Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 129 of 290
Found at i:40428814 original size:41 final size:40
Alignment explanation
Indices: 40428761--40428930 Score: 143
Period size: 41 Copynumber: 4.2 Consensus size: 40
40428751 AGTCTGACTC
* *
40428761 TTAG-CACCGGCTCAAAAGCCCTTCGAGACCAAGCTCAGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
* * *
40428800 TTAGACTACTGGCTCGAAGGCCCTTCG-GAACTAAG-TCCGG-
1 TTAGAC-ACTGGCTCAAAAGCCCTTCGAG-ACCAAGCT-CGGA
* * *
40428840 TTATGACACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTA-GACACTGGCTC--AAAAGCCCTTCGAGACCAAGCTCGG--A
*
40428885 TTAG-CACTGGCTCAAAAGCACTTCGAGACCAAGCTCGGA
1 TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
40428924 TTTAGAC
1 -TTAGAC
40428931 CCCGATTAGC
Statistics
Matches: 105, Mismatches: 12, Indels: 26
0.73 0.08 0.18
Matches are distributed among these distances:
39 5 0.05
40 18 0.17
41 49 0.47
42 19 0.18
43 10 0.10
44 1 0.01
45 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (40 bp):
TTAGACACTGGCTCAAAAGCCCTTCGAGACCAAGCTCGGA
Found at i:40432083 original size:14 final size:15
Alignment explanation
Indices: 40432066--40432094 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40432056 TCACGAAAAT
40432066 TTCACACAT-ATAAA
1 TTCACACATAATAAA
40432080 TTCACACATAATAAA
1 TTCACACATAATAAA
40432095 CACAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:40434890 original size:47 final size:44
Alignment explanation
Indices: 40434820--40434987 Score: 133
Period size: 44 Copynumber: 3.6 Consensus size: 44
40434810 GGATAAACCT
*
40434820 TAAGACATGTTTGGGACATGCATCGGCCTCGACAGAGATAT-CCAGTG
1 TAAGACATGTCTGGGACATGCATCGG-CT--A-AGAGATATGCCAGTG
* * * * *
40434867 TAAGACGTGTCTGGGACACGCATCGGCTAAGAGTTGTGCTAGTG
1 TAAGACATGTCTGGGACATGCATCGGCTAAGAGATATGCCAGTG
* * *
40434911 TAAGACATGTCTGGGACATGCATCAGC-ACGCATATATGAGAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGGCTAAG-AGATAT----GCCAGTG
*
40434959 TAAGACCATGTCTCGGACATGGCATCGGC
1 TAAGA-CATGTCTGGGACAT-GCATCGGC
40434988 AATTTATCCC
Statistics
Matches: 97, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
43 8 0.08
44 33 0.34
46 2 0.02
47 23 0.24
48 11 0.11
49 13 0.13
50 7 0.07
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (44 bp):
TAAGACATGTCTGGGACATGCATCGGCTAAGAGATATGCCAGTG
Found at i:40435016 original size:42 final size:42
Alignment explanation
Indices: 40434957--40435043 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
40434947 TGAGAGCCAG
40434957 TGTAAGACCATGTCTCGGACATGGCATCGGCAATTTATCCCA
1 TGTAAGACCATGTCTCGGACATGGCATCGGCAATTTATCCCA
*
40434999 TGTAAGCCCATGTCTCGGACATGGCATCGGCAATTTATCCCA
1 TGTAAGACCATGTCTCGGACATGGCATCGGCAATTTATCCCA
40435041 TGT
1 TGT
40435044 TGATGGTTCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (42 bp):
TGTAAGACCATGTCTCGGACATGGCATCGGCAATTTATCCCA
Found at i:40452565 original size:39 final size:38
Alignment explanation
Indices: 40452509--40452671 Score: 202
Period size: 39 Copynumber: 4.2 Consensus size: 38
40452499 ATATTTGATG
* *
40452509 TGTATCCGGACTTAGGGTCCGCAGGTTATGTGCTGGAAT
1 TGTATCCGGACTTAGGGTCCGCAGGTT-CGTGCTGGAAA
* *
40452548 TATATCCGGACTTAGGGTCCGCAAGCTTCGTGCTGGAAA
1 TGTATCCGGACTTAGGGTCCGC-AGGTTCGTGCTGGAAA
40452587 TGTATCCGGACTTAGGGTCCGCAGGCTTCGTGCTGGAAA
1 TGTATCCGGACTTAGGGTCCGCAGG-TTCGTGCTGGAAA
* * **
40452626 TGTATCCGGGC-CAAAGTCCCGCAGGCTTCGTGCTGGAAA
1 TGTATCCGGACTTAGGGT-CCGCAGG-TTCGTGCTGGAAA
40452665 TGTATCC
1 TGTATCC
40452672 AGGTTAAAGT
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
38 5 0.05
39 102 0.92
40 4 0.04
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (38 bp):
TGTATCCGGACTTAGGGTCCGCAGGTTCGTGCTGGAAA
Found at i:40452681 original size:39 final size:38
Alignment explanation
Indices: 40452566--40452699 Score: 171
Period size: 39 Copynumber: 3.4 Consensus size: 38
40452556 GACTTAGGGT
* **
40452566 CCGCAAGCTTCGTGCTGGAAATGTATCCGGACTTAGGGT-
1 CCGCAGGCTTCGTGCTGGAAATGTATCCGG--TTAAAGTC
**
40452605 CCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGTC
1 CCGCAGGCTTCGTGCTGGAAATGTATCC-GGTTAAAGTC
40452644 CCGCAGGCTTCGTGCTGGAAATGTATCCAGGTTAAAGTC
1 CCGCAGGCTTCGTGCTGGAAATGTATCC-GGTTAAAGTC
*
40452683 CCGCAGGCTTTGTGCTG
1 CCGCAGGCTTCGTGCTG
40452700 ATAATATAAC
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
38 3 0.04
39 79 0.94
40 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (38 bp):
CCGCAGGCTTCGTGCTGGAAATGTATCCGGTTAAAGTC
Found at i:40466804 original size:40 final size:40
Alignment explanation
Indices: 40466752--40466943 Score: 231
Period size: 40 Copynumber: 4.8 Consensus size: 40
40466742 TATAACCACA
** *
40466752 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * *
40466792 CGCACAAATGCCTTCGGATCTTAGTCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * * **
40466832 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
40466872 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
40466912 AGCACAATTGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
40466944 TCATTCAAAT
Statistics
Matches: 124, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 124 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
Found at i:40466885 original size:80 final size:80
Alignment explanation
Indices: 40466752--40466944 Score: 314
Period size: 80 Copynumber: 2.4 Consensus size: 80
40466742 TATAACCACA
* * * *
40466752 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGT
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGC
40466817 CCGGATAAAATCACT
66 CCGGATAAAATCACT
* * *
40466832 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGC
40466897 CCGGATAAAATCACT
66 CCGGATAAAATCACT
*
40466912 AGCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 AGCACAATTGCCTTCGGGTCTTAGCCCGGATAT
40466945 CATTCAAATG
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 103 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
AGCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGATCTTAGC
CCGGATAAAATCACT
Found at i:40473398 original size:40 final size:40
Alignment explanation
Indices: 40473353--40473541 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
40473343 TATAACCACA
** *
40473353 AGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGTAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * *
40473393 CGCACAAATGCCTTCGGATCTTAGTCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* * * * **
40473433 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
40473473 CGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
* *
40473513 AGCACAATTGCCTTCGGGACTTAGCCCGG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGG
40473542 GAGACTTTAA
Statistics
Matches: 121, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 121 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATAACT
Found at i:40473473 original size:80 final size:79
Alignment explanation
Indices: 40473325--40473542 Score: 312
Period size: 80 Copynumber: 2.7 Consensus size: 79
40473315 ACCCAAGTTT
* * * * * * *
40473325 CTTCGGAAT-TTAGCCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAGT
1 CTTCGG-ATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGGTATAGC
40473389 AACTCGCACAAATGC
65 AACTCGCACAAATGC
*
40473404 CTTCGGATCTTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGGTATAGC
40473469 AACTCGCACAAATGC
65 AACTCGCACAAATGC
* *
40473484 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGGG
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGG
40473543 AGACTTTAAC
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
78 2 0.02
79 10 0.08
80 113 0.90
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CTTCGGATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAGCCCGGGTATAGCA
ACTCGCACAAATGC
Found at i:40477753 original size:46 final size:46
Alignment explanation
Indices: 40477601--40477811 Score: 169
Period size: 46 Copynumber: 4.5 Consensus size: 46
40477591 TGTGTGAGCT
* * * * * *
40477601 AGTGTAAGACATGTATGGGGCATGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTACGA-GACGATAGCC
* * * * ** *
40477647 AATGTAAGACCATGTCTGGGACATGGCATCAAC-ATTGAGACAAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTA-CGAGACGATAGCC
* * *
40477695 AGTGTAAGACATGTTTGGGACATGCATCGGCCT-CGAGATG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGACGAT-AGCC
* *
40477741 AGTGCAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGCC
40477787 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
40477812 GAATCAACTT
Statistics
Matches: 129, Mismatches: 26, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
45 2 0.02
46 63 0.49
47 43 0.33
48 20 0.16
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCTACGAGACGATAGCC
Found at i:40477842 original size:47 final size:47
Alignment explanation
Indices: 40477642--40477862 Score: 191
Period size: 47 Copynumber: 4.7 Consensus size: 47
40477632 CACATTATGA
* * * *
40477642 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCAACATTGAGACAA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAAC-TCGAGATAT
* * * ** *
40477690 GGGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAGATGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-AACTCGAGATAT
* * * *
40477736 AAGCCAGTGCAAGA-CATGTCTGGGACAT-GCATCAGCTACGAGACGAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACT-CGAGA-TAT
* * *
40477783 -AGTCAGTGTAAGACCATGTCTGGGACATGGAATCAACTTGAGATAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGAGATAT
* * *
40477829 GAGCCAGTATAAGACCATGCCTAGGACATGGCAT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
40477863 TGGCACCTTA
Statistics
Matches: 137, Mismatches: 30, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
45 2 0.01
46 56 0.41
47 61 0.45
48 18 0.13
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGAGATAT
Found at i:40487288 original size:23 final size:23
Alignment explanation
Indices: 40487234--40487329 Score: 131
Period size: 23 Copynumber: 4.1 Consensus size: 23
40487224 CCTAGCCTCT
*
40487234 TTTAATAACTGGGGCA-AAAGTCCT
1 TTTAATAACTGGGGCATAAA--CCC
40487258 TTTAATAACTGGGGCATAAACCC
1 TTTAATAACTGGGGCATAAACCC
* *
40487281 TTTAATAACTGGGGCACAAGCCC
1 TTTAATAACTGGGGCATAAACCC
*
40487304 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAACCC
40487327 TTT
1 TTT
40487330 TTCACTTCCT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 48 0.72
24 16 0.24
25 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAACCC
Found at i:40487328 original size:46 final size:47
Alignment explanation
Indices: 40487234--40487329 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 47
40487224 CCTAGCCTCT
*
40487234 TTTAATAACTGGGGCAAAAGTCCTTTTAATAACTGGGGCATAAACCC
1 TTTAATAACTGGGGCAAAAGTCCCTTTAATAACTGGGGCATAAACCC
* *
40487281 TTTAATAACTGGGGCACAAG-CCCTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCAAAAGTCCCTTTAATAACTGGGGCATAAACCC
40487327 TTT
1 TTT
40487330 TTCACTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 27 0.59
47 19 0.41
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (47 bp):
TTTAATAACTGGGGCAAAAGTCCCTTTAATAACTGGGGCATAAACCC
Found at i:40487445 original size:20 final size:20
Alignment explanation
Indices: 40487389--40487446 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
40487379 CATCACGTGG
*
40487389 ATATCATACATATAATGTGC
1 ATATCATACATATCATGTGC
*
40487409 ATATCATACATGTCATGTGC
1 ATATCATACATATCATGTGC
*
40487429 ATATCATACATACCATGT
1 ATATCATACATATCATGT
40487447 TTATCAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATCATACATATCATGTGC
Found at i:40493127 original size:26 final size:26
Alignment explanation
Indices: 40493091--40493152 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
40493081 GGGTGTTACA
* *
40493091 AAAAATTTGACAATTTTACCCTTAAT
1 AAAATTTTGACAATTTTACCCTCAAT
*
40493117 AAAATTTTGACAATTTTACCCTCAGT
1 AAAATTTTGACAATTTTACCCTCAAT
*
40493143 AAGATTTTGA
1 AAAATTTTGA
40493153 GAAAAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCTCAAT
Found at i:40493292 original size:6 final size:6
Alignment explanation
Indices: 40493281--40493325 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
40493271 GGATTGCAAG
* * *
40493281 TTTCGA TTTCGA TTTCCA TTTCCA TTTCCA TTTCCA TTTCTA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
40493326 TTTGAAACCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTCCA
Found at i:40497329 original size:34 final size:34
Alignment explanation
Indices: 40497286--40497351 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
40497276 AGTGTTTTGT
* *
40497286 AAATAATGAGTTATTTTATGGCTGAATGTTGTGC
1 AAATAATGAGTTATTTTACGACTGAATGTTGTGC
* *
40497320 AAATGATGAGTTCTTTTACGACTGAATGTTGT
1 AAATAATGAGTTATTTTACGACTGAATGTTGT
40497352 TGTATCATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.41
Consensus pattern (34 bp):
AAATAATGAGTTATTTTACGACTGAATGTTGTGC
Found at i:40503867 original size:161 final size:161
Alignment explanation
Indices: 40503602--40503924 Score: 628
Period size: 161 Copynumber: 2.0 Consensus size: 161
40503592 ATGAATGAGA
40503602 AAGATTTTAGCAGAATTAACACAATAAGCAACAATTTTAACATAAATAAGCTAGGACAATTACTT
1 AAGATTTTAGCAGAATTAACACAATAAGCAACAATTTTAACATAAATAAGCTAGGACAATTACTT
*
40503667 TAATTAAACTCAAATTATTATCAACATACTTACCAATATTCGAAAAAAATTTCATGGCAACTCGA
66 TAATTAAACTCAAATTATTATCAACATACTTACCAATATTCGAAAAAAATTCCATGGCAACTCGA
*
40503732 TCTTTCATGAGTTTGGAAACCACGTTAGGTC
131 TCTTTCATGAGTTTGGAAACCACATTAGGTC
40503763 AAGATTTTAGCAGAATTAACACAATAAGCAACAATTTTAACATAAATAAGCTAGGACAATTACTT
1 AAGATTTTAGCAGAATTAACACAATAAGCAACAATTTTAACATAAATAAGCTAGGACAATTACTT
40503828 TAATTAAACTCAAATTATTATCAACATACTTACCAATATTCGAAAAAAATTCCATGGCAACTCGA
66 TAATTAAACTCAAATTATTATCAACATACTTACCAATATTCGAAAAAAATTCCATGGCAACTCGA
40503893 TCTTTCATGAGTTTGGAAACCACATTAGGTC
131 TCTTTCATGAGTTTGGAAACCACATTAGGTC
40503924 A
1 A
40503925 TTTCGGAATC
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (161 bp):
AAGATTTTAGCAGAATTAACACAATAAGCAACAATTTTAACATAAATAAGCTAGGACAATTACTT
TAATTAAACTCAAATTATTATCAACATACTTACCAATATTCGAAAAAAATTCCATGGCAACTCGA
TCTTTCATGAGTTTGGAAACCACATTAGGTC
Found at i:40532088 original size:37 final size:37
Alignment explanation
Indices: 40532006--40532158 Score: 159
Period size: 37 Copynumber: 4.2 Consensus size: 37
40531996 GTACATGGCT
* *
40532006 ATGGCATAATCCAAGG-AGGTTCGCCAGA-TTGCCTAC
1 ATGGCATAAT-CTAGGAAGGTTCGCCAAACTTGCCTAC
* * *
40532042 ATGGCATAATCTAGGGAGGTTCGCCAAACTTTCTTAC
1 ATGGCATAATCTAGGAAGGTTCGCCAAACTTGCCTAC
* **
40532079 ATGGCATAATCAAGGAAGG-TCTGTTAAACTTGCCTAC
1 ATGGCATAATCTAGGAAGGTTC-GCCAAACTTGCCTAC
* * * *
40532116 ATGGCATAATCTAGGAAGGTCCACCAAACTTTCATAC
1 ATGGCATAATCTAGGAAGGTTCGCCAAACTTGCCTAC
40532153 ATGGCA
1 ATGGCA
40532159 AGATCCAAGG
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
35 4 0.04
36 23 0.24
37 68 0.71
38 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (37 bp):
ATGGCATAATCTAGGAAGGTTCGCCAAACTTGCCTAC
Found at i:40532198 original size:74 final size:73
Alignment explanation
Indices: 40532006--40532188 Score: 237
Period size: 74 Copynumber: 2.5 Consensus size: 73
40531996 GTACATGGCT
* * * *
40532006 ATGGCATAATCCAAGGAGGT-TCGCCAGATTGCCTACATGGCATAATCTAGGGAGGTTCGCCAAA
1 ATGGCATAATCCAAGGAGGTCT-GCTAGATTGCCTACATGGCATAATCTAGGAAGGTCCACCAAA
*
40532070 CTTTCTTAC
65 CTTTCATAC
* *
40532079 ATGGCATAAT-CAAGGAAGGTCTGTTAAACTTGCCTACATGGCATAATCTAGGAAGGTCCACCAA
1 ATGGCATAATCCAAGG-AGGTCTGCTAGA-TTGCCTACATGGCATAATCTAGGAAGGTCCACCAA
40532143 ACTTTCATAC
64 ACTTTCATAC
40532153 ATGGCA-AGATCCAAGGAGGTCTGCTAGATTTGCCTA
1 ATGGCATA-ATCCAAGGAGGTCTGCTAGA-TTGCCTA
40532189 GGTGACATAA
Statistics
Matches: 95, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
72 5 0.05
73 18 0.19
74 67 0.71
75 5 0.05
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (73 bp):
ATGGCATAATCCAAGGAGGTCTGCTAGATTGCCTACATGGCATAATCTAGGAAGGTCCACCAAAC
TTTCATAC
Found at i:40534370 original size:34 final size:34
Alignment explanation
Indices: 40534327--40534429 Score: 163
Period size: 34 Copynumber: 3.0 Consensus size: 34
40534317 TAAGTAGTTA
*
40534327 ATTAAGTAAAAAGGAATAAATCGTAAAATA-TGTG
1 ATTAAGTAAAAAGGACTAAATCGTAAAA-AGTGTG
*
40534361 ATTAAGTAAAAAGGACTCAATCGTAAAAAGTGTG
1 ATTAAGTAAAAAGGACTAAATCGTAAAAAGTGTG
*
40534395 ATTAAGTAAAAATGACTAAATCGTAAAAAGTGTG
1 ATTAAGTAAAAAGGACTAAATCGTAAAAAGTGTG
40534429 A
1 A
40534430 AAGTTGAGTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 1 0.02
34 63 0.98
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.25
Consensus pattern (34 bp):
ATTAAGTAAAAAGGACTAAATCGTAAAAAGTGTG
Found at i:40534590 original size:16 final size:15
Alignment explanation
Indices: 40534569--40534612 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
40534559 TTTTAAAAGT
*
40534569 TAATTAAGTAATTTGA
1 TAATTAAGTAA-ATGA
*
40534585 TAATTAAGTTAAATGT
1 TAATTAAG-TAAATGA
40534601 TAATTAAGTAAA
1 TAATTAAGTAAA
40534613 AGATGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.16
16 18 0.72
17 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (15 bp):
TAATTAAGTAAATGA
Found at i:40534603 original size:32 final size:31
Alignment explanation
Indices: 40534540--40534611 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
40534530 TGGATAGGTT
*
40534540 TTAATGTAATTATGATAATTTTTAAAAGTTAA
1 TTAA-GTAATTATGATAATTGTTAAAAGTTAA
*
40534572 TTAAGTAATT-TGATAATTAAGTTAAATGTTAA
1 TTAAGTAATTATGATAATT--GTTAAAAGTTAA
40534604 TTAAGTAA
1 TTAAGTAA
40534612 AAGATGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 8 0.22
31 6 0.17
32 22 0.61
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (31 bp):
TTAAGTAATTATGATAATTGTTAAAAGTTAA
Found at i:40535460 original size:40 final size:40
Alignment explanation
Indices: 40535362--40535512 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 40
40535352 AATTATTTTA
* ** * * *
40535362 TGATTGCACATAAGTGCCTTTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGCAACCC
* * *
40535402 TAATTGTACATACATGCCCCTGTTTGTACTTTGGCAACCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGCAACCC
* * * * *
40535442 TGATTGCACGTACGTGCCCCTATTTGTACTTTAGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTTGGCAACCC
* * * **
40535482 AGATTGCACATATGTACCCCTAATTGTACTT
1 TGATTGCACATACGTGCCCCTGTTTGTACTT
40535513 CGGTGCCCTG
Statistics
Matches: 89, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 89 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTTGGCAACCC
Found at i:40542294 original size:16 final size:16
Alignment explanation
Indices: 40542273--40542306 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40542263 AGTACTAATT
*
40542273 TAGTTGATTGTTAAAC
1 TAGTTGATTATTAAAC
40542289 TAGTTGATTATTAAAC
1 TAGTTGATTATTAAAC
40542305 TA
1 TA
40542307 TGAGCCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (16 bp):
TAGTTGATTATTAAAC
Found at i:40543461 original size:54 final size:54
Alignment explanation
Indices: 40543392--40543502 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
40543382 TGTACTTTCC
*
40543392 ACACGGCCTGCGACACAGCCATGTGACCCT-A-GTCAATGAGTTACACGGGTAGAG
1 ACACGGCCTGCGACAC-GAC-TGTGACCCTCAGGTCAATGAGTTACACGGGTAGAG
* * *** *
40543446 ACACGGGCTGGGACACGACTGTGTGTCTCAGGTCAATGAGTTACATGGGTAGAG
1 ACACGGCCTGCGACACGACTGTGACCCTCAGGTCAATGAGTTACACGGGTAGAG
40543500 ACA
1 ACA
40543503 TGAGTTGGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
52 6 0.12
53 3 0.06
54 39 0.81
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.19
Consensus pattern (54 bp):
ACACGGCCTGCGACACGACTGTGACCCTCAGGTCAATGAGTTACACGGGTAGAG
Found at i:40546102 original size:24 final size:22
Alignment explanation
Indices: 40546075--40546128 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
40546065 TAAGGATGTT
40546075 TAAAAATAAAATTTAAGAACTAA
1 TAAAAATAAAATTTAA-AACTAA
* **
40546098 CTAAACATAATGTTTAAAACTAA
1 -TAAAAATAAAATTTAAAACTAA
*
40546121 TAATAATA
1 TAAAAATA
40546129 CATATGTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 6 0.24
23 6 0.24
24 13 0.52
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (22 bp):
TAAAAATAAAATTTAAAACTAA
Found at i:40552743 original size:3 final size:3
Alignment explanation
Indices: 40552737--40552767 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
40552727 TCATGATTTG
40552737 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
40552768 CTGCAGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:40553753 original size:12 final size:12
Alignment explanation
Indices: 40553736--40553764 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40553726 GTATATTTTC
40553736 GCATATTGCATT
1 GCATATTGCATT
40553748 GCATATTGCATT
1 GCATATTGCATT
40553760 GCATA
1 GCATA
40553765 GTCGTTCGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (12 bp):
GCATATTGCATT
Found at i:40554765 original size:41 final size:41
Alignment explanation
Indices: 40554706--40554788 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
40554696 AAAAAGTAGA
* **
40554706 TAGTAAATGTATCGCTTGGAAAAGCTTGCGGGATTTGATCT
1 TAGTAAATGTATCCCTTGGAAAAGCTTGCAAGATTTGATCT
40554747 TAGTAAATGTATCCCTTGGAAAAGCTTGCAAGATTTGATCT
1 TAGTAAATGTATCCCTTGGAAAAGCTTGCAAGATTTGATCT
40554788 T
1 T
40554789 GGCACATTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (41 bp):
TAGTAAATGTATCCCTTGGAAAAGCTTGCAAGATTTGATCT
Found at i:40555799 original size:22 final size:22
Alignment explanation
Indices: 40555740--40555800 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
40555730 AAAGTGGCCC
*
40555740 AAGTTGTAAAGTTTTATTTTTATT
1 AAGTT-TAAATTTTTA-TTTTATT
* *
40555764 TA-TTT-ATTTATTTATTTTATT
1 AAGTTTAAATT-TTTATTTTATT
40555785 AAGTTTAAATTTTTAT
1 AAGTTTAAATTTTTAT
40555801 ATTCAGTCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
21 10 0.34
22 13 0.45
23 5 0.17
24 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
AAGTTTAAATTTTTATTTTATT
Found at i:40559576 original size:12 final size:13
Alignment explanation
Indices: 40559553--40559585 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
40559543 AGTTGTAAAG
40559553 TTTTATTTTATTTA
1 TTTTA-TTTATTTA
40559567 -TTTATTTATTTA
1 TTTTATTTATTTA
40559579 TTTTATT
1 TTTTATT
40559586 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:40559599 original size:21 final size:22
Alignment explanation
Indices: 40559543--40559600 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
40559533 AAGTGGCCCA
*
40559543 AGTTGTAAAGTTTTATTTTATTT
1 AGTT-TAAATTTTTATTTTATTT
*
40559566 A-TTT-ATTTATTTATTTTA-TT
1 AGTTTAAATT-TTTATTTTATTT
40559586 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
40559601 ATTCAGTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
20 5 0.17
21 18 0.62
22 5 0.17
23 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:40580537 original size:27 final size:27
Alignment explanation
Indices: 40580506--40580557 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40580496 ACAAGTGAGG
40580506 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
40580533 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
40580558 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:40592632 original size:53 final size:55
Alignment explanation
Indices: 40592563--40592769 Score: 195
Period size: 53 Copynumber: 3.8 Consensus size: 55
40592553 TTCCTTTTTA
*
40592563 AACTTACCATTTCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATCGT
* * * *
40592616 AACTCACCATTGCCATGTCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCGT
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATCGT
** * * * * * * **
40592671 AGTTTATCAATGCCATGTCTTGACATGGTCTCACATGATTTCCTTGCCTTGT-AA
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATCGT
* * * * * * *
40592725 AACTTACCAATGTCTTGCCTTGGCATGTTCTTACTTGGTATCCTT
1 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTT
40592770 AAACCTTAAT
Statistics
Matches: 121, Mismatches: 31, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 47 0.39
54 34 0.28
55 40 0.33
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (55 bp):
AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATCGT
Found at i:40592718 original size:55 final size:53
Alignment explanation
Indices: 40592575--40592769 Score: 183
Period size: 55 Copynumber: 3.6 Consensus size: 53
40592565 CTTACCATTT
*
40592575 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCATTG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
* * * ** * *
40592628 CCATGTCTTGGCATGGTCTTACATGGGATCTTTGCCTTATCGTAGTTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-G-AACTCACCAATG
* * * * * *
40592683 CCATGTCTTGACATGGTCTCACATGATTTCCTTGCCTTGTAAAACTTACCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACTCACCAATG
* * * * * *
40592737 TCTTGCCTTGGCATGTTCTTACTTGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTT
40592770 AAACCTTAAT
Statistics
Matches: 111, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
53 37 0.33
54 34 0.31
55 40 0.36
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
Found at i:40595837 original size:44 final size:44
Alignment explanation
Indices: 40595792--40596424 Score: 433
Period size: 44 Copynumber: 13.9 Consensus size: 44
40595782 TCTTGAAGTA
* *
40595792 GAGCAGATTAAAGCTGTAAATCTTATCTCTCTGAAGTTGCAGTA
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
* *
40595836 GAGCAGATTGAAGCTACAAATCTTATCT-TCCTGAAGTTGCAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCT-CTGAAGTTGCAGTG
* *
40595880 GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
**
40595924 GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTT-CAAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGC-AGTG
* * * * *
40595968 GAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTACAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
*
40596012 GAGCAGATTAAAGCTGTAAATTACAAATCTTACCT-TCTTGAAGTTGCAGTG
1 GAGCAGATTAAAGC--T--A-T--AAATCTTATCTCTC-TGAAGTTGCAGTG
* * *
40596063 GAGTAGATTGAAA--TGATAAGTCCTATAC-CTCTGAAGTTGCAGTAG
1 GAGCAGATT-AAAGCT-ATAAATCTTAT-CTCTCTGAAGTTGCAGT-G
* *
40596108 G-TCAGATTAAATCTACCATAGCAAGTCTTATCTC-CTTGAAGTTGCAGTG
1 GAGCAGATTAAAGCT---ATA--AA-TCTTATCTCTC-TGAAGTTGCAGTG
* * * *
40596157 GAATAGACTAAAGCTACAAGCTACAAATCTTATCTC-CTTGAAATTGCAGTG
1 G---AG-C-AGA-TTA-AAGCTATAAATCTTATCTCTC-TGAAGTTGCAGTG
* * * ** * * *
40596208 GAGTAGATTGAAGATACGAGTCTCATCTCCCTGAAGTTGCAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
* * * * * * * *
40596252 GAACAGATTGAAGTTACAATTCTTATCTCCCTGAAGTTGTAGTT
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
* ** * * * *
40596296 GAGCGGATTGGAGCTACAAATTTTATCTCCCTGAAGTTGTAGTG
1 GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
* * *
40596340 GAGCAGATTGAAA-TTACAAATCTTATCTCTTTGAAGTTGCAGTG
1 GAGCAGATT-AAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
* * * *
40596384 GAGCAGATTAAAACTACAAGTCTAATCTC-CTTGAAGTTGCA
1 GAGCAGATTAAAGCTATAAATCTTATCTCTC-TGAAGTTGCA
40596425 ATGGGTTAGA
Statistics
Matches: 480, Mismatches: 72, Indels: 74
0.77 0.12 0.12
Matches are distributed among these distances:
43 8 0.02
44 357 0.74
45 10 0.02
46 4 0.01
47 4 0.01
48 4 0.01
49 5 0.01
50 19 0.04
51 53 0.11
52 5 0.01
54 3 0.01
55 2 0.00
56 2 0.00
57 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
GAGCAGATTAAAGCTATAAATCTTATCTCTCTGAAGTTGCAGTG
Found at i:40595884 original size:88 final size:88
Alignment explanation
Indices: 40595792--40596424 Score: 487
Period size: 88 Copynumber: 7.0 Consensus size: 88
40595782 TCTTGAAGTA
* * *
40595792 GAGCAGATTAAAGCTGTAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTACAAAT
1 GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
40595857 CTTATCTTCCTGAAGTTGCAGTG
66 CTTATCTTCCTGAAGTTGCAGTG
*
40595880 GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGCAAAT
1 GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
40595945 CTTATC-TCTCTGAAGTT-CAAGTG
66 CTTATCTTC-CTGAAGTTGC-AGTG
* ** * *
40595968 GAGCAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTGTAAAT
1 GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC-------
* *
40596033 TACAAATCTTACCTTCTTGAAGTTGCAGTG
59 TACAAATCTTATCTTCCTGAAGTTGCAGTG
* * * * * *
40596063 GAGTAGATTGAAA--TGATAAGTCCTATAC-CTCTGAAGTTGCAGTAGG-TCAGATTAAATCTAC
1 GAGCAGATT-AAAGCTG-TAAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGCTA-
40596124 CATAGCAAGTCTTATC-TCCTTGAAGTTGCAGTG
61 C--A--AA-TCTTATCTTCC-TGAAGTTGCAGTG
** * * * * * *
40596157 GAATAGACTAAAGCTACAAGCTACAAATCTTATCTCCTTGAAATTGCAGTGGAGTAGATTGAAGA
1 GAGCAGATTAAAGCT----G-T--AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
* * * *
40596222 TACGAGTCTCATCTCCCTGAAGTTGCAGTG
59 TACAAATCTTATCTTCCTGAAGTTGCAGTG
* * * * * **
40596252 GAACAGATTGAAG-T-TACAATTCTTATCTCCCTGAAGTTGTAGTTGAGCGGATTGGAGCTACAA
1 GAGCAGATTAAAGCTGTA-AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAA
* * *
40596315 ATTTTATCTCCCTGAAGTTGTAGTG
64 ATCTTATCTTCCTGAAGTTGCAGTG
* ** ** * *
40596340 GAGCAGATTGAAA-TTACAAATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAACTACAAG
1 GAGCAGATT-AAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
*
40596404 TCTAATC-TCCTTGAAGTTGCA
65 TCTTATCTTCC-TGAAGTTGCA
40596425 ATGGGTTAGA
Statistics
Matches: 432, Mismatches: 74, Indels: 78
0.74 0.13 0.13
Matches are distributed among these distances:
86 1 0.00
87 7 0.02
88 247 0.57
89 6 0.01
90 1 0.00
91 1 0.00
93 7 0.02
94 28 0.06
95 89 0.21
96 11 0.03
99 2 0.00
100 4 0.01
101 28 0.06
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (88 bp):
GAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAAT
CTTATCTTCCTGAAGTTGCAGTG
Found at i:40595928 original size:132 final size:132
Alignment explanation
Indices: 40595792--40596424 Score: 537
Period size: 132 Copynumber: 4.6 Consensus size: 132
40595782 TCTTGAAGTA
* *
40595792 GAGCAGATTAAAGCTGTAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTGAAGCTACAAAT
1 GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
40595857 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAG
66 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAG
40595922 TG
131 TG
40595924 GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTT-CAAGTGGAGCAGATTGAAGCTACAAA
1 GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGC-AGTGGAGCAGATTGAAGCTACAAA
* * * **
40595988 TCTTATCTCCCTAAAGTTACAGTGGAGCAGATTAAAGCTGTAAATTACAAATCTTACCTTCTTGA
65 TCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGTAAA-T-CTTATC-T-CC--C-TGA
40596053 AGTTGCAGTG
123 AGTTGCAGTG
* * * * *
40596063 GAGTAGATTGAAA--TG-ATAAGTCCTATAC-CTCTGAAGTTGCAGTAGG-TCAGATTAAATCTA
1 GAGCAGATT-AAAGCTGCA-AA-TCTTAT-CTCTCTGAAGTTGCAGT-GGAGCAGATTGAAGCTA
** *
40596123 CCATAGCAAGTCTTATC-TCCTTGAAGTTGCAGTGGAATAGACTAAAGCTACAAGCTACAAATCT
61 -C--A--AA-TCTTATCTTCC-TGAAGTTGCAGTGGAGCAGATTAAAGCT----G-T--AAATCT
* *
40596187 TATCTCCTTGAAATTGCAGTG
112 TATCTCCCTGAAGTTGCAGTG
* * * * * * * * * * *
40596208 GAGTAGATTGAAGATACGAGTCTCATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGTTACAATT
1 GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
* * * * ** ** * *
40596273 CTTATCTCCCTGAAGTTGTAGTTGAGCGGATTGGAGCTACAAATTTTATCTCCCTGAAGTTGTAG
66 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAG
40596338 TG
131 TG
* * * * * *
40596340 GAGCAGATTGAAA-TTACAAATCTTATCTCTTTGAAGTTGCAGTGGAGCAGATTAAAACTACAAG
1 GAGCAGATT-AAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAA
*
40596404 TCTAATC-TCCTTGAAGTTGCA
65 TCTTATCTTCC-TGAAGTTGCA
40596425 ATGGGTTAGA
Statistics
Matches: 400, Mismatches: 65, Indels: 72
0.74 0.12 0.13
Matches are distributed among these distances:
131 3 0.01
132 187 0.47
133 3 0.01
134 4 0.01
135 1 0.00
136 2 0.00
137 1 0.00
138 5 0.01
139 77 0.19
140 11 0.03
142 2 0.00
144 10 0.03
145 79 0.20
146 2 0.00
148 2 0.00
149 2 0.00
150 5 0.01
151 1 0.00
152 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (132 bp):
GAGCAGATTAAAGCTGCAAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGTAAATCTTATCTCCCTGAAGTTGCAG
TG
Found at i:40596155 original size:50 final size:49
Alignment explanation
Indices: 40596094--40596214 Score: 129
Period size: 51 Copynumber: 2.4 Consensus size: 49
40596084 CCTATACCTC
* * * *
40596094 TGAAGTTGCAGTAGG-TCAGATTAAATCTACCA-TAGCAAGTCTTATCTCCT
1 TGAAGTTGCAGT-GGAT-AGACTAAAGCTACAACTA-CAAATCTTATCTCCT
40596144 TGAAGTTGCAGTGGAATAGACTAAAGCTACAAGCTACAAATCTTATCTCCT
1 TGAAGTTGCAGTGG-ATAGACTAAAGCTACAA-CTACAAATCTTATCTCCT
*
40596195 TGAAATTGCAGTGGAGTAGA
1 TGAAGTTGCAGTGGA-TAGA
40596215 TTGAAGATAC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
49 2 0.03
50 25 0.41
51 32 0.52
52 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (49 bp):
TGAAGTTGCAGTGGATAGACTAAAGCTACAACTACAAATCTTATCTCCT
Found at i:40598266 original size:14 final size:14
Alignment explanation
Indices: 40598247--40598275 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40598237 GATGGCTTCC
40598247 ATGTTTCTTGTGGG
1 ATGTTTCTTGTGGG
40598261 ATGTTTCTTGTGGG
1 ATGTTTCTTGTGGG
40598275 A
1 A
40598276 CTAGTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.34, T:0.48
Consensus pattern (14 bp):
ATGTTTCTTGTGGG
Found at i:40601880 original size:23 final size:22
Alignment explanation
Indices: 40601829--40601880 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
40601819 CCTCATCTTT
*
40601829 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
40601851 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
40601874 TTCTTTT
1 TTCTTTT
40601881 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:40601895 original size:18 final size:18
Alignment explanation
Indices: 40601874--40601912 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40601864 TTTCTTCAAC
* *
40601874 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
40601892 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
40601910 TTC
1 TTC
40601913 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:40605322 original size:41 final size:41
Alignment explanation
Indices: 40605276--40605358 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
40605266 CAAATGTGCC
** *
40605276 AAGATCAAATCTTGCAAGCTTTTCCAAGGGATACATTTACT
1 AAGATCAAATCCCGCAAGCTTTTCCAAGCGATACATTTACT
40605317 AAGATCAAATCCCGCAAGCTTTTCCAAGCGATACATTTACT
1 AAGATCAAATCCCGCAAGCTTTTCCAAGCGATACATTTACT
40605358 A
1 A
40605359 TCTACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (41 bp):
AAGATCAAATCCCGCAAGCTTTTCCAAGCGATACATTTACT
Found at i:40606317 original size:12 final size:12
Alignment explanation
Indices: 40606300--40606328 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40606290 ATCGAACGAC
40606300 TATGCAATGCAA
1 TATGCAATGCAA
40606312 TATGCAATGCAA
1 TATGCAATGCAA
40606324 TATGC
1 TATGC
40606329 GAAAATATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (12 bp):
TATGCAATGCAA
Found at i:40607342 original size:3 final size:3
Alignment explanation
Indices: 40607296--40607323 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40607286 AATACTGCAG
40607296 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40607324 CAAATCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40614661 original size:106 final size:106
Alignment explanation
Indices: 40614476--40614686 Score: 422
Period size: 106 Copynumber: 2.0 Consensus size: 106
40614466 ATCTTTTACT
40614476 TAATTTAAATTTGAAGTTTCATTCTTTAGGTTATTAAATTATGCAGTGATAATTGTCTGAAATTA
1 TAATTTAAATTTGAAGTTTCATTCTTTAGGTTATTAAATTATGCAGTGATAATTGTCTGAAATTA
40614541 TGTGAAATTTGATTCAATTGTGAGTGGCTAAATTTCTCTTC
66 TGTGAAATTTGATTCAATTGTGAGTGGCTAAATTTCTCTTC
40614582 TAATTTAAATTTGAAGTTTCATTCTTTAGGTTATTAAATTATGCAGTGATAATTGTCTGAAATTA
1 TAATTTAAATTTGAAGTTTCATTCTTTAGGTTATTAAATTATGCAGTGATAATTGTCTGAAATTA
40614647 TGTGAAATTTGATTCAATTGTGAGTGGCTAAATTTCTCTT
66 TGTGAAATTTGATTCAATTGTGAGTGGCTAAATTTCTCTT
40614687 TTATTTCCTA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.45
Consensus pattern (106 bp):
TAATTTAAATTTGAAGTTTCATTCTTTAGGTTATTAAATTATGCAGTGATAATTGTCTGAAATTA
TGTGAAATTTGATTCAATTGTGAGTGGCTAAATTTCTCTTC
Found at i:40617079 original size:33 final size:33
Alignment explanation
Indices: 40617037--40617103 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
40617027 AATGTGGAAG
40617037 TGTGCTCTTGTTTCCTCCTTTTTTGACTTGTCA
1 TGTGCTCTTGTTTCCTCCTTTTTTGACTTGTCA
40617070 TGTGCTCTTGTTTCCTCCTTTTTTGACTTGTCA
1 TGTGCTCTTGTTTCCTCCTTTTTTGACTTGTCA
40617103 T
1 T
40617104 ACTTCCAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (33 bp):
TGTGCTCTTGTTTCCTCCTTTTTTGACTTGTCA
Found at i:40628321 original size:7 final size:7
Alignment explanation
Indices: 40628306--40628336 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
40628296 ATGATGGAAT
*
40628306 TGTGTGA
1 TGTGAGA
40628313 TGTGAGA
1 TGTGAGA
40628320 TGTGAGA
1 TGTGAGA
40628327 TGTGAGA
1 TGTGAGA
40628334 TGT
1 TGT
40628337 CTAGGGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (7 bp):
TGTGAGA
Found at i:40629652 original size:63 final size:62
Alignment explanation
Indices: 40629455--40629653 Score: 179
Period size: 63 Copynumber: 3.2 Consensus size: 62
40629445 GCTGTGTGGT
* * * *
40629455 AGGCCGTGTAACTTACTATTTTCGAATTTGAGG-CACACGGGCTAAGGACACAGGCGTGTGTCC
1 AGGCCGTGTAACTCATTGTTTT-GAATTT-AGGTCACACGGGCTAAGGACACGGGCGTGTGTCC
* * * * * * *
40629518 AGGCCGAGTAAGTCATTG-TTTGTATTGTTGGTCACACGAGCTACA-GACACGGGTGTGTGCCC
1 AGGCCGTGTAACTCATTGTTTTGAATT-TAGGTCACACGGGCTA-AGGACACGGGCGTGTGTCC
* * * * *
40629580 AAGCTGTGTAACTCATTGTTTTGGATTTAAGGTCACACGGGCCAGGGACACGGGCGTGTGTCC
1 AGGCCGTGTAACTCATTGTTTTGAATTT-AGGTCACACGGGCTAAGGACACGGGCGTGTGTCC
*
40629643 TGGCCGTGTAA
1 AGGCCGTGTAA
40629654 GGGGTTATAA
Statistics
Matches: 105, Mismatches: 25, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
61 6 0.06
62 43 0.41
63 56 0.53
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.27
Consensus pattern (62 bp):
AGGCCGTGTAACTCATTGTTTTGAATTTAGGTCACACGGGCTAAGGACACGGGCGTGTGTCC
Found at i:40636587 original size:132 final size:132
Alignment explanation
Indices: 40636350--40636614 Score: 467
Period size: 132 Copynumber: 2.0 Consensus size: 132
40636340 TTGACTAATT
* *
40636350 TTGTACTATCAAATATTGGAATAATATTTGATTGATTTCGTACCAAATAAGATAAATGCTTTCTA
1 TTGTACTATCAAATATTGGAATAATATTTGATTGATTTCATACCAAATAAGATAAATACTTTCTA
* *
40636415 TCTATATTGATAGAATTTATTACTACATTCTCATATCCTTCCTCAAAGAATATTAACAGAAACAA
66 TCTATAATGATAGAATTTATTACTACATTCTCATATCCTTCCTCAAAAAATATTAACAGAAACAA
40636480 AA
131 AA
* *
40636482 TTGTACTATCAAATATTGGAATAATTTTTGTTTGATTTCATACCAAATAAGATAAATACTTTCTA
1 TTGTACTATCAAATATTGGAATAATATTTGATTGATTTCATACCAAATAAGATAAATACTTTCTA
*
40636547 TCTATAATGATAGAATTTATTACTACATTCTCATATCCTTCCTCAAAAAATATTAACAGAAATAA
66 TCTATAATGATAGAATTTATTACTACATTCTCATATCCTTCCTCAAAAAATATTAACAGAAACAA
40636612 AA
131 AA
40636614 T
1 T
40636615 ATTTGGGCAT
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 126 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (132 bp):
TTGTACTATCAAATATTGGAATAATATTTGATTGATTTCATACCAAATAAGATAAATACTTTCTA
TCTATAATGATAGAATTTATTACTACATTCTCATATCCTTCCTCAAAAAATATTAACAGAAACAA
AA
Found at i:40650152 original size:41 final size:40
Alignment explanation
Indices: 40650058--40650216 Score: 140
Period size: 41 Copynumber: 3.9 Consensus size: 40
40650048 AATACTCAAT
* * * * *
40650058 ATCTCACACACTAAGTGCCATACATAGCTGAAGCTATCTC-
1 ATCTCGCACACTAAG-GTCATATATAGCCGAAGCTATCACG
** * *
40650098 AAATCGCACACTAAGCGTCATGTATAACCGAAGCTATCACG
1 ATCTCGCACACTAAG-GTCATATATAGCCGAAGCTATCACG
* * * *
40650139 ATCTCGCACACTAAGTTCCATATATAGCTGAAACTATCTCG
1 ATCTCGCACACTAAGGT-CATATATAGCCGAAGCTATCACG
* *
40650180 ATCTTGCACACTAAGTGCCATATATAGCCGAAGCTAT
1 ATCTCGCACACTAAG-GTCATATATAGCCGAAGCTAT
40650217 GTCGAATTGC
Statistics
Matches: 93, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
40 31 0.33
41 62 0.67
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (40 bp):
ATCTCGCACACTAAGGTCATATATAGCCGAAGCTATCACG
Found at i:40650229 original size:81 final size:81
Alignment explanation
Indices: 40650058--40650248 Score: 217
Period size: 81 Copynumber: 2.4 Consensus size: 81
40650048 AATACTCAAT
* * * * *
40650058 ATCTCACACACTAAGTGCCATACATAGCTGAAGCTATCTCAAATCGCACACTAAGCGTCATGTAT
1 ATCTCGCACACTAAGTGCCATATATAGCTGAAACTATCTCAAATCGCACACTAAGCGCCATATAT
40650123 AACCGAAGCTATCACG
66 AACCGAAGCTATCACG
* * *
40650139 ATCTCGCACACTAAGTTCCATATATAGCTGAAACTATCTC-GATCTTGCACACTAAGTGCCATAT
1 ATCTCGCACACTAAGTGCCATATATAGCTGAAACTATCTCAAATC--GCACACTAAGCGCCATAT
* **
40650203 ATAGCCGAAGCTATGTCG
64 ATAACCGAAGCTATCACG
* *
40650221 AAT-T-GCACACTTAGTGCCACATATAGCT
1 -ATCTCGCACACTAAGTGCCATATATAGCT
40650249 AATTTGTCGT
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
80 3 0.03
81 57 0.61
82 31 0.33
83 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (81 bp):
ATCTCGCACACTAAGTGCCATATATAGCTGAAACTATCTCAAATCGCACACTAAGCGCCATATAT
AACCGAAGCTATCACG
Found at i:40656559 original size:13 final size:13
Alignment explanation
Indices: 40656543--40656569 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40656533 AAGCCAATTT
40656543 ACACGGCTGAGAC
1 ACACGGCTGAGAC
40656556 ACACGGCTGAGAC
1 ACACGGCTGAGAC
40656569 A
1 A
40656570 TGCTCGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.30, T:0.07
Consensus pattern (13 bp):
ACACGGCTGAGAC
Found at i:40657351 original size:41 final size:41
Alignment explanation
Indices: 40657265--40657447 Score: 203
Period size: 41 Copynumber: 4.5 Consensus size: 41
40657255 AATACCTTAT
* * *
40657265 ACACTAAGTGCCATACATAGACAAAGCTATCTCAAAT-T-GC
1 ACACTAAGTGCCATATATAGCCGAAGCTATCTC-AATCTCGC
* * * * * **
40657305 ACACTAACTGTCATGTATAGCAGAAGCTATTTTGATCTCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATCTCAATCTCGC
40657346 ACACTAAGTGCCATATATAGCCGAAGCTATCTCAATCTCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATCTCAATCTCGC
*
40657387 ACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA--TCGC
1 ACACTAAGTGCCATATATAGCCGAAGCTATCTC-AATCTCGC
* *
40657427 ACATTAAGTGCCACATATAGC
1 ACACTAAGTGCCATATATAGC
40657448 TGATTTTTCA
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 48 0.40
41 68 0.57
42 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (41 bp):
ACACTAAGTGCCATATATAGCCGAAGCTATCTCAATCTCGC
Found at i:40657427 original size:81 final size:81
Alignment explanation
Indices: 40657265--40657447 Score: 226
Period size: 81 Copynumber: 2.3 Consensus size: 81
40657255 AATACCTTAT
* * * *
40657265 ACACTAAGTGCCATACATAGACAAAGCTATCTCAAATTGCACACTAACTGTCATGTATAGCAGAA
1 ACACTAAGTGCCATATATAGCCAAAGCTATCTCAAATTGCACACTAACTGCCATATATAGCAGAA
* * *
40657330 GCTATTTTGATCTCGC
66 GCTATGTCGATATCGC
* * *
40657346 ACACTAAGTGCCATATATAGCCGAAGCTATCTC-AATCTCGCACACTAAGTGCCATATATAGCCG
1 ACACTAAGTGCCATATATAGCCAAAGCTATCTCAAAT-T-GCACACTAACTGCCATATATAGCAG
40657410 AAGCTATGTCGA-ATCGC
64 AAGCTATGTCGATATCGC
* *
40657427 ACATTAAGTGCCACATATAGC
1 ACACTAAGTGCCATATATAGC
40657448 TGATTTTTCA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
80 3 0.03
81 54 0.61
82 31 0.35
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (81 bp):
ACACTAAGTGCCATATATAGCCAAAGCTATCTCAAATTGCACACTAACTGCCATATATAGCAGAA
GCTATGTCGATATCGC
Found at i:40658271 original size:13 final size:14
Alignment explanation
Indices: 40658247--40658275 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
40658237 ATTTACTAAT
40658247 TTACTAAATTAACC
1 TTACTAAATTAACC
40658261 TTACT-AATTAACC
1 TTACTAAATTAACC
40658274 TT
1 TT
40658276 TAAAACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
TTACTAAATTAACC
Found at i:40658406 original size:34 final size:34
Alignment explanation
Indices: 40658363--40658427 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
40658353 TAAGGTTTTA
40658363 TAGCTATTAGAACTCAAGTTTTACGCTTTACCTT
1 TAGCTATTAGAACTCAAGTTTTACGCTTTACCTT
40658397 TAGCTATTAGAACTCAAGTTTTACGCTTTAC
1 TAGCTATTAGAACTCAAGTTTTACGCTTTAC
40658428 GCGATTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (34 bp):
TAGCTATTAGAACTCAAGTTTTACGCTTTACCTT
Found at i:40658889 original size:18 final size:18
Alignment explanation
Indices: 40658868--40658912 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
40658858 ACTCCCCACT
40658868 ATCCCACTAACCAATCTA
1 ATCCCACTAACCAATCTA
40658886 ATCCCAC-AA--AATCTA
1 ATCCCACTAACCAATCTA
*
40658901 A-CTCACTAACCA
1 ATCCCACTAACCA
40658913 CTTCCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
17 3 0.13
18 7 0.30
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (18 bp):
ATCCCACTAACCAATCTA
Found at i:40663677 original size:44 final size:44
Alignment explanation
Indices: 40663612--40663695 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
40663602 TCATAAATGT
*
40663612 TAGTTTGTGTGTTAAATTGATCTACGTTAATTTT-TTAAAGCCAC
1 TAGTTTGTGTGTTAAACTGATCTACGTT-ATTTTCTTAAAGCCAC
*
40663656 TAGTTTGTGTTTTAAACTGATCTACGTTATTTTCTTAAAG
1 TAGTTTGTGTGTTAAACTGATCTACGTTATTTTCTTAAAG
40663696 TCACAACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 5 0.14
44 32 0.86
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (44 bp):
TAGTTTGTGTGTTAAACTGATCTACGTTATTTTCTTAAAGCCAC
Found at i:40667475 original size:41 final size:41
Alignment explanation
Indices: 40667385--40667634 Score: 270
Period size: 41 Copynumber: 6.1 Consensus size: 41
40667375 ATATAACTTA
* * * * *
40667385 CCTGATACAATACATTGGCACGAAGACTGCTAGGCTCAACG
1 CCTGATATAATACATCGGCACGAAGCCTGCTAGGCACAAAG
* * **
40667426 CTTGATATAACACATCGGCATAAAGCCTGCTAGGCACAAAG
1 CCTGATATAATACATCGGCACGAAGCCTGCTAGGCACAAAG
* * * *
40667467 CCTAATATAGTACACTAGG-ACGAAGCCTTCTAGGCACAAAG
1 CCTGATATAATACA-TCGGCACGAAGCCTGCTAGGCACAAAG
* * *
40667508 CCTGACATAATACATTGACACGAAGCCTGCTAGGCACAAAG
1 CCTGATATAATACATCGGCACGAAGCCTGCTAGGCACAAAG
* * * *
40667549 CTTGATATAATACACCGGTACGAAGCCTGCTAGGCACCAAG
1 CCTGATATAATACATCGGCACGAAGCCTGCTAGGCACAAAG
* *
40667590 CCTGATATAATACA-CTGACACGAAGCCTACTAGGCACAAAG
1 CCTGATATAATACATC-GGCACGAAGCCTGCTAGGCACAAAG
40667631 CCTG
1 CCTG
40667635 CTAGGCACAA
Statistics
Matches: 171, Mismatches: 35, Indels: 6
0.81 0.17 0.03
Matches are distributed among these distances:
40 3 0.02
41 165 0.96
42 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (41 bp):
CCTGATATAATACATCGGCACGAAGCCTGCTAGGCACAAAG
Found at i:40667604 original size:123 final size:123
Alignment explanation
Indices: 40667393--40667634 Score: 342
Period size: 123 Copynumber: 2.0 Consensus size: 123
40667383 TACCTGATAC
* * * * *
40667393 AATACATTGGCACGAAGACTGCTAGGCTCAACGCTTGATATAACACATCGGCATAAAGCCTGCTA
1 AATACATTGACACGAAGACTGCTAGGCACAAAGCTTGATATAACACACCGGCACAAAGCCTGCTA
* * *
40667458 GGCACAAAGCCTAATATAGTACACT-AGGACGAAGCCTTCTAGGCACAAAGCCTGACAT
66 GGCACAAAGCCTAATATAATACACTGA-CACGAAGCCTACTAGGCACAAAGCCTGACAT
* * * *
40667516 AATACATTGACACGAAGCCTGCTAGGCACAAAGCTTGATATAATACACCGGTACGAAGCCTGCTA
1 AATACATTGACACGAAGACTGCTAGGCACAAAGCTTGATATAACACACCGGCACAAAGCCTGCTA
* *
40667581 GGCACCAAGCCTGATATAATACACTGACACGAAGCCTACTAGGCACAAAGCCTG
66 GGCACAAAGCCTAATATAATACACTGACACGAAGCCTACTAGGCACAAAGCCTG
40667635 CTAGGCACAA
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
123 103 0.99
124 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (123 bp):
AATACATTGACACGAAGACTGCTAGGCACAAAGCTTGATATAACACACCGGCACAAAGCCTGCTA
GGCACAAAGCCTAATATAATACACTGACACGAAGCCTACTAGGCACAAAGCCTGACAT
Found at i:40667638 original size:57 final size:55
Alignment explanation
Indices: 40667571--40667687 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 55
40667561 CACCGGTACG
* * *
40667571 AAGCCTGCTAGGCACCAAGCCTGATATAATACACTGACACGAAGCCTACTAGGCACA
1 AAGCCTGCTAGGCACAAAGCCTGATAT-AT-CACCGACACAAAGCCTACTAGGCACA
* * *
40667628 AAGCCTGCTAGGCACAAAGCCTGATATATCACCGGCACAAAGCTTGCTAGGCACA
1 AAGCCTGCTAGGCACAAAGCCTGATATATCACCGACACAAAGCCTACTAGGCACA
40667683 AAGCC
1 AAGCC
40667688 CAAATATCAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 26 0.48
56 2 0.04
57 26 0.48
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (55 bp):
AAGCCTGCTAGGCACAAAGCCTGATATATCACCGACACAAAGCCTACTAGGCACA
Found at i:40667650 original size:16 final size:16
Alignment explanation
Indices: 40667612--40667650 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40667602 CACTGACACG
*
40667612 AAGCCTACTAGGCACA
1 AAGCCTGCTAGGCACA
40667628 AAGCCTGCTAGGCACA
1 AAGCCTGCTAGGCACA
40667644 AAGCCTG
1 AAGCCTG
40667651 ATATATCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.31, G:0.23, T:0.13
Consensus pattern (16 bp):
AAGCCTGCTAGGCACA
Found at i:40667770 original size:76 final size:77
Alignment explanation
Indices: 40667625--40667772 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 77
40667615 CCTACTAGGC
* * *
40667625 ACAAAGCCTGCTAGGCACAAAGCCTGATATATCACCGGCACAAAGCTTGCTAGGCACAAAGCCCA
1 ACAAAGCCTGCTAGGCACAAAGCCTGAAATATCACCGGCACAAAGCCTGCTAAGCACAAAGCCCA
40667690 AATATCATCTGT
66 AATATCATCTGT
** * * * * *
40667702 ACAAAGCCTGCTAGGCACGGAGCCT-AAATATCAGCGGCACAAAGCCTGCTAAGTACGAAGCTCG
1 ACAAAGCCTGCTAGGCACAAAGCCTGAAATATCACCGGCACAAAGCCTGCTAAGCACAAAGCCCA
40667766 AATATCA
66 AATATCA
40667773 CTACGTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
76 38 0.62
77 23 0.38
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (77 bp):
ACAAAGCCTGCTAGGCACAAAGCCTGAAATATCACCGGCACAAAGCCTGCTAAGCACAAAGCCCA
AATATCATCTGT
Found at i:40667772 original size:38 final size:38
Alignment explanation
Indices: 40667622--40667752 Score: 172
Period size: 38 Copynumber: 3.4 Consensus size: 38
40667612 AAGCCTACTA
*
40667622 GGCACAAAGCCTGCTAGGCACAAAGCCTGATATATCACC
1 GGCACAAAGCCTGCTAGGCACAAAGCCT-AAATATCACC
* * *
40667661 GGCACAAAGCTTGCTAGGCACAAAGCCCAAATATCATC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTAAATATCACC
* * ** *
40667699 TGTACAAAGCCTGCTAGGCACGGAGCCTAAATATCAGC
1 GGCACAAAGCCTGCTAGGCACAAAGCCTAAATATCACC
40667737 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
40667753 AGTACGAAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 53 0.67
39 26 0.33
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (38 bp):
GGCACAAAGCCTGCTAGGCACAAAGCCTAAATATCACC
Found at i:40670058 original size:96 final size:96
Alignment explanation
Indices: 40669880--40670089 Score: 262
Period size: 96 Copynumber: 2.2 Consensus size: 96
40669870 ACCTTTAAAC
** * *
40669880 CACGTTGTGGATGAACCACTAATTGTTGTAGATGAACTGCTAACGATAAGATTATTGGTGGATGA
1 CACGTTGTGGATGAACCACTAATCATTGTAGATGAACTGCTAACGATAAAAATATTGGTGGATGA
*
40669945 ACCATCCATCGTAGAAGATGAAAGCTACTAG
66 ACCATCCATCGTAGAAGATCAAAGCTACTAG
* * *
40669976 TACGTTGTGGATGAACCACTGATCATTGTAGATGAACTGCTAACTATAAAAATATTGGTAGG-TG
1 CACGTTGTGGATGAACCACTAATCATTGTAGATGAACTGCTAACGATAAAAATATTGGT-GGATG
* * * *
40670040 AACTATCTATCGGT-GAAGATCAAAGTTGCTAG
65 AACCATCCATC-GTAGAAGATCAAAGCTACTAG
* *
40670072 CACATTGTGGATTAACCA
1 CACGTTGTGGATGAACCA
40670090 ATAGTCATAC
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
96 93 0.96
97 4 0.04
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (96 bp):
CACGTTGTGGATGAACCACTAATCATTGTAGATGAACTGCTAACGATAAAAATATTGGTGGATGA
ACCATCCATCGTAGAAGATCAAAGCTACTAG
Found at i:40671679 original size:34 final size:33
Alignment explanation
Indices: 40671574--40671680 Score: 78
Period size: 33 Copynumber: 3.2 Consensus size: 33
40671564 GCAATATGAA
* * *
40671574 ATGCTTATAACAGATCAATATGGTAGCAAT-AAC
1 ATGCTTA-AAAAGATCAATACGATAGCAATAAAC
* * *
40671607 ATACTTATAACAAG-TCGATAC-AGTAGCAATTATA-
1 ATGCTTA-AA-AAGATCAATACGA-TAGCAA-TAAAC
40671641 ATGCTTAAAATAGATCAATACGATAGCAATAAAC
1 ATGCTTAAAA-AGATCAATACGATAGCAATAAAC
40671675 ATGCTT
1 ATGCTT
40671681 GTGACAAGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
32 1 0.02
33 27 0.47
34 27 0.47
35 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (33 bp):
ATGCTTAAAAAGATCAATACGATAGCAATAAAC
Found at i:40671696 original size:68 final size:66
Alignment explanation
Indices: 40671572--40671723 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 66
40671562 ATGCAATATG
* * *
40671572 AAATGCTTATAACAGATCAATATGGTAGCAATAACATACTTATAACAAGTCGATACAGTAGCAAT
1 AAATGCTTATAATAGATCAATACGATAGCAATAACATACTTATAACAAGTCGATACAGTAGCAAT
40671637 T
66 T
* * * *
40671638 ATAATGCTTAAAATAGATCAATACGATAGCAATAAACATGCTTGTGACAAGTCGATACAGTAGCA
1 A-AATGCTTATAATAGATCAATACGATAGCAAT-AACATACTTATAACAAGTCGATACAGTAGCA
40671703 ATT
64 ATT
40671706 AACATGCTTATAATAGAT
1 AA-ATGCTTATAATAGAT
40671724 AATTACAGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 1 0.01
67 28 0.37
68 46 0.61
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (66 bp):
AAATGCTTATAATAGATCAATACGATAGCAATAACATACTTATAACAAGTCGATACAGTAGCAAT
T
Found at i:40671731 original size:34 final size:34
Alignment explanation
Indices: 40671574--40671740 Score: 134
Period size: 34 Copynumber: 5.0 Consensus size: 34
40671564 GCAATATGAA
* **
40671574 ATGCTTATAACAGATCAATATGGTAGCAA-TAAC
1 ATGCTTATAATAGATCAATACAGTAGCAATTAAC
* * *
40671607 ATACTTATAACA-AGTCGATACAGTAGCAATTATA-
1 ATGCTTATAATAGA-TCAATACAGTAGCAATTA-AC
* *
40671641 ATGCTTAAAATAGATCAATAC-GATAGCAATAAAC
1 ATGCTTATAATAGATCAATACAG-TAGCAATTAAC
* *
40671675 ATGCTTGTGACA-AG-TCGATACAGTAGCAATTAAC
1 ATGCTTAT-A-ATAGATCAATACAGTAGCAATTAAC
40671709 ATGCTTATAATAGAT-AATTACAGTAGC-ATTAA
1 ATGCTTATAATAGATCAA-TACAGTAGCAATTAA
40671741 ACTAGTTTAA
Statistics
Matches: 107, Mismatches: 15, Indels: 24
0.73 0.10 0.16
Matches are distributed among these distances:
32 2 0.02
33 34 0.32
34 64 0.60
35 6 0.06
36 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.28
Consensus pattern (34 bp):
ATGCTTATAATAGATCAATACAGTAGCAATTAAC
Found at i:40671736 original size:68 final size:67
Alignment explanation
Indices: 40671573--40671742 Score: 211
Period size: 68 Copynumber: 2.5 Consensus size: 67
40671563 TGCAATATGA
* *
40671573 AATGCTTATAACAGATCAATATGGTAGCAAT-AACATACTTATAACAAGTCGATACAGTAGCAAT
1 AATGCTTATAATAGATCAATA-CGTAGCAATAAACATACTTATAACAAGTCGATACAGTAGCAAT
40671637 TAT
65 TAT
* * * *
40671640 AATGCTTAAAATAGATCAATACGATAGCAATAAACATGCTTGTGACAAGTCGATACAGTAGCAAT
1 AATGCTTATAATAGATCAATACG-TAGCAATAAACATACTTATAACAAGTCGATACAGTAGCAAT
40671705 TA-
65 TAT
*
40671707 ACATGCTTATAATAGAT-AATTACAGTAGCATTAAAC
1 A-ATGCTTATAATAGATCAA-TAC-GTAGCAATAAAC
40671743 TAGTTTAATG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
66 1 0.01
67 29 0.32
68 59 0.66
69 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.28
Consensus pattern (67 bp):
AATGCTTATAATAGATCAATACGTAGCAATAAACATACTTATAACAAGTCGATACAGTAGCAATT
AT
Found at i:40673852 original size:54 final size:54
Alignment explanation
Indices: 40673765--40673868 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
40673755 CTTAATTTTT
* *
40673765 TCATTGTTTTAGGGGAGTTTTCTTAACCATAAAAAACTGAGGTCAAATGATCGA
1 TCATAGTTTTAGGGGAGTTTTCTTAACCATAAAAAACGGAGGTCAAATGATCGA
40673819 TCATAGTTTTAGGGGAGTTTTCTTAACCATAAAAAACGGAGGTCAAATGA
1 TCATAGTTTTAGGGGAGTTTTCTTAACCATAAAAAACGGAGGTCAAATGA
40673869 GTTAAATGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (54 bp):
TCATAGTTTTAGGGGAGTTTTCTTAACCATAAAAAACGGAGGTCAAATGATCGA
Found at i:40676591 original size:42 final size:42
Alignment explanation
Indices: 40676532--40676614 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
40676522 TGGGTACATG
40676532 GTAAGTGTTATTTTCTATATCATTAGTTAATATATATTTTTA
1 GTAAGTGTTATTTTCTATATCATTAGTTAATATATATTTTTA
*
40676574 GTAAGTGTTATTTTCTATATCATTAGTTAATATATTTTTTT
1 GTAAGTGTTATTTTCTATATCATTAGTTAATATATATTTTT
40676615 TCAATCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (42 bp):
GTAAGTGTTATTTTCTATATCATTAGTTAATATATATTTTTA
Found at i:40679776 original size:13 final size:13
Alignment explanation
Indices: 40679758--40679784 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40679748 CACAAACGAT
40679758 AAAATTTTCACAC
1 AAAATTTTCACAC
40679771 AAAATTTTCACAC
1 AAAATTTTCACAC
40679784 A
1 A
40679785 TATTAATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTTTCACAC
Found at i:40683455 original size:42 final size:44
Alignment explanation
Indices: 40683377--40683479 Score: 113
Period size: 42 Copynumber: 2.4 Consensus size: 44
40683367 ATCGATTTGA
* ***
40683377 GATTTATGTGTAAGACCATGTTTGAGACATCGGCATCG-TATTT
1 GATTTATGTGTAAGACCATGTCTGAGACAGAAGCATCGATATTT
* *
40683420 GATTT-TGTGTAAGACCCTGTCTGGGACAGAAGCATCGATATTT
1 GATTTATGTGTAAGACCATGTCTGAGACAGAAGCATCGATATTT
**
40683463 GA-TTACATGTAAGACCA
1 GATTTATGTGTAAGACCA
40683480 CATTTGGGAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 28 0.57
43 21 0.43
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (44 bp):
GATTTATGTGTAAGACCATGTCTGAGACAGAAGCATCGATATTT
Found at i:40685638 original size:93 final size:93
Alignment explanation
Indices: 40685531--40685701 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40685521 GCCCCTAAGT
* *
40685531 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40685596 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
40685624 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40685689 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40685702 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40685698 original size:46 final size:46
Alignment explanation
Indices: 40685526--40685698 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
40685516 AACCCGCCCC
* * *
40685526 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
40685572 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
40685620 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
40685665 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40685699 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 61 0.57
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:40688120 original size:14 final size:15
Alignment explanation
Indices: 40688077--40688131 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
40688067 CAAGGAAACC
40688077 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
40688092 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
40688107 GAATAAAG-AATCCA
1 GAATAAAGAAATCCA
40688121 GAATAAAGAAA
1 GAATAAAGAAA
40688132 CCCAAGATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 15 0.43
15 19 0.54
16 1 0.03
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:40691255 original size:93 final size:92
Alignment explanation
Indices: 40691097--40691266 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 92
40691087 GCCCCTAAGT
*
40691097 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
40691162 GAGTTCGGATGCCTAGTTACATTTCAC
66 GAGTTCGGATGCCTAGTTACATTTCAC
*
40691189 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40691254 CGAGTTCGGATGC
65 CGAGTTCGGATGC
40691267 TCAACCATCC
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40691282 original size:46 final size:46
Alignment explanation
Indices: 40691091--40691275 Score: 159
Period size: 45 Copynumber: 4.0 Consensus size: 46
40691081 TAACCCGCCC
* * * * *
40691091 CTAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCTCAACCAT
40691137 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCAT
* * * * * *
40691184 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA-
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCAT
40691230 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
40691275 C
1 C
40691276 CTAGTGACAT
Statistics
Matches: 113, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
43 1 0.01
44 11 0.10
45 34 0.30
46 30 0.27
47 30 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
Found at i:40692596 original size:23 final size:22
Alignment explanation
Indices: 40692565--40692607 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40692555 TTATGAATAA
* *
40692565 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGATATGA-TTTGGCT
40692588 TATGATTTGATATGATTTGG
1 TATGATTTGATATGATTTGG
40692608 TATGGATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.51
Consensus pattern (22 bp):
TATGATTTGATATGATTTGGCT
Found at i:40697225 original size:45 final size:45
Alignment explanation
Indices: 40697157--40697310 Score: 229
Period size: 45 Copynumber: 3.4 Consensus size: 45
40697147 AGGATTTCGT
* *
40697157 TATGTGTTTTCGTGTAAGGCCACGTCTGGGACATTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATA
* *
40697202 TATGTGTTTTTGTGTAAGACCACGTTTGGGACGTTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATA
* *
40697247 TATGTGTTTTCGTGTAAAACCACGTCTAGGACGTTGGCATCGATA
1 TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATA
*
40697292 TATGTGGTTAT-GTGTAAGA
1 TATGT-GTTTTCGTGTAAGA
40697311 GGATGTTTGG
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 94 0.96
46 4 0.04
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (45 bp):
TATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATA
Found at i:40697333 original size:90 final size:90
Alignment explanation
Indices: 40697157--40697333 Score: 246
Period size: 90 Copynumber: 2.0 Consensus size: 90
40697147 AGGATTTCGT
** * * *
40697157 TATGTGTTTTCGTGTAAGGCCACGTCTGGGACATTGGCATCGATATATGTGTTTTTGTGTAAGAC
1 TATGTGTTTTCGTGTAAAACCACGTCTAGGACATTGGCATCGATATATGTGGTTATGTGTAAGAC
* * *
40697222 CACGTTTGGGACGTTGGCATCGATA
66 CACGTTTGGGACATCGACATCGATA
* *
40697247 TATGTGTTTTCGTGTAAAACCACGTCTAGGACGTTGGCATCGATATATGTGGTTATGTGTAAGAG
1 TATGTGTTTTCGTGTAAAACCACGTCTAGGACATTGGCATCGATATATGTGGTTATGTGTAAGAC
* *
40697312 GATGTTTGGGACATCGACATCG
66 CACGTTTGGGACATCGACATCG
40697334 TATTGATTCG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (90 bp):
TATGTGTTTTCGTGTAAAACCACGTCTAGGACATTGGCATCGATATATGTGGTTATGTGTAAGAC
CACGTTTGGGACATCGACATCGATA
Found at i:40732786 original size:39 final size:39
Alignment explanation
Indices: 40732743--40732831 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
40732733 CATACTTTGA
* *
40732743 TACCCTTGGTCACACTTACATGCCTCTT-TCGTACTTCGG
1 TACCCCTGATCACACTTACATGCC-CTTGTCGTACTTCGG
* * * *
40732782 TACCCCTGATCGCACTTACGTTCCCTTGTTGTACTTCGG
1 TACCCCTGATCACACTTACATGCCCTTGTCGTACTTCGG
*
40732821 TACTCCTGATC
1 TACCCCTGATC
40732832 GTACGTGCCC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 3 0.07
39 39 0.93
ACGTcount: A:0.15, C:0.34, G:0.16, T:0.36
Consensus pattern (39 bp):
TACCCCTGATCACACTTACATGCCCTTGTCGTACTTCGG
Found at i:40732849 original size:35 final size:36
Alignment explanation
Indices: 40732773--40732859 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 36
40732763 TGCCTCTTTC
* * * *
40732773 GTACTTCGGTACCCCTGATCGCACTTACGTTCCCTTGTT
1 GTACTTCGGTACTCCTGATCG--C-TACGTGCCCCTCTT
40732812 GTACTTCGGTACTCCTGATCG-TACGTGCCCCTCTT
1 GTACTTCGGTACTCCTGATCGCTACGTGCCCCTCTT
*
40732847 GTACTTCGATACT
1 GTACTTCGGTACT
40732860 GTTGATGGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
35 23 0.53
39 20 0.47
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.36
Consensus pattern (36 bp):
GTACTTCGGTACTCCTGATCGCTACGTGCCCCTCTT
Found at i:40734684 original size:27 final size:26
Alignment explanation
Indices: 40734628--40734738 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
40734618 AGCATGACTG
* * *
40734628 CCAGAACAAATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
40734654 CCAGAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
40734681 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
40734708 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGAT-AATGTGGCAGAGCCA
40734735 CCAG
1 CCAG
40734739 TATGCTTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.17
27 61 0.79
28 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40736198 original size:24 final size:24
Alignment explanation
Indices: 40736170--40736270 Score: 166
Period size: 24 Copynumber: 4.2 Consensus size: 24
40736160 CCAACACCGT
*
40736170 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
40736194 TCTCCCTTATCAGCTCCTACATCC
1 TCTCCCTTATCAGCTCCTAAATCC
40736218 TCTCCCTTATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
* *
40736242 TCTCCCTTATTAGCTCCTAAATCT
1 TCTCCCTTATCAGCTCCTAAATCC
40736266 TCTCC
1 TCTCC
40736271 TGACAGCCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.20, C:0.42, G:0.04, T:0.35
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:40740812 original size:15 final size:15
Alignment explanation
Indices: 40740790--40740834 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
40740780 GAAAATCGAG
*
40740790 TTTT-TTTTTTTAAA
1 TTTTGTTTTTGTAAA
*
40740804 TTTTGTTTTTGAAAA
1 TTTTGTTTTTGTAAA
40740819 TCTTTGTTTTTGTAAA
1 T-TTTGTTTTTGTAAA
40740835 CCCATTCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 13 0.50
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (15 bp):
TTTTGTTTTTGTAAA
Found at i:40741856 original size:27 final size:26
Alignment explanation
Indices: 40741802--40741912 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
40741792 AGCATGGCTG
* * *
40741802 CCAGAATAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
40741828 CCAAAACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAAT-GTGGCAGAGCCA
40741855 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
40741882 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGAT-AATGTGGCAGAGCCA
40741909 CCAG
1 CCAG
40741913 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 12 0.16
27 60 0.80
28 3 0.04
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:40743443 original size:24 final size:24
Alignment explanation
Indices: 40743344--40743436 Score: 150
Period size: 24 Copynumber: 3.9 Consensus size: 24
40743334 CCAACACCGT
*
40743344 TCTCCCTAATCAGCTCCTAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
40743368 TCTCCCTTATCAGCTCCTACATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
40743392 TCTCCCTTATCAGCTCATAAATCC
1 TCTCCCTTATCAGCTCCTAAATCC
*
40743416 TCTCTCTTATCAGCTCCTAAA
1 TCTCCCTTATCAGCTCCTAAA
40743437 ACTTCTCCTG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.23, C:0.40, G:0.04, T:0.33
Consensus pattern (24 bp):
TCTCCCTTATCAGCTCCTAAATCC
Found at i:40760658 original size:22 final size:21
Alignment explanation
Indices: 40760633--40760687 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
40760623 CCTCCTATAT
40760633 TTTTATTATTATTTATTCTTA
1 TTTTATTATTATTTATTCTTA
40760654 -TTT-TTATT-TTTATTCTTA
1 TTTTATTATTATTTATTCTTA
40760672 TTTTATT-TTATTTATT
1 TTTTATTATTATTTATT
40760688 TTTGCTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
20 11 0.35
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTATTATTATTTATTCTTA
Found at i:40760659 original size:12 final size:11
Alignment explanation
Indices: 40760630--40760732 Score: 70
Period size: 12 Copynumber: 9.1 Consensus size: 11
40760620 AATCCTCCTA
40760630 TATTTTTA--T
1 TATTTTTATTT
40760639 TATTATTTATTCT
1 TATT-TTTATT-T
40760652 TATTTTTATTTT
1 TATTTTTA-TTT
*
40760664 TATTCTTATTT
1 TATTTTTATTT
40760675 TA-TTTTA-TT
1 TATTTTTATTT
*
40760684 TATTTTTGCTTT
1 TATTTTT-ATTT
*
40760696 GATTTTTATTT
1 TATTTTTATTT
**
40760707 TCATTTCAATTT
1 T-ATTTTTATTT
40760719 TATTATTTTATTT
1 TA-T-TTTTATTT
40760732 T
1 T
40760733 GAAAGACATA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.11
10 12 0.16
11 9 0.12
12 30 0.41
13 14 0.19
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:40760667 original size:18 final size:17
Alignment explanation
Indices: 40760638--40760680 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 17
40760628 TATATTTTTA
40760638 TTATTATTTATTCTTATTT
1 TTATT-TTTATTCTTA-TT
40760657 TTATTTTTATTCTTATT
1 TTATTTTTATTCTTATT
40760674 TTATTTT
1 TTATTTT
40760681 ATTTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.38
18 10 0.42
19 5 0.21
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTTATTCTTATT
Found at i:40760672 original size:28 final size:28
Alignment explanation
Indices: 40760630--40760684 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
40760620 AATCCTCCTA
40760630 TATTTTTATTATTA-TTTATTCTTATTTT
1 TATTTTTATTATTATTTTATT-TTATTTT
*
40760658 TATTTTTATTCTTATTTTATTTTATTT
1 TATTTTTATTATTATTTTATTTTATTT
40760685 ATTTTTGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (28 bp):
TATTTTTATTATTATTTTATTTTATTTT
Found at i:40760701 original size:38 final size:38
Alignment explanation
Indices: 40760633--40760727 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 38
40760623 CCTCCTATAT
* * *
40760633 TTTTATTATTATTTATTCTTATTTTTATTTTTATTCTT-A
1 TTTTATT-TTATTTATTTTTACTTTGATTTTTATT-TTCA
*
40760672 TTTTATTTTATTTATTTTTGCTTTGATTTTTATTTTCA
1 TTTTATTTTATTTATTTTTACTTTGATTTTTATTTTCA
*
40760710 TTTCAATTTTA-TTATTTT
1 TTT-TATTTTATTTATTTT
40760728 ATTTTGAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
37 2 0.04
38 34 0.69
39 13 0.27
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (38 bp):
TTTTATTTTATTTATTTTTACTTTGATTTTTATTTTCA
Found at i:40763449 original size:13 final size:13
Alignment explanation
Indices: 40763433--40763465 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
40763423 TTTAATTAAA
*
40763433 TTAGTTAATTAGT
1 TTAGATAATTAGT
40763446 TTAGATAATTAGT
1 TTAGATAATTAGT
40763459 TTA-ATAA
1 TTAGATAA
40763466 ACAAAGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:40768094 original size:28 final size:28
Alignment explanation
Indices: 40768026--40768263 Score: 379
Period size: 28 Copynumber: 8.5 Consensus size: 28
40768016 CATGAGATTG
* * * *
40768026 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40768055 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40768083 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
40768111 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40768139 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40768167 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40768195 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40768223 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40768250 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40768264 GACTTAACAT
Statistics
Matches: 200, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.12
28 158 0.79
29 18 0.09
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40776031 original size:27 final size:28
Alignment explanation
Indices: 40775942--40776169 Score: 301
Period size: 28 Copynumber: 8.4 Consensus size: 28
40775932 CATGAGATTG
* * * *
40775942 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40775971 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40775999 GCACTAAGTGTGCGAGTTTGA-TATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40776026 GCACTAAGTGTGC-AGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40776053 GCACTAAGTGTGCGAG---GATTATGT-
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
40776077 GAACT-AGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40776104 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40776132 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40776159 GCACTGAGTGT
1 GCACTAAGTGT
40776170 CGGACTTAAA
Statistics
Matches: 183, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.05
24 4 0.02
25 8 0.04
26 15 0.08
27 61 0.33
28 67 0.37
29 18 0.10
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40779576 original size:27 final size:27
Alignment explanation
Indices: 40779546--40779749 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
40779536 ATATTAAGTC
* * *
40779546 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
40779573 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
40779601 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
40779628 CGCACACTTAGTGC-GCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
40779654 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
40779681 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
*
40779708 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
40779735 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40779750 GTACAATTTA
Statistics
Matches: 158, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.15
27 109 0.69
28 26 0.16
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:40779745 original size:107 final size:108
Alignment explanation
Indices: 40779546--40779748 Score: 320
Period size: 108 Copynumber: 1.9 Consensus size: 108
40779536 ATATTAAGTC
*
40779546 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAATCAAACTCGCACACTTA
*
40779611 GTGCTACATAGTCAACTCGCACACTTAGTGCGCATGGTCAATT
66 GTGCTACATAGTCAAATCGCACACTTAGTGCGCATGGTCAATT
* * ** *
40779654 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTT
1 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCAACATAATCAAACTCGCACACTT
40779717 AGTGCTACATAGTCAAATCGCACACTTAGTGC
65 AGTGCTACATAGTCAAATCGCACACTTAGTGC
40779749 TGTACAATTT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 43 0.49
108 44 0.51
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.26
Consensus pattern (108 bp):
CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCAACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAAATCGCACACTTAGTGCGCATGGTCAATT
Found at i:40786711 original size:28 final size:28
Alignment explanation
Indices: 40786643--40786877 Score: 355
Period size: 28 Copynumber: 8.4 Consensus size: 28
40786633 CATGAGATTG
* * * *
40786643 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
40786672 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40786700 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
40786728 GCACTAAGTGTGCAAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40786756 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
* *
40786784 GAACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40786812 GCACTAAGTGTGCGAGTTTGATTATGTA
1 GCACTAAGTGTGCGAGTTTGATTATATA
40786840 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
40786867 GCACTGAGTGT
1 GCACTAAGTGT
40786878 CCGGACTTAA
Statistics
Matches: 195, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
27 20 0.10
28 157 0.81
29 18 0.09
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:40798543 original size:25 final size:25
Alignment explanation
Indices: 40798515--40798580 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
40798505 CTGTAGACCG
* * *
40798515 GTATGGTCTCACGAGCTATAAATTA
1 GTATGCTCTCACGAGCTACAAATCA
40798540 GTATGCTCTCACGAGCTACAAATCA
1 GTATGCTCTCACGAGCTACAAATCA
* *
40798565 GCATGCTCTCAAGAGC
1 GTATGCTCTCACGAGC
40798581 GGTGGAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTACAAATCA
Found at i:40807303 original size:32 final size:32
Alignment explanation
Indices: 40807267--40807328 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
40807257 TAACACATGC
*
40807267 ACACCTGGGTAGACCACACAATTATACAATGG
1 ACACCTGGCTAGACCACACAATTATACAATGG
*
40807299 ACACCTGGCTAGACTACACAATTATACAAT
1 ACACCTGGCTAGACCACACAATTATACAAT
40807329 ACACCGCACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.21
Consensus pattern (32 bp):
ACACCTGGCTAGACCACACAATTATACAATGG
Found at i:40809798 original size:36 final size:36
Alignment explanation
Indices: 40809751--40809823 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
40809741 ATTTTGGAGT
40809751 AGCAATTGAGTGTTCATAGAAGCCTTGATCAGTGAG
1 AGCAATTGAGTGTTCATAGAAGCCTTGATCAGTGAG
*
40809787 AGCAATTGAGTGTTCATAGAAGCCTTGATCGGTGAG
1 AGCAATTGAGTGTTCATAGAAGCCTTGATCAGTGAG
40809823 A
1 A
40809824 ACAACAGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (36 bp):
AGCAATTGAGTGTTCATAGAAGCCTTGATCAGTGAG
Found at i:40831883 original size:27 final size:27
Alignment explanation
Indices: 40831822--40831943 Score: 129
Period size: 27 Copynumber: 4.5 Consensus size: 27
40831812 TACCCTTGTA
* * * *
40831822 AGGTAAAATAACTGTAATT-CCCCTATA
1 AGGTAAAATGACTGT-TTTGCCCTTATG
* *
40831849 AGGCAAAATGACTGTTTTGCCTTTATG
1 AGGTAAAATGACTGTTTTGCCCTTATG
*
40831876 AGGTAAAATGACTATTTTGCCCTTATG
1 AGGTAAAATGACTGTTTTGCCCTTATG
** *
40831903 AGGTGCAATGACTGTTTTTCCCTTATG
1 AGGTAAAATGACTGTTTTGCCCTTATG
*
40831930 TGGTAAAATGACTG
1 AGGTAAAATGACTG
40831944 AAATGCCCCT
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 2 0.03
27 76 0.97
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (27 bp):
AGGTAAAATGACTGTTTTGCCCTTATG
Found at i:40832401 original size:18 final size:18
Alignment explanation
Indices: 40832343--40832402 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
40832333 GTTTAAATTT
*
40832343 TTACTGCACTGATTACTG
1 TTACTGTACTGATTACTG
* *
40832361 TTACCGTACTGATTACTA
1 TTACTGTACTGATTACTG
* *
40832379 TTACTGTTCTGTTTACTG
1 TTACTGTACTGATTACTG
40832397 TTACTG
1 TTACTG
40832403 CAATGGGCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (18 bp):
TTACTGTACTGATTACTG
Found at i:40850260 original size:22 final size:24
Alignment explanation
Indices: 40850234--40850277 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
40850224 ATATAGTTCA
40850234 ATTTTAATTT-TTAT-TCAAAAAC
1 ATTTTAATTTGTTATATCAAAAAC
40850256 ATTTTAATTTGTTATATCAAAA
1 ATTTTAATTTGTTATATCAAAA
40850278 TATTTTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTTTAATTTGTTATATCAAAAAC
Found at i:40851340 original size:115 final size:115
Alignment explanation
Indices: 40851215--40851445 Score: 417
Period size: 115 Copynumber: 2.0 Consensus size: 115
40851205 TTTATGTGTT
* * *
40851215 AAAAAAATGTTCTTAAATAAAAGAAAAAAGCATATGTACTTTTAAACATAAAAAGAACTATGATA
1 AAAAAAATGTTATTAAATAAAAGAAAAAAGCATATGTACTTTAAAAAATAAAAAGAACTATGATA
40851280 TTCTTCCCATTATCGTTTCCAACATTGTTTAACATCAAAGGATTTGGCCA
66 TTCTTCCCATTATCGTTTCCAACATTGTTTAACATCAAAGGATTTGGCCA
*
40851330 AAAAAAATGTTATTAAATAAAAGAAAAATGCATATGTACTTTAAAAAATAAAAAGAACTATGATA
1 AAAAAAATGTTATTAAATAAAAGAAAAAAGCATATGTACTTTAAAAAATAAAAAGAACTATGATA
*
40851395 TTCTTCCCATTATCGTTTCCACCATTGTTTAACATCAAAGGATTTGGCCA
66 TTCTTCCCATTATCGTTTCCAACATTGTTTAACATCAAAGGATTTGGCCA
40851445 A
1 A
40851446 CTTAGGGTCT
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (115 bp):
AAAAAAATGTTATTAAATAAAAGAAAAAAGCATATGTACTTTAAAAAATAAAAAGAACTATGATA
TTCTTCCCATTATCGTTTCCAACATTGTTTAACATCAAAGGATTTGGCCA
Found at i:40859625 original size:106 final size:106
Alignment explanation
Indices: 40859440--40859658 Score: 429
Period size: 106 Copynumber: 2.1 Consensus size: 106
40859430 TGACTATTAG
*
40859440 ATAAATTATAATGATTTCATATACATAAAAATATAAAGAGGAAGCACAATGCATATGATTCATAA
1 ATAAAGTATAATGATTTCATATACATAAAAATATAAAGAGGAAGCACAATGCATATGATTCATAA
40859505 ATTACAATAAGTTCATTCAAAATATTGACTAAGTTAACTAA
66 ATTACAATAAGTTCATTCAAAATATTGACTAAGTTAACTAA
40859546 ATAAAGTATAATGATTTCATATACATAAAAATATAAAGAGGAAGCACAATGCATATGATTCATAA
1 ATAAAGTATAATGATTTCATATACATAAAAATATAAAGAGGAAGCACAATGCATATGATTCATAA
40859611 ATTACAATAAGTTCATTCAAAATATTGACTAAGTTAACTAA
66 ATTACAATAAGTTCATTCAAAATATTGACTAAGTTAACTAA
40859652 ATAAAGT
1 ATAAAGT
40859659 TCACTTTAAC
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (106 bp):
ATAAAGTATAATGATTTCATATACATAAAAATATAAAGAGGAAGCACAATGCATATGATTCATAA
ATTACAATAAGTTCATTCAAAATATTGACTAAGTTAACTAA
Found at i:40865169 original size:46 final size:46
Alignment explanation
Indices: 40865045--40865211 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
40865035 TGATATGTGT
* * * *
40865045 GCTATTGTAAGACATGTCTAGGACATGCATCGACCACATT---ATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCG---GCATTGAGAAGAGA
* *
40865091 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAAGAGA
* *
40865137 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC-TTCGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATT-GAGA-AGA-GA
* *
40865185 GCTAGTGTAAGACCTGTCTGGTACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
40865212 GCGTCAGCTT
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 71 0.68
47 1 0.01
48 26 0.25
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAAGAGA
Found at i:40865353 original size:142 final size:138
Alignment explanation
Indices: 40865093--40865355 Score: 314
Period size: 142 Copynumber: 1.9 Consensus size: 138
40865083 TTATGAGAGC
* * ** * *
40865093 CAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGG
1 CAGTGTAAGACATGTCCGGGACATGCATCGACACCGAGAAGAGAGCCAGTGTAAGACATGTCTGG
* * * * *
40865158 GACATGCATCGGCTTCGAGATATACAAGCTAGTGTAAGACCTGTCTGGTACATGGCGTCAGCTTG
66 GACAGGCATCGGCTTCGAGAAATAAAAGCTAGTGGAAGACCTGTCTGGGACATGGCGTCAGCTTG
40865223 TTGTGTGT
131 TTGTGTGT
* * *
40865231 CAGTGTAAGACCTGTCCGGGACATGGCATCGACACCGATAGAAGAGAGCCAGTGTAAGACCTGTT
1 CAGTGTAAGACATGTCCGGGACAT-GCATCGACACCG--AGAAGAGAGCCAGTGTAAGACATGTC
* *
40865296 TGGGACACGGCATCGGCCTT-GATAAATAAAAG-TCAGTGGAAGACCTTTCTGGGACATGGC
63 TGGGACA-GGCATCGG-CTTCGAGAAATAAAAGCT-AGTGGAAGACCTGTCTGGGACATGGC
40865356 AACGACTTTG
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
138 22 0.21
139 9 0.09
141 30 0.29
142 39 0.38
143 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (138 bp):
CAGTGTAAGACATGTCCGGGACATGCATCGACACCGAGAAGAGAGCCAGTGTAAGACATGTCTGG
GACAGGCATCGGCTTCGAGAAATAAAAGCTAGTGGAAGACCTGTCTGGGACATGGCGTCAGCTTG
TTGTGTGT
Found at i:40871969 original size:27 final size:27
Alignment explanation
Indices: 40871932--40872134 Score: 257
Period size: 27 Copynumber: 7.6 Consensus size: 27
40871922 TAAATTGTAC
40871932 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
40871959 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40871986 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40872012 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
40872040 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40872067 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40872094 -GCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40872120 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40872135 GACTTAATAT
Statistics
Matches: 155, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 24 0.15
27 131 0.85
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40879962 original size:27 final size:27
Alignment explanation
Indices: 40879863--40880019 Score: 174
Period size: 27 Copynumber: 5.8 Consensus size: 27
40879853 GGCATATTGT
* **
40879863 ACTATGTTGCACTAAGTGTGCGAAATG
1 ACTATGTAGCACTAAGTGTGCGAGTTG
* * *
40879890 AATATGAATGCACTAAGTGTGCGAATTG
1 ACTATGTA-GCACTAAGTGTGCGAGTTG
*
40879918 AC-ATG-CGCACTAAGTGTGCGAGTTG
1 ACTATGTAGCACTAAGTGTGCGAGTTG
40879943 ACTATGTAGCACTAAGTGTGCGAGTTTG
1 ACTATGTAGCACTAAGTGTGCGAG-TTG
* *
40879971 ATTATGTGGCACTAAGTGTGCGAGTTG
1 ACTATGTAGCACTAAGTGTGCGAGTTG
* * *
40879998 ATTATATAGCACTGAGTGTGCG
1 ACTATGTAGCACTAAGTGTGCG
40880020 GACTTAATAT
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
25 20 0.18
26 3 0.03
27 46 0.41
28 44 0.39
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (27 bp):
ACTATGTAGCACTAAGTGTGCGAGTTG
Found at i:40896134 original size:27 final size:27
Alignment explanation
Indices: 40896097--40896301 Score: 250
Period size: 27 Copynumber: 7.6 Consensus size: 27
40896087 TAAATTGTAC
40896097 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
40896124 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40896151 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40896177 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
40896205 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40896232 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
40896260 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40896287 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40896302 GACTTAATAT
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
27 131 0.85
28 24 0.15
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40902235 original size:30 final size:30
Alignment explanation
Indices: 40902199--40902259 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40902189 TCCTTAACTC
40902199 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40902229 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40902259 A
1 A
40902260 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40903227 original size:51 final size:51
Alignment explanation
Indices: 40903151--40903249 Score: 189
Period size: 51 Copynumber: 1.9 Consensus size: 51
40903141 CCATGATCAG
*
40903151 AAGTCAGTACGTTACTGTTAACCTCATCATTGTCAGCATGATCAAATCTGT
1 AAGTCAGTACGTTACTGTTAACCTCATCATTGCCAGCATGATCAAATCTGT
40903202 AAGTCAGTACGTTACTGTTAACCTCATCATTGCCAGCATGATCAAATC
1 AAGTCAGTACGTTACTGTTAACCTCATCATTGCCAGCATGATCAAATC
40903250 CGTCTGATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (51 bp):
AAGTCAGTACGTTACTGTTAACCTCATCATTGCCAGCATGATCAAATCTGT
Found at i:40904920 original size:43 final size:43
Alignment explanation
Indices: 40904859--40904940 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
40904849 AATACAAATG
* *
40904859 TTAAATTTTAATCGTACAAACTTATTGGACTAAATTGTACTCA
1 TTAAATTTTAACCGTACAAACTTACTGGACTAAATTGTACTCA
40904902 TTAAATTTTAACCGTACAAACTTACTGGACTAAATTGTA
1 TTAAATTTTAACCGTACAAACTTACTGGACTAAATTGTA
40904941 GTCGTTGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (43 bp):
TTAAATTTTAACCGTACAAACTTACTGGACTAAATTGTACTCA
Found at i:40935275 original size:18 final size:18
Alignment explanation
Indices: 40935252--40935286 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40935242 GATATGATAC
40935252 TAAAAT-TATTAAAAAAAT
1 TAAAATATA-TAAAAAAAT
40935270 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
40935287 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:40935575 original size:22 final size:21
Alignment explanation
Indices: 40935540--40935615 Score: 68
Period size: 22 Copynumber: 3.7 Consensus size: 21
40935530 AAAAGGTATC
* *
40935540 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
40935561 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
40935584 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
40935603 TGC-AATCATATCT
1 TACAAATCATATCT
40935616 AAGATTGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Done.