Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 144 of 378
Found at i:41166618 original size:53 final size:54
Alignment explanation
Indices: 41166537--41166744 Score: 204
Period size: 53 Copynumber: 3.9 Consensus size: 54
41166527 TTTGCTTTTT
* * * **
41166537 GAACTTACCATTGCCATGTCTTGACATGGTCTTATGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* *
41166590 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
** * * * * *
41166644 GTAACTCATGAATTCCATGTCTTGACATGGTATTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * * * *
41166699 GAACTTATCAATGCCATGCTTTGGCGTGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
41166745 ATCTTACCAA
Statistics
Matches: 126, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
52 2 0.02
53 43 0.34
54 37 0.29
55 42 0.33
56 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:41166780 original size:47 final size:47
Alignment explanation
Indices: 41166725--41166844 Score: 222
Period size: 47 Copynumber: 2.6 Consensus size: 47
41166715 TGCTTTGGCG
*
41166725 TGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACA
*
41166772 TGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAACA
1 TGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACA
41166819 TGGTCTTACATGGTATCCTTATCTTA
1 TGGTCTTACATGGTATCCTTATCTTA
41166845 GTGCCAATGC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (47 bp):
TGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAACA
Found at i:41166922 original size:47 final size:46
Alignment explanation
Indices: 41166816--41166970 Score: 136
Period size: 47 Copynumber: 3.3 Consensus size: 46
41166806 CATGTTCCAA
* * **
41166816 ACATGGTCTTACATGGTA-TCCTTATCTTAGTGCCAATGCCACATCTTG
1 ACATGGTCTTACATGG-AGTCCTTATC--AATGCTAATGCCATGTCTTG
* * *
41166864 ATATGGCCTTACATGGAGTCCTTAATCAATGCTGATGCCATGTCTTG
1 ACATGGTCTTACATGGAGTCCTT-ATCAATGCTAATGCCATGTCTTG
* * ** *
41166911 ACATGGTCTTACACGG-GATCCTT-GCCTTACTAATGCCATGTCTTG
1 ACATGGTCTTACATGGAG-TCCTTATCAATGCTAATGCCATGTCTTG
41166956 ACATGGTCTTACATG
1 ACATGGTCTTACATG
41166971 ATATCCTTAA
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
45 31 0.35
46 1 0.01
47 34 0.39
48 19 0.22
49 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (46 bp):
ACATGGTCTTACATGGAGTCCTTATCAATGCTAATGCCATGTCTTG
Found at i:41167628 original size:31 final size:30
Alignment explanation
Indices: 41167587--41167650 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
41167577 CATTCCCTAA
41167587 CTAAAACTTTGGCTA-AATTATAATTTTGCAC
1 CTAAAACTTT-GC-AGAATTATAATTTTGCAC
* * *
41167618 CTAAACCTTTGCAGAATTATGATTTTGCCC
1 CTAAAACTTTGCAGAATTATAATTTTGCAC
41167648 CTA
1 CTA
41167651 GGCTCGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 19 0.66
31 9 0.31
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (30 bp):
CTAAAACTTTGCAGAATTATAATTTTGCAC
Found at i:41180667 original size:143 final size:141
Alignment explanation
Indices: 41180459--41180753 Score: 563
Period size: 143 Copynumber: 2.1 Consensus size: 141
41180449 TGAGTTAAAT
*
41180459 TTCGGCCATGCATGTTGTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
41180524 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTA--TGTGT
41180589 GTGTGCATGAGTA
129 GTGTGCATGAGTA
41180602 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
41180667 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
41180732 GTGCATGAGTA
131 GTGCATGAGTA
41180743 TTCGGCCATGC
1 TTCGGCCATGC
41180754 TATAGAATTT
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 29 0.19
143 122 0.81
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (141 bp):
TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
GTGCATGAGTA
Found at i:41181430 original size:29 final size:29
Alignment explanation
Indices: 41181397--41181508 Score: 161
Period size: 29 Copynumber: 3.9 Consensus size: 29
41181387 GTGACGAGAT
*
41181397 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
41181426 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* *
41181455 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
* * *
41181484 TGACACTATGTGTGCAAGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
41181509 AATACAGCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:41181525 original size:29 final size:29
Alignment explanation
Indices: 41181400--41181526 Score: 94
Period size: 29 Copynumber: 4.4 Consensus size: 29
41181390 ACGAGATTGG
* ** * * *
41181400 CACTAAGTGTGCGTGCTGGAAATATATGG
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
* ** * *
41181429 CACTAAGTGTGCGTGCTGGAAATATAAGG
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
* * *
41181458 CACTAAGTGTGCATGCTGGAAAAATATGA
1 CACTAGGTGTGCAAGCTGGAAAAATAAGA
*
41181487 CACTATGTGTGCAAGCTGGAAAAATACAG-
1 CACTAGGTGTGCAAGCTGGAAAAATA-AGA
*
41181516 CACTGGGTGTG
1 CACTAGGTGTG
41181527 AGAGCTCGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 86 0.99
30 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.24
Consensus pattern (29 bp):
CACTAGGTGTGCAAGCTGGAAAAATAAGA
Found at i:41188618 original size:143 final size:141
Alignment explanation
Indices: 41188410--41188704 Score: 563
Period size: 143 Copynumber: 2.1 Consensus size: 141
41188400 TGAGTTAAAT
*
41188410 TTCGGCCATGCATGTTGTTTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
41188475 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTA--TGTGT
41188540 GTGTGCATGAGTA
129 GTGTGCATGAGTA
41188553 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
1 TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
41188618 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
66 GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
41188683 GTGCATGAGTA
131 GTGCATGAGTA
41188694 TTCGGCCATGC
1 TTCGGCCATGC
41188705 TATAGAATTT
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
141 29 0.19
143 122 0.81
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (141 bp):
TTCGGCCATGCATGTTGTCTTCCTTGGTGAGTGTTTTGATGTTGTTGTGATGAAAGCATGGAGAT
GAGTGAGTTCGAATGTTTAACAAAAAGGAAATTTTGTGCCATTGAGTTCTTGTTGTTATGTGTGT
GTGCATGAGTA
Found at i:41189481 original size:29 final size:29
Alignment explanation
Indices: 41189346--41189477 Score: 174
Period size: 29 Copynumber: 4.6 Consensus size: 29
41189336 GTGACGAGAT
*
41189346 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41189375 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41189404 AGGCACTAAGTGTGCGTGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
41189433 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
41189462 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
41189478 AGCTCGAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:41191419 original size:20 final size:20
Alignment explanation
Indices: 41191368--41191420 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
41191358 GTTCGCTTCT
*
41191368 CCCACGCCCATGTATGTAGA
1 CCCACGCCCGTGTATGTAGA
41191388 CCCACGCCCGTGTATGTAGA
1 CCCACGCCCGTGTATGTAGA
*
41191408 CCCACGCTCGTGT
1 CCCACGCCCGTGT
41191421 CAATCTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.21
Consensus pattern (20 bp):
CCCACGCCCGTGTATGTAGA
Found at i:41197280 original size:48 final size:47
Alignment explanation
Indices: 41197163--41197494 Score: 342
Period size: 48 Copynumber: 6.9 Consensus size: 47
41197153 GTAAGATGCT
* * * *
41197163 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAT-ATCGGTGCC
1 GATGCCATGT-CCAAACATGGTCTTACACTAGCTCACATATCA--AG-GCC
* * * * *
41197213 GATGCCATGTTCCAAACATGGTCTTACAATAGCCCACATGTCGAGACC
1 GATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATATCAAGGCC
* * * ** * * *
41197261 GATGCCATGTCCTAGACATGGTCTTAGACTAGTTTTCCTATCAATGTC
1 GATGCCATGTCC-AAACATGGTCTTACACTAGCTCACATATCAAGGCC
* *
41197309 GATGGCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGAGGCC
1 GATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATATCAAGGCC
* * *
41197357 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCC
1 GATGCCATGT-CCAAACATGGTCTTACACTAGCTCACATATCAAGGCC
* *
41197405 GATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATCAAGGCC
1 GATGCCATG-TCCAAACATGGTCTTACACTAGCTCACATATCAAGGCC
*
41197453 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
1 GATGCCATGT-CCAAACATGGTCTTACACTAGCTCACATATC
41197495 CCTAGTATCA
Statistics
Matches: 232, Mismatches: 43, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.02
48 188 0.81
49 5 0.02
50 33 0.14
51 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (47 bp):
GATGCCATGTCCAAACATGGTCTTACACTAGCTCACATATCAAGGCC
Found at i:41197333 original size:96 final size:96
Alignment explanation
Indices: 41197163--41197494 Score: 466
Period size: 96 Copynumber: 3.4 Consensus size: 96
41197153 GTAAGATGCT
* **
41197163 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTC--ATATCAATGCCGATGCCATGTTCCAA
* * *
41197228 ACATGGTCTTACAATAGCCCACATGTCGAGACC
64 ACATGGTCTTACAATAGCTCACATATCGAGGCC
* * * * * * *
41197261 GATGCCATGTCCTAGACATGGTCTTAGACTAGTTTTCCTATCAATGTCGATGGCATGTTCCAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAAC
*
41197326 ATGGTCTTACACTAGCTCACATATCGAGGCC
66 ATGGTCTTACAATAGCTCACATATCGAGGCC
41197357 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAAC
* * *
41197422 ATGGTCTTACATTGGCTCACATATCAAGGCC
66 ATGGTCTTACAATAGCTCACATATCGAGGCC
* * *
41197453 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
41197495 CCTAGTATCA
Statistics
Matches: 207, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 175 0.85
98 32 0.15
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (96 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAAC
ATGGTCTTACAATAGCTCACATATCGAGGCC
Found at i:41197430 original size:144 final size:144
Alignment explanation
Indices: 41197163--41197494 Score: 400
Period size: 144 Copynumber: 2.3 Consensus size: 144
41197153 GTAAGATGCT
* * *
41197163 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATATCGGTGCCGATGCCATGTTCCAA
1 GATGCCATGTCCCAAACATGGTCTTACACTGG--CTCACATATCGGTGCCGATGCCATGTCCCAA
* * * *
41197228 ACATGGTCTTACAATAGCCCACATGTCGAGACCGATGCCATGTCCTAGACATGGTCTTAGACTAG
64 ACATGGTCTTACAATAGCCCACATATCAAGACCGATGCCATGTCCTAAACATGGTCTTACACTAG
* ** * * *
41197293 TTTTCCTATCAATGTC
129 CTCACATATCAAGGCC
* * * *
41197309 GATGGCATGTTCCAAACATGGTCTTACACTAGCTCACATATCGAG-GCCGATGCCATGTCCCAGA
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCG-GTGCCGATGCCATGTCCCAAA
* * * * *
41197373 CATGGTCTTACACTAGCTCTCATATCAATG-CCGATGCCATGTTCC-AAACATGGTCTTACATTG
65 CATGGTCTTACAATAGCCCACATATCAA-GACCGATGCCATG-TCCTAAACATGGTCTTACACTA
41197436 GCTCACATATCAAGGCC
128 GCTCACATATCAAGGCC
41197453 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
1 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
41197495 CCTAGTATCA
Statistics
Matches: 158, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
144 125 0.79
145 5 0.03
146 28 0.18
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (144 bp):
GATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGGTGCCGATGCCATGTCCCAAAC
ATGGTCTTACAATAGCCCACATATCAAGACCGATGCCATGTCCTAAACATGGTCTTACACTAGCT
CACATATCAAGGCC
Found at i:41205710 original size:58 final size:57
Alignment explanation
Indices: 41205561--41205710 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 57
41205551 ATCATATAAT
* * * * *
41205561 AGGATTACCAGTCTAGGTTAAATCCTTTATATAACGTAAGCTCAGAGGAGCTCGATT
1 AGGATTACCAGTCCAGGCTAAATCCTTTCTATAACGTAAGCTCAGAGGAGCTAGATC
* * * * *
41205618 AGGATTACCAGTCCAGGCTAAACCCTAATC-ATAACGTATGCTCGAGAGGTA-TTATATC
1 AGGATTACCAGTCCAGGCTAAATCCT-TTCTATAACGTAAGCTC-AGAGG-AGCTAGATC
* *
41205676 GGGATTACCCGTCCAGGCTAAATCCTTTCTATAAC
1 AGGATTACCAGTCCAGGCTAAATCCTTTCTATAAC
41205711 AAGGTCAATG
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
57 37 0.49
58 37 0.49
59 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (57 bp):
AGGATTACCAGTCCAGGCTAAATCCTTTCTATAACGTAAGCTCAGAGGAGCTAGATC
Found at i:41206280 original size:20 final size:20
Alignment explanation
Indices: 41206251--41206291 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
41206241 CAGCACTGTA
*
41206251 TTCATAAAATTTTAGAACTT
1 TTCATAAAATTTTACAACTT
*
41206271 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
41206291 T
1 T
41206292 ACATTTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:41212274 original size:46 final size:46
Alignment explanation
Indices: 41212207--41212378 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
41212197 AACCCGCCCC
*
41212207 TAAGTGAACTCGGACTCAACTCAATGAGCTT-GGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGGCGTTCACATCCA
41212253 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACATCCA
* * * * *
41212301 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
41212346 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
41212379 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 3 0.03
46 57 0.53
47 28 0.26
48 3 0.03
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
Found at i:41212344 original size:93 final size:93
Alignment explanation
Indices: 41212212--41212382 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
41212202 GCCCCTAAGT
* * *
41212212 GAACTCGGACTCAACTCAATGAGCTTGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
41212277 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
41212305 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTT-GGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
41212369 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
41212383 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41212835 original size:30 final size:30
Alignment explanation
Indices: 41212801--41212860 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41212791 ATTTAATACG
41212801 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
41212831 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
41212861 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:41216083 original size:49 final size:49
Alignment explanation
Indices: 41215968--41216180 Score: 349
Period size: 49 Copynumber: 4.4 Consensus size: 49
41215958 TACATATATG
* * * *
41215968 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGCA--TATG
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
41216015 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
*
41216064 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
* *
41216113 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
41216162 TGTGATAAGGCCTAATGGC
1 TGTGATAAGGCCTAATGGC
41216181 TAATGTAAAA
Statistics
Matches: 158, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
47 40 0.25
49 118 0.75
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.29
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
Found at i:41216332 original size:37 final size:37
Alignment explanation
Indices: 41216282--41216366 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
41216272 GGAATATGTT
*
41216282 CCGGGTGAGACCCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
*
41216319 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
41216356 CCGGGTAAGAC
1 CCGGGTAAGAC
41216367 TTCGTAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:41223952 original size:46 final size:45
Alignment explanation
Indices: 41223885--41224054 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 45
41223875 AACCCGCCCC
*
41223885 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT-CA
* *
41223931 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCATCA
* * * *
41223979 TCA-CGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT-CA
41224023 T-AGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
41224055 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 10, Indels: 17
0.80 0.08 0.13
Matches are distributed among these distances:
42 5 0.05
43 3 0.03
44 7 0.07
45 21 0.20
46 53 0.50
47 6 0.06
48 3 0.03
49 2 0.02
50 6 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCA
Found at i:41224053 original size:91 final size:93
Alignment explanation
Indices: 41223890--41224058 Score: 288
Period size: 91 Copynumber: 1.8 Consensus size: 93
41223880 GCCCCTAAGT
* *
41223890 GAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCATACATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATACATAAGTGAACTCGGACTCAACTCAA
41223955 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
41223983 GAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATACATAAGTGAACTCGGACTCAACTCAA
41224046 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41224059 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 35 0.49
92 31 0.43
93 6 0.08
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATACATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:41224507 original size:30 final size:30
Alignment explanation
Indices: 41224473--41224533 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
41224463 CATTTAATAC
41224473 AAACTTTGGAAAAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
* * *
41224503 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACACTTTTGCCCCT
41224533 A
1 A
41224534 GGCTCAGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACACTTTTGCCCCT
Found at i:41232338 original size:16 final size:16
Alignment explanation
Indices: 41232317--41232347 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41232307 ATTTCGATAG
*
41232317 CATAAATATTCATAAA
1 CATAAAAATTCATAAA
41232333 CATAAAAATTCATAA
1 CATAAAAATTCATAA
41232348 GCATGTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (16 bp):
CATAAAAATTCATAAA
Found at i:41234612 original size:47 final size:45
Alignment explanation
Indices: 41234541--41234807 Score: 234
Period size: 47 Copynumber: 5.7 Consensus size: 45
41234531 TGTGTTGTGT
* *
41234541 GCCAGTGTAAGACATGTCTGGGACATGCTTCGGCCACATTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACA-GATGAGA
* *
41234587 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAGATGAGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-CACAGATGAGA
* ** * *
41234635 GCTAAAGTAAGACATGTCTGGGACATGCATCAGCCTCGACAG-TGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGC-C-ACAGATGAGA
* * * *
41234682 GCCAGTGTAAGACATGTCTGGGACACGCATCGGCTA-AGA-GTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATG-AGA
* ** *
41234726 GCTAGTGTAAGACATGTCTGGGACATGCATCAGAACGCATGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-GGCCACA-G-ATGAGA
*
41234774 GCCAGTGTAAGACCATGTCTGAGACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
41234808 TCAATTTATC
Statistics
Matches: 176, Mismatches: 31, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.02
44 30 0.17
45 1 0.01
46 20 0.11
47 62 0.35
48 37 0.21
49 18 0.10
50 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.22
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCACAGATGAGA
Found at i:41244512 original size:21 final size:21
Alignment explanation
Indices: 41244486--41244527 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41244476 CCATGGTGAG
41244486 GGCATTTCTGTAATAATTCTT
1 GGCATTTCTGTAATAATTCTT
41244507 GGCATTTCTGTAATAATTCTT
1 GGCATTTCTGTAATAATTCTT
41244528 TGTATCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (21 bp):
GGCATTTCTGTAATAATTCTT
Found at i:41251878 original size:115 final size:116
Alignment explanation
Indices: 41251653--41251889 Score: 248
Period size: 115 Copynumber: 2.1 Consensus size: 116
41251643 TAGGCCACGT
* * *
41251653 TGGGCCCAATGGGCCCGTGAGCCCATATGGGTGAATCTCACTGTCAGATGGGAAAGGTTGGGCTA
1 TGGGCCCAATGGGCCCGTGAGCCCACATGGGTAAATCTCACTGTAAGATGGGAAAGGTTGGGCTA
* *
41251718 GCCATGTCACACACATGGCTTAGGACATTTCTAGGCCTCAATGGGCTA-AA
66 GCCATGTCACACACATGACTTAGGACATTTCTAGGCCACAATGGGCTAGAA
* * *
41251768 TGGGCCCAATGGGTCCGTGGGCCCGCATGGGTAAATCTCACTGTTAAG-TGGG-AAGTAGTTGGG
1 TGGGCCCAATGGGCCCGTGAGCCCACATGGGTAAATCTCACTG-TAAGATGGGAAAG--GTTGGG
* * *** *** * *
41251831 CTTGTCATGTCACGTGCATGACTTAGGTTGTTT-TCGGCCACATTGGGCTAGAA
63 CTAGCCATGTCACACACATGACTTAGGACATTTCTAGGCCACAATGGGCTAGAA
*
41251884 TAGGCC
1 TGGGCC
41251890 GTGCGGGCCA
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
114 3 0.03
115 56 0.57
116 40 0.40
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (116 bp):
TGGGCCCAATGGGCCCGTGAGCCCACATGGGTAAATCTCACTGTAAGATGGGAAAGGTTGGGCTA
GCCATGTCACACACATGACTTAGGACATTTCTAGGCCACAATGGGCTAGAA
Found at i:41252220 original size:27 final size:26
Alignment explanation
Indices: 41252126--41252221 Score: 111
Period size: 26 Copynumber: 3.7 Consensus size: 26
41252116 GGTCGTTAAG
* *
41252126 ACCCCGGTTTGTAAAATTACCCAAAT
1 ACCCCGATTTGTAAAATTACCAAAAT
*
41252152 ACCCAGATTTGTAAAATTACCAAAAT
1 ACCCCGATTTGTAAAATTACCAAAAT
* * * *
41252178 ATCTCGATTTGCAAAATTACTAAAAT
1 ACCCCGATTTGTAAAATTACCAAAAT
*
41252204 ACCCTCGGTTTGTAAAAT
1 ACCC-CGATTTGTAAAAT
41252222 GATCATAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
26 46 0.81
27 11 0.19
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (26 bp):
ACCCCGATTTGTAAAATTACCAAAAT
Found at i:41252337 original size:26 final size:27
Alignment explanation
Indices: 41252215--41252340 Score: 157
Period size: 27 Copynumber: 4.7 Consensus size: 27
41252205 CCCTCGGTTT
* *
41252215 GTAAAATGATCATAAT-ACCCTGTAGG
1 GTAAAATGATCGTAATGCCCCTGTAGG
* *
41252241 GTAAAATAATCGTAATGCCCCAGTAGG
1 GTAAAATGATCGTAATGCCCCTGTAGG
* *
41252268 GTAAAAAGACCGTAATGCCCCTGTAGG
1 GTAAAATGATCGTAATGCCCCTGTAGG
* *
41252295 TTAAAATGATCGTAATGCCCTTGTAGG
1 GTAAAATGATCGTAATGCCCCTGTAGG
*
41252322 GTAAAATGA-CGAAATGCCC
1 GTAAAATGATCGTAATGCCC
41252341 TTATGTTATG
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 23 0.27
27 62 0.73
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (27 bp):
GTAAAATGATCGTAATGCCCCTGTAGG
Found at i:41252557 original size:27 final size:27
Alignment explanation
Indices: 41252471--41252543 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
41252461 GGAAGTTCTG
* *
41252471 TACTGGTGACTATGTCAC-ATTCACT-A
1 TACTGGTGGCTATGCCACAATT-ACTGA
41252497 TTACTGGTGGCTATGCCACAATTACTGA
1 -TACTGGTGGCTATGCCACAATTACTGA
*
41252525 TACTGGTGGCTTTGCCACA
1 TACTGGTGGCTATGCCACA
41252544 TCTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 37 0.90
28 4 0.10
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACAATTACTGA
Found at i:41256960 original size:27 final size:27
Alignment explanation
Indices: 41256928--41257033 Score: 117
Period size: 27 Copynumber: 3.9 Consensus size: 27
41256918 AAGACCCTCG
41256928 TTTGTAAAATTACCGAAATATCCCTGA
1 TTTGTAAAATTACCGAAATATCCCTGA
** *
41256955 TTTGTAAAATTACTAAAATACCCCTGA
1 TTTGTAAAATTACCGAAATATCCCTGA
* **
41256982 TTTGCAAAATTATTGAAATA-CCCTCGA
1 TTTGTAAAATTACCGAAATATCCCT-GA
*
41257009 TTTGTAAAATGACC-ATAATATCCCT
1 TTTGTAAAATTACCGA-AATATCCCT
41257034 ATAGGGTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
26 5 0.08
27 57 0.86
28 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (27 bp):
TTTGTAAAATTACCGAAATATCCCTGA
Found at i:41257042 original size:27 final size:27
Alignment explanation
Indices: 41257012--41257165 Score: 211
Period size: 27 Copynumber: 5.7 Consensus size: 27
41257002 CCCTCGATTT
* ** *
41257012 GTAAAATGACCATAATATCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
41257039 GTAAAATGACCGTAATGCCCCTGTAAG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
41257066 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
41257093 TTAAAATGATCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
41257120 GTAAAATGACCGTAATGCCCTTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
41257147 GTAAAATGA-CGAAATGCCC
1 GTAAAATGACCGTAATGCCC
41257166 TTATGTTCCG
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 9 0.08
27 104 0.92
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCCTGTAGG
Found at i:41257374 original size:27 final size:26
Alignment explanation
Indices: 41257295--41257375 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 26
41257285 AGGAAGTTCT
* *
41257295 ATACTGGTGACTATGTCACATTCACTG
1 ATACTGGTGGCTATGCCACATT-ACTG
* *
41257322 TTACTTGTGGCTATGCCACAATTACTG
1 ATACTGGTGGCTATGCCAC-ATTACTG
*
41257349 ATACTGGTGGCTTTGCCACATGTACTG
1 ATACTGGTGGCTATGCCACAT-TACTG
41257376 TTTCTAGCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
27 40 0.89
28 3 0.07
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (26 bp):
ATACTGGTGGCTATGCCACATTACTG
Found at i:41257581 original size:32 final size:34
Alignment explanation
Indices: 41257540--41257611 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
41257530 TTAGGCCCAC
* * *
41257540 ACTGCTACTGTATAGGGC-AAGGCCCAGA-CTGT
1 ACTGATACTGAATAAGGCTAAGGCCCAGACCTGT
* *
41257572 ACTGATACTGAATAAGGCTCAGGCCCAGACCTTT
1 ACTGATACTGAATAAGGCTAAGGCCCAGACCTGT
41257606 ACTGAT
1 ACTGAT
41257612 CTGGGCTTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 15 0.45
33 9 0.27
34 9 0.27
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (34 bp):
ACTGATACTGAATAAGGCTAAGGCCCAGACCTGT
Found at i:41265123 original size:40 final size:40
Alignment explanation
Indices: 41265068--41265277 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41265058 AACATTGGAA
41265068 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41265108 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41265148 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41265188 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
41265227 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41265268 CTATATCCGG
1 ATATATCCGG
41265278 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41273258 original size:40 final size:40
Alignment explanation
Indices: 41273203--41273411 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
41273193 AACATTGGAA
41273203 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41273243 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
41273283 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
41273323 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * *
41273362 ACCA-ATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
41273402 CTATATCCGG
1 ATATATCCGG
41273412 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 30 0.20
40 121 0.80
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:41279502 original size:60 final size:60
Alignment explanation
Indices: 41279433--41279551 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
41279423 TATGTATGTG
41279433 TATGAAAGTGCATACTCTTATTGTTTATTAATTACATACAAGATTACTAAGATTTATGCT
1 TATGAAAGTGCATACTCTTATTGTTTATTAATTACATACAAGATTACTAAGATTTATGCT
* * * *
41279493 TATGAAAGTGCATACTCTTATTTTTTATTAATTATATACAAGATTACTATGCTTTATGC
1 TATGAAAGTGCATACTCTTATTGTTTATTAATTACATACAAGATTACTAAGATTTATGC
41279552 GTATTCCCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (60 bp):
TATGAAAGTGCATACTCTTATTGTTTATTAATTACATACAAGATTACTAAGATTTATGCT
Found at i:41284466 original size:60 final size:60
Alignment explanation
Indices: 41284390--41284508 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
41284380 GAGGGAATAC
41284390 GCATAAAGCATAGTAATCTTGTATATAATTAATAAAAAATAAGAGTATGCACTTTCATAA
1 GCATAAAGCATAGTAATCTTGTATATAATTAATAAAAAATAAGAGTATGCACTTTCATAA
* * * *
41284450 GCATAAATCTTAGTAATCTTGTATGTAATTAATAAACAATAAGAGTATGCACTTTCATA
1 GCATAAAGCATAGTAATCTTGTATATAATTAATAAAAAATAAGAGTATGCACTTTCATA
41284509 CACATACATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (60 bp):
GCATAAAGCATAGTAATCTTGTATATAATTAATAAAAAATAAGAGTATGCACTTTCATAA
Found at i:41286261 original size:43 final size:43
Alignment explanation
Indices: 41286180--41286264 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
41286170 ATCAACATCA
* * * *
41286180 TATTTGATTTCTTGTAAGACCCTGTCTGGGACAGTGGCATTGG
1 TATTTGATTACATGTAAGACCCTATCTAGGACAGTGGCATTGG
41286223 TATTTGATTACATGTAAGACCAC-ATCTAGGAC-GTTGGCATTG
1 TATTTGATTACATGTAAGACC-CTATCTAGGACAG-TGGCATTG
41286265 TACGAGCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 34 0.94
44 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (43 bp):
TATTTGATTACATGTAAGACCCTATCTAGGACAGTGGCATTGG
Found at i:41294575 original size:29 final size:30
Alignment explanation
Indices: 41294519--41294581 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
41294509 ATTTGATCTT
* * *
41294519 ATTTGATTCTTTTTAATAGTACATGGATTA
1 ATTTGATTCTATTTAATAATACAGGGATTA
*
41294549 ATTTGATTC-ATTTAATAATAGAGGGATTA
1 ATTTGATTCTATTTAATAATACAGGGATTA
41294578 ATTT
1 ATTT
41294582 AATCTAATCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATACAGGGATTA
Found at i:41295331 original size:30 final size:29
Alignment explanation
Indices: 41295295--41295365 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
41295285 AATTTTTATA
41295295 TTTTTATATTTTTAAAATATTAAAAAATAT
1 TTTTTATATTTTTAAAAT-TTAAAAAATAT
* * * *
41295325 TTTTTATATTTTTTAAATTTTAAGAATTT
1 TTTTTATATTTTTAAAATTTAAAAAATAT
41295354 TTTTTCATATTT
1 TTTTT-ATATTT
41295366 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (29 bp):
TTTTTATATTTTTAAAATTTAAAAAATAT
Found at i:41295582 original size:14 final size:14
Alignment explanation
Indices: 41295563--41295589 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41295553 CTAAATTAGT
41295563 CATAGAGGTTAAAA
1 CATAGAGGTTAAAA
41295577 CATAGAGGTTAAA
1 CATAGAGGTTAAA
41295590 TTTAAAATTA
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:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (14 bp):
CATAGAGGTTAAAA
Found at i:41295607 original size:26 final size:26
Alignment explanation
Indices: 41295571--41295624 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
41295561 GTCATAGAGG
41295571 TTAAAACATAGAGGTTAAATTTAAAA
1 TTAAAACATAGAGGTTAAATTTAAAA
*
41295597 TTAAAGCATAGAGGTTAAATTTAAAA
1 TTAAAACATAGAGGTTAAATTTAAAA
41295623 TT
1 TT
41295625 TAACAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (26 bp):
TTAAAACATAGAGGTTAAATTTAAAA
Found at i:41295719 original size:26 final size:27
Alignment explanation
Indices: 41295679--41295750 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
41295669 TTTTTCCCGC
*
41295679 TCAATTAGTAATTGTACTTTAATTTTA
1 TCAATTAGTCATTGTACTTTAATTTTA
* * *
41295706 -GATTTAGTCATTGTATTTTAATTTTA
1 TCAATTAGTCATTGTACTTTAATTTTA
41295732 TCAATTAGTC-TTGTACTTT
1 TCAATTAGTCATTGTACTTT
41295751 TTGAAATGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 30 0.81
27 7 0.19
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (27 bp):
TCAATTAGTCATTGTACTTTAATTTTA
Found at i:41296335 original size:24 final size:23
Alignment explanation
Indices: 41296299--41296345 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
41296289 AGTATAATGA
41296299 TTTATTTTTTGATATTTTAAATT
1 TTTATTTTTTGATATTTTAAATT
*
41296322 TTTATTATTTTGATATTTTTAATT
1 TTTATT-TTTTGATATTTTAAATT
41296346 AACATTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTATTTTTTGATATTTTAAATT
Found at i:41296555 original size:24 final size:25
Alignment explanation
Indices: 41296502--41296557 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
41296492 TAAATAGTTC
41296502 AAAAATTATAAAAATAAAAATACAT
1 AAAAATTATAAAAATAAAAATACAT
* ** *
41296527 CAAAATTA-AAATTTAAAAATATAT
1 AAAAATTATAAAAATAAAAATACAT
41296551 AAAAATT
1 AAAAATT
41296558 TCATAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATTATAAAAATAAAAATACAT
Found at i:41297967 original size:27 final size:26
Alignment explanation
Indices: 41297930--41297982 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
41297920 GAATCTTTGA
*
41297930 GATTCTTAATAAATTTTTA-GGTTTT
1 GATTCTTAATAAAGTTTTAGGGTTTT
41297955 GATTCTTTAAATAAAGTTTTAGGGTTTT
1 GATTC-TT-AATAAAGTTTTAGGGTTTT
41297983 ATAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 5 0.21
26 2 0.08
27 11 0.46
28 6 0.25
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (26 bp):
GATTCTTAATAAAGTTTTAGGGTTTT
Found at i:41298042 original size:4 final size:4
Alignment explanation
Indices: 41298033--41298057 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
41298023 AAGATGAAGG
41298033 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
41298058 AATCAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:41298701 original size:15 final size:15
Alignment explanation
Indices: 41298681--41298709 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41298671 TTATTATAAT
41298681 TGTGTGTATATATTA
1 TGTGTGTATATATTA
41298696 TGTGTGTATATATT
1 TGTGTGTATATATT
41298710 TTATATGCAT
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:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (15 bp):
TGTGTGTATATATTA
Found at i:41304151 original size:29 final size:29
Alignment explanation
Indices: 41304065--41304172 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
41304055 ACGTTATTTC
* * * *
41304065 GATTTTGGTTTAAGGTTTTAGAGTTT-GTG
1 GATTTTGGGTTAGGGTTTTTGAATTTAG-G
* *
41304094 GATTTTGGGTTTAGGGTTATCGAATTTAGG
1 GATTTTGGG-TTAGGGTTTTTGAATTTAGG
41304124 GATTTTGGGTTAGGGTTTTTG-ATATTAGG
1 GATTTTGGGTTAGGGTTTTTGAAT-TTAGG
* *
41304153 GATTTTTGTTTAGGGTTTTT
1 GATTTTGGGTTAGGGTTTTT
41304173 TATTTTTGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.03
29 41 0.61
30 23 0.34
31 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.31, T:0.51
Consensus pattern (29 bp):
GATTTTGGGTTAGGGTTTTTGAATTTAGG
Found at i:41304173 original size:14 final size:14
Alignment explanation
Indices: 41304118--41304172 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
41304108 GGTTATCGAA
*
41304118 TTTAGGGATTTTGG
1 TTTAGGGATTTTTG
*
41304132 GTTAGGG-TTTTTG
1 TTTAGGGATTTTTG
41304145 ATATTAGGGATTTTTG
1 -T-TTAGGGATTTTTG
41304161 TTTAGGG-TTTTT
1 TTTAGGGATTTTT
41304173 TATTTTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 10 0.29
14 12 0.34
15 7 0.20
16 6 0.17
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.55
Consensus pattern (14 bp):
TTTAGGGATTTTTG
Found at i:41305368 original size:57 final size:58
Alignment explanation
Indices: 41305292--41305418 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 58
41305282 GTGACAGTGG
* * * * * *
41305292 TAAATGTGGTGA-AGGTTTTGAAAGG-TTAAATGGAGAGGGTGTTGAGGTTGTTGGCAC
1 TAAAGGTGGTGAGAGGTTTTG-AAGGTTTAAATGGAGAGGGCGTTAAGGTTGCTAGCAA
*
41305349 TAAAGGTGGTGAGA-GTTTTGAAGGTTTAAATGGGGAGGGCGTTAAGGTTGCTAGCAA
1 TAAAGGTGGTGAGAGGTTTTGAAGGTTTAAATGGAGAGGGCGTTAAGGTTGCTAGCAA
41305406 TAAAGGTGGTGAG
1 TAAAGGTGGTGAG
41305419 GGTGGTGAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
56 4 0.07
57 56 0.92
58 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.29
Consensus pattern (58 bp):
TAAAGGTGGTGAGAGGTTTTGAAGGTTTAAATGGAGAGGGCGTTAAGGTTGCTAGCAA
Found at i:41305424 original size:9 final size:9
Alignment explanation
Indices: 41305410--41305452 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
41305400 TAGCAATAAA
41305410 GGTGGTGAG
1 GGTGGTGAG
41305419 GGTGGTGA-
1 GGTGGTGAG
41305427 GGT--TGAG
1 GGTGGTGAG
*
41305434 GGTGGTGAA
1 GGTGGTGAG
41305443 GGTGGTGAG
1 GGTGGTGAG
41305452 G
1 G
41305453 ATTTTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 3 0.10
9 20 0.69
ACGTcount: A:0.14, C:0.00, G:0.63, T:0.23
Consensus pattern (9 bp):
GGTGGTGAG
Found at i:41309393 original size:158 final size:158
Alignment explanation
Indices: 41309081--41309397 Score: 492
Period size: 158 Copynumber: 2.0 Consensus size: 158
41309071 GGTAAAGGTC
* * * *
41309081 ACAACAGAGGATCATGCAATCAATCTAACACAATTGGATCACAGGTATATCTTAAACACTTTTTC
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCTTAAACACTTTTTC
* *
41309146 ACTGTTAAGTTTCAAAATATTTAAATCTAATTTGGGGTTGTGCATTTTTTTCTCAGTCTGGTACG
66 ACTGTCAAGTTTCAAAATATTTAAATCTAATTTGGGGTTGGGCATTTTTTTCTCAGTCTGGTACG
41309211 AGTACAAGAACTAGAAGCCAAAAAAGGA
131 AGTACAAGAACTAGAAGCCAAAAAAGGA
*
41309239 ACAACAGAAGATCATGCAATCAACCTAACACAACTAGATCATAGGTATAT-TGTAAACACTTTTT
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCT-TAAACACTTTTT
* * * *
41309303 TAGTGTCAAGTTTCAAAATATTTAAATCTAATTTGGGGTTGGGCATTTTTTTCCTTAGTTTGGTA
65 CACTGTCAAGTTTCAAAATATTTAAATCTAATTTGGGGTTGGGCATTTTTTT-CTCAGTCTGGTA
* *
41309368 CGAGTACAATAACTAGAAGCTAAAAAAGGA
129 CGAGTACAAGAACTAGAAGCCAAAAAAGGA
41309398 TAGCATATCA
Statistics
Matches: 144, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
157 1 0.01
158 105 0.73
159 38 0.26
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (158 bp):
ACAACAGAAGATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCTTAAACACTTTTTC
ACTGTCAAGTTTCAAAATATTTAAATCTAATTTGGGGTTGGGCATTTTTTTCTCAGTCTGGTACG
AGTACAAGAACTAGAAGCCAAAAAAGGA
Found at i:41326338 original size:43 final size:43
Alignment explanation
Indices: 41326234--41326351 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 43
41326224 TGGATTTACG
* * * *
41326234 ATATGTGATTGCGTGTAAGACCATGTCTAGGACATCGGCATCGT
1 ATATGTGATT-CATGTAAGACCCTGTCTGGGACATCGGCATCGA
* *
41326278 ATATGTAATTCACGTAAGACCCTGTCTGGGACAGT-GGCATC-A
1 ATATGTGATTCATGTAAGACCCTGTCTGGGACA-TCGGCATCGA
*
41326320 ATCTGTGATTACATGTAAGACCAC-GTCTGGGA
1 ATATGTGATT-CATGTAAGACC-CTGTCTGGGA
41326352 TGTTGGCATT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
42 8 0.13
43 43 0.69
44 11 0.18
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
ATATGTGATTCATGTAAGACCCTGTCTGGGACATCGGCATCGA
Found at i:41330852 original size:29 final size:29
Alignment explanation
Indices: 41330777--41330871 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
41330767 TACAAAACTC
* *
41330777 AACCCATCTCGT-CAAAATTATTTCTTCAG
1 AACCCATCTTGTAC-AAATTATTTTTTCAG
* *
41330806 AAACCATCCCCT-TA-AAATTATTTTTTCAG
1 AACCCAT--CTTGTACAAATTATTTTTTCAG
*
41330835 AACCCATCTTGTACAAATTATTTTTTTTAG
1 AACCCATCTTGTACAAATTA-TTTTTTCAG
41330865 AACCCAT
1 AACCCAT
41330872 AAACCCTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 32 0.60
30 16 0.30
31 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
AACCCATCTTGTACAAATTATTTTTTCAG
Found at i:41335755 original size:9 final size:9
Alignment explanation
Indices: 41335741--41335782 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
41335731 TTTCTTTTTA
41335741 TTTATAATT
1 TTTATAATT
41335750 TTTAT-ATT
1 TTTATAATT
*
41335758 TTTAAATCATT
1 TTT--ATAATT
41335769 TTTATAATT
1 TTTATAATT
41335778 TTTAT
1 TTTAT
41335783 CAAAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 6 0.21
9 15 0.52
10 2 0.07
11 6 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTATAATT
Found at i:41336059 original size:23 final size:23
Alignment explanation
Indices: 41336013--41336061 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
41336003 AGTTAATTTC
41336013 AAAAAGTTGGGTAACTAAATAAAA
1 AAAAAGTTGGGTAACTAAA-AAAA
* *
41336037 AAATAGTTGGGTGAC-AAAAAAA
1 AAAAAGTTGGGTAACTAAAAAAA
41336059 AAA
1 AAA
41336062 CCAAATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 7 0.30
23 3 0.13
24 13 0.57
ACGTcount: A:0.59, C:0.04, G:0.18, T:0.18
Consensus pattern (23 bp):
AAAAAGTTGGGTAACTAAAAAAA
Found at i:41337821 original size:58 final size:58
Alignment explanation
Indices: 41337758--41337875 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
41337748 TGCTTATAAG
41337758 ATGTTAATTGTATCATGGATGGTATTTTTGGGTTATGTTATGTATTAGGAAATATGTT
1 ATGTTAATTGTATCATGGATGGTATTTTTGGGTTATGTTATGTATTAGGAAATATGTT
41337816 ATGTTAATTGTATCATGGATGGTATTTTTGGGTTATGTTATGTATTAGGAAATATGTT
1 ATGTTAATTGTATCATGGATGGTATTTTTGGGTTATGTTATGTATTAGGAAATATGTT
41337874 AT
1 AT
41337876 TGATGGTGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (58 bp):
ATGTTAATTGTATCATGGATGGTATTTTTGGGTTATGTTATGTATTAGGAAATATGTT
Found at i:41340502 original size:25 final size:26
Alignment explanation
Indices: 41340474--41340535 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
41340464 TTAATATTGT
*
41340474 ATAAAT-TGTGAAAAC-GAGATTATAG
1 ATAAATGTATGAAAACAG-GATTATAG
*
41340499 AT-AATGTATTAAAACAGGATTATAG
1 ATAAATGTATGAAAACAGGATTATAG
41340524 AT-AATGTATGAA
1 ATAAATGTATGAA
41340536 GTGTGAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 3 0.09
25 28 0.88
26 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (26 bp):
ATAAATGTATGAAAACAGGATTATAG
Found at i:41343148 original size:22 final size:22
Alignment explanation
Indices: 41343077--41343181 Score: 88
Period size: 23 Copynumber: 4.6 Consensus size: 22
41343067 ACAGCTTATA
* * *
41343077 AGAGCTTATTGTTTCAGCTTATT
1 AGAGCTTACTG-TTCAGCTCAAT
*
41343100 GGAGCTTACTGATTCAGCTCGAA-
1 AGAGCTTACTG-TTCAGCTC-AAT
*
41343123 AGAGCTTACTGTTCATCTCAAT
1 AGAGCTTACTGTTCAGCTCAAT
41343145 AGAGCTTATCAT-TTCTAGCTCAAT
1 AGAGCTTA-C-TGTTC-AGCTCAAT
*
41343169 AGAGCTTATTGTT
1 AGAGCTTACTGTT
41343182 TATCAGCTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.03
22 16 0.24
23 32 0.48
24 17 0.25
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:41347820 original size:47 final size:46
Alignment explanation
Indices: 41347703--41347875 Score: 187
Period size: 45 Copynumber: 3.8 Consensus size: 46
41347693 GGATGGTTGA
*
41347703 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAT
* *
41347750 G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA-T
* * *
41347793 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAC
1 --GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGC-AAT
*
41347843 GC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
41347876 TAGGGGCGGG
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 30 0.28
46 29 0.27
47 30 0.28
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAT
Found at i:41347871 original size:46 final size:45
Alignment explanation
Indices: 41347707--41347877 Score: 204
Period size: 46 Copynumber: 3.7 Consensus size: 45
41347697 GGTTGAGCAT
* *
41347707 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
* * *
41347752 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAC---GC
*
41347797 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGC
*
41347845 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41347878 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
42 6 0.06
44 2 0.02
45 29 0.27
46 31 0.29
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGC
Found at i:41348138 original size:19 final size:20
Alignment explanation
Indices: 41348101--41348138 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41348091 ATAAGGTGGT
41348101 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
41348121 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
41348139 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:41355316 original size:46 final size:46
Alignment explanation
Indices: 41355266--41355438 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
41355256 TGGTTGAGCA
*
41355266 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
41355312 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
41355359 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
41355405 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41355439 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:41355422 original size:93 final size:93
Alignment explanation
Indices: 41355263--41355433 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41355253 GGATGGTTGA
* *
41355263 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
41355328 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
41355356 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
41355421 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41355434 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41355700 original size:19 final size:20
Alignment explanation
Indices: 41355663--41355700 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
41355653 ATAAGGTGGT
41355663 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
41355683 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
41355701 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:41360189 original size:24 final size:24
Alignment explanation
Indices: 41359970--41360187 Score: 384
Period size: 24 Copynumber: 9.1 Consensus size: 24
41359960 GCAAAGACCA
41359970 TATGGCACTATGTGTGCGA-TTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41359993 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41360017 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41360041 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41360065 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41360089 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41360113 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41360137 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
41360161 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
41360185 TAT
1 TAT
41360188 AGTCACATTC
Statistics
Matches: 188, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
23 19 0.10
24 169 0.90
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:41368170 original size:24 final size:24
Alignment explanation
Indices: 41367950--41368168 Score: 384
Period size: 24 Copynumber: 9.1 Consensus size: 24
41367940 GCAAAGACCA
*
41367950 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
*
41367974 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41367998 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41368022 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41368046 TATGGCACTATGTGTGCGATTCAC
1 TATGGCACTATGTGTGCGATTTAC
41368070 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
41368094 TATGGCACTATGTGTGCGATTTAC
1 TATGGCACTATGTGTGCGATTTAC
*
41368118 TATGGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
* *
41368142 TATAGCACTATGTGTGCGATTTGC
1 TATGGCACTATGTGTGCGATTTAC
41368166 TAT
1 TAT
41368169 AGTCACATTC
Statistics
Matches: 190, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 190 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (24 bp):
TATGGCACTATGTGTGCGATTTAC
Found at i:41370822 original size:19 final size:21
Alignment explanation
Indices: 41370798--41370838 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41370788 TTTGGCATAA
41370798 ACATGGG-ACC-GAGGAAGCT
1 ACATGGGAACCTGAGGAAGCT
41370817 ACATGGGAACCTGAGGAAGCT
1 ACATGGGAACCTGAGGAAGCT
41370838 A
1 A
41370839 TGTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.34, C:0.20, G:0.34, T:0.12
Consensus pattern (21 bp):
ACATGGGAACCTGAGGAAGCT
Found at i:41372250 original size:24 final size:23
Alignment explanation
Indices: 41372168--41372250 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
41372158 TTACTATTTC
* * *
41372168 AGAGCTTATCGATTCAGCTGGAA-
1 AGAGCTTATTGTTTCAGCT-CAAT
*
41372191 AGAGCTTATT-ATTCAGCTCAAT
1 AGAGCTTATTGTTTCAGCTCAAT
**
41372213 AGAGCTTACCGTTTCCAGCTCAAT
1 AGAGCTTATTGTTT-CAGCTCAAT
41372237 AGAGCTTATTGTTT
1 AGAGCTTATTGTTT
41372251 ATCAGCTTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.04
22 16 0.32
23 11 0.22
24 21 0.42
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (23 bp):
AGAGCTTATTGTTTCAGCTCAAT
Found at i:41385293 original size:27 final size:27
Alignment explanation
Indices: 41385243--41385372 Score: 179
Period size: 27 Copynumber: 4.8 Consensus size: 27
41385233 ATTACCAAAG
* *
41385243 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
41385270 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
41385297 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
41385324 TACCCTTGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
41385351 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
41385373 TAAAATACCC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 91 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:41385351 original size:54 final size:54
Alignment explanation
Indices: 41385243--41385392 Score: 183
Period size: 54 Copynumber: 2.8 Consensus size: 54
41385233 ATTACCAAAG
* * ** *
41385243 TACCCCCGATTTACATAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTTGATTTACAGAATTACCGTTT
* * **
41385297 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTATTTTACCCTTGATTTACAGAATTACCGTTT
*** *
41385351 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACA
1 TACCCTCGATTTACAAAATTACTATTTTACCCTTGATTTACA
41385393 AAATACCAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTACAAAATTACTATTTTACCCTTGATTTACAGAATTACCGTTT
Found at i:41385381 original size:27 final size:27
Alignment explanation
Indices: 41385230--41385570 Score: 149
Period size: 27 Copynumber: 12.7 Consensus size: 27
41385220 ATCGACTTGT
* *
41385230 AAAATTACCAAAGTACCCCCGATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* ****
41385257 ATAATTACCGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* **** *
41385284 AGAATTACCGTTTTACCCTCGATTTAT
1 AAAATTACCAAAATACCCTCGATTTAC
* * *** *
41385311 AGAATTACTATTTTACCCTTGATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* ******
41385338 AGAATTATTGTTTTACCCTCGATTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* * *
41385365 AAAATTACTAAAATACCCTTGGTTTAC
1 AAAATTACCAAAATACCCTCGATTTAC
* *
41385392 AAAA-TACCAAAATACCCTCGA-TCAGT
1 AAAATTACCAAAATACCCTCGATTTA-C
* * *
41385418 AAAATTACCAAAATACCCT-GGTCTAT
1 AAAATTACCAAAATACCCTCGATTTAC
* * * **
41385444 AAAATTGCTAAAATACCC-CTGGTTTGT
1 AAAATTACCAAAATACCCTC-GATTTAC
* **
41385471 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCTCGA-TTTAC
* **
41385498 AAAATTACCAAAATACCACT-GGTTTGT
1 AAAATTACCAAAATACC-CTCGATTTAC
* *
41385525 GAAATTACCAGAATACCC-CTGATTTAC
1 AAAATTACCAAAATACCCTC-GATTTAC
41385552 AAAATTA-CAGAAATACCCT
1 AAAATTACCA-AAATACCCT
41385571 TGACTTTCTA
Statistics
Matches: 254, Mismatches: 48, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
25 2 0.01
26 39 0.15
27 212 0.83
28 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCGATTTAC
Found at i:41385431 original size:53 final size:54
Alignment explanation
Indices: 41385351--41385652 Score: 229
Period size: 54 Copynumber: 5.6 Consensus size: 54
41385341 ATTATTGTTT
* ** * *
41385351 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAA-TACCAAAA
1 TACCCTCGGTTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAA
* ** * * * *
41385404 TACCCTCGATCAGTAAAATTACCAAAATA-CCCTGGTCTATAAAATTGCTAAAA
1 TACCCTCGGTTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAA
* **
41385457 TACCC-CTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTC-GGTTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAA
* * *
41385511 TACCACT-GGTTTGTGAAATTACCAGAATACCCCTGATTTACAAAATTA-CAGAAA
1 TACC-CTCGGTTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCA-AAA
* * * * * ** **
41385565 TACCCTTGACTTTCTAAAAATTA-TAGGAATACCATTGGTTTACAAAATTACTGAAA
1 TACCCTCG-GTTTGT-AAAATTACCA-AAATACCCCTGGTTTACAAAATTACCAAAA
* * * *
41385621 TACCCTTGGTTTGTAGATTTACCAAAACACCC
1 TACCCTCGGTTTGTAAAATTACCAAAATACCC
41385653 TTGTTGGGTG
Statistics
Matches: 196, Mismatches: 41, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
52 13 0.07
53 58 0.30
54 76 0.39
55 11 0.06
56 38 0.19
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (54 bp):
TACCCTCGGTTTGTAAAATTACCAAAATACCCCTGGTTTACAAAATTACCAAAA
Found at i:41385566 original size:81 final size:80
Alignment explanation
Indices: 41385365--41385569 Score: 227
Period size: 81 Copynumber: 2.6 Consensus size: 80
41385355 CTCGATTTAC
* * * * **
41385365 AAAATTACTAAAATACCCTTGGTTTACAAAA-TACCAAAATA-CCCTCGATCAGTAAAATTACCA
1 AAAATTACCAAAATACCCCTGATTTACAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCA
41385428 AAATACCCTGGTCTAT
65 AAATACCCTGGTCTAT
* * * **
41385444 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCTGATTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
* *
41385509 AATACCACTGGTTTGT
66 AATACC-CTGGTCTAT
* *
41385525 GAAATTACCAGAATACCCCTGATTTACAAAATTA-CAGAAATACCC
1 AAAATTACCAAAATACCCCTGATTTACAAAATTACCA-AAATACCC
41385570 TTGACTTTCT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
79 27 0.25
80 32 0.30
81 47 0.44
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.27
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTGATTTACAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAA
AATACCCTGGTCTAT
Found at i:41385622 original size:27 final size:27
Alignment explanation
Indices: 41385324--41385632 Score: 128
Period size: 27 Copynumber: 11.4 Consensus size: 27
41385314 ATTACTATTT
* * * ***
41385324 TACCCTTGATTTACAGAATTATTGTTT
1 TACCCTTGGTTTACAAAATTACTGAAA
* * *
41385351 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
**
41385378 TACCCTTGGTTTACAAAA-TACCAAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
* * * * **
41385404 TACCC-TCGATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTA-CAAAATTACTGAAA
* * * *
41385431 TACCC-TGGTCTATAAAATTGCTAAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
* ** **
41385457 TACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
* * ** **
41385484 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
*** *
41385511 TACCAC-TGGTTTGTGAAATTAC-CAGAA
1 TACC-CTTGGTTTACAAAATTACTGA-AA
* * *
41385538 TACCCCTGATTTACAAAATTACAGAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
* *
41385565 TACCCTTGACTTT-CTAAAAATTA-TAGGAA
1 TACCCTTG-GTTTAC--AAAATTACT-GAAA
*
41385594 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACTGAAA
41385621 TACCCTTGGTTT
1 TACCCTTGGTTT
41385633 GTAGATTTAC
Statistics
Matches: 228, Mismatches: 41, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
25 4 0.02
26 35 0.15
27 162 0.71
28 9 0.04
29 18 0.08
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACTGAAA
Found at i:41385716 original size:26 final size:26
Alignment explanation
Indices: 41385687--41385745 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
41385677 CCCCTATTAT
41385687 GTAAAAAGACCGT-TAGCCCCTGTAGG
1 GTAAAAAGACCGTATA-CCCCTGTAGG
** *
41385713 GTAAAGTGACCGTAATACCCCTGTATG
1 GTAAAAAGACCGT-ATACCCCTGTAGG
41385740 GTAAAA
1 GTAAAA
41385746 TGACGAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 11 0.41
27 14 0.52
28 2 0.07
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (26 bp):
GTAAAAAGACCGTATACCCCTGTAGG
Found at i:41386596 original size:25 final size:25
Alignment explanation
Indices: 41386558--41386627 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41386548 AGGAAGTGCT
*
41386558 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
41386583 AAAAGGCCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
41386608 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
41386628 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:41386881 original size:31 final size:31
Alignment explanation
Indices: 41386846--41387079 Score: 387
Period size: 31 Copynumber: 7.5 Consensus size: 31
41386836 TGTTTACAGT
*
41386846 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41386877 AAAGGATTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41386908 AAAGGCTTCGGCCCAGAGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41386939 TAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41386970 TAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
41387001 TAAGGCTTCGACCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41387032 TAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
41387063 AAAGGATTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
41387080 AACCGTTAAA
Statistics
Matches: 193, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 193 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:41389701 original size:48 final size:48
Alignment explanation
Indices: 41389643--41389827 Score: 228
Period size: 48 Copynumber: 3.8 Consensus size: 48
41389633 GATACTAGGG
* *
41389643 ATATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATTT
1 ATATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTT
* * * *
41389691 ATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGTATCGGCCTTG
1 ATATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTT
* * * *
41389739 ACATGTAG-GCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCATCGAT
1 ATATG-AGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCAT--TT
* *
41389789 ATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCA
1 ATATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCA
41389828 CCAGCATCTT
Statistics
Matches: 115, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
48 79 0.69
49 4 0.03
50 32 0.28
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (48 bp):
ATATGAGAGCTAGTGTAAGACCATGTCTGGAACATGGCATCGGCATTT
Found at i:41398981 original size:68 final size:71
Alignment explanation
Indices: 41398896--41399031 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 71
41398886 TTTTTTAAAT
41398896 TTAATATTAAATTTAATTTAATACTTATCTT-AAGAGT-AT-TT-TATTAATTCAATATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATCTTGAAGA-TAATATTCTATTAATTCAATATTAAAGT
41398957 GATTATC
65 GATTATC
** * *
41398964 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATATTAAAGT
1 TTAATATTAAATTTAATTTAATACTTATCTTGAAGAT-AATATTCTATTAATTCAATATTAAAGT
41399029 GAT
65 GAT
41399032 CAAGTTTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
68 30 0.51
69 3 0.05
70 2 0.03
71 2 0.03
72 22 0.37
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (71 bp):
TTAATATTAAATTTAATTTAATACTTATCTTGAAGATAATATTCTATTAATTCAATATTAAAGTG
ATTATC
Found at i:41408903 original size:12 final size:12
Alignment explanation
Indices: 41408860--41408905 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
41408850 TGTAAAGAGA
41408860 AAATTTTCTAAAG
1 AAATTTT-TAAAG
*
41408873 AAATTATTAAAGG
1 AAATTTTTAAA-G
41408886 AAATTTTTAAAG
1 AAATTTTTAAAG
*
41408898 ATATTTTT
1 AAATTTTT
41408906 CTTATTTACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (12 bp):
AAATTTTTAAAG
Found at i:41410497 original size:14 final size:15
Alignment explanation
Indices: 41410473--41410501 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41410463 TTGAGATATG
41410473 AAATGTATGTTTTTA
1 AAATGTATGTTTTTA
41410488 AAAT-TATGTTTTTA
1 AAATGTATGTTTTTA
41410502 CAGTAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
AAATGTATGTTTTTA
Found at i:41411892 original size:42 final size:44
Alignment explanation
Indices: 41411776--41411909 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 44
41411766 ATATAGGATT
* * * *
41411776 TCGATATG-TGATTTCGTGTAAGACCAC-ATTAGGGACGTTGGCA
1 TCGATGTGATGATTTCGTGTAAGA-CACTGTTTGGGACATTGGCA
* *
41411819 TCGATTTGA-GATCTACGTGTAAGAC-CATGTTTGGGACATTGGCA
1 TCGATGTGATGAT-TTCGTGTAAGACAC-TGTTTGGGACATTGGCA
*
41411863 TCG-TGT-ATGATTTCGTGTAAGACACTGTTTGGGACAGTGGCA
1 TCGATGTGATGATTTCGTGTAAGACACTGTTTGGGACATTGGCA
41411905 TCGAT
1 TCGAT
41411910 ATTTGATTAC
Statistics
Matches: 76, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
42 32 0.42
43 18 0.24
44 26 0.34
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (44 bp):
TCGATGTGATGATTTCGTGTAAGACACTGTTTGGGACATTGGCA
Found at i:41411939 original size:43 final size:41
Alignment explanation
Indices: 41411814--41411939 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 41
41411804 TTAGGGACGT
* *
41411814 TGGCATCGATTTGAGATCTACGTGTAAGACCATGTTTGGGACAT
1 TGGCATCGATTT-TGAT-TACGTGTAAGACC-TGTTTGGGACAG
* *
41411858 TGGCATCG-TGTATGATTTCGTGTAAGACACTGTTTGGGACAG
1 TGGCATCGAT-TTTGATTACGTGTAAGAC-CTGTTTGGGACAG
* *
41411900 TGGCATCGATATTTGATTACATGTAAGACCTCGTCTGGGA
1 TGGCATCGAT-TTTGATTACGTGTAAGACCT-GTTTGGGA
41411940 TGTTGGCATT
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 32 0.46
43 28 0.41
44 9 0.13
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (41 bp):
TGGCATCGATTTTGATTACGTGTAAGACCTGTTTGGGACAG
Found at i:41419527 original size:42 final size:44
Alignment explanation
Indices: 41419418--41419542 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 44
41419408 TTCCGATATG
* *
41419418 TGATTTCGTGTAAGACCAC-GTCT-GGACGTTGGCATCGATTTGA
1 TGATTTCGTGTAAGACC-CTGTCTGGGACATTGGCATCGATGTGA
* * * * *
41419461 -GATCTACATGTAAGACCATTTCTGGGACATTAGCATCG-TGT-A
1 TGAT-TTCGTGTAAGACCCTGTCTGGGACATTGGCATCGATGTGA
*
41419503 TGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCGAT
1 TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGAT
41419543 ATTTGATTAC
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
42 32 0.50
43 20 0.31
44 12 0.19
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (44 bp):
TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGATGTGA
Found at i:41419569 original size:43 final size:42
Alignment explanation
Indices: 41419411--41419581 Score: 102
Period size: 43 Copynumber: 4.0 Consensus size: 42
41419401 CATGGGATTC
* * * **
41419411 CGATATGTGATTTCGTGTAAGACCACGTCT-GGACGTTGGCAT
1 CGATATTTGATTACATGTAAGACTTCGTCTGGGACG-TGGCAT
* * *
41419453 CGAT-TTGAGATCTACATGTAAGACCATT--TCTGGGACATTAGCAT
1 CGATATT-TGAT-TACATGTAAGA-C-TTCGTCTGGGAC-GTGGCAT
* * * * *
41419497 CG-TGTATGATTTCGTGTAAGAC-CCTGTCTGGGACAGTGGCAT
1 CGATATTTGATTACATGTAAGACTTC-GTCTGGGAC-GTGGCAT
41419539 CGATATTTGATTACATGTAAGACTTCGTCTGGGACGTGTGCAT
1 CGATATTTGATTACATGTAAGACTTCGTCTGGGACGTG-GCAT
41419582 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 20, Indels: 25
0.68 0.14 0.18
Matches are distributed among these distances:
41 2 0.02
42 35 0.36
43 45 0.47
44 14 0.15
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (42 bp):
CGATATTTGATTACATGTAAGACTTCGTCTGGGACGTGGCAT
Found at i:41422375 original size:40 final size:40
Alignment explanation
Indices: 41422313--41422492 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
41422303 TATTCGGATG
* *
41422313 ATATCCGGGCT-AGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
41422352 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
**
41422392 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
41422432 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
41422472 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
41422493 ATACTTGGGT
Statistics
Matches: 129, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
39 24 0.19
40 103 0.80
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:41430559 original size:40 final size:40
Alignment explanation
Indices: 41430504--41430727 Score: 306
Period size: 40 Copynumber: 5.5 Consensus size: 40
41430494 TATTCGGATG
41430504 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
41430544 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
41430587 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
41430627 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
41430667 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
41430707 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
41430728 ATACTTGGGT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.69
41 1 0.01
43 37 0.22
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:41430647 original size:83 final size:80
Alignment explanation
Indices: 41430508--41430727 Score: 302
Period size: 83 Copynumber: 2.7 Consensus size: 80
41430498 CGGATGATAT
* **
41430508 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
41430573 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
41430591 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
41430656 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * *
41430671 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
41430728 ATACTTGGGT
Statistics
Matches: 127, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
79 16 0.13
80 45 0.35
81 2 0.02
83 64 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:41434386 original size:25 final size:25
Alignment explanation
Indices: 41434348--41434472 Score: 105
Period size: 25 Copynumber: 5.0 Consensus size: 25
41434338 GGACTAACAC
* *
41434348 GAATTATCTGGAAAGCCTTTGTGGT
1 GAATTCTCTTGAAAGCCTTTGTGGT
41434373 GAATTCTCTTGAAAGCCTTTAG-GG-
1 GAATTCTCTTGAAAGCCTTT-GTGGT
* * *
41434397 AAATTCTCTAGAAAGCCTTTGTGGC
1 GAATTCTCTTGAAAGCCTTTGTGGT
* * *
41434422 GAATACTC-TGTAAGGCCTTTGTGGA
1 GAATTCTCTTG-AAAGCCTTTGTGGT
* *
41434447 GAACTCTC-TGTAAAACCTTTGTGGT
1 GAATTCTCTTG-AAAGCCTTTGTGGT
41434472 G
1 G
41434473 TTCTATTTAG
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.01
24 21 0.26
25 59 0.72
26 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (25 bp):
GAATTCTCTTGAAAGCCTTTGTGGT
Found at i:41434414 original size:49 final size:49
Alignment explanation
Indices: 41434348--41434472 Score: 130
Period size: 49 Copynumber: 2.5 Consensus size: 49
41434338 GGACTAACAC
* *
41434348 GAATTATCTGGAAAGCCTTTGTGGTGAATTCTCT-TGAAAGCCTTTAG-GGA
1 GAATTCTCT-GAAAGCCTTTGTGGTGAATACTCTGT-AAAGCCTTT-GTGGA
* *
41434398 -AATTCTCTAGAAAGCCTTTGTGGCGAATACTCTGTAAGGCCTTTGTGGA
1 GAATTCTCT-GAAAGCCTTTGTGGTGAATACTCTGTAAAGCCTTTGTGGA
* *
41434447 GAACTCTCTGTAAAACCTTTGTGGTG
1 GAATTCTCTG-AAAGCCTTTGTGGTG
41434473 TTCTATTTAG
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
48 1 0.02
49 41 0.65
50 21 0.33
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (49 bp):
GAATTCTCTGAAAGCCTTTGTGGTGAATACTCTGTAAAGCCTTTGTGGA
Found at i:41435074 original size:26 final size:24
Alignment explanation
Indices: 41435027--41435074 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
41435017 CAAGGTTTGA
*
41435027 AAGGATGTCCAGAATCTTAAAATC
1 AAGGATGTCCAGAATATTAAAATC
*
41435051 AAGGATTTCGCAGTAATATTAAAA
1 AAGGATGTC-CAG-AATATTAAAA
41435075 AGGTAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 3 0.15
26 9 0.45
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (24 bp):
AAGGATGTCCAGAATATTAAAATC
Found at i:41436894 original size:46 final size:46
Alignment explanation
Indices: 41436779--41436989 Score: 173
Period size: 46 Copynumber: 4.6 Consensus size: 46
41436769 GTGTATACGT
* * **
41436779 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-ACGA-AATTTAG
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCAAC-ATCATTGCG
* *
41436824 GC-GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCATCGCG
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGC-AACATCATTGCG
* * * * *
41436870 GCTGATGCATGT-CCAGACATGTCTTACATTGGCACTCACCTTTAC-
1 GCTGATGCATGTCCCAGACATGTCTTACACTGGCA-ACATCATTGCG
* * * *
41436915 GCCGATGCCATGTCCCAGACGTGGTCTTACACTGGCTATCATGA-TGCG
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTGGC-AACATCATTGCG
* *
41436963 ACTGATGCATGTCCCAGACACGTCTTA
1 GCTGATGCATGTCCCAGACATGTCTTA
41436990 TACTAGCCCT
Statistics
Matches: 132, Mismatches: 24, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
44 29 0.22
45 10 0.08
46 42 0.32
47 30 0.23
48 20 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (46 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTGGCAACATCATTGCG
Found at i:41436976 original size:47 final size:43
Alignment explanation
Indices: 41436779--41436981 Score: 130
Period size: 47 Copynumber: 4.4 Consensus size: 43
41436769 GTGTATACGT
* *
41436779 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-A-CGAAATTTAG-
1 GCTGATGCATGTCCCAGAC-TGTCTTACACTGGCTATC---ATAT-GC
* *
41436824 GC-GATGCATGTCCCAGACACGTCTTACACTGGCTAACATCATCGC
1 GCTGATGCATGTCCCAGAC-TGTCTTACACTGGCTATCAT-AT-GC
* * *
41436869 GGCTGATGCATGT-CCAGACATGTCTTACATTGGC-ACTCACCTTTAC
1 -GCTGATGCATGTCCCAGAC-TGTCTTACACTGGCTA-TCA--TATGC
*
41436915 GCCGATGCCATGTCCCAGACGTGGTCTTACACTGGCTATCATGATGC
1 GCTGATG-CATGTCCCAGAC-T-GTCTTACACTGGCTATCAT-ATGC
41436962 GACTGATGCATGTCCCAGAC
1 G-CTGATGCATGTCCCAGAC
41436982 ACGTCTTATA
Statistics
Matches: 128, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
43 2 0.02
44 31 0.24
45 10 0.08
46 31 0.24
47 32 0.25
48 21 0.16
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (43 bp):
GCTGATGCATGTCCCAGACTGTCTTACACTGGCTATCATATGC
Found at i:41437013 original size:94 final size:92
Alignment explanation
Indices: 41436731--41437050 Score: 308
Period size: 94 Copynumber: 3.4 Consensus size: 92
41436721 CCATCGAGGT
* * * ** *
41436731 CGATGCCATGTCCGAGACATGGTCTTACACTAGCTCTTGTGTATACGTGCTGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATG-ATGCG-GCTGATGCATGTCCCAG
* *
41436796 ACATGTCTTACACTAG-CACGAAATTTAGG
64 ACATGTCTTACACTAGCCTCG-AATTTAGC
* * *
41436825 CGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACATCATCGCGGCTGATGCATGT-CCAGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGAT-GCGGCTGATGCATGTCCCAGA
* * *
41436887 CATGTCTTACATTGGCACTC-ACCTTTACGC
65 CATGTCTTACACTAGC-CTCGA-ATTTA-GC
* *
41436917 CGATGCCATGTCCCAGACGTGGTCTTACACTGGCTATCATGATGCGACTGATGCATGTCCCAGAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGATGCGGCTGATGCATGTCCCAGAC
* * * **
41436982 ACGTCTTATACTAGCCCTCGTATCAATGC
66 ATGTCTTACACTAG-CCTCGAATTTA-GC
* * *
41437011 CGATGCCATGTCCCAGACATGTTCTTATACTGGCTCTCAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCAT
41437051 ATAACCCAAT
Statistics
Matches: 184, Mismatches: 32, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
90 19 0.10
91 18 0.10
92 24 0.13
93 38 0.21
94 84 0.46
95 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (92 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTATCATGATGCGGCTGATGCATGTCCCAGAC
ATGTCTTACACTAGCCTCGAATTTAGC
Found at i:41438360 original size:20 final size:20
Alignment explanation
Indices: 41438335--41438373 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41438325 TAACTTAGAA
*
41438335 TTATTA-AAACTATGTTCATC
1 TTATTACAAA-TAAGTTCATC
41438355 TTATTACAAATAAGTTCAT
1 TTATTACAAATAAGTTCAT
41438374 TGCAACTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (20 bp):
TTATTACAAATAAGTTCATC
Found at i:41439110 original size:23 final size:23
Alignment explanation
Indices: 41439071--41439119 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
41439061 TCAAGATGGG
* *
41439071 AAATAGGAAAGAGAAAGAATAGA
1 AAATAGGAAAGAAAAAGAAGAGA
*
41439094 AAAT-GGAAAGACAAAAGGAGAGA
1 AAATAGGAAAGA-AAAAGAAGAGA
41439117 AAA
1 AAA
41439120 GAATAGATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (23 bp):
AAATAGGAAAGAAAAAGAAGAGA
Found at i:41444331 original size:24 final size:24
Alignment explanation
Indices: 41444301--41444626 Score: 480
Period size: 24 Copynumber: 14.1 Consensus size: 24
41444291 GAATGTGACT
* *
41444301 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
41444325 ATAGCAAATCGCACAC--A-TGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41444346 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444370 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444394 ATAGT-AATCGCACACATA-TGCC
1 ATAGTAAATCGCACACATAGTGCC
41444416 ATAGTAAAT--CACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444438 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41444462 ATAGTGAATCGCACAC--A----C
1 ATAGTAAATCGCACACATAGTGCC
*
41444480 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41444504 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444528 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41444552 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41444576 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444600 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41444624 ATA
1 ATA
41444627 TGGTCTTTGC
Statistics
Matches: 283, Mismatches: 6, Indels: 26
0.90 0.02 0.08
Matches are distributed among these distances:
18 17 0.06
20 1 0.00
21 27 0.10
22 24 0.08
23 17 0.06
24 197 0.70
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:41444484 original size:18 final size:18
Alignment explanation
Indices: 41444461--41444496 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41444451 CACATAGTGC
41444461 CATAGTGAATCGCACACA
1 CATAGTGAATCGCACACA
41444479 CATAGTGAATCGCACACA
1 CATAGTGAATCGCACACA
41444497 TAGTGCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (18 bp):
CATAGTGAATCGCACACA
Found at i:41444496 original size:16 final size:17
Alignment explanation
Indices: 41444461--41444501 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
41444451 CACATAGTGC
41444461 CATAGTGAATCGCACACA
1 CATAGTGAATCG-ACACA
41444479 CATAGTGAATCG-CACA
1 CATAGTGAATCGACACA
41444495 CATAGTG
1 CATAGTG
41444502 CCATAGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.48
18 12 0.52
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (17 bp):
CATAGTGAATCGACACA
Found at i:41452417 original size:24 final size:24
Alignment explanation
Indices: 41452387--41452723 Score: 579
Period size: 24 Copynumber: 14.1 Consensus size: 24
41452377 GAATGTGACT
* *
41452387 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
41452411 ATAGCAAATCGCACACAT-GTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452434 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452458 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452482 ATA-TGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452505 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452529 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452553 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452577 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452601 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452625 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452649 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
41452673 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452697 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
41452721 ATA
1 ATA
41452724 TGGTCTTTGC
Statistics
Matches: 303, Mismatches: 8, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
23 43 0.14
24 260 0.86
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:41456016 original size:29 final size:28
Alignment explanation
Indices: 41455982--41456084 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41455972 TACTCAATCA
*
41455982 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41456011 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41456040 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41456069 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41456085 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41463476 original size:14 final size:14
Alignment explanation
Indices: 41463457--41463484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41463447 AGAAATCCCT
41463457 AATTTATATTATTA
1 AATTTATATTATTA
41463471 AATTTATATTATTA
1 AATTTATATTATTA
41463485 TCTCTCTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTTATATTATTA
Found at i:41465360 original size:23 final size:24
Alignment explanation
Indices: 41465257--41465375 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
41465247 GCTTTATCAT
*
41465257 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
41465282 ATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
41465306 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
41465330 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
41465353 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
41465376 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
23 22 0.25
24 53 0.61
25 12 0.14
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:41465451 original size:20 final size:20
Alignment explanation
Indices: 41465428--41465465 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41465418 ATGAACATCA
41465428 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATGT
41465448 CATGTGCATATCATACAT
1 CATGTGCATATCATACAT
41465466 ACCATGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
CATGTGCATATCATACATGT
Found at i:41465471 original size:20 final size:20
Alignment explanation
Indices: 41465428--41465472 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41465418 ATGAACATCA
**
41465428 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
41465448 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
41465468 CATGT
1 CATGT
41465473 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:41465537 original size:25 final size:25
Alignment explanation
Indices: 41465509--41465556 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
41465499 ATGTATAAAC
* *
41465509 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
41465534 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
41465557 AATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:41466816 original size:27 final size:27
Alignment explanation
Indices: 41466795--41467298 Score: 543
Period size: 27 Copynumber: 18.7 Consensus size: 27
41466785 AAGGGTATTT
*
41466795 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
41466822 CAGTAATTCTGTAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
41466849 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
41466876 TGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
**
41466903 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* * *
41466930 -CGATAATTATGTAAATCGGGGGTAAAA
1 TAG-TAATTCTGTAAATCGAGGGTAAAA
* * *
41466957 TGGTAATTATGTAAAT-TAGGGGTAAAA
1 TAGTAATTCTGTAAATCGA-GGGTAAAA
** * *
41466984 CGGTAATTCTATAAATTGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
41467011 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
** *
41467038 CGGTAATTCTGTAAATTGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
41467065 TGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* * *
41467092 CAGTAATTCTATAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
41467119 CAATAATTCTGTAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
**
41467146 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
41467173 TAGTAATTCTGTAAA-CTGAAGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
**
41467200 CGGTAATTCTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
** * **
41467227 CGGTAATTTTACAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
41467254 CAGTAATTCTATAAA-CTGAGGGTAAAA
1 TAGTAATTCTGTAAATC-GAGGGTAAAA
**
41467281 CGGTAATTCTGTAAATCG
1 TAGTAATTCTGTAAATCG
41467299 GGAGTACTTT
Statistics
Matches: 414, Mismatches: 51, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.01
27 405 0.98
28 5 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:41467315 original size:54 final size:54
Alignment explanation
Indices: 41466797--41467298 Score: 636
Period size: 54 Copynumber: 9.3 Consensus size: 54
41466787 GGGTATTTTA
* * * *
41466797 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* * *
41466851 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* * *
41466905 GTAATTCTGTAAATCGAGGGTAAAACGATAATTATGTAAATCGGGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* * * * *
41466959 GTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATA
1 GTAATTCTGTAAATCGA-GGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
*
41467013 GTAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* * * * **
41467067 GTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* *
41467121 ATAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* *
41467175 GTAATTCTGTAAA-CTGAAGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
* ** * * *
41467229 GTAATTTTACAAATCGAGGGTAAAACAGTAATTCTATAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATC-GAGGGTAAAATG
41467283 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
41467299 GGAGTACTTT
Statistics
Matches: 390, Mismatches: 51, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
53 3 0.01
54 384 0.98
55 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (54 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATG
Found at i:41467321 original size:81 final size:81
Alignment explanation
Indices: 41466797--41467298 Score: 665
Period size: 81 Copynumber: 6.2 Consensus size: 81
41466787 GGGTATTTTA
* * * * *
41466797 GTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATA
*
41466862 AATCGAGGGTAAAATG
66 AATCGAGGGTAAAACG
* * *
41466878 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAC-GATAATTATGT
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAG-TAATTCTAT
* *
41466942 AAATCGGGGGTAAAATG
65 AAATCGAGGGTAAAACG
* * * * *
41466959 GTAATTATGTAAAT-TAGGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATAGTAATTCTGT
1 GTAATTCTGTAAATCGA-GGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
41467023 AAA-CTGAGGGTAAAACG
65 AAATC-GAGGGTAAAACG
* *
41467040 GTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATA
* *
41467105 AATCAAGGGTAAAACA
66 AATCGAGGGTAAAACG
* * * *
41467121 ATAATTCTGTAAA-CTGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTGT
1 GTAATTCTGTAAATC-GAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTAT
*
41467185 AAA-CTGAAGGTAAAACG
65 AAATC-GAGGGTAAAACG
* *
41467202 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTTTACAAATCGAGGGTAAAACAGTAATTCTATA
1 GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATA
41467267 AA-CTGAGGGTAAAACG
66 AATC-GAGGGTAAAACG
41467283 GTAATTCTGTAAATCG
1 GTAATTCTGTAAATCG
41467299 GGAGTACTTT
Statistics
Matches: 373, Mismatches: 39, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
80 4 0.01
81 365 0.98
82 4 0.01
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (81 bp):
GTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACAGTAATTCTATA
AATCGAGGGTAAAACG
Found at i:41474666 original size:23 final size:23
Alignment explanation
Indices: 41474640--41474686 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41474630 GTTACTAGGT
41474640 AGACTTCTTGGTGGTCTTTCTAA
1 AGACTTCTTGGTGGTCTTTCTAA
41474663 AGACTTCTTGGTGGTCTTTCTAA
1 AGACTTCTTGGTGGTCTTTCTAA
41474686 A
1 A
41474687 ATCATCTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (23 bp):
AGACTTCTTGGTGGTCTTTCTAA
Found at i:41474694 original size:23 final size:23
Alignment explanation
Indices: 41474640--41474694 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
41474630 GTTACTAGGT
*
41474640 AGACTTCTTGGTGGTCTTTCTAA
1 AGACATCTTGGTGGTCTTTCTAA
*
41474663 AGACTTCTTGGTGGTCTTTCTAA
1 AGACATCTTGGTGGTCTTTCTAA
41474686 A-ATCATCTT
1 AGA-CATCTT
41474695 AGCCAGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (23 bp):
AGACATCTTGGTGGTCTTTCTAA
Found at i:41476821 original size:40 final size:38
Alignment explanation
Indices: 41476772--41476879 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
41476762 ATCACGATTT
*
41476772 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
41476812 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
41476852 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
41476880 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:41476839 original size:80 final size:80
Alignment explanation
Indices: 41476731--41476879 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
41476721 TATGGTAACC
* * * *
41476731 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
41476795 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
41476811 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
41476876 CCGG
66 CCGG
41476880 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:41488471 original size:40 final size:40
Alignment explanation
Indices: 41488412--41488618 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
41488402 CAATTGAATG
* * * *
41488412 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
41488452 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41488492 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
41488532 AAAT-CGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
41488571 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
41488611 ATATCCGG
1 ATATCCGG
41488619 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 26, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
39 34 0.24
40 106 0.76
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:41488577 original size:79 final size:78
Alignment explanation
Indices: 41488413--41488603 Score: 222
Period size: 79 Copynumber: 2.4 Consensus size: 78
41488403 AATTGAATGA
* * ** * * *
41488413 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGCAA
*
41488478 TTGTGCTAGTGAC
66 TTGTGCAAGTGAC
** *
41488491 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAAT-CGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGC
* *
41488555 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGT-G-AC
41488572 TATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCA
41488604 TGTGGTTATA
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
78 1 0.01
79 58 0.60
80 35 0.36
81 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (78 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATTAAATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTGAC
Found at i:41490729 original size:47 final size:47
Alignment explanation
Indices: 41490676--41490768 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
41490666 TTCAATTATG
* *
41490676 ATAACTTAGACAAAGAGCACTCATCCAATCCTCATAGGAATGATACT
1 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATAGGAACGATACT
41490723 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATAGGAACGATAC
1 ATAACTTAGACAAAAAGCACTCATCCAATCCTCATAGGAACGATAC
41490769 CCACTCATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.22
Consensus pattern (47 bp):
ATAACTTAGACAAAAAGCACTCATCCAATCCTCATAGGAACGATACT
Found at i:41492832 original size:50 final size:50
Alignment explanation
Indices: 41492750--41492844 Score: 163
Period size: 50 Copynumber: 1.9 Consensus size: 50
41492740 GCCAAGTTTA
41492750 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
1 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
* **
41492800 TGAAGGACATACTTTCAAAGAAAAGATGATTGTGAGAATTTGAAA
1 TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAA
41492845 TAATCACACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.26
Consensus pattern (50 bp):
TGAAAGACATACTTTCAAAGAAAAGACAATTGTGAGAATTTGAAACAATT
Done.