Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 32 of 91
Found at i:11194515 original size:15 final size:15
Alignment explanation
Indices: 11194477--11194516 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
11194467 GAGATTTTGG
*
11194477 TTTTAAAGCTTTAGA
1 TTTTAAAGTTTTAGA
**
11194492 TTTTAAAGTTTTTTA
1 TTTTAAAGTTTTAGA
11194507 TTTTAAAGTT
1 TTTTAAAGTT
11194517 GCTTTAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (15 bp):
TTTTAAAGTTTTAGA
Found at i:11196908 original size:28 final size:28
Alignment explanation
Indices: 11196877--11196935 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
11196867 TTTGGAGCAT
* *
11196877 AGGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGGCAAAATGATAATTTT-CCACCACC
*
11196905 AGGGGCAAAATTATAATTTTCCACCACC
1 AGGGGCAAAATGATAATTTTCCACCACC
11196933 AGG
1 AGG
11196936 ACATTTGTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (28 bp):
AGGGGCAAAATGATAATTTTCCACCACC
Found at i:11204020 original size:31 final size:31
Alignment explanation
Indices: 11203979--11204085 Score: 133
Period size: 31 Copynumber: 3.5 Consensus size: 31
11203969 ATGGTTTGAC
* * *
11203979 CCCCATTGCACCTTAGGCTAGCAATGTATAT
1 CCCCATTGCACCTTAGGTTGGCAATGTACAT
* **
11204010 CCCCACTGCACCTTAGGTTGGGGATGTACAT
1 CCCCATTGCACCTTAGGTTGGCAATGTACAT
* * *
11204041 CCCTATTGCACCTTAAGTTGGCAACGTACAT
1 CCCCATTGCACCTTAGGTTGGCAATGTACAT
11204072 CCCCATTGCACCTT
1 CCCCATTGCACCTT
11204086 GAGCTGCATT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (31 bp):
CCCCATTGCACCTTAGGTTGGCAATGTACAT
Found at i:11204291 original size:68 final size:68
Alignment explanation
Indices: 11204214--11204548 Score: 411
Period size: 68 Copynumber: 4.9 Consensus size: 68
11204204 CGGATACATG
* * * * *
11204214 CTTACTCATCTCATAAGATATATGGAATTTACATCATGTACATAATCTCATGGCATTTATCATGC
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
* *
11204279 TTG
66 ATA
* * * * *
11204282 CTTAATCATCTCATGTAGTATATGCAATATACATCATATACATAATCTCATGGCATTAATCGTGC
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
11204347 ATA
66 ATA
* * * * *
11204350 CTTAATCACCTCATGTGGTATATGGAATATACATCATAAACAAAATCTCATGGCATTAATCATGC
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
11204415 ATA
66 ATA
* * * * * *
11204418 CTTAATCACCTCATATGGTATATGGAATTTACATCATATACACAATCTTATAGTA-TACATCATT
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTA-ATCATG
11204482 CATA
65 CATA
* * * *
11204486 CTTGATCATCTCATATGGTATATGGAATTTACATCATACACATAATCTTATGGCATTCATCAT
1 CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCAT
11204549 ACCCAACATG
Statistics
Matches: 232, Mismatches: 33, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
67 2 0.01
68 229 0.99
69 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (68 bp):
CTTAATCATCTCATATGGTATATGGAATTTACATCATATACATAATCTCATGGCATTAATCATGC
ATA
Found at i:11205772 original size:16 final size:16
Alignment explanation
Indices: 11205747--11205778 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11205737 ATAAAAATAT
11205747 CAAAAAAATCAAAATC
1 CAAAAAAATCAAAATC
*
11205763 CAAAAGAATCAAAATC
1 CAAAAAAATCAAAATC
11205779 TAAGTTTTGG
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:0.66, C:0.19, G:0.03, T:0.12
Consensus pattern (16 bp):
CAAAAAAATCAAAATC
Found at i:11207265 original size:55 final size:54
Alignment explanation
Indices: 11207178--11207332 Score: 194
Period size: 55 Copynumber: 2.9 Consensus size: 54
11207168 ATGTATACAA
* * *
11207178 CCACCAGTTATCAGCTCATGTACACTCTCACACCGCACATAGCTGGAATCATCAC
1 CCACCA-TCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
*
11207233 CCACCGATCATCAGCTCATGTGCACTCCCACACCGTACATAGCTGG-A--ATCAC
1 CCACC-ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
* * *
11207285 CCATCATCA-CCG-GCATGTGCACTCCCACACCGCACATAGCTGGAATCA
1 CCACCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCA
11207333 CCCATTATCA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
49 29 0.33
50 3 0.03
51 4 0.05
52 10 0.11
54 1 0.01
55 40 0.45
56 1 0.01
ACGTcount: A:0.28, C:0.38, G:0.15, T:0.19
Consensus pattern (54 bp):
CCACCATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGAATCATCAC
Found at i:11207305 original size:49 final size:49
Alignment explanation
Indices: 11207249--11207369 Score: 206
Period size: 49 Copynumber: 2.5 Consensus size: 49
11207239 ATCATCAGCT
*
11207249 CATGTGCACTCCCACACCGTACATAGCTGGAATCACCCATCATCACCGG
1 CATGTGCACTCCCACACCGCACATAGCTGGAATCACCCATCATCACCGG
*
11207298 CATGTGCACTCCCACACCGCACATAGCTGGAATCACCCATTATCACCGG
1 CATGTGCACTCCCACACCGCACATAGCTGGAATCACCCATCATCACCGG
* *
11207347 CATGTGCACTCTCACACCTCACA
1 CATGTGCACTCCCACACCGCACA
11207370 CGCGCAGTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.26, C:0.40, G:0.15, T:0.19
Consensus pattern (49 bp):
CATGTGCACTCCCACACCGCACATAGCTGGAATCACCCATCATCACCGG
Found at i:11208161 original size:19 final size:19
Alignment explanation
Indices: 11208137--11208174 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
11208127 CCATTTGATT
11208137 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
11208156 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
11208175 GTTTATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:11210400 original size:20 final size:21
Alignment explanation
Indices: 11210371--11210416 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11210361 TTTATTAAGT
*
11210371 ATTATTATTTTA-TTCAAACA
1 ATTATAATTTTATTTCAAACA
*
11210391 ATTATAATTTTATTTCAAATA
1 ATTATAATTTTATTTCAAACA
11210412 ATTAT
1 ATTAT
11210417 TTTAGACATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATAATTTTATTTCAAACA
Found at i:11214026 original size:25 final size:27
Alignment explanation
Indices: 11213977--11214032 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
11213967 TTTTTTATGT
*
11213977 TTTTAGGTTAGTTTATTTTCATT-AAA
1 TTTTAGGTCAGTTTATTTTCATTAAAA
**
11214003 TTTT-GGTCAGTTTATTTTTGTTAAAA
1 TTTTAGGTCAGTTTATTTTCATTAAAA
11214029 TTTT
1 TTTT
11214033 TGTTCATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.23, C:0.04, G:0.12, T:0.61
Consensus pattern (27 bp):
TTTTAGGTCAGTTTATTTTCATTAAAA
Found at i:11216091 original size:71 final size:72
Alignment explanation
Indices: 11215927--11216106 Score: 206
Period size: 71 Copynumber: 2.5 Consensus size: 72
11215917 AAGATCATAA
* * * ** *
11215927 AGCCCTAGTCGACTA-GAGAGGAAGCACAGTCGACCCCATCCCAAAAAGATCAAGAAAATCAACT
1 AGCCATAGTCGACTACTAGAGGAAGCATAGTCGACCCTGTCCCAAAAAGATCAAGAAAACCAACT
*
11215991 TCAAAAT
66 TCAAAAC
* *
11215998 AGCCATAGTCGACTACTA-AGGAAGCATAGTCGACCCTGTTCCAAAAAGATCAAGAAAACCAAGT
1 AGCCATAGTCGACTACTAGAGGAAGCATAGTCGACCCTGTCCCAAAAAGATCAAGAAAACCAACT
*
11216062 TTAAAAC
66 TCAAAAC
* * *
11216069 AGCCATAGTTGA-TGAC-AGAGGAAGTATAGTCAACCCTG
1 AGCCATAGTCGACT-ACTAGAGGAAGCATAGTCGACCCTG
11216107 ACAAGTCAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
70 2 0.02
71 90 0.97
72 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (72 bp):
AGCCATAGTCGACTACTAGAGGAAGCATAGTCGACCCTGTCCCAAAAAGATCAAGAAAACCAACT
TCAAAAC
Found at i:11216304 original size:21 final size:21
Alignment explanation
Indices: 11216278--11216327 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
11216268 TTGAAGAACA
11216278 TAGTCGACCCTAAAAGCATTG
1 TAGTCGACCCTAAAAGCATTG
* *
11216299 TAGTCGACCCTAAGAGCGTTG
1 TAGTCGACCCTAAAAGCATTG
11216320 TAGTCGAC
1 TAGTCGAC
11216328 TCTGAAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TAGTCGACCCTAAAAGCATTG
Found at i:11217029 original size:14 final size:14
Alignment explanation
Indices: 11217012--11217038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11217002 CAAATTTAAT
11217012 TAATTAACTAAAAC
1 TAATTAACTAAAAC
11217026 TAATTAACTAAAA
1 TAATTAACTAAAA
11217039 TTTAAAATAA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:11220532 original size:22 final size:22
Alignment explanation
Indices: 11220507--11220578 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
11220497 ATTATTTAAT
* *
11220507 TTAATCGATTAGGCCTAATAAC
1 TTAATCAATTAGGCCCAATAAC
* * * *
11220529 TTAATTAATTAAGCCCAACAATT
1 TTAATCAATTAGGCCCAATAA-C
11220552 TTAATCAATTAGGCCCAATAAC
1 TTAATCAATTAGGCCCAATAAC
11220574 TTAAT
1 TTAAT
11220579 TAAACAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 21 0.54
23 18 0.46
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (22 bp):
TTAATCAATTAGGCCCAATAAC
Found at i:11220597 original size:35 final size:35
Alignment explanation
Indices: 11220545--11220655 Score: 138
Period size: 35 Copynumber: 3.2 Consensus size: 35
11220535 AATTAAGCCC
*
11220545 AACAATTTTAATCAATTAGGCCCAATAACTTAATTA
1 AACAA-TTTAATTAATTAGGCCCAATAACTTAATTA
* *
11220581 AACAATTTAATTAATTAGGCCCAATGATTTAATTA
1 AACAATTTAATTAATTAGGCCCAATAACTTAATTA
* * *
11220616 AACAATTTAGTTAATTAAG--C-ACAACTTAATTA
1 AACAATTTAATTAATTAGGCCCAATAACTTAATTA
11220648 AACAATTT
1 AACAATTT
11220656 TAATCAAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
32 17 0.25
33 1 0.01
35 44 0.66
36 5 0.07
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (35 bp):
AACAATTTAATTAATTAGGCCCAATAACTTAATTA
Found at i:11224227 original size:20 final size:20
Alignment explanation
Indices: 11224202--11224247 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
11224192 TTTTGGCCTC
11224202 ATTTGACTTATTGGAGTATA-
1 ATTTGACTTATTGGAGT-TAG
*
11224222 ATTTGACTTATTTGAGTTAG
1 ATTTGACTTATTGGAGTTAG
11224242 ATTTGA
1 ATTTGA
11224248 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTTAG
Found at i:11255735 original size:19 final size:19
Alignment explanation
Indices: 11255711--11255760 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
11255701 TTTTCTTTCG
11255711 ATTTAAAGCTTCCCTTCCA
1 ATTTAAAGCTTCCCTTCCA
11255730 ATTTAAAGCTTCCCTTCCA
1 ATTTAAAGCTTCCCTTCCA
11255749 ATTTAAAGCTTC
1 ATTTAAAGCTTC
11255761 ATCCTATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.38
Consensus pattern (19 bp):
ATTTAAAGCTTCCCTTCCA
Found at i:11257973 original size:20 final size:20
Alignment explanation
Indices: 11257950--11257989 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11257940 ATTAAACTTA
*
11257950 AAACTAAAACTAAAACTAAT
1 AAACTAAAAATAAAACTAAT
*
11257970 AAACTAAAAATAAAATTAAT
1 AAACTAAAAATAAAACTAAT
11257990 CTAAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (20 bp):
AAACTAAAAATAAAACTAAT
Found at i:11260247 original size:23 final size:23
Alignment explanation
Indices: 11260217--11260276 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
11260207 TGAGCTGGTG
* * *
11260217 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGC
11260240 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGC
*
11260263 ATGATAATGATGGG
1 ATGATGATGATGGG
11260277 TATACGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGC
Found at i:11263124 original size:35 final size:35
Alignment explanation
Indices: 11263053--11263301 Score: 261
Period size: 35 Copynumber: 7.1 Consensus size: 35
11263043 CACTTGATTA
* * *
11263053 AAATTGTTTAATTAA---ATTGTGCCTTATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
11263085 AAATTGTTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11263120 AAATTATTTAATTAAGTCATTAGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * * *
11263155 AAATTAAATAATTAAGTTATTGTGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11263190 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** **
11263226 AAAATTGTTTAATTAAATTGTTGGGTTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* * *
11263262 AAATTGTTTAATTAAGTTATTGAGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
11263297 AAATT
1 AAATT
11263302 AAACAATTAA
Statistics
Matches: 181, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
32 15 0.08
35 112 0.62
36 51 0.28
37 3 0.02
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:11263274 original size:107 final size:106
Alignment explanation
Indices: 11263053--11263301 Score: 308
Period size: 107 Copynumber: 2.4 Consensus size: 106
11263043 CACTTGATTA
* * *
11263053 AAATTGTTTAATTAA---ATTGTGCCTTATTAACTAAA-TTGTTTAATTAAATCATTGGGCCTAA
1 AAATTGTTTAATTAAGTTATTGTGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
*
11263114 TTAATTAAATTATTTAATTAAGTCATTAGGCCTAATTAATT
66 TTAATTAAATTATTTAATTAAATCATTAGGCCTAATTAATT
*** * *
11263155 AAATTAAATAATTAAGTTATTGTGCCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAG
1 AAATTGTTTAATTAAGTTATTGTGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
* * ** * **
11263220 TTGATTAAAATTGTTTAATTAAATTGTTGGGTTTAATTAATT
66 TTAATT-AAATTATTTAATTAAATCATTAGGCCTAATTAATT
*
11263262 AAATTGTTTAATTAAGTTATTGAGCCTAATTGATTAAATT
1 AAATTGTTTAATTAAGTTATTGTGCCTAATTGATTAAATT
11263302 AAACAATTAA
Statistics
Matches: 122, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
102 12 0.10
105 17 0.14
106 29 0.24
107 64 0.52
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (106 bp):
AAATTGTTTAATTAAGTTATTGTGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
TTAATTAAATTATTTAATTAAATCATTAGGCCTAATTAATT
Found at i:11264021 original size:144 final size:144
Alignment explanation
Indices: 11263835--11264118 Score: 498
Period size: 144 Copynumber: 2.0 Consensus size: 144
11263825 ATCATATACT
*
11263835 TTTATTTTAATTTAATTCTGTACTCAATTTGGCATGAAAGAGATCCTAGGAAGGTGAGGTGTAAA
1 TTTATTTTAATTTAATTCTGTACTCAAGTTGGCATGAAAGAGATCCTAGGAAGGTGAGGTGTAAA
*
11263900 TTTAATTTTTAAATTTATTT-TCGCTGCATTTTATTCGTATATGATGCATGATCAACCCTCACCC
66 TTTAATTTTTAAATTTATTTCT-ACTGCATTTTATTCGTATATGATGCATGATCAACCCTCACCC
11263964 AACAATGGTATCAAC
130 AACAATGGTATCAAC
*
11263979 TTTATTTTAATTTAATTCTGTACTCGAGTTGGCATGAAAGAGATCCTAGGAAGGTGAGGTGTAAA
1 TTTATTTTAATTTAATTCTGTACTCAAGTTGGCATGAAAGAGATCCTAGGAAGGTGAGGTGTAAA
* * *
11264044 TTTAATTTTTAAATTTATTTCTACTGCATTTTATTTGTATATGATGCATGATCAGCCTTCACCCA
66 TTTAATTTTTAAATTTATTTCTACTGCATTTTATTCGTATATGATGCATGATCAACCCTCACCCA
11264109 ACAATGGTAT
131 ACAATGGTAT
11264119 TGTAGACACT
Statistics
Matches: 133, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
144 132 0.99
145 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (144 bp):
TTTATTTTAATTTAATTCTGTACTCAAGTTGGCATGAAAGAGATCCTAGGAAGGTGAGGTGTAAA
TTTAATTTTTAAATTTATTTCTACTGCATTTTATTCGTATATGATGCATGATCAACCCTCACCCA
ACAATGGTATCAAC
Found at i:11265258 original size:18 final size:18
Alignment explanation
Indices: 11265233--11265275 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11265223 TAATGATACA
11265233 AAAAAAATGA-ATGATGAT
1 AAAAAAATGAGATGA-GAT
*
11265251 AAAAAAATGAGATTAGAT
1 AAAAAAATGAGATGAGAT
11265269 AAAAAAA
1 AAAAAAA
11265276 AAAGAGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (18 bp):
AAAAAAATGAGATGAGAT
Found at i:11265275 original size:21 final size:18
Alignment explanation
Indices: 11265224--11265278 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
11265214 TAGGATATTT
*
11265224 AATGATACAAAAAAAATG
1 AATGATAAAAAAAAAATG
* *
11265242 AATGATGATAAAAAAATG
1 AATGATAAAAAAAAAATG
11265260 AGATTAGATAAAAAAAAAA
1 A-A-T-GATAAAAAAAAAA
11265279 GAGTATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 16 0.55
19 1 0.03
20 1 0.03
21 11 0.38
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.18
Consensus pattern (18 bp):
AATGATAAAAAAAAAATG
Found at i:11266263 original size:27 final size:26
Alignment explanation
Indices: 11266233--11266327 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 26
11266223 GTAAAGTATG
11266233 AAAAAATAATAACTAAAAATAAAATAA
1 AAAAAATAATAA-TAAAAATAAAATAA
11266260 AAAATATGATAATAA-AAAAATAAAATAAA
1 AAAA-A--ATAATAATAAAAATAAAAT-AA
*
11266289 ATAAAAATAATAATTAAATAATAATAACTGA
1 A-AAAAATAATAA-TAAA-AATAA-AA-TAA
11266320 AAAAAATA
1 AAAAAATA
11266328 GGTAATTGCA
Statistics
Matches: 57, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
27 11 0.19
28 12 0.21
29 7 0.12
30 22 0.39
31 4 0.07
32 1 0.02
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (26 bp):
AAAAAATAATAATAAAAATAAAATAA
Found at i:11266311 original size:14 final size:14
Alignment explanation
Indices: 11266236--11266315 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 14
11266226 AAGTATGAAA
11266236 AAATAATAACT-AA-
1 AAATAATAA-TAAAT
11266249 AAATAA-AATAAA-
1 AAATAATAATAAAT
*
11266261 AAATATGATAATAAAA
1 AAATA--ATAATAAAT
11266277 AAATAA-AATAAAAT
1 AAATAATAAT-AAAT
*
11266291 AAA-AATAATAATT
1 AAATAATAATAAAT
11266304 AAATAATAATAA
1 AAATAATAATAA
11266316 CTGAAAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
11 1 0.02
12 9 0.16
13 17 0.30
14 19 0.33
15 6 0.11
16 5 0.09
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (14 bp):
AAATAATAATAAAT
Found at i:11266315 original size:33 final size:34
Alignment explanation
Indices: 11266236--11266315 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
11266226 AAGTATGAAA
11266236 AAATAATAACTAAAAATAAAATAAAAAATATGATAAT
1 AAATAATAA-T-AAAATAAAATAAAAAATA-GATAAT
11266273 AAA-AA-AATAAAATAAAAT-AAAAATA-ATAATT
1 AAATAATAATAAAATAAAATAAAAAATAGATAA-T
11266304 AAATAATAATAA
1 AAATAATAATAA
11266316 CTGAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 15 0.38
34 1 0.03
35 2 0.05
36 2 0.05
37 3 0.08
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.24
Consensus pattern (34 bp):
AAATAATAATAAAATAAAATAAAAAATAGATAAT
Found at i:11278202 original size:37 final size:38
Alignment explanation
Indices: 11278161--11278412 Score: 269
Period size: 37 Copynumber: 6.7 Consensus size: 38
11278151 AAAAAAAAGN
*
11278161 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGT-TCG
1 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
* * *
11278198 TTGCCTCAGCTTTGAAGAGTTCACTTTTAAAAATCTCA
1 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
** * *
11278236 TTGCCTCATTTTTGAGGAGTTTA-TTTTAAAAGTGTCA
1 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
*
11278273 TTGCCTCAGCTTTGAAGAGTTCATTTTTAAAAGTCTCA
1 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
** * * *
11278311 TTGCCTCATTTTTTAGGAGTGT-A-TTTTAAAAATGTCA
1 TTGCCTCAGCTTTGAGGAGT-TCATTTTTAAAAGTCTCA
* * * * *
11278348 TTGCCTCAGCTTTGAGAAATTCATTTTTAGAAGTTTCG
1 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
* *
11278386 TTGCCTCAGCTTTAAAGAGTTTCATTT
1 TTGCCTCAGCTTTGAGGAG-TTCATTT
11278413 AAAAAAAAAT
Statistics
Matches: 175, Mismatches: 34, Indels: 10
0.80 0.16 0.05
Matches are distributed among these distances:
36 1 0.01
37 90 0.51
38 76 0.43
39 8 0.05
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (38 bp):
TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCA
Found at i:11278241 original size:75 final size:75
Alignment explanation
Indices: 11278161--11278417 Score: 304
Period size: 75 Copynumber: 3.4 Consensus size: 75
11278151 AAAAAAAAGN
* *
11278161 TTGCCTCAGCTTTGAGGAGTTCATTTTTAAAAGT-TCGTTGCCTCAGCTTTGAAGAGTTCACTTT
1 TTGCCTCAGCTTTGAGGAGTTCA-TTTTAAAAGTGTCATTGCCTCAGCTTTGAAGAGTTCATTTT
*
11278225 TAAAAATCTCA
65 TAAAAGTCTCA
** *
11278236 TTGCCTCATTTTTGAGGAGTTTATTTTAAAAGTGTCATTGCCTCAGCTTTGAAGAGTTCATTTTT
1 TTGCCTCAGCTTTGAGGAGTTCATTTTAAAAGTGTCATTGCCTCAGCTTTGAAGAGTTCATTTTT
11278301 AAAAGTCTCA
66 AAAAGTCTCA
** * * *
11278311 TTGCCTCATTTTTTAGGAGTGT-ATTTTAAAAATGTCATTGCCTCAGCTTTG-AGAAATTCATTT
1 TTGCCTCAGCTTTGAGGAGT-TCATTTTAAAAGTGTCATTGCCTCAGCTTTGAAG-AGTTCATTT
* * *
11278374 TTAGAAGTTTCG
64 TTAAAAGTCTCA
* * *
11278386 TTGCCTCAGCTTTAAAGAGTTTCATTTAAAAA
1 TTGCCTCAGCTTTGAGGAG-TTCATTTTAAAA
11278418 AAAATAAAAA
Statistics
Matches: 160, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
74 12 0.08
75 138 0.86
76 10 0.06
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (75 bp):
TTGCCTCAGCTTTGAGGAGTTCATTTTAAAAGTGTCATTGCCTCAGCTTTGAAGAGTTCATTTTT
AAAAGTCTCA
Found at i:11278503 original size:1 final size:1
Alignment explanation
Indices: 11278497--11278567 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
11278487 AGTCTCACTT
* * * * * * * * * *
11278497 AAAAAAAAAAACAAAAAAAAGACAAACAAAAAAAAAAAAACAAAAACAGAAAAAAAATAATAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11278562 AAAAAA
1 AAAAAA
11278568 TTTGGTAAGA
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.07, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:11278532 original size:18 final size:19
Alignment explanation
Indices: 11278497--11278553 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
11278487 AGTCTCACTT
11278497 AAAAAA-AAAAAC--AAAA
1 AAAAAACAAAAACAGAAAA
*
11278513 AAAAGACAAACAA-A-AAAA
1 AAAAAACAAA-AACAGAAAA
11278531 AAAAAACAAAAACAGAAAA
1 AAAAAACAAAAACAGAAAA
11278550 AAAA
1 AAAA
11278554 TAATAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
16 5 0.15
17 5 0.15
18 16 0.47
19 8 0.24
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAACAAAAACAGAAAA
Found at i:11278532 original size:20 final size:20
Alignment explanation
Indices: 11278497--11278553 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
11278487 AGTCTCACTT
* *
11278497 AAAAAAAAAAACAAAAAAAAG
1 AAAAACAAAAA-AAAAAAAAC
*
11278518 ACAAACAAAAAAAAAAAAAC
1 AAAAACAAAAAAAAAAAAAC
*
11278538 AAAAACAGAAAAAAAA
1 AAAAACAAAAAAAAAA
11278554 TAATAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.88, C:0.09, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAACAAAAAAAAAAAAAC
Found at i:11278745 original size:24 final size:25
Alignment explanation
Indices: 11278693--11278745 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
11278683 ATTTTATTAA
*
11278693 AAAAATCATAAACAAAAAATGAATG
1 AAAAATCATAAACAAAAAATGAAAG
*
11278718 -AAAATGATAAA-AAAATAAT-AAAG
1 AAAAATCATAAACAAAA-AATGAAAG
11278741 AAAAA
1 AAAAA
11278746 AAGAGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.15
Consensus pattern (25 bp):
AAAAATCATAAACAAAAAATGAAAG
Found at i:11279342 original size:66 final size:65
Alignment explanation
Indices: 11279210--11279377 Score: 177
Period size: 66 Copynumber: 2.6 Consensus size: 65
11279200 GCCGACGCTG
* * * *
11279210 AAGGGAGACCGATCGACGACTAGA-A-AG--ATAGAGAGAGTGAAAGAGGGAGGATCGATCGGGC
1 AAGGGAGACCGATCG-CGGCTAGAGAGAGAAAGAGAGAGAGTGAAAGAGGGACGATCGATCAGGC
11279271 C
65 C
*
11279272 AAGGGAGACCGGTCGACGG-TCAGAGAGAGAAAGAGAGAGAGTGAAAGAGGGACGA-CTGATCAG
1 AAGGGAGACCGATCG-CGGCT-AGAGAGAGAAAGAGAGAGAGTGAAAGAGGGACGATC-GATCAG
*
11279335 GCT
63 GCC
* * *
11279338 AAGGGAGACTGATCGTGGCTAGAGAGAGAGAGAGAGAGAG
1 AAGGGAGACCGATCGCGGCTAGAGAGAGAAAGAGAGAGAG
11279378 AGAGAGAGAG
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
61 1 0.01
62 20 0.22
63 1 0.01
64 2 0.02
65 22 0.25
66 43 0.48
ACGTcount: A:0.37, C:0.12, G:0.41, T:0.10
Consensus pattern (65 bp):
AAGGGAGACCGATCGCGGCTAGAGAGAGAAAGAGAGAGAGTGAAAGAGGGACGATCGATCAGGCC
Found at i:11279365 original size:2 final size:2
Alignment explanation
Indices: 11279358--11279415 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
11279348 GATCGTGGCT
11279358 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
11279400 AG AG TG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG
11279416 GACCGATCGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:11279930 original size:4 final size:4
Alignment explanation
Indices: 11279923--11279962 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
11279913 ACAAAAAAAA
*
11279923 AATG AATG -ATG AATG GATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG A
11279963 TGATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:11280929 original size:28 final size:28
Alignment explanation
Indices: 11280894--11280957 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
11280884 ATAGATTAAT
11280894 AAATATCATGTAAAAATGATAAGATAAG
1 AAATATCATGTAAAAATGATAAGATAAG
11280922 AAATATCATGTAAAAATGATAAGATAAG
1 AAATATCATGTAAAAATGATAAGATAAG
11280950 AAATATCA
1 AAATATCA
11280958 AGGAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.58, C:0.05, G:0.12, T:0.25
Consensus pattern (28 bp):
AAATATCATGTAAAAATGATAAGATAAG
Found at i:11281075 original size:17 final size:16
Alignment explanation
Indices: 11281017--11281084 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
11281007 TAATAACTAG
11281017 AAATAAAATAGAAAATA
1 AAATAAAAT-GAAAATA
** *
11281034 TGATAATAA-AAAAATA
1 AAATAA-AATGAAAATA
11281050 AAATAAAATGAAAATA
1 AAATAAAATGAAAATA
*
11281066 ATAATTAAAT-AATAATA
1 A-AATAAAATGAA-AATA
11281083 AA
1 AA
11281085 TGAAAAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
15 2 0.05
16 20 0.50
17 16 0.40
18 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (16 bp):
AAATAAAATGAAAATA
Found at i:11281075 original size:27 final size:27
Alignment explanation
Indices: 11281036--11281095 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
11281026 AGAAAATATG
11281036 ATAATAAAAAAATAA-AATAAAATGAAA
1 ATAATAAAAAAATAATAAT-AAATGAAA
**
11281063 ATAATAATTAAATAATAATAAATGAAA
1 ATAATAAAAAAATAATAATAAATGAAA
*
11281090 AAAATA
1 ATAATA
11281096 GATAATTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (27 bp):
ATAATAAAAAAATAATAATAAATGAAA
Found at i:11281083 original size:33 final size:34
Alignment explanation
Indices: 11281004--11281084 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 34
11280994 AAGTATGAAA
11281004 AAATAATAACTAGAAATAAAATAGAAAATATGATAAT
1 AAATAATAA-TA-AAATAAAATAGAAAATA-GATAAT
11281041 AAA-AA-AATAAAATAAAAT-GAAAATA-ATAATT
1 AAATAATAATAAAATAAAATAGAAAATAGATAA-T
11281072 AAATAATAATAAA
1 AAATAATAATAAA
11281085 TGAAAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 15 0.37
34 2 0.05
35 2 0.05
36 2 0.05
37 3 0.07
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (34 bp):
AAATAATAATAAAATAAAATAGAAAATAGATAAT
Found at i:11285720 original size:14 final size:14
Alignment explanation
Indices: 11285701--11285727 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11285691 TTATGTTCGT
11285701 TTGATCAAAAGGTA
1 TTGATCAAAAGGTA
11285715 TTGATCAAAAGGT
1 TTGATCAAAAGGT
11285728 TGAATATTGA
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:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (14 bp):
TTGATCAAAAGGTA
Found at i:11287625 original size:35 final size:35
Alignment explanation
Indices: 11287555--11287803 Score: 279
Period size: 35 Copynumber: 7.1 Consensus size: 35
11287545 CACTTGATTA
* * *
11287555 AAATTATTTAATTAAG---TTGTGCCTAATTAACT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*
11287587 AAATTGTTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11287622 AAATTATTTAATTAAGTCATTGGGCCTAATCAATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
*** * *
11287657 AAATTAAATAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11287692 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATT
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTAATT
* ** * *
11287728 AAAATTGTTTAATTAAATTGTTGAGCTTAATTAATT
1 -AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
* *
11287764 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
11287799 AAATT
1 AAATT
11287804 AAACAATTAA
Statistics
Matches: 183, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
32 14 0.08
35 114 0.62
36 52 0.28
37 3 0.02
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:11287771 original size:71 final size:71
Alignment explanation
Indices: 11287555--11287801 Score: 288
Period size: 71 Copynumber: 3.5 Consensus size: 71
11287545 CACTTGATTA
* * * * *
11287555 AAATTATTTAATTAAG---TTGTGCCTAATTAACT-AAATTGTTTAATTAAATCATTGGGCCTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTGGGCCTAA
11287616 TTAATT
66 TTAATT
* ** *** *
11287622 AAATTATTTAATTAAGTCATTGGGCCTAATCAATT-AAATTAAATAATTAAGTTATTGGGCCTAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTGGGCCTAA
*
11287686 TTGATT
66 TTAATT
* * * *
11287692 AAATTTGTTTAATTAAGTCATTGGGCCTAGTTGATTAAAATTGTTTAATTAAATTGTTGAGCTTA
1 AAA-TTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTGGGCCTA
11287757 ATTAATT
65 ATTAATT
*
11287764 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAA
1 AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAA
11287802 TTAAACAATT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
67 16 0.11
70 45 0.30
71 61 0.40
72 30 0.20
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (71 bp):
AAATTGTTTAATTAAGTCATTGGGCCTAATTGATTAAAATTGTTTAATTAAATTATTGGGCCTAA
TTAATT
Found at i:11287778 original size:107 final size:106
Alignment explanation
Indices: 11287555--11287803 Score: 317
Period size: 107 Copynumber: 2.4 Consensus size: 106
11287545 CACTTGATTA
* * *
11287555 AAATTATTTAATTAAG---TTGTGCCTAATTAACTAAA-TTGTTTAATTAAATCATTGGGCCTAA
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
* *
11287616 TTAATTAAATTATTTAATTAAGTCATTGGGCCTAATCAATT
66 TTAATTAAATTATTTAATTAAATCATTGAGCCTAATCAATT
** * *
11287657 AAATTAAATAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAGTCATTGGGCCTAG
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
* * ** * *
11287722 TTGATTAAAATTGTTTAATTAAATTGTTGAGCTTAATTAATT
66 TTAATT-AAATTATTTAATTAAATCATTGAGCCTAATCAATT
*
11287764 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
11287804 AAACAATTAA
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
102 14 0.11
105 16 0.13
106 29 0.23
107 65 0.52
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.43
Consensus pattern (106 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATTAAATCATTGGGCCTAA
TTAATTAAATTATTTAATTAAATCATTGAGCCTAATCAATT
Found at i:11293220 original size:35 final size:36
Alignment explanation
Indices: 11293181--11293278 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 36
11293171 TGATGTGGGT
*
11293181 GGGAGTGCGTG-TGATGATATTGAAATGTGCT-AGTA
1 GGGAGTGCATGATGATGATATTGAAATGTG-TGAGTA
11293216 GGGAGTGCACATGATGATGATATTGAAATGTGTGAGTA
1 GGGAGTG--CATGATGATGATATTGAAATGTGTGAGTA
11293254 GGGAGTGCACATGATGATGATATTG
1 GGGAGTG--CATGATGATGATATTG
11293279 CCTTTCGCGT
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
35 7 0.12
37 4 0.07
38 47 0.81
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (36 bp):
GGGAGTGCATGATGATGATATTGAAATGTGTGAGTA
Found at i:11293243 original size:38 final size:38
Alignment explanation
Indices: 11293192--11293278 Score: 158
Period size: 38 Copynumber: 2.3 Consensus size: 38
11293182 GGAGTGCGTG
11293192 TGATGATATTGAAATGTGCT-AGTAGGGAGTGCACATGA
1 TGATGATATTGAAATGTG-TGAGTAGGGAGTGCACATGA
11293230 TGATGATATTGAAATGTGTGAGTAGGGAGTGCACATGA
1 TGATGATATTGAAATGTGTGAGTAGGGAGTGCACATGA
11293268 TGATGATATTG
1 TGATGATATTG
11293279 CCTTTCGCGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 1 0.02
38 47 0.98
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (38 bp):
TGATGATATTGAAATGTGTGAGTAGGGAGTGCACATGA
Found at i:11293463 original size:24 final size:23
Alignment explanation
Indices: 11293431--11293477 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
11293421 AGTTGTTCCG
* *
11293431 AAATTGCTTTTTATTTCAACAAGA
1 AAATGGCTTTTGATTT-AACAAGA
11293455 AAATGGCTTTTGATTTAACAAGA
1 AAATGGCTTTTGATTTAACAAGA
11293478 CCCCTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (23 bp):
AAATGGCTTTTGATTTAACAAGA
Found at i:11297666 original size:42 final size:42
Alignment explanation
Indices: 11297614--11297761 Score: 147
Period size: 42 Copynumber: 3.5 Consensus size: 42
11297604 TGTTGTGTAA
* *
11297614 TGATATTGACCCAACTATGTGCGAGTAGGAGTGCGTATAAGC
1 TGATGTTGACCCAACTATGTGCGAGTAGGAGTGCGCATAAGC
*** * *
11297656 TGATGTTGACCTGGCTATGTGCGAGT-GGAAATGCACATAAGC
1 TGATGTTGACCCAACTATGTGCGAGTAGG-AGTGCGCATAAGC
* * * *
11297698 CGATGCTGACCCGACTATGTGCGAGTAAGAGTGCGCATAAG-
1 TGATGTTGACCCAACTATGTGCGAGTAGGAGTGCGCATAAGC
* *
11297739 TCGATGTTGACCCAGCCATGTGC
1 T-GATGTTGACCCAACTATGTGC
11297762 TAGTGGGGAG
Statistics
Matches: 84, Mismatches: 19, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.02
42 81 0.96
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (42 bp):
TGATGTTGACCCAACTATGTGCGAGTAGGAGTGCGCATAAGC
Found at i:11297822 original size:2 final size:2
Alignment explanation
Indices: 11297817--11297856 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
11297807 ATGGTGATGG
* *
11297817 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11297857 GTGTATTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:11300647 original size:73 final size:72
Alignment explanation
Indices: 11300528--11300709 Score: 183
Period size: 73 Copynumber: 2.5 Consensus size: 72
11300518 GTAAAATGCT
* * * **
11300528 CTTAGTCGACTAATTTATGTCTTAGTTGACTAAGTTGTCTCTATTTT-CTGTTTCCA-ATTTCTG
1 CTTAGTCGACTAACTTAT-TCTTGGTTGACTAAGTCGTCTCTATTTTGAAG-TT-CAGATTTCTG
11300591 ATAGTGAGC-A
63 ATAGT-AGCTA
* *
11300601 CTTAGTCGACTAACTTACTTCTTGGTTAACTAAGTCGAT-TCTATTTTGAAGTTCAGATTTCTGG
1 CTTAGTCGACTAACTTA-TTCTTGGTTGACTAAGTCG-TCTCTATTTTGAAGTTCAGATTTCTGA
*
11300665 TAGTAGCTT
64 TAGTAGCTA
**
11300674 CTTAGTCGACTAACCCATTTCTTGGTTGACTAAGTC
1 CTTAGTCGACTAACTTA-TTCTTGGTTGACTAAGTC
11300710 TTTTCTGTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
72 5 0.05
73 84 0.91
74 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (72 bp):
CTTAGTCGACTAACTTATTCTTGGTTGACTAAGTCGTCTCTATTTTGAAGTTCAGATTTCTGATA
GTAGCTA
Found at i:11306758 original size:18 final size:19
Alignment explanation
Indices: 11306717--11306758 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
11306707 TCTACGCCCT
*
11306717 ACTCACTGAGTCAATGATT
1 ACTCACTGAGTCAATGATG
*
11306736 A-TCACTGAGTCTATGA-G
1 ACTCACTGAGTCAATGATG
11306753 ACTCAC
1 ACTCAC
11306759 ACCTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (19 bp):
ACTCACTGAGTCAATGATG
Found at i:11319523 original size:22 final size:22
Alignment explanation
Indices: 11319498--11319542 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
11319488 AAAGGAAAAC
11319498 ATGTGGACCAAAAGCTCTATAG
1 ATGTGGACCAAAAGCTCTATAG
*
11319520 ATGTGGACCAAAAGTTCTATAG
1 ATGTGGACCAAAAGCTCTATAG
11319542 A
1 A
11319543 GATATCTTAT
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:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (22 bp):
ATGTGGACCAAAAGCTCTATAG
Found at i:11320429 original size:14 final size:15
Alignment explanation
Indices: 11320397--11320429 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11320387 CCTCTGAATC
*
11320397 TAAAAACATGAAGTT
1 TAAAAACATGAAGTA
11320412 TAAAAACATG-AGTA
1 TAAAAACATGAAGTA
11320426 TAAA
1 TAAA
11320430 CTTAGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (15 bp):
TAAAAACATGAAGTA
Found at i:11320915 original size:22 final size:22
Alignment explanation
Indices: 11320890--11320945 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
11320880 GAGTTTCTCG
11320890 CTGCAGCGAGAATCCATTTTCA
1 CTGCAGCGAGAATCCATTTTCA
* * *
11320912 CTGCAGCGAGAATTCTTTTTCG
1 CTGCAGCGAGAATCCATTTTCA
11320934 CTGCAGCGAGAA
1 CTGCAGCGAGAA
11320946 ACATGGTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CTGCAGCGAGAATCCATTTTCA
Found at i:11321155 original size:26 final size:27
Alignment explanation
Indices: 11321105--11321157 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
11321095 TCATTATTCA
11321105 TTTCAATCACATATTACAATCATAAAC
1 TTTCAATCACATATTACAATCATAAAC
*
11321132 TTTCTATCACATA-TACATAT-ATAAAC
1 TTTCAATCACATATTACA-ATCATAAAC
11321158 ATATATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (27 bp):
TTTCAATCACATATTACAATCATAAAC
Found at i:11321273 original size:43 final size:43
Alignment explanation
Indices: 11321209--11321344 Score: 175
Period size: 43 Copynumber: 3.2 Consensus size: 43
11321199 AGTCAGGTCA
*
11321209 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCTAGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCTGGG
* * * * *
11321252 TCCTCATTGGCTTATGGGCACTCCCTACTCGCACATAACCGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCTGGG
* * *
11321295 TCATCATCAGCTCATGTGCACTCCC-ACATCGCACATAGCTGGG
1 TCATCATCGGCTTATGCGCACTCCCTAC-TCGCACATAGCTGGG
11321338 TCATCAT
1 TCATCAT
11321345 TATCACACAA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 2 0.03
43 77 0.97
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (43 bp):
TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCTGGG
Found at i:11323020 original size:37 final size:37
Alignment explanation
Indices: 11322947--11323020 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
11322937 GTAATGATGT
* *
11322947 TGTCACGATCCAAATTTCGGGCCATAACCGGTGCATG
1 TGTCACGACCCAAATTTCGGGCCATAACCGGCGCATG
* * *
11322984 TGTCACGACCCAAATTTCGGGTCATGACTGGCGCATG
1 TGTCACGACCCAAATTTCGGGCCATAACCGGCGCATG
11323021 GGCCCAATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (37 bp):
TGTCACGACCCAAATTTCGGGCCATAACCGGCGCATG
Found at i:11324295 original size:43 final size:44
Alignment explanation
Indices: 11324194--11324317 Score: 137
Period size: 43 Copynumber: 2.9 Consensus size: 44
11324184 CCCATCATCA
* * * **
11324194 TCATCACCAGCTCATGCGCACTCCCTACTCGCACA-AGGCTGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGACCAGG
*
11324237 TCATCACCGGGTTATGCGCACTCCCTACTCGCACATA-ACCAGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGACCAGG
* * *
11324280 TTATC-CTCGGCTTATGCTCACTCCTTACTCGCACATAG
1 TCATCAC-CGGCTTATGCGCACTCCCTACTCGCACATAG
11324318 CTCAGTTAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.01
43 66 0.97
44 1 0.01
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (44 bp):
TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAGACCAGG
Found at i:11326530 original size:21 final size:21
Alignment explanation
Indices: 11326504--11326546 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11326494 GCTACAGTAA
* **
11326504 CATTCTTGCTGTAGTGAGATT
1 CATTCTCGCTGTAACGAGATT
11326525 CATTCTCGCTGTAACGAGATT
1 CATTCTCGCTGTAACGAGATT
11326546 C
1 C
11326547 CCAGCTAGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (21 bp):
CATTCTCGCTGTAACGAGATT
Found at i:11326923 original size:20 final size:20
Alignment explanation
Indices: 11326898--11326937 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11326888 NNNNNNNCAC
11326898 CACCCTCCCATCATCATGCA
1 CACCCTCCCATCATCATGCA
11326918 CACCCTCCCATCATCATGCA
1 CACCCTCCCATCATCATGCA
11326938 ACGACTTATG
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:0.25, C:0.50, G:0.05, T:0.20
Consensus pattern (20 bp):
CACCCTCCCATCATCATGCA
Found at i:11326982 original size:42 final size:42
Alignment explanation
Indices: 11326935--11327101 Score: 237
Period size: 42 Copynumber: 4.0 Consensus size: 42
11326925 CCATCATCAT
* * **
11326935 GCAACGACTTATGCT-CATTCCTACTCACACATAGCTTGGTCA
1 GCAACGACTTATG-TGCACTCCTACTCGCACATAGCCGGGTCA
11326977 GCAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
1 GCAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
* *
11327019 GCATCGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
1 GCAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
* * *
11327061 GCATCGGCTTATGTGCACTCCTACTCGCACATAGCCAGGTC
1 GCAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTC
11327102 CACATCAACA
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
41 1 0.01
42 116 0.99
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (42 bp):
GCAACGACTTATGTGCACTCCTACTCGCACATAGCCGGGTCA
Found at i:11330254 original size:39 final size:39
Alignment explanation
Indices: 11330164--11330254 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 39
11330154 AAAAGAACAG
* * *
11330164 GAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAA
1 GAAAAAGAAAAAGAATCACCCACAGAAGAGAATGAAAAA
11330203 GAAAAAGAAAAAGAAT-ACACCACAGAAGAGAATGAAAAA
1 GAAAAAGAAAAAGAATCAC-CCACAGAAGAGAATGAAAAA
11330242 GAGAAAA-AAAAAG
1 GA-AAAAGAAAAAG
11330255 GGAAAAAGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.04
39 41 0.87
40 4 0.09
ACGTcount: A:0.65, C:0.11, G:0.19, T:0.05
Consensus pattern (39 bp):
GAAAAAGAAAAAGAATCACCCACAGAAGAGAATGAAAAA
Found at i:11330528 original size:39 final size:39
Alignment explanation
Indices: 11330485--11330575 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
11330475 AAAAGAACAG
* *
11330485 GAAAAAGAAAAACAAT-CACCCACTGAAGAGGATGAAAAA
1 GAAAAAGAAAAACAATACA-CCACAGAAGAGAATGAAAAA
*
11330524 GAAAAAGAAAAAGAATACACCACAGAAGAGAATGAAAAA
1 GAAAAAGAAAAACAATACACCACAGAAGAGAATGAAAAA
*
11330563 GAGAAAAAAAAAA
1 GA-AAAAGAAAAA
11330576 AGGGAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 35 0.76
40 11 0.24
ACGTcount: A:0.66, C:0.11, G:0.18, T:0.05
Consensus pattern (39 bp):
GAAAAAGAAAAACAATACACCACAGAAGAGAATGAAAAA
Found at i:11330534 original size:321 final size:320
Alignment explanation
Indices: 11329951--11330574 Score: 1239
Period size: 321 Copynumber: 1.9 Consensus size: 320
11329941 TCAACAGCTT
11329951 AAAGCTTTGTTAAATCTAGCTAAGGAAATCAAAGTTCTCGAAGTCTTTGTCTTTGCTACAAGTTA
1 AAAGCTTTGTTAAATCTAGCTAAGGAAATCAAAGTTCTCGAAGTCTTTGTCTTTGCTACAAGTTA
11330016 ATAAAGTGAGAGGACTGCTACAGAACAATTTGAAAGTGCTGCTTCTGGTCGTGACAGGTTAATTG
66 ATAAAGTGAGAGGACTGCTACAGAACAATTTGAAAGTGCTGCTTCTGGTCGTGACAGGTTAATTG
11330081 AAAAGGAAATACCTGAAAATTTAAATGTGACTCAAGTTGGAATTAAGGAATCTGAAAAGAAGAAT
131 AAAAGGAAATACCTGAAAATTTAAATGTGACTCAAGTTGGAATTAAGGAATCTGAAAAGAAGAAT
11330146 GCTGAACAAAAAGAACAGGAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAAGAAAAAGA
196 GCTGAACAAAAAGAACAGGAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAAGAAAAAGA
11330211 AAAAGAATACACCACAGAAGAGAATGAAAAAGAGAAAAAAAAAGGGAAAAAGGAAACCCA
261 AAAAGAATACACCACAGAAGAGAATGAAAAAGAGAAAAAAAAAGGGAAAAAGGAAACCCA
11330271 ANAAGCTTTGTTAAATCTAGCTAAGGAAATCAAAGTTCTCGAAGTCTTTGTCTTTGCTACAAGTT
1 A-AAGCTTTGTTAAATCTAGCTAAGGAAATCAAAGTTCTCGAAGTCTTTGTCTTTGCTACAAGTT
11330336 AATAAAGTGAGAGGACTGCTACAGAACAATTTGAAAGTGCTGCTTCTGGTCGTGACAGGTTAATT
65 AATAAAGTGAGAGGACTGCTACAGAACAATTTGAAAGTGCTGCTTCTGGTCGTGACAGGTTAATT
11330401 GAAAAGGAAATACCTGAAAATTTAAATGTGACTCAAGTTGGAATTAAGGAATCTGAAAAGAAGAA
130 GAAAAGGAAATACCTGAAAATTTAAATGTGACTCAAGTTGGAATTAAGGAATCTGAAAAGAAGAA
11330466 TGCTGAACAAAAAGAACAGGAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAAGAAAAAG
195 TGCTGAACAAAAAGAACAGGAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAAGAAAAAG
11330531 AAAAAGAATACACCACAGAAGAGAATGAAAAAGAGAAAAAAAAA
260 AAAAAGAATACACCACAGAAGAGAATGAAAAAGAGAAAAAAAAA
11330575 AAGGGAAAGA
Statistics
Matches: 303, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
320 1 0.00
321 302 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (320 bp):
AAAGCTTTGTTAAATCTAGCTAAGGAAATCAAAGTTCTCGAAGTCTTTGTCTTTGCTACAAGTTA
ATAAAGTGAGAGGACTGCTACAGAACAATTTGAAAGTGCTGCTTCTGGTCGTGACAGGTTAATTG
AAAAGGAAATACCTGAAAATTTAAATGTGACTCAAGTTGGAATTAAGGAATCTGAAAAGAAGAAT
GCTGAACAAAAAGAACAGGAAAAAGAAAAACAATCACCCACTGAAGAGGATGAAAAAGAAAAAGA
AAAAGAATACACCACAGAAGAGAATGAAAAAGAGAAAAAAAAAGGGAAAAAGGAAACCCA
Found at i:11342396 original size:14 final size:15
Alignment explanation
Indices: 11342360--11342397 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
11342350 AGTTTTAATT
**
11342360 ATGGAAAGAATTAAA
1 ATGGAAAGTCTTAAA
11342375 ATGGAAAGTCTTAAA
1 ATGGAAAGTCTTAAA
11342390 A-GGAAAGT
1 ATGGAAAGT
11342398 TTTATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (15 bp):
ATGGAAAGTCTTAAA
Found at i:11343949 original size:43 final size:43
Alignment explanation
Indices: 11343879--11343997 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 43
11343869 GTAATGACAT
* *
11343879 TGACTCGGCTATGTGCGAGTAGGGAGTGTGCATAAGC-CGGGGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAA-CTCGGGGA
* * *
11343922 TGACCCGGTTATGTACGAGTAGGGAGTGCGCATAACTCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACTCGGGGA
* *
11343965 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
11343998 GAGCTGGTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACTCGGGGA
Found at i:11344007 original size:43 final size:42
Alignment explanation
Indices: 11343889--11344010 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 42
11343879 TGACTCGGCT
* * * * **
11343889 ATGTGCGAGTAGGGAGTGTGCATAAGCCGGGGATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCAT-AGCTGGTGATGACCCAGCC
* *
11343932 ATGTACGAGTAGGGAGTGCGCATAACTCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAGCT-GGTGATGACCCAGCC
11343975 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCAT-AGCTGGTGATGA
11344011 TAATGATGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 62 0.93
44 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
ATGTGCGAGTAGGGAGTGCGCATAGCTGGTGATGACCCAGCC
Found at i:11344420 original size:39 final size:39
Alignment explanation
Indices: 11344366--11344442 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
11344356 GTAGCTTCTC
* * *
11344366 GCTGCACCGAGAAACCTTTTGTTTCTGGGTTGCAATTTT
1 GCTGCACCGAGAAACCTTCTATTTCTGGGTTACAATTTT
*
11344405 GCTGCAGCGAGAAACCTTCTATTTCTGGGTTACAATTT
1 GCTGCACCGAGAAACCTTCTATTTCTGGGTTACAATTT
11344443 CTCTGAATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (39 bp):
GCTGCACCGAGAAACCTTCTATTTCTGGGTTACAATTTT
Found at i:11347113 original size:33 final size:33
Alignment explanation
Indices: 11347076--11347147 Score: 135
Period size: 33 Copynumber: 2.2 Consensus size: 33
11347066 CGAGTCCTCA
*
11347076 CTGCAGCGAAAAGGCATTCTCGTTGCAGTGTAG
1 CTGCAGCGAAAAGGCATTCTCGCTGCAGTGTAG
11347109 CTGCAGCGAAAAGGCATTCTCGCTGCAGTGTAG
1 CTGCAGCGAAAAGGCATTCTCGCTGCAGTGTAG
11347142 CTGCAG
1 CTGCAG
11347148 TGAGAATGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.22
Consensus pattern (33 bp):
CTGCAGCGAAAAGGCATTCTCGCTGCAGTGTAG
Found at i:11347745 original size:42 final size:42
Alignment explanation
Indices: 11347693--11347810 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
11347683 CAGCTCATAT
* * * *
11347693 GCATCGGCTTATGTGCACTCCCACTCGCACATAGTTGGGTCA
1 GCATTGGCTTATGCGCACTCCCACTCGCACATAGTCGAGTCA
* *
11347735 GCATTGGCTTATGCGTACTCCCACTTGCACATAGTCGAGTCA
1 GCATTGGCTTATGCGCACTCCCACTCGCACATAGTCGAGTCA
* *
11347777 GCATCT-GCTTATGCACACTCCTACTCGCACATAG
1 GCAT-TGGCTTATGCGCACTCCCACTCGCACATAG
11347811 CCGGGTCAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.27
Consensus pattern (42 bp):
GCATTGGCTTATGCGCACTCCCACTCGCACATAGTCGAGTCA
Found at i:11348563 original size:3 final size:3
Alignment explanation
Indices: 11348555--11348579 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11348545 AACGTGAAAG
11348555 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
11348580 AGCTGCTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:11350122 original size:2 final size:2
Alignment explanation
Indices: 11350115--11350161 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
11350105 ATGCTTAGCT
* * *
11350115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA CA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11350157 TA TA T
1 TA TA T
11350162 TTACATTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:11357633 original size:13 final size:13
Alignment explanation
Indices: 11357615--11357639 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11357605 ATTTTCAAAA
11357615 ATTTTATAAAATT
1 ATTTTATAAAATT
11357628 ATTTTATAAAAT
1 ATTTTATAAAAT
11357640 CTCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:11360644 original size:23 final size:23
Alignment explanation
Indices: 11360614--11360668 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
11360604 CTAAGGAATG
11360614 AATGAATGATGTTTATGATGCTA
1 AATGAATGATGTTTATGATGCTA
*
11360637 AATGAATGATGTTTATGATGGTA
1 AATGAATGATGTTTATGATGCTA
*
11360660 AATAAATGA
1 AATGAATGA
11360669 GGAAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (23 bp):
AATGAATGATGTTTATGATGCTA
Found at i:11365600 original size:24 final size:24
Alignment explanation
Indices: 11365564--11365609 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
11365554 GCCATGTTGA
11365564 TTATTTGAGTGAAATGAATTTATT
1 TTATTTGAGTGAAATGAATTTATT
*
11365588 TTATTT-AGTTGAAATGAGTTTA
1 TTATTTGAG-TGAAATGAATTTA
11365610 AAACGTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (24 bp):
TTATTTGAGTGAAATGAATTTATT
Found at i:11370410 original size:22 final size:22
Alignment explanation
Indices: 11370385--11370428 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11370375 GTTGGTTGTT
11370385 GGGTTTTGGTTTATCCTGGTAA
1 GGGTTTTGGTTTATCCTGGTAA
11370407 GGGTTTTGGTTTATCCTGGTAA
1 GGGTTTTGGTTTATCCTGGTAA
11370429 AAGCCATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.32, T:0.45
Consensus pattern (22 bp):
GGGTTTTGGTTTATCCTGGTAA
Found at i:11370558 original size:66 final size:67
Alignment explanation
Indices: 11370440--11370565 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 67
11370430 AGCCATTGTG
* *
11370440 AAAGGTTGTGGTTGAGCCTTTGAAAAATCACTTTAGGTTTTAATTTAGCCCGTGAAAAACTAGTG
1 AAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGGTTTTAATTGAGCCCGTGAAAAACTAGTG
11370505 TA
66 TA
* ** *
11370507 AAAGGTTGTGGTTGAGCC-TTGAAAAACCACTTTGGGTTTTGGTTGATCCCGTGAAAAAC
1 AAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGGTTTTAATTGAGCCCGTGAAAAAC
11370566 CATTTCTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
66 35 0.66
67 18 0.34
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (67 bp):
AAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTAGGTTTTAATTGAGCCCGTGAAAAACTAGTG
TA
Found at i:11378210 original size:10 final size:10
Alignment explanation
Indices: 11378197--11378226 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
11378187 ATTTTTTTCC
11378197 TTCCTTTCTT
1 TTCCTTTCTT
11378207 TTCCTTTCTT
1 TTCCTTTCTT
*
11378217 TTCTTTTCTT
1 TTCCTTTCTT
11378227 ACTTCTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCCTTTCTT
Found at i:11378219 original size:15 final size:14
Alignment explanation
Indices: 11378191--11378224 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
11378181 TTTTTCATTT
11378191 TTTTCCTTCCTTTC
1 TTTTCCTTCCTTTC
*
11378205 TTTTCCTTTCTTTTC
1 TTTTCC-TTCCTTTC
11378220 TTTTC
1 TTTTC
11378225 TTACTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCCTTCCTTTC
Found at i:11379484 original size:36 final size:37
Alignment explanation
Indices: 11379480--11379654 Score: 126
Period size: 42 Copynumber: 4.5 Consensus size: 37
11379470 GTGATGGTGG
*
11379480 TGTGCGGTGTGGGAGTGCACATGATGATGATGATATTTGCCA
1 TGTGCGGTGTGGGAGTGCACATGATG--G-TGATAGTTG--A
* * * *
11379522 TGTGCGGAGTTGGG-GTGCACATGATGGGGACA--TGG
1 TGTGCGGTG-TGGGAGTGCACATGATGGTGATAGTTGA
* *
11379557 TGTGTGGTGTGGGAGTGCACATGATGATGATGATATTTGCCA
1 TGTGCGGTGTGGGAGTGCACATGATG--G-TGATAGTTG--A
* *
11379599 TGTGCGGTGTGGAAGTGCACATGATGGT-ATTAGCT-A
1 TGTGCGGTGTGGGAGTGCACATGATGGTGA-TAGTTGA
11379635 TGTGCGGTGTGGGAGTGCAC
1 TGTGCGGTGTGGGAGTGCAC
11379655 GTGAGATGAG
Statistics
Matches: 109, Mismatches: 14, Indels: 26
0.73 0.09 0.17
Matches are distributed among these distances:
34 4 0.04
35 19 0.17
36 20 0.18
37 3 0.03
38 4 0.04
39 7 0.06
40 4 0.04
42 44 0.40
43 4 0.04
ACGTcount: A:0.19, C:0.11, G:0.40, T:0.29
Consensus pattern (37 bp):
TGTGCGGTGTGGGAGTGCACATGATGGTGATAGTTGA
Found at i:11379576 original size:77 final size:77
Alignment explanation
Indices: 11379442--11379663 Score: 281
Period size: 77 Copynumber: 2.9 Consensus size: 77
11379432 TATAACCGTG
* **
11379442 CATGTGCGGTGTGGGAGTGCACATGATGGTGATGGTGGTGTGCGGTGTGGGAGTGCACATGATGA
1 CATGTGCGGTGTGGG-GTGCACATGATGGGGATCATGGTGTGCGGTGTGGGAGTGCACATGATGA
11379507 TGATGATATTTGC
65 TGATGATATTTGC
* *
11379520 CATGTGCGGAGTTGGGGTGCACATGATGGGGA-CATGGTGTGTGGTGTGGGAGTGCACATGATGA
1 CATGTGCGGTG-TGGGGTGCACATGATGGGGATCATGGTGTGCGGTGTGGGAGTGCACATGATGA
11379584 TGATGATATTTGC
65 TGATGATATTTGC
* * * * *
11379597 CATGTGCGGTGTGGAAGTGCACATGAT-GGTATTA-GCTATGTGCGGTGTGGGAGTGCACGTGA-
1 CATGTGCGGTGTGG-GGTGCACATGATGGGGATCATG--GTGTGCGGTGTGGGAGTGCACATGAT
11379659 GATGA
63 GATGA
11379664 GTTGCAAATG
Statistics
Matches: 127, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
76 7 0.06
77 69 0.54
78 47 0.37
79 4 0.03
ACGTcount: A:0.19, C:0.11, G:0.41, T:0.28
Consensus pattern (77 bp):
CATGTGCGGTGTGGGGTGCACATGATGGGGATCATGGTGTGCGGTGTGGGAGTGCACATGATGAT
GATGATATTTGC
Found at i:11379754 original size:2 final size:2
Alignment explanation
Indices: 11379742--11379809 Score: 95
Period size: 2 Copynumber: 34.5 Consensus size: 2
11379732 TATGTTTGAA
* *
11379742 AT AT CT AT AT AT AT ACT -T AT AT TT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
11379783 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11379810 CATGAATTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
1 2 0.03
2 56 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11392898 original size:42 final size:42
Alignment explanation
Indices: 11392842--11392940 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
11392832 CTCCCCACTA
* * * * *
11392842 GCACATGGCTGGGTCAGCAACGGCTTATGCGCACTCCTACTT
1 GCACATAGCCGGGTCAGCAACGACGTATGCGCACTCCTACTC
* *
11392884 GCACATAGCCGGGTCATCATCGACGTATGCGCACTCCTACTC
1 GCACATAGCCGGGTCAGCAACGACGTATGCGCACTCCTACTC
11392926 GCACATAGCCGGGTC
1 GCACATAGCCGGGTC
11392941 CACATCAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.21
Consensus pattern (42 bp):
GCACATAGCCGGGTCAGCAACGACGTATGCGCACTCCTACTC
Found at i:11399961 original size:42 final size:42
Alignment explanation
Indices: 11399897--11399978 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
11399887 TCATGGCTGG
*
11399897 GTCAGCATCGGCTTATGCGCACTCCTACTCGCACATAGCCAA
1 GTCAGCATCGGCGTATGCGCACTCCTACTCGCACATAGCCAA
*
11399939 GTCATCATCGGCGTATGCGCACTCCTACTCGCACATAGCC
1 GTCAGCATCGGCGTATGCGCACTCCTACTCGCACATAGCC
11399979 GGGTCCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.37, G:0.20, T:0.22
Consensus pattern (42 bp):
GTCAGCATCGGCGTATGCGCACTCCTACTCGCACATAGCCAA
Found at i:11405633 original size:21 final size:19
Alignment explanation
Indices: 11405607--11405647 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
11405597 AATTTAAAAC
11405607 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
11405628 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
11405647 A
1 A
11405648 TTCAACGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:11407317 original size:32 final size:32
Alignment explanation
Indices: 11407275--11407375 Score: 103
Period size: 32 Copynumber: 3.1 Consensus size: 32
11407265 AACCTTTCAC
*
11407275 AATGGTTTTTCACGGGATCAACAAAAACCCAA
1 AATGGTTTTTCACGGGATCAACCAAAACCCAA
* ** * * *
11407307 AATGGCTTTTCAAAGGCTCAACCATAACCTTTAA
1 AATGGTTTTTCACGGGATCAACCAAAACC--CAA
*
11407341 CAATGGTTTTTCACGAGATCAACCAAAACCCAA
1 -AATGGTTTTTCACGGGATCAACCAAAACCCAA
11407374 AA
1 AA
11407376 CTAACTTTTC
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
32 25 0.48
33 2 0.04
34 2 0.04
35 23 0.44
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (32 bp):
AATGGTTTTTCACGGGATCAACCAAAACCCAA
Found at i:11407326 original size:67 final size:67
Alignment explanation
Indices: 11407240--11407375 Score: 211
Period size: 67 Copynumber: 2.0 Consensus size: 67
11407230 AAGCTTTTAC
* * *
11407240 AATGGCTTTTCACAAGCTCAGCCACAACCTTTCACAATGGTTTTTCACGGGATCAACAAAAACCC
1 AATGGCTTTTCACAAGCTCAACCACAACCTTTAACAATGGTTTTTCACGAGATCAACAAAAACCC
11407305 AA
66 AA
* *
11407307 AATGGCTTTTCA-AAGGCTCAACCATAACCTTTAACAATGGTTTTTCACGAGATCAACCAAAACC
1 AATGGCTTTTCACAA-GCTCAACCACAACCTTTAACAATGGTTTTTCACGAGATCAACAAAAACC
11407371 CAA
65 CAA
11407374 AA
1 AA
11407376 CTAACTTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 2 0.03
67 61 0.97
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.24
Consensus pattern (67 bp):
AATGGCTTTTCACAAGCTCAACCACAACCTTTAACAATGGTTTTTCACGAGATCAACAAAAACCC
AA
Found at i:11407352 original size:35 final size:35
Alignment explanation
Indices: 11407233--11407370 Score: 97
Period size: 35 Copynumber: 4.0 Consensus size: 35
11407223 TTCCACTAAG
* * *
11407233 CTTTTACAATGGCTTTTCACAA-GCTCAGCCACAAC
1 CTTTAACAATGGCTTTTCA-AAGGCTCAACCAAAAC
* * ** * *
11407268 CTTTCACAATGGTTTTTCACGGGATCAACAAAAAC
1 CTTTAACAATGGCTTTTCAAAGGCTCAACCAAAAC
* *
11407303 C--CAA-AATGGCTTTTCAAAGGCTCAACCATAAC
1 CTTTAACAATGGCTTTTCAAAGGCTCAACCAAAAC
* * *
11407335 CTTTAACAATGGTTTTTC-ACGAGATCAACCAAAAC
1 CTTTAACAATGGCTTTTCAAAG-GCTCAACCAAAAC
11407370 C
1 C
11407371 CAAAACTAAC
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
32 23 0.30
33 1 0.01
34 4 0.05
35 49 0.64
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (35 bp):
CTTTAACAATGGCTTTTCAAAGGCTCAACCAAAAC
Found at i:11407881 original size:73 final size:73
Alignment explanation
Indices: 11407784--11407952 Score: 177
Period size: 73 Copynumber: 2.3 Consensus size: 73
11407774 AATTGCGCTT
*
11407784 TTAGTCGACTAAGTCATTTTTGTCTTCTG-A-TCCTAG-TTTCCGGCAGT-GAGCACTTAGTCGA
1 TTAGTCGACTAAGTCATTTCTGTC-T-TGAAGT-CTAGATTTCCGGCAGTAG-GCACTTAGTCGA
*
11407845 CTAACTTCCTTC
62 CTAACTTACTTC
* ** * *
11407857 TTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCTAGATTTCTGGCAGTAGGCTCTTAGTCGACTAA
1 TTAGTCGACTAAGTCATTTCTGTCTTGAAGTCTAGATTTCCGGCAGTAGGCACTTAGTCGACTAA
11407922 CTTACTTC
66 CTTACTTC
* *
11407930 TTGGTTGACTAAGTC-TTCTCTGT
1 TTAGTCGACTAAGTCATT-TCTGT
11407953 TTCTGAACCA
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
71 2 0.03
72 8 0.10
73 69 0.86
74 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (73 bp):
TTAGTCGACTAAGTCATTTCTGTCTTGAAGTCTAGATTTCCGGCAGTAGGCACTTAGTCGACTAA
CTTACTTC
Found at i:11409750 original size:20 final size:20
Alignment explanation
Indices: 11409713--11409751 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11409703 CTTCAAGCAC
* * *
11409713 TATTCTCAATTATCATCAAG
1 TATTATCAATCATAATCAAG
11409733 TATTATCAATCATAATCAA
1 TATTATCAATCATAATCAA
11409752 CATTCATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATAATCAAG
Found at i:11414551 original size:35 final size:35
Alignment explanation
Indices: 11414506--11414620 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 35
11414496 AAGCTTTTAC
*
11414506 AATGGCTTTTCACAAGCTCAGCCACAACCTTTCAA
1 AATGGCTTTTCACAAGCTCAACCACAACCTTTCAA
* * * *
11414541 AATGGTTTTTCACGAGATCAACCAAAACC---CAA
1 AATGGCTTTTCACAAGCTCAACCACAACCTTTCAA
* *
11414573 AATGGCTTTTCGA-AGGCTCAACAACAACCTTT-AA
1 AATGGCTTTTC-ACAAGCTCAACCACAACCTTTCAA
*
11414607 CAATGGTTTTTCAC
1 -AATGGCTTTTCAC
11414621 GGGATCAACC
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
32 24 0.39
33 1 0.02
34 3 0.05
35 34 0.55
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (35 bp):
AATGGCTTTTCACAAGCTCAACCACAACCTTTCAA
Found at i:11414583 original size:32 final size:33
Alignment explanation
Indices: 11414506--11414641 Score: 100
Period size: 35 Copynumber: 4.1 Consensus size: 33
11414496 AAGCTTTTAC
* * * *
11414506 AATGGCTTTTCACAAGCTCAGCCACAACCTTTCAA
1 AATGGCTTTTCACGAGATCAACCAAAACC--TCAA
*
11414541 AATGGTTTTTCACGAGATCAACCAAAACC-CAA
1 AATGGCTTTTCACGAGATCAACCAAAACCTCAA
* * *
11414573 AATGGCTTTTCGAAG-GCTCAA-CAACAACCTTTAA
1 AATGGCTTTTC-ACGAGATCAACCAA-AACC-TCAA
* *
11414607 CAATGGTTTTTCACGGGATCAACCAAAACCT-AA
1 -AATGGCTTTTCACGAGATCAACCAAAACCTCAA
11414640 AA
1 AA
11414642 CTAACTTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
31 3 0.04
32 24 0.29
33 4 0.05
34 5 0.06
35 43 0.52
36 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (33 bp):
AATGGCTTTTCACGAGATCAACCAAAACCTCAA
Found at i:11414592 original size:67 final size:67
Alignment explanation
Indices: 11414506--11414641 Score: 195
Period size: 67 Copynumber: 2.0 Consensus size: 67
11414496 AAGCTTTTAC
* *
11414506 AATGGCTTTTCACAAGCTCAGCCACAACCTTTCAA-AATGGTTTTTCACGAGATCAACCAAAACC
1 AATGGCTTTTCACAAGCTCAACAACAACCTTT-AACAATGGTTTTTCACGAGATCAACCAAAACC
11414570 CAA
65 CAA
* *
11414573 AATGGCTTTTCGA-AGGCTCAACAACAACCTTTAACAATGGTTTTTCACGGGATCAACCAAAACC
1 AATGGCTTTTC-ACAAGCTCAACAACAACCTTTAACAATGGTTTTTCACGAGATCAACCAAAACC
*
11414637 TAA
65 CAA
11414640 AA
1 AA
11414642 CTAACTTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
66 2 0.03
67 59 0.95
68 1 0.02
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (67 bp):
AATGGCTTTTCACAAGCTCAACAACAACCTTTAACAATGGTTTTTCACGAGATCAACCAAAACCC
AA
Found at i:11414629 original size:35 final size:34
Alignment explanation
Indices: 11414531--11414637 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 34
11414521 GCTCAGCCAC
*
11414531 AACCTTTCAAAATGGTTTTTCACGAGATCAACCAA
1 AACCTTT-AAAATGGTTTTTCACGGGATCAACCAA
* * * *
11414566 AACC--CAAAATGGCTTTTCGA-AGGCTCAA-CAA
1 AACCTTTAAAATGGTTTTTC-ACGGGATCAACCAA
11414597 CAACCTTTAACAATGGTTTTTCACGGGATCAACCAA
1 -AACCTTTAA-AATGGTTTTTCACGGGATCAACCAA
11414633 AACCT
1 AACCT
11414638 AAAACTAACT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
31 3 0.05
32 21 0.38
33 1 0.02
34 3 0.05
35 25 0.45
36 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (34 bp):
AACCTTTAAAATGGTTTTTCACGGGATCAACCAA
Found at i:11415069 original size:19 final size:20
Alignment explanation
Indices: 11415030--11415070 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
11415020 AAGAATAATC
*
11415030 TTAGTTGACTAACTGCGCTT
1 TTAGTCGACTAACTGCGCTT
*
11415050 TTAGTCGACTAAGT-CGCTT
1 TTAGTCGACTAACTGCGCTT
11415069 TT
1 TT
11415071 GTCTTCTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTAGTCGACTAACTGCGCTT
Found at i:11415136 original size:73 final size:73
Alignment explanation
Indices: 11415029--11415218 Score: 187
Period size: 73 Copynumber: 2.6 Consensus size: 73
11415019 AAAGAATAAT
* *
11415029 CTTAGTTGACTAACTGCGCTT-TTAGTCGACTAAGTCGCTTT-TGTCTTCTG-A-TCCCAG-TTT
1 CTTAGTCGACTAACTTC-CTTCTTAGTCGACTAAGTCG-TTTCTGTC-T-TGAAGT-CCAGATTT
11415089 CTGACAGT-GAGCA
61 CTGACAGTAG-GCA
* * * *
11415102 CTTAGTCGACTAACTTCCTTCTTAGTCGATTAAGTTGTTTCTGTCTTGAAGTCTAGATTTCTGGC
1 CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTCGTTTCTGTCTTGAAGTCCAGATTTCTGAC
*
11415167 AGTAGGCT
66 AGTAGGCA
* *
11415175 CTTAGTCGACTAACTTACTTCTTGGTCGACTAAGTC-TTCTCTGT
1 CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTCGTT-TCTGT
11415219 TCCTAAACCA
Statistics
Matches: 99, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
71 2 0.02
72 13 0.13
73 83 0.84
74 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (73 bp):
CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTCGTTTCTGTCTTGAAGTCCAGATTTCTGAC
AGTAGGCA
Found at i:11427206 original size:42 final size:41
Alignment explanation
Indices: 11427120--11427245 Score: 135
Period size: 42 Copynumber: 3.0 Consensus size: 41
11427110 TCTCCCATCG
* * * * *
11427120 TCATCAGCTCATGTGCACTCCCCACTAGCACATGGCTAGGTCA
1 TCATCGGCTTATGTGCACT--CCACTCGCACATAGCCAGGTCA
11427163 TCATCGGCTTATGTGCACTCACACTCGCACATAGCCAGGTCA
1 TCATCGGCTTATGTGCACTC-CACTCGCACATAGCCAGGTCA
* * * *
11427205 TCATCGACTTATGTACACTCCTACTCGTACATAGCCTGGTC
1 TCATCGGCTTATGTGCACTCC-ACTCGCACATAGCCAGGTC
11427246 CACATCAACA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.03
42 53 0.74
43 17 0.24
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.26
Consensus pattern (41 bp):
TCATCGGCTTATGTGCACTCCACTCGCACATAGCCAGGTCA
Found at i:11432758 original size:27 final size:27
Alignment explanation
Indices: 11432707--11432760 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
11432697 TCACTATCTA
11432707 GGGGCAAAACGGTAATTTTGCCACCCCG
1 GGGGCAAAACGGTAATTTT-CCACCCCG
*
11432735 GGGGCAAATCGGTAAATTTT-CACCCC
1 GGGGCAAAACGGT-AATTTTCCACCCC
11432761 CGACACCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 12 0.50
29 6 0.25
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (27 bp):
GGGGCAAAACGGTAATTTTCCACCCCG
Found at i:11434888 original size:17 final size:18
Alignment explanation
Indices: 11434868--11434901 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11434858 TTTTTTAGAA
11434868 AATA-TAATATTTTATTG
1 AATATTAATATTTTATTG
*
11434885 AATATTATTATTTTATT
1 AATATTAATATTTTATT
11434902 CAAACAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATATTAATATTTTATTG
Found at i:11437914 original size:261 final size:261
Alignment explanation
Indices: 11437450--11437929 Score: 843
Period size: 261 Copynumber: 1.8 Consensus size: 261
11437440 ATAGCACTCC
11437450 ACACATAAGATAACCTGGTGTCTTAAGTATAGGGAGTATTTACACAACTGACACATGAGAAGTAT
1 ACACATAAGATAACCTGGTGTCTTAAGTATAGGGAGTATTTACACAACTGACACATGAGAAGTAT
**
11437515 TGCATAGACACTTAAGTGAAATTTCAAATGCACTTCTCATGGCGTGTCATGTTCAGTGAACTTGC
66 TGCATAGACACTTAAGTGAAATACCAAATGCACTTCTCATGGCGTGTCATGTTCAGTGAACTTGC
* * * *
11437580 TCTCCTAGGCAAACATCTACATTCTAGTTTCAAGTATCTCTATACTTCAACCTATTAGATCAGTT
131 TCCCCTAGGCAAACACCTACATTATAGTTTCAAGTATCTCTATACTTCAACCTATTAGATCAATT
*
11437645 GCTTACTACCCAAGTAAGAAACATGACAAGTAAGTATCTCTATATTCTAGTTTCAAGTATCTCTA
196 GCTTACTACCCAAGGAAGAAACATGACAAGTAAGTATCTCTATATTCTAGTTTCAAGTATCTCTA
11437710 T
261 T
* *
11437711 ACACATAAGATAACTTGGTGTCTTAAGTCTAGGGAGTATTTACACAACTGACACATGAGAAGTAT
1 ACACATAAGATAACCTGGTGTCTTAAGTATAGGGAGTATTTACACAACTGACACATGAGAAGTAT
* *
11437776 TGCATAGACACTTGAGTGAAATACCAAATGCACTTCTCATGGCGTGTCATGTTCAGTGAACTTGG
66 TGCATAGACACTTAAGTGAAATACCAAATGCACTTCTCATGGCGTGTCATGTTCAGTGAACTTGC
*
11437841 TCCCCTAGGCAAACACCTATATTATAGTTTCAAGTATCTCTATACTTCAACCTATTAGATCAATT
131 TCCCCTAGGCAAACACCTACATTATAGTTTCAAGTATCTCTATACTTCAACCTATTAGATCAATT
*
11437906 GTTTACTACCCAAGGAAGAAACAT
196 GCTTACTACCCAAGGAAGAAACAT
11437930 AGAATGTACC
Statistics
Matches: 206, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
261 206 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (261 bp):
ACACATAAGATAACCTGGTGTCTTAAGTATAGGGAGTATTTACACAACTGACACATGAGAAGTAT
TGCATAGACACTTAAGTGAAATACCAAATGCACTTCTCATGGCGTGTCATGTTCAGTGAACTTGC
TCCCCTAGGCAAACACCTACATTATAGTTTCAAGTATCTCTATACTTCAACCTATTAGATCAATT
GCTTACTACCCAAGGAAGAAACATGACAAGTAAGTATCTCTATATTCTAGTTTCAAGTATCTCTA
T
Found at i:11456931 original size:42 final size:42
Alignment explanation
Indices: 11456867--11456991 Score: 187
Period size: 42 Copynumber: 3.0 Consensus size: 42
11456857 TGTTGATGTG
* *
11456867 GACCTGGCTATGTGCGAGTGGGAGTGCACCTAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
*
11456909 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCATTGCT
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
* * * *
11456951 GACCCGACTATGTGCGAGTTGGAGTACGCATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
11456992 ATATGAGATG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.22
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCT
Found at i:11458953 original size:180 final size:180
Alignment explanation
Indices: 11458708--11459036 Score: 505
Period size: 180 Copynumber: 1.8 Consensus size: 180
11458698 TTAATAGCTT
* ** *
11458708 AAATCAGCTTGTTTGCCCATGAAAATTTCCAAAAATAATTCTCATTGAACATTTTAATAAAGATA
1 AAATCAGCTTATTTGAACATGAAAATTTCCAAAAATAATCCTCATTGAACATTTTAATAAAGATA
* * * *
11458773 ATTTTTCTGGAATTTTTCAGAATTAATTTTTGAGAATTTCTTGTCAATTAATACTGAAATTCATG
66 ATTTTCCTGGAATTTTTCAGAATTAATTTCTAAGAATTTCTTGTCAATTAAAACTGAAATTCATG
11458838 CCAAAACAGTGAGCTGGACAGATTTACATTTGCACCAATTTTCTTGCTCG
131 CCAAAACAGTGAGCTGGACAGATTTACATTTGCACCAATTTTCTTGCTCG
* * * * *
11458888 AAATCAGCTTATTTGAACATGATATTTTCCAGAAATAATCCTTATTGAATATTTTAATAAAGATA
1 AAATCAGCTTATTTGAACATGAAAATTTCCAAAAATAATCCTCATTGAACATTTTAATAAAGATA
* *
11458953 ATTTTCCTGGAATTTTTCAGAATTAATTTCTAAGACTTTCTTGTTAATTAAAACTGAAATTCATG
66 ATTTTCCTGGAATTTTTCAGAATTAATTTCTAAGAATTTCTTGTCAATTAAAACTGAAATTCATG
* *
11459018 TCATAACAGTGAGCTGGAC
131 CCAAAACAGTGAGCTGGAC
11459037 TGCTTTCACT
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
180 132 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (180 bp):
AAATCAGCTTATTTGAACATGAAAATTTCCAAAAATAATCCTCATTGAACATTTTAATAAAGATA
ATTTTCCTGGAATTTTTCAGAATTAATTTCTAAGAATTTCTTGTCAATTAAAACTGAAATTCATG
CCAAAACAGTGAGCTGGACAGATTTACATTTGCACCAATTTTCTTGCTCG
Found at i:11460189 original size:35 final size:35
Alignment explanation
Indices: 11460143--11460391 Score: 264
Period size: 35 Copynumber: 7.0 Consensus size: 35
11460133 TCATTAAGAA
*** *
11460143 GCCCAATTAACTTAATTGTTTAATTTAATCGATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATCAATTAG
* *
11460179 GCCCAATAACTTAATTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* *
11460214 GCCCAATAATTTAATTAAACAATTTTAATCAATTAG
1 GCCCAATAACTTAATTAAATAA-TTTAATCAATTAG
* * *
11460250 GCCCAATGACTTAACTAAACAAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAA-TAATTTAATCAATTAG
* *** *
11460286 GCCTAATAACTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * *
11460321 GCCCAATGACTTAATTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
11460356 GCCTAATGATTTAATTAAATAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
11460391 G
1 G
11460392 GACAACTTAA
Statistics
Matches: 180, Mismatches: 31, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
35 119 0.66
36 59 0.33
37 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATCAATTAG
Found at i:11460285 original size:107 final size:105
Alignment explanation
Indices: 11460164--11460391 Score: 294
Period size: 107 Copynumber: 2.2 Consensus size: 105
11460154 TTAATTGTTT
* *
11460164 AATTTAATCGATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAATAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAATAACTTAAT
*
11460229 TAAACAATTTTAATCAATTAGGCCCAATGACTTAACTAAACA
66 TAAACAA-TTTAATCAATTAAGCCCAATGACTTAACTAAA-A
* *** * *
11460271 AATTTAATCAATTAGGCCTAATAACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAATAACTTAAT
* * * * * *
11460336 TAAATAATTTAATTAATTAAGCCTAATGATTTAATTAAAT
66 TAAACAATTTAATCAATTAAGCCCAATGACTTAACTAAAA
*
11460376 AATTTAATTAATTAGG
1 AATTTAATCAATTAGG
11460392 GACAACTTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 15 0.14
106 27 0.26
107 63 0.60
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAATAACTTAAT
TAAACAATTTAATCAATTAAGCCCAATGACTTAACTAAAA
Found at i:11461788 original size:73 final size:73
Alignment explanation
Indices: 11461711--11461870 Score: 196
Period size: 73 Copynumber: 2.2 Consensus size: 73
11461701 GTAGTGAGCA
* * * *
11461711 CTTAGTTGAGTAACTTCCTTCTTAGTCGATTAAGTT-GTTTCTGTCTTAAAGTCCAGATTTCTGG
1 CTTAGTCGACTAACTTACTTCTTAGTCGATTAAGTTGGTTT-TGTCTTAAAGTCAAGATTTCTGG
11461775 CAGTAGGGT
65 CAGTAGGGT
* * * * *
11461784 CTTAGTCGACTAACTTACTTCTTGGTTGATTAAGTTGGTTTTGTCTTGAAGTCAAGATTTTTGGT
1 CTTAGTCGACTAACTTACTTCTTAGTCGATTAAGTTGGTTTTGTCTTAAAGTCAAGATTTCTGGC
**
11461849 AGTAGACT
66 AGTAGGGT
*
11461857 TTTAGTCGACTAAC
1 CTTAGTCGACTAAC
11461871 CCATTTCTTG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
73 70 0.95
74 4 0.05
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (73 bp):
CTTAGTCGACTAACTTACTTCTTAGTCGATTAAGTTGGTTTTGTCTTAAAGTCAAGATTTCTGGC
AGTAGGGT
Found at i:11461879 original size:73 final size:73
Alignment explanation
Indices: 11461728--11461891 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
11461718 GAGTAACTTC
* * **
11461728 CTTCTTAGTCGATTAAGTTGTTTCTGTCTTAAAGTCCAGATTTCTGGCAGTAGGGTCTTAGTCGA
1 CTTCTTGGTCGATTAAGTTGTTTCTGTCTTAAAGTCAAGATTTCTGGCAGTAGACTCTTAGTCGA
**
11461793 CTAACTTA
66 CTAACCCA
* * * * *
11461801 CTTCTTGGTTGATTAAGTTGGTTT-TGTCTTGAAGTCAAGATTTTTGGTAGTAGACTTTTAGTCG
1 CTTCTTGGTCGATTAAGTT-GTTTCTGTCTTAAAGTCAAGATTTCTGGCAGTAGACTCTTAGTCG
11461865 ACTAACCCA
65 ACTAACCCA
* *
11461874 TTTCTTGGTCGACTAAGT
1 CTTCTTGGTCGATTAAGT
11461892 CTTCTCTATT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 72 0.95
74 4 0.05
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.41
Consensus pattern (73 bp):
CTTCTTGGTCGATTAAGTTGTTTCTGTCTTAAAGTCAAGATTTCTGGCAGTAGACTCTTAGTCGA
CTAACCCA
Found at i:11464076 original size:38 final size:39
Alignment explanation
Indices: 11463980--11464083 Score: 113
Period size: 38 Copynumber: 2.7 Consensus size: 39
11463970 CACCTAGCTT
* *
11463980 ATGTACATCCCCCCACATCGTGCA-AATAGCCGACACCCTC
1 ATGTACATCCCCCCACATCGTGCACAATA--CAACACCATC
* * **
11464020 CTGTGCATCCCCCCACATCGTGCACAAT-CAATGCCATC
1 ATGTACATCCCCCCACATCGTGCACAATACAACACCATC
*
11464058 ATGTACATCCCCCCACATCATGCACA
1 ATGTACATCCCCCCACATCGTGCACA
11464084 CTGGCACTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 29 0.54
40 22 0.41
41 3 0.06
ACGTcount: A:0.27, C:0.42, G:0.12, T:0.19
Consensus pattern (39 bp):
ATGTACATCCCCCCACATCGTGCACAATACAACACCATC
Found at i:11467269 original size:31 final size:31
Alignment explanation
Indices: 11467231--11467293 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
11467221 GAATAGCCAT
11467231 TTGATATAGTTGGAAGCCAATTAGGAATGAC
1 TTGATATAGTTGGAAGCCAATTAGGAATGAC
11467262 TTGATATAGTTGGAAGCCAATTAGGAATGAC
1 TTGATATAGTTGGAAGCCAATTAGGAATGAC
11467293 T
1 T
11467294 AGTAGAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (31 bp):
TTGATATAGTTGGAAGCCAATTAGGAATGAC
Found at i:11467724 original size:37 final size:37
Alignment explanation
Indices: 11467683--11467792 Score: 121
Period size: 37 Copynumber: 3.0 Consensus size: 37
11467673 ATAATGTTGT
* **
11467683 ATGATGATAATGAGGTGTGCGAGTAGGGAGTGCACAC
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
* * *
11467720 ATGATGACATTGAAATGTGTGAGTAGGGAGTGCACAT
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
* *** *
11467757 ATGATGGTATTGCCTTGTGCGTGTAGGGAGTGCACA
1 ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACA
11467793 AGAACTGAGG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.26
Consensus pattern (37 bp):
ATGATGATATTGAAATGTGCGAGTAGGGAGTGCACAC
Found at i:11475694 original size:2 final size:2
Alignment explanation
Indices: 11475682--11475723 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
11475672 ACATTATTCG
*
11475682 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11475724 NTCCCAAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:11481371 original size:35 final size:35
Alignment explanation
Indices: 11481326--11481396 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
11481316 TTTCACCAAG
* * *
11481326 CTTTGACAATGGCTTTTACCAAGCTCAGCCAAAAC
1 CTTTCACAATGGCTTTTACCAAGATCAACCAAAAC
*
11481361 CTTTCACAATGGTTTTTACCAAGATCAACCAAAAC
1 CTTTCACAATGGCTTTTACCAAGATCAACCAAAAC
11481396 C
1 C
11481397 CAAAGTGGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (35 bp):
CTTTCACAATGGCTTTTACCAAGATCAACCAAAAC
Found at i:11484185 original size:40 final size:39
Alignment explanation
Indices: 11484137--11484240 Score: 122
Period size: 38 Copynumber: 2.7 Consensus size: 39
11484127 AACCGGCTCA
* * *
11484137 TGTACATCCCCCCACATAGTGGACATAGCCG-GCACCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGTG--CCATCG
* * *
11484177 TGTGCATCCCCTCACATCGTGCACA-ATCAGTGCCATCG
1 TGTACATCCCCCCACATCGTGCACATAGCAGTGCCATCG
11484215 TGTACATCCCCCCACATCGTGCACAT
1 TGTACATCCCCCCACATCGTGCACAT
11484241 GGGTACTATC
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
38 29 0.54
39 3 0.06
40 22 0.41
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACATAGCAGTGCCATCG
Found at i:11484232 original size:19 final size:19
Alignment explanation
Indices: 11484137--11484240 Score: 57
Period size: 19 Copynumber: 5.4 Consensus size: 19
11484127 AACCGGCTCA
*
11484137 TGTACATCCCCCCACATAG
1 TGTACATCCCCCCACATCG
* * **
11484156 TGGACATAGCCGGCACCATCG
1 TGTACAT-CCCCCCA-CATCG
* *
11484177 TGTGCATCCCCTCACATCG
1 TGTACATCCCCCCACATCG
* ****
11484196 TGCACAATCAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
11484215 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
*
11484234 TGCACAT
1 TGTACAT
11484241 GGGTACTATC
Statistics
Matches: 59, Mismatches: 22, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
18 4 0.07
19 34 0.58
20 12 0.20
21 9 0.15
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:11485659 original size:43 final size:41
Alignment explanation
Indices: 11485588--11485681 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 41
11485578 ACAATGCACT
11485588 ATCATCATCATGTGAACTCCCTACTCGCACATAGCCGGGTC
1 ATCATCATCATGTGAACTCCCTACTCGCACATAGCCGGGTC
* * *
11485629 ATCATCAGCTCATGTGCACTCTC-ACATCGCACATAGCTGGGTC
1 ATCATCA--TCATGTGAACTCCCTAC-TCGCACATAGCCGGGTC
*
11485672 ATCATTATCA
1 ATCATCATCA
11485682 CACAAAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
41 10 0.22
42 2 0.04
43 34 0.74
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (41 bp):
ATCATCATCATGTGAACTCCCTACTCGCACATAGCCGGGTC
Found at i:11486847 original size:73 final size:72
Alignment explanation
Indices: 11486770--11486966 Score: 204
Period size: 73 Copynumber: 2.7 Consensus size: 72
11486760 CTGATCTCAG
*
11486770 TTTCTAGTAGTGAGCACTTAGTCGACTAACTTCCTTCTTAGTCAATTAAGTT-ATTTCTATCTTG
1 TTTCTAGTAGT-AGCTCTTAGTCGACTAACTTCCTTCTTAGTCAATTAAGTTGATTT-TATCTTG
*
11486834 AAGTC-TAGA
64 AAG-CACAGA
* * * * * *
11486843 TTTCTAATAGTAGGCTCTTAGTCGACTAACTTACTTCTTGGTCGATTAAGTTGGTTTTGTCTTGA
1 TTTCTAGTAGTA-GCTCTTAGTCGACTAACTTCCTTCTTAGTCAATTAAGTTGATTTTATCTTGA
11486908 AGCACAGA
65 AGCACAGA
* * *
11486916 TTTCTAGCAATAGACTCTTAGTCGACTAAC--CCATTTCTTAGTCAACTAAGT
1 TTTCTAGTAGTAG-CTCTTAGTCGACTAACTTCC--TTCTTAGTCAATTAAGT
11486967 CTTTTTTGTT
Statistics
Matches: 103, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
71 1 0.01
72 3 0.03
73 96 0.93
74 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (72 bp):
TTTCTAGTAGTAGCTCTTAGTCGACTAACTTCCTTCTTAGTCAATTAAGTTGATTTTATCTTGAA
GCACAGA
Found at i:11491639 original size:24 final size:25
Alignment explanation
Indices: 11491607--11491653 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
11491597 CTCAAATTTT
11491607 CAGCAACAAAACT-TCTCAATTTTGG
1 CAGCAACAAAACTGTC-CAATTTTGG
*
11491632 CAGC-ACAAAGCTGTCCAATTTT
1 CAGCAACAAAACTGTCCAATTTT
11491654 CCTGCACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (25 bp):
CAGCAACAAAACTGTCCAATTTTGG
Found at i:11496462 original size:35 final size:35
Alignment explanation
Indices: 11496423--11496495 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
11496413 GGAGTGCGTG
* *
11496423 TGATGATATTGAAATGTGCATGTATGGAGTGTACA
1 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
*** *
11496458 TGATGATATTGCCTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
11496493 TGA
1 TGA
11496496 GCTGAGTAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.33
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
Found at i:11496772 original size:21 final size:21
Alignment explanation
Indices: 11496742--11496791 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
11496732 TTACAAGAAA
*
11496742 TTAAACTAAATTGCAT-TGTTT
1 TTAAAATAAA-TGCATCTGTTT
11496763 TTAAAATAAATGCATCGTGTTT
1 TTAAAATAAATGCATC-TGTTT
*
11496785 TCAAAAT
1 TTAAAAT
11496792 CTTTTCGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 9 0.36
22 11 0.44
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (21 bp):
TTAAAATAAATGCATCTGTTT
Found at i:11501666 original size:2 final size:2
Alignment explanation
Indices: 11501621--11501657 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11501611 TACATAGTAA
11501621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11501658 CACATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11501767 original size:36 final size:36
Alignment explanation
Indices: 11501722--11501822 Score: 157
Period size: 36 Copynumber: 2.8 Consensus size: 36
11501712 TAGCCGGAGT
* * *
11501722 CATCGTGTGCACCCCTACATTGCGCACAGCTAATAC
1 CATCATGTGCACCCCCACATCGCGCACAGCTAATAC
* *
11501758 CATCATGTGCACCCCCACATCGCGCACAGCTCATGC
1 CATCATGTGCACCCCCACATCGCGCACAGCTAATAC
11501794 CATCATGTGCACCCCCACATCGCGCACAG
1 CATCATGTGCACCCCCACATCGCGCACAG
11501823 GCAATATCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.24, C:0.42, G:0.17, T:0.18
Consensus pattern (36 bp):
CATCATGTGCACCCCCACATCGCGCACAGCTAATAC
Done.