Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 59 of 187
Found at i:17352408 original size:43 final size:43
Alignment explanation
Indices: 17352361--17352444 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
17352351 TTGTAGAAAG
*
17352361 GAAAGAAATCAATTGAAACAAAATCT-CAATCGAGAAACCTAAA
1 GAAAGAAATCAAGTGAAACAAAAT-TACAATCGAGAAACCTAAA
* * *
17352404 GAAAGAAATCTAGTGAAATAAAATTACAATTGAGAAACCTA
1 GAAAGAAATCAAGTGAAACAAAATTACAATCGAGAAACCTA
17352445 TTAGAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (43 bp):
GAAAGAAATCAAGTGAAACAAAATTACAATCGAGAAACCTAAA
Found at i:17369094 original size:6 final size:6
Alignment explanation
Indices: 17369083--17369123 Score: 55
Period size: 6 Copynumber: 6.3 Consensus size: 6
17369073 ATCTACATTT
17369083 AAAATA AAAATA CGTAAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA ---AAAATA AAAATA AAAATA AAAATA AA
17369124 TAAAATCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 26 0.81
9 6 0.19
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:17369128 original size:15 final size:14
Alignment explanation
Indices: 17369082--17369129 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
17369072 TATCTACATT
*
17369082 TAAAATAAAAATACG
1 TAAAATAAAAATA-A
17369097 TAAAATAAAAAT-A
1 TAAAATAAAAATAA
17369110 -AAAATAAAAATAAA
1 TAAAATAAAAAT-AA
17369124 TAAAAT
1 TAAAAT
17369130 CCACAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 11 0.38
14 1 0.03
15 17 0.59
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAAATAAAAATAA
Found at i:17369233 original size:7 final size:7
Alignment explanation
Indices: 17369221--17369260 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
17369211 AAGTTGCGAA
17369221 TGCCTAT
1 TGCCTAT
17369228 TGCCTAT
1 TGCCTAT
17369235 TGCCTAT
1 TGCCTAT
17369242 TGCCTAT
1 TGCCTAT
17369249 TGCCTAT
1 TGCCTAT
17369256 TGCCT
1 TGCCT
17369261 GTGCCGGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.12, C:0.30, G:0.15, T:0.42
Consensus pattern (7 bp):
TGCCTAT
Found at i:17373470 original size:3 final size:3
Alignment explanation
Indices: 17373462--17373509 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
17373452 GAAAAAGTAA
* *
17373462 AAG AAG AAG AAG AAG -AG GAG AAG AAG AAG AAG AAG AAG AAG GAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
17373509 A
1 A
17373510 GGAAAAATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17374116 original size:11 final size:11
Alignment explanation
Indices: 17374100--17374190 Score: 65
Period size: 11 Copynumber: 8.9 Consensus size: 11
17374090 TTAAAAGAAG
17374100 TATTTTAAAAA
1 TATTTTAAAAA
17374111 TATTTT--AAA
1 TATTTTAAAAA
17374120 -A--TTAAAAA
1 TATTTTAAAAA
* **
17374128 AATTAAAAAAA
1 TATTTTAAAAA
17374139 GTATTTT--AAA
1 -TATTTTAAAAA
17374149 -ATTTTAAAAA
1 TATTTTAAAAA
*
17374159 -ATTTAAAAAA
1 TATTTTAAAAA
17374169 GTATTTTAAAAA
1 -TATTTTAAAAA
17374181 TATTTTAAAA
1 TATTTTAAAA
17374191 TTAAAAAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
6 2 0.03
8 9 0.14
9 4 0.06
10 15 0.24
11 21 0.33
12 12 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:17374160 original size:30 final size:30
Alignment explanation
Indices: 17374106--17374199 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
17374096 GAAGTATTTT
*
17374106 AAAAA-TATTTTAAAA-TTAAAAAAATTAA
1 AAAAAGTATTTTAAAATTTTAAAAAATTAA
*
17374134 AAAAAGTATTTTAAAATTTTAAAAAATTTA
1 AAAAAGTATTTTAAAATTTTAAAAAATTAA
*
17374164 AAAAAGTATTTTAAAAATATTT-TAAAATTAA
1 AAAAAGTATTTT-AAAAT-TTTAAAAAATTAA
17374195 AAAAA
1 AAAAA
17374200 TAAATATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
28 5 0.09
29 10 0.17
30 23 0.40
31 17 0.29
32 3 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAAAGTATTTTAAAATTTTAAAAAATTAA
Found at i:17374165 original size:40 final size:40
Alignment explanation
Indices: 17374085--17374200 Score: 123
Period size: 40 Copynumber: 2.9 Consensus size: 40
17374075 AATTTATTTT
* *
17374085 AAAAATTAAAAGAAGTATTTTAAAAATATTT-TAAAA-TTAA
1 AAAAATTAAAAAAAGTATTTT-AAAAT-TTTAAAAAATTTAA
17374125 AAAAATTAAAAAAAGTATTTTAAAATTTTAAAAAATTTAA
1 AAAAATTAAAAAAAGTATTTTAAAATTTTAAAAAATTTAA
** *
17374165 AAAAGTATTTTAAAAA-TATTTTAAAA-TTAAAAAAAT
1 AAAA--ATTAAAAAAAGTATTTTAAAATTTTAAAAAAT
17374201 AAATATATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
38 3 0.04
39 9 0.13
40 37 0.55
41 10 0.15
42 8 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAATTTTAAAAAATTTAA
Found at i:17374441 original size:36 final size:36
Alignment explanation
Indices: 17374394--17374466 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
17374384 AGCACCTCTA
17374394 ATTGTTGCTTATGTTGGTATACATGGCTGCTAGTAT
1 ATTGTTGCTTATGTTGGTATACATGGCTGCTAGTAT
* *
17374430 ATTGTTGCTTATGTTGTTATACATGGCTGCTGGTAT
1 ATTGTTGCTTATGTTGGTATACATGGCTGCTAGTAT
17374466 A
1 A
17374467 AATGGCTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.45
Consensus pattern (36 bp):
ATTGTTGCTTATGTTGGTATACATGGCTGCTAGTAT
Found at i:17388164 original size:36 final size:37
Alignment explanation
Indices: 17388118--17388213 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
17388108 GTCTCCAATT
* *
17388118 TCACATTTCAATTCAATGTCACTTTTTCAATTTCAA-
1 TCACAATTCAATTCAATGTCACTTTTCCAATTTCAAG
* * *
17388154 TCACAATTCAATTCAAAAGTTACTTTTCCATTTTCAAG
1 TCACAATTCAATTC-AATGTCACTTTTCCAATTTCAAG
* *
17388192 TCA-ATATTCATTTCAATTTCAC
1 TCACA-ATTCAATTCAATGTCAC
17388214 ACATATATTC
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
36 13 0.27
37 24 0.50
38 11 0.23
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (37 bp):
TCACAATTCAATTCAATGTCACTTTTCCAATTTCAAG
Found at i:17389034 original size:21 final size:23
Alignment explanation
Indices: 17388987--17389031 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
17388977 ACTTTACTTT
17388987 ATATATAATATAATAATAATAAA
1 ATATATAATATAATAATAATAAA
17389010 ATATATAATA-AA-ACATAATAAA
1 ATATATAATATAATA-ATAATAAA
17389032 TATCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.05
22 10 0.48
23 10 0.48
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
ATATATAATATAATAATAATAAA
Found at i:17389463 original size:25 final size:25
Alignment explanation
Indices: 17389421--17389469 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17389411 TTTGTCACTA
17389421 TTTTAATATAAAACCATAATAATAT
1 TTTTAATATAAAACCATAATAATAT
*
17389446 TTTTATATATAATA-CATAATAATA
1 TTTTA-ATATAAAACCATAATAATA
17389470 AAAAAATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTAATATAAAACCATAATAATAT
Found at i:17391967 original size:18 final size:18
Alignment explanation
Indices: 17391944--17391978 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17391934 TAACCAAACC
* *
17391944 GAAATCCAAATCGAAATT
1 GAAATCAAAATCAAAATT
17391962 GAAATCAAAATCAAAAT
1 GAAATCAAAATCAAAAT
17391979 CAAAATCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (18 bp):
GAAATCAAAATCAAAATT
Found at i:17392027 original size:48 final size:48
Alignment explanation
Indices: 17391963--17392074 Score: 224
Period size: 48 Copynumber: 2.3 Consensus size: 48
17391953 ATCGAAATTG
17391963 AAATCAAAATCAAAATCAAAATCAGTGAGTGTTTCAAAATTGAAATCA
1 AAATCAAAATCAAAATCAAAATCAGTGAGTGTTTCAAAATTGAAATCA
17392011 AAATCAAAATCAAAATCAAAATCAGTGAGTGTTTCAAAATTGAAATCA
1 AAATCAAAATCAAAATCAAAATCAGTGAGTGTTTCAAAATTGAAATCA
17392059 AAATCAAAATCAAAAT
1 AAATCAAAATCAAAAT
17392075 TAGAATCGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.24
Consensus pattern (48 bp):
AAATCAAAATCAAAATCAAAATCAGTGAGTGTTTCAAAATTGAAATCA
Found at i:17392099 original size:6 final size:6
Alignment explanation
Indices: 17392005--17392098 Score: 62
Period size: 6 Copynumber: 14.7 Consensus size: 6
17391995 TTCAAAATTG
** **
17392005 AAATCA AAATCA AAATCA AAATCA AAATCA GTGAGTGTTTCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA ---A---AATCA AAATCA
* * * *
17392053 AAATCA AAATCA AAATCA AAATTA GAATCG AAATCA AAATTA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
17392099 TGAAATAACC
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
6 62 0.93
9 2 0.03
12 3 0.04
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:17392103 original size:18 final size:18
Alignment explanation
Indices: 17392053--17392104 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
17392043 TTCAAAATTG
* *
17392053 AAATCAAAATCAAAATCA
1 AAATTAAAATCGAAATCA
*
17392071 AAATTAGAATCGAAATCA
1 AAATTAAAATCGAAATCA
*
17392089 AAATTAAAATTGAAAT
1 AAATTAAAATCGAAAT
17392105 AACCCTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.62, C:0.10, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATTAAAATCGAAATCA
Found at i:17395088 original size:17 final size:17
Alignment explanation
Indices: 17395066--17395103 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
17395056 AGACAAAAAA
*
17395066 ACAACTTATATTAGTAG
1 ACAACTTATAATAGTAG
17395083 ACAACTTATAATAGTAG
1 ACAACTTATAATAGTAG
17395100 ACAA
1 ACAA
17395104 ACCTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (17 bp):
ACAACTTATAATAGTAG
Found at i:17395112 original size:17 final size:17
Alignment explanation
Indices: 17395066--17395112 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
17395056 AGACAAAAAA
* *
17395066 ACAACTTATATTAGTAG
1 ACAACCTATAATAGTAG
*
17395083 ACAACTTATAATAGTAG
1 ACAACCTATAATAGTAG
17395100 ACAAACCTA-AATA
1 AC-AACCTATAATA
17395113 TGTCCTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 22 0.81
18 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.28
Consensus pattern (17 bp):
ACAACCTATAATAGTAG
Found at i:17396097 original size:12 final size:12
Alignment explanation
Indices: 17396080--17396139 Score: 84
Period size: 12 Copynumber: 4.9 Consensus size: 12
17396070 TGGTTTTCTC
*
17396080 GAAAATGGAAGT
1 GAAAATGGAAAT
17396092 GAAAATGGAAAT
1 GAAAATGGAAAT
*
17396104 GGAAATGGAAAT
1 GAAAATGGAAAT
*
17396116 GAAAATGAAAAT
1 GAAAATGGAAAT
17396128 GAAAATGAGAAA
1 GAAAATG-GAAA
17396140 CAAATTCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
12 39 0.93
13 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (12 bp):
GAAAATGGAAAT
Found at i:17396105 original size:6 final size:6
Alignment explanation
Indices: 17396082--17396139 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
17396072 GTTTTCTCGA
* * * * *
17396082 AAATGG AAGTGA AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
17396130 AAATGAG AAA
1 AAATG-G AAA
17396140 CAAATTCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
6 42 0.93
7 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.16
Consensus pattern (6 bp):
AAATGG
Found at i:17396105 original size:18 final size:18
Alignment explanation
Indices: 17396082--17396139 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
17396072 GTTTTCTCGA
*
17396082 AAATGGAAGTGAAAATGG
1 AAATGGAAATGAAAATGG
* *
17396100 AAATGGAAATGGAAATGA
1 AAATGGAAATGAAAATGG
*
17396118 AAATGAAAATGAAAATGAG
1 AAATGGAAATGAAAATG-G
17396137 AAA
1 AAA
17396140 CAAATTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 30 0.91
19 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.16
Consensus pattern (18 bp):
AAATGGAAATGAAAATGG
Found at i:17408052 original size:13 final size:13
Alignment explanation
Indices: 17408034--17408060 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17408024 AACCTAATCT
17408034 TAAATAAATAAAA
1 TAAATAAATAAAA
17408047 TAAATAAATAAAA
1 TAAATAAATAAAA
17408060 T
1 T
17408061 GTAATATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:17409516 original size:43 final size:43
Alignment explanation
Indices: 17409437--17409537 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
17409427 GCTCCCAGTA
*
17409437 TCGCACACTTAGTG-CCTGTTATTCAACATCTCCATTTTAATT
1 TCGCACACTTAGTGCCCTGTTATTCAACACCTCCATTTTAATT
* * *
17409479 TCGCACACTTAGTGCCCTTTTATTCAACCCCAT-CATTTTAGTT
1 TCGCACACTTAGTGCCCTGTTATTCAACACC-TCCATTTTAATT
*
17409522 CCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
17409538 GTTTACATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 14 0.27
43 37 0.71
44 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.37
Consensus pattern (43 bp):
TCGCACACTTAGTGCCCTGTTATTCAACACCTCCATTTTAATT
Found at i:17420869 original size:15 final size:14
Alignment explanation
Indices: 17420837--17420871 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
17420827 TGGATGTGGG
17420837 TTTTTAAGACGTAA
1 TTTTTAAGACGTAA
17420851 TTTTTAAGAAC-TAA
1 TTTTTAAG-ACGTAA
17420865 TTTTTAA
1 TTTTTAA
17420872 ATATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.90
15 2 0.10
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (14 bp):
TTTTTAAGACGTAA
Found at i:17433572 original size:33 final size:34
Alignment explanation
Indices: 17433504--17433572 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
17433494 TACACATTAC
* * * *
17433504 CATAAACATATGTCAGATCGGAATATCATATTTT
1 CATAAACATATATCAGAACGAAATATCATAATTT
*
17433538 CATAATCATATATCAGAACGAAAT-TCATAATTT
1 CATAAACATATATCAGAACGAAATATCATAATTT
17433571 CA
1 CA
17433573 AAATAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (34 bp):
CATAAACATATATCAGAACGAAATATCATAATTT
Found at i:17436074 original size:61 final size:61
Alignment explanation
Indices: 17435979--17436101 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
17435969 GGTATTTTAT
17435979 TATTTATCGAAATGGGCCATTTTCCATAAAATCGAGTCCACATCAGAGCGCTTTACTGACG
1 TATTTATCGAAATGGGCCATTTTCCATAAAATCGAGTCCACATCAGAGCGCTTTACTGACG
17436040 TATTTATCGAAATGGGCCATTTTCCATAAAATCGAGTCCACATCAGAGCGCTTTACTGACG
1 TATTTATCGAAATGGGCCATTTTCCATAAAATCGAGTCCACATCAGAGCGCTTTACTGACG
17436101 T
1 T
17436102 GGACGTGATT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (61 bp):
TATTTATCGAAATGGGCCATTTTCCATAAAATCGAGTCCACATCAGAGCGCTTTACTGACG
Found at i:17436182 original size:9 final size:9
Alignment explanation
Indices: 17436168--17436218 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
17436158 CCACATTAGG
17436168 TTTAGGGTT
1 TTTAGGGTT
17436177 TTTAGGG--
1 TTTAGGGTT
17436184 -TTAGGG--
1 TTTAGGGTT
17436190 TTTAGGGTT
1 TTTAGGGTT
*
17436199 TTTAGGATT
1 TTTAGGGTT
17436208 TTTAGGGTT
1 TTTAGGGTT
17436217 TT
1 TT
17436219 AGAGAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
9 25 0.68
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (9 bp):
TTTAGGGTT
Found at i:17436187 original size:15 final size:15
Alignment explanation
Indices: 17436163--17436192 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17436153 TCATCCCACA
*
17436163 TTAGGTTTAGGGTTT
1 TTAGGGTTAGGGTTT
17436178 TTAGGGTTAGGGTTT
1 TTAGGGTTAGGGTTT
17436193 AGGGTTTTTA
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:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (15 bp):
TTAGGGTTAGGGTTT
Found at i:17436564 original size:126 final size:126
Alignment explanation
Indices: 17436335--17436779 Score: 601
Period size: 126 Copynumber: 3.5 Consensus size: 126
17436325 ATAAAAATCA
* * * * * * * * *
17436335 AAGC-GGATGCTTTATCAGAAGAATTTATGAAGTCGCGCCCACATGTATGAGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGATGCGCTTTTACTACAGT
17436399 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* *
17436460 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATAGCGCCCTCGTGGATGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGATGCGCTTTTACTACAGT
* * * *
17436525 AGGTCCTGGAAGAAATAA-TTCTGACTCGATGTTTCTGAGCAAATAGTTTAAAAAAATGCTTC
66 AGGTCCTGGAAGAAATAATTTC-GACTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTC
* *
17436587 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGATGCGCTTTTACTACAGT
* *
17436652 AGGTCCTGGAAAAAATAATTTCGACTTGACGTTTCTGAGAAAATAGTAT-AAAAACGCTTC
66 AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
*** * * *
17436712 AAGCAGGATGCGACATTGAGAAGAATTTGTGAAATCGAG-CCTACGTGGATGCACTTTTACTATA
1 AAGCAGGATGCTTTA-TGAGAAGAATTTGTGAAATCGCGCCCT-CGTGGATGCGCTTTTACTACA
17436776 GTAG
64 GTAG
17436780 CATGTTTGGG
Statistics
Matches: 282, Mismatches: 32, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
125 32 0.11
126 135 0.48
127 112 0.40
128 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGATGCGCTTTTACTACAGT
AGGTCCTGGAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:17439844 original size:22 final size:21
Alignment explanation
Indices: 17439813--17439960 Score: 111
Period size: 22 Copynumber: 6.6 Consensus size: 21
17439803 GGTTAGGGTT
17439813 AGGGTTAGGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
*
17439834 AGGGTTTAGGGTTTCTAAGTTA
1 AGGG-TTAGGGTTTTTAAGTTA
* *
17439856 AGGGTTAAGG--TTTAAGTTTT
1 AGGGTTAGGGTTTTTAAG-TTA
17439876 AGGGTTAGGGGGTTTTTAAGTTAAGTTA
1 AGGGTTA--GGG--TTT---TTAAGTTA
* *
17439904 AGGGTTTATGGTTTATAAGTTAA
1 AGGG-TTAGGGTTTTTAAGTT-A
* * *
17439927 AAGTTTAAGGTTTTTAAGTTA
1 AGGGTTAGGGTTTTTAAGTTA
17439948 AGGGTTAGGGTTT
1 AGGGTTAGGGTTT
17439961 AAGATTTACA
Statistics
Matches: 99, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
19 5 0.05
20 9 0.09
21 20 0.20
22 42 0.42
23 3 0.03
25 3 0.03
26 1 0.01
27 2 0.02
28 6 0.06
29 8 0.08
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.43
Consensus pattern (21 bp):
AGGGTTAGGGTTTTTAAGTTA
Found at i:17439974 original size:49 final size:48
Alignment explanation
Indices: 17439886--17439987 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 48
17439876 AGGGTTAGGG
* *
17439886 GGTTTTTAAGTTAAGTTAAGGGTTTATGGTTTATAAGTTAAAAGTTTAA
1 GGTTTTTAAGTTAAGTTAAGGGTTTAAGATTTATAAGTT-AAAGTTTAA
* **
17439935 GGTTTTTAAGTTAAGGGTT-AGGGTTTAAGATTTA-CAGTTAGTGTTTAA
1 GGTTTTTAAGTTAA--GTTAAGGGTTTAAGATTTATAAGTTAAAGTTTAA
17439983 GGTTT
1 GGTTT
17439988 AGGGTTTAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 12 0.26
49 18 0.39
50 13 0.28
51 3 0.07
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.45
Consensus pattern (48 bp):
GGTTTTTAAGTTAAGTTAAGGGTTTAAGATTTATAAGTTAAAGTTTAA
Found at i:17439980 original size:20 final size:20
Alignment explanation
Indices: 17439951--17440002 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17439941 TAAGTTAAGG
17439951 GTTAGGGTTTAAGATTTACA
1 GTTAGGGTTTAAGATTTACA
* * **
17439971 GTTAGTGTTTAAGGTTTAGG
1 GTTAGGGTTTAAGATTTACA
17439991 GTTTAGGGTTTA
1 G-TTAGGGTTTA
17440003 TCAATTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (20 bp):
GTTAGGGTTTAAGATTTACA
Found at i:17441454 original size:20 final size:20
Alignment explanation
Indices: 17441417--17441454 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17441407 ATTATTTTTA
*
17441417 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
17441437 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
17441455 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:17442448 original size:11 final size:11
Alignment explanation
Indices: 17442415--17442442 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17442405 TAAGAGAAAT
17442415 TTGAGAGCAAA
1 TTGAGAGCAAA
17442426 TTGAGAGCAAA
1 TTGAGAGCAAA
17442437 TTGAGA
1 TTGAGA
17442443 TTAAATATGG
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:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (11 bp):
TTGAGAGCAAA
Found at i:17442483 original size:12 final size:12
Alignment explanation
Indices: 17442453--17442486 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17442443 TTAAATATGG
*
17442453 ATTTGAGAGCAA
1 ATTTGAGAGGAA
17442465 A-TTGAGAGGAA
1 ATTTGAGAGGAA
17442476 ATTTGAGAGGA
1 ATTTGAGAGGA
17442487 TTAGTTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.03, G:0.32, T:0.24
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:17443345 original size:24 final size:23
Alignment explanation
Indices: 17443314--17443360 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
17443304 ACACTTTTTA
17443314 ATTATATTATTAAGTAATAATTT
1 ATTATATTATTAAGTAATAATTT
* * *
17443337 ATTAGTATTGTTATGTGATAATTT
1 ATTA-TATTATTAAGTAATAATTT
17443361 TGATGAAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTATATTATTAAGTAATAATTT
Found at i:17444463 original size:24 final size:23
Alignment explanation
Indices: 17444421--17444479 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
17444411 ACGACACATA
* *
17444421 ATTTTTATAAAAAATAAATATAT
1 ATTTATATAAAAAAAAAATATAT
17444444 ATTTATATAAAAATAAAAATATAT
1 ATTTATATAAAAA-AAAAATATAT
*
17444468 ATTTATGTAAAA
1 ATTTATATAAAA
17444480 TACTTTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATTTATATAAAAAAAAAATATAT
Found at i:17448889 original size:18 final size:19
Alignment explanation
Indices: 17448868--17448905 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17448858 TTAGTTTCGG
* *
17448868 TATTTTAAATTTTG-AATT
1 TATTTGAAAGTTTGTAATT
17448886 TATTTGAAAGTTTGTAATT
1 TATTTGAAAGTTTGTAATT
17448905 T
1 T
17448906 TTGGGACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TATTTGAAAGTTTGTAATT
Found at i:17450986 original size:41 final size:41
Alignment explanation
Indices: 17450870--17450986 Score: 128
Period size: 40 Copynumber: 2.9 Consensus size: 41
17450860 ACATCCAGGA
* * * *
17450870 GTACCGAAGTACAAACAGGTGCACGTATGTGCAATATAGGG
1 GTACCGAAGTACAAATAGGGGCACGTATGTGCAATTTAAGG
** * * *
17450911 GTTTCGAAGTACAAATA-AGACATGTATGTGCAATTTAAGG
1 GTACCGAAGTACAAATAGGGGCACGTATGTGCAATTTAAGG
* *
17450951 GTACCAAAGTTCAAATAGGGGCACGTATGTGCAATT
1 GTACCGAAGTACAAATAGGGGCACGTATGTGCAATT
17450987 CTTTATTATT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
40 30 0.51
41 29 0.49
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.25
Consensus pattern (41 bp):
GTACCGAAGTACAAATAGGGGCACGTATGTGCAATTTAAGG
Found at i:17452690 original size:20 final size:20
Alignment explanation
Indices: 17452665--17452707 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17452655 AAAACTTAGA
* *
17452665 CTTGTTGATAAAACTCGTTT
1 CTTGTTGATAAAAATCATTT
17452685 CTTGTTGATAAAAATCATTT
1 CTTGTTGATAAAAATCATTT
17452705 CTT
1 CTT
17452708 AACTTTGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (20 bp):
CTTGTTGATAAAAATCATTT
Found at i:17453394 original size:26 final size:26
Alignment explanation
Indices: 17453365--17453426 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
17453355 TAAAACTACT
*
17453365 AGTAATAG-AATCCCAGCAAAGCTGTC
1 AGTAATAGTAA-CCCAGCAAAGCTGCC
* *
17453391 AGTAATAGTAACGCAGCAAAGTTGCC
1 AGTAATAGTAACCCAGCAAAGCTGCC
*
17453417 AGTAACAGTA
1 AGTAATAGTA
17453427 TATGTGGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (26 bp):
AGTAATAGTAACCCAGCAAAGCTGCC
Found at i:17453634 original size:27 final size:27
Alignment explanation
Indices: 17453604--17453666 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
17453594 TTTCATCTTC
*
17453604 TAGGGGTATAACGGTTATTTTACCCTA
1 TAGGGGTATAACGGTCATTTTACCCTA
** *
17453631 TAGGGGTATTTCGGTCATTTTACCCTT
1 TAGGGGTATAACGGTCATTTTACCCTA
*
17453658 TAGCGGTAT
1 TAGGGGTAT
17453667 TTTGATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (27 bp):
TAGGGGTATAACGGTCATTTTACCCTA
Found at i:17453667 original size:27 final size:27
Alignment explanation
Indices: 17453615--17453994 Score: 300
Period size: 27 Copynumber: 14.0 Consensus size: 27
17453605 AGGGGTATAA
* * *
17453615 CGGTTATTTTACCCTATAGGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
*
17453642 CGGTCATTTTACCCTTT-AGCGGTATTT
1 CGGTAATTTTACCCTTTAAG-GGTATTT
* * * *
17453669 TGATAATTTTACCCTTTGAGGGCATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
** *
17453696 CAATAATTTTA-CCTTTCAAGGCTATTT
1 CGGTAATTTTACCCTTT-AAGGGTATTT
* **
17453723 TGGTAATTTTA-CCTTTCAAGGCCATTT
1 CGGTAATTTTACCCTTT-AAGGGTATTT
* ** *
17453750 TGGTAATTTTACCCTTCGAGGGTGTTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* *
17453777 CAGTAATTTTACTCTTTAAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* **
17453804 CGGTAATTTTATCCTTCGAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* * *
17453831 CGATAAATTTATCCTTTAAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* *
17453858 CGATAATTTTACCCTTCAAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* * * *
17453885 CCGTTATTTTACCTTTTGAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
* * *
17453912 TGGTTATTTTACCCCTTTAGGGGTATTT
1 CGGTAATTTTA-CCCTTTAAGGGTATTT
* * **
17453940 CAGTCATTTTA-CCTTTCGGAGGTATTT
1 CGGTAATTTTACCCTTTAAG-GGTATTT
* * **
17453967 CGGTCATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCTTTAAGGGTATTT
17453994 C
1 C
17453995 AGTCATTTAC
Statistics
Matches: 287, Mismatches: 59, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
26 13 0.05
27 243 0.85
28 31 0.11
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.45
Consensus pattern (27 bp):
CGGTAATTTTACCCTTTAAGGGTATTT
Found at i:17453757 original size:81 final size:81
Alignment explanation
Indices: 17453634--17453993 Score: 363
Period size: 81 Copynumber: 4.4 Consensus size: 81
17453624 TACCCTATAG
* *
17453634 GGGTATTTCGGTCATTTTACCCTTT--AGCGGTATTTTGATAATTTTACCCTTTGAGGGCATTTC
1 GGGTATTTCGGTAATTTTA-CCTTTCGAG-GGTATTTTGATAATTTTACCCTTTGAGGGTATTTC
17453697 AATAATTTTACCTTTCAA
64 AATAATTTTACCTTTCAA
* * * ** * * * *
17453715 GGCTATTTTGGTAATTTTACCTTTCAAGGCCATTTTGGTAATTTTACCCTTCGAGGGTGTTTCAG
1 GGGTATTTCGGTAATTTTACCTTTCGAGGGTATTTTGATAATTTTACCCTTTGAGGGTATTTCAA
17453780 TAATTTTACTCTTT-AA
66 TAATTTTAC-CTTTCAA
* * * * *
17453796 GGGTATTTCGGTAATTTTATCC-TTCGAGGGTATTTCGATAAATTTATCCTTTAAGGGTATTTCG
1 GGGTATTTCGGTAATTTTA-CCTTTCGAGGGTATTTTGATAATTTTACCCTTTGAGGGTATTTCA
*
17453860 ATAATTTTACCCTTCAA
65 ATAATTTTACCTTTCAA
* * * * *
17453877 GGGTATTTCCGTTATTTTACCTTTTGAGGGTATTTTGGTTATTTTACCCCTTT-AGGGGTATTTC
1 GGGTATTTCGGTAATTTTACCTTTCGAGGGTATTTTGATAATTTTA-CCCTTTGA-GGGTATTTC
* * *
17453941 AGTCATTTTACCTTTC-G
64 AATAATTTTACCTTTCAA
* **
17453958 GAGGTATTTCGGTCATTTTACCCATCGAGGGTATTT
1 G-GGTATTTCGGTAATTTTACCTTTCGAGGGTATTT
17453994 CAGTCATTTA
Statistics
Matches: 227, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
80 10 0.04
81 154 0.68
82 63 0.28
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (81 bp):
GGGTATTTCGGTAATTTTACCTTTCGAGGGTATTTTGATAATTTTACCCTTTGAGGGTATTTCAA
TAATTTTACCTTTCAA
Found at i:17454005 original size:26 final size:26
Alignment explanation
Indices: 17453931--17454002 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 26
17453921 TACCCCTTTA
**
17453931 GGGGTATTTCAGTCATTTTACCTTTC
1 GGGGTATTTCAGTCATTTTACCCATC
*
17453957 GGAGGTATTTCGGTCATTTTACCCATC
1 GG-GGTATTTCAGTCATTTTACCCATC
17453984 GAGGGTATTTCAGTCATTT
1 G-GGGTATTTCAGTCATTT
17454003 ACCTACGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 2 0.05
27 37 0.93
28 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (26 bp):
GGGGTATTTCAGTCATTTTACCCATC
Found at i:17458698 original size:25 final size:25
Alignment explanation
Indices: 17458639--17458723 Score: 73
Period size: 25 Copynumber: 3.4 Consensus size: 25
17458629 ACATGTATGT
*
17458639 TCATATGAG-CATATAAACGAGAAGC
1 TCATATGAGCCATAT-AACGGGAAGC
* **
17458664 TCTTCCGAGCCATATAACGGGAAGC
1 TCATATGAGCCATATAACGGGAAGC
* ** *
17458689 TCATGTGAGCTGTATAAAGGGAAGC
1 TCATATGAGCCATATAACGGGAAGC
*
17458714 TCATTTGAGC
1 TCATATGAGC
17458724 TGAGAATCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 43 0.90
26 5 0.10
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.24
Consensus pattern (25 bp):
TCATATGAGCCATATAACGGGAAGC
Found at i:17458724 original size:25 final size:25
Alignment explanation
Indices: 17458676--17458725 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
17458666 TTCCGAGCCA
*
17458676 TATAACGGGAAGCTCATGTGAGCTG
1 TATAAAGGGAAGCTCATGTGAGCTG
*
17458701 TATAAAGGGAAGCTCATTTGAGCTG
1 TATAAAGGGAAGCTCATGTGAGCTG
17458726 AGAATCAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.26
Consensus pattern (25 bp):
TATAAAGGGAAGCTCATGTGAGCTG
Found at i:17458737 original size:25 final size:25
Alignment explanation
Indices: 17458684--17458773 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 25
17458674 CATATAACGG
* *
17458684 GAAGCTCATGTGAGCTGTATAA--AGG
1 GAAGCTCATATGAGCTGTA-AATCA-A
*
17458709 GAAGCTCATTTGAGCTG-AGAATCAA
1 GAAGCTCATATGAGCTGTA-AATCAA
* *
17458734 GAAGCTCATAAGAGCTGTAAATCAG
1 GAAGCTCATATGAGCTGTAAATCAA
17458759 GAAGCTCATATGAGC
1 GAAGCTCATATGAGC
17458774 CAATATTGAG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
24 3 0.05
25 50 0.91
26 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (25 bp):
GAAGCTCATATGAGCTGTAAATCAA
Found at i:17458813 original size:25 final size:24
Alignment explanation
Indices: 17458759--17458880 Score: 97
Period size: 25 Copynumber: 4.9 Consensus size: 24
17458749 TGTAAATCAG
* *
17458759 GAAGCTCAT-ATGAGCCAATATTGA
1 GAAGCTCATGA-GAGCCATTATCGA
17458783 GAAGCTC-TGGAGAGCCATTAATCGA
1 GAAGCTCAT-GAGAGCCATT-ATCGA
* *
17458808 GAAGCTCATAAGAGCAAATTATCGA
1 GAAGCTCATGAGAGC-CATTATCGA
* *
17458833 GAAGCTCATGAGAGCCAAATAACG-
1 GAAGCTCATGAGAGCC-ATTATCGA
*
17458857 GCAAGCTCAAGAGAGCCATATATC
1 G-AAGCTCATGAGAGCCAT-TATC
17458881 AGGATGCTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 15
0.75 0.10 0.14
Matches are distributed among these distances:
23 1 0.01
24 16 0.20
25 58 0.73
26 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (24 bp):
GAAGCTCATGAGAGCCATTATCGA
Found at i:17463488 original size:18 final size:18
Alignment explanation
Indices: 17463465--17463503 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
17463455 TTAAGATTTA
17463465 TTGGACCGTACGAGATTG
1 TTGGACCGTACGAGATTG
17463483 TTGGACCGTACGAGATTG
1 TTGGACCGTACGAGATTG
17463501 TTG
1 TTG
17463504 AGCATATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (18 bp):
TTGGACCGTACGAGATTG
Found at i:17466716 original size:22 final size:22
Alignment explanation
Indices: 17466689--17466734 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17466679 ATATGTTTCG
*
17466689 ATATATGTCAT-ATTAGATTGAA
1 ATATATG-CATGATTAGACTGAA
*
17466711 ATATATGCATGATTATACTGAA
1 ATATATGCATGATTAGACTGAA
17466733 AT
1 AT
17466735 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (22 bp):
ATATATGCATGATTAGACTGAA
Found at i:17469785 original size:17 final size:18
Alignment explanation
Indices: 17469745--17469785 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
17469735 TATCAATTTC
*
17469745 ACATTTTATTTTAAAATA
1 ACATTTTATTTAAAAATA
*
17469763 AC-TTTTA-TTAAAAATT
1 ACATTTTATTTAAAAATA
17469779 ACATTTT
1 ACATTTT
17469786 TTACATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.45
17 9 0.45
18 2 0.10
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (18 bp):
ACATTTTATTTAAAAATA
Found at i:17472950 original size:72 final size:72
Alignment explanation
Indices: 17472825--17472964 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
17472815 AGCTTACCGT
* * * * * *
17472825 TACAACGTTAACGATAATTAACGACTCAGTGACTAAAATGGTACAATATGATAACATAAGTGATT
1 TACAACGTTAACGACAATTAAAGACTCAATGACTAAAATGGTACAACACGATAACACAAGTGATT
17472890 AAACTGC
66 AAACTGC
* * * * *
17472897 TACACCGTTAATGACAATTAAAGACTCAATTACTAAAATGTTACAACACGATAACGCAAGTGATT
1 TACAACGTTAACGACAATTAAAGACTCAATGACTAAAATGGTACAACACGATAACACAAGTGATT
17472962 AAA
66 AAA
17472965 ACGTAACATT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (72 bp):
TACAACGTTAACGACAATTAAAGACTCAATGACTAAAATGGTACAACACGATAACACAAGTGATT
AAACTGC
Found at i:17474773 original size:16 final size:18
Alignment explanation
Indices: 17474752--17474785 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17474742 GACTTGTTAC
17474752 ATTAA-TAA-TACGAAAA
1 ATTAATTAATTACGAAAA
17474768 ATTAATTAATTACGAAAA
1 ATTAATTAATTACGAAAA
17474786 TAAAATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 3 0.19
18 8 0.50
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
ATTAATTAATTACGAAAA
Found at i:17475445 original size:25 final size:23
Alignment explanation
Indices: 17475407--17475458 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
17475397 TCATTATTCT
*
17475407 AAATATTCAAAAATTTATAATTATA
1 AAATATTCAAAAA-TTA-AAATATA
17475432 AAATATT-ACAAAATTAAAATATA
1 AAATATTCA-AAAATTAAAATATA
17475455 AAAT
1 AAAT
17475459 TAAAAGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 11 0.44
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATATTCAAAAATTAAAATATA
Found at i:17475459 original size:13 final size:13
Alignment explanation
Indices: 17475441--17475470 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17475431 AAAATATTAC
*
17475441 AAAATTAAAATAT
1 AAAATTAAAAGAT
17475454 AAAATTAAAAGAT
1 AAAATTAAAAGAT
17475467 AAAA
1 AAAA
17475471 CAACTCAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAATTAAAAGAT
Found at i:17475722 original size:7 final size:7
Alignment explanation
Indices: 17475689--17475745 Score: 55
Period size: 7 Copynumber: 8.0 Consensus size: 7
17475679 TTTTTATTAA
17475689 ATAAAAT
1 ATAAAAT
*
17475696 A-AAATT
1 ATAAAAT
17475702 ATAAAAACT
1 AT-AAAA-T
17475711 ATAAAAT
1 ATAAAAT
17475718 ATAAAA-
1 ATAAAAT
17475724 ATAAAACT
1 ATAAAA-T
*
17475732 AAAAAAT
1 ATAAAAT
17475739 ATAAAAT
1 ATAAAAT
17475746 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 11 0.27
7 15 0.37
8 12 0.29
9 3 0.07
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (7 bp):
ATAAAAT
Found at i:17475731 original size:21 final size:21
Alignment explanation
Indices: 17475705--17475744 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17475695 TAAAATTATA
*
17475705 AAAACTATAAAATATAAAAAT
1 AAAACTAAAAAATATAAAAAT
17475726 AAAACTAAAAAATATAAAA
1 AAAACTAAAAAATATAAAA
17475745 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAACTAAAAAATATAAAAAT
Found at i:17476954 original size:9 final size:9
Alignment explanation
Indices: 17476937--17476967 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17476927 TCAAGTTGAT
17476937 TCGAATAAC
1 TCGAATAAC
*
17476946 TCGATTAAC
1 TCGAATAAC
17476955 TCGAATAAC
1 TCGAATAAC
17476964 TCGA
1 TCGA
17476968 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17477374 original size:41 final size:41
Alignment explanation
Indices: 17477329--17477419 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
17477319 GTCCACGTCA
17477329 GCGCGCTTTATCTGACGTGGCAACAAAACGCGTACTCAAGG
1 GCGCGCTTTATCTGACGTGGCAACAAAACGCGTACTCAAGG
17477370 GCGCGCTTTATCTGACGTGGCAACAAAACGCGTACTCAAGG
1 GCGCGCTTTATCTGACGTGGCAACAAAACGCGTACTCAAGG
17477411 GCGCGCTTT
1 GCGCGCTTT
17477420 GTCCACGTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (41 bp):
GCGCGCTTTATCTGACGTGGCAACAAAACGCGTACTCAAGG
Found at i:17477635 original size:11 final size:11
Alignment explanation
Indices: 17477608--17477641 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17477598 ATTAATCCTT
*
17477608 TCTCAATTATTC
1 TCTCAATT-TCC
17477620 TCTCAATTTCC
1 TCTCAATTTCC
17477631 TCTCAATTTCC
1 TCTCAATTTCC
17477642 AATTTGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:17477646 original size:18 final size:18
Alignment explanation
Indices: 17477623--17477657 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17477613 ATTATTCTCT
17477623 CAATTTCCTCTCAATTTC
1 CAATTTCCTCTCAATTTC
*
17477641 CAATTTGCTCTCAATTT
1 CAATTTCCTCTCAATTT
17477658 TCTTCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.29, G:0.03, T:0.46
Consensus pattern (18 bp):
CAATTTCCTCTCAATTTC
Found at i:17477652 original size:29 final size:30
Alignment explanation
Indices: 17477619--17477699 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
17477609 CTCAATTATT
*
17477619 CTCTCAATTTCCTCTCAATTTCCA-ATTTG
1 CTCTCAATTTCCTCTCAATTTCCATATTTA
* *
17477648 CTCTCAATTTTCT-TCCAA-ATCCATATTTA
1 CTCTCAATTTCCTCT-CAATTTCCATATTTA
*
17477677 ATCTCAATTTCCTCTCAAATTTC
1 CTCTCAATTTCCTCTC-AATTTC
17477700 TCTTAAATCT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 5 0.12
29 31 0.76
30 3 0.07
31 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.01, T:0.44
Consensus pattern (30 bp):
CTCTCAATTTCCTCTCAATTTCCATATTTA
Found at i:17478868 original size:7 final size:7
Alignment explanation
Indices: 17478856--17478898 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
17478846 AGCTAGTTGA
17478856 TTAGTAT
1 TTAGTAT
17478863 TTAGTAT
1 TTAGTAT
17478870 TTAGTAT
1 TTAGTAT
17478877 TTAGTAT
1 TTAGTAT
17478884 TTAGTAT
1 TTAGTAT
17478891 TTAGTAT
1 TTAGTAT
17478898 T
1 T
17478899 ATATATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (7 bp):
TTAGTAT
Found at i:17479569 original size:18 final size:18
Alignment explanation
Indices: 17479546--17479589 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17479536 TGTCAGGTGC
*
17479546 GTATCCTTACCCTTTTAT
1 GTATCCTTACCCTTATAT
* *
17479564 GTATCCTAATCCTTATAT
1 GTATCCTTACCCTTATAT
*
17479582 GTTTCCTT
1 GTATCCTT
17479590 TTCCGAGTCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.07, T:0.50
Consensus pattern (18 bp):
GTATCCTTACCCTTATAT
Found at i:17479868 original size:21 final size:21
Alignment explanation
Indices: 17479844--17479890 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17479834 AGATACCCTA
* * *
17479844 CCGGAGGAACCAGAATCCCCG
1 CCGGAGCAACCACAACCCCCG
*
17479865 CCGGATCAACCACAACCCCCG
1 CCGGAGCAACCACAACCCCCG
17479886 CCGGA
1 CCGGA
17479891 AGCTAGACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.45, G:0.23, T:0.04
Consensus pattern (21 bp):
CCGGAGCAACCACAACCCCCG
Found at i:17481368 original size:15 final size:15
Alignment explanation
Indices: 17481348--17481376 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17481338 TAATTTTTAA
17481348 CCTAAACCCTAAAAC
1 CCTAAACCCTAAAAC
17481363 CCTAAACCCTAAAA
1 CCTAAACCCTAAAA
17481377 GCAATGAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.38, G:0.00, T:0.14
Consensus pattern (15 bp):
CCTAAACCCTAAAAC
Found at i:17481921 original size:16 final size:16
Alignment explanation
Indices: 17481900--17481931 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17481890 ATTTTTTAAA
*
17481900 AATTAATTAATATTTT
1 AATTAATAAATATTTT
17481916 AATTAATAAATATTTT
1 AATTAATAAATATTTT
17481932 GTTTTTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAATAAATATTTT
Found at i:17482034 original size:19 final size:19
Alignment explanation
Indices: 17482010--17482048 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17482000 TATAGTCACG
17482010 ATTCATATTAAAAAATGAT
1 ATTCATATTAAAAAATGAT
* *
17482029 ATTCATGTTCAAAAATGAT
1 ATTCATATTAAAAAATGAT
17482048 A
1 A
17482049 AAATTACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTCATATTAAAAAATGAT
Found at i:17484855 original size:3 final size:3
Alignment explanation
Indices: 17484842--17484911 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
17484832 TAATATTAAT
* * * * *
17484842 TTA TCA TTA TTA TTTA TTA CTA TTA TTA CTA TCA TTA TTT TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
17484888 TTA TTA TTA GTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
17484912 ATATATTAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:17484966 original size:23 final size:24
Alignment explanation
Indices: 17484940--17484984 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
17484930 CCTTTTACTA
*
17484940 TTATCATATATTGTTAT-TTAAGT
1 TTATAATATATTGTTATATTAAGT
* *
17484963 TTATAATGTATTTTTATATTAA
1 TTATAATATATTGTTATATTAA
17484985 TCCAATATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (24 bp):
TTATAATATATTGTTATATTAAGT
Found at i:17492605 original size:13 final size:13
Alignment explanation
Indices: 17492587--17492611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17492577 CTAAAAATCT
17492587 TTTTATAATTTTA
1 TTTTATAATTTTA
17492600 TTTTATAATTTT
1 TTTTATAATTTT
17492612 TTAAATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTATAATTTTA
Found at i:17495815 original size:3 final size:3
Alignment explanation
Indices: 17495809--17495863 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
17495799 TTCTTATTTT
17495809 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
17495857 TTA TTA T
1 TTA TTA T
17495864 CTTTTGTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17502011 original size:2 final size:2
Alignment explanation
Indices: 17502000--17502040 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
17501990 ATATGAATAC
17502000 AT AT -T 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
17502041 TCTTCATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17502422 original size:14 final size:14
Alignment explanation
Indices: 17502403--17502441 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17502393 TGGTATATTG
17502403 TATTTGTATATATA
1 TATTTGTATATATA
* *
17502417 TATTTGTAAATATT
1 TATTTGTATATATA
*
17502431 TATTCGTATAT
1 TATTTGTATAT
17502442 GCTATAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (14 bp):
TATTTGTATATATA
Found at i:17508125 original size:19 final size:17
Alignment explanation
Indices: 17508101--17508137 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
17508091 TGATGATAGA
17508101 AATAAATTTTATGATTTTT
1 AATAAATTTT-T-ATTTTT
17508120 AATAAATTTTTATTTTT
1 AATAAATTTTTATTTTT
17508137 A
1 A
17508138 TGGATTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 1 0.06
19 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
AATAAATTTTTATTTTT
Found at i:17511162 original size:22 final size:22
Alignment explanation
Indices: 17511137--17511181 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17511127 AACTAACTGC
17511137 ACAACTAACTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
*
17511159 ACAACTAATTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
17511181 A
1 A
17511182 ACAGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
ACAACTAACTAACTGATAAGCT
Found at i:17515801 original size:22 final size:22
Alignment explanation
Indices: 17515776--17515820 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
17515766 AACTAACTGC
17515776 ACAACTAACTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
*
17515798 ACAACTAATTAACTGATAAGCT
1 ACAACTAACTAACTGATAAGCT
17515820 A
1 A
17515821 ACAGTTAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
ACAACTAACTAACTGATAAGCT
Found at i:17529636 original size:14 final size:14
Alignment explanation
Indices: 17529617--17529643 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17529607 GTCGTGCTGC
17529617 CATCATTAGTATGT
1 CATCATTAGTATGT
17529631 CATCATTAGTATG
1 CATCATTAGTATG
17529644 AGTCCTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (14 bp):
CATCATTAGTATGT
Found at i:17533123 original size:6 final size:6
Alignment explanation
Indices: 17533112--17533140 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17533102 GGAAGATTTT
17533112 GATGAG GATGAG GATGAG GATGAG GATGA
1 GATGAG GATGAG GATGAG GATGAG GATGA
17533141 TGAATGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.48, T:0.17
Consensus pattern (6 bp):
GATGAG
Found at i:17535638 original size:94 final size:92
Alignment explanation
Indices: 17535455--17535642 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 92
17535445 GTACACCACT
* *
17535455 TCTCCTGGAAGATACAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
1 TCTCCTGGAAGAGAAAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
17535520 GCCAGTATATAAAGAATTATCTAATCC
66 GCCAGTATATAAAGAATTATCTAATCC
* * *
17535547 TCTCCTGGAAGAGAAAATCTAGATTTGGGTGTTCTTTTTTCCCCTTTTTTTTCCATTATGCAACA
1 TCTCCTGGAAGAGAAAATCTAGATCTGGGTGTTCCTTTTTCCCC--TTTTTTCCAATATGCAACA
17535612 CAGCCAGTATATAAAGAATTATCTAATCC
64 CAGCCAGTATATAAAGAATTATCTAATCC
17535641 TC
1 TC
17535643 ATCTTTGTCA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 40 0.45
94 49 0.55
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (92 bp):
TCTCCTGGAAGAGAAAATCTAGATCTGGGTGTTCCTTTTTCCCCTTTTTTCCAATATGCAACACA
GCCAGTATATAAAGAATTATCTAATCC
Found at i:17536214 original size:20 final size:20
Alignment explanation
Indices: 17536189--17536228 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17536179 TCCTCTCTCC
17536189 CTCAAGGCAACACCTTTTAT
1 CTCAAGGCAACACCTTTTAT
17536209 CTCAAGGCAACACCTTTTAT
1 CTCAAGGCAACACCTTTTAT
17536229 GCTGAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (20 bp):
CTCAAGGCAACACCTTTTAT
Found at i:17540646 original size:9 final size:9
Alignment explanation
Indices: 17540632--17540710 Score: 52
Period size: 9 Copynumber: 9.8 Consensus size: 9
17540622 AACAATTTTA
17540632 AAAAATTAT
1 AAAAATTAT
17540641 AAAAA-TAT
1 AAAAATTAT
17540649 AAAAATT-T
1 AAAAATTAT
17540657 AGAAAA-TAT
1 A-AAAATTAT
* *
17540666 --ACATAAT
1 AAAAATTAT
*
17540673 AAAAAGTAT
1 AAAAATTAT
17540682 -AAAA--AT
1 AAAAATTAT
17540688 AAAAATTAT
1 AAAAATTAT
17540697 AAAAA--AT
1 AAAAATTAT
17540704 AAAAATT
1 AAAAATT
17540711 CATTAATTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
6 4 0.07
7 13 0.24
8 15 0.28
9 22 0.41
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:17540686 original size:24 final size:22
Alignment explanation
Indices: 17540639--17540709 Score: 63
Period size: 24 Copynumber: 3.1 Consensus size: 22
17540629 TTAAAAAATT
*
17540639 ATAAAAAT-ATAAAAATTTAGAAA
1 ATAAAAATAATAAAAA-ATA-AAA
* *
17540662 ATATACATAATAAAAAGTATAAAA
1 ATAAAAATAATAAAAA--ATAAAA
*
17540686 ATAAAAATTATAAAAAATAAAA
1 ATAAAAATAATAAAAAATAAAA
17540708 AT
1 AT
17540710 TCATTAATTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 8 0.20
23 6 0.15
24 23 0.57
25 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (22 bp):
ATAAAAATAATAAAAAATAAAA
Found at i:17540688 original size:15 final size:14
Alignment explanation
Indices: 17540639--17540709 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 14
17540629 TTAAAAAATT
17540639 ATAAAAATATAAAA
1 ATAAAAATATAAAA
*
17540653 ATTTAGAAAATATACATA
1 A--TA-AAAATATA-AAA
17540671 ATAAAAAGTATAAAA
1 ATAAAAA-TATAAAA
17540686 ATAAAAATTATAAAAA
1 ATAAAAA-TAT-AAAA
17540702 ATAAAAAT
1 ATAAAAAT
17540710 TCATTAATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 1 0.02
15 17 0.35
16 19 0.40
17 8 0.17
18 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (14 bp):
ATAAAAATATAAAA
Found at i:17540709 original size:16 final size:16
Alignment explanation
Indices: 17540620--17540710 Score: 69
Period size: 16 Copynumber: 5.6 Consensus size: 16
17540610 ATATATTTAT
* *
17540620 ATAACAATTTTAAAAA
1 ATAAAAATTATAAAAA
*
17540636 ATTATAAAAATATAAAAA
1 A-TA-AAAATTATAAAAA
* * *
17540654 TTTAGAAAA-TATACATA
1 -ATA-AAAATTATAAAAA
*
17540671 ATAAAAAGTAT-AAAA
1 ATAAAAATTATAAAAA
17540686 ATAAAAATTATAAAAA
1 ATAAAAATTATAAAAA
17540702 ATAAAAATT
1 ATAAAAATT
17540711 CATTAATTCC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
15 16 0.27
16 19 0.32
17 8 0.14
18 16 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
ATAAAAATTATAAAAA
Found at i:17547040 original size:16 final size:17
Alignment explanation
Indices: 17546995--17547040 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
17546985 TAATTAAATT
*
17546995 AAATTTTAA-TAAATAT
1 AAATTTTAAGTAAATAA
*
17547011 ATATTTTCAAGTAAA-AA
1 AAATTTT-AAGTAAATAA
17547028 AAATTTTAAGTAA
1 AAATTTTAAGTAA
17547041 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 12 0.48
17 9 0.36
18 4 0.16
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
AAATTTTAAGTAAATAA
Found at i:17547868 original size:17 final size:18
Alignment explanation
Indices: 17547848--17547881 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17547838 AAAATGAACT
17547848 AAAAATAAAAA-ATAAAG
1 AAAAATAAAAAGATAAAG
*
17547865 AAAATTAAAAAGATAAA
1 AAAAATAAAAAGATAAA
17547882 ATAATTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAAATAAAAAGATAAAG
Found at i:17556354 original size:62 final size:62
Alignment explanation
Indices: 17556257--17556380 Score: 178
Period size: 62 Copynumber: 2.0 Consensus size: 62
17556247 ATGTTATTTG
* * ** *
17556257 AATGAGTAATCGGGTTCAAGTGGTAAATACTTAAAGTCAAGTGGTTTTCGAAAATGGGGTAT
1 AATGAGTAATCAGGTTCAAGTGGTAAATACTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
*
17556319 AATGAGTAATTAGGTTCAAGTGGTAAAT-CTTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
1 AATGAGTAATCAGGTTCAAGTGGTAAATAC-TTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
17556381 TGGGACCTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 1 0.02
62 54 0.98
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.31
Consensus pattern (62 bp):
AATGAGTAATCAGGTTCAAGTGGTAAATACTTAAAGTCAAGCGGTTTTAAAAAATGAGGTAT
Found at i:17559328 original size:50 final size:49
Alignment explanation
Indices: 17559266--17559428 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 49
17559256 GATCTGTAAT
* * *
17559266 CTTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAA-TGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* * * *** ** *
17559316 CTTCAATCTGTTCCATCGCACTTTCAGGGAAGTAAGATCCGCCGTTATGG
1 CTTCAATCTGTTCAAT-GCAATATCAGGGAAACCAGATCCGCCGTCGTAG
* *
17559366 CTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAA-TGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
*
17559416 CTTCAATTTGTTC
1 CTTCAATCTGTTC
17559429 CGCTGTACTG
Statistics
Matches: 86, Mismatches: 25, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
49 1 0.01
50 84 0.98
51 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (49 bp):
CTTCAATCTGTTCAATGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
Found at i:17559414 original size:100 final size:99
Alignment explanation
Indices: 17559282--17559481 Score: 287
Period size: 100 Copynumber: 2.0 Consensus size: 99
17559272 TTTGTTCAAC
* * * * *
17559282 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCC-ATCGCACT-TTCAGGG
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCT-GCACTGCT-AAGG
17559345 AAGTAAGATCCGCCGTTATGGCTTCAATCTTTTTAAT
64 AAGTAAGATCCGCCGTTATGGCTTCAATC-TTTTAAT
* *
17559382 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATTTGTTCCGCTGTACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAA
*
17559447 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTAAT
66 GTAAGATCCGCCGTTATGGCTTCAATCTTTTAAT
17559481 T
1 T
17559482 TTTCAACCCG
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 8 0.09
100 80 0.89
101 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.30
Consensus pattern (99 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCACTGCTAAGGAA
GTAAGATCCGCCGTTATGGCTTCAATCTTTTAAT
Found at i:17567574 original size:20 final size:20
Alignment explanation
Indices: 17567549--17567608 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
17567539 TAAAGGTCTT
*
17567549 TAATGCATATGATGCGGTGC
1 TAATGCATATGATGCGATGC
17567569 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
17567589 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
17567609 ATGAGGTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:17572816 original size:9 final size:9
Alignment explanation
Indices: 17572770--17572812 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
17572760 TATTTTCTCC
17572770 TTATTATAA
1 TTATTATAA
17572779 TTATTATAA
1 TTATTATAA
* *
17572788 TAATAATAA
1 TTATTATAA
* *
17572797 TAATTATTA
1 TTATTATAA
17572806 TTATTAT
1 TTATTAT
17572813 TATTGTTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTATTATAA
Found at i:17572821 original size:3 final size:3
Alignment explanation
Indices: 17572815--17572847 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17572805 ATTATTATTA
17572815 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
17572848 ATATTGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:17573144 original size:18 final size:18
Alignment explanation
Indices: 17573121--17573155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17573111 ATATTCTTAA
17573121 ATTATTATAAACATATTT
1 ATTATTATAAACATATTT
* *
17573139 ATTATTTTATACATATT
1 ATTATTATAAACATATT
17573156 GTACATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTATAAACATATTT
Found at i:17575316 original size:23 final size:22
Alignment explanation
Indices: 17575263--17575321 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
17575253 TAAATATTAG
*
17575263 TTTATTAATATTTTAATTTGAT
1 TTTATTAATATATTAATTTGAT
* *
17575285 TTTTTTAATGATATT-ATTTTAT
1 TTTATTAAT-ATATTAATTTGAT
*
17575307 TGTTATTAATTTATT
1 T-TTATTAATATATT
17575322 TAGTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (22 bp):
TTTATTAATATATTAATTTGAT
Found at i:17581111 original size:43 final size:44
Alignment explanation
Indices: 17580970--17581139 Score: 146
Period size: 43 Copynumber: 3.9 Consensus size: 44
17580960 CCTGCACCGA
* * * *
17580970 CAGTGAAGCAGATTGAAGACACCAG-CCTTACCTCCCTGGGTTG
1 CAGTGAAGCAGATTAAAAACACCAGACCTTGCCTTCCTGGGTTG
* * * * * * ***
17581013 CAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCTTGCACTG
1 CAGTGAAGCAGATTAAAAACACCAGACCTTGCCTTCCTGGGTTG
*
17581057 ACAGTGAAGCAGATCAAAAACACCAG-CCTTGCCTTCCTGGGTTG
1 -CAGTGAAGCAGATTAAAAACACCAGACCTTGCCTTCCTGGGTTG
* * * * *
17581101 CAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTG
1 CAGTGAAGCAGATTAAAAACACCAGACCTTGCCTTCCTG
17581140 CACCGACAGC
Statistics
Matches: 95, Mismatches: 29, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
43 39 0.41
44 36 0.38
45 20 0.21
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (44 bp):
CAGTGAAGCAGATTAAAAACACCAGACCTTGCCTTCCTGGGTTG
Found at i:17581132 original size:44 final size:44
Alignment explanation
Indices: 17581004--17581139 Score: 166
Period size: 44 Copynumber: 3.1 Consensus size: 44
17580994 GCCTTACCTC
17581004 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
* *** * * * * * *
17581048 CTTGCACTGACAGTGAAGCAGATCAAAAACACCAG-CCTTGCCTT
1 CCTGGGTTG-CAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
17581092 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
17581136 CCTG
1 CCTG
17581140 CACCGACAGC
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
43 20 0.29
44 30 0.43
45 20 0.29
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (44 bp):
CCTGGGTTGCAGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
Found at i:17581171 original size:88 final size:88
Alignment explanation
Indices: 17580938--17581205 Score: 385
Period size: 88 Copynumber: 3.0 Consensus size: 88
17580928 AGCAGATCAG
*
17580938 TAAAAATAGCAGATTTTGCCTTCCTGCACCGACAGTGAAGCAGATTGAAGACACCAGCCTTACCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATTGAAGACACCAGCCTTACCT
*
17581003 CCCTGGGTTGCAGTGGAGCAGGT
66 TCCTGGGTTGCAGTGGAGCAGGT
* * ** * *
17581026 TAAAAATAGCAGATCTTGCCTTCTTGCACTGACAGTGAAGCAGATCAAAAACACCAGCCTTGCCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATTGAAGACACCAGCCTTACCT
17581091 TCCTGGGTTGCAGTGGAGCAGGT
66 TCCTGGGTTGCAGTGGAGCAGGT
* * * * *
17581114 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATTGATGACCCCAGCCCTATCT
1 TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATTGAAGACACCAGCCTTACCT
**
17581179 TCCT-GGTTAGCAGTGGAAAAGGT
66 TCCTGGGTT-GCAGTGGAGCAGGT
17581202 TAAA
1 TAAA
17581206 GATTGTGAAT
Statistics
Matches: 158, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
87 4 0.03
88 154 0.97
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (88 bp):
TAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGTGAAGCAGATTGAAGACACCAGCCTTACCT
TCCTGGGTTGCAGTGGAGCAGGT
Found at i:17581220 original size:44 final size:44
Alignment explanation
Indices: 17581172--17581547 Score: 439
Period size: 44 Copynumber: 8.7 Consensus size: 44
17581162 TGACCCCAGC
* * *
17581172 CCTATCTTCCTGGTTAGCAGTGGAAAAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
17581216 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
17581260 TCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAA-ATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTT-AAAGATTGTGAAT
* * *
17581304 TCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
17581342 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
17581386 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAA-ATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTT-AAAGATTGTGAAT
* * * * * *
17581430 TCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * * *
17581474 TCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
17581518 CCTATCTCTCTGAG-CAGCAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
17581548 GGAAAATAGC
Statistics
Matches: 290, Mismatches: 30, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
38 32 0.11
39 2 0.01
40 1 0.00
42 3 0.01
43 3 0.01
44 241 0.83
45 8 0.03
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:17581373 original size:126 final size:129
Alignment explanation
Indices: 17581211--17581554 Score: 525
Period size: 126 Copynumber: 2.7 Consensus size: 129
17581201 TTAAAGATTG
*
17581211 TGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATTCTATCTCCCTGGTCA
1 TGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
*
17581276 GCAGTGGAATAGGTTGAAAATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATT-AA-A
66 GCAGTGGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGA
17581338 -GAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
1 TGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
17581402 GCAGTGGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGA
66 GCAGTGGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGA
* * * * * * *
17581466 TTGTAGGTTCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAACCCTATCTCTCTGA
1 -TG-A-ATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTG-
* *
17581531 G-CAGCAGTGGAGTAGGTGGAAAAT
62 GTCAGCAGTGGAATAGGTTGAAAAT
17581555 AGCAGATCTT
Statistics
Matches: 199, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
126 121 0.61
127 2 0.01
128 1 0.01
130 1 0.01
131 1 0.01
132 72 0.36
133 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (129 bp):
TGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCA
GCAGTGGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGA
Found at i:17581380 original size:170 final size:170
Alignment explanation
Indices: 17581172--17581501 Score: 520
Period size: 170 Copynumber: 1.9 Consensus size: 170
17581162 TGACCCCAGC
* **
17581172 CCTATCTTCCTGGTTAGCAGTGGAAAAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
1 CCTATCTCCCTGGACAGCAGTGGAAAAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
* * * *
17581237 GGAATAGGTT-AAAGATTGTGAATTCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAAATTG-A
66 GGAATAGGTTGAAA-ATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAAATTGTA
17581300 GAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
130 G-ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
* *
17581342 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTGGACAGCAGTGGAAAAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
*
17581407 GGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG
66 GGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAAATTGTAG
* *
17581472 GTTCTATCTCCCTGGTCAGCAGTGGAATAG
131 ATTCTATCTCCCTGGGCAGCAGTGGAATAG
17581502 GTTGAAGATC
Statistics
Matches: 146, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
170 141 0.97
171 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (170 bp):
CCTATCTCCCTGGACAGCAGTGGAAAAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
GGAATAGGTTGAAAATTGAGAATTCTATATCCCTGGGCAGCAGTGGAATAGATTGAAAATTGTAG
ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
Found at i:17581919 original size:44 final size:43
Alignment explanation
Indices: 17581854--17582007 Score: 129
Period size: 44 Copynumber: 3.6 Consensus size: 43
17581844 ATGGCAATTT
*
17581854 TTATCTCCCTGAAGTTACAGTGGAGCCGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCCGATTAAAGCC-ATAATC
* ** * * *
17581898 TTATCTCCCTGAAGTTGCAGTGAAGTGGATTAAAACCTTGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCCGATTAAAGCCAT-AATC
* * * * *
17581942 TTATCTCTCTGAAGTTGCAG-AGAG-C-A-GAACG-CATCTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCCGATTAAAGCCA--TAATC
17581982 TTATCTCCCTGAAGTTGCAGTGGAGC
1 TTATCTCCCTGAAGTTGCAGTGGAGC
17582008 AGACTAAATA
Statistics
Matches: 86, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
39 1 0.01
40 23 0.27
41 5 0.06
43 3 0.03
44 54 0.63
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCCGATTAAAGCCATAATC
Found at i:17583413 original size:3 final size:3
Alignment explanation
Indices: 17583407--17583454 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
17583397 ATTATTATTA
17583407 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
17583455 ATATTGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:17583761 original size:18 final size:18
Alignment explanation
Indices: 17583738--17583772 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17583728 ATATTCTTAA
17583738 ATTATTATAAACATATTT
1 ATTATTATAAACATATTT
* *
17583756 ATTATTTTATACATATT
1 ATTATTATAAACATATT
17583773 GTACATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTATAAACATATTT
Found at i:17585294 original size:17 final size:18
Alignment explanation
Indices: 17585255--17585294 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
17585245 GTTTGTTTGG
*
17585255 ATTAAACTTTAGTTATGA
1 ATTAAACTTTAGTTATAA
17585273 A-TAAACTTTAGTTA-AA
1 ATTAAACTTTAGTTATAA
17585289 ATTAAA
1 ATTAAA
17585295 ATTTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 17 0.85
18 1 0.05
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (18 bp):
ATTAAACTTTAGTTATAA
Found at i:17587815 original size:28 final size:28
Alignment explanation
Indices: 17587783--17587838 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
17587773 GCGGAGTTTC
17587783 CCTCTTCATTGTTTTACAATATTTTATG
1 CCTCTTCATTGTTTTACAATATTTTATG
17587811 CCTCTTCATTGTTTTACAATATTTTATG
1 CCTCTTCATTGTTTTACAATATTTTATG
17587839 TAGTTGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (28 bp):
CCTCTTCATTGTTTTACAATATTTTATG
Found at i:17589422 original size:14 final size:14
Alignment explanation
Indices: 17589405--17589435 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17589395 ACTTTTGTAT
17589405 CTTATCTTTTAATC
1 CTTATCTTTTAATC
17589419 CTTATCTTTTAATC
1 CTTATCTTTTAATC
17589433 CTT
1 CTT
17589436 TCCATCTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (14 bp):
CTTATCTTTTAATC
Found at i:17595502 original size:8 final size:8
Alignment explanation
Indices: 17595483--17595528 Score: 51
Period size: 7 Copynumber: 5.8 Consensus size: 8
17595473 ATAAGCCTTA
17595483 AAAAAATT
1 AAAAAATT
17595491 -AAAAATT
1 AAAAAATT
17595498 -AAAAATT
1 AAAAAATT
*
17595505 AAAAATATA
1 AAAAA-ATT
17595514 AAAAAATT
1 AAAAAATT
17595522 CAAAAAA
1 -AAAAAA
17595529 AAGTATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 14 0.42
8 6 0.18
9 13 0.39
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:17595526 original size:7 final size:7
Alignment explanation
Indices: 17595484--17595517 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
17595474 TAAGCCTTAA
17595484 AAAAATT
1 AAAAATT
17595491 AAAAATT
1 AAAAATT
17595498 AAAAATT
1 AAAAATT
17595505 AAAAATAT
1 AAAAAT-T
17595513 AAAAA
1 AAAAA
17595518 AATTCAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:17600707 original size:15 final size:15
Alignment explanation
Indices: 17600702--17600733 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
17600692 AATAATTGTG
17600702 ATAATAATAATACTA
1 ATAATAATAATACTA
17600717 ATAATAATAATATCTA
1 ATAATAATAATA-CTA
17600733 A
1 A
17600734 ATTTTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATAATACTA
Found at i:17603330 original size:16 final size:17
Alignment explanation
Indices: 17603298--17603331 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17603288 CTTTTTAAAT
*
17603298 AATTTTATTATTTTTTA
1 AATTTTATTAATTTTTA
17603315 AATTTTA-TAATTTTTA
1 AATTTTATTAATTTTTA
17603331 A
1 A
17603332 CAAATTAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATTTTATTAATTTTTA
Found at i:17607602 original size:21 final size:21
Alignment explanation
Indices: 17607578--17607618 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17607568 TCAAAATGAC
*
17607578 ATAGTTTAGCCTTTTAACTTA
1 ATAGTTTAGACTTTTAACTTA
*
17607599 ATAGTTTTGACTTTTAACTT
1 ATAGTTTAGACTTTTAACTT
17607619 TAGAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAGTTTAGACTTTTAACTTA
Found at i:17608975 original size:19 final size:20
Alignment explanation
Indices: 17608951--17608988 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17608941 TGTTATGGTT
17608951 TAGGG-TTAAGGTTTTAAAG
1 TAGGGTTTAAGGTTTTAAAG
*
17608970 TAGGGTTTAGGGTTTTAAA
1 TAGGGTTTAAGGTTTTAAA
17608989 ATTTAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (20 bp):
TAGGGTTTAAGGTTTTAAAG
Found at i:17621172 original size:31 final size:31
Alignment explanation
Indices: 17621134--17621199 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
17621124 ACGATGAAAA
*
17621134 TTATCTTATTAAAGCTTATATGCCACATGAC
1 TTATCTTATTAAAGCTTATACGCCACATGAC
17621165 TTATCTTATTAAAGCTTATACGCCACATGAC
1 TTATCTTATTAAAGCTTATACGCCACATGAC
17621196 TTAT
1 TTAT
17621200 ACTTTATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (31 bp):
TTATCTTATTAAAGCTTATACGCCACATGAC
Found at i:17622559 original size:8 final size:8
Alignment explanation
Indices: 17622546--17622571 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17622536 GATAGAGAGA
17622546 AAAAAAAT
1 AAAAAAAT
17622554 AAAAAAAT
1 AAAAAAAT
17622562 AAAAAAAT
1 AAAAAAAT
17622570 AA
1 AA
17622572 TTATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17628490 original size:11 final size:11
Alignment explanation
Indices: 17628474--17628503 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
17628464 GTGAGATTAT
17628474 ATACTGTAACG
1 ATACTGTAACG
17628485 ATACTGTAACG
1 ATACTGTAACG
17628496 ATACTGTA
1 ATACTGTA
17628504 GCATGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (11 bp):
ATACTGTAACG
Found at i:17628967 original size:18 final size:18
Alignment explanation
Indices: 17628933--17628967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17628923 GTTATTATTA
*
17628933 AGGTTTGCACAACAACAT
1 AGGTTTGCACAAAAACAT
*
17628951 AGGTTTGCATAAAAACA
1 AGGTTTGCACAAAAACA
17628968 CAATTGCACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (18 bp):
AGGTTTGCACAAAAACAT
Found at i:17633436 original size:14 final size:14
Alignment explanation
Indices: 17633417--17633446 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17633407 CATAAGATAC
17633417 AATAAAGTAAATAA
1 AATAAAGTAAATAA
17633431 AATAAAGTAAATAA
1 AATAAAGTAAATAA
17633445 AA
1 AA
17633447 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAGTAAATAA
Found at i:17633464 original size:18 final size:18
Alignment explanation
Indices: 17633433--17633487 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
17633423 GTAAATAAAA
*
17633433 TAAAGTAAATAAAAGAAAC
1 TAAAG-AAAGAAAAGAAAC
*
17633452 TAAAGAAAGAAAAGAAAG
1 TAAAGAAAGAAAAGAAAC
*
17633470 AAAAG-AAGTAAAAGAAAC
1 TAAAGAAAG-AAAAGAAAC
17633488 AAAAAGAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 23 0.74
19 5 0.16
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.09
Consensus pattern (18 bp):
TAAAGAAAGAAAAGAAAC
Done.