Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 73 of 318
Found at i:21186479 original size:15 final size:16
Alignment explanation
Indices: 21186459--21186495 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
21186449 TCTTCTTGAG
*
21186459 TTTCTTT-TTTTCTCT
1 TTTCTTTCTTTTCCCT
21186474 TTTCTTTCTTTTCCCT
1 TTTCTTTCTTTTCCCT
21186490 TTTCTT
1 TTTCTT
21186496 CTTGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTCTTTTCCCT
Found at i:21187128 original size:19 final size:17
Alignment explanation
Indices: 21187084--21187130 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
21187074 AGGCCAAGTT
*
21187084 GGGCGTGTAGGCCACAC
1 GGGCGTGTGGGCCACAC
*
21187101 GGGCATGTGGGCCCACAC
1 GGGCGTGTGGG-CCACAC
21187119 AGGGCGTGTGGG
1 -GGGCGTGTGGG
21187131 TTTTTGGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.36
18 6 0.24
19 10 0.40
ACGTcount: A:0.15, C:0.26, G:0.47, T:0.13
Consensus pattern (17 bp):
GGGCGTGTGGGCCACAC
Found at i:21189722 original size:46 final size:45
Alignment explanation
Indices: 21189671--21189801 Score: 156
Period size: 46 Copynumber: 2.8 Consensus size: 45
21189661 GATGGTTGAG
*
21189671 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA-A
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGGA-ACGAGA
* * * * * *
21189717 TATCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCCT-TATGGAACGAGA
21189763 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-CTTATGG
21189802 GCGGGTTACA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
45 3 0.04
46 67 0.94
47 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (45 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCCTTATGGAACGAGA
Found at i:21192766 original size:15 final size:15
Alignment explanation
Indices: 21192696--21192771 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
21192686 CATAGTATCG
*
21192696 TATCTTGGGTTT-TT
1 TATCTTGGATTTCTT
* *
21192710 TATCCTGGATCTCTT
1 TATCTTGGATTTCTT
21192725 TAT-TTGGATTTCTT
1 TATCTTGGATTTCTT
* * *
21192739 TAT-TCCGGGTTTCTC
1 TATCT-TGGATTTCTT
21192754 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
21192769 TAT
1 TAT
21192772 TCGGTTTTCT
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
14 22 0.46
15 25 0.52
16 1 0.02
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.57
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:21192782 original size:14 final size:14
Alignment explanation
Indices: 21192716--21192782 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
21192706 TTTTTATCCT
* *
21192716 GGATCTCTTTATTT
1 GGATTTCTTTATTC
21192730 GGATTTCTTTATTCC
1 GGATTTCTTTATT-C
* * *
21192745 GGGTTTCTCTATCTT
1 GGATTTCTTTAT-TC
21192760 GGATTTCTTTATTC
1 GGATTTCTTTATTC
*
21192774 GGTTTTCTT
1 GGATTTCTT
21192783 GTTATCTTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
14 21 0.50
15 20 0.48
16 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (14 bp):
GGATTTCTTTATTC
Found at i:21195216 original size:45 final size:45
Alignment explanation
Indices: 21195166--21195337 Score: 208
Period size: 45 Copynumber: 3.8 Consensus size: 45
21195156 GGTTGAGCAT
21195166 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * *
21195211 TCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCAT-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAATG
21195257 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
21195301 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21195338 GCGGTTACAT
Statistics
Matches: 106, Mismatches: 12, Indels: 17
0.79 0.09 0.13
Matches are distributed among these distances:
42 1 0.01
43 4 0.04
44 2 0.02
45 61 0.58
46 33 0.31
47 4 0.04
48 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:21195317 original size:91 final size:91
Alignment explanation
Indices: 21195162--21195330 Score: 304
Period size: 91 Copynumber: 1.9 Consensus size: 91
21195152 GGATGGTTGA
*
21195162 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCGAACTCGTTGAGTT
21195227 GAGTCCGAGTTCGTGAATGTAACTAG
66 GAGTCCGAGTTCGTGAATGTAACTAG
*
21195253 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCGAACTCGTTGAGT
21195317 TGAGTCCGAGTTCG
65 TGAGTCCGAGTTCG
21195331 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
90 14 0.19
91 61 0.81
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (91 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAATGTAACTAG
Found at i:21203735 original size:18 final size:18
Alignment explanation
Indices: 21203708--21203748 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
21203698 ATGGAATTTG
21203708 AAAT-AAAATAGAAACAA
1 AAATAAAAATAGAAACAA
*
21203725 AAATAAAAATAGAAATAA
1 AAATAAAAATAGAAACAA
21203743 AAATAA
1 AAATAA
21203749 TAGTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (18 bp):
AAATAAAAATAGAAACAA
Found at i:21211682 original size:41 final size:41
Alignment explanation
Indices: 21211638--21211888 Score: 412
Period size: 41 Copynumber: 6.1 Consensus size: 41
21211628 CAAAAATTGT
*
21211638 AAAACACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTA
1 AAAAC-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
*
21211680 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCAA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
* *
21211721 AAAACCAGAGCATTAGCGGCGCTTTTGATAAAACGCCGCAA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
* *
21211762 AAAACCAGAGCATTGGCGGCGCTTTTGATAAAACGCCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
*
21211803 AAAACCAGAGCATTAGCGGCGCTTTTTGGTAAAACGCAGCTA
1 AAAACCAGAGCATTAGCGGCGC-TTTTGGTAAAACGCCGCTA
*
21211845 AAAACCAAAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
1 AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
21211886 AAA
1 AAA
21211889 GTCATATAAC
Statistics
Matches: 198, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
41 155 0.78
42 43 0.22
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (41 bp):
AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTA
Found at i:21212068 original size:14 final size:14
Alignment explanation
Indices: 21212046--21212150 Score: 66
Period size: 14 Copynumber: 7.2 Consensus size: 14
21212036 TTAATTATCA
*
21212046 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
21212060 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* * *
21212074 ATATGATTTAGGGT
1 TTATGGTTTAAGGT
* *
21212088 TTAAGGTTTAGGAGT
1 TTATGGTTTAAG-GT
*
21212103 TAACTATGGTTTAAGAT
1 T---TATGGTTTAAGGT
* * *
21212120 ATATGATTTAGGGT
1 TTATGGTTTAAGGT
*
21212134 TTAAGGTTTAAGGT
1 TTATGGTTTAAGGT
21212148 TTA
1 TTA
21212151 GGAGTTAACT
Statistics
Matches: 67, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
14 54 0.81
15 3 0.04
17 1 0.01
18 9 0.13
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.45
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:21212088 original size:21 final size:21
Alignment explanation
Indices: 21212059--21212138 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 21
21212049 TAGTTTAAGG
*
21212059 TTTATGGTTTAAGATATATGA
1 TTTAGGGTTTAAGATATATGA
* * *
21212080 TTTAGGGTTTAAGGTTTAGGA
1 TTTAGGGTTTAAGATATATGA
*
21212101 GTTAACTATGGTTTAAGATATATGA
1 -TT---TAGGGTTTAAGATATATGA
21212126 TTTAGGGTTTAAG
1 TTTAGGGTTTAAG
21212139 GTTTAAGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
21 27 0.59
22 2 0.04
24 2 0.04
25 15 0.33
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (21 bp):
TTTAGGGTTTAAGATATATGA
Found at i:21217122 original size:28 final size:27
Alignment explanation
Indices: 21217059--21217128 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21217049 ATAGTGAGTC
*
21217059 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
21217086 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
21217114 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21217129 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:21225059 original size:28 final size:27
Alignment explanation
Indices: 21224996--21225065 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21224986 ATAGTGAGTC
*
21224996 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
21225023 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
21225051 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21225066 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:21228371 original size:27 final size:27
Alignment explanation
Indices: 21228353--21228422 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21228343 ATAGTGAGTC
21228353 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
21228380 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
21228408 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21228423 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:21228416 original size:28 final size:28
Alignment explanation
Indices: 21228353--21228451 Score: 119
Period size: 30 Copynumber: 3.5 Consensus size: 28
21228343 ATAGTGAGTC
* *
21228353 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATGATCAAACT
21228380 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATGATCAAACT
* * * *
21228408 CGCACACTTAGTGCTGTACAAGTTTAAACC
1 CGCACACTTAGTGC--TACATGATCAAACT
21228438 CGCACACTTAGTGC
1 CGCACACTTAGTGC
21228452 CATTCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 21 0.33
28 18 0.29
30 24 0.38
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATGATCAAACT
Found at i:21236350 original size:28 final size:27
Alignment explanation
Indices: 21236287--21236356 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
21236277 ATAGTGAGTC
*
21236287 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
21236314 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
21236342 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
21236357 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:21240090 original size:19 final size:19
Alignment explanation
Indices: 21240068--21240108 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21240058 TTTATTGATA
21240068 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
21240086 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
21240105 TTTT
1 TTTT
21240109 GACTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:21240416 original size:43 final size:43
Alignment explanation
Indices: 21240355--21240500 Score: 213
Period size: 43 Copynumber: 3.4 Consensus size: 43
21240345 TTTTTGAATT
* *
21240355 TCATGACCTTTAACGGCGTTTGTGGGAAAAGTGCCGCTAAAGG
1 TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
* *
21240398 TCATGGCCTTTAGCGGCGTTTGT-GGAAAAGCGCTGCTAAAGG
1 TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
* * *
21240440 TCATGATCTTTAGCGGCGTTTGTGCGAAAAGCGCCACTAAAGG
1 TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
*
21240483 TCATGATCTTTAGCGGCG
1 TCATGACCTTTAGCGGCG
21240501 CTTTTTTTCA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 38 0.41
43 55 0.59
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
TCATGACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGG
Found at i:21244021 original size:24 final size:24
Alignment explanation
Indices: 21243991--21244209 Score: 357
Period size: 24 Copynumber: 9.1 Consensus size: 24
21243981 GAATGTGACT
* *
21243991 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
21244015 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
21244039 ATAGTAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
21244063 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
21244087 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
* *
21244111 ATAGTGAATCGCACACCTAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
21244135 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
21244159 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
21244183 ATAGTAAACCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
21244207 ATA
1 ATA
21244210 TGGTCTTTGC
Statistics
Matches: 184, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 184 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:21246905 original size:41 final size:41
Alignment explanation
Indices: 21246860--21246938 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
21246850 AAACTATCAA
*
21246860 TACTATACATGAATATTAAATTGAGTGTGTTTCTAACAGAT
1 TACTATACACGAATATTAAATTGAGTGTGTTTCTAACAGAT
*
21246901 TACTATACCCGAATATTAAATTGAGTGTGTTTCTAACA
1 TACTATACACGAATATTAAATTGAGTGTGTTTCTAACA
21246939 AATTTTATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (41 bp):
TACTATACACGAATATTAAATTGAGTGTGTTTCTAACAGAT
Found at i:21257445 original size:44 final size:44
Alignment explanation
Indices: 21257303--21257501 Score: 196
Period size: 44 Copynumber: 4.6 Consensus size: 44
21257293 TCATACAATT
* * * *
21257303 CCAACGTCTCAGACGTGGTCTTACATGT-AATCA-AATATCGATG
1 CCAACGTCCCAGACGTGGTCTTACACGTAAATCATAA-GTCGATA
* *
21257346 CC-ACTGTCCCAGACAG-AGTCTTACACG-AAATCA-AA-TACGATG
1 CCAAC-GTCCCAGAC-GTGGTCTTACACGTAAATCATAAGT-CGATA
* * *
21257388 CCAACGTCCCAGACGTGGTCTTATACGTCAATCATAAGTTGATA
1 CCAACGTCCCAGACGTGGTCTTACACGTAAATCATAAGTCGATA
* *
21257432 CCAACGTCTCAGACGTGGTCTTACACGTAAATCATAAGTCGATG
1 CCAACGTCCCAGACGTGGTCTTACACGTAAATCATAAGTCGATA
* *
21257476 CCAATGTCCCAGACATGGTCTTACAC
1 CCAACGTCCCAGACGTGGTCTTACAC
21257502 AATAACATAT
Statistics
Matches: 131, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.02
42 27 0.21
43 33 0.25
44 68 0.52
45 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.25
Consensus pattern (44 bp):
CCAACGTCCCAGACGTGGTCTTACACGTAAATCATAAGTCGATA
Found at i:21262171 original size:2 final size:2
Alignment explanation
Indices: 21262164--21262198 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21262154 TTGAAAATGA
21262164 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21262199 AAGCCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21262795 original size:68 final size:67
Alignment explanation
Indices: 21262715--21262843 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 67
21262705 TCTAAATAAG
* *
21262715 AAAAGGTAAAACTACACCGTTTTGATAAATGTTCACTTT-TTAAAGTTAAAAGTCAAAACCATTA
1 AAAAGGCAAAACTACACCGTTTTGATAAATGTTCA-TTTATTAAA-TTAAAAGCCAAAACCATTA
21262779 AGTT
64 AGTT
**** *
21262783 AAAAGGCAAAACTATGTTGTTTTGATAAATGTTTATTTATTAAATTAAAAGCCAAAACCAT
1 AAAAGGCAAAACTACACCGTTTTGATAAATGTTCATTTATTAAATTAAAAGCCAAAACCAT
21262844 GATGTAGTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 19 0.36
68 34 0.64
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (67 bp):
AAAAGGCAAAACTACACCGTTTTGATAAATGTTCATTTATTAAATTAAAAGCCAAAACCATTAAG
TT
Found at i:21266950 original size:21 final size:21
Alignment explanation
Indices: 21266924--21266973 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
21266914 TGTGTGTTGG
21266924 ATTAAATTAAATATGAATTAT
1 ATTAAATTAAATATGAATTAT
21266945 ATTAAATTAAATATGAATTAT
1 ATTAAATTAAATATGAATTAT
21266966 ATTAAATT
1 ATTAAATT
21266974 GAGTTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
ATTAAATTAAATATGAATTAT
Found at i:21266964 original size:16 final size:15
Alignment explanation
Indices: 21266945--21266983 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
21266935 TATGAATTAT
21266945 ATTAAATTAAATATGA
1 ATTAAATTAAAT-TGA
*
21266961 ATTATATTAAATTGA
1 ATTAAATTAAATTGA
*
21266976 GTTAAATT
1 ATTAAATT
21266984 CATTCATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (15 bp):
ATTAAATTAAATTGA
Found at i:21268455 original size:2 final size:2
Alignment explanation
Indices: 21268395--21268436 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
21268385 ATATCTTATC
21268395 AT AT 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 AT AT
21268437 CATACCAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21269385 original size:46 final size:46
Alignment explanation
Indices: 21269317--21269481 Score: 231
Period size: 46 Copynumber: 3.6 Consensus size: 46
21269307 CCATAGTGTT
* * **
21269317 TTTCAACTATGGTCTTACTCATTTCCTATCATGTTGTTATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
* * *
21269363 TTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
** *
21269409 TTTCAACCATGGTCTTACAAATTTCATATTATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
*
21269455 TTTCAACCATGGTCTTACACATTTCAT
1 TTTCAACCATGGTCTTACTCATTTCAT
21269482 TTCAGAAAGC
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATC
Found at i:21273141 original size:45 final size:45
Alignment explanation
Indices: 21273091--21273212 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 45
21273081 CAATACCGAT
* * ** * * *
21273091 GTCCCAGACATGGTCTTACTCGTAACCATATATATCGATACCAAC
1 GTCCCAGACGTGGTCTTACACAAAAACACATATATCGACACCAAC
*
21273136 GTCCCAGACGTGGTCTTACACAAAAACACATATATCGACGCCAAC
1 GTCCCAGACGTGGTCTTACACAAAAACACATATATCGACACCAAC
*
21273181 GTCCCAGACGTGGTCTTACACGAAAACACATA
1 GTCCCAGACGTGGTCTTACACAAAAACACATA
21273213 GCATAGTCCT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.21
Consensus pattern (45 bp):
GTCCCAGACGTGGTCTTACACAAAAACACATATATCGACACCAAC
Found at i:21276408 original size:19 final size:19
Alignment explanation
Indices: 21276384--21276422 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
21276374 TCCATCAGAT
21276384 TCTCCTCATCAAGGTCAAC
1 TCTCCTCATCAAGGTCAAC
21276403 TCTCCTCATCAAGGTCAAC
1 TCTCCTCATCAAGGTCAAC
21276422 T
1 T
21276423 GAGGTCTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.36, G:0.10, T:0.28
Consensus pattern (19 bp):
TCTCCTCATCAAGGTCAAC
Found at i:21281492 original size:126 final size:127
Alignment explanation
Indices: 21281324--21281575 Score: 402
Period size: 127 Copynumber: 2.0 Consensus size: 127
21281314 TGAGGGCTCC
* *
21281324 ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTC-AAACCACAAA-AATATTTGCTTTC
1 ACCATGGACAACAGGAGTTATTGCAACTAAAGTATGTGTCAAAACCA-AAATAATATTTGCCTTC
* * * * *
21281387 TAAATAATGTAATAAAGTAATTAACAAAAATTGCCTTCAGGAAAATTTTCACACTTTTACAGCT
65 TAAACAATGTAATAAAGTAACTAACAAAAATTGCATTCAAG-AAATTTTCACACTTTGACAGCT
21281451 ACCAT-GACAACAGGAGTTATTGCAACTAAAGTATGTGTCAAAACCAAAATAATATTTGCCTTCT
1 ACCATGGACAACAGGAGTTATTGCAACTAAAGTATGTGTCAAAACCAAAATAATATTTGCCTTCT
21281515 AAACAATGTAATAAAGTAACTAACAAAAATTGCATTCAAGAAATTTTCACACTTTGACAGC
66 AAACAATGTAATAAAGTAACTAACAAAAATTGCATTCAAGAAATTTTCACACTTTGACAGC
21281576 AAGGTTCAGA
Statistics
Matches: 116, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
126 56 0.48
127 60 0.52
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.29
Consensus pattern (127 bp):
ACCATGGACAACAGGAGTTATTGCAACTAAAGTATGTGTCAAAACCAAAATAATATTTGCCTTCT
AAACAATGTAATAAAGTAACTAACAAAAATTGCATTCAAGAAATTTTCACACTTTGACAGCT
Found at i:21284638 original size:2 final size:2
Alignment explanation
Indices: 21284631--21284657 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21284621 TCCGATAGAT
21284631 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
21284658 TCATAAAATG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21291598 original size:69 final size:69
Alignment explanation
Indices: 21291487--21291621 Score: 252
Period size: 69 Copynumber: 2.0 Consensus size: 69
21291477 ACTCTATCAA
*
21291487 CCCTACCACCACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTATTTTGGAACCTG
1 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTATTTTGGAACCTG
21291552 TCAG
66 TCAG
*
21291556 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTGTTTTGGAACCTG
1 CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTATTTTGGAACCTG
21291621 T
66 T
21291622 TTTTCCTATC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.27
Consensus pattern (69 bp):
CCCTACCACAACTACAAAACCTGCTGAAAATCCTACAGCCACTGTTATTCCTATTTTGGAACCTG
TCAG
Found at i:21296442 original size:42 final size:42
Alignment explanation
Indices: 21296335--21296435 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
21296325 GTACATATCT
* *
21296335 TTTACTTTATTTATTGAAGAGATAATTTTTTAAATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
21296377 TTTACTTTATATATTAAAGAGATAATTTTTT-AATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
21296418 -TTACTCTTTATATATTAA
1 TTTA--CTTTATATATTAA
21296436 TTAGATACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
40 3 0.05
41 10 0.18
42 42 0.76
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (42 bp):
TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
Found at i:21298093 original size:87 final size:86
Alignment explanation
Indices: 21297947--21298108 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 86
21297937 TTTAAATTCG
*
21297947 GTGAATTCATCAAGTCCGTCCCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAGAGTA
1 GTGAATTCATCAAGTCCGTCCCAATAGGACCACCCAAACCCTAGGATATGAACTCATTAAGAGTA
*
21298012 AGAAATTCAACATCACATGTCA
66 A-AAACTCAACATCACATGTCA
* * * * * *
21298034 GTGAATTCATCAAGTTCGTCTCAATAGGATCGCCCAAACCCTGGGATATGAATTCATTAAGAGTA
1 GTGAATTCATCAAGTCCGTCCCAATAGGACCACCCAAACCCTAGGATATGAACTCATTAAGAGTA
21298099 AAAACTCAAC
66 AAAACTCAAC
21298109 TTTATGCATG
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 8 0.12
87 59 0.88
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (86 bp):
GTGAATTCATCAAGTCCGTCCCAATAGGACCACCCAAACCCTAGGATATGAACTCATTAAGAGTA
AAAACTCAACATCACATGTCA
Found at i:21302810 original size:11 final size:11
Alignment explanation
Indices: 21302794--21302821 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21302784 GTGTATACTG
21302794 AAACTGTAGTA
1 AAACTGTAGTA
21302805 AAACTGTAGTA
1 AAACTGTAGTA
21302816 AAACTG
1 AAACTG
21302822 AGATTGTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (11 bp):
AAACTGTAGTA
Found at i:21310167 original size:27 final size:27
Alignment explanation
Indices: 21310125--21310227 Score: 134
Period size: 27 Copynumber: 3.8 Consensus size: 27
21310115 AACACGCTAG
* *
21310125 GAAAGGAATGCTTTTGTGGCAATACAT
1 GAAAGGAATGCCTTCGTGGCAATACAT
*
21310152 GAAAGGAATGCCTTTGTGGCAATACAT
1 GAAAGGAATGCCTTCGTGGCAATACAT
* * *
21310179 GAAAGGAGTGCCTTCATGGAAATACAT
1 GAAAGGAATGCCTTCGTGGCAATACAT
* *
21310206 GAAAGGAAAGCCTCCGTGGCAA
1 GAAAGGAATGCCTTCGTGGCAA
21310228 ACTCCAAAAG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (27 bp):
GAAAGGAATGCCTTCGTGGCAATACAT
Found at i:21321309 original size:5 final size:5
Alignment explanation
Indices: 21321299--21321416 Score: 227
Period size: 5 Copynumber: 23.6 Consensus size: 5
21321289 TCTATATAGA
*
21321299 CATAT CATAT CATAT CATAT TATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
21321349 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT
21321399 CATAT CATAT CATAT CAT
1 CATAT CATAT CATAT CAT
21321417 GCCATGGGTC
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 111 1.00
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.41
Consensus pattern (5 bp):
CATAT
Found at i:21326984 original size:3 final size:3
Alignment explanation
Indices: 21326976--21327025 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
21326966 CTTTTTCTCT
21326976 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21327024 TT
1 TT
21327026 TCCTTCTTCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21328937 original size:34 final size:34
Alignment explanation
Indices: 21328888--21328955 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
21328878 TTTGGAAAAT
** *
21328888 GTTAAGTTCTGTTTGAATGATGAGTTTTAATGGA
1 GTTAAGTTCCATTTGAATGATGAATTTTAATGGA
*
21328922 GTTAAGTTCCATTTGAATGATGAATTTTGATGGA
1 GTTAAGTTCCATTTGAATGATGAATTTTAATGGA
21328956 TATATGTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.43
Consensus pattern (34 bp):
GTTAAGTTCCATTTGAATGATGAATTTTAATGGA
Found at i:21328969 original size:42 final size:42
Alignment explanation
Indices: 21328923--21329008 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
21328913 TTTAATGGAG
* *
21328923 TTAAGTTCCATTTGAATGATGAATTTTGATGGATATATGTGA
1 TTAAGCTCCATTTGAATGATGAATTTCGATGGATATATGTGA
*
21328965 TTAAGCTCCGTTTGAATGATGAATTTCGATGGATATATGTGA
1 TTAAGCTCCATTTGAATGATGAATTTCGATGGATATATGTGA
21329007 TT
1 TT
21329009 TCCCGTATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (42 bp):
TTAAGCTCCATTTGAATGATGAATTTCGATGGATATATGTGA
Found at i:21341225 original size:19 final size:19
Alignment explanation
Indices: 21341201--21341246 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
21341191 GTACACAAGA
*
21341201 AAAATTTTGAAATTTTGCG
1 AAAATTTTGAAATTTTACG
21341220 AAAATTTTGAAATTTTACG
1 AAAATTTTGAAATTTTACG
21341239 AAAATTTT
1 AAAATTTT
21341247 TTTGAGTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (19 bp):
AAAATTTTGAAATTTTACG
Found at i:21344352 original size:20 final size:20
Alignment explanation
Indices: 21344300--21344341 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
21344290 ACTGATGAAA
21344300 AAACTATAGAAATTAAATAT
1 AAACTATAGAAATTAAATAT
21344320 AAACTATAGAAATTAAATAT
1 AAACTATAGAAATTAAATAT
21344340 AA
1 AA
21344342 CTAAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (20 bp):
AAACTATAGAAATTAAATAT
Found at i:21345589 original size:43 final size:43
Alignment explanation
Indices: 21345541--21345656 Score: 205
Period size: 43 Copynumber: 2.7 Consensus size: 43
21345531 GGGTAAATCC
* * *
21345541 AACAACCCATGTTTATCTTCTCTTCTTTTTAAATTCTTTTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTTT
21345584 AACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTTT
21345627 AACAACCCAAGATTATCTTCTCCTCTTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTT
21345657 TAGGTAGATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.49
Consensus pattern (43 bp):
AACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTTT
Found at i:21345669 original size:43 final size:43
Alignment explanation
Indices: 21345541--21345669 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 43
21345531 GGGTAAATCC
* * * * ***
21345541 AACAACCCATGTTTATCTTCTCTTCTTTTTAAATTCTTTTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTTAAAGTAGATTTTT
* ***
21345584 AACAACCCAAGATTATCTTCTCCTCTTTTTAAATTCTTTTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTTAAAGTAGATTTTT
* *
21345627 AACAACCCAAGATTATCTTCTCCTCTTTTTTAGGTAGATTTTT
1 AACAACCCAAGATTATCTTCTCCTCTTTTTAAAGTAGATTTTT
21345670 CTGGTATAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.50
Consensus pattern (43 bp):
AACAACCCAAGATTATCTTCTCCTCTTTTTAAAGTAGATTTTT
Found at i:21348692 original size:69 final size:69
Alignment explanation
Indices: 21348502--21348699 Score: 180
Period size: 69 Copynumber: 2.9 Consensus size: 69
21348492 TTAGTATGAA
* * * * *
21348502 CCCATGTTTAATGTCCTAGCGGACTCTTATTGGTTGCCACAGTCGAGCTATGGTCTTACACCTCG
1 CCCATGTTTACTGTCCCAACAGACT-TTATTGGTTGCCATAGTCGAGCTATGGTCTTACACCTCG
21348567 TAATT
65 TAATT
* **** * ** * **
21348572 CCTATGTTTACTGTCCCGGTGGACTCTATCAGTTGCCATAGTTGAAATATGGTCTTACACCTCGT
1 CCCATGTTTACTGTCCCAACAGACTTTATTGGTTGCCATAGTCGAGCTATGGTCTTACACCTCGT
21348637 AATT
66 AATT
* * * * ** *
21348641 CCCCTGTTTATTGTCCTAACAGATTTTATTGGTCACCATAGTCGAGCTATGGTGTTACA
1 CCCATGTTTACTGTCCCAACAGACTTTATTGGTTGCCATAGTCGAGCTATGGTCTTACA
21348700 ACTTAAACAT
Statistics
Matches: 98, Mismatches: 30, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
69 78 0.80
70 20 0.20
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (69 bp):
CCCATGTTTACTGTCCCAACAGACTTTATTGGTTGCCATAGTCGAGCTATGGTCTTACACCTCGT
AATT
Found at i:21352275 original size:42 final size:42
Alignment explanation
Indices: 21352201--21352364 Score: 105
Period size: 42 Copynumber: 3.8 Consensus size: 42
21352191 GGGTTATGTG
* * *
21352201 TGATTTCGTGTAAGACCATATTTAGGATATGGCATCGATATT
1 TGATTTCATGTAAGACCATATCTAGGACATGGCATCGATATT
* * * * **
21352243 TGATTTCATGTAAGACTATGTCTGGGACATGGCATTGATACG
1 TGATTTCATGTAAGACCATATCTAGGACATGGCATCGATATT
* * * * * *
21352285 AGATATCGTGTAAGACCATAGCT-GGGCTATCGGCATCGATCTATG
1 TGATTTCATGTAAGACCATATCTAGGAC-AT-GGCATCGA--TATT
** * * *
21352330 TGATCCCATGTAAAACCATATCTGGGATATGGCAT
1 TGATTTCATGTAAGACCATATCTAGGACATGGCAT
21352365 TGGCATCTTA
Statistics
Matches: 91, Mismatches: 26, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
41 3 0.03
42 52 0.57
43 7 0.08
44 5 0.05
45 22 0.24
46 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (42 bp):
TGATTTCATGTAAGACCATATCTAGGACATGGCATCGATATT
Found at i:21352362 original size:87 final size:84
Alignment explanation
Indices: 21352206--21352366 Score: 196
Period size: 87 Copynumber: 1.9 Consensus size: 84
21352196 ATGTGTGATT
** * ** * * *
21352206 TCGTGTAAGACCATATTTAGGATATGGCATCGATATTTGATTTCATGTAAGACTATGTCTGGGAC
1 TCGTGTAAGACCATAGCTAGGATATGGCATCGATATGTGATCCCATGTAAAACCATATCTGGGAC
21352271 ATGGCATTGATACGAGATA
66 ATGGCATTGATACGAGATA
* *
21352290 TCGTGTAAGACCATAGCTGGGCTATCGGCATCGATCTATGTGATCCCATGTAAAACCATATCTGG
1 TCGTGTAAGACCATAGCTAGGATAT-GGCATCGA--TATGTGATCCCATGTAAAACCATATCTGG
*
21352355 GATATGGCATTG
63 GACATGGCATTG
21352367 GCATCTTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 21 0.33
85 8 0.13
87 34 0.54
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (84 bp):
TCGTGTAAGACCATAGCTAGGATATGGCATCGATATGTGATCCCATGTAAAACCATATCTGGGAC
ATGGCATTGATACGAGATA
Found at i:21358686 original size:2 final size:2
Alignment explanation
Indices: 21358681--21358709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21358671 CTACATTTAC
21358681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21358710 AAACCCAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21362519 original size:29 final size:29
Alignment explanation
Indices: 21362483--21362641 Score: 173
Period size: 29 Copynumber: 5.6 Consensus size: 29
21362473 AGCGATCACC
*
21362483 GAATATGAAAAGGGATAGCTTCGGTTATT
1 GAATATGAAAAGGGATAGCTTCGGCTATT
* * * * *
21362512 GATTATGAAAAGGGACAG-TGACGACCATT
1 GAATATGAAAAGGGATAGCT-TCGGCTATT
21362541 G-AT-TGAAAAGGGATAGCTTCGGCTATT
1 GAATATGAAAAGGGATAGCTTCGGCTATT
* *
21362568 GAATATGAAAAGGGATAGCTTCAGCTATC
1 GAATATGAAAAGGGATAGCTTCGGCTATT
* *
21362597 GAATATGAAAAGGGATAGCTTTGGTTA-T
1 GAATATGAAAAGGGATAGCTTCGGCTATT
*
21362625 CAATTATGAAAAGGGAT
1 GAA-TATGAAAAGGGAT
21362642 GGTGAAGACT
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
27 19 0.18
28 7 0.07
29 81 0.76
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (29 bp):
GAATATGAAAAGGGATAGCTTCGGCTATT
Found at i:21362555 original size:56 final size:58
Alignment explanation
Indices: 21362482--21362640 Score: 191
Period size: 56 Copynumber: 2.8 Consensus size: 58
21362472 CAGCGATCAC
21362482 CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGACAG-TGAC-GACCAT
1 CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGACAGCT-ACAG-CCAT
* * * * * *
21362540 TG-AT-TGAAAAGGGATAGCTTCGGCTATTGAATATGAAAAGGGATAGCTTCAGCTAT
1 CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGACAGCTACAGCCAT
* **
21362596 CGAATATGAAAAGGGATAGCTTTGGTTATCAATTATGAAAAGGGA
1 CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGA
21362641 TGGTGAAGAC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
56 44 0.52
57 6 0.07
58 35 0.41
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.26
Consensus pattern (58 bp):
CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGACAGCTACAGCCAT
Found at i:21362654 original size:58 final size:58
Alignment explanation
Indices: 21362482--21362671 Score: 199
Period size: 58 Copynumber: 3.3 Consensus size: 58
21362472 CAGCGATCAC
** ** * *
21362482 CGAATATGAAAAGGGATAGCTTCGGTTATTGATTATGAAAAGGGACAGTGACGACCAT
1 CGAATATGAAAAGGGATAGCTTCGGTTATCAATTATGAAAAGGGATGGTGAAGACTAT
* * * * **
21362540 TG-AT-TGAAAAGGGATAGCTTCGGCTATTGAA-TATGAAAAGGGATAGCTTCAG-CTAT
1 CGAATATGAAAAGGGATAGCTTCGGTTA-TCAATTATGAAAAGGGAT-GGTGAAGACTAT
*
21362596 CGAATATGAAAAGGGATAGCTTTGGTTATCAATTATGAAAAGGGATGGTGAAGACTAT
1 CGAATATGAAAAGGGATAGCTTCGGTTATCAATTATGAAAAGGGATGGTGAAGACTAT
*
21362654 CGATTAATGAAAAGGGAT
1 CGAAT-ATGAAAAGGGAT
21362672 GGTTTTGACC
Statistics
Matches: 106, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
56 37 0.35
57 15 0.14
58 42 0.40
59 12 0.11
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.26
Consensus pattern (58 bp):
CGAATATGAAAAGGGATAGCTTCGGTTATCAATTATGAAAAGGGATGGTGAAGACTAT
Found at i:21375249 original size:30 final size:29
Alignment explanation
Indices: 21375215--21375272 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
21375205 ACAAAAAAAA
*
21375215 ATCT-AATCTAAAAAGAAAATAGAAAACCTT
1 ATCTAAATATAAAAAG-AAA-AGAAAACCTT
*
21375245 ATCTAAATATGAAAAGAAAAGAAAACCT
1 ATCTAAATATAAAAAGAAAAGAAAACCT
21375273 AACCCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 7 0.28
31 9 0.36
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (29 bp):
ATCTAAATATAAAAAGAAAAGAAAACCTT
Found at i:21378040 original size:13 final size:13
Alignment explanation
Indices: 21378017--21378052 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21378007 AATGCATGTG
21378017 TAATG-TAATGGT
1 TAATGTTAATGGT
21378029 TAATGTTAATGGT
1 TAATGTTAATGGT
21378042 TAATGTGTAAT
1 TAATGT-TAAT
21378053 CATGAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
TAATGTTAATGGT
Found at i:21387470 original size:21 final size:20
Alignment explanation
Indices: 21387434--21387473 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
21387424 TAAATTTTAA
21387434 TTTTATTTAATTAATTATTT
1 TTTTATTTAATTAATTATTT
21387454 TTTTAATTT-ATTGAATTATT
1 TTTT-ATTTAATT-AATTATT
21387474 AATATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTTATTTAATTAATTATTT
Found at i:21387481 original size:25 final size:26
Alignment explanation
Indices: 21387428--21387481 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
21387418 TTCTCCTAAA
* *
21387428 TTTTAATTTTATTTAATTAATTATTT
1 TTTTAATTTTATTGAATTAATTATAT
21387454 TTTTAA-TTTATTGAATT-ATTAATAT
1 TTTTAATTTTATTGAATTAATT-ATAT
21387479 TTT
1 TTT
21387482 ATATTGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 16 0.64
26 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTAATTTTATTGAATTAATTATAT
Found at i:21388385 original size:3 final size:3
Alignment explanation
Indices: 21388377--21388408 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
21388367 CGAGGATCCT
*
21388377 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
21388409 TCCCACAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21389191 original size:23 final size:23
Alignment explanation
Indices: 21389161--21389204 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
21389151 TCTTTCAATT
21389161 ATGATTGGGTTATATTTTGTTAA
1 ATGATTGGGTTATATTTTGTTAA
21389184 ATGATTGGGTTATATTTTGTT
1 ATGATTGGGTTATATTTTGTT
21389205 CAAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (23 bp):
ATGATTGGGTTATATTTTGTTAA
Found at i:21390438 original size:11 final size:11
Alignment explanation
Indices: 21390413--21390459 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
21390403 TAAAATGTTG
21390413 AATTTTAT-TT
1 AATTTTATATT
*
21390423 AATTTTATAAT
1 AATTTTATATT
*
21390434 AATTTTTTATT
1 AATTTTATATT
21390445 AATTTTA-ATT
1 AATTTTATATT
21390455 -ATTTT
1 AATTTT
21390460 CGATAGATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 5 0.16
10 11 0.34
11 16 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
AATTTTATATT
Found at i:21393227 original size:38 final size:38
Alignment explanation
Indices: 21393176--21393251 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21393166 GTCGTTTGTC
21393176 TTTGTGATGAATGACTTAATTACTATATGATAGTAATT
1 TTTGTGATGAATGACTTAATTACTATATGATAGTAATT
21393214 TTTGTGATGAATGACTTAATTACTATATGATAGTAATT
1 TTTGTGATGAATGACTTAATTACTATATGATAGTAATT
21393252 GACTTTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (38 bp):
TTTGTGATGAATGACTTAATTACTATATGATAGTAATT
Found at i:21397988 original size:22 final size:22
Alignment explanation
Indices: 21397961--21398004 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21397951 GAAAAACAAG
*
21397961 TCCCTACAAATCAATTCTATGA
1 TCCCTACAAATCAACTCTATGA
*
21397983 TCCCTACAAATCAGCTCTATGA
1 TCCCTACAAATCAACTCTATGA
21398005 ATCAGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
TCCCTACAAATCAACTCTATGA
Found at i:21399690 original size:84 final size:83
Alignment explanation
Indices: 21399585--21399740 Score: 192
Period size: 84 Copynumber: 1.9 Consensus size: 83
21399575 TCAACAAAAA
*
21399585 ATTGGGGACTATCAACCTCAGAT-TCACTGAATGTAGGAATTTAAGATCTCAGA-TAAATAGAAG
1 ATTGGGGACTATCAACCTCAGATCTC-CT-AATGTAGGAATTAAAGATCTCA-ACTAAATAGAAG
*
21399648 ATTGGATAGTTTAAACCAAAG
63 ATTGAATAGTTTAAACCAAAG
* * * *
21399669 ATTGGAGG-CTATCAACGTCAGATCCTCCTATTGTTGGAATTAAAGATTTCAACTAAATAGAAGA
1 ATTGG-GGACTATCAACCTCAGAT-CTCCTAATGTAGGAATTAAAGATCTCAACTAAATAGAAGA
21399733 TTGAATAG
64 TTGAATAG
21399741 CTCAACTAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
83 1 0.02
84 55 0.89
85 4 0.06
86 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (83 bp):
ATTGGGGACTATCAACCTCAGATCTCCTAATGTAGGAATTAAAGATCTCAACTAAATAGAAGATT
GAATAGTTTAAACCAAAG
Found at i:21405712 original size:32 final size:32
Alignment explanation
Indices: 21405676--21405835 Score: 248
Period size: 32 Copynumber: 5.0 Consensus size: 32
21405666 TATAACTATG
21405676 CTACTTTTTTATATGTAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
21405708 CTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
*
21405740 CTACTTTTTTATATGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* * *
21405772 ATAATTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
* *
21405804 CTACTTTTTTATAGGTAAACCTAATGTATGAT
1 CTACTTTTTTATATGTAAAACTAATGTATGAT
21405836 ATTTTTTATG
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 114 1.00
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (32 bp):
CTACTTTTTTATATGTAAAACTAATGTATGAT
Found at i:21405780 original size:64 final size:64
Alignment explanation
Indices: 21405676--21405837 Score: 279
Period size: 64 Copynumber: 2.5 Consensus size: 64
21405666 TATAACTATG
* * *
21405676 CTACTTTTTTATATGTAAAACTAATGTATGATCTACTTTTTCATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATAATTTTTCATATGCAAAACTAATGTATGAT
*
21405740 CTACTTTTTTATATGTAAACCTAATGTATGATATAATTTTTTATATGCAAAACTAATGTATGAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATATAATTTTTCATATGCAAAACTAATGTATGAT
*
21405804 CTACTTTTTTATAGGTAAACCTAATGTATGATAT
1 CTACTTTTTTATATGTAAACCTAATGTATGATAT
21405838 TTTTTATGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 93 1.00
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (64 bp):
CTACTTTTTTATATGTAAACCTAATGTATGATATAATTTTTCATATGCAAAACTAATGTATGAT
Found at i:21410855 original size:53 final size:54
Alignment explanation
Indices: 21410793--21411102 Score: 353
Period size: 55 Copynumber: 5.7 Consensus size: 54
21410783 TTATGAAATT
* * *
21410793 ACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTC
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTC
* *
21410846 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTC
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATAG-AACTC
* * *
21410901 ATCAATGCGATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTC
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTC
*
21410954 ACCAATGCCATGCCTT-AGCATGATCTTACATAGG-A-CCTTTGCCTTATAGTAACTC
1 ACCAATGCCATGCCTTGA-CATGGTCTTACAT-GGTATCC-TTGCCTTATAG-AACTC
* * * * *
21411009 ATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTC
* * * * *
21411063 ATCAATGCTATGCCTTGGCGTGGTCTTACATGATATCCTT
1 ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
21411103 ATCTTACCAA
Statistics
Matches: 220, Mismatches: 25, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
52 5 0.02
53 79 0.36
54 45 0.20
55 86 0.39
56 5 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (54 bp):
ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACTC
Found at i:21410991 original size:108 final size:108
Alignment explanation
Indices: 21410798--21411093 Score: 484
Period size: 108 Copynumber: 2.7 Consensus size: 108
21410788 AAATTACCAT
*
21410798 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
*
21410863 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
* *
21410906 TGCGATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTA
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
*
21410971 GCATGATCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
* * * * *
21411014 TGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCTATGCCTT
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTT
*
21411079 GGCGTGGTCTTACAT
65 GGCATGGTCTTACAT
21411094 GATATCCTTA
Statistics
Matches: 173, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 142 0.82
109 31 0.18
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
GCATGGTCTTACATAGGACCTTTGCCTTATAGTAACTCATCAA
Found at i:21411135 original size:47 final size:47
Alignment explanation
Indices: 21411083--21411202 Score: 213
Period size: 47 Copynumber: 2.6 Consensus size: 47
21411073 TGCCTTGGCG
* *
21411083 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACA
21411130 TGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACA
*
21411177 TGGTCTTATATGGTATCCTTGTCTTA
1 TGGTCTTACATGGTATCCTTGTCTTA
21411203 GTGCCAATGC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (47 bp):
TGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACA
Found at i:21411345 original size:44 final size:44
Alignment explanation
Indices: 21411294--21411380 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
21411284 GTATCCTTAA
*
21411294 CCGTCAATTCCTCCTTAAATGCCATGTTACGAA-CATGGACTTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTAC-AACCATGGACTTTT
* *
21411338 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
21411381 GAAATATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
43 2 0.05
44 37 0.95
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (44 bp):
CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTT
Found at i:21415746 original size:40 final size:40
Alignment explanation
Indices: 21415672--21415812 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
21415662 CCGCACCAAG
* * * * * *
21415672 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
21415712 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
21415752 GCCTTCGGGTCTT-GCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
21415791 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
21415813 GTAATTTCAG
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 33 0.39
40 52 0.61
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:21415794 original size:39 final size:40
Alignment explanation
Indices: 21415672--21415853 Score: 163
Period size: 39 Copynumber: 4.6 Consensus size: 40
21415662 CCGCACCAAG
* * * * * * * *
21415672 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * *
21415712 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
21415752 GCCTTCGGGTCTT-GCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * * *
21415791 GCCTTCGGGTCTTAACCCGGATGTAATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
21415830 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
21415854 CATTCAATTT
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
38 2 0.02
39 60 0.51
40 54 0.46
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:21428833 original size:40 final size:40
Alignment explanation
Indices: 21428748--21428898 Score: 134
Period size: 40 Copynumber: 3.8 Consensus size: 40
21428738 AATTGAATGA
* * *
21428748 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
21428788 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
21428829 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
21428868 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
21428899 ACATGGTTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 79 0.86
41 4 0.04
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:21428912 original size:40 final size:40
Alignment explanation
Indices: 21428785--21428914 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
21428775 ATGCTGGAAA
* * * *
21428785 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
21428825 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
21428865 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
21428905 TTATATCCGG
1 TTATATCCGG
21428915 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:21430688 original size:37 final size:38
Alignment explanation
Indices: 21430602--21430676 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
21430592 TGTTTAACCT
*
21430602 TACAATCTCTCTTAAGACTTATACCCCAAAATCTTAAGA
1 TACAA-CTCTCTTAAGACTTATACCCCAAAACCTTAAGA
* *
21430641 TACAACTCTCTTAAGATTTTTA-CCC-AAACCTTAAGA
1 TACAACTCTCTTAAGACTTATACCCCAAAACCTTAAGA
21430677 ATAAACCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 10 0.30
37 3 0.09
38 15 0.45
39 5 0.15
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.32
Consensus pattern (38 bp):
TACAACTCTCTTAAGACTTATACCCCAAAACCTTAAGA
Found at i:21432184 original size:45 final size:45
Alignment explanation
Indices: 21432088--21432214 Score: 152
Period size: 45 Copynumber: 2.9 Consensus size: 45
21432078 TTTTATTAAT
* * * *
21432088 TCACCGGTATT-TTGCCTGCTAGGCTC-AAGGCTCG-ATAACATG
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
* **
21432130 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
* *
21432175 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCTGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATA
21432215 TAATACCAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 10 0.14
43 13 0.18
44 7 0.10
45 42 0.58
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATC
Found at i:21432255 original size:38 final size:38
Alignment explanation
Indices: 21432212--21432675 Score: 678
Period size: 38 Copynumber: 12.1 Consensus size: 38
21432202 AAAGGCCTGA
* * * * *
21432212 ATATAATACCAGTACTAGGCCTGCGGGATTTAACTCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
21432250 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
21432288 ATATATTACCAGCACGAAGCCTAC-GGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
21432325 ATATATCACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
21432363 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGG
1 ATATATTACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
*
21432403 ATATATTACTAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
21432441 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
21432479 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * *
21432517 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGG
1 ATATATTACCAGCACGAAGCCTGCGGG-ATTTAA-CCCGG
*
21432557 ATATATTACCAGCACGAAGCCTGTGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
*
21432595 ATATATTACCAGCACGAAGCCTGTGGGATTTAACCCGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
* * **
21432633 ATATATTACTAGCACAAAGCCTGCAGGTCTTTAAGCCCGG
1 ATATATTACCAGCACGAAGCCTGC-GGGATTTAA-CCCGG
21432673 ATA
1 ATA
21432676 CACATCAAAT
Statistics
Matches: 390, Mismatches: 29, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
37 35 0.09
38 262 0.67
39 27 0.07
40 66 0.17
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGG
Found at i:21432471 original size:116 final size:115
Alignment explanation
Indices: 21432212--21432675 Score: 682
Period size: 116 Copynumber: 4.0 Consensus size: 115
21432202 AAAGGCCTGA
* * * * *
21432212 ATATAATACCAGTACTAGGCCTGCGGGATTTAACTCGGATATAATACCAGCACGAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGG
* *
21432277 ATTTAACCCGGATATATTACCAGCACGAAGCCTAC-GGATTTAA-CCCGG
66 ATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGGATTTAAGCCCGG
* *
21432325 ATATATCACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACAAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGG
* * *
21432390 TCTTTAAGCCCGGATATATTACTAGCACGAAGCCTGCGGGATTTAA-CCCGG
66 -ATTTAA-CCCGGATATATTACCAGCACAAAGCCTGCGGGATTTAAGCCCGG
*
21432441 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGG
* *
21432506 ATTTAACCCGGATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGG
66 ATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGG-ATTTAAGCCCGG
* * *
21432557 ATATATTACCAGCACGAAGCCTGTGGGATTTAACCCGGATATATTACCAGCACGAAGCCTGTGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGG
* **
21432622 ATTTAACCCGGATATATTACTAGCACAAAGCCTGCAGGTCTTTAAGCCCGG
66 ATTTAACCCGGATATATTACCAGCACAAAGCCTGC-GGGATTTAAGCCCGG
21432673 ATA
1 ATA
21432676 CACATCAAAT
Statistics
Matches: 322, Mismatches: 23, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
113 58 0.18
114 34 0.11
115 37 0.11
116 191 0.59
117 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (115 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAATACCAGCACGAAGCCTGCGGG
ATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGGATTTAAGCCCGG
Found at i:21432524 original size:154 final size:154
Alignment explanation
Indices: 21432212--21432675 Score: 754
Period size: 154 Copynumber: 3.0 Consensus size: 154
21432202 AAAGGCCTGA
* * * * * *
21432212 ATATAATACCAGTACTAGGCCTGCGGG-ATTTAA-CTCGGATATAATACCAGCACGAAGCCTGCG
1 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACCAGCACGAAGCCTGCG
* *
21432275 GGATTTAACCCGGATATATTACCAGCACGAAGCCTAC-GGATTTAACCCGGATATATCACCAGCA
66 GGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCA
21432339 CGAAGCCTGCGGGATTTAACCCGG
131 CGAAGCCTGCGGGATTTAACCCGG
*
21432363 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACTAGCACGAAGCCTGCG
1 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACCAGCACGAAGCCTGCG
21432428 GGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCA
66 GGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCA
21432493 CGAAGCCTGCGGGATTTAACCCGG
131 CGAAGCCTGCGGGATTTAACCCGG
*
21432517 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACCAGCACGAAGCCTGTG
1 ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACCAGCACGAAGCCTGCG
* *
21432582 GGATTTAACCCGGATATATTACCAGCACGAAGCCTGTGGGATTTAACCCGGATATATTACTAGCA
66 GGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCA
* **
21432647 CAAAGCCTGCAGGTCTTTAAGCCCGG
131 CGAAGCCTGC-GGGATTTAA-CCCGG
21432673 ATA
1 ATA
21432676 CACATCAAAT
Statistics
Matches: 292, Mismatches: 16, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
151 24 0.08
152 5 0.02
153 63 0.22
154 185 0.63
155 7 0.02
156 8 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (154 bp):
ATATAATACCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATATTACCAGCACGAAGCCTGCG
GGATTTAACCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCA
CGAAGCCTGCGGGATTTAACCCGG
Found at i:21433009 original size:43 final size:44
Alignment explanation
Indices: 21432956--21433039 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
21432946 ACATTTCATT
*
21432956 TCACCGGCATTATAACCTGCTAGGCTCAAAGCCCG-ATATCGTC
1 TCACCGGCATTATAACCTGCTAGGCCCAAAGCCCGAATATCGTC
* * * *
21432999 TCACTGGCATTATAGCTTGCTAGGCCCGAAGCCCGAATATC
1 TCACCGGCATTATAACCTGCTAGGCCCAAAGCCCGAATATC
21433040 ATATTTCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 30 0.86
44 5 0.14
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (44 bp):
TCACCGGCATTATAACCTGCTAGGCCCAAAGCCCGAATATCGTC
Found at i:21434106 original size:2 final size:2
Alignment explanation
Indices: 21434094--21434128 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
21434084 CACTTTCAGA
21434094 AT AT AT A- 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
21434129 TCGACTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21456114 original size:21 final size:20
Alignment explanation
Indices: 21456084--21456122 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21456074 CCAAACTTGT
21456084 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
21456104 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
21456123 CAAAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:21457721 original size:26 final size:27
Alignment explanation
Indices: 21457679--21457746 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 27
21457669 ATCATAATAC
* *
21457679 GCCACAAAAGTTATTCTTTCAGAGTTT
1 GCCACAAAGGCTATTCTTTCAGAGTTT
*
21457706 TCCAC-AAGGCTATTCTTTCAGAGTTT
1 GCCACAAAGGCTATTCTTTCAGAGTTT
21457732 GCCACAAAGGCTATT
1 GCCACAAAGGCTATT
21457747 TCTTAGCTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 23 0.64
27 13 0.36
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (27 bp):
GCCACAAAGGCTATTCTTTCAGAGTTT
Found at i:21464294 original size:35 final size:35
Alignment explanation
Indices: 21464230--21464334 Score: 113
Period size: 35 Copynumber: 3.0 Consensus size: 35
21464220 ATATAAAATC
* *
21464230 AATATAGTGGCATACTTAACATACAAACTAGAATT
1 AATATAGTGGCATGCTTAACATGCAAACTAGAATT
* * *
21464265 AATATAGTGCCATGCTTAACATGCGAACTATAA-T
1 AATATAGTGGCATGCTTAACATGCAAACTAGAATT
* * *
21464299 AAGTAATAATGGAATGCTTAACATGCAAATTAGAAT
1 AA-T-ATAGTGGCATGCTTAACATGCAAACTAGAAT
21464335 ATCAACAGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 3 0.05
35 29 0.52
36 24 0.43
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (35 bp):
AATATAGTGGCATGCTTAACATGCAAACTAGAATT
Found at i:21465079 original size:20 final size:19
Alignment explanation
Indices: 21465056--21465097 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
21465046 TGGCGACGCA
21465056 GGTGCGGTGATGAAAATGGT
1 GGTGCGGTGATG-AAATGGT
* *
21465076 GGTGTGGTGGTGAAATGGT
1 GGTGCGGTGATGAAATGGT
21465095 GGT
1 GGT
21465098 TCAGTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.19, C:0.02, G:0.50, T:0.29
Consensus pattern (19 bp):
GGTGCGGTGATGAAATGGT
Found at i:21469188 original size:15 final size:15
Alignment explanation
Indices: 21469168--21469208 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
21469158 ATTACTTATA
*
21469168 CAAATTCATAAAATT
1 CAAATTCAAAAAATT
21469183 CAAATTCAAAAAATT
1 CAAATTCAAAAAATT
21469198 CAAATTCAAAA
1 CAAATTCAAAA
21469209 TCAGCATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (15 bp):
CAAATTCAAAAAATT
Found at i:21478006 original size:40 final size:39
Alignment explanation
Indices: 21477951--21478158 Score: 231
Period size: 40 Copynumber: 5.2 Consensus size: 39
21477941 TGAATGATAC
* * *
21477951 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
* *
21477991 CCGGGCTAAGACCCGAAGGCATTCGTACGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
*
21478031 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * *
21478071 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGT--TATAT
* * **
21478111 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
21478151 CC-GGCTAA
1 CCGGGCTAA
21478159 ATTTCGAAGA
Statistics
Matches: 146, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 6 0.04
40 136 0.93
41 2 0.01
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:21485035 original size:40 final size:39
Alignment explanation
Indices: 21484977--21485179 Score: 201
Period size: 40 Copynumber: 5.1 Consensus size: 39
21484967 TGAATGATAC
* * *
21484977 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
* *
21485017 CCAGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * *
21485057 TCGGGCTAAGACCCAAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* * * *
21485097 CCGGGCTAAGACCCAAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGT--TATAT
* * **
21485137 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
21485177 CCG
1 CCG
21485180 ACTAAATTCC
Statistics
Matches: 138, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 133 0.96
41 2 0.01
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:21492962 original size:16 final size:16
Alignment explanation
Indices: 21492932--21493001 Score: 65
Period size: 15 Copynumber: 4.5 Consensus size: 16
21492922 ATAGTTTCAG
*
21492932 TATAG-TTTCAAAATC
1 TATAGTTTTCATAATC
21492947 TATAGTTTTCATAATC
1 TATAGTTTTCATAATC
* * * *
21492963 TTAAAGTTTTCACAGTT
1 -TATAGTTTTCATAATC
21492980 TATAG-TTTCATAATC
1 TATAGTTTTCATAATC
21492995 TA-AGTTT
1 TATAGTTT
21493002 CAGTATGTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
14 2 0.05
15 16 0.37
16 13 0.30
17 12 0.28
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (16 bp):
TATAGTTTTCATAATC
Found at i:21492971 original size:32 final size:29
Alignment explanation
Indices: 21492935--21493003 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 29
21492925 GTTTCAGTAT
21492935 AGTTTCAAAATCTATAGTTTTCATAATCTTAA
1 AGTTTCAAAATCTATAG-TTTCATAATC-T-A
* * *
21492967 AGTTTTCACAGTTTATAGTTTCATAATCTA
1 AG-TTTCAAAATCTATAGTTTCATAATCTA
21492997 AGTTTCA
1 AGTTTCA
21493004 GTATGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 5 0.15
30 3 0.09
31 1 0.03
32 12 0.36
33 12 0.36
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (29 bp):
AGTTTCAAAATCTATAGTTTCATAATCTA
Found at i:21494289 original size:24 final size:24
Alignment explanation
Indices: 21494210--21494309 Score: 119
Period size: 24 Copynumber: 4.0 Consensus size: 24
21494200 TGACATTGTG
* * *
21494210 CTAAGTGAAACAAGACCATGACAT
1 CTAAGTGAAATAAGTCCATGGCAT
*
21494234 TTAAGTGAAATAAGTCCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGC-A--T
*
21494261 GCTAAATGAAATAAGTCCATGGCAT
1 -CTAAGTGAAATAAGTCCATGGCAT
21494286 CTAAGTGAAATAAGTCCATGGCAT
1 CTAAGTGAAATAAGTCCATGGCAT
21494310 TGTCCTACGT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
24 41 0.63
25 2 0.03
27 2 0.03
28 20 0.31
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (24 bp):
CTAAGTGAAATAAGTCCATGGCAT
Found at i:21494291 original size:52 final size:52
Alignment explanation
Indices: 21494206--21494308 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
21494196 GATATGACAT
* *
21494206 TGTGCTAAGTGAAACAAGACCATGACATTTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAATGAAACAAGACCATGACATCTAAGTGAAATAAGTCCATGGCAA
* * *
21494258 TGTGCTAAATGAAATAAGTCCATGGCATCTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAATGAAACAAGACCATGACATCTAAGTGAAATAAGTCCATGGCA
21494309 TTGTCCTACG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (52 bp):
TGTGCTAAATGAAACAAGACCATGACATCTAAGTGAAATAAGTCCATGGCAA
Found at i:21494427 original size:51 final size:51
Alignment explanation
Indices: 21494345--21494532 Score: 238
Period size: 51 Copynumber: 3.7 Consensus size: 51
21494335 TGAACCTTAG
* *
21494345 GAATAAAATAGCTTTGGAAACAAAT-CTGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGC-GGTACTATGTGAAGGCCACTTTGT
*
21494396 GAATATAATAGCTTTGGACACAAGTGCGGTACTATGTGAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGCGGTACTATGTGAAGGCCACTTTGT
* * *
21494447 GAATAAAATAACTTTGGACACAAGTGTGGTACTA-GATAAAGGCCACTTTGT
1 GAATAAAATAGCTTTGGACACAAGTGCGGTACTATG-TGAAGGCCACTTTGT
** * *
21494498 GAATAAGGTAGCTTT-GACTACAAGGGTGGTACTAT
1 GAATAAAATAGCTTTGGAC-ACAAGTGCGGTACTAT
21494533 ATGCAAGCCA
Statistics
Matches: 122, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
50 4 0.03
51 117 0.96
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTGGACACAAGTGCGGTACTATGTGAAGGCCACTTTGT
Found at i:21496845 original size:28 final size:28
Alignment explanation
Indices: 21496814--21496896 Score: 157
Period size: 28 Copynumber: 3.0 Consensus size: 28
21496804 CATGGCTATA
21496814 CACATAACTAAACATACTTCATTTACAT
1 CACATAACTAAACATACTTCATTTACAT
21496842 CACATAACTAAACATACTTCATTTACAT
1 CACATAACTAAACATACTTCATTTACAT
*
21496870 CATATAACTAAACATACTTCATTTACA
1 CACATAACTAAACATACTTCATTTACA
21496897 ATGCCAAATC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (28 bp):
CACATAACTAAACATACTTCATTTACAT
Found at i:21505226 original size:5 final size:5
Alignment explanation
Indices: 21505196--21505225 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21505186 GCATCATACA
*
21505196 GTCAT GTCAT GTCAT GTCAT GTCAT ATCAT
1 GTCAT GTCAT GTCAT GTCAT GTCAT GTCAT
21505226 AAAATCATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (5 bp):
GTCAT
Found at i:21505340 original size:27 final size:27
Alignment explanation
Indices: 21505304--21505510 Score: 199
Period size: 27 Copynumber: 7.7 Consensus size: 27
21505294 TACATCACAT
* *
21505304 AGGGCTAAACAGTCATCTTACCAT-ATA
1 AGGGCAAAACAGTCATTTTACC-TCATA
*
21505331 AGGGCAAAACAGTCATTTTACCTCATG
1 AGGGCAAAACAGTCATTTTACCTCATA
* *
21505358 AGGGTAAAACAGTCATCTTA-CT-ATTTA
1 AGGGCAAAACAGTCATTTTACCTCA--TA
* * *
21505385 AGGG-ATAAATAGCCATTTTACCTCATG
1 AGGGCA-AAACAGTCATTTTACCTCATA
* *
21505412 AGGGAAAAACAATCATTTTACCAT-ATA
1 AGGGCAAAACAGTCATTTTACC-TCATA
*
21505439 AGGGCAAAACAGTCATTTTACCTCATG
1 AGGGCAAAACAGTCATTTTACCTCATA
* *
21505466 AGGGCAAAACAATCATTTTACCTCATG
1 AGGGCAAAACAGTCATTTTACCTCATA
* *
21505493 AGGGAAAAATAGTCATTT
1 AGGGCAAAACAGTCATTT
21505511 ATCAATCTGG
Statistics
Matches: 150, Mismatches: 21, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
25 1 0.01
26 5 0.03
27 139 0.93
28 4 0.03
29 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (27 bp):
AGGGCAAAACAGTCATTTTACCTCATA
Found at i:21505402 original size:54 final size:54
Alignment explanation
Indices: 21505310--21505510 Score: 253
Period size: 54 Copynumber: 3.7 Consensus size: 54
21505300 ACATAGGGCT
* *
21505310 AAACAGTCATCTTACCATATAAGGGCAAAACAGTCATTTTACCTCATGAGGGTA
1 AAACAATCATCTTACCATATAAGGGCAAAACAGTCATTTTACCTCATGAGGGAA
* * * * *
21505364 AAACAGTCATCTTACTATTTAAGGG-ATAAATAGCCATTTTACCTCATGAGGGAA
1 AAACAATCATCTTACCATATAAGGGCA-AAACAGTCATTTTACCTCATGAGGGAA
* *
21505418 AAACAATCATTTTACCATATAAGGGCAAAACAGTCATTTTACCTCATGAGGGCA
1 AAACAATCATCTTACCATATAAGGGCAAAACAGTCATTTTACCTCATGAGGGAA
* * * *
21505472 AAACAATCATTTTACC-TCATGAGGGAAAAATAGTCATTT
1 AAACAATCATCTTACCAT-ATAAGGGCAAAACAGTCATTT
21505511 ATCAATCTGG
Statistics
Matches: 129, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.02
54 126 0.98
55 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (54 bp):
AAACAATCATCTTACCATATAAGGGCAAAACAGTCATTTTACCTCATGAGGGAA
Found at i:21508775 original size:18 final size:18
Alignment explanation
Indices: 21508752--21508795 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
21508742 TGGCCCAATA
21508752 CAGTAACAATAAACAGTG
1 CAGTAACAATAAACAGTG
* *
21508770 CAGTAACAGTAATCAGTG
1 CAGTAACAATAAACAGTG
*
21508788 CAATAACA
1 CAGTAACA
21508796 GAATACAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (18 bp):
CAGTAACAATAAACAGTG
Found at i:21509153 original size:27 final size:27
Alignment explanation
Indices: 21509118--21509295 Score: 257
Period size: 27 Copynumber: 6.6 Consensus size: 27
21509108 CATCACAAAA
* * *
21509118 GGCAAAACAGTCATCTTACCTTATAAG
1 GGCAAAACAGTCATTTTACCTCATGAG
*
21509145 GGCAAAACAGTCATCTTACCTCATGAG
1 GGCAAAACAGTCATTTTACCTCATGAG
* *
21509172 GGCAAAACACTCATTTTACCTCGTGAG
1 GGCAAAACAGTCATTTTACCTCATGAG
*
21509199 GGCAAAACAATCATTTTACCTCATGAG
1 GGCAAAACAGTCATTTTACCTCATGAG
*
21509226 GGCAAAACAGTCATTTTACCTCATGAA
1 GGCAAAACAGTCATTTTACCTCATGAG
*
21509253 GGCAAAACAATCATTTTACCTCATGAG
1 GGCAAAACAGTCATTTTACCTCATGAG
* *
21509280 GGCAAAATAATCATTT
1 GGCAAAACAGTCATTT
21509296 ATCAATCTGG
Statistics
Matches: 139, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (27 bp):
GGCAAAACAGTCATTTTACCTCATGAG
Found at i:21509514 original size:18 final size:18
Alignment explanation
Indices: 21509476--21509510 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
21509466 ATGTGATTTA
*
21509476 CCCGTGTGGGCCCACATG
1 CCCGTGTGGGCCCAAATG
21509494 CCCGTG-GGGCCCAAATG
1 CCCGTGTGGGCCCAAATG
21509511 GCCCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.14, C:0.37, G:0.34, T:0.14
Consensus pattern (18 bp):
CCCGTGTGGGCCCAAATG
Found at i:21518638 original size:19 final size:19
Alignment explanation
Indices: 21518614--21518725 Score: 156
Period size: 19 Copynumber: 5.8 Consensus size: 19
21518604 AATCTTTAAG
21518614 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21518633 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21518652 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
21518669 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
21518688 GAAATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
* *
21518709 GATCTTGTAATCTTAGA
1 GAT-ATGCAATCTTAGA
21518726 GATTTAATTT
Statistics
Matches: 84, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.20
19 48 0.57
20 3 0.04
21 8 0.10
22 8 0.10
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:21518644 original size:36 final size:35
Alignment explanation
Indices: 21518604--21518689 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 35
21518594 ATGGAAATAT
21518604 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTT-A-GATATGACAATCTTAGATATGATATGC
21518640 AATC-TTAGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAGATATG--ACAATCTTAGATATGATATGC
21518676 AATC-TTAGATATGA
1 AATCTTTAGATATGA
21518690 AATGCAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
33 6 0.13
34 2 0.04
35 2 0.04
36 37 0.79
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
AATCTTTAGATATGACAATCTTAGATATGATATGC
Found at i:21519105 original size:2 final size:2
Alignment explanation
Indices: 21519100--21519148 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
21519090 TCTATGCATG
* *
21519100 TA TA TA TA T- TA TA T- TA TA TT TT TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21519139 TA TA T- TA TA T
1 TA TA TA TA TA T
21519149 TTTTATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (2 bp):
TA
Found at i:21519118 original size:31 final size:30
Alignment explanation
Indices: 21519100--21519157 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
21519090 TCTATGCATG
21519100 TATATATAT-TATATTATATTTTTATATTA
1 TATATATATATATATTATATTTTTATATTA
21519129 TATATATATATATATTATATTTTTATATT
1 TATATATATATATATTATATTTTTATATT
21519158 TTAGTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATATATATATATATTATATTTTTATATTA
Found at i:21519126 original size:13 final size:13
Alignment explanation
Indices: 21519108--21519157 Score: 64
Period size: 13 Copynumber: 3.5 Consensus size: 13
21519098 TGTATATATA
21519108 TTATATTATATTT
1 TTATATTATATTT
21519121 TTATATTATATATAT
1 TTATATTATAT-T-T
21519136 ATATATATTATATTT
1 -T-TATATTATATTT
21519151 TTATATT
1 TTATATT
21519158 TTAGTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 17 0.52
14 2 0.06
15 2 0.06
16 2 0.06
17 10 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATATTATATTT
Found at i:21524984 original size:33 final size:32
Alignment explanation
Indices: 21524943--21525004 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
21524933 AATTTATTGT
*
21524943 TTTCCTATTGT-TTCCTCACTATTTTGTTGCCA
1 TTTCCTATTATATTCCT-ACTATTTTGTTGCCA
*
21524975 TTTCACTATTATATTTCTACTATTTTGTTG
1 TTTC-CTATTATATTCCTACTATTTTGTTG
21525005 TTGTTATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 18 0.69
34 4 0.15
ACGTcount: A:0.16, C:0.19, G:0.08, T:0.56
Consensus pattern (32 bp):
TTTCCTATTATATTCCTACTATTTTGTTGCCA
Found at i:21527199 original size:40 final size:40
Alignment explanation
Indices: 21526968--21527192 Score: 316
Period size: 40 Copynumber: 5.7 Consensus size: 40
21526958 TCGAATGATG
* * * *
21526968 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
21527008 TCCGGAG-TAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGG-GTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
21527048 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
21527087 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
21527127 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
21527168 -CCGGGCTATGTCCCGAAGACATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTG
21527193 AACGAGTAGC
Statistics
Matches: 173, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
39 41 0.24
40 121 0.70
41 11 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:21527223 original size:119 final size:119
Alignment explanation
Indices: 21526968--21527225 Score: 296
Period size: 119 Copynumber: 2.2 Consensus size: 119
21526958 TCGAATGATG
* * *
21526968 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGAGTAAGATCCGAAGGCATTT
1 TCCGGGTTAACTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAGTAAGATCCGAAGGCATTT
* * **
21527033 GTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGACATTTGAACGAGTTACTAAA
* * *
21527087 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGG-GTTAAG-TCCCGAAGGCA
1 TCCGGGTTAACTCCCGAAGGC-TTTGTGCTAAGTGACTAAATCCGGAG-TAAGAT-CCGAAGGCA
* *
21527149 TTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGACATTTGAACGAG-TAGCTATA
63 TTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGACATTTGAACGAGTTA-CTAAA
21527207 TCC-GGTTAAACT-CCGAAGG
1 TCCGGGTT-AACTCCCGAAGG
21527226 TACGTGATTC
Statistics
Matches: 121, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
118 2 0.02
119 84 0.69
120 35 0.29
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAACTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGAGTAAGATCCGAAGGCATTT
GTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGACATTTGAACGAGTTACTAAA
Found at i:21531351 original size:18 final size:18
Alignment explanation
Indices: 21531328--21531365 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
21531318 TAAAAATATG
21531328 TTGTGTTCTTTATTTTTA
1 TTGTGTTCTTTATTTTTA
21531346 TTGTGTTCTTTATTTTTA
1 TTGTGTTCTTTATTTTTA
21531364 TT
1 TT
21531366 TCTCATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (18 bp):
TTGTGTTCTTTATTTTTA
Found at i:21532677 original size:22 final size:22
Alignment explanation
Indices: 21532632--21532693 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
21532622 CTATAGGCCT
21532632 TAAAT-CTCAAAC-CTTAAACTA
1 TAAATCCT-AAACTCTTAAACTA
21532653 TAAATCCTAAACTCTTAAA-TCA
1 TAAATCCTAAACTCTTAAACT-A
* *
21532675 TAAACCCTAAAATCTTAAA
1 TAAATCCTAAACTCTTAAA
21532694 AATAAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATCCTAAACTCTTAAACTA
Found at i:21533106 original size:34 final size:34
Alignment explanation
Indices: 21533063--21533131 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
21533053 GGGGTTAAGA
*
21533063 TTTAAAATTTAAG-TT-TAAGGTTTAGGGTATTGGG
1 TTTAAAATTT-AGTTTATAAGGTTTA-GGAATTGGG
*
21533097 TTTAGAATTTAGTTTATAAGGTTTAGGAATTGGG
1 TTTAAAATTTAGTTTATAAGGTTTAGGAATTGGG
21533131 T
1 T
21533132 ATTGGGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 2 0.06
34 20 0.65
35 9 0.29
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.45
Consensus pattern (34 bp):
TTTAAAATTTAGTTTATAAGGTTTAGGAATTGGG
Found at i:21533107 original size:21 final size:21
Alignment explanation
Indices: 21533083--21533177 Score: 68
Period size: 21 Copynumber: 4.6 Consensus size: 21
21533073 AAGTTTAAGG
21533083 TTTAGGGTATTGGGTTTAGAA
1 TTTAGGGTATTGGGTTTAGAA
** **
21533104 TTTAGTTTATAAGGTTTAGGAA
1 TTTAGGGTATTGGGTTTA-GAA
**
21533126 -TT-GGGTATTGGGTTTAGGG
1 TTTAGGGTATTGGGTTTAGAA
** * **
21533145 TTTAGTCTATAGGGTTTAGGG
1 TTTAGGGTATTGGGTTTAGAA
21533166 TTTAGGGTATTG
1 TTTAGGGTATTG
21533178 TGTATTTGGT
Statistics
Matches: 55, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.02
20 12 0.22
21 39 0.71
22 3 0.05
ACGTcount: A:0.21, C:0.01, G:0.34, T:0.44
Consensus pattern (21 bp):
TTTAGGGTATTGGGTTTAGAA
Found at i:21533132 original size:41 final size:41
Alignment explanation
Indices: 21533087--21533164 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
21533077 TTAAGGTTTA
*
21533087 GGGTATTGGGTTTAGAATTTAGTTTATAAGGTTTAGGAATT
1 GGGTATTGGGTTTAGAATTTAGTCTATAAGGTTTAGGAATT
** *
21533128 GGGTATTGGGTTTAGGGTTTAGTCTATAGGGTTTAGG
1 GGGTATTGGGTTTAGAATTTAGTCTATAAGGTTTAGG
21533165 GTTTAGGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.22, C:0.01, G:0.35, T:0.42
Consensus pattern (41 bp):
GGGTATTGGGTTTAGAATTTAGTCTATAAGGTTTAGGAATT
Found at i:21533145 original size:7 final size:7
Alignment explanation
Indices: 21533135--21533227 Score: 55
Period size: 7 Copynumber: 13.1 Consensus size: 7
21533125 ATTGGGTATT
21533135 GGGTTTA
1 GGGTTTA
21533142 GGGTTTA
1 GGGTTTA
** *
21533149 GTCTATA
1 GGGTTTA
21533156 GGGTTTA
1 GGGTTTA
21533163 GGGTTTA
1 GGGTTTA
21533170 GGGTATT-
1 GGGT-TTA
*
21533177 GTGTATT-
1 GGGT-TTA
*
21533184 TGGTTTA
1 GGGTTTA
*
21533191 GGTTTTA
1 GGGTTTA
** *
21533198 GTCTCTA
1 GGGTTTA
21533205 GGGTTTA
1 GGGTTTA
*
21533212 GGGTATTG
1 GGGT-TTA
21533220 GGGTTTA
1 GGGTTTA
21533227 G
1 G
21533228 TGTATTGGTT
Statistics
Matches: 64, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
6 2 0.03
7 54 0.84
8 8 0.12
ACGTcount: A:0.15, C:0.03, G:0.37, T:0.45
Consensus pattern (7 bp):
GGGTTTA
Found at i:21533189 original size:42 final size:40
Alignment explanation
Indices: 21533075--21533227 Score: 137
Period size: 42 Copynumber: 3.7 Consensus size: 40
21533065 TAAAATTTAA
* * *
21533075 GTTTAAGGTTTAGGGTATTGGGTTTAGAATTTAGTTTATAAG
1 GTTTAGGGTTTAGGGTATTGGGTTTAG-GTTTAG-TTATAGG
**
21533117 GTTTAGGAATT-GGGTATTGGGTTTAGGGTTTAGTCTATAGG
1 GTTTAGGGTTTAGGGTATTGGGTTTA-GGTTTAGT-TATAGG
* * * *
21533158 GTTTAGGGTTTAGGGTATTGTGTATTTGGTTTAGGTTTTAGT
1 GTTTAGGGTTTAGGGTATTGGGT-TTAGGTTTA-GTTATAGG
* *
21533200 CTCTAGGGTTTAGGGTATTGGGGTTTAG
1 GTTTAGGGTTTAGGGTATT-GGGTTTAG
21533228 TGTATTGGTT
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
40 1 0.01
41 33 0.37
42 49 0.54
43 7 0.08
ACGTcount: A:0.19, C:0.02, G:0.34, T:0.45
Consensus pattern (40 bp):
GTTTAGGGTTTAGGGTATTGGGTTTAGGTTTAGTTATAGG
Found at i:21533198 original size:49 final size:49
Alignment explanation
Indices: 21533116--21533238 Score: 153
Period size: 49 Copynumber: 2.5 Consensus size: 49
21533106 TAGTTTATAA
* * *
21533116 GGTTTA-GGAATTGGGTATTGGGTTTAGGGTTTAGTCTATAGGGTTTAG
1 GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTTTAG
* *
21533164 GGTTTAGGGTATTGTGTATTTGGTTTAGGTTTTAGTCTCTAGGGTTTAG
1 GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTTTAG
*
21533213 GGTATTGGGGT-TTAGTGTA-TTGGTTT
1 GGT-TTAGGGTATT-GTGTATTTGGTTT
21533239 TGGGATTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 6 0.09
49 49 0.74
50 11 0.17
ACGTcount: A:0.15, C:0.02, G:0.36, T:0.46
Consensus pattern (49 bp):
GGTTTAGGGTATTGTGTATTTGGTTTAGGGTTTAGTCTATAGGGTTTAG
Found at i:21533223 original size:15 final size:15
Alignment explanation
Indices: 21533205--21533235 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21533195 TTAGTCTCTA
21533205 GGGTTTAGGGTATTG
1 GGGTTTAGGGTATTG
*
21533220 GGGTTTAGTGTATTG
1 GGGTTTAGGGTATTG
21533235 G
1 G
21533236 TTTTGGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.45, T:0.42
Consensus pattern (15 bp):
GGGTTTAGGGTATTG
Found at i:21533586 original size:83 final size:84
Alignment explanation
Indices: 21533499--21533716 Score: 244
Period size: 84 Copynumber: 2.6 Consensus size: 84
21533489 TGAAACGTCG
* * * * * *
21533499 TCGTTTTATTTCGCG-GGTAGT-GGATTTAGTGGTGCTATCTTATAAACGCCACTAATAATATGA
1 TCGTTTTATGTCGCGCGAT-GTAGGAATTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGA
21533562 AAAATCGAATGAAAACTACA
65 AAAATCGAATGAAAACTACA
* * *
21533582 TCGTTTTATGTGGCGCGATTTAGGAATTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAG
1 TCGTTTTATGTCGCGCGATGTAGGAATTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAA
* *
21533647 AAATCGAATTAAAACTACG
66 AAATCGAATGAAAACTACA
* * * * * *
21533666 TCATTTTATGTGGCACGGTTTAGGAATTAGTGGCGCTATCC-TAAAAACGCC
1 TCGTTTTATGTCGCGCGATGTAGGAATTAGTGGCGCTA-CCTTATAAACGCC
21533717 GCAAAAAAAC
Statistics
Matches: 117, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
83 14 0.12
84 101 0.86
85 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (84 bp):
TCGTTTTATGTCGCGCGATGTAGGAATTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAA
AAATCGAATGAAAACTACA
Found at i:21533673 original size:84 final size:84
Alignment explanation
Indices: 21533524--21533716 Score: 280
Period size: 84 Copynumber: 2.3 Consensus size: 84
21533514 GGTAGTGGAT
* * * *
21533524 TTAGTGGTGCTATCTTATAAACGCCACTAATAATATGAAAAATCGAATGAAAACTACATCGTTTT
1 TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAATCGAATGAAAACTACATCATTTT
*
21533589 ATGTGGCGCGATTTAGGAA
66 ATGTGGCACGATTTAGGAA
* * *
21533608 TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAGAAATCGAATTAAAACTACGTCATTTT
1 TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAATCGAATGAAAACTACATCATTTT
*
21533673 ATGTGGCACGGTTTAGGAA
66 ATGTGGCACGATTTAGGAA
*
21533692 TTAGTGGCGCTATCC-TAAAAACGCC
1 TTAGTGGCGCTA-CCTTATAAACGCC
21533717 GCAAAAAAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 96 0.98
85 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (84 bp):
TTAGTGGCGCTACCTTATAAACGCCACTAAGAATATGAAAAATCGAATGAAAACTACATCATTTT
ATGTGGCACGATTTAGGAA
Found at i:21536022 original size:29 final size:29
Alignment explanation
Indices: 21535983--21536061 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
21535973 CTTAATAATC
*
21535983 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
21536013 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
21536042 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
21536062 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:21536181 original size:10 final size:10
Alignment explanation
Indices: 21536168--21536196 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
21536158 TCTACATACA
21536168 TATACATTTG
1 TATACATTTG
21536178 TATACATTTG
1 TATACATTTG
21536188 TATACATTT
1 TATACATTT
21536197 CATCTCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (10 bp):
TATACATTTG
Found at i:21540450 original size:9 final size:9
Alignment explanation
Indices: 21540427--21540502 Score: 71
Period size: 9 Copynumber: 8.1 Consensus size: 9
21540417 ATTGATCATT
*
21540427 ACTTAAATA
1 ACTTACATA
*
21540436 AATTACATA
1 ACTTACATA
21540445 ACTTACATA
1 ACTTACATA
* *
21540454 ACTCATATA
1 ACTTACATA
21540463 ACTTACATA
1 ACTTACATA
*
21540472 ATTTACATAACA
1 ACTTACAT---A
21540484 ACTTACATA
1 ACTTACATA
*
21540493 ACTCACATA
1 ACTTACATA
21540502 A
1 A
21540503 TTTCCTTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 46 0.85
12 8 0.15
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:21540488 original size:21 final size:21
Alignment explanation
Indices: 21540444--21540502 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
21540434 TAAATTACAT
*
21540444 AACTTACATAACT--CAT-AT
1 AACTTACATAACTCACATAAC
* *
21540462 AACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAAC
21540483 AACTTACATAACTCACATAA
1 AACTTACATAACTCACATAA
21540503 TTTCCTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.35
20 3 0.09
21 19 0.56
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (21 bp):
AACTTACATAACTCACATAAC
Done.