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.35
16 6 0.23
17 2 0.08
18 4 0.15
19 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATATTTTAATA
Found at i:1079347 original size:13 final size:13
Alignment explanation
Indices: 1079329--1079353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1079319 TACCAAGAAC
1079329 ATGTATCGATACA
1 ATGTATCGATACA
1079342 ATGTATCGATAC
1 ATGTATCGATAC
1079354 TAAGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1079370 original size:33 final size:32
Alignment explanation
Indices: 1079313--1079374 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
1079303 ATTCACTGTA
1079313 TATCGATACCAAGAACATGTATCGATACAATG
1 TATCGATACCAAGAACATGTATCGATACAATG
* *
1079345 TATCGATACTAAGCAATATGTATCGATACA
1 TATCGATACCAAG-AACATGTATCGATACA
1079375 TCTGGATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (32 bp):
TATCGATACCAAGAACATGTATCGATACAATG
Found at i:1081031 original size:79 final size:79
Alignment explanation
Indices: 1080876--1081023 Score: 206
Period size: 79 Copynumber: 1.9 Consensus size: 79
1080866 AAAAATTTAA
* * * *
1080876 TATTTTGAAGATAAAAACGAGGTTAGAGTATCCCCTAAAAAATAACGAGGTTGAAGTATCCCCGA
1 TATTTTAAAAATAAAAACGAGATTAGAGTATCCCCTAAAAAATAACGAGGTTGAAGTATCCCCAA
*
1080941 TTATAAAAAATCAG
66 TGATAAAAAATCAG
* * * * *
1080955 TATTTTAAAAATAAAATCGAGATTGGAGTATCCCCTTAGAAATAACGAGGTTGCAGTATCCCCAA
1 TATTTTAAAAATAAAAACGAGATTAGAGTATCCCCTAAAAAATAACGAGGTTGAAGTATCCCCAA
1081020 TGAT
66 TGAT
1081024 GGAAAATCGG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (79 bp):
TATTTTAAAAATAAAAACGAGATTAGAGTATCCCCTAAAAAATAACGAGGTTGAAGTATCCCCAA
TGATAAAAAATCAG
Found at i:1081145 original size:79 final size:78
Alignment explanation
Indices: 1081032--1081499 Score: 397
Period size: 79 Copynumber: 5.9 Consensus size: 78
1081022 ATGGAAAATC
* * * * *
1081032 GGAGTATCTCCTCGAAAAA-AACGGGGTTGAAGTATCTTCGATTGTGGAAAATCAGTGTTTTAGA
1 GGAGTATCCCCTC-AAAAATAA-TGGGTTGGAGTATCTTCGATGGTGGAAAATCGGTGTTTTAGA
1081096 AATAAAA-CAGAGGTT
64 AATAAAATCAG-GGTT
* * *
1081111 GGAGTGTCCCCTCAAAAATAATGGGATTGGAGTATC-CCTGATGGTGGAAGATCGGTGTTTTAGA
1 GGAGTATCCCCTCAAAAATAATGGG-TTGGAGTATCTTC-GATGGTGGAAAATCGGTGTTTTAGA
*
1081175 AATAAAATCGGGGTT
64 AATAAAATCAGGGTT
* * * ** * *
1081190 GGAGTATCTCTTCAAAAATAACGGTTGGGTTAGAGTATCCCCGATGGTGAAAAATCGGTATTTTA
1 GGAGTATCCCCTCAAAAATAA----TGGGTTGGAGTATCTTCGATGGTGGAAAATCGGTGTTTTA
*
1081255 GAAATAAAA-CCGGGATT
62 GAAATAAAATCAGGG-TT
** * ** * *** *
1081272 AAAGTATCTCCTCGGAAATAACAGGGTTGGAGTATCTTCGATGGTGGAAAATTTTTGTTTCAGAA
1 GGAGTATCCCCTCAAAAATAA-TGGGTTGGAGTATCTTCGATGGTGGAAAATCGGTGTTTTAGAA
1081337 ATAAAATCAGGGTT
65 ATAAAATCAGGGTT
** * * * *
1081351 GGAGTATCCTTTCAAAAATAATGGGGTTGGAGTAT-TCTCGATTGTGAAAAATTGGTGTTTTGGA
1 GGAGTATCCCCTCAAAAATAAT-GGGTTGGAGTATCT-TCGATGGTGGAAAATCGGTGTTTTAGA
* *
1081415 AATAAAACCAGAGTT
64 AATAAAATCAGGGTT
* * ** * * * *
1081430 AGAGTATCCCATCGGAAATAAAGGGTTGGAGTATCCTCGATGGTGGAAAATCGATATTTTAGAAA
1 GGAGTATCCCCTCAAAAATAATGGGTTGGAGTATCTTCGATGGTGGAAAATCGGTGTTTTAGAAA
1081495 TAAAA
66 TAAAA
1081500 CATCAATGGA
Statistics
Matches: 312, Mismatches: 63, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
78 50 0.16
79 190 0.61
80 6 0.02
81 4 0.01
82 56 0.18
83 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (78 bp):
GGAGTATCCCCTCAAAAATAATGGGTTGGAGTATCTTCGATGGTGGAAAATCGGTGTTTTAGAAA
TAAAATCAGGGTT
Found at i:1081202 original size:132 final size:131
Alignment explanation
Indices: 1080913--1081198 Score: 294
Period size: 132 Copynumber: 2.2 Consensus size: 131
1080903 GTATCCCCTA
* ** * **
1080913 AAAAATAACGAGGTTGAAGTATCCCCGATTATAAAAAATCAGTATTTTAAAAATAAAATCGAGAT
1 AAAAA-AACGGGGTTGAAGTATCTTCGATTGTGGAAAATCAGTATTTTAAAAATAAAATCGAGAT
* *
1080978 TGGAGTATCCCCTTAGAAATAACGAGGTTGCAGTATCCCCAATGATGGAAAATCGGAGTATCTCC
65 TGGAGTATCCCCTCAAAAATAACGAGGTTGCAGTATCCCCAATGATGGAAAATCGGAGTATCT-C
*
1081043 TCG
129 TAG
* * *
1081046 AAAAAAACGGGGTTGAAGTATCTTCGATTGTGGAAAATCAGTGTTTTAGAAATAAAA-CAGAGGT
1 AAAAAAACGGGGTTGAAGTATCTTCGATTGTGGAAAATCAGTATTTTAAAAATAAAATC-GAGAT
* * * ** * * *
1081110 TGGAGTGTCCCCTCAAAAATAATG-GGATTGGAGTATCCCTGATGGTGGAAGATCGGTGT-T-T-
65 TGGAGTATCCCCTCAAAAATAACGAGG-TTGCAGTATCCCCAATGATGGAAAATCGGAGTATCTC
1081171 TAG
129 TAG
*
1081174 AAATAAAATCGGGGTTGGAGTATCT
1 AAA-AAAA-CGGGGTTGAAGTATCT
1081199 CTTCAAAAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
128 5 0.04
129 4 0.03
130 16 0.12
131 4 0.03
132 94 0.73
133 5 0.04
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (131 bp):
AAAAAAACGGGGTTGAAGTATCTTCGATTGTGGAAAATCAGTATTTTAAAAATAAAATCGAGATT
GGAGTATCCCCTCAAAAATAACGAGGTTGCAGTATCCCCAATGATGGAAAATCGGAGTATCTCTA
G
Found at i:1081304 original size:161 final size:157
Alignment explanation
Indices: 1081070--1081499 Score: 465
Period size: 161 Copynumber: 2.7 Consensus size: 157
1081060 GAAGTATCTT
* * * * ** * * ** *
1081070 CGATTGTGGAAAATCAGTGTTTTAGAAATAAAA-CAGAGGTTGGAGTGTCCCCTCAAAAATAATG
1 CGATGGTGAAAAATCGGTATTTTAGAAATAAAACCAGA-GTTAAAGTATCCCATCGGAAATAAAG
* * *
1081134 GGATTGGAGTATCC-CTGATGGTGGAAGATCGGTGTTTTAGAAATAAAATCGGGGTTGGAGTAT-
65 GG-TTGGAGTATCCTC-GATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATC
*
1081197 CTCTTCAAAAATAACGGTTGGGTTAGAGTATCCC
128 CT-TTCAAAAATAA---TGGGGTTAGAGTATCCC
*
1081231 CGATGGTGAAAAATCGGTATTTTAGAAATAAAACC-GGGATTAAAGTATCTCC-TCGGAAATAAC
1 CGATGGTGAAAAATCGGTATTTTAGAAATAAAACCAGAG-TTAAAGTATC-CCATCGGAAATAA-
* *** *
1081294 AGGGTTGGAGTATCTTCGATGGTGGAAAATTTTTGTTTCAGAAATAAAATCAGGGTTGGAGTATC
63 AGGGTTGGAGTATCCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATC
* * *
1081359 CTTTCAAAAATAATGGGGTTGGAGTATTCT
128 CTTTCAAAAATAATGGGGTTAGAGTATCCC
* * * * *
1081389 CGATTGTGAAAAATTGGTGTTTTGGAAATAAAACCAGAGTTAGAGTATCCCATCGGAAATAAAGG
1 CGATGGTGAAAAATCGGTATTTTAGAAATAAAACCAGAGTTAAAGTATCCCATCGGAAATAAAGG
*
1081454 GTTGGAGTATCCTCGATGGTGGAAAATCGATATTTTAGAAATAAAA
66 GTTGGAGTATCCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAA
1081500 CATCAATGGA
Statistics
Matches: 227, Mismatches: 34, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
157 45 0.20
158 63 0.28
159 2 0.01
160 1 0.00
161 107 0.47
162 9 0.04
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (157 bp):
CGATGGTGAAAAATCGGTATTTTAGAAATAAAACCAGAGTTAAAGTATCCCATCGGAAATAAAGG
GTTGGAGTATCCTCGATGGTGGAAAATCGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCTT
TCAAAAATAATGGGGTTAGAGTATCCC
Found at i:1090802 original size:3 final size:3
Alignment explanation
Indices: 1090794--1090827 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1090784 TAAGTCAACT
1090794 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1090828 TATCTTTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1092533 original size:19 final size:20
Alignment explanation
Indices: 1092509--1092557 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1092499 CAATTCACTG
1092509 TGTATCGATACCAAG-AACA
1 TGTATCGATACCAAGCAACA
* **
1092528 TGTATCGATACTAAGCAATT
1 TGTATCGATACCAAGCAACA
1092548 TGTATCGATA
1 TGTATCGATA
1092558 TATCTAGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
TGTATCGATACCAAGCAACA
Found at i:1096328 original size:20 final size:20
Alignment explanation
Indices: 1096283--1096339 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1096273 GCCAGAGAAA
* **
1096283 TGTATCGATACATTTAGTGTT
1 TGTATCGATACATTT-TTCAT
1096304 TGTATCGATACATTTTTCAT
1 TGTATCGATACATTTTTCAT
*
1096324 TGTATCGATATATTTT
1 TGTATCGATACATTTT
1096340 AGGTTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.51
Consensus pattern (20 bp):
TGTATCGATACATTTTTCAT
Found at i:1098918 original size:80 final size:79
Alignment explanation
Indices: 1098743--1099233 Score: 507
Period size: 79 Copynumber: 6.2 Consensus size: 79
1098733 TCATTGATGT
* * * * * *
1098743 TTTTATTTCTAAAACACCGATTTTTCATCATCGGGGATACTCCAAAACCTTGTTATTTTCGAGAG
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCC--AACCCTGTTATTTTTGAGGG
* *
1098808 GATACTTCAACCCCGA
64 GATACTCCAACCCCGG
* * * * *
1098824 TTTTATTTTTAAAACACTAATTTTTCACCATTGGGGATACTCCAACCCCGTTATTTTTCGAGGGG
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTT-GAGGGG
* *
1098889 ATACTTCAACCTCGG
65 ATACTCCAACCCCGG
* * * ** * * * *
1098904 TTTTATCTCCAAAACACCGATTTTTCACCATCAAAGATACTCTAACCCTGATATTTTTTAGAGGA
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTTGAGGGGA
1098969 TACTCCAACCCCGG
66 TACTCCAACCCCGG
* * * * * * * *
1098983 TTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATATTTCAACCATGTTATTTATGATGGGA
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTTGAGGGGA
1099048 TACTCCAACCCCGG
66 TACTCCAACCCCGG
* * * * *
1099062 TTTTATTTCTAAAACATCAATTTTTCACAATCGGAGATACTCCAATCCTATTATTTCCT-AGGGG
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTT-TTGAGGGG
*
1099126 ATACTCCAACCCCAG
65 ATACTCCAACCCCGG
* * * * * *
1099141 TTTTATTTCCAAAACATCGATTTTTCACTATCGAAGATACTCCAACCCCGTTATTTTTGAGGGGA
1 TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTTGAGGGGA
* * *
1099206 TACTCTAACCCTGT
66 TACTCCAACCCCGG
*
1099220 TTTTATCTCTAAAA
1 TTTTATTTCTAAAA
1099234 TATTAAAATT
Statistics
Matches: 338, Mismatches: 69, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
78 1 0.00
79 234 0.69
80 65 0.19
81 38 0.11
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTATTTCTAAAACACCAATTTTTCACCATCGGAGATACTCCAACCCTGTTATTTTTGAGGGGA
TACTCCAACCCCGG
Found at i:1099209 original size:237 final size:239
Alignment explanation
Indices: 1098743--1099235 Score: 611
Period size: 237 Copynumber: 2.1 Consensus size: 239
1098733 TCATTGATGT
* * *
1098743 TTTTATTTCTAAAACACCGATTTTTCATCATCGGGGATACTCCAAAACCTTGTTATTTTCGAGAG
1 TTTTATTTCTAAAATACCAATTTTTCATCATCGGGGATACTCC-AAACCATGTTATTTTCGAGAG
* * * * *
1098808 GATACTTCAACCCCGATTTTATTTTTAAAACACTAATTTTTCACCATTGGGGATACTCCAACCCC
65 GATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCACAATCGGAGATACTCCAACCCC
* * * * *
1098873 GTTATTTTTCGAGGGGATACTTCAACCTCGGTTTTATCTCCAAAACACCGATTTTTCACCATCAA
130 ATTATTTTCCGAGGGGATACTCCAACCCCAGTTTTATCTCCAAAACACCGATTTTTCACCATCAA
* * *
1098938 AGATACTCTAACCCTGATATTTTTTAGAGGATACTCCAACCCCGG
195 AGATACTCCAACCCCGATATTTTTGAGAGGATACTCCAACCCCGG
* *
1098983 TTTTATTTCTAAAATACCAATTTTTCA-CAATCGGGGATATTTC-AACCATGTTATTTAT-GATG
1 TTTTATTTCTAAAATACCAATTTTTCATC-ATCGGGGATACTCCAAACCATGTTATTT-TCGA-G
* *
1099045 -GGATACTCCAACCCCGGTTTTATTTCTAAAACA-TCAATTTTTCACAATCGGAGATACTCCAAT
63 AGGATACTCCAACCCCGATTTTATTTCTAAAACACT-AATTTTTCACAATCGGAGATACTCCAAC
* * * * *
1099108 CCTATTA-TTTCCTAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCGATTTTTCACTAT
127 CCCATTATTTTCCGAGGGGATACTCCAACCCCAGTTTTATCTCCAAAACACCGATTTTTCACCAT
* * * * * *
1099172 CGAAGATACTCCAACCCCGTTATTTTTGAGGGGATACTCTAACCCTGT
192 CAAAGATACTCCAACCCCGATATTTTTGAGAGGATACTCCAACCCCGG
*
1099220 TTTTATCTCTAAAATA
1 TTTTATTTCTAAAATA
1099236 TTAAAATTTT
Statistics
Matches: 217, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
237 104 0.48
238 73 0.34
239 3 0.01
240 37 0.17
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (239 bp):
TTTTATTTCTAAAATACCAATTTTTCATCATCGGGGATACTCCAAACCATGTTATTTTCGAGAGG
ATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTTCACAATCGGAGATACTCCAACCCCA
TTATTTTCCGAGGGGATACTCCAACCCCAGTTTTATCTCCAAAACACCGATTTTTCACCATCAAA
GATACTCCAACCCCGATATTTTTGAGAGGATACTCCAACCCCGG
Found at i:1102145 original size:2 final size:2
Alignment explanation
Indices: 1102138--1102169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1102128 ATTGCAAAAC
1102138 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
1102170 TATTTAGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1103119 original size:21 final size:21
Alignment explanation
Indices: 1103073--1103123 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1103063 TAGAAGAAAC
1103073 ATTATTTTTTATTTTTAATAT
1 ATTATTTTTTATTTTTAATAT
*
1103094 TTTATTTTTTATTCATTT-AT-T
1 ATTATTTTTTATT--TTTAATAT
1103115 ATTATTTTT
1 ATTATTTTT
1103124 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 21 0.81
22 2 0.08
23 3 0.12
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTATTTTTTATTTTTAATAT
Found at i:1103132 original size:21 final size:20
Alignment explanation
Indices: 1103091--1103128 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1103081 TTATTTTTAA
*
1103091 TATTTTATTTTTTATTCATT
1 TATTTTATTTTTTATTAATT
1103111 TATTATTA-TTTTTATTAA
1 TATT-TTATTTTTTATTAA
1103129 ATTTTGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTATTTTTTATTAATT
Found at i:1103184 original size:31 final size:30
Alignment explanation
Indices: 1103149--1103212 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
1103139 CAAATTGTTT
1103149 AAAAT-AAAAGTTGAATGACAAAATTCAATAC
1 AAAATCAAAA-TTGAATGACAAAATTCAAT-C
* *
1103180 AAAATCAAAATTTAATGACAAATTTCAATC
1 AAAATCAAAATTGAATGACAAAATTCAATC
1103210 AAA
1 AAA
1103213 TAAGAATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 4 0.13
31 22 0.73
32 4 0.13
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (30 bp):
AAAATCAAAATTGAATGACAAAATTCAATC
Found at i:1116877 original size:40 final size:40
Alignment explanation
Indices: 1116822--1116938 Score: 225
Period size: 40 Copynumber: 2.9 Consensus size: 40
1116812 CTTATGACTT
*
1116822 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCAGTC
1 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCAATC
1116862 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCAATC
1 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCAATC
1116902 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCA
1 TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCA
1116939 TCATTTTGGC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (40 bp):
TTCTCTTTTTGCTCGCATCTATATCTTGTCTCTGCCAATC
Found at i:1116940 original size:20 final size:20
Alignment explanation
Indices: 1116837--1116940 Score: 76
Period size: 20 Copynumber: 5.2 Consensus size: 20
1116827 TTTTTGCTCG
1116837 CATCTATATCTTGTCTCTGC
1 CATCTATATCTTGTCTCTGC
* *
1116857 CAGTCT-TCTCTT-TTTGCT-C
1 CA-TCTATATCTTGTCT-CTGC
1116876 GCATCTATATCTTGTCTCTGC
1 -CATCTATATCTTGTCTCTGC
* *
1116897 CAATCT-TCTCTT-TTTGCT-C
1 C-ATCTATATCTTGTCT-CTGC
1116916 GCATCTATATCTTGTCTCTGC
1 -CATCTATATCTTGTCTCTGC
1116937 CATC
1 CATC
1116941 ATTTTGGCAA
Statistics
Matches: 64, Mismatches: 8, Indels: 24
0.67 0.08 0.25
Matches are distributed among these distances:
19 13 0.20
20 38 0.59
21 13 0.20
ACGTcount: A:0.12, C:0.31, G:0.11, T:0.46
Consensus pattern (20 bp):
CATCTATATCTTGTCTCTGC
Found at i:1130285 original size:19 final size:19
Alignment explanation
Indices: 1130257--1130298 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1130247 GAATTTGAGG
*
1130257 AAATGAATTTGAAATATTGA
1 AAATGAATTTCAAA-ATTGA
*
1130277 AAATG-ATTTCAAAGTTGA
1 AAATGAATTTCAAAATTGA
1130295 AAAT
1 AAAT
1130299 AAAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 7 0.35
20 5 0.25
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33
Consensus pattern (19 bp):
AAATGAATTTCAAAATTGA
Found at i:1130812 original size:25 final size:23
Alignment explanation
Indices: 1130777--1130822 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
1130767 TTTAAAATGC
1130777 TTTTATGAAAACT-ATTTTAATAT
1 TTTTATGAAAA-TGATTTTAATAT
1130800 TTTTAATGTAAAATGATTTTAAT
1 TTTT-ATG-AAAATGATTTTAAT
1130823 GAAAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTATGAAAATGATTTTAATAT
Found at i:1131934 original size:20 final size:21
Alignment explanation
Indices: 1131911--1131958 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1131901 AAAAAAACTA
* *
1131911 AGAAAATAA-GAAAATAAGAG
1 AGAAAATAAGGAAAAAAAAAG
1131931 AGAAAA-AAGGAAAAAAAAAG
1 AGAAAATAAGGAAAAAAAAAG
*
1131951 AAAAAATA
1 AGAAAATA
1131959 TATATTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (21 bp):
AGAAAATAAGGAAAAAAAAAG
Found at i:1131985 original size:13 final size:14
Alignment explanation
Indices: 1131957--1132029 Score: 53
Period size: 14 Copynumber: 5.2 Consensus size: 14
1131947 AAAGAAAAAA
1131957 TATATATTTATATT
1 TATATATTTATATT
*
1131971 TATAT-TTTTTATT
1 TATATATTTATATT
1131984 TATA-ATATTATATT
1 TATATAT-TTATATT
* **
1131998 T-TTTATAAATATTT
1 TATATATTTATA-TT
*
1132012 TATATATTAATAATT
1 TATATATTTAT-ATT
1132027 TAT
1 TAT
1132030 TTTATTTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
13 16 0.35
14 17 0.37
15 12 0.26
16 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATATATTTATATT
Found at i:1132003 original size:21 final size:20
Alignment explanation
Indices: 1131961--1132001 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1131951 AAAAAATATA
1131961 TATTTATATTTATA-TTTTT
1 TATTTATATTTATATTTTTT
1131980 TATTTATAATATTATATTTTTT
1 TATTTAT-AT-TTATATTTTTT
1132002 ATAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 5 0.26
22 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTATATTTATATTTTTT
Found at i:1132025 original size:36 final size:34
Alignment explanation
Indices: 1131972--1132049 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
1131962 ATTTATATTT
*
1131972 ATATTTTTTATTTATAATATTATATT-TTTTATAA
1 ATATTTTTTATTAATAAT-TTATATTATTTTATAA
* **
1132006 ATATTTTATATATTAATAATTTATTTTATTTTATGT
1 ATATTTT-T-TATTAATAATTTATATTATTTTATAA
1132042 ATATTTTT
1 ATATTTTT
1132050 GTACGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.19
35 8 0.22
36 22 0.59
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (34 bp):
ATATTTTTTATTAATAATTTATATTATTTTATAA
Found at i:1132606 original size:10 final size:10
Alignment explanation
Indices: 1132591--1132617 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1132581 GAGGAGAGAG
1132591 AAAAAAGGAA
1 AAAAAAGGAA
1132601 AAAAAAGGAA
1 AAAAAAGGAA
1132611 AAAAAAG
1 AAAAAAG
1132618 AAAGACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAGGAA
Found at i:1133527 original size:15 final size:17
Alignment explanation
Indices: 1133495--1133531 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1133485 AATATTTTTT
*
1133495 TATATTTTTATATATTA
1 TATAATTTTATATATTA
1133512 TATAATTTT-TAT-TTA
1 TATAATTTTATATATTA
1133527 TATAA
1 TATAA
1133532 AATATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTTTATATATTA
Found at i:1142134 original size:14 final size:14
Alignment explanation
Indices: 1142117--1142146 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1142107 AATTAATGTT
1142117 AGCTGAATTATAGG
1 AGCTGAATTATAGG
1142131 AGCTGAATTATAGG
1 AGCTGAATTATAGG
1142145 AG
1 AG
1142147 TTCCTAGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.30, T:0.27
Consensus pattern (14 bp):
AGCTGAATTATAGG
Found at i:1154930 original size:7 final size:7
Alignment explanation
Indices: 1154914--1154943 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1154904 AGACCAGTCC
1154914 TTTGCCT
1 TTTGCCT
*
1154921 TTTGCGT
1 TTTGCCT
1154928 TTTGCCT
1 TTTGCCT
1154935 TTTGCCT
1 TTTGCCT
1154942 TT
1 TT
1154944 CGCTGGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.17, T:0.60
Consensus pattern (7 bp):
TTTGCCT
Found at i:1157600 original size:76 final size:78
Alignment explanation
Indices: 1157450--1157601 Score: 186
Period size: 76 Copynumber: 2.0 Consensus size: 78
1157440 AATAAAAGTT
* * * * *
1157450 CTCAATTTTAAGGTACTATTACTTAAATATCCCTAAGAGACTTGTTTTAACATGAAAATTCTCAC
1 CTCAATTTTAAGGTACTATTACTAAAATACCCCTAAGAGACATGTTTCAACATGAAAATTCCCAC
*
1157515 ATGATCCTAAGGA
66 ATGAACCTAAGGA
* *
1157528 CTCAATTTT-A-GTACTATTACTAAAATACCCCTAA-AGGACATGTTTCGACTTGAAAATTCCCA
1 CTCAATTTTAAGGTACTATTACTAAAATACCCCTAAGA-GACATGTTTCAACATGAAAATTCCCA
1157590 CA-GAAACCTAAG
65 CATG-AACCTAAG
1157602 AACTTGGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 2 0.03
76 52 0.81
77 1 0.02
78 9 0.14
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (78 bp):
CTCAATTTTAAGGTACTATTACTAAAATACCCCTAAGAGACATGTTTCAACATGAAAATTCCCAC
ATGAACCTAAGGA
Found at i:1162981 original size:52 final size:52
Alignment explanation
Indices: 1162900--1163020 Score: 206
Period size: 52 Copynumber: 2.3 Consensus size: 52
1162890 GAAAAGTTGT
* * *
1162900 CTGCATGTATCGATACATTTAATAGTGTATCGATACATTTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
*
1162952 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
1163004 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1163021 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGC
Found at i:1163033 original size:52 final size:51
Alignment explanation
Indices: 1162900--1163040 Score: 194
Period size: 52 Copynumber: 2.7 Consensus size: 51
1162890 GAAAAGTTGT
* *
1162900 CTGCATGTATCGATACATTTAATAGTGTATCGATACATTTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
* *
1162952 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGC
*
1163004 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1163041 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAATTTGC
Found at i:1163034 original size:20 final size:20
Alignment explanation
Indices: 1163009--1163074 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1162999 TTTGCCTGCA
1163009 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
1163029 TGTATCGATAC----A--A-
1 TGTATCGATACAAAGATCAG
1163042 TGTATCGATACAAAGATCAG
1 TGTATCGATACAAAGATCAG
1163062 TGTATCGATACAA
1 TGTATCGATACAA
1163075 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 24 0.62
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGATCAG
Found at i:1163047 original size:13 final size:13
Alignment explanation
Indices: 1163029--1163086 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1163019 CAAAGATCAG
1163029 TGTATCGATACAA
1 TGTATCGATACAA
1163042 TGTATCGATACAA
1 TGTATCGATACAA
*
1163055 ---A--GAT-CAG
1 TGTATCGATACAA
1163062 TGTATCGATACAA
1 TGTATCGATACAA
1163075 TGTATCGATACA
1 TGTATCGATACA
1163087 TTTGAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 27 0.73
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1163050 original size:33 final size:33
Alignment explanation
Indices: 1163008--1163086 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1162998 ATTTGCCTGC
1163008 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
1163041 ATGTATCGATACAAAGATCAGTGTATCGATACA
1 ATGTATCGATACAAAGATCAGTGTATCGATACA
1163074 ATGTATCGATACA
1 ATGTATCGATACA
1163087 TTTGAGTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAGTGTATCGATACA
Found at i:1163145 original size:13 final size:13
Alignment explanation
Indices: 1163127--1163185 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 13
1163117 AGTAGCTTAA
1163127 ATTGTATCGATAC
1 ATTGTATCGATAC
1163140 ATTGTATCGATACAAC
1 ATTGTATCGAT---AC
1163156 ACTTATGTATCGATAC
1 A--T-TGTATCGATAC
1163172 ATTGTATCGATAC
1 ATTGTATCGATAC
1163185 A
1 A
1163186 ACACTTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 23 0.57
14 1 0.03
16 6 0.15
18 1 0.03
19 9 0.22
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:1163166 original size:19 final size:19
Alignment explanation
Indices: 1163142--1163225 Score: 117
Period size: 19 Copynumber: 4.7 Consensus size: 19
1163132 ATCGATACAT
1163142 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1163161 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1163174 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1163193 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
1163213 TGTATCGATACAA
1 TGTATCGATACAA
1163226 GTCGTTGAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 6 0.10
18 1 0.02
19 25 0.43
20 16 0.28
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1163170 original size:32 final size:32
Alignment explanation
Indices: 1163129--1163204 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
1163119 TAGCTTAAAT
1163129 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1163161 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1163193 TGTATCGATACA
1 TGTATCGATACA
1163205 ACACTTTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1164323 original size:25 final size:25
Alignment explanation
Indices: 1164295--1164357 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 25
1164285 CATTTGGTAT
1164295 CGAAAAATTACAAACTATACCTTTC
1 CGAAAAATTACAAACTATACCTTTC
*
1164320 CGAAAAGGTAATTACAAACTATACTTTTC
1 CG-AAA---AATTACAAACTATACCTTTC
1164349 CAGAAAAAT
1 C-GAAAAAT
1164358 CATCTAGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
29 23 0.72
30 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (25 bp):
CGAAAAATTACAAACTATACCTTTC
Found at i:1165570 original size:13 final size:13
Alignment explanation
Indices: 1165548--1165600 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
1165538 TTTGTTTCTA
*
1165548 TTTC-TTCTCTCT
1 TTTCTTTCTCTTT
1165560 TTTCTTTCTCTTT
1 TTTCTTTCTCTTT
* *
1165573 TTTTTTTTTCTTT
1 TTTCTTTCTCTTT
1165586 TTTCTTTCT-TTT
1 TTTCTTTCTCTTT
1165598 TTT
1 TTT
1165601 AGTTGAACCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTCTCTTT
Found at i:1165582 original size:15 final size:14
Alignment explanation
Indices: 1165559--1165600 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1165549 TTCTTCTCTC
*
1165559 TTTTCTTTCTCTTT
1 TTTTCTTTCTTTTT
*
1165573 TTTT-TTT-TTCTT
1 TTTTCTTTCTTTTT
1165585 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
1165599 TT
1 TT
1165601 AGTTGAACCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 7 0.30
13 6 0.26
14 10 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTCTTTTT
Found at i:1165583 original size:19 final size:21
Alignment explanation
Indices: 1165559--1165600 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1165549 TTCTTCTCTC
1165559 TTTTC-TTTCTCTTT-TTTTT
1 TTTTCTTTTCTCTTTCTTTTT
*
1165578 TTTTCTTTTTTCTTTCTTTTT
1 TTTTCTTTTCTCTTTCTTTTT
1165599 TT
1 TT
1165601 AGTTGAACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (21 bp):
TTTTCTTTTCTCTTTCTTTTT
Found at i:1166978 original size:32 final size:32
Alignment explanation
Indices: 1166903--1167020 Score: 123
Period size: 32 Copynumber: 3.7 Consensus size: 32
1166893 CGGACATAGG
* ****
1166903 TGCCACCAACTTGTGTGGGCTTT-AAAAAAAA
1 TGCCACCAACTTGTGTGGGCTTTGGAAAGGGT
* *
1166934 TGCCACAAACTTGTGTGGGCTTT-GAAGGGGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAA-AGGGT
* * *
1166966 TGCCATCGACTTGTGTGGACTTTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGGAAAGGGT
1166998 TGCCACCAACTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
1167021 AGAGAAGGAT
Statistics
Matches: 70, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
31 24 0.34
32 43 0.61
33 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGGAAAGGGT
Found at i:1167034 original size:32 final size:30
Alignment explanation
Indices: 1166903--1167608 Score: 246
Period size: 28 Copynumber: 24.2 Consensus size: 30
1166893 CGGACATAGG
* **
1166903 TGCCACCAACTTGTGTGGGCTTTAAAAAAAA
1 TGCCACCAACTTGTGTGGGCTTT-GAAAGGA
* * *
1166934 TGCCACAAACTTGTGTGGGCTTTGAAGGGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAA--AGGA
* * * *
1166966 TGCCATCGACTTGTGTGGACTTTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAA-GGA
1166998 TGCCACCAACTTGTGTGGGCTTTAGAGAAGGA
1 TGCCACCAACTTGTGTGGGCTTT-GA-AAGGA
**
1167030 TGCCACTGAC-T-TGTGGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
* ** * * * *
1167058 TGTCACGGA-GT-TGTCGAC-TTAAAAGGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAA-GGA
* * * **
1167086 TGCCACTAAC-T-TGTAGACTTTGAAAACA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** *
1167114 GTGCCACTGACTTGT-T-GGCTTTGAAAAAGAATA
1 -TGCCACCAACTTGTGTGGGCTTTG--AAAG--GA
** *
1167147 TGCCATTAAC-T-TGTGGGCTTTTGAAAAGA
1 TGCCACCAACTTGTGTGGGC-TTTGAAAGGA
** * *
1167176 TGCCACTGAC-T-TGTAGACTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** * *
1167204 TGCCACTGAC-T-TGTAGGCTTTGAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
*** * *
1167232 TGCCATTGAC-T-TATAGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** * *
1167260 TGCCACTGAC-T-TATGGGCTTTGAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** * *
1167288 TGCCACTGAC--CTATGGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
* * *
1167316 CGCCACTAAC-T-TGTGGGCTTTGAAAGGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
* * * *
1167344 TGCCACCGATTTGTGTGGGTTTTTGAAAGGG
1 TGCCACCAACTTGTGTGGG-CTTTGAAAGGA
* **
1167375 TACCACTGAC-T-TGTGGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
* ** * *
1167403 TGCGACTGAC-T-TGTGCGCTTTGAAAGAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
***
1167431 TGCCATTGAC-T-TGTGGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** * *
1167459 TGCCACTGAC-T-TATGGGCTTTGAAAAGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
** * *
1167487 TGCCACTGATTTGTATGGG-TTTGAGAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGA-AAGGA
**
1167517 TGCCACTGAC-T-TGTGGGCTTTGAGAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGA-AAGGA
*
1167546 TGCCACTAAC-T-TGTGGGCTTTGAGAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGA-AAGGA
**
1167575 TGCCACTGAC-T-TGTGGGCTTTGAAAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGA
1167603 TGCCAC
1 TGCCAC
1167609 TGACTTATGA
Statistics
Matches: 564, Mismatches: 83, Indels: 59
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.01
28 282 0.50
29 112 0.20
30 41 0.07
31 49 0.09
32 65 0.12
33 10 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGA
Found at i:1167034 original size:64 final size:61
Alignment explanation
Indices: 1166934--1167683 Score: 294
Period size: 56 Copynumber: 12.9 Consensus size: 61
1166924 TTAAAAAAAA
** *
1166934 TGCCACAAACTTGTGTGGGCTTTGAAGGGGGTTGCCA-TCGACTTGTGTGGACTTTGGAAAGGGT
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACT-GACTTGTG-GG-CTTT-GAAAGGGT
* *
1166998 TGCCACCAACTTGTGTGGGCTTT-AGAGAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGA
1 TGCCACAAACTTGTGTGGGCTTTGA-AGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
* ** * * * * * * **
1167058 TGTCACGGA-GT-TGTCGAC-TT-AA-AAGGGATGCCACTAACTTGTAGACTTTGAAAACAG-
1 TGCCACAAACTTGTGTGGGCTTTGAAGAA-GGATGCCACTGACTTGTGGGCTTTG-AAAGGGT
** * * * * * *
1167115 TGCCACTGACTTGT-T-GGCTTTGAAAAAGAATATGCCATTAACTTGTGGGCTTTTGAAA-AGA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAG--GATGCCACTGACTTGTGGGC-TTTGAAAGGGT
** * * *
1167176 TGCCACTGAC-T-TGTAGACTTTG-A-AAGGATGCCACTGACTTGTAGGCTTTGAAAGGG-
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
*** * * *
1167232 TGCCATTGAC-T-TATAGGCTTTG-A-AAGGATGCCACTGACTTATGGGCTTTGAAAGGG-
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
** * * * *
1167288 TGCCACTGAC--CTATGGGCTTTG-A-AAGGACGCCACTAACTTGTGGGCTTTGAAAGGG-
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
** * * * * *
1167344 TGCCACCGATTTGTGTGGGTTTTTG-A-AAGGGTACCACTGACTTGTGGGCTTTGAAA-GGA
1 TGCCACAAACTTGTGTGGG-CTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
* ** * * * *
1167403 TGCGACTGAC-T-TGTGCGCTTTG-A-AAGAATGCCATTGACTTGTGGGCTTTGAAA-GGA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
** * * *
1167459 TGCCACTGAC-T-TATGGGCTTTGAA-AA-GATGCCACTGATTTGTATGGG-TTTGAGAA-GGA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTG--TGGGCTTTGA-AAGGGT
** * *
1167517 TGCCACTGAC-T-TGTGGGCTTTG-AGAAGGATGCCACTAACTTGTGGGCTTTGAGAA-GGA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGA-AAGGGT
** * *** * *
1167575 TGCCACTGAC-T-TGTGGGCTTTG-A-AAGGATGCCACTGACTTATGATTTTTTG-AAGAGA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTG-GGCTTTGAAAGGGT
** * *
1167632 TGCCACTGAC-T-TGTGGGCTTTG-A-AAGGATGCCACTGACCTATGGGCTTTGAA
1 TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAA
1167684 GAGATAAATG
Statistics
Matches: 578, Mismatches: 76, Indels: 71
0.80 0.10 0.10
Matches are distributed among these distances:
55 2 0.00
56 210 0.36
57 113 0.20
58 88 0.15
59 60 0.10
60 15 0.03
61 39 0.07
62 8 0.01
63 3 0.01
64 39 0.07
65 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (61 bp):
TGCCACAAACTTGTGTGGGCTTTGAAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGT
Found at i:1167157 original size:61 final size:61
Alignment explanation
Indices: 1167085--1167200 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1167075 CTTAAAAGGG
* *
1167085 ATGCCACTAACTTGTAGAC-TTTGAAAACAGTGCCACTGACTTGTTGGCTTTGAAAAAGAAT
1 ATGCCACTAACTTGTAGACTTTTGAAAACA-TGCCACTGACTTGTAGACTTTGAAAAAGAAT
* * * *
1167146 ATGCCATTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAA
1 ATGCCACTAACTTGTAGACTTTTGAAAACATGCCACTGACTTGTAGACTTTGAAA
1167201 GGATGCCACT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 39 0.81
62 9 0.19
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (61 bp):
ATGCCACTAACTTGTAGACTTTTGAAAACATGCCACTGACTTGTAGACTTTGAAAAAGAAT
Found at i:1167411 original size:143 final size:141
Alignment explanation
Indices: 1167011--1167683 Score: 699
Period size: 143 Copynumber: 4.7 Consensus size: 141
1167001 CACCAACTTG
* * * *
1167011 TGTGGGCTTTAGAGAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGTCACGGA-GT-TGTCG
1 TGTGGGCTTT-GA-AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTGTGTGG
** * * * * ** *
1167074 ACTTAAAAGGGATGCCACTAACTTGTAGACTTTGAAAACAGTGCCACTGACTTGTTGGCTTTGAA
64 GTTTGAAAGGG-TGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTG--
* * *
1167139 AAAGAATATGCCATTAACT
125 AAAG--GATGCCACTGACT
* * * * * *
1167158 TGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGACTTTGAAAGGATGCCACTGACTTGT-AGGC
1 TGTGGGC-TTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTGTGTGGG
* * * *
1167222 TTTGAAAGGGTGCCATTGACTTATAGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAGG
65 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGG
* *
1167287 GTGCCACTGACC
130 ATGCCACTGACT
* * * * *
1167299 TATGGGCTTTGAAAGGACGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACCGATTTGTGTGGGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTGTGTGGG-
* * *
1167364 TTTTGAAAGGGTACCACTGACTTGTGGGCTTTGAAAGGATGCGACTGACTTGTGCGCTTTGAAAG
65 -TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
* *
1167429 AATGCCATTGACT
129 GATGCCACTGACT
* * *
1167442 TGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGATTTGTATGGGT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTGTGTGGGT
* *
1167507 TTGAGAAGGATGCCACTGACTTGTGGGCTTTGAGAAGGATGCCACTAACTTGTGGGCTTTGAGAA
66 TTGA-AAGGGTGCCACTGACTTGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGA-AA
1167572 GGATGCCACTGACT
128 GGATGCCACTGACT
* *** *
1167586 TGTGGGCTTTGAAAGGATGCCACTGACTTATGATTTTTTG-AAGAGATGCCACTGACTTGTG-GG
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTG-GGCTTTGAAAG-GATGCCACTGATTTGTGTGG
* * * *
1167649 CTTTGAAAGGATGCCACTGACCTATGGGCTTTGAA
64 GTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
1167684 GAGATAAATG
Statistics
Matches: 445, Mismatches: 70, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
140 44 0.10
141 21 0.05
142 27 0.06
143 177 0.40
144 55 0.12
145 39 0.09
146 59 0.13
147 19 0.04
148 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (141 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGATTTGTGTGGGT
TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGA
TGCCACTGACT
Found at i:1167681 original size:28 final size:28
Alignment explanation
Indices: 1167011--1167683 Score: 713
Period size: 28 Copynumber: 23.5 Consensus size: 28
1167001 CACCAACTTG
1167011 TGTGGGCTTTAGAGAAGGATGCCACTGACT
1 TGTGGGCTTT-GA-AAGGATGCCACTGACT
* * *
1167041 TGTGGGCTTTGAAAGGATGTCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
1167069 TGTCGAC-TTAAAAGGGATGCCACTAACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
* * **
1167097 TGTAGACTTTGAAAACAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
1167126 TGTTGGCTTTGAAAAAGAATATGCCATTAACT
1 TGTGGGCTTTG--AAAG--GATGCCACTGACT
*
1167158 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGC-TTTGAAAGGATGCCACTGACT
* *
1167187 TGTAGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167215 TGTAGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1167243 TATAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167271 TATGGGCTTTGAAAGGGTGCCACTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167299 TATGGGCTTTGAAAGGACGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167327 TGTGGGCTTTGAAAGGGTGCCACCGATTT
1 TGTGGGCTTTGAAAGGATGCCACTGA-CT
* * *
1167356 GTGTGGGTTTTTGAAAGGGTACCACTGACT
1 -TGTGGG-CTTTGAAAGGATGCCACTGACT
*
1167386 TGTGGGCTTTGAAAGGATGCGACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167414 TGTGCGCTTTGAAAGAATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1167442 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1167470 TATGGGCTTTGAAAAGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1167498 TGTATGGG-TTTGAGAAGGATGCCACTGACT
1 TG--TGGGCTTTGA-AAGGATGCCACTGACT
*
1167528 TGTGGGCTTTGAGAAGGATGCCACTAACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
1167557 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
1167586 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* ***
1167614 TATGATTTTTTG-AAGAGATGCCACTGACT
1 TGTG-GGCTTTGAAAG-GATGCCACTGACT
*
1167643 TGTGGGCTTTGAAAGGATGCCACTGACC
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1167671 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1167684 GAGATAAATG
Statistics
Matches: 544, Mismatches: 81, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.01
28 322 0.59
29 137 0.25
30 37 0.07
31 23 0.04
32 15 0.03
33 5 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1168981 original size:13 final size:13
Alignment explanation
Indices: 1168963--1169002 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1168953 TGTTTGTTTG
1168963 TTTTTTTTATTTT
1 TTTTTTTTATTTT
*
1168976 TTTTTTCTATTTT
1 TTTTTTTTATTTT
* *
1168989 TTTGTTTTCTTTT
1 TTTTTTTTATTTT
1169002 T
1 T
1169003 GTATGAAGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.05, C:0.05, G:0.03, T:0.88
Consensus pattern (13 bp):
TTTTTTTTATTTT
Found at i:1168990 original size:15 final size:14
Alignment explanation
Indices: 1168959--1169002 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1168949 TGTTTGTTTG
*
1168959 TTTGTTTTTTTTATT
1 TTTGTTTTCTTT-TT
*
1168974 TTTTTTTTCTATTTT
1 TTTGTTTTCT-TTTT
1168989 TTTGTTTTCTTTTT
1 TTTGTTTTCTTTTT
1169003 GTATGAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.16
15 19 0.76
16 2 0.08
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.86
Consensus pattern (14 bp):
TTTGTTTTCTTTTT
Found at i:1172548 original size:34 final size:35
Alignment explanation
Indices: 1172510--1172576 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1172500 CCTTACAACA
1172510 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1172544 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1172577 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1173073 original size:13 final size:13
Alignment explanation
Indices: 1173055--1173080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1173045 CTATTTATGA
1173055 TGTATCGATACAC
1 TGTATCGATACAC
1173068 TGTATCGATACAC
1 TGTATCGATACAC
1173081 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1173203 original size:21 final size:21
Alignment explanation
Indices: 1173177--1173218 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1173167 CCTATGAAAC
*
1173177 AGTGATTTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
1173198 AGTGATGTATCGATACATGAA
1 AGTGATGTATCGATACATGAA
1173219 CAGTTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTGATGTATCGATACATGAA
Found at i:1173332 original size:53 final size:53
Alignment explanation
Indices: 1173268--1173404 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1173258 CTACTTTCAA
1173268 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1173321 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1173374 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1173405 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1173437 original size:20 final size:20
Alignment explanation
Indices: 1173374--1173444 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1173364 GCCAATGTCC
**
1173374 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1173394 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1173414 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1173434 TGTATCGATAC
1 TGTATCGATAC
1173445 TTTTCAAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1173508 original size:21 final size:21
Alignment explanation
Indices: 1173484--1173524 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1173474 GTCAACCTTG
1173484 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1173505 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1173525 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1175173 original size:13 final size:13
Alignment explanation
Indices: 1175155--1175179 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1175145 ACTGAAGTAA
1175155 TGTATCGATACAT
1 TGTATCGATACAT
1175168 TGTATCGATACA
1 TGTATCGATACA
1175180 ATCTGGAAAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.