Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 55 of 59
Found at i:19914972 original size:34 final size:35
Alignment explanation
Indices: 19914898--19914983 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 35
19914888 AATTTAAAAT
*
19914898 TAATATTTTATTTATAATTTAAAATATTAATAATTGA
1 TAATATATT-TTTA-AATTTAAAATATTAATAATTGA
** *
19914935 TAAT-TATTTTTAAATTTAAAATATTAATTTTTTA
1 TAATATATTTTTAAATTTAAAATATTAATAATTGA
*
19914969 TAATATATTATTAAA
1 TAATATATTTTTAAA
19914984 AACTTAAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
34 23 0.53
35 13 0.30
36 3 0.07
37 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (35 bp):
TAATATATTTTTAAATTTAAAATATTAATAATTGA
Found at i:19915056 original size:42 final size:42
Alignment explanation
Indices: 19915010--19915178 Score: 139
Period size: 42 Copynumber: 3.9 Consensus size: 42
19915000 CTTTTTTATA
19915010 ATAATATTAATAATTGATCATTTAAATATTAATATTTTATTT
1 ATAATATTAATAATTGATCATTTAAATATTAATATTTTATTT
* * *
19915052 ATAAT-TCAATCATTAAT-ATTTTAAATTATTAATATTTTATTT
1 ATAATATTAATAATTGATCA-TTTAAA-TATTAATATTTTATTT
* * **
19915094 ACAATTGNTATTAATAATTGATCATTTAAATATTAACATTTTTAAGT
1 ATAA----TATTAATAATTGATCATTTAAATATTAATA-TTTTATTT
* * * *
19915141 ATTAATATT--TTATTTATAATTTAATTATTAATATTTTA
1 A-TAATATTAATAATTGATCATTTAAATATTAATATTTTA
19915179 AAATATTAAT
Statistics
Matches: 101, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
40 1 0.01
41 20 0.20
42 43 0.43
44 4 0.04
46 8 0.08
47 22 0.22
48 3 0.03
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (42 bp):
ATAATATTAATAATTGATCATTTAAATATTAATATTTTATTT
Found at i:19915084 original size:16 final size:15
Alignment explanation
Indices: 19915030--19915199 Score: 74
Period size: 16 Copynumber: 11.6 Consensus size: 15
19915020 TAATTGATCA
*
19915030 TTTAAATATTAATAT
1 TTTAATTATTAATAT
*
19915045 TTT-A-T-TT-ATAA
1 TTTAATTATTAATAT
* *
19915056 TTCAATCATTAATAT
1 TTTAATTATTAATAT
19915071 TTTAAATTATTAATAT
1 TTT-AATTATTAATAT
* *
19915087 TTTATTTA-CAAT-T
1 TTTAATTATTAATAT
* *
19915100 GNTATTAATAATTGATCA-
1 --T-TTAATTATTAAT-AT
* *
19915118 TTTAAATATTAACATT
1 TTTAATTATTAATA-T
*
19915134 TTTAAGTATTAATAT
1 TTTAATTATTAATAT
*
19915149 TTT-A-T-TT-ATAA
1 TTTAATTATTAATAT
19915160 TTTAATTATTAATAT
1 TTTAATTATTAATAT
*
19915175 TTTAAAATATTAATAT
1 TTT-AATTATTAATAT
*
19915191 TTTATTTAT
1 TTTAATTAT
19915200 CATTTCAATA
Statistics
Matches: 114, Mismatches: 23, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
11 11 0.10
12 6 0.05
13 4 0.04
14 10 0.09
15 35 0.31
16 46 0.40
17 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTAATTATTAATAT
Found at i:19915167 original size:88 final size:86
Alignment explanation
Indices: 19915014--19915178 Score: 208
Period size: 88 Copynumber: 1.9 Consensus size: 86
19915004 TTTATAATAA
* ** *
19915014 TATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTCAATCATTAATATTTTAAATT
1 TATTAATAATTGATCATTTAAATATTAACATTTTAAGTATAATT-AATCATTAATAATTTAAATT
19915079 ATTAATATTTTATTTACAATTG
65 ATTAATATTTTATTTACAATTG
* * *
19915101 NTATTAATAATTGATCATTTAAATATTAACATTTTTAAGTATTAA-TATTTTATTTATAATTT-A
1 -TATTAATAATTGATCATTTAAATATTAACA-TTTTAAGTA-TAATTA-ATCATTAATAATTTAA
19915164 ATTATTAATATTTTA
62 ATTATTAATATTTTA
19915179 AAATATTAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
88 46 0.69
89 18 0.27
90 3 0.04
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (86 bp):
TATTAATAATTGATCATTTAAATATTAACATTTTAAGTATAATTAATCATTAATAATTTAAATTA
TTAATATTTTATTTACAATTG
Found at i:19915186 original size:42 final size:41
Alignment explanation
Indices: 19915117--19915238 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 41
19915107 ATAATTGATC
* * *
19915117 ATTTAAATATTAACATTTTTAAGTATTAATATTTTATTTATA
1 ATTT-AATATTAATATTTTAAAATATTAATATTTTATTTATA
*
19915159 ATTTAATTATTAATATTTTAAAATATTAATATTTTATTTATC
1 ATTTAA-TATTAATATTTTAAAATATTAATATTTTATTTATA
* *
19915201 ATTTCAATATTATTATGGTTAAAATATTAATAATTTTA
1 ATTT-AATATTAATAT-TTTAAAATATTAAT-ATTTTA
19915239 ATTGATTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
41 2 0.03
42 47 0.67
43 15 0.21
44 6 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (41 bp):
ATTTAATATTAATATTTTAAAATATTAATATTTTATTTATA
Found at i:19918020 original size:27 final size:28
Alignment explanation
Indices: 19917952--19918020 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
19917942 TTTTTATTTT
* * *
19917952 ATTTTTTAATATTAATAATTTATAATTT
1 ATTTTTAAATATTAATAATTGATAATTA
*
19917980 A-TTTAAAATATTAATAATTGATAATTA
1 ATTTTTAAATATTAATAATTGATAATTA
19918007 ATTTTTAAAT-TTAA
1 ATTTTTAAATATTAA
19918021 ATATTAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 27 0.77
28 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTTAAATATTAATAATTGATAATTA
Found at i:19918147 original size:19 final size:18
Alignment explanation
Indices: 19918111--19918149 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
19918101 TTTTTTAAAT
19918111 ATTAATAATTTATAATTG
1 ATTAATAATTTATAATTG
19918129 ATTAA-AATATTACTAATTG
1 ATTAATAAT-TTA-TAATTG
19918148 AT
1 AT
19918150 CATTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTAATAATTTATAATTG
Found at i:19918193 original size:41 final size:42
Alignment explanation
Indices: 19918164--19918254 Score: 127
Period size: 41 Copynumber: 2.2 Consensus size: 42
19918154 TAAATATTTC
*
19918164 AATATTAATATTTTCTTTA-AATTTAATCATTAATATTTTAA
1 AATATTAATATTTTATTTATAATTTAATCATTAATATTTTAA
*
19918205 AATATTAATATTTTATTTATAATTTAAAT-ATT-AT-TATTAA
1 AATATTAATATTTTATTTATAATTT-AATCATTAATATTTTAA
19918245 AATATTAATA
1 AATATTAATA
19918255 ATTATTATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
40 15 0.33
41 20 0.43
42 8 0.17
43 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (42 bp):
AATATTAATATTTTATTTATAATTTAATCATTAATATTTTAA
Found at i:19918258 original size:21 final size:21
Alignment explanation
Indices: 19918197--19918262 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
19918187 TAATCATTAA
19918197 TATT-TTAAAATATTAAT-AT
1 TATTATTAAAATATTAATAAT
*
19918216 T-TTATTTATAAT-TTAA-ATAT
1 TATTA-TTAAAATATTAATA-AT
19918236 TATTATTAAAATATTAATAAT
1 TATTATTAAAATATTAATAAT
19918257 TATTAT
1 TATTAT
19918263 GTTCTTTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
18 2 0.05
19 5 0.13
20 15 0.39
21 15 0.39
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTATTAAAATATTAATAAT
Found at i:19926229 original size:24 final size:24
Alignment explanation
Indices: 19926190--19926248 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
19926180 TTGTTACTCC
* *
19926190 TGCTACTCCTCCTCCTGCTTCTGG
1 TGCTACCCCTCCTCCTGCTTCAGG
* *
19926214 TGTTGCCCCTCCTCCTGCTTCAGG
1 TGCTACCCCTCCTCCTGCTTCAGG
19926238 TGCTACCCCTC
1 TGCTACCCCTC
19926249 ATGTTAAATC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.05, C:0.44, G:0.17, T:0.34
Consensus pattern (24 bp):
TGCTACCCCTCCTCCTGCTTCAGG
Found at i:19926407 original size:24 final size:24
Alignment explanation
Indices: 19926379--19926425 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19926369 GTAGATGCAG
*
19926379 TCAATGCAGTTGGAGATCCAGCAA
1 TCAATGCAGTTAGAGATCCAGCAA
*
19926403 TCAATGCAGTTAGAGATTCAGCA
1 TCAATGCAGTTAGAGATCCAGCA
19926426 GGCGATGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (24 bp):
TCAATGCAGTTAGAGATCCAGCAA
Found at i:19926433 original size:24 final size:24
Alignment explanation
Indices: 19926380--19926435 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
19926370 TAGATGCAGT
* *
19926380 CAATGCAGTTGGAGATCCAGCAAT
1 CAATGCAGTTAGAGATCCAGCAAG
* *
19926404 CAATGCAGTTAGAGATTCAGCAGG
1 CAATGCAGTTAGAGATCCAGCAAG
*
19926428 CGATGCAG
1 CAATGCAG
19926436 ATACAAACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.29, T:0.20
Consensus pattern (24 bp):
CAATGCAGTTAGAGATCCAGCAAG
Found at i:19928084 original size:26 final size:26
Alignment explanation
Indices: 19928055--19928106 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
19928045 AACATTATTC
*
19928055 TGTATCATTTCCATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
19928081 TGTATCATTTACATATTATTCTTTGT
1 TGTATCATTTACATATTATTCTTTGT
19928107 ATTCATTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (26 bp):
TGTATCATTTACATATTATTCTTTGT
Found at i:19928106 original size:23 final size:23
Alignment explanation
Indices: 19928048--19928113 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 23
19928038 TAACATTAAC
*
19928048 ATTATTC--TGTATCATTTCCAT
1 ATTATTCTTTGTATCATTTACAT
19928069 ATTATTCTTTGTTGTATCATTTACAT
1 ATTATTC--T-TTGTATCATTTACAT
19928095 ATTATTCTTTGTATTCATT
1 ATTATTCTTTGTA-TCATT
19928114 CATGTGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 7 0.18
23 5 0.13
24 6 0.16
26 20 0.53
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.58
Consensus pattern (23 bp):
ATTATTCTTTGTATCATTTACAT
Found at i:19928470 original size:92 final size:92
Alignment explanation
Indices: 19928346--19928526 Score: 326
Period size: 92 Copynumber: 2.0 Consensus size: 92
19928336 TGGAATCAAG
* *
19928346 TCACCAGTTGATATTGATTCGCGGGAGTATTTGTTATGGAGTCATGCGAGTACTAAATGTTGAAT
1 TCACCAGTTGATATTGATTCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAAT
19928411 CACGTTGGTAATTAATATGGAATCGCA
66 CACGTTGGTAATTAATATGGAATCGCA
*
19928438 TCACCAGTTGATATTGATTCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATTTTGAAT
1 TCACCAGTTGATATTGATTCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAAT
*
19928503 CACGTTGGTAGTTAATATGGAATC
66 CACGTTGGTAATTAATATGGAATC
19928527 ACGTCATTAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 85 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (92 bp):
TCACCAGTTGATATTGATTCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAAT
CACGTTGGTAATTAATATGGAATCGCA
Found at i:19928558 original size:92 final size:92
Alignment explanation
Indices: 19928364--19928550 Score: 257
Period size: 92 Copynumber: 2.0 Consensus size: 92
19928354 TGATATTGAT
* *
19928364 TCGCGGGAGTATTTGTTATGGAGTCATGCGAGTACTAAATGTTGAATCACGTTGGTAATTAATAT
1 TCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAATCACGTTGGTAATTAATAT
* * * * * *
19928429 GGAATCGCATCACCAGTTGATATTGAT
66 GGAATCACATCACCAATTCACATGGAA
* *
19928456 TCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATTTTGAATCACGTTGGTAGTTAATAT
1 TCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAATCACGTTGGTAATTAATAT
* **
19928521 GGAATCACGTCATTAATTCACATGGAA
66 GGAATCACATCACCAATTCACATGGAA
19928548 TCG
1 TCG
19928551 TGTGAGTAGT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (92 bp):
TCGCGGGAGTATTTGTTATAGAGTCATGCAAGTACTAAATGTTGAATCACGTTGGTAATTAATAT
GGAATCACATCACCAATTCACATGGAA
Found at i:19930855 original size:63 final size:62
Alignment explanation
Indices: 19930755--19930873 Score: 184
Period size: 63 Copynumber: 1.9 Consensus size: 62
19930745 TCTTGTGTTT
*
19930755 TAGATTTGCTTGTCCCCCAATCACCGCACTCAGTTTGCTTCGTTGTACTGGTCACAGTTGCTA
1 TAGATTTGCTTGTCCCCCAATCACAGCACTCAGTTTGCTTCGTTGT-CTGGTCACAGTTGCTA
* * * *
19930818 TAGATTTGCTTGTCCCTCAATCACAGCAGTCATTTTGCTTCGTTGTTTGGTCACAG
1 TAGATTTGCTTGTCCCCCAATCACAGCACTCAGTTTGCTTCGTTGTCTGGTCACAG
19930874 CTATTGCAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
62 9 0.18
63 42 0.82
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (62 bp):
TAGATTTGCTTGTCCCCCAATCACAGCACTCAGTTTGCTTCGTTGTCTGGTCACAGTTGCTA
Found at i:19931707 original size:48 final size:48
Alignment explanation
Indices: 19931642--19931828 Score: 178
Period size: 48 Copynumber: 3.8 Consensus size: 48
19931632 AACGCCTGTA
*
19931642 ACGCAACGCTCAACAAATATTAAGTCACGTAATGCCTATAAAGAACTC
1 ACGCAACGCTCAACAAATATTCAGTCACGTAATGCCTATAAAGAACTC
* * * ** * *
19931690 ACGCAATGTTCAACAAATATTCAGTCAGGTAAT-TTTCAGTCACGTAATACCTGTC
1 ACGCAACGCTCAACAAATATTCAGTCACGTAATGCCT-A-T-A---AAGAAC--TC
* *
19931745 ACGCAACACTCAACATATATTCAGTCACGTAATGCCTATAAAGAACTC
1 ACGCAACGCTCAACAAATATTCAGTCACGTAATGCCTATAAAGAACTC
* * *
19931793 ACGCAATGCTCAACAAATATTCAGGCACCTAATGCC
1 ACGCAACGCTCAACAAATATTCAGTCACGTAATGCC
19931829 AAATAAACAG
Statistics
Matches: 108, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
47 1 0.01
48 63 0.58
49 1 0.01
50 5 0.05
53 5 0.05
54 1 0.01
55 31 0.29
56 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (48 bp):
ACGCAACGCTCAACAAATATTCAGTCACGTAATGCCTATAAAGAACTC
Found at i:19931771 original size:103 final size:101
Alignment explanation
Indices: 19931562--19931825 Score: 348
Period size: 103 Copynumber: 2.6 Consensus size: 101
19931552 TAGGTAGCTA
* * * ** *
19931562 AAGTCACGCAATGCCTAAAAACAGGTCACGCAATGCTCAATAAATATTCAGTCACATAATTCAGT
1 AAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCACATAATTCAGT
* * *
19931627 CATGTAACGCCTGTAACGCAACGCTCAACAAATATT
66 CACGTAACACCTGTAACGCAACACTCAACAAATATT
* **
19931663 AAGTCACGTAATGCCTATAAAGAACTCACGCAATGTTCAACAAATATTCAGTCAGGTAATTTTCA
1 AAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCACATAA--TTCA
* * *
19931728 GTCACGTAATACCTGTCACGCAACACTCAACATATATT
64 GTCACGTAACACCTGTAACGCAACACTCAACAAATATT
* * *
19931766 CAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGGCACCTAAT
1 AAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCACATAAT
19931826 GCCAAATAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
101 51 0.36
103 90 0.64
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (101 bp):
AAGTCACGTAATGCCTATAAAGAACTCACGCAATGCTCAACAAATATTCAGTCACATAATTCAGT
CACGTAACACCTGTAACGCAACACTCAACAAATATT
Found at i:19934459 original size:23 final size:23
Alignment explanation
Indices: 19934425--19934472 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
19934415 AACTAAGTTA
*
19934425 GATAAACCTTGGGGCAAAACCAG
1 GATAAACCTTGGAGCAAAACCAG
* *
19934448 GATAAACGTTGGAGCAAAACTAG
1 GATAAACCTTGGAGCAAAACCAG
19934471 GA
1 GA
19934473 GAACCAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.27, T:0.15
Consensus pattern (23 bp):
GATAAACCTTGGAGCAAAACCAG
Found at i:19944961 original size:25 final size:23
Alignment explanation
Indices: 19944920--19944965 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
19944910 AGAATTTATA
* *
19944920 AATTTATAATAATTATACTAAATT
1 AATTTATAAAAAATATA-TAAATT
19944944 AATTATATAAAAAATATATAAA
1 AATT-TATAAAAAATATATAAA
19944966 AATTGTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AATTTATAAAAAATATATAAATT
Found at i:19949770 original size:13 final size:13
Alignment explanation
Indices: 19949752--19949789 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
19949742 CTAACTTTTA
19949752 ATAAAATAATAAT
1 ATAAAATAATAAT
*
19949765 ATAAAATTATAA-
1 ATAAAATAATAAT
*
19949777 ATAAAATATTAAT
1 ATAAAATAATAAT
19949790 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAAATAATAAT
Found at i:19950288 original size:23 final size:23
Alignment explanation
Indices: 19950262--19950323 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
19950252 TGAAAANTAA
*
19950262 TAATATTTAAATTAAATAAATGT
1 TAATATTTAAATTAAATAAATAT
* * *
19950285 TAATATTTAAA-TGATTAATTAT
1 TAATATTTAAATTAAATAAATAT
*
19950307 TAATATTTTAATTAAAT
1 TAATATTTAAATTAAAT
19950324 TCTAGATTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (23 bp):
TAATATTTAAATTAAATAAATAT
Found at i:19954396 original size:13 final size:13
Alignment explanation
Indices: 19954375--19954422 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
19954365 ATTTAGTTTG
*
19954375 TTTAATTGTTTAT
1 TTTATTTGTTTAT
19954388 TTTATTTGTTT-T
1 TTTATTTGTTTAT
*
19954400 TTTATTTAGTCTAT
1 TTTATTT-GTTTAT
*
19954414 ATTATTTGT
1 TTTATTTGT
19954423 AAAAAAAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 8 0.27
13 15 0.50
14 7 0.23
ACGTcount: A:0.19, C:0.02, G:0.08, T:0.71
Consensus pattern (13 bp):
TTTATTTGTTTAT
Found at i:19960964 original size:66 final size:66
Alignment explanation
Indices: 19960876--19961030 Score: 188
Period size: 66 Copynumber: 2.4 Consensus size: 66
19960866 TTACAATGGC
* * * * * *
19960876 TTTT-CAAGGCTCAGCCAAAACCTTTTACACTAG-TTTTCACGAGCTCAACTAAAACCCAAGGTG
1 TTTTCCAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGAGCTCAACCAAAACCCAAAGTG
19960939 G
66 G
* * * *
19960940 TTTTCCAAAGGCTCAATCACAACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGT
1 TTTTCC-AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGAGCTCAACCAAAACCCAAAGT
19961005 GG
65 GG
*
19961007 TTTTCCAAGGTTCAACCACAACCT
1 TTTTCCAAGGCTCAACCACAACCT
19961031 ACAACAATCA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 4 0.05
65 1 0.01
66 38 0.50
67 33 0.43
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (66 bp):
TTTTCCAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGAGCTCAACCAAAACCCAAAGTG
G
Found at i:19961557 original size:25 final size:25
Alignment explanation
Indices: 19961529--19961579 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
19961519 CTTCAGTCCG
19961529 CTATTTCTTCAATTTGAAATTTGAT
1 CTATTTCTTCAATTTGAAATTTGAT
19961554 CTATTTCTTCAATTTGAAATTTGAT
1 CTATTTCTTCAATTTGAAATTTGAT
19961579 C
1 C
19961580 AACCAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (25 bp):
CTATTTCTTCAATTTGAAATTTGAT
Found at i:19968828 original size:32 final size:31
Alignment explanation
Indices: 19968782--19968885 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 31
19968772 TTTTACACTA
** *
19968782 GTTTTTCATTGGCTCAACTAAAACCCAAGGTG
1 GTTTTTCAAAGGCTCAACCAAAACCCAA-GTG
* *
19968814 GTTTTTCAAAGGCTCAACCACAACCTTTCACAATG
1 GTTTTTCAAAGGCTCAACCAAAACC---CA-AGTG
**
19968849 GTTTTTCACGGGCTCAACCAAAACCCAAAGTG
1 GTTTTTCAAAGGCTCAACCAAAACCC-AAGTG
19968881 GTTTT
1 GTTTT
19968886 CCAATGTTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
32 30 0.52
33 1 0.02
35 26 0.45
36 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (31 bp):
GTTTTTCAAAGGCTCAACCAAAACCCAAGTG
Found at i:19968863 original size:67 final size:65
Alignment explanation
Indices: 19968750--19968905 Score: 186
Period size: 67 Copynumber: 2.4 Consensus size: 65
19968740 TTACAATGGC
* * * * ** * *
19968750 TTTTCAAGGCTCAGCCAAAACCTTTTACACTAGTTTTTCATTGGCTCAACTAAAACCCAAGGTGG
1 TTTTCAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTCAACCAAAACCCAAAGTGG
*
19968815 TTTTTCAAAGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGT
1 -TTTTC-AAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTCAACCAAAACCCAAAGT
19968880 GG
64 GG
* *
19968882 TTTTCCAATGTTCAACCACAACCT
1 TTTT-CAAGGCTCAACCACAACCT
19968906 ACAACAATCA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
66 25 0.32
67 52 0.68
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (65 bp):
TTTTCAAGGCTCAACCACAACCTTTCACAATAGTTTTTCACGGGCTCAACCAAAACCCAAAGTGG
Found at i:19977917 original size:20 final size:19
Alignment explanation
Indices: 19977855--19977943 Score: 61
Period size: 20 Copynumber: 4.4 Consensus size: 19
19977845 AGAAACTTAG
* *
19977855 AATAAAAATAAAATAGAAAAG
1 AATAAAAA-AAAA-ATAAAAT
* **
19977876 AATAAAATAAAAGATATGAT
1 AATAAAA-AAAAAATAAAAT
19977896 AATAAAAAATAAAATAAAAT
1 AATAAAAAA-AAAATAAAAT
**
19977916 AATAATTAAAAAATAATAAT
1 AATAAAAAAAAAATAA-AAT
*
19977936 GATAAAAA
1 AATAAAAA
19977944 TAGTTAATTG
Statistics
Matches: 52, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
19 9 0.17
20 32 0.62
21 10 0.19
22 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AATAAAAAAAAAATAAAAT
Found at i:19977925 original size:17 final size:18
Alignment explanation
Indices: 19977894--19977945 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
19977884 AAAAGATATG
* *
19977894 ATAATAAAAAATAAAATA
1 ATAATAATAATTAAAATA
19977912 A-AATAATAATTAAAA-A
1 ATAATAATAATTAAAATA
* *
19977928 ATAATAATGATAAAAATA
1 ATAATAATAATTAAAATA
19977946 GTTAATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAATAATAATTAAAATA
Found at i:19977930 original size:14 final size:15
Alignment explanation
Indices: 19977911--19977945 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19977901 AAAATAAAAT
*
19977911 AAAATAATAATTA-A
1 AAAATAATAATGATA
19977925 AAAATAATAATGATA
1 AAAATAATAATGATA
19977940 AAAATA
1 AAAATA
19977946 GTTAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAATAATAATGATA
Found at i:19977933 original size:27 final size:25
Alignment explanation
Indices: 19977859--19977934 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
19977849 ACTTAGAATA
*
19977859 AAAATAA-AATAGAAAAGAATAAAAT
1 AAAATAATAATA-AAAAAAATAAAAT
* *
19977884 AAAAGATATGATAATAAAAAATAAAAT
1 AAAATA-ATAATAA-AAAAAATAAAAT
19977911 AAAATAATAATTAAAAAATAATAA
1 AAAATAATAA-TAAAAAA-AATAA
19977935 TGATAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 5 0.12
26 9 0.22
27 27 0.66
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAATAATAATAAAAAAAATAAAAT
Found at i:19990144 original size:8 final size:8
Alignment explanation
Indices: 19990129--19990216 Score: 78
Period size: 8 Copynumber: 11.1 Consensus size: 8
19990119 ACAAAAAAAT
19990129 AAAA-ATA
1 AAAATATA
19990136 AAAATAT-
1 AAAATATA
*
19990143 AATA-ATA
1 AAAATATA
19990150 AAAATATAA
1 AAAATAT-A
19990159 AAAATATA
1 AAAATATA
19990167 AAAATAATA
1 AAAAT-ATA
19990176 AATAATATA
1 AA-AATATA
*
19990185 AAAATATG
1 AAAATATA
19990193 AAAATA-A
1 AAAATATA
*
19990200 AGAATAGTA
1 AAAATA-TA
19990209 AAAA-ATA
1 AAAATATA
19990216 A
1 A
19990217 TAAAATTTGT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.03
7 18 0.27
8 22 0.33
9 22 0.33
10 3 0.04
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (8 bp):
AAAATATA
Found at i:19990161 original size:9 final size:9
Alignment explanation
Indices: 19990149--19990221 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 9
19990139 ATATAATAAT
19990149 AAAAATATA
1 AAAAATATA
19990158 AAAAATAT-
1 AAAAATATA
19990166 AAAAATAATA
1 AAAAAT-ATA
*
19990176 AATAATAT-
1 AAAAATATA
19990184 AAAAATAT-
1 AAAAATATA
*
19990192 -GAAA-ATA
1 AAAAATATA
*
19990199 AAGAATAGTA
1 AAAAATA-TA
19990209 AAAAATAATA
1 AAAAAT-ATA
19990219 AAA
1 AAA
19990222 TTTGTGTCCA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 15 0.29
9 13 0.25
10 17 0.33
11 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (9 bp):
AAAAATATA
Found at i:19990165 original size:23 final size:22
Alignment explanation
Indices: 19990125--19990222 Score: 66
Period size: 20 Copynumber: 4.5 Consensus size: 22
19990115 GCTTACAAAA
19990125 AAATA-AAAATAAAAATAT-AA
1 AAATATAAAATAAAAATATAAA
* * *
19990145 TAATA-AAAATATAAAAAATATA
1 AAATATAAAATA-AAAATATAAA
19990167 AAA-AT--AATAAATAATAT-AA
1 AAATATAAAATAAA-AATATAAA
19990186 AAATATGAAAATAAAGAATAGTAAA
1 AAATAT-AAAATAAA-AATA-TAAA
19990211 AAATAATAAAAT
1 AAAT-ATAAAAT
19990223 TTGTGTCCAC
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
19 6 0.10
20 20 0.33
21 7 0.12
22 3 0.05
23 10 0.17
24 1 0.02
25 11 0.18
26 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (22 bp):
AAATATAAAATAAAAATATAAA
Found at i:19990170 original size:18 final size:17
Alignment explanation
Indices: 19990121--19990221 Score: 91
Period size: 18 Copynumber: 5.8 Consensus size: 17
19990111 GATTGCTTAC
*
19990121 AAAAAA-ATAAAAATAA
1 AAAAAATATAAAAATAT
19990137 AAATATAATAATAAAAATAT
1 AAA-A-AAT-ATAAAAATAT
19990157 AAAAAATATAAAAATAAT
1 AAAAAATATAAAAAT-AT
*
19990175 AAATAATATAAAAATAT
1 AAAAAATATAAAAATAT
* *
19990192 -GAAAATA-AAGAATAGT
1 AAAAAATATAAAAATA-T
19990208 AAAAAATAATAAAA
1 AAAAAAT-ATAAAA
19990222 TTTGTGTCCA
Statistics
Matches: 69, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.09
16 9 0.13
17 16 0.23
18 22 0.32
19 4 0.06
20 12 0.17
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAAAATATAAAAATAT
Found at i:19990172 original size:26 final size:26
Alignment explanation
Indices: 19990143--19990221 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 26
19990133 ATAAAAATAT
19990143 AATAATAAAAATATAAAAAATATAAA
1 AATAATAAAAATATAAAAAATATAAA
*
19990169 AATAATAAATAATAT-AAAAATATGAA
1 AATAATAAA-AATATAAAAAATATAAA
*
19990195 AAT-A-AAGAATAGTAAAAAATAATAAA
1 AATAATAAAAATA-TAAAAAAT-ATAAA
19990221 A
1 A
19990222 TTTGTGTCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.09
24 3 0.07
25 7 0.15
26 27 0.59
27 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (26 bp):
AATAATAAAAATATAAAAAATATAAA
Found at i:19990213 original size:43 final size:40
Alignment explanation
Indices: 19990132--19990221 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 40
19990122 AAAAAATAAA
*
19990132 AATAAAAATATAATAATAAAAATATAAAAAATATAAAAAT
1 AATAAAAATATAAAAATAAAAATATAAAAAATATAAAAAT
* *
19990172 AATAAATAATATAAAAATATGAAA-ATAAAGAATAGTAAAAAAT
1 AATAAA-AATATAAAAATA-AAAATATAAAAAATA-T-AAAAAT
19990215 AATAAAA
1 AATAAAA
19990222 TTTGTGTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
40 6 0.14
41 20 0.47
42 5 0.12
43 12 0.28
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (40 bp):
AATAAAAATATAAAAATAAAAATATAAAAAATATAAAAAT
Found at i:19990377 original size:9 final size:9
Alignment explanation
Indices: 19990349--19990423 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 9
19990339 AAATATGATA
*
19990349 AAAAAGAAT
1 AAAAATAAT
*
19990358 AAAACAAAAT
1 AAAA-ATAAT
19990368 AAAAATAAT
1 AAAAATAAT
19990377 AATTAAATAAT
1 AA--AAATAAT
*
19990388 --AAATGA-
1 AAAAATAAT
*
19990394 CAAAA-AAT
1 AAAAATAAT
19990402 AAAAATAAT
1 AAAAATAAT
*
19990411 AAAAACAAT
1 AAAAATAAT
19990420 AAAA
1 AAAA
19990424 TAGATAATCG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
7 6 0.11
8 7 0.13
9 25 0.47
10 8 0.15
11 7 0.13
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:19990423 original size:23 final size:23
Alignment explanation
Indices: 19990364--19990425 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
19990354 GAATAAAACA
*
19990364 AAATAA-AAATAATAATTAAATAAT
1 AAATAACAAAAAATAA--AAATAAT
*
19990388 AAATGACAAAAAATAAAAATAAT
1 AAATAACAAAAAATAAAAATAAT
19990411 AAA-AACAATAAAATA
1 AAATAACAA-AAAATA
19990426 GATAATCGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 4 0.12
23 16 0.48
24 5 0.15
25 8 0.24
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (23 bp):
AAATAACAAAAAATAAAAATAAT
Found at i:19992985 original size:75 final size:75
Alignment explanation
Indices: 19992900--19993137 Score: 318
Period size: 75 Copynumber: 3.1 Consensus size: 75
19992890 ATTATTTTTC
*
19992900 AAGTTTCGTTGCCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGT
1 AAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGT
19992965 TCATTTTTAA
66 TCATTTTTAA
** * * *
19992975 AAGTTTCGTTGTTTCAATTTTGAGGAGTTTATTTTTCAAGTTTCGTTGCCTCAATTTTGAGGAGT
1 AAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGT
19993040 TCATTTTTTAAAAA
66 TCA-TTTTT---AA
* * * *
19993054 AAGTTTCGTTGCCTTAGTTTTGAGGAGTCTCATTTTTAAAGTTTCATTGCCTTAGTTTTGAGGAG
1 AAGTTTCGTTGCCTCAGTTTTGAGGAGT-TCATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAG
19993119 TTTCA-TTTT-A
65 -TTCATTTTTAA
19993129 AAGTTTCGT
1 AAGTTTCGT
19993138 AATGCTTAGC
Statistics
Matches: 142, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
75 72 0.51
76 5 0.04
79 30 0.21
80 31 0.22
81 4 0.03
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (75 bp):
AAGTTTCGTTGCCTCAGTTTTGAGGAGTTCATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGT
TCATTTTTAA
Found at i:19992992 original size:38 final size:37
Alignment explanation
Indices: 19992893--19993137 Score: 303
Period size: 37 Copynumber: 6.4 Consensus size: 37
19992883 AGGGTTGATT
* **
19992893 ATTTTTCAAGTTTCGTTGCCTCAGCTTTGAGGAGTTC
1 ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
19992930 ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
1 ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
** *
19992967 ATTTTTAAAAGTTTCGTTGTTTCAATTTTGAGGAGTTT
1 ATTTTT-AAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
*
19993005 ATTTTTCAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
1 ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
* *
19993042 ATTTTTTAAAAAAAGTTTCGTTGCCTTAGTTTTGAGGAGTCTC
1 A-TTTTT----AAAGTTTCGTTGCCTCAATTTTGAGGAGT-TC
* * *
19993085 ATTTTTAAAGTTTCATTGCCTTAGTTTTGAGGAGTTTC
1 ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAG-TTC
19993123 A-TTTTAAAGTTTCGT
1 ATTTTTAAAGTTTCGT
19993138 AATGCTTAGC
Statistics
Matches: 185, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
37 81 0.44
38 69 0.37
39 1 0.01
42 31 0.17
43 3 0.02
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (37 bp):
ATTTTTAAAGTTTCGTTGCCTCAATTTTGAGGAGTTC
Found at i:19995304 original size:20 final size:19
Alignment explanation
Indices: 19995242--19995330 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 19
19995232 AGAAATTTAG
*
19995242 AATAAAAATAAAATATAAAAG
1 AATAAAAA-AAAA-ATAAAAT
* **
19995263 AATAAAATAAAAGATATGAT
1 AATAAAA-AAAAAATAAAAT
19995283 AATAAAAAATAAAATAAAAT
1 AATAAAAAA-AAAATAAAAT
**
19995303 AATAATTAAAAAATAATAAT
1 AATAAAAAAAAAATAA-AAT
*
19995323 GATAAAAA
1 AATAAAAA
19995331 TAGTTAATTG
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
19 9 0.17
20 33 0.62
21 10 0.19
22 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
AATAAAAAAAAAATAAAAT
Found at i:19995312 original size:17 final size:18
Alignment explanation
Indices: 19995281--19995332 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
19995271 AAAAGATATG
* *
19995281 ATAATAAAAAATAAAATA
1 ATAATAATAATTAAAATA
19995299 A-AATAATAATTAAAA-A
1 ATAATAATAATTAAAATA
* *
19995315 ATAATAATGATAAAAATA
1 ATAATAATAATTAAAATA
19995333 GTTAATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAATAATAATTAAAATA
Found at i:19995320 original size:27 final size:25
Alignment explanation
Indices: 19995246--19995321 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
19995236 ATTTAGAATA
*
19995246 AAAATAA-AATATAAAAGAATAAAAT
1 AAAATAATAATA-AAAAAAATAAAAT
* *
19995271 AAAAGATATGATAATAAAAAATAAAAT
1 AAAATA-ATAATAA-AAAAAATAAAAT
19995298 AAAATAATAATTAAAAAATAATAA
1 AAAATAATAA-TAAAAAA-AATAA
19995322 TGATAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 5 0.12
26 9 0.22
27 27 0.66
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
AAAATAATAATAAAAAAAATAAAAT
Found at i:19998655 original size:63 final size:64
Alignment explanation
Indices: 19998549--19998673 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 64
19998539 TTGTTCTAAG
* * * *
19998549 GAATTCAAAGTTTATGGACATCACAATATATTTCATCATATAT-ATTTGAAAATGATGGTTTAA
1 GAATTCAAAGTTTACGGACATCACAATATATTTCATCAAATATAATGTGAAAACGATGGTTTAA
* * *
19998612 GAATTCAAAGTTTACGGACCTCAGAATAT-GTTCTATCAAATATAAATGTGAAAACGATGGTT
1 GAATTCAAAGTTTACGGACATCACAATATATTTC-ATCAAATAT-AATGTGAAAACGATGGTT
19998674 GAATAGAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 3 0.06
63 34 0.65
65 15 0.29
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (64 bp):
GAATTCAAAGTTTACGGACATCACAATATATTTCATCAAATATAATGTGAAAACGATGGTTTAA
Found at i:20008909 original size:17 final size:16
Alignment explanation
Indices: 20008876--20008910 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
20008866 AGAGATAAAT
*
20008876 AAAATTAAATTAGGTA
1 AAAATTAAATAAGGTA
20008892 AAAATTAAATAAAGGTA
1 AAAATTAAAT-AAGGTA
20008909 AA
1 AA
20008911 CAAAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (16 bp):
AAAATTAAATAAGGTA
Found at i:20008915 original size:20 final size:19
Alignment explanation
Indices: 20008856--20008915 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 19
20008846 TCCTTAGGTG
* *
20008856 AAAATTAAATAGAGATAAA
1 AAAATTAAATAAAGGTAAA
*
20008875 TAAAATTAAAT-TAGGT--A
1 -AAAATTAAATAAAGGTAAA
20008892 AAAATTAAATAAAGGTAAA
1 AAAATTAAATAAAGGTAAA
20008911 CAAAA
1 -AAAA
20008916 ATAAGAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 10 0.30
17 5 0.15
19 4 0.12
20 14 0.42
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (19 bp):
AAAATTAAATAAAGGTAAA
Found at i:20021486 original size:36 final size:36
Alignment explanation
Indices: 20021446--20021516 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
20021436 GAATGGTAAG
20021446 ATTGATTCCTAACCTGGTGAATCTTGGGTTTGAGAT
1 ATTGATTCCTAACCTGGTGAATCTTGGGTTTGAGAT
20021482 ATTGATTCCTAACCTGGTGAATCTTGGGTTTGAGA
1 ATTGATTCCTAACCTGGTGAATCTTGGGTTTGAGA
20021517 AAAGCTCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (36 bp):
ATTGATTCCTAACCTGGTGAATCTTGGGTTTGAGAT
Found at i:20022876 original size:2 final size:2
Alignment explanation
Indices: 20022871--20022904 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20022861 ACACACACAC
20022871 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
20022905 TAAATAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20047533 original size:16 final size:16
Alignment explanation
Indices: 20047512--20047558 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
20047502 ATTTAGAGAA
20047512 AATAAAATAAATAAAT
1 AATAAAATAAATAAAT
20047528 AATAAAATAAAT-AAT
1 AATAAAATAAATAAAT
*
20047543 AA-AAAATAAAAAAAT
1 AATAAAATAAATAAAT
20047558 A
1 A
20047559 GAAAGAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 12 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAAAATAAATAAAT
Found at i:20047537 original size:12 final size:12
Alignment explanation
Indices: 20047520--20047558 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
20047510 AAAATAAAAT
20047520 AAATAAATAATA
1 AAATAAATAATA
20047532 AAATAAATAAT-
1 AAATAAATAATA
*
20047543 AAA-AAATAAAA
1 AAATAAATAATA
20047554 AAATA
1 AAATA
20047559 GAAAGAGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 6 0.25
11 6 0.25
12 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:20047553 original size:7 final size:7
Alignment explanation
Indices: 20047515--20047555 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
20047505 TAGAGAAAAT
20047515 AAAATAA
1 AAAATAA
20047522 ATAAATAA
1 A-AAATAA
20047530 TAAAATAA
1 -AAAATAA
*
20047538 ATAATAA
1 AAAATAA
20047545 AAAATAA
1 AAAATAA
20047552 AAAA
1 AAAA
20047556 ATAGAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 17 0.57
8 12 0.40
9 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:20065422 original size:2 final size:2
Alignment explanation
Indices: 20065415--20065468 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
20065405 TAATATTATG
* *
20065415 TA TA TA TA TA T- TA TGA TT TA TA TA -A AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20065456 TA TT TA TA TA TA T
1 TA TA TA TA TA TA T
20065469 TTGTTATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20071750 original size:2 final size:2
Alignment explanation
Indices: 20071745--20071782 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20071735 TGATATATTG
20071745 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
20071783 GTGGTAGATG
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:20079438 original size:2 final size:2
Alignment explanation
Indices: 20079431--20079483 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
20079421 ATCTTACTTT
* * *
20079431 TA TA TA TA T- TA TA GA TA TT TA TA TA -A TA CA 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
20079471 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
20079484 GTATTTGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20091328 original size:407 final size:406
Alignment explanation
Indices: 20090561--20091371 Score: 1460
Period size: 407 Copynumber: 2.0 Consensus size: 406
20090551 CCTCCACCTT
*
20090561 GACATCAACCTTCTTCAACTGATCAATGATCCCATCAAATTCATTCATATGCTTCATGAGGTCTC
1 GACATCAACCTTCTTCAACTGATCAATGATCCCATCAAATTCATTCATATGCTTCACGAGGTCTC
* *
20090626 CATTCTTCTCCATCTTTAAGCAATACAACTTTCGCCTAAGCTGCAACTTGTTAGAAAGACTTTTC
66 CATTCTCCTCCATCTTTAAGCAATACAACTTTCACCTAAGCTGCAACTTGTTAGAAAGACTTTTC
20090691 GTCAAGTAAATTTTCTCTAACTTTGCCCATAATCTTAGAGCAGAATCCTCATCAATAACATGATT
131 GTCAAGTAAATTTTCTCTAACTTTGCCCATAATCTTAGAGCAGAATCCTCATCAATAACATGATT
*
20090756 AAACACATTATCTCCAATGCAAAGCCGAATAGTGCTCACACACCTTTGCTTCAACTATGCCCATT
196 AAACACATTATCTCCAATGCAAAGCCGAATAGTGCTCACACACCTTTGCTCCAACTATGCCCATT
20090821 CAACATCCTTCATGTCATCTGGTTGCCCTTCCTCATTTCCTAGCAAGGGGCGCATTAAACCTTGC
261 CAACATCCTTCATGTCATCTGGTTGCCCTTCCTCATTTCCTAGCAAGGGGCGCATTAAACCTTGC
*
20090886 TGTACAAGGAGATCTTTCATCATTCTTTACCACTGCGTGAAACTAGTCTTACCATCAAACTTCTC
326 TGTACAAGGAGATCTTTCATCATTCTCTACCACTGCGTGAAACTAGTCTTACCATCAAACTTCTC
20090951 AATTGAAAAATTCGTA
391 AATTGAAAAATTCGTA
* * *
20090967 GNACATCACCCTTCTTCAACTGATCAATGATTCCATCGAATTCATTCATATGCTTCACGAGGTCT
1 G-ACATCAACCTTCTTCAACTGATCAATGATCCCATCAAATTCATTCATATGCTTCACGAGGTCT
** *
20091032 CCATTCTCCTTTATCTTTAAGCGATACAACTTTCACCTAAGCTGCAACTTGTTAGAAAGACTTTT
65 CCATTCTCCTCCATCTTTAAGCAATACAACTTTCACCTAAGCTGCAACTTGTTAGAAAGACTTTT
*
20091097 CGTCAAGTAAATTTTCTCTAACTTTGCCCATAATCTTAGAGCAGAATCCTCATCAATAACATGGT
130 CGTCAAGTAAATTTTCTCTAACTTTGCCCATAATCTTAGAGCAGAATCCTCATCAATAACATGAT
*
20091162 TAAACACATTATCTCCAATGCAAAGCCGAATAGTGCTCACACACCTTTGCTCCAACTCTGCCCAT
195 TAAACACATTATCTCCAATGCAAAGCCGAATAGTGCTCACACACCTTTGCTCCAACTATGCCCAT
*
20091227 TCAACATCCTTCATGTCATCTGGTTGCTCTTCCTCATTTCCTAGCAAGGGGCGCATTAAACCTTG
260 TCAACATCCTTCATGTCATCTGGTTGCCCTTCCTCATTTCCTAGCAAGGGGCGCATTAAACCTTG
* * *
20091292 CTGTACAAGGAGATCTTTCATCCTTCTCTGCCACTGCGTGAAACTAGTCTTCCCATCAAACTTCT
325 CTGTACAAGGAGATCTTTCATCATTCTCTACCACTGCGTGAAACTAGTCTTACCATCAAACTTCT
20091357 CAATTGAAAAATTCG
390 CAATTGAAAAATTCG
20091372 CAGAACTAGT
Statistics
Matches: 387, Mismatches: 17, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
406 1 0.00
407 386 1.00
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.32
Consensus pattern (406 bp):
GACATCAACCTTCTTCAACTGATCAATGATCCCATCAAATTCATTCATATGCTTCACGAGGTCTC
CATTCTCCTCCATCTTTAAGCAATACAACTTTCACCTAAGCTGCAACTTGTTAGAAAGACTTTTC
GTCAAGTAAATTTTCTCTAACTTTGCCCATAATCTTAGAGCAGAATCCTCATCAATAACATGATT
AAACACATTATCTCCAATGCAAAGCCGAATAGTGCTCACACACCTTTGCTCCAACTATGCCCATT
CAACATCCTTCATGTCATCTGGTTGCCCTTCCTCATTTCCTAGCAAGGGGCGCATTAAACCTTGC
TGTACAAGGAGATCTTTCATCATTCTCTACCACTGCGTGAAACTAGTCTTACCATCAAACTTCTC
AATTGAAAAATTCGTA
Found at i:20094572 original size:22 final size:20
Alignment explanation
Indices: 20094547--20094600 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
20094537 TAATGGGGGC
20094547 ATAAAGAAAAAAAAACATAATA
1 ATAAA-AAAAAAAAACATAA-A
* *
20094569 ATAATAAAATAAAAATATAAA
1 ATAA-AAAAAAAAAACATAAA
20094590 ATAAAATAAAA
1 ATAAAA-AAAA
20094601 TNGAGGAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.07
21 8 0.30
22 16 0.59
23 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
ATAAAAAAAAAAAACATAAA
Found at i:20094711 original size:14 final size:14
Alignment explanation
Indices: 20094692--20094736 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
20094682 AAACATAAAT
20094692 AATAAATAAAATAA
1 AATAAATAAAATAA
20094706 AATAAATAAAATAA
1 AATAAATAAAATAA
20094720 AATAAAATAAAAGTAA
1 AAT-AAATAAAA-TAA
20094736 A
1 A
20094737 GTAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 17 0.59
15 8 0.28
16 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
AATAAATAAAATAA
Found at i:20094740 original size:5 final size:5
Alignment explanation
Indices: 20094695--20094736 Score: 68
Period size: 5 Copynumber: 8.4 Consensus size: 5
20094685 CATAAATAAT
20094695 AAATA AAATA AAAT- AAATA AAATA AAATA AAATA AAAGTA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAA-TA AA
20094737 GTAATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
6 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:20094747 original size:2 final size:2
Alignment explanation
Indices: 20094740--20094771 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20094730 AAGTAAAGTA
20094740 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
20094772 TAATGGGGTT
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:20116920 original size:29 final size:29
Alignment explanation
Indices: 20116885--20116964 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
20116875 AAAAAAGAGT
*
20116885 TGTATGTGAACAGGTACAAGAGAAGAAAC
1 TGTATGTGAATAGGTACAAGAGAAGAAAC
* * *
20116914 TGTATGTGAATAGGTATAAGATAAGAAGC
1 TGTATGTGAATAGGTACAAGAGAAGAAAC
* *
20116943 TATACGTGAATAGGTACAAGAG
1 TGTATGTGAATAGGTACAAGAG
20116965 GACAAGGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.07, G:0.28, T:0.23
Consensus pattern (29 bp):
TGTATGTGAATAGGTACAAGAGAAGAAAC
Found at i:20120241 original size:36 final size:36
Alignment explanation
Indices: 20120194--20120310 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 36
20120184 TTATAACATC
* *
20120194 TAAAAAGAAAATCAATCAGTTTTACCTTATCATATT
1 TAAAAAAAAAATCAATCAGTTTTATCTTATCATATT
* * *
20120230 TAAAAAAAAAATCAATCAATTTTATCTTAGCATGTT
1 TAAAAAAAAAATCAATCAGTTTTATCTTATCATATT
* * * *
20120266 T-AAAAGAAAAGCAGTCAG-TTAATCTTATCATATT
1 TAAAAAAAAAATCAATCAGTTTTATCTTATCATATT
20120300 TAAAAAAAAAA
1 TAAAAAAAAAA
20120311 AAGCAATTAG
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
34 14 0.21
35 21 0.31
36 32 0.48
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (36 bp):
TAAAAAAAAAATCAATCAGTTTTATCTTATCATATT
Found at i:20120325 original size:71 final size:70
Alignment explanation
Indices: 20120196--20120353 Score: 185
Period size: 71 Copynumber: 2.2 Consensus size: 70
20120186 ATAACATCTA
* * * * *
20120196 AAAAGAAAATCAATCAGTTTTACCTTATCATATTTAAAAAAAAAATCAATCAATTTTATCTTAGC
1 AAAAGAAAAGCAATCAGTTTAACCTTATCATATTTAAAAAAAAAA-CAAGCAATTTTATCTCAAC
**
20120261 ATGTTT
65 ACATTT
* *
20120267 AAAAGAAAAGCAGTCAG-TTAATCTTATCATATTTAAAAAAAAAA-AAGCAATTAGTTTATCTCA
1 AAAAGAAAAGCAATCAGTTTAACCTTATCATATTTAAAAAAAAAACAAGCAA-T--TTTATCTCA
20120330 ACACATTT
63 ACACATTT
20120338 AAAAGAAAAGCAATCA
1 AAAAGAAAAGCAATCA
20120354 TATTCATATT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
68 5 0.07
69 1 0.01
70 25 0.34
71 43 0.58
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.30
Consensus pattern (70 bp):
AAAAGAAAAGCAATCAGTTTAACCTTATCATATTTAAAAAAAAAACAAGCAATTTTATCTCAACA
CATTT
Found at i:20120848 original size:42 final size:42
Alignment explanation
Indices: 20120794--20120973 Score: 143
Period size: 42 Copynumber: 4.5 Consensus size: 42
20120784 TGGTTGCTTC
* *
20120794 TGATATACTTATGACCTATGACACTAGGGTTAATTGTGGTTT
1 TGATATAATTATGACCTATGCCACTAGGGTTAATTGTGGTTT
*
20120836 TGATATAATTATGAACC-ATGCCACTGGGGTTAA-T-T-G---
1 TGATATAATTATG-ACCTATGCCACTAGGGTTAATTGTGGTTT
* *
20120872 TG-----ATTATGACCTATGCCATTAAGGTTAATTGTGGTTT
1 TGATATAATTATGACCTATGCCACTAGGGTTAATTGTGGTTT
* * *
20120909 CGATATGATTATGAACC-ATGCCATTAGGGTTAATTGTGGTTTT
1 TGATATAATTATG-ACCTATGCCACTAGGGTTAATTGTGG-TTT
* * *
20120952 TGTTATGATTATGACTTATGCC
1 TGATATAATTATGACCTATGCC
20120974 TTAAGGGTTA
Statistics
Matches: 111, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
30 3 0.03
31 19 0.17
32 1 0.01
33 1 0.01
34 1 0.01
36 2 0.02
37 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 55 0.50
43 25 0.23
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (42 bp):
TGATATAATTATGACCTATGCCACTAGGGTTAATTGTGGTTT
Found at i:20120878 original size:31 final size:31
Alignment explanation
Indices: 20120843--20120904 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
20120833 TTTTGATATA
**
20120843 ATTATGAACC-ATGCCACTGGGGTTAATTGTG
1 ATTATG-ACCTATGCCACTAAGGTTAATTGTG
*
20120874 ATTATGACCTATGCCATTAAGGTTAATTGTG
1 ATTATGACCTATGCCACTAAGGTTAATTGTG
20120905 GTTTCGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (31 bp):
ATTATGACCTATGCCACTAAGGTTAATTGTG
Found at i:20120898 original size:73 final size:73
Alignment explanation
Indices: 20120802--20120946 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 73
20120792 TCTGATATAC
* * *
20120802 TTATGACCTATGACACTAGGGTTAATTGTGGTTTTGATATAATTATGAACCATGCCACTGGGGTT
1 TTATGACCTATGACACTAAGGTTAATTGTGGTTTCGATATAATTATGAACCATGCCACTAGGGTT
20120867 AATTGTGA
66 AATTGTGA
* * * *
20120875 TTATGACCTATGCCATTAAGGTTAATTGTGGTTTCGATATGATTATGAACCATGCCATTAGGGTT
1 TTATGACCTATGACACTAAGGTTAATTGTGGTTTCGATATAATTATGAACCATGCCACTAGGGTT
20120940 AATTGTG
66 AATTGTG
20120947 GTTTTTGTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (73 bp):
TTATGACCTATGACACTAAGGTTAATTGTGGTTTCGATATAATTATGAACCATGCCACTAGGGTT
AATTGTGA
Found at i:20126388 original size:16 final size:15
Alignment explanation
Indices: 20126367--20126405 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
20126357 CTTTAAGGAA
20126367 AAAAAGAGAAAAAAAG
1 AAAAAGA-AAAAAAAG
*
20126383 AAAAAGTAATAAAAAG
1 AAAAAG-AAAAAAAAG
20126399 AAAAAGA
1 AAAAAGA
20126406 CAGGGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:20127124 original size:6 final size:6
Alignment explanation
Indices: 20127105--20127189 Score: 52
Period size: 6 Copynumber: 13.8 Consensus size: 6
20127095 AAAAATTAAG
*
20127105 AAAG-A AAA-AA AAAGAA AAAGAA AAAGAAA AAATGTAA AAGGAA AAA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AAA-G-AA AAAGAA AAAGAA
* * *
20127153 AGAGAA AACA-AA AAGGAAA GAAAGAA GAAGAA AAAGA
1 AAAGAA AA-AGAA AAAG-AA -AAAGAA AAAGAA AAAGA
20127190 TGAAAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
5 11 0.18
6 32 0.52
7 11 0.18
8 8 0.13
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:20127187 original size:22 final size:23
Alignment explanation
Indices: 20127140--20127186 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 23
20127130 GAAAAAATGT
20127140 AAAAGGAAAAAAAAGAGAAAACA
1 AAAAGGAAAAAAAAGAGAAAACA
20127163 AAAAGGAAAGAAAGAAGAAGAAAA
1 AAAAGGAAA-AAA-AAG-AGAAAA
20127187 AGATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 3 0.14
25 3 0.14
26 6 0.29
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAGGAAAAAAAAGAGAAAACA
Found at i:20134346 original size:24 final size:24
Alignment explanation
Indices: 20134319--20134367 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20134309 ACAAGGAAAA
20134319 GAAACCGCGTGGAAAATATTGCAT
1 GAAACCGCGTGGAAAATATTGCAT
20134343 GAAACCGCGTGGAAAATATTGCAT
1 GAAACCGCGTGGAAAATATTGCAT
20134367 G
1 G
20134368 CATCCTGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.27, T:0.20
Consensus pattern (24 bp):
GAAACCGCGTGGAAAATATTGCAT
Found at i:20134424 original size:14 final size:14
Alignment explanation
Indices: 20134405--20134441 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
20134395 CCTTTGTCAC
20134405 ACGTCAGTGCATCT
1 ACGTCAGTGCATCT
20134419 ACGTCAGTGCATCT
1 ACGTCAGTGCATCT
20134433 ACGTCAGTG
1 ACGTCAGTG
20134442 ACTTGGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (14 bp):
ACGTCAGTGCATCT
Found at i:20134515 original size:14 final size:14
Alignment explanation
Indices: 20134496--20134537 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
20134486 GTAATTTTAA
*
20134496 TATTTAATATTTTT
1 TATTTAGTATTTTT
*
20134510 TATTTAGT-TTTTAG
1 TATTTAGTATTTT-T
20134524 TATTTAGTATTTTT
1 TATTTAGTATTTTT
20134538 AGGATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 15 0.65
15 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
TATTTAGTATTTTT
Found at i:20137957 original size:17 final size:19
Alignment explanation
Indices: 20137930--20137964 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20137920 GTTCTCATTT
20137930 TTTTATTCCTCT-TTTTTG
1 TTTTATTCCTCTATTTTTG
20137948 TTTT-TTCCTCTATTTTT
1 TTTTATTCCTCTATTTTT
20137965 ACTTCTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTATTCCTCTATTTTTG
Found at i:20151558 original size:59 final size:58
Alignment explanation
Indices: 20151444--20151562 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 58
20151434 ATCATTTAAT
* ** * *
20151444 AATTATCATGAAAGTGTGAAGCTCAAATTCCGTTGTTAGCACCATAACTTGACCAACC
1 AATTATCAAGAAAGTGTGAAGCTCAAATTCCACTGTTAGCACCACAACATGACCAACC
* * *
20151502 AATTGTCAAGAAAGTGTGGAGTTTCAAATTCCACTGTTAGCACCACAA-ATGCACCAACC
1 AATTATCAAGAAAGTGTGAAG-CTCAAATTCCACTGTTAGCACCACAACATG-ACCAACC
20151561 AA
1 AA
20151563 AATGCTAGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 20 0.39
59 31 0.61
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (58 bp):
AATTATCAAGAAAGTGTGAAGCTCAAATTCCACTGTTAGCACCACAACATGACCAACC
Found at i:20155202 original size:2 final size:2
Alignment explanation
Indices: 20155195--20155261 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
20155185 ATCTTACTTT
* * *
20155195 TA TA TA TA T- TA TA GA TA TT TA TA TA -A TA TA TA CA 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
20155235 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 T
20155262 GTTATTGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20172208 original size:48 final size:48
Alignment explanation
Indices: 20172137--20172281 Score: 290
Period size: 48 Copynumber: 3.0 Consensus size: 48
20172127 ACGGGACCAG
20172137 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
1 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
20172185 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
1 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
20172233 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
1 TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
20172281 T
1 T
20172282 CCCTATTAAT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (48 bp):
TAGTTGGACTTAGATCGTTACAGTGATATAAACAACAAATCAACCGTA
Found at i:20173764 original size:22 final size:22
Alignment explanation
Indices: 20173732--20173774 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20173722 AGCTAAAAGA
*
20173732 AATTTACTTCAACCAAAAGAAG
1 AATTTAATTCAACCAAAAGAAG
**
20173754 AATTTAATTCAATTAAAAGAA
1 AATTTAATTCAACCAAAAGAA
20173775 ATTTACCTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (22 bp):
AATTTAATTCAACCAAAAGAAG
Found at i:20175315 original size:18 final size:17
Alignment explanation
Indices: 20175292--20175331 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
20175282 GAAGACAATA
20175292 AGAAGAGAATTAGAGAG
1 AGAAGAGAATTAGAGAG
*
20175309 TAGAAGATAATTAGAGAG
1 -AGAAGAGAATTAGAGAG
20175327 AGAAG
1 AGAAG
20175332 CTCTCAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.15
Consensus pattern (17 bp):
AGAAGAGAATTAGAGAG
Found at i:20175876 original size:35 final size:35
Alignment explanation
Indices: 20175837--20175957 Score: 134
Period size: 35 Copynumber: 3.5 Consensus size: 35
20175827 GTAATGCTTT
* * *
20175837 ACTTATTCTAATTGTTTTGCTTTAAGTAGTACTTC
1 ACTTATTCTAATTGTTTTGCGTGAAGTAGCACTTC
* *
20175872 ACTTATTCTAGTTGTTTTGCGTGAAGTAGCGCTTC
1 ACTTATTCTAATTGTTTTGCGTGAAGTAGCACTTC
* * * * *
20175907 ACTTATTTTAGTTATTCTGCGTGAAGTAACACTTC
1 ACTTATTCTAATTGTTTTGCGTGAAGTAGCACTTC
* *
20175942 ACTTGTTCTAGTTGTT
1 ACTTATTCTAATTGTT
20175958 CTCTGTACAA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 73 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.47
Consensus pattern (35 bp):
ACTTATTCTAATTGTTTTGCGTGAAGTAGCACTTC
Found at i:20178337 original size:34 final size:34
Alignment explanation
Indices: 20178298--20178365 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
20178288 ATCATAACAG
*
20178298 AAACCACAATTAACCCCAGTGGCATGGGTCATAA
1 AAACCACAATTAACCCCAATGGCATGGGTCATAA
20178332 AAACCACAATTAACCCCAATGGCATGGGTCATAA
1 AAACCACAATTAACCCCAATGGCATGGGTCATAA
20178366 GTATATCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (34 bp):
AAACCACAATTAACCCCAATGGCATGGGTCATAA
Found at i:20179113 original size:3 final size:3
Alignment explanation
Indices: 20179105--20179164 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
20179095 ATAGGTAATA
20179105 TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
20179150 TAT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
20179165 TGAGTTAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:20186963 original size:27 final size:27
Alignment explanation
Indices: 20186919--20186970 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
20186909 TGTCCTGGTC
* *
20186919 GTGGAAAAATTATAATTTTTCCCCTGG
1 GTGGAAAAATTACAATTTTACCCCTGG
*
20186946 GTGGAAAAATTACCATTTTACCCCT
1 GTGGAAAAATTACAATTTTACCCCT
20186971 ATGCTCCGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (27 bp):
GTGGAAAAATTACAATTTTACCCCTGG
Found at i:20193133 original size:18 final size:16
Alignment explanation
Indices: 20193094--20193135 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
20193084 TACTTACAAA
20193094 GTTATTTAACTTTTTG
1 GTTATTTAACTTTTTG
*
20193110 GTTATTTCAACTTTCTTT
1 GTTATTT-AACTTT-TTG
20193128 GTTATTTA
1 GTTATTTA
20193136 GTTTTTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.62
Consensus pattern (16 bp):
GTTATTTAACTTTTTG
Found at i:20205116 original size:15 final size:15
Alignment explanation
Indices: 20205082--20205133 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20205072 TTTCTGTATG
*
20205082 AAAATAATAATATTATA
1 AAAATAA-AA-ATAATA
20205099 AAAATAAAAATAATA
1 AAAATAAAAATAATA
** *
20205114 AAAATCTAGATAATA
1 AAAATAAAAATAATA
20205129 AAAAT
1 AAAAT
20205134 TTGAATAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 22 0.71
16 2 0.06
17 7 0.23
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAATAAAAATAATA
Found at i:20215071 original size:13 final size:14
Alignment explanation
Indices: 20215043--20215083 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
20215033 ACCATAATAA
*
20215043 ATAATGATATGA-T
1 ATAATAATATGATT
*
20215056 ATATTAATAT-ATT
1 ATAATAATATGATT
20215069 ATAATAATATGATT
1 ATAATAATATGATT
20215083 A
1 A
20215084 CGAAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
12 1 0.04
13 18 0.78
14 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
ATAATAATATGATT
Found at i:20216194 original size:2 final size:2
Alignment explanation
Indices: 20216187--20216211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20216177 CTCTAAAATG
20216187 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 T
20216212 TATGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20216936 original size:14 final size:14
Alignment explanation
Indices: 20216914--20216969 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
20216904 GATCTCATTC
*
20216914 TTTTATTATTTTAT
1 TTTTATTATTTAAT
*
20216928 TTTTTTTATTTAAT
1 TTTTATTATTTAAT
20216942 TTTGT-TGTATTTAAT
1 TTT-TAT-TATTTAAT
20216957 TATTTATT-TTTAA
1 T-TTTATTATTTAA
20216970 GTGCAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 21 0.58
15 12 0.33
16 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (14 bp):
TTTTATTATTTAAT
Found at i:20242220 original size:21 final size:21
Alignment explanation
Indices: 20242169--20242220 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
20242159 CAAACGAATA
* *
20242169 TGTTTTGATATGCACGATATG
1 TGTTTTGATGTGCACAATATG
20242190 TGTTTTGATGTGCACAATATG
1 TGTTTTGATGTGCACAATATG
20242211 TGTTTTGATG
1 TGTTTTGATG
20242221 AAAATGGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (21 bp):
TGTTTTGATGTGCACAATATG
Found at i:20242482 original size:38 final size:38
Alignment explanation
Indices: 20242439--20242564 Score: 144
Period size: 38 Copynumber: 3.2 Consensus size: 38
20242429 TCTGATAAAC
* **
20242439 TTATGACCCATGTCATTGATGTTAATTGTAGTTTATGA
1 TTATGACCCATGCCATTGGGGTTAATTGTAGTTTATGA
* *
20242477 TTATGACCCACGCCACTGGGGTTAATTGTGGTTTAGTTTATGA
1 TTATGACCCATGCCATTGGGGTTAA-T-T-G--TAGTTTATGA
* *
20242520 TAATGACCCATGCCATTGGGGTTAATTGTGGTTTATGA
1 TTATGACCCATGCCATTGGGGTTAATTGTAGTTTATGA
20242558 TTATGAC
1 TTATGAC
20242565 TTATGCTACA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
38 35 0.48
39 1 0.01
40 2 0.03
41 2 0.03
42 1 0.01
43 32 0.44
ACGTcount: A:0.24, C:0.13, G:0.23, T:0.40
Consensus pattern (38 bp):
TTATGACCCATGCCATTGGGGTTAATTGTAGTTTATGA
Found at i:20242528 original size:43 final size:43
Alignment explanation
Indices: 20242467--20242563 Score: 149
Period size: 43 Copynumber: 2.2 Consensus size: 43
20242457 ATGTTAATTG
*
20242467 TAGTTTATGATTATGACCCACGCCACTGGGGTTAATTGTGGTT
1 TAGTTTATGATAATGACCCACGCCACTGGGGTTAATTGTGGTT
* *
20242510 TAGTTTATGATAATGACCCATGCCATTGGGGTTAATTGTGGTT
1 TAGTTTATGATAATGACCCACGCCACTGGGGTTAATTGTGGTT
*
20242553 TATGATTATGA
1 TA-GTTTATGA
20242564 CTTATGCTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 42 0.86
44 7 0.14
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (43 bp):
TAGTTTATGATAATGACCCACGCCACTGGGGTTAATTGTGGTT
Found at i:20242581 original size:81 final size:81
Alignment explanation
Indices: 20242441--20242589 Score: 190
Period size: 81 Copynumber: 1.8 Consensus size: 81
20242431 TGATAAACTT
* * *** *
20242441 ATGACCCATGTCATTGATGTTAATTGTAGTTTATGATTATGACCCACGCCACTGGGGTTAATTGT
1 ATGACCCATGCCATTGAGGTTAATTGTAGTTTATGATTATGACCCACGCCACAAAGGTTAAGTGT
20242506 GGTTTAGTTTATGATA
66 GGTTTAGTTTATGATA
* * ** * *
20242522 ATGACCCATGCCATTGGGGTTAATTGTGGTTTATGATTATGACTTATGCTACAAAGGTTAAGTGT
1 ATGACCCATGCCATTGAGGTTAATTGTAGTTTATGATTATGACCCACGCCACAAAGGTTAAGTGT
20242587 GGT
66 GGT
20242590 CATAATAAGT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (81 bp):
ATGACCCATGCCATTGAGGTTAATTGTAGTTTATGATTATGACCCACGCCACAAAGGTTAAGTGT
GGTTTAGTTTATGATA
Found at i:20251141 original size:23 final size:23
Alignment explanation
Indices: 20251090--20251133 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
20251080 CTTATGTGTC
*
20251090 ATTTGAAATTAATATAATTCAAA
1 ATTTGAAAATAATATAATTCAAA
*
20251113 ACTTGAAAAT-AT-TAATTCAAA
1 ATTTGAAAATAATATAATTCAAA
20251134 TAATTTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 2 0.11
23 8 0.42
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (23 bp):
ATTTGAAAATAATATAATTCAAA
Found at i:20267015 original size:4 final size:4
Alignment explanation
Indices: 20267003--20267049 Score: 58
Period size: 4 Copynumber: 10.8 Consensus size: 4
20266993 CGATTTTTTT
20267003 TTTA TTTTA TTTA TTTTA TTTA TTTAA TTTA TTTAA TTTA TTTA TTT
1 TTTA -TTTA TTTA -TTTA TTTA TTT-A TTTA TTT-A TTTA TTTA TTT
20267050 TTTTTTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
4 23 0.59
5 16 0.41
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:20267015 original size:9 final size:9
Alignment explanation
Indices: 20266995--20267053 Score: 72
Period size: 9 Copynumber: 7.0 Consensus size: 9
20266985 AGCCATCCCG
20266995 ATTT-TTTT
1 ATTTATTTT
20267003 -TTTATTTT
1 ATTTATTTT
20267011 ATTTATTTT
1 ATTTATTTT
*
20267020 ATTTATTTA
1 ATTTATTTT
*
20267029 ATTTATTTA
1 ATTTATTTT
20267038 ATTTA-TTT
1 ATTTATTTT
20267046 ATTT-TTTT
1 ATTTATTTT
20267054 TTAAATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
7 3 0.07
8 13 0.28
9 30 0.65
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTATTTT
Found at i:20274444 original size:22 final size:22
Alignment explanation
Indices: 20274391--20274445 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20274381 TGGTCCAACA
* *
20274391 TCACGCTATACATAACAATAAG
1 TCACGCAATACATAACAACAAG
* * *
20274413 TCATGAAATACATAACAACCAG
1 TCACGCAATACATAACAACAAG
20274435 TCACGCAATAC
1 TCACGCAATAC
20274446 CTAAAAAAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.20
Consensus pattern (22 bp):
TCACGCAATACATAACAACAAG
Found at i:20274579 original size:212 final size:208
Alignment explanation
Indices: 20274146--20274661 Score: 549
Period size: 212 Copynumber: 2.5 Consensus size: 208
20274136 AGTTATTCAT
* * * * * *
20274146 GTTATACCAAAATAACTAGTCACGTATTAGCCTAACGTCACGTAATACATAATAATAAGTCACGG
1 GTTATGCCAAAATAACCAGTCACGTATTGGCCTAACATCACGTAATACATAACAATAAGTCACGA
* * * * * *
20274211 AATATATACCAACCAGTCACGTAATGACTAAAAAACAGTAAGAGATGTCTCAAAATAAGATGTGT
66 AATACATAACAACCAGTCACGCAATGACTAAAAAACAGTAAGAAATGTCTCAAAACAAGATATGT
* ** * * *
20274276 TGCACAATTCACACAACGTATATAAGTCAGTCTCGCAATACCTAATAATAAGTCACTCAATGCCT
131 TGCAAAATTCACACAACACATATAAGTCAGTCTCACAATACCTAATAATAAGTCACGCAACGCCT
20274341 AATATCCACTCAC
196 AATATCCACTCAC
* *
20274354 GTTATGGCAAAATAACCAGTCACGTATTGGTCC-AACATCACGCT-ATACATAACAATAAGTCAT
1 GTTATGCCAAAATAACCAGTCACGTATTGG-CCTAACATCACG-TAATACATAACAATAAGTCAC
* * *
20274417 GAAATACATAACAACCAGTCACGCAAT-ACCTAAAAAAAGAGTAAAGAAATGTCTTAAAACAATA
64 GAAATACATAACAACCAGTCACGCAATGA-CT-AAAAAACAGT-AAGAAATGTCTCAAAACAAGA
** * *
20274481 TATGCATTGCAAAATTCATGCAGCACCTATAAG-CTAGTCTCACAATACCTAATAATAAGTCACG
126 TATG--TTGCAAAATTCACACAACACATATAAGTC-AGTCTCACAATACCTAATAATAAGTCACG
20274545 CAACGCCTAATATCCACTCAC
188 CAACGCCTAATATCCACTCAC
* * * ** * *
20274566 GTTATGCCAAAAT-ACACAGTCACGCATTGGCCTTATATCACACAATACATAAAAACCAA-TCAC
1 GTTATGCCAAAATAAC-CAGTCACGTATTGGCCTAACATCACGTAATACATAACAA-TAAGTCAC
* * * * *
20274629 GGAATACATAACAACTAGACATGCAATGCCTAA
64 GAAATACATAACAACCAGTCACGCAATGACTAA
20274662 TATCCATTCA
Statistics
Matches: 254, Mismatches: 41, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
207 1 0.00
208 76 0.30
209 12 0.05
210 20 0.08
211 7 0.03
212 136 0.54
213 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (208 bp):
GTTATGCCAAAATAACCAGTCACGTATTGGCCTAACATCACGTAATACATAACAATAAGTCACGA
AATACATAACAACCAGTCACGCAATGACTAAAAAACAGTAAGAAATGTCTCAAAACAAGATATGT
TGCAAAATTCACACAACACATATAAGTCAGTCTCACAATACCTAATAATAAGTCACGCAACGCCT
AATATCCACTCAC
Found at i:20274701 original size:27 final size:22
Alignment explanation
Indices: 20274648--20274693 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
20274638 AACAACTAGA
*
20274648 CATGCAATGCCTAATATCCATT
1 CATGCAATGCATAATATCCATT
20274670 CATGCAATGCATAATATCCATT
1 CATGCAATGCATAATATCCATT
20274692 CA
1 CA
20274694 CTTAATGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (22 bp):
CATGCAATGCATAATATCCATT
Found at i:20277056 original size:16 final size:17
Alignment explanation
Indices: 20277024--20277057 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20277014 CGTTTTTTCC
20277024 TTTCTCTTCTACTTTTTT
1 TTTCTCTTC-ACTTTTTT
20277042 TTTCTCTTC-CTTTTTT
1 TTTCTCTTCACTTTTTT
20277058 CTCCCTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTCTTCACTTTTTT
Found at i:20278424 original size:22 final size:21
Alignment explanation
Indices: 20278398--20278461 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
20278388 GCAATAACTA
*
20278398 AAAACCAGTCACGCAATGCTT
1 AAAACCAGTCAAGCAATGCTT
* *
20278419 ACAAACTAGTCAAGCAAATTCTT
1 A-AAACCAGTCAAGC-AATGCTT
* *
20278442 AAAACCTCGTCATGCAATGC
1 AAAACC-AGTCAAGCAATGC
20278462 ACAACTCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.03
22 19 0.58
23 13 0.39
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAACCAGTCAAGCAATGCTT
Found at i:20290465 original size:32 final size:32
Alignment explanation
Indices: 20290424--20290486 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
20290414 CGTGAACAAA
*
20290424 CCCATCCCAAATGTAGCAGGCACTATTAAGTC
1 CCCATCCCAAATGTAGCAGGCACCATTAAGTC
20290456 CCCATCCCAAATGTAGCAGGCACCATTAAGT
1 CCCATCCCAAATGTAGCAGGCACCATTAAGT
20290487 ACTAAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (32 bp):
CCCATCCCAAATGTAGCAGGCACCATTAAGTC
Found at i:20293745 original size:17 final size:17
Alignment explanation
Indices: 20293723--20293758 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20293713 TCTGCTTTGA
20293723 TTGCATTTCAATTTCAT
1 TTGCATTTCAATTTCAT
*
20293740 TTGCATTTCAGTTTCAT
1 TTGCATTTCAATTTCAT
20293757 TT
1 TT
20293759 TGACGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.56
Consensus pattern (17 bp):
TTGCATTTCAATTTCAT
Found at i:20298939 original size:15 final size:15
Alignment explanation
Indices: 20298906--20298938 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
20298896 TTGATCTCGG
*
20298906 TTTTGTAGTTTTTGT
1 TTTTGGAGTTTTTGT
20298921 TTTTGGAGTTTTT-T
1 TTTTGGAGTTTTTGT
20298935 TTTT
1 TTTT
20298939 TTTTGCTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (15 bp):
TTTTGGAGTTTTTGT
Found at i:20301488 original size:11 final size:11
Alignment explanation
Indices: 20301473--20301509 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20301463 TAAAACATGT
20301473 TAAAAATGTG-
1 TAAAAATGTGC
20301483 TGAAAAATGTGC
1 T-AAAAATGTGC
20301495 TAAAAATGTGC
1 TAAAAATGTGC
20301506 -AAAA
1 TAAAA
20301510 GATGGCGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 19 0.76
12 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (11 bp):
TAAAAATGTGC
Found at i:20302348 original size:127 final size:128
Alignment explanation
Indices: 20302117--20302370 Score: 372
Period size: 127 Copynumber: 2.0 Consensus size: 128
20302107 CAATTGCCTA
*
20302117 CACAAAAGAGTTATTGTGTGAAGCAACTTAGAGTGGGACATGAAGTATCATAATTGAGGATATAC
1 CACAAAAGAGTTATTGTGTGAAGCAACTTAGAGTGGGACATGAAATATCATAATTGAGGATATAC
* * * * *
20302182 CGGTCTAGAGGTTTATTTGCCCAAAAGGGATAGATTTTTT-GAAAAGTAGCTAGGATGTTCTG
66 CGGTCTAAAGGTCTATATGCCCAAAAGGGATAGATTTTTTCGAAAAATAGCTAGGATATTCTG
* *
20302244 CACAAAGGAGTTATTGTGTGGAGCAACTTAGAGT-GGAGCATGAAATATCATAATTGAGGGA-AT
1 CACAAAAGAGTTATTGTGTGAAGCAACTTAGAGTGGGA-CATGAAATATCATAATTGA-GGATAT
*
20302307 ACCGGTCTAAAAGGTCTATATGCCCAAAGGGGATAGA-TTTTTCGAAAAATAGCTAGGATATTCT
64 ACCGGTCT-AAAGGTCTATATGCCCAAAAGGGATAGATTTTTTCGAAAAATAGCTAGGATATTCT
20302371 CATATTAGTT
Statistics
Matches: 114, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
126 3 0.03
127 65 0.57
128 46 0.40
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (128 bp):
CACAAAAGAGTTATTGTGTGAAGCAACTTAGAGTGGGACATGAAATATCATAATTGAGGATATAC
CGGTCTAAAGGTCTATATGCCCAAAAGGGATAGATTTTTTCGAAAAATAGCTAGGATATTCTG
Found at i:20306858 original size:29 final size:28
Alignment explanation
Indices: 20306788--20306850 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
20306778 GATAAGACAG
* *
20306788 AATATGTTGCAGACTTAAATAGTATGGA
1 AATATGTTGCAGACTTAAACAATATGGA
*
20306816 AACATGGTTGCAGACTTAAACAATATGGA
1 AATAT-GTTGCAGACTTAAACAATATGGA
*
20306845 GATATG
1 AATATG
20306851 ATTTCAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.29
Consensus pattern (28 bp):
AATATGTTGCAGACTTAAACAATATGGA
Found at i:20322076 original size:15 final size:15
Alignment explanation
Indices: 20322058--20322087 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20322048 GCATTTCTGA
20322058 CTTTAATATTAGTAG
1 CTTTAATATTAGTAG
*
20322073 CTTTAATATTGGTAG
1 CTTTAATATTAGTAG
20322088 ATTTTTGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (15 bp):
CTTTAATATTAGTAG
Found at i:20324941 original size:23 final size:23
Alignment explanation
Indices: 20324905--20324969 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
20324895 AAAATTATTT
*
20324905 TTTTAGTTTAATTTAGTCTCTAAG
1 TTTTA-TTCAATTTAGTCTCTAAG
*
20324929 TTTTATTCAATTTACTCTCTAAG
1 TTTTATTCAATTTAGTCTCTAAG
20324952 TTTTATTCAATTTAGTCT
1 TTTTATTCAATTTAGTCT
20324970 TCGTACTCTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (23 bp):
TTTTATTCAATTTAGTCTCTAAG
Found at i:20330342 original size:16 final size:16
Alignment explanation
Indices: 20330321--20330351 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20330311 ATTACAGGAG
20330321 ATTACAAAAATAAATC
1 ATTACAAAAATAAATC
20330337 ATTACAAAAATAAAT
1 ATTACAAAAATAAAT
20330352 TTTATTACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTACAAAAATAAATC
Found at i:20331625 original size:31 final size:30
Alignment explanation
Indices: 20331553--20331636 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
20331543 GTCACGTCAT
*
20331553 AAGGATTAAATTGAACAAAAATATATAGTA
1 AAGGATTAAATTGAACAAAAATAGATAGTA
*
20331583 AATGGATTAAATTGAACAAAATTAAGAT-GTTA
1 AA-GGATTAAATTGAACAAAAAT-AGATAG-TA
* *
20331615 AAGGACTAAATTGAAAAAAAAT
1 AAGGATTAAATTGAACAAAAAT
20331637 TTGAAAAATG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.04
31 37 0.80
32 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.26
Consensus pattern (30 bp):
AAGGATTAAATTGAACAAAAATAGATAGTA
Found at i:20332315 original size:18 final size:19
Alignment explanation
Indices: 20332292--20332337 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
20332282 ATATAACCTG
*
20332292 AAATATTAAACA-AAATAA
1 AAATATTAAAAATAAATAA
*
20332310 AAATATAAAAAATAAATAA
1 AAATATTAAAAATAAATAA
20332329 AAA-ATTAAA
1 AAATATTAAA
20332338 GGGGTGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATATTAAAAATAAATAA
Found at i:20332899 original size:31 final size:31
Alignment explanation
Indices: 20332856--20332934 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
20332846 TATTTTTTAA
*
20332856 ATATCTTT-TTCAATTTAATCCCTCAATATCT-T
1 ATATTTTTGTTCAATTTAATCCC-C-ATA-CTAT
20332888 A-A-TTTTGTTCAATTTAATCCCCATACTAT
1 ATATTTTTGTTCAATTTAATCCCCATACTAT
20332917 ATATTTTTGTTCAATTTA
1 ATATTTTTGTTCAATTTA
20332935 GTCTCTATGA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
30 5 0.12
31 29 0.69
32 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.03, T:0.51
Consensus pattern (31 bp):
ATATTTTTGTTCAATTTAATCCCCATACTAT
Found at i:20334905 original size:26 final size:26
Alignment explanation
Indices: 20334849--20334898 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
20334839 AACAATATTT
*
20334849 TTTTTTTCAACATGGTGTGTAATAAC
1 TTTTTTTCAACATGGTGTGTAACAAC
20334875 TTTTTTT-AATCATGGTGTGTAACA
1 TTTTTTTCAA-CATGGTGTGTAACA
20334899 TGTTTTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (26 bp):
TTTTTTTCAACATGGTGTGTAACAAC
Found at i:20334996 original size:76 final size:78
Alignment explanation
Indices: 20334833--20335076 Score: 246
Period size: 76 Copynumber: 3.1 Consensus size: 78
20334823 CAACATAACG
* * * *
20334833 TGTAACAACAATATTTTTTTTTTCAACATGGTGTGTAATAACTTTTTTTAATCATGGTGTGTAAC
1 TGTAACAACAATA-TTTTTTTTTCAACATGATGTGTAACAAC----TCTAACCATGGTGTGTAAC
* *
20334898 ATGTTTTTGTATATGACG
61 ATATTTTTGTATATGACA
*
20334916 TGTAACAACAATA-TTTTTTTTCAACATGATGTGTAACAAC-CTAACCATGGTGTGTAACGTATT
1 TGTAACAACAATATTTTTTTTTCAACATGATGTGTAACAACTCTAACCATGGTGTGTAACATATT
*
20334979 TTTGTACT-TGGCA
66 TTTGTA-TATGACA
* * * ** * *
20334992 TGTAACAACAATATTTTTTTTTC-ACATAATGTGTAACAA-TATAATCATGGCATGTTACATGTT
1 TGTAACAACAATATTTTTTTTTCAACATGATGTGTAACAACTCTAACCATGGTGTGTAACATATT
* *
20335055 TTTATACATGACA
66 TTTGTATATGACA
20335068 TGTAACAAC
1 TGTAACAAC
20335077 CTAACTATGA
Statistics
Matches: 138, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
76 90 0.65
77 10 0.07
81 25 0.18
83 13 0.09
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (78 bp):
TGTAACAACAATATTTTTTTTTCAACATGATGTGTAACAACTCTAACCATGGTGTGTAACATATT
TTTGTATATGACA
Found at i:20335072 original size:45 final size:45
Alignment explanation
Indices: 20335023--20335122 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
20335013 TCACATAATG
* * * *
20335023 TGTAACAATATAA-TCATGGCATGTTACATGTTTTTATACATGACA
1 TGTAACAACATAACT-ATGACATGTAACATGTCTTTATACATGACA
* * * *
20335068 TGTAACAACCTAACTATGACGTGTAACATGTCTTTGTATATGACA
1 TGTAACAACATAACTATGACATGTAACATGTCTTTATACATGACA
20335113 TGTAACAACA
1 TGTAACAACA
20335123 GTATTTATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (45 bp):
TGTAACAACATAACTATGACATGTAACATGTCTTTATACATGACA
Found at i:20335072 original size:121 final size:121
Alignment explanation
Indices: 20334947--20335238 Score: 329
Period size: 121 Copynumber: 2.4 Consensus size: 121
20334937 CAACATGATG
* * * * *
20334947 TGTAACAACCTAACCATGGTGTGTAACGTATTTTTGTACT-TGGCATGTAACAACAATATTTTTT
1 TGTAACAACCTAACCATGATGTGTAACATGTTTTTGTA-TATGACATGTAACAACAATATTTATT
* * **
20335011 TTTCACATAATGTGTAACAA-TATAATCATGGCATGTTACATGTTTTTATACAT-GACA
65 TTTAACATAACGTGTAACAACT-TAATCATGGCATGACACATGTTTTTATACATAG-CA
* * * *
20335068 TGTAACAACCTAACTATGACGTGTAACATGTCTTTGTATATGACATGTAACAACAGTATTTATTT
1 TGTAACAACCTAACCATGATGTGTAACATGTTTTTGTATATGACATGTAACAACAATATTTATTT
* * * * * *
20335133 TTAATATGACGTGTATCAACTTAATCATGGCTTGACACATGTTTTTGTACATAGCG
66 TTAACATAACGTGTAACAACTTAATCATGGCATGACACATGTTTTTATACATAGCA
* * * *
20335189 TGTAACAATCTAATCATGATGTGTCACATGTTTTTGTATATGACGTGTAA
1 TGTAACAACCTAACCATGATGTGTAACATGTTTTTGTATATGACATGTAA
20335239 TATTATAACG
Statistics
Matches: 142, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
120 1 0.01
121 139 0.98
122 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (121 bp):
TGTAACAACCTAACCATGATGTGTAACATGTTTTTGTATATGACATGTAACAACAATATTTATTT
TTAACATAACGTGTAACAACTTAATCATGGCATGACACATGTTTTTATACATAGCA
Found at i:20335236 original size:45 final size:45
Alignment explanation
Indices: 20335136--20335238 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
20335126 TTTATTTTTA
* *
20335136 ATATGACGTGTATCAACTTAATCATGGCTTGACACATGTTTTTGT
1 ATATGACGTGTAACAACTTAATCATGGATTGACACATGTTTTTGT
* *
20335181 ACAT-AGCGTGTAACAA-TCTAATCAT-GATGTGTCACATGTTTTTGT
1 ATATGA-CGTGTAACAACT-TAATCATGGAT-TGACACATGTTTTTGT
20335226 ATATGACGTGTAA
1 ATATGACGTGTAA
20335239 TATTATAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
44 4 0.08
45 44 0.90
46 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (45 bp):
ATATGACGTGTAACAACTTAATCATGGATTGACACATGTTTTTGT
Found at i:20337754 original size:3 final size:3
Alignment explanation
Indices: 20337739--20337776 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
20337729 GCACTACCAA
*
20337739 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20337777 AAGGTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:20340659 original size:201 final size:201
Alignment explanation
Indices: 20340273--20340664 Score: 558
Period size: 201 Copynumber: 2.0 Consensus size: 201
20340263 GACCTAATGG
* * * * * *
20340273 GTTTAATATGAAAGCCAAAGAGAATATCCATATGCCTATACGACAAACTGGGTTTGGTCCATGTA
1 GTTTAATATGAAAGCCAAAGAAAATATCCATATACCTATACAACAAACTGGGATCGGTCCATGGA
* * *
20340338 TTGGCTTGCTTTGTTTGCAAAATGGTTATAGGATTACCGTTTGGAATCCTTCCACAGAGAAGTTA
66 ATGGCTTGCTTTGTTTACAAAATGGTTATAGGATTACCCTTTGGAATCCTTCCACAGAGAAGTTA
* * ** *
20340403 AGCTTCTTCCTGAATCCACCATCTTTCATCCTCCTTTCGCATTTCACACTTTTTTTTATGCGTTG
131 AACTTCTTCCTGAAGCCACCATCTCACATCCTCCTTTCGCATCTCACACTTTTTTTTATGCGTTG
20340468 GGACAT
196 GGACAT
*
20340474 GTTTAATATGAAAGTCAAAGAAAATATCCATATACCTATACAACAAA-TGGGGATCGGTCCATGG
1 GTTTAATATGAAAGCCAAAGAAAATATCCATATACCTATACAACAAACT-GGGATCGGTCCATGG
**
20340538 AATGGCTTG-TTCTGTTTACATGATGGTTATAGGATTACCCTTTGGAATCCTTCCACGAGAGAAG
65 AATGGCTTGCTT-TGTTTACAAAATGGTTATAGGATTACCCTTTGGAATCCTTCCAC-AGAGAAG
*
20340602 TTAAACTTCTTCCTGAAGCCACCATCTCACGTCCT-CTTTCTGCATCTCACA-TTTTTTTTATGC
128 TTAAACTTCTTCCTGAAGCCACCATCTCACATCCTCCTTTC-GCATCTCACACTTTTTTTTATGC
20340665 ATCGGGTTCG
Statistics
Matches: 169, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
200 3 0.02
201 120 0.71
202 46 0.27
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (201 bp):
GTTTAATATGAAAGCCAAAGAAAATATCCATATACCTATACAACAAACTGGGATCGGTCCATGGA
ATGGCTTGCTTTGTTTACAAAATGGTTATAGGATTACCCTTTGGAATCCTTCCACAGAGAAGTTA
AACTTCTTCCTGAAGCCACCATCTCACATCCTCCTTTCGCATCTCACACTTTTTTTTATGCGTTG
GGACAT
Found at i:20341346 original size:16 final size:16
Alignment explanation
Indices: 20341318--20341360 Score: 70
Period size: 15 Copynumber: 2.7 Consensus size: 16
20341308 AATTAATTAT
20341318 ATTAAAAATATATAAAA
1 ATTAAAAA-ATATAAAA
20341335 ATTAAAAAATATAAAA
1 ATTAAAAAATATAAAA
20341351 A-TAAAAAATA
1 ATTAAAAAATA
20341361 ATTAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATTAAAAAATATAAAA
Done.