Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 25 of 50
Found at i:6202003 original size:22 final size:22
Alignment explanation
Indices: 6201978--6202031 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
6201968 GCCTCAACAT
* *
6201978 TGATATAAATGTGCATTCGCAC
1 TGATATAAAAGTGCATTCACAC
* *
6202000 TGATTTAAAAGTTCATTCACAC
1 TGATATAAAAGTGCATTCACAC
6202022 TGATACTAAA
1 TGATA-TAAA
6202032 GTACCTTAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (22 bp):
TGATATAAAAGTGCATTCACAC
Found at i:6203159 original size:31 final size:31
Alignment explanation
Indices: 6203094--6203159 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
6203084 TTCTGTTGCG
* * * ***
6203094 AAAATGGGGCCTTAGTGTCGATACTGTTGTA
1 AAAACGGGGCCTCAGTATCGATACTGTCACA
6203125 AAAACGGGGCCTCAGTATCGATACTGTCACA
1 AAAACGGGGCCTCAGTATCGATACTGTCACA
6203156 AAAA
1 AAAA
6203160 ATTTGGACTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAACGGGGCCTCAGTATCGATACTGTCACA
Found at i:6204646 original size:43 final size:50
Alignment explanation
Indices: 6204593--6204699 Score: 129
Period size: 51 Copynumber: 2.3 Consensus size: 50
6204583 TTAATTAATG
*
6204593 AATAAAATAATAACAAAC-AA-AA-CATGTCTT-A-AC-TC-TAATTCCT
1 AATAAAATAATAACAAACTAAGAATAATGTCTTAACACATCTTAATTCCT
* *
6204636 AATAAAATAATAATAAACTAAGAATAATGTTTTAACACAATCTTAATTCCT
1 AATAAAATAATAACAAACTAAGAATAATGTCTTAACAC-ATCTTAATTCCT
6204687 AATAAAATAATAA
1 AATAAAATAATAA
6204700 ATCTAATCCT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
43 17 0.32
44 2 0.04
45 2 0.04
46 6 0.11
47 1 0.02
48 2 0.04
50 2 0.04
51 21 0.40
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (50 bp):
AATAAAATAATAACAAACTAAGAATAATGTCTTAACACATCTTAATTCCT
Found at i:6204702 original size:25 final size:22
Alignment explanation
Indices: 6204674--6204719 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6204664 GTTTTAACAC
6204674 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
6204699 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
6204720 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:6205633 original size:30 final size:30
Alignment explanation
Indices: 6205597--6205657 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
6205587 TTTAAAAACA
6205597 ATGTCAACGGGTTTGTTAAAGTAACCCCTT
1 ATGTCAACGGGTTTGTTAAAGTAACCCCTT
* *
6205627 ATGTCAACTGGTTTGTTAAAGTAATCCCTT
1 ATGTCAACGGGTTTGTTAAAGTAACCCCTT
6205657 A
1 A
6205658 AGTCTCCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (30 bp):
ATGTCAACGGGTTTGTTAAAGTAACCCCTT
Found at i:6208701 original size:13 final size:13
Alignment explanation
Indices: 6208683--6208756 Score: 112
Period size: 13 Copynumber: 5.7 Consensus size: 13
6208673 TGCGTCATAA
6208683 ATTTATGACGCGC
1 ATTTATGACGCGC
*
6208696 ATTTATGACACGC
1 ATTTATGACGCGC
*
6208709 ATTTATGACACGC
1 ATTTATGACGCGC
*
6208722 ATTTATGACGTGC
1 ATTTATGACGCGC
*
6208735 ATTTATGACGCAC
1 ATTTATGACGCGC
6208748 ATTTATGAC
1 ATTTATGAC
6208757 TTACATTGCG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 56 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:6208858 original size:85 final size:85
Alignment explanation
Indices: 6208747--6208902 Score: 251
Period size: 85 Copynumber: 1.8 Consensus size: 85
6208737 TTATGACGCA
* *
6208747 CATTTATGACTTACATTGCGCTTCATTAAAGCCCCCGTCATAAATGAAAATGACACACATTTGTG
1 CATTTATGACTTACATTGCGATTCATTAAAGCCCCCGTCATAAATGAAAATGACACACATTCGTG
6208812 TGTCATAAATTTATGGCACG
66 TGTCATAAATTTATGGCACG
* * *
6208832 CATTTATGATTTACATTGC-ATGTCATTGAAGCCTCCGTCATAAATGAAAATGACACACATTCGT
1 CATTTATGACTTACATTGCGAT-TCATTAAAGCCCCCGTCATAAATGAAAATGACACACATTCGT
6208896 GTGTCAT
65 GTGTCAT
6208903 GATTGTATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
84 1 0.02
85 64 0.98
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (85 bp):
CATTTATGACTTACATTGCGATTCATTAAAGCCCCCGTCATAAATGAAAATGACACACATTCGTG
TGTCATAAATTTATGGCACG
Found at i:6215058 original size:25 final size:23
Alignment explanation
Indices: 6215009--6215058 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
6214999 TTTCGTTTGC
** *
6215009 AATTTTTGGCTTTTTTTTTTTAA
1 AATTTTTGGCTTTTTTTAATGAA
6215032 AATTTTTCGGTCTTTTTTTAATGAA
1 AATTTTT-GG-CTTTTTTTAATGAA
6215057 AA
1 AA
6215059 AAAAGAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 2 0.09
25 13 0.59
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.60
Consensus pattern (23 bp):
AATTTTTGGCTTTTTTTAATGAA
Found at i:6217219 original size:43 final size:42
Alignment explanation
Indices: 6217157--6217420 Score: 316
Period size: 43 Copynumber: 6.2 Consensus size: 42
6217147 AACAAAAAAT
*** * *
6217157 GCCGCAATAGGTAACGATATATAGCGGTGTTTGTCCAACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTT-TCCAACAAAC
* * * *
6217200 GTCGCAATAGGTGTTGATATTTGGTGGCTTTTTCCAACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCCAACAAAC
*
6217242 GCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCAACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTT-CCAACAAAC
*
6217285 GCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-ACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCG--TTTTCCAACAAAC
6217328 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCC-ACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCG-TTT-TCCAACAAAC
* * *
6217371 GCCGTAATAGGTCTTGATATTTAGCGGCGTTTTTCCCACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCG-TTTTCCAACAAAC
*
6217414 ACCGCAA
1 GCCGCAA
6217421 AAAATCTGGT
Statistics
Matches: 197, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
42 45 0.23
43 146 0.74
44 2 0.01
45 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (42 bp):
GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTCCAACAAAC
Found at i:6217455 original size:129 final size:128
Alignment explanation
Indices: 6217194--6217461 Score: 319
Period size: 129 Copynumber: 2.1 Consensus size: 128
6217184 TGTTTGTCCA
* * * *
6217194 ACAAACGTCGCAATAGGTGTTGATATTTGGTGGCTTTTTCCAACAAACGCCGCAATAGGTGTTGA
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCTTTTTCCAACAAACGCCGCAATAGGTCTTGA
* * ** * * ***
6217259 GATTTAGCGGCGTTTTCCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC
66 GATTTAGCGGCGTTTTCCCAACAAACACCGCAAAAAATGCTGAGATATAGCGGCGTTTTAGAC
*
6217322 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTGTCC-ACAAACGCCGTAATAGGTCTT
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGC-TTTT-TCCAACAAACGCCGCAATAGGTCTT
*
6217386 GATATTTAGCGGCGTTTTTCCC-ACAAACACCGCAAAAAAT-CTG-GTATATAGCGGCGTTTTAA
64 GAGATTTAGCGGCG-TTTTCCCAACAAACACCGCAAAAAATGCTGAG-ATATAGCGGCGTTTT-A
*
6217448 GAT
126 GAC
6217451 ACAAACGCCGC
1 ACAAACGCCGC
6217462 TAATTACCTC
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
127 1 0.01
128 47 0.39
129 61 0.51
130 10 0.08
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (128 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCTTTTTCCAACAAACGCCGCAATAGGTCTTGA
GATTTAGCGGCGTTTTCCCAACAAACACCGCAAAAAATGCTGAGATATAGCGGCGTTTTAGAC
Found at i:6217599 original size:21 final size:21
Alignment explanation
Indices: 6217573--6217631 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
6217563 ATTTTCCAAT
*
6217573 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
6217594 AAACTTAAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
**
6217615 AAAAATGAAATCCATAA
1 AAACTTGAAATCCATAA
6217632 TAATAAATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:6222058 original size:83 final size:82
Alignment explanation
Indices: 6221935--6222338 Score: 415
Period size: 83 Copynumber: 4.9 Consensus size: 82
6221925 TATGACAATT
*
6221935 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATTATTAAAATGCC
1 GCGGCGTTTGGTA-TAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-TTATTAAAACGCC
6222000 ACAAAAGTACGTGTCTATA
64 ACAAAAGTACGTGTCTATA
* * * *
6222019 GCGGCGTTTGTGTA-AAAACGCAACTAAAGTACGAATCTATAGCGGCGTTTGGTATTAAAACACC
1 GCGGCGTTTG-GTATAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-TTATTAAAACGCC
6222083 AC-AAAGTACGTGTCTATA
64 ACAAAAGTACGTGTCTATA
* * * * * * *
6222101 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCATTTGTGTAAAAATGCCA
1 GCGGCGTTTGGTA-TAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATTAAAACGCCA
* * *
6222166 CTAAAGTATGAGTCTATA
65 CAAAAGTACGTGTCTATA
** * * * * *
6222184 GCATCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCAGCGTTTGTATAAAAACGCCA
1 GCGGCGTTTGGTA-TAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATTAAAACGCCA
*
6222249 CTAAAA-TAC-TAGTTTATA
65 C-AAAAGTACGT-GTCTATA
* * * * *
6222267 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTCTTTAGCGGCGTTTTTA-TACAAACGAC
1 GCGGCGTTTGGTAT-AAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATTA-AAACGCC
*
6222330 ACTAAAGTA
64 ACAAAAGTA
6222339 TAGTATTTTG
Statistics
Matches: 271, Mismatches: 40, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
81 8 0.03
82 81 0.30
83 166 0.61
84 13 0.05
85 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (82 bp):
GCGGCGTTTGGTATAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTTTATTAAAACGCCAC
AAAAGTACGTGTCTATA
Found at i:6222060 original size:41 final size:42
Alignment explanation
Indices: 6221935--6222338 Score: 418
Period size: 41 Copynumber: 9.8 Consensus size: 42
6221925 TATGACAATT
6221935 GCGGCGTTTG-GTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGTGTA-TAAAACGCCACTAAAGTACGAGTCTATA
* * * *
6221977 GCGGCGTTTAT-TATTAAAATGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGTGTA-TAAAACGCCACTAAAGTACGAGTCTATA
* *
6222019 GCGGCGTTTGTGTA-AAAACGCAACTAAAGTACGAATCTATA
1 GCGGCGTTTGTGTATAAAACGCCACTAAAGTACGAGTCTATA
* *
6222060 GCGGCGTTTG-GTATTAAAACACCAC-AAAGTACGTGTCTATA
1 GCGGCGTTTGTGTA-TAAAACGCCACTAAAGTACGAGTCTATA
* *
6222101 GCGGCGTTTG-GTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGTGTA-TAAAACGCCACTAAAGTACGAGTCTATA
* * *
6222143 GCGGCATTTGTGTA-AAAATGCCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTGTATAAAACGCCACTAAAGTACGAGTCTATA
** * *
6222184 GCATCGTTTG-GTATTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGTGTA-TAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
6222226 GCAGCGTTTGTATA-AAAACGCCACTAAAATACTAGTTTATA
1 GCGGCGTTTGTGTATAAAACGCCACTAAAGTACGAGTCTATA
* * * * *
6222267 GCGGCGTTTGTATA-AAAACGCCACTACATTACGATTCTTTA
1 GCGGCGTTTGTGTATAAAACGCCACTAAAGTACGAGTCTATA
*
6222308 GCGGCGTTT-T-TATACAAACGACACTAAAGTA
1 GCGGCGTTTGTGTATA-AAACGCCACTAAAGTA
6222339 TAGTATTTTG
Statistics
Matches: 307, Mismatches: 44, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.01
40 8 0.03
41 178 0.58
42 112 0.36
43 7 0.02
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGTGTATAAAACGCCACTAAAGTACGAGTCTATA
Found at i:6222116 original size:124 final size:124
Alignment explanation
Indices: 6221935--6222316 Score: 527
Period size: 124 Copynumber: 3.1 Consensus size: 124
6221925 TATGACAATT
* * * *
6221935 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTATTATTAAAATGCC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT-GTATTAAAACGCC
*
6222000 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCAACTAAAGTACGAATCTATA
65 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
*
6222060 GCGGCGTTTGGTATTAAAACACCAC-AAAGTACGTGTCTATAGCGGCGTTTGGTATTAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTT-GTATTAAAACGCC
* * * *
6222124 ACAAAAGTACGTGTCTATAGCGGCATTTGTGTAAAAATGCCACTAAAGTATGAGTCTATA
65 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
** * *
6222184 GCATCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCAGCGTTTGTATAAAAACGCCA
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTATTAAAACGCCA
* * * * * *
6222249 CTAAAA-TAC-TAGTTTATAGCGGCGTTTGTATAAAAACGCCACTACATTACGATTCTTTA
66 C-AAAAGTACGT-GTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
6222308 GCGGCGTTT
1 GCGGCGTTT
6222317 TTATACAAAC
Statistics
Matches: 228, Mismatches: 26, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
123 1 0.00
124 175 0.77
125 52 0.23
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (124 bp):
GCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGTATTAAAACGCCA
CAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
Found at i:6225934 original size:18 final size:19
Alignment explanation
Indices: 6225911--6225950 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
6225901 TATATATAAT
6225911 ATTTT-ATAATTTCGGTTA
1 ATTTTAATAATTTCGGTTA
6225929 ATTTTAATAATTTCGGTTA
1 ATTTTAATAATTTCGGTTA
6225948 ATT
1 ATT
6225951 AATCGACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (19 bp):
ATTTTAATAATTTCGGTTA
Found at i:6227346 original size:15 final size:15
Alignment explanation
Indices: 6227326--6227357 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6227316 TTCTCTTGAC
6227326 TTACATTTACAAAAG
1 TTACATTTACAAAAG
*
6227341 TTACATTTAGAAAAG
1 TTACATTTACAAAAG
6227356 TT
1 TT
6227358 TCTACTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (15 bp):
TTACATTTACAAAAG
Found at i:6227996 original size:87 final size:87
Alignment explanation
Indices: 6227836--6227998 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
6227826 TATGTTATAT
6227836 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
**
6227901 AGTGCTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* *
6227923 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
6227988 AGCACTTATAT
66 AGCACTTATAT
6227999 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCACTTATATAATAAAATAGG
Found at i:6228441 original size:182 final size:182
Alignment explanation
Indices: 6228134--6229337 Score: 2085
Period size: 182 Copynumber: 6.6 Consensus size: 182
6228124 TGCGTTCACC
** * * *
6228134 TTTTGTCATTTATAGACAGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
6228199 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTTCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
6228263 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
6228316 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
6228381 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
6228446 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
6228498 TTTTTTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
6228563 TTTATAAAGTATCGACACTTTATTGGCACTATAACTTATTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* * *
6228628 TACTTATAATAAATTATCGACCCTTTCAACATATCCGGTAGCGCTTTACCTA
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
6228680 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
6228745 TTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
6228810 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAACGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
6228862 TTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
6228927 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
* *
6228989 ATACTTATAATAAATTATCGACACTTTCAACATAACTGGAAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* **
6229042 TTTTGTCATTTTGAGACTAGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
6229107 TTTATAAAGTATCTACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGCCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
6229171 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
6229223 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
6229288 TTTATAAAGTATCAACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
6229338 AAAGGTAAAA
Statistics
Matches: 970, Mismatches: 46, Indels: 12
0.94 0.04 0.01
Matches are distributed among these distances:
178 2 0.00
179 19 0.02
180 148 0.15
181 150 0.15
182 649 0.67
183 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:6229389 original size:21 final size:22
Alignment explanation
Indices: 6229364--6229408 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
6229354 TGATATGTTG
6229364 AAAATG-TCCATACTTTTTATA
1 AAAATGATCCATACTTTTTATA
*
6229385 AAAATGATCCATACTTTTTTTA
1 AAAATGATCCATACTTTTTATA
6229407 AA
1 AA
6229409 GTTATGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATGATCCATACTTTTTATA
Found at i:6232354 original size:184 final size:184
Alignment explanation
Indices: 6232045--6232384 Score: 617
Period size: 184 Copynumber: 1.8 Consensus size: 184
6232035 AAAAGTATGG
* *
6232045 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTTTCTCATAAAACCGGTATATTTAT
1 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCTCTCATAAAACCGGTATATCTAT
* *
6232110 ACCGGTTATATTAAAAAATTACCTATTACATTATAATTGTGGGTTCCTATGTTTTTTCAATCGAC
66 ACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCAATGTTTTTTCAATCGAC
6232175 ACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCA
131 ACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCA
* *
6232229 ACACAATATTAAAAAGTGTCGATATAGGTTGTATACCTATTCTCTCATAAAACCGGTATATCTAT
1 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCTCTCATAAAACCGGTATATCTAT
*
6232294 ACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCAATGTTTTTTCAATCGAC
66 ACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCAATGTTTTTTCAATCGAC
6232359 ACTTTTTGAAAAGGTATCGACACTTT
131 ACTTTTTGAAAAGGTATCGACACTTT
6232385 ATGCTGATAT
Statistics
Matches: 149, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 149 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (184 bp):
ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACATATTCTCTCATAAAACCGGTATATCTAT
ACCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTCCAATGTTTTTTCAATCGAC
ACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACATAAAGTAGCA
Found at i:6234385 original size:19 final size:19
Alignment explanation
Indices: 6234361--6234409 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
6234351 TTACATTCAC
6234361 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
6234380 ATACAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
6234399 ATACAAAATTA
1 ATACAAAATTA
6234410 ACCCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:6236012 original size:33 final size:33
Alignment explanation
Indices: 6235975--6236047 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
6235965 TTCCTCCTTA
*
6235975 TTTCTTCCATCTCTTCTTCTTCCTCCTCCCTCT
1 TTTCTTCCATCTCTTCTTATTCCTCCTCCCTCT
*
6236008 TTTCTTCCATCTTTTCTTATTCCTCCTCCCTCT
1 TTTCTTCCATCTCTTCTTATTCCTCCTCCCTCT
6236041 TTTCTTC
1 TTTCTTC
6236048 TTCATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTCTTCCATCTCTTCTTATTCCTCCTCCCTCT
Found at i:6236272 original size:33 final size:33
Alignment explanation
Indices: 6236235--6236300 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
6236225 CATCTTAAGA
*
6236235 TCACCCCTTAACACCT-TAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCT-ACTTCTTTCACCACT
6236268 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCTACTTCTTTCACCACT
6236301 CCATCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTCAACACCTCTACTTCTTTCACCACT
Found at i:6236361 original size:21 final size:21
Alignment explanation
Indices: 6236337--6236377 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6236327 CTTATGCCTC
6236337 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
6236358 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
6236378 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:6238679 original size:20 final size:19
Alignment explanation
Indices: 6238633--6238679 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
6238623 TCCGATATCA
*
6238633 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
6238652 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
6238673 TTTTACC
1 TTTTACC
6238680 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:6238979 original size:182 final size:180
Alignment explanation
Indices: 6238609--6239073 Score: 644
Period size: 182 Copynumber: 2.6 Consensus size: 180
6238599 GAAAGCATCG
* * * * *
6238609 ACACTTTTAATATATCCGATATCATTTTACCGGTTTTATCATTTTGATACCGATTTTATCATATT
1 ACACTTTAAATATATCTGGTACCGTTTTACCGGTTTTATCATTTTGATACCG-TTTTATCATATT
*
6238674 TTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTATAAGCGCTA
65 TTTACCTGTTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCGACACTTTATAAGCGCTA
* ** *
6238739 AAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGTTTCG
129 AAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGTACCA
* * *
6238791 ACACTTTCAATATATCTGGTAGCGTTTTACCGGTTTCATCATTTTGATACCAGTTTTATCATATT
1 ACACTTTAAATATATCTGGTACCGTTTTACCGGTTTTATCATTTTGATACC-GTTTTATCATATT
* *
6238856 TTTACCTGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTATAGGCGCTAA
65 TTTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATAAGCGCTAA
* * *
6238921 AATTGCTTTTCTTTTAAATTAACGAAGTGTCGATCCTTATATTAAAGTACCA
130 AACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATA-TAAAGTACCA
* ** * * *
6238973 ACACTTTAAATATAT-TCGGTACCGCTTTACCGGTTTTATCATTTCAATACTGGTTTTGTCATAG
1 ACACTTTAAATATATCT-GGTACCGTTTTACCGGTTTTATCATTTTGATAC-CGTTTTATCATAT
*
6239037 TTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
64 TTTTACCTGTTATATCGTTGTTGATCGATACATTTTT
6239074 AATTTGGATC
Statistics
Matches: 252, Mismatches: 27, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
181 81 0.32
182 170 0.67
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.44
Consensus pattern (180 bp):
ACACTTTAAATATATCTGGTACCGTTTTACCGGTTTTATCATTTTGATACCGTTTTATCATATTT
TTACCTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATAAGCGCTAAA
ACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATAAAGTACCA
Found at i:6239629 original size:24 final size:24
Alignment explanation
Indices: 6239602--6239650 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6239592 TTGTGTTTGA
6239602 TATGAAAATAGACTTGGATGTATT
1 TATGAAAATAGACTTGGATGTATT
*
6239626 TATGAAAATAGGCTTGGATGTATT
1 TATGAAAATAGACTTGGATGTATT
6239650 T
1 T
6239651 GGATTTCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (24 bp):
TATGAAAATAGACTTGGATGTATT
Found at i:6245932 original size:20 final size:20
Alignment explanation
Indices: 6245907--6245952 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6245897 TTAAGATCGA
6245907 GTTCTTATGAAGAATTACTT
1 GTTCTTATGAAGAATTACTT
*
6245927 GTTCTTCTGAAGAATTACTT
1 GTTCTTATGAAGAATTACTT
6245947 GTTCTT
1 GTTCTT
6245953 GTGATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
GTTCTTATGAAGAATTACTT
Found at i:6249335 original size:14 final size:13
Alignment explanation
Indices: 6249316--6249365 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
6249306 GGTCTGAACC
*
6249316 GAGTCAACTTGATT
1 GAGTCAACTCG-TT
6249330 GAGTCAACTCGTCT
1 GAGTCAACTCGT-T
6249344 GAGTCAACTCGTTT
1 GAGTCAACTCG-TT
6249358 GAGTCAAC
1 GAGTCAAC
6249366 CCATTGACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 1 0.03
14 31 0.94
15 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (13 bp):
GAGTCAACTCGTT
Found at i:6255465 original size:20 final size:20
Alignment explanation
Indices: 6255440--6255496 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
6255430 AAAACCCGAT
6255440 GAGTGTATCGATGCACAACA
1 GAGTGTATCGATGCACAACA
6255460 GAGTGTATCGATGCACAACA
1 GAGTGTATCGATGCACAACA
*
6255480 GAGTATATCGATGCACA
1 GAGTGTATCGATGCACA
6255497 TTCAATGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (20 bp):
GAGTGTATCGATGCACAACA
Found at i:6255517 original size:23 final size:23
Alignment explanation
Indices: 6255486--6255556 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 23
6255476 AACAGAGTAT
6255486 ATCGATGCACATTCAATGAATGC
1 ATCGATGCACATTCAATGAATGC
* * * *
6255509 ATCGGTGCACCTTC-AT-AGTGT
1 ATCGATGCACATTCAATGAATGC
* * *
6255530 ATCGATGCATATTCAAGGGATGC
1 ATCGATGCACATTCAATGAATGC
6255553 ATCG
1 ATCG
6255557 GTACACTTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
21 14 0.40
22 3 0.09
23 18 0.51
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (23 bp):
ATCGATGCACATTCAATGAATGC
Found at i:6255583 original size:44 final size:44
Alignment explanation
Indices: 6255485--6255584 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 44
6255475 CAACAGAGTA
* * *
6255485 TATCGATGCACATTCAATGAATGCATCGGTGCACCTTCATAGTG
1 TATCGATGCATATTCAAGGAATGCATCGGTACACCTTCATAGTG
* * *
6255529 TATCGATGCATATTCAAGGGATGCATCGGTACACTTTTATAGTG
1 TATCGATGCATATTCAAGGAATGCATCGGTACACCTTCATAGTG
6255573 TATCGATGCATA
1 TATCGATGCATA
6255585 GTGCACAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (44 bp):
TATCGATGCATATTCAAGGAATGCATCGGTACACCTTCATAGTG
Found at i:6261415 original size:65 final size:65
Alignment explanation
Indices: 6261297--6261517 Score: 315
Period size: 65 Copynumber: 3.4 Consensus size: 65
6261287 TACACTTGGG
* * * *
6261297 GTGCATTGGTACACT-AATTACATTCGATGTTTCAA-AAGAGC-CAGGAGTACATCGATGCATGG
1 GTGCATTGGTACA-TAAAATCCATTCGATGTTTCAATAA-A-CTCAAGAGTGCATCGATGCATGG
6261359 TAT
63 TAT
6261362 GTGCATTGGTACATAAAATCCATTCGATGTTTCAATAAACTCAAGAGTGCATCGATGCATGGTAT
1 GTGCATTGGTACATAAAATCCATTCGATGTTTCAATAAACTCAAGAGTGCATCGATGCATGGTAT
*
6261427 GTGCATTGGTACATAAAATCCATTCGATGTTTCAATAAACTCAAGAGTGCATCGATGCATAG-AT
1 GTGCATTGGTACATAAAATCCATTCGATGTTTCAATAAACTCAAGAGTGCATCGATGCATGGTAT
** *
6261491 GTGCATCAGTACATAAAATGCATTCGA
1 GTGCATTGGTACATAAAATCCATTCGA
6261518 AATAGGGTGT
Statistics
Matches: 145, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
64 28 0.19
65 115 0.79
66 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (65 bp):
GTGCATTGGTACATAAAATCCATTCGATGTTTCAATAAACTCAAGAGTGCATCGATGCATGGTAT
Found at i:6263258 original size:26 final size:27
Alignment explanation
Indices: 6263220--6263272 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
6263210 ATGCATATGA
*
6263220 AAATATTATCAT-ATGATATG-TATTGT
1 AAATATTAACATAAT-ATATGTTATTGT
*
6263246 AAATTTTAACATAATATATGTTATTGT
1 AAATATTAACATAATATATGTTATTGT
6263273 TTTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (27 bp):
AAATATTAACATAATATATGTTATTGT
Found at i:6264132 original size:23 final size:23
Alignment explanation
Indices: 6264074--6264133 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
6264064 CTCGGCTTCC
* **
6264074 CTCGGATTCCCTCTTATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
*
6264097 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
6264120 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
6264134 GTCGGATGGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.10, C:0.35, G:0.25, T:0.30
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:6264138 original size:14 final size:14
Alignment explanation
Indices: 6264116--6264162 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
6264106 CCTCGCATAG
*
6264116 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
6264130 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
*
6264144 CTTGGTCGGATGGC
1 CTCGGTCGGATGGC
6264158 CTCGG
1 CTCGG
6264163 ATGCCCAGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.06, C:0.28, G:0.40, T:0.26
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:6267447 original size:14 final size:15
Alignment explanation
Indices: 6267397--6267449 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
6267387 CCCGACTTAA
*
6267397 TTAAATATTTAGTAAAT
1 TTAAATATTTA-T-TAT
* *
6267414 TTATATATTTTTTAT
1 TTAAATATTTATTAT
6267429 TTAAATATTTATT-T
1 TTAAATATTTATTAT
6267443 TTAAATA
1 TTAAATA
6267450 AACTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 8 0.26
15 13 0.42
16 1 0.03
17 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTAAATATTTATTAT
Found at i:6271542 original size:76 final size:76
Alignment explanation
Indices: 6271455--6271607 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
6271445 AGACTTAGTC
6271455 GTGCATTTATATATATGATATAATTTATGATTAAGTTATATTATAAAGTCCTAAAATTATGTTTT
1 GTGCATTTATATATATGATATAATTTATGATTAAGTTATATTATAAAGTCCTAAAATTATGTTTT
6271520 GTTTGAATTAA
66 GTTTGAATTAA
*
6271531 GTGCATTTATATATATGATATAATTTATGATTAAGTTATATTATAAAGTCCTAACATTATGTTTT
1 GTGCATTTATATATATGATATAATTTATGATTAAGTTATATTATAAAGTCCTAAAATTATGTTTT
6271596 GTTTGAATTAA
66 GTTTGAATTAA
6271607 G
1 G
6271608 GAGGAAACAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (76 bp):
GTGCATTTATATATATGATATAATTTATGATTAAGTTATATTATAAAGTCCTAAAATTATGTTTT
GTTTGAATTAA
Found at i:6271799 original size:33 final size:34
Alignment explanation
Indices: 6271752--6271836 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 34
6271742 CATGAAGAGT
6271752 CATGA-CTCTTCACCAAAAGGTGTCATTTCAAGC
1 CATGACCTCTTCACCAAAAGGTGTCATTTCAAGC
*
6271785 CAT-ACCTCTTCACCAAAAGGTGTCATTTCAAGT
1 CATGACCTCTTCACCAAAAGGTGTCATTTCAAGC
6271818 CATGACCT-TTCACCAAAAG
1 CATGACCTCTTCACCAAAAG
6271837 TTGTGATTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 1 0.02
33 44 0.90
34 4 0.08
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (34 bp):
CATGACCTCTTCACCAAAAGGTGTCATTTCAAGC
Found at i:6277775 original size:8 final size:9
Alignment explanation
Indices: 6277758--6277813 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 9
6277748 ATAATAAAAA
6277758 ATAT-TAAT
1 ATATATAAT
6277766 ATA-ATAAT
1 ATATATAAT
6277774 AT-TAATAA-
1 ATAT-ATAAT
6277782 ATATAT-AT
1 ATATATAAT
6277790 ATATAT-AT
1 ATATATAAT
6277798 ATATAT-AT
1 ATATATAAT
6277806 ATATATAA
1 ATATATAA
6277814 CAATGTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.02
8 35 0.83
9 6 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATAAT
Found at i:6277776 original size:14 final size:13
Alignment explanation
Indices: 6277749--6277789 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
6277739 AAGAAAAGAA
*
6277749 TAATAAAAAATAT
1 TAATAAATAATAT
6277762 TAATATAATAATAT
1 TAATA-AATAATAT
6277776 TAATAAATATATAT
1 TAATAAATA-ATAT
6277790 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAAATAATAT
Found at i:6277783 original size:24 final size:24
Alignment explanation
Indices: 6277730--6277803 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
6277720 TAAAAATGAA
* * * *
6277730 AATAAATA-TAAGAAAAGAATAAT
1 AATAAATATTAATATAATAATATT
*
6277753 AAAAAATATTAATATAATAATATT
1 AATAAATATTAATATAATAATATT
6277777 AATAAATATATATATATATATATATAT
1 AATAAATAT-TA-ATATA-ATA-ATAT
6277804 ATATATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 7 0.17
24 19 0.47
25 2 0.05
26 5 0.12
27 3 0.08
28 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (24 bp):
AATAAATATTAATATAATAATATT
Found at i:6277789 original size:2 final size:2
Alignment explanation
Indices: 6277782--6277812 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6277772 ATATTAATAA
6277782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6277813 ACAATGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6278189 original size:34 final size:34
Alignment explanation
Indices: 6278151--6278237 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 34
6278141 AGTTTTACTT
*
6278151 GGACTCAAAATGC-TTCGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACGTT-GGTTTTAGTGTTTCAATA
* *
6278185 GGACT-TAAATACGTTGGTTTTAGTGTTTTAATA
1 GGACTCAAAATACGTTGGTTTTAGTGTTTCAATA
*
6278218 GGACTC-AAATATGTTGGTTT
1 GGACTCAAAATACGTTGGTTT
6278238 ATTTTCTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 40 0.85
34 7 0.15
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.41
Consensus pattern (34 bp):
GGACTCAAAATACGTTGGTTTTAGTGTTTCAATA
Found at i:6278208 original size:33 final size:33
Alignment explanation
Indices: 6278167--6278237 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6278157 AAAATGCTTC
*
6278167 GGTTTTAGTGTTTCAATAGGACTTAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
* *
6278200 GGTTTTAGTGTTTTAATAGGACTCAAATATGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
6278233 GGTTT
1 GGTTT
6278238 ATTTTCTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
Found at i:6278303 original size:14 final size:14
Alignment explanation
Indices: 6278284--6278331 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
6278274 CGAGGCCTAC
6278284 AAAAATAATAAAAT
1 AAAAATAATAAAAT
6278298 AAAAATATATTAATAAT
1 AAAAATA-A-TAA-AAT
6278315 AATAAATAAT-AAAT
1 AA-AAATAATAAAAT
6278329 AAA
1 AAA
6278332 TAAAGAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.03
14 12 0.40
15 2 0.07
16 4 0.13
17 6 0.20
18 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:6278841 original size:84 final size:83
Alignment explanation
Indices: 6278703--6279788 Score: 982
Period size: 84 Copynumber: 13.1 Consensus size: 83
6278693 AATGGAATCA
* * * * * *
6278703 AACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGGTTCC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGAT-GTGCC
* *
6278765 TTTGAGCTGAGTGGAGTCG
65 TTGGAGCTGAGTGTAGTCG
* * *
6278784 AACTCGAAGGTCTTTGTTGAGAGATAACCCTTCTAGCCTTGAGTTATG-TCGTAAATGATGTGCC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCT-GTAAATGATGTG-C
* * *
6278848 CTTGAAGCTGAGTGTAATCA
64 CTTGGAGCTGAGTGTAGTCG
* * * * * * * *
6278868 AACTCGAGGGTCTTTG--G-CAAATAGCCCTTCTCGACTTAAGCTGTGCTATAAATGATATGCCT
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCT
* *
6278930 TGGAGCTGAGCGTAGTCA
66 TGGAGCTGAGTGTAGTCG
* * * * * *
6278948 AACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATTCC
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC
*
6279013 TTGGAGCTGAGTGTAGTCA
65 TTGGAGCTGAGTGTAGTCG
* * * * * *
6279032 AACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGATTTATGCTATAAATGATGTGCC
1 AACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTG-C
* * * *
6279097 CTCGAAGTTGAGTGTAATCG
64 CTTGGAGCTGAGTGTAGTCG
* * * * *
6279117 AACTCGAGGGTCTTTGTTGACAAATAACCCTTCTAGCCTTGAGTTATG-TCGAAAATGATGTGCC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCT-GTAAATGATGTG-C
* * * *
6279181 CTCGAAGCTGAGTGTAATCA
64 CTTGGAGCTGAGTGTAGTCG
* * * * *
6279201 AACTCG-AGGGCTTTG--GA-AGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCCT
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCT
*
6279262 TGGAGCTGAGCGTAGTCG
66 TGGAGCTGAGTGTAGTCG
* * * *
6279280 AACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATGCTGTAAATGATATGCC
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC
* *
6279345 TTGGAGTTGAGCGTAGTCG
65 TTGGAGCTGAGTGTAGTCG
* * * * *
6279364 AACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCC
1 AACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTG-C
* * *
6279429 CTCGAAGCTGAGTGTAATCG
64 CTTGGAGCTGAGTGTAGTCG
* * * * * * * **
6279449 AACTCGAGGGACTTTG--G-CAGATATCCCTTTTCA-ACTTAAGCTATACTGCAAATGATGTATC
1 AACTCGAAGGTCTTTGTTGACAGATAACCCTTCT-AGACTTAAGTTATGCTGTAAATGATGTGCC
* *
6279510 TTGGAGCTGAGCGTAATCG
65 TTGGAGCTGAGTGTAGTCG
* * * * *
6279529 AACTCGAAGGTCTTTGGTTGCCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATATGCC
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC
* *
6279594 TTAGAGCTGAGCGTAGTCG
65 TTGGAGCTGAGTGTAGTCG
* * * * *
6279613 AACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGTC
1 AACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTG-C
* * *
6279678 CTCGAAGCTGAGTGTAATCG
64 CTTGGAGCTGAGTGTAGTCG
* * * * *
6279698 AACTC-AAGGGCTTTGGTTGGCAGATAACCCTTATTGACTTAAGTTATACTGTAAATGATGTGCC
1 AACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCC
* *
6279762 TTGGAGCTGAGCGTAGTCA
65 TTGGAGCTGAGTGTAGTCG
6279781 AACTCGAA
1 AACTCGAA
6279789 TGCCTTTGGT
Statistics
Matches: 822, Mismatches: 152, Indels: 59
0.80 0.15 0.06
Matches are distributed among these distances:
79 22 0.03
80 101 0.12
81 83 0.10
82 3 0.00
83 39 0.05
84 491 0.60
85 83 0.10
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (83 bp):
AACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGCCT
TGGAGCTGAGTGTAGTCG
Found at i:6279576 original size:249 final size:247
Alignment explanation
Indices: 6278698--6279798 Score: 1152
Period size: 249 Copynumber: 4.4 Consensus size: 247
6278688 CTCTGAATGG
* * *
6278698 AATCAAACTCGAAGGTCTTTGGCAGATAACCCTTCTT-GCCTTGAGCTATGCTGCAAATGATGGT
1 AATCAAACTCG-AGGGCTTTGGCAGATAACCCTT-TTCGACTTAAGCTATGCTGCAAATGAT-GT
* * * ** * *
6278762 TCCTTTGAGCTGAGTGGAGTCGAACTCGAAGGTCTTT-GTTGAGAGATAACCCTTCTAGCCTTGA
63 T-CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGCCAGATAACCCTTCTAGACTTAA
* * * *
6278826 GTTATG-TCGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGG-CA-A
127 GTTATGCT-GTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTCACA
* * * * * * * * * *
6278888 -ATAGCCCTTCTCGACTTAAGCTGTGCTA-TAAATGATATG-CCTTGGAGCTGAGCGT
191 GATAACCCTTCTAGCCTTGAGTTATGC-AGTAAATGATGTGCCCTCGAAGCTGAGTGT
* * * * *
6278943 AGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGAT
1 AATCAAACTCG-AGGGC--T--TTGGCAGATAACCCTTTTCGACTTAAGCTATGCTGCAAATGAT
* * * *
6279008 ATTCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTTGG-T-CACAGATAACCCTTCTAGCC
61 GTT-CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGC-CAGATAACCCTTCTAGAC
* * * * * * * * * *
6279071 TTGATTTATGCTATAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAGGGTCTTTGTTG
123 TTAAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTC
* *
6279136 ACAAATAACCCTTCTAGCCTTGAGTTATGTC-GAAAATGATGTGCCCTCGAAGCTGAGTGT
188 ACAGATAACCCTTCTAGCCTTGAGTTATG-CAGTAAATGATGTGCCCTCGAAGCTGAGTGT
* * * * * *
6279196 AATCAAACTCGAGGGCTTTGGAAGATAGCCCTTCTCGACTTAAGCTATGTTGTAAATGATGTGCC
1 AATCAAACTCGAGGGCTTTGGCAGATAACCCTTTTCGACTTAAGCTATGCTGCAAATGATGT-TC
* * *
6279261 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTT
65 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGCCAGATAACCCTTCTAGACTTAAGTT
* * *
6279326 ATGCTGTAAATGATATG-CCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGAT
130 ATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTCACAGAT
6279390 AACCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCGAAGCTGAGTGT
194 AACCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCGAAGCTGAGTGT
* * * *
6279444 AATCGAACTCGAGGGACTTTGGCAGATATCCCTTTTCAACTTAAGCTATACTGCAAATGATGTAT
1 AATCAAACTCGAGGG-CTTTGGCAGATAACCCTTTTCGACTTAAGCTATGCTGCAAATGATGT-T
* * *
6279509 CTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGCCAGATAACCCTTATCGACTTAAGT
64 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGCCAGATAACCCTTCTAGACTTAAGT
* *
6279574 TATGCTGCAAATGATATG-CCTT-AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAG
129 TATGCTGTAAATGATATGCCCTTGA-AGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTCACAG
* * *
6279637 ATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGTCCTCGAAGCTGAGTGT
192 ATAACCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCGAAGCTGAGTGT
* * * * *
6279693 AATCGAACTCAAGGGCTTTGGTTGGCAGATAACCCTTATT-GACTTAAGTTATACTGTAAATGAT
1 AATCAAACTCGAGGGC--T--TTGGCAGATAACCCTT-TTCGACTTAAGCTATGCTGCAAATGAT
* * * *
6279757 GTGCCTTGGAGCTGAGCGTAGTCAAACTCGAATGCCTTTGGT
61 GT-TCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
6279799 GGGAATGATT
Statistics
Matches: 741, Mismatches: 88, Indels: 47
0.85 0.10 0.05
Matches are distributed among these distances:
245 16 0.02
247 35 0.05
248 215 0.29
249 339 0.46
250 5 0.01
251 1 0.00
252 104 0.14
253 26 0.04
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (247 bp):
AATCAAACTCGAGGGCTTTGGCAGATAACCCTTTTCGACTTAAGCTATGCTGCAAATGATGTTCT
TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGCCAGATAACCCTTCTAGACTTAAGTTA
TGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTCACAGATAA
CCCTTCTAGCCTTGAGTTATGCAGTAAATGATGTGCCCTCGAAGCTGAGTGT
Found at i:6280223 original size:110 final size:110
Alignment explanation
Indices: 6279907--6280888 Score: 1481
Period size: 110 Copynumber: 9.0 Consensus size: 110
6279897 CAAATATTTT
* * * * * *
6279907 TGTTGTTTCGAGGCCAATATCCTTCACCGTGAAGTTAAAATTGACTC----TGAAACTGGAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* ** * *
6279968 TGTTTGTTGACAGCCAACCACCCCTTCGCTGTGAAGTTAAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* *
6280013 TGTTATCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT-AATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
6280077 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
6280122 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
6280187 TGTTTGTTGACAGTCAGTCTCCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* * *
6280232 TGTTGTCTCGAGTCCAATATTCTTCGCTATGAAATTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
*
6280297 TATTTGTTGACAGTCAGTCGCCCCTTCAG-TGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTC-GCTGTGAAGTTGAGCTTG
* * *
6280342 TGTTGTCTCTAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACCCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* * *
6280407 TGTTTGTTGACTGTCAGTCGCCCATTCACTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* * * *
6280452 TGTTGTCTTGAGTCCAATATCATTCGCTTTGAAATTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* * * * *
6280517 TATTTATTGACAATCAGCCACCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* *
6280562 TGTTGTCTCGAGTCCAATATTCTTCGCTGCGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* *
6280627 TATTTGTTGATAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
*
6280672 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* *
6280737 TGTTTATTGACAGTCAGTCGGCCCTTCGCTGTGAAGTTGAGCTTG
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
* * * * *
6280782 TGTTCTCTTGAGTCCAATATTCTTCACTGTGAAGTTTAAATTGACTCTGAATGAAACTGAAAAGT
1 TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
* * *
6280847 TGTTTGTTGACCGTCAGTCGCCTCTTCGTTGTGAAGTTGAGC
66 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
6280889 AACCACCATC
Statistics
Matches: 797, Mismatches: 73, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
106 40 0.05
109 99 0.12
110 657 0.82
111 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (110 bp):
TGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGT
TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTG
Found at i:6285110 original size:8 final size:8
Alignment explanation
Indices: 6285097--6285132 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
6285087 GAGGCCTGCA
6285097 AAAATAAT
1 AAAATAAT
6285105 AAAATAAT
1 AAAATAAT
*
6285113 AAAATATT
1 AAAATAAT
6285121 AATAATAAT
1 AA-AATAAT
6285130 AAA
1 AAA
6285133 TAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:6287606 original size:31 final size:31
Alignment explanation
Indices: 6287542--6287609 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6287532 CCGGTCAGGA
* *
6287542 CGGGTCGGGTTTCTAAGTCATATATTCACGT
1 CGGGTCAGGTTTCTAAGTCATATATTCAAGT
*
6287573 CGGGTCAGGTTTCTAAGTTATATATT-AGAGT
1 CGGGTCAGGTTTCTAAGTCATATATTCA-AGT
6287604 CGGGTC
1 CGGGTC
6287610 GGGTCATGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (31 bp):
CGGGTCAGGTTTCTAAGTCATATATTCAAGT
Found at i:6293748 original size:23 final size:26
Alignment explanation
Indices: 6293721--6293776 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 26
6293711 GAATAATAAG
6293721 AATAAGAA-TAAAG-AAAAC-AAAGA
1 AATAAGAACTAAAGCAAAACAAAAGA
6293744 AATAA-AACTAAAGACCAAAACAAAAGA
1 AATAAGAACTAAAG--CAAAACAAAAGA
6293771 AATAAG
1 AATAAG
6293777 TGAATCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 2 0.07
23 10 0.37
26 5 0.19
27 10 0.37
ACGTcount: A:0.71, C:0.09, G:0.11, T:0.09
Consensus pattern (26 bp):
AATAAGAACTAAAGCAAAACAAAAGA
Found at i:6293846 original size:13 final size:14
Alignment explanation
Indices: 6293823--6293851 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6293813 AACAAATACG
6293823 AAGAATAAAAATAA
1 AAGAATAAAAATAA
6293837 AAGAAT-AAAATAA
1 AAGAATAAAAATAA
6293850 AA
1 AA
6293852 TAGATAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
AAGAATAAAAATAA
Found at i:6293969 original size:2 final size:2
Alignment explanation
Indices: 6293962--6293998 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6293952 AAATAAAATA
* *
6293962 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6293999 ATAGAATAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6294142 original size:2 final size:2
Alignment explanation
Indices: 6294135--6294201 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
6294125 AAATGAGGAA
6294135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6294177 AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6294202 TTAGAAAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6296378 original size:84 final size:84
Alignment explanation
Indices: 6296003--6296801 Score: 880
Period size: 84 Copynumber: 9.5 Consensus size: 84
6295993 TTATTGACAT
* * * * * * * *
6296003 ATAACCCTTCTTGCCTTAAGCTATGCTGTAAATTTGATTTGCCTCT-TAGCTGAGTGTAATCGAA
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCT-TGGAGCTGAGCGTAGTCGAA
*
6296067 CTCGAAGGTATTTGGTTGGCAG
63 CTCGAAGGTCTTTGGTTGGCAG
* * * * * * * * * * * *
6296089 ATAGCCGTTCTCGACTTAAGCTATGCTACAAACGATGTACCTTTGG-GTTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACT
6296153 CGAAGGTCTTTGGTTGGCAG
65 CGAAGGTCTTTGGTTGGCAG
* * * * * *
6296173 AT-----TTATAACCTTTAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCATAGTCAAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
6296233 AAAGGTCTTTTGGTTGGCAG
66 GAAGGTC-TTTGGTTGGCAG
* * * * *
6296253 ATAACCCTTGTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
6296318 GAAGGACTTTGGTTGGCAG
66 GAAGGTCTTTGGTTGGCAG
* * * *
6296337 ATAACCTTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTGGAGTTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
6296402 GAAGATCTTTTGG-TGGCAG
66 GAAGGTC-TTTGGTTGGCAG
** * * *
6296421 ATAGGCCTTATAGCCTTGAGTTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTTGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* * *
6296486 AAAGGTCTTTAGTTGGAAG
66 GAAGGTCTTTGGTTGGCAG
* * * *
6296505 ATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCTAGGAGCTAAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
6296570 GAAGGTCTTTTGG-TGGCAG
66 GAAGGTC-TTTGGTTGGCAG
* ** *
6296589 ATAGCCCTTCTAGCCTTGACCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* *
6296654 AAAGGTCTTTGGTTGGCAC
66 GAAGGTCTTTGGTTGGCAG
* * *
6296673 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAAGGATGTGCCTTGGAGCTGAGGGTAGTCGAACCC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
6296738 AAAGGTCTTTGG-TGGCAG
66 GAAGGTCTTTGGTTGGCAG
* * * *
6296756 ATATCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCATTGGA
1 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGA
6296802 ACTCGAAGGT
Statistics
Matches: 602, Mismatches: 98, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
78 4 0.01
79 44 0.07
80 14 0.02
83 55 0.09
84 395 0.66
85 64 0.11
86 26 0.04
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (84 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTGGTTGGCAG
Found at i:6298168 original size:96 final size:96
Alignment explanation
Indices: 6297978--6298223 Score: 311
Period size: 96 Copynumber: 2.6 Consensus size: 96
6297968 TGGCTAGATG
* * *
6297978 TATCCATAAAGCCGGG-GTATTAACCAATTACTCTAGAGGGACAACTCAATATCATTATATAGAT
1 TATCCATAAAGCAGGGCGTTTTAACCAATTACTCTAGAGGGACAACTC-A-AGCATTATATAGAT
*
6298042 GTTATAATCACCTTTATCAGGCTAGCTGAATAT
64 ATTATAATCACCTTTATCAGGCTAGCTGAATAT
* *
6298075 TATCCATAAAGTCGGGGCGTTTTAACCAATTACTCTAGAGGGACAACTCAAGC-TT-TATTGTAT
1 TATCCATAAAG-CAGGGCGTTTTAACCAATTACTCTAGAGGGACAACTCAAGCATTATATAG-AT
*
6298138 ATTATAATCACCTTTATCAGGCTAGCTGAATCT
64 ATTATAATCACCTTTATCAGGCTAGCTGAATAT
* * * * *
6298171 TATCTATAAAGCCAGGGCG-TTTAACCAATTGCTTTACAGGGACAGCTCAAGCA
1 TATCCATAAAG-CAGGGCGTTTTAACCAATTACTCTAGAGGGACAACTCAAGCA
6298224 ATAACGACAA
Statistics
Matches: 132, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
95 33 0.25
96 51 0.39
97 13 0.10
98 5 0.04
99 30 0.23
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (96 bp):
TATCCATAAAGCAGGGCGTTTTAACCAATTACTCTAGAGGGACAACTCAAGCATTATATAGATAT
TATAATCACCTTTATCAGGCTAGCTGAATAT
Found at i:6302674 original size:20 final size:20
Alignment explanation
Indices: 6302643--6302694 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
6302633 GAATAAAAAT
6302643 GAAAGAATAAAATA-AAATAGA
1 GAAA-AATAAAATATAAA-AGA
* *
6302664 GAAATATAAAATATACAAGA
1 GAAAAATAAAATATAAAAGA
6302684 GAAAAATAAAA
1 GAAAAATAAAA
6302695 AGTAAAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (20 bp):
GAAAAATAAAATATAAAAGA
Found at i:6302774 original size:2 final size:2
Alignment explanation
Indices: 6302767--6302799 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6302757 TAAATAAATA
6302767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6302800 AAATGTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6302813 original size:17 final size:18
Alignment explanation
Indices: 6302786--6302821 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6302776 TATATATATA
*
6302786 TATATATATATATAAAATG
1 TATACATATA-ATAAAATG
6302805 TATACATATAATAAAAT
1 TATACATATAATAAAAT
6302822 AAAATACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (18 bp):
TATACATATAATAAAATG
Found at i:6302892 original size:18 final size:19
Alignment explanation
Indices: 6302845--6302892 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
6302835 TAATAATAAT
*
6302845 AAATAAATGATAAACAGAAA
1 AAATAAA-GAAAAACAGAAA
*
6302865 AAA-AAGGAAAAACA-AAA
1 AAATAAAGAAAAACAGAAA
6302882 AAATAAAGAAA
1 AAATAAAGAAA
6302893 TAATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 2 0.08
20 3 0.12
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (19 bp):
AAATAAAGAAAAACAGAAA
Found at i:6302942 original size:2 final size:2
Alignment explanation
Indices: 6302935--6303015 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
6302925 ACATACATAC
6302935 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6302977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6303016 ATACTAATGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6303073 original size:35 final size:35
Alignment explanation
Indices: 6303003--6303073 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
6302993 ATATATATAT
* *
6303003 ATATATATATATAATACTAATGTAAAATGAGGAAA
1 ATATATATATATAATACTAATGAAAAATAAGGAAA
* *
6303038 ATATATATATATAATATTTA-GAAAAATAAGAGAAA
1 ATATATATATATAATACTAATGAAAAATAAG-GAAA
6303073 A
1 A
6303074 AAATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (35 bp):
ATATATATATATAATACTAATGAAAAATAAGGAAA
Found at i:6304242 original size:23 final size:23
Alignment explanation
Indices: 6304216--6304265 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
6304206 GCTTGAAAAA
*
6304216 TATAATGTAAATAAATGTA-AAT
1 TATAATATAAATAAATGTAGAAT
* *
6304238 GTATAGTATATATAAATGTAGAAT
1 -TATAATATAAATAAATGTAGAAT
6304262 TATA
1 TATA
6304266 TAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (23 bp):
TATAATATAAATAAATGTAGAAT
Found at i:6306975 original size:25 final size:25
Alignment explanation
Indices: 6306947--6307034 Score: 176
Period size: 25 Copynumber: 3.5 Consensus size: 25
6306937 AAAAACAAAT
6306947 CACCTTTCGGTGCATTAATTGTATG
1 CACCTTTCGGTGCATTAATTGTATG
6306972 CACCTTTCGGTGCATTAATTGTATG
1 CACCTTTCGGTGCATTAATTGTATG
6306997 CACCTTTCGGTGCATTAATTGTATG
1 CACCTTTCGGTGCATTAATTGTATG
6307022 CACCTTTCGGTGC
1 CACCTTTCGGTGC
6307035 TTTAGTTAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 63 1.00
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
CACCTTTCGGTGCATTAATTGTATG
Found at i:6319803 original size:2 final size:2
Alignment explanation
Indices: 6319796--6319823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6319786 CTTACCTTAG
6319796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6319824 TCAAAATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6321581 original size:24 final size:24
Alignment explanation
Indices: 6321554--6321605 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6321544 CGTTCATTTA
* *
6321554 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
6321578 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
6321602 CGTT
1 CGTT
6321606 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:6321592 original size:14 final size:14
Alignment explanation
Indices: 6321575--6321605 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6321565 GTTCGGTTAT
*
6321575 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
6321589 GTTCGATTATGTTC
1 GTTCGATTATGTTC
6321603 GTT
1 GTT
6321606 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:6321606 original size:24 final size:24
Alignment explanation
Indices: 6321564--6321625 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
6321554 CGTTCGTGAA
*
6321564 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
6321588 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
6321612 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
6321626 TAACCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:6322368 original size:10 final size:10
Alignment explanation
Indices: 6322353--6322426 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
6322343 GGGTCTCCAA
6322353 CGTTTATGTT
1 CGTTTATGTT
6322363 CGTTTATGTT
1 CGTTTATGTT
6322373 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
6322384 ATGTTCGTGTT
1 -CGTTTATGTT
6322395 CGTTTATGTT
1 CGTTTATGTT
6322405 CG----TGTT
1 CGTTTATGTT
6322411 CGTTTATGTT
1 CGTTTATGTT
6322421 CGTTTA
1 CGTTTA
6322427 ATTATTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.66
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:6322384 original size:16 final size:16
Alignment explanation
Indices: 6322359--6322423 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
6322349 CCAACGTTTA
6322359 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
6322375 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
6322391 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6322407 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
6322423 T
1 T
6322424 TTAATTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:6325759 original size:20 final size:20
Alignment explanation
Indices: 6325731--6325769 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6325721 ATACTTGACC
* *
6325731 CTAGGGTATTGATACTACAA
1 CTAGAGTATCGATACTACAA
6325751 CTAGAGTATCGATACTACA
1 CTAGAGTATCGATACTACA
6325770 CCCGATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (20 bp):
CTAGAGTATCGATACTACAA
Found at i:6326374 original size:16 final size:16
Alignment explanation
Indices: 6326355--6326388 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6326345 CAACTAGAAA
*
6326355 TAGAAACAGTAATAGC
1 TAGAAACAATAATAGC
*
6326371 TAGATACAATAATAGC
1 TAGAAACAATAATAGC
6326387 TA
1 TA
6326389 TGATGTCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (16 bp):
TAGAAACAATAATAGC
Found at i:6333344 original size:2 final size:2
Alignment explanation
Indices: 6333337--6333412 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
6333327 TTTACATGTA
6333337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6333379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6333413 TATTATTATC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6334278 original size:24 final size:20
Alignment explanation
Indices: 6334225--6334282 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
6334215 TTCCCCTTGA
*
6334225 AGTGCATTGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
6334245 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
6334268 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
6334283 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:6334344 original size:64 final size:63
Alignment explanation
Indices: 6334270--6334410 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
6334260 TCTTTAACAT
* * *
6334270 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * *
6334333 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
6334397 GTGCATCGATGCAC
1 GTGCATCGATGCAC
6334411 ATTGAATATG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:6335224 original size:2 final size:2
Alignment explanation
Indices: 6335217--6335262 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
6335207 CTTTTTCCTT
6335217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
6335260 TA T
1 TA T
6335263 CATGTCACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6338270 original size:20 final size:22
Alignment explanation
Indices: 6338239--6338302 Score: 89
Period size: 20 Copynumber: 3.0 Consensus size: 22
6338229 TTCAATTTCC
6338239 TCTTAA-AGTGCATCGATGCAT
1 TCTTAACAGTGCATCGATGCAT
6338260 TC-T-ACAGTGCATCGATGCAT
1 TCTTAACAGTGCATCGATGCAT
6338280 TCTTTAACATGTGCATCGATGCA
1 TC-TTAACA-GTGCATCGATGCA
6338303 CTATCCATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.03
20 18 0.47
21 2 0.05
22 1 0.03
23 3 0.08
24 13 0.34
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (22 bp):
TCTTAACAGTGCATCGATGCAT
Found at i:6341075 original size:17 final size:17
Alignment explanation
Indices: 6341053--6341087 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6341043 GGTCAACGGA
6341053 CAACGGTCGGGTCAGGT
1 CAACGGTCGGGTCAGGT
*
6341070 CAACGGTCGGGTCGGGT
1 CAACGGTCGGGTCAGGT
6341087 C
1 C
6341088 GGGTCAGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.26, G:0.43, T:0.17
Consensus pattern (17 bp):
CAACGGTCGGGTCAGGT
Found at i:6341077 original size:7 final size:7
Alignment explanation
Indices: 6341010--6341060 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
6341000 GTAAAAGAAA
6341010 GTCAACG
1 GTCAACG
* *
6341017 GTTAATG
1 GTCAACG
*
6341024 GTC-GCG
1 GTCAACG
6341030 GTCAACG
1 GTCAACG
*
6341037 GTCAATG
1 GTCAACG
6341044 GTCAACG
1 GTCAACG
*
6341051 GACAACG
1 GTCAACG
6341058 GTC
1 GTC
6341061 GGGTCAGGTC
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
6 4 0.12
7 29 0.88
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.20
Consensus pattern (7 bp):
GTCAACG
Found at i:6347611 original size:5 final size:5
Alignment explanation
Indices: 6347601--6347655 Score: 67
Period size: 5 Copynumber: 10.8 Consensus size: 5
6347591 CGCGGTCAAC
* *
6347601 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
6347652 GGTC
1 GGTC
6347656 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
4 3 0.07
5 36 0.84
7 4 0.09
ACGTcount: A:0.05, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:6347621 original size:22 final size:23
Alignment explanation
Indices: 6347588--6347636 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
6347578 AACGATCAAC
6347588 GGTCGCGGTCAACGGTCGGGTCG
1 GGTCGCGGTCAACGGTCGGGTCG
6347611 GGTCG-GGTCAACGGTCGGGTCG
1 GGTCGCGGTCAACGGTCGGGTCG
6347633 GGTC
1 GGTC
6347637 AGTCGGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.08, C:0.24, G:0.49, T:0.18
Consensus pattern (23 bp):
GGTCGCGGTCAACGGTCGGGTCG
Found at i:6347664 original size:9 final size:9
Alignment explanation
Indices: 6347652--6347714 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
6347642 GGTCGGGTCG
6347652 GGTCAGACC
1 GGTCAGACC
*
6347661 GGTCAAACC
1 GGTCAGACC
6347670 GGTTCAGACC
1 GG-TCAGACC
* *
6347680 AGTCAAACC
1 GGTCAGACC
*
6347689 GGTTCTGACC
1 GG-TCAGACC
*
6347699 GGTCAAACC
1 GGTCAGACC
6347708 GGTCAGA
1 GGTCAGA
6347715 ACAGGTTTCC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 28 0.67
10 14 0.33
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAGACC
Found at i:6347664 original size:19 final size:19
Alignment explanation
Indices: 6347606--6347664 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
6347596 TCAACGGTCG
6347606 GGTCGGGTCGGGTCA-A-C
1 GGTCGGGTCGGGTCAGACC
* *
6347623 GGTCGGGTCGGGTCAGTCG
1 GGTCGGGTCGGGTCAGACC
6347642 GGTCGGGTCGGGTCAGACC
1 GGTCGGGTCGGGTCAGACC
6347661 GGTC
1 GGTC
6347665 AAACCGGTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 15 0.42
19 21 0.58
ACGTcount: A:0.08, C:0.24, G:0.49, T:0.19
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGACC
Found at i:6347676 original size:19 final size:19
Alignment explanation
Indices: 6347654--6347714 Score: 97
Period size: 19 Copynumber: 3.3 Consensus size: 19
6347644 TCGGGTCGGG
6347654 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
6347673 TCAGACCAGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
6347692 TCTGACCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
6347710 TCAGA
1 TCAGA
6347715 ACAGGTTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 4 0.11
19 34 0.89
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:6349219 original size:13 final size:14
Alignment explanation
Indices: 6349201--6349230 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
6349191 TGTTTTTAGA
6349201 ATTATCCTTA-GTT
1 ATTATCCTTAGGTT
6349214 ATTATCCTTAGGTT
1 ATTATCCTTAGGTT
6349228 ATT
1 ATT
6349231 TGAAAGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.53
Consensus pattern (14 bp):
ATTATCCTTAGGTT
Found at i:6350322 original size:18 final size:18
Alignment explanation
Indices: 6350295--6350329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6350285 ATTATGTCCT
* *
6350295 TTCATGAAAAGTTTAAGC
1 TTCATCAAAAGGTTAAGC
6350313 TTCATCAAAAGGTTAAG
1 TTCATCAAAAGGTTAAG
6350330 TCCATTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
TTCATCAAAAGGTTAAGC
Found at i:6354144 original size:21 final size:20
Alignment explanation
Indices: 6354109--6354147 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6354099 CTAGAGGAGA
*
6354109 AAAAGAAGCAGGAAGAAGCG
1 AAAAGAAGCAAGAAGAAGCG
6354129 AAAAGAATGCAAGAAGAAG
1 AAAAGAA-GCAAGAAGAAG
6354148 AGGAGAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.08, G:0.31, T:0.03
Consensus pattern (20 bp):
AAAAGAAGCAAGAAGAAGCG
Found at i:6355063 original size:20 final size:21
Alignment explanation
Indices: 6355038--6355086 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
6355028 TTTGGTTAGC
*
6355038 GAGAAAATGA-AGGAATCGAT
1 GAGAAAATGAGAGGAATCAAT
6355058 GAG-AAATGAGAGGAATCAAT
1 GAGAAAATGAGAGGAATCAAT
*
6355078 TAGAAAATG
1 GAGAAAATG
6355087 GGAGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.24
20 14 0.56
21 5 0.20
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (21 bp):
GAGAAAATGAGAGGAATCAAT
Found at i:6355296 original size:2 final size:2
Alignment explanation
Indices: 6355289--6355344 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
6355279 ACAAAATTGA
6355289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6355331 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6355345 TTGGGTCGGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6356000 original size:17 final size:18
Alignment explanation
Indices: 6355978--6356026 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
6355968 CAAAGATGTT
6355978 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTGATA
* *
6355995 TTATATTTGATTTTGATT
1 TTATATTTAATTTTGATA
6356013 TTA-ATATTAATTTT
1 TTATAT-TTAATTTT
6356027 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTATATTTAATTTTGATA
Found at i:6356078 original size:28 final size:28
Alignment explanation
Indices: 6356016--6356106 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 28
6356006 TTTGATTTTA
*
6356016 ATATTAATTTTTTTAA-A-TAAATTA-A-
1 ATATTAA-TTTTTTAATATTATATTATAG
6356041 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
6356069 ATATTAA--TTTTAATATTATATTATAG
1 ATATTAATTTTTTAATATTATATTATAG
6356095 ATATTTAATTTT
1 ATA-TTAATTTT
6356107 ATAGCATATA
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
24 8 0.14
25 8 0.14
26 28 0.48
27 5 0.09
28 7 0.12
29 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTAATTTTTTAATATTATATTATAG
Found at i:6356115 original size:26 final size:26
Alignment explanation
Indices: 6356041--6356115 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
6356031 AATAAATTAA
**
6356041 ATATTAATTTTTTAATATTATATTATAG
1 ATATTAA--TTTTAATAGCATATTATAG
**
6356069 ATATTAATTTTAATATTATATTATAG
1 ATATTAATTTTAATAGCATATTATAG
6356095 ATATTTAATTTT-ATAGCATAT
1 ATA-TTAATTTTAATAGCATAT
6356116 AAATTATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 29 0.66
27 8 0.18
28 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (26 bp):
ATATTAATTTTAATAGCATATTATAG
Found at i:6356162 original size:20 final size:19
Alignment explanation
Indices: 6356117--6356163 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
6356107 ATAGCATATA
6356117 AATTATTTTATATATTATT
1 AATTATTTTATATATTATT
*
6356136 AA-AATTTTATAT-TTATTTT
1 AATTATTTTATATATTA--TT
6356155 AATTATTTT
1 AATTATTTT
6356164 GATTTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 9 0.39
19 6 0.26
20 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATTTTATATATTATT
Found at i:6356398 original size:19 final size:20
Alignment explanation
Indices: 6356364--6356404 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6356354 AATAAAAAAT
*
6356364 AATTATAAAATAATTTTATA
1 AATTAAAAAATAATTTTATA
*
6356384 AATTAAAAAAT-ATTTTCTA
1 AATTAAAAAATAATTTTATA
6356403 AA
1 AA
6356405 AATATCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAAAAAATAATTTTATA
Found at i:6356664 original size:31 final size:31
Alignment explanation
Indices: 6356627--6356686 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
6356617 TAGTTGTATG
* * *
6356627 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
6356658 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
6356687 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:6357223 original size:23 final size:23
Alignment explanation
Indices: 6357197--6357244 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6357187 ATAAAGTACA
*
6357197 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
6357220 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
6357243 AT
1 AT
6357245 TTACTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:6357756 original size:23 final size:23
Alignment explanation
Indices: 6357721--6357793 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
6357711 ATACTTTACA
*
6357721 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
6357744 ATATAAACGCTACTTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
6357767 ATATAAGCGCTATCTATTACATC
1 ATATAAGCGCTACCTATTACATT
6357790 ATAT
1 ATAT
6357794 TTTTACCTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:6358214 original size:23 final size:23
Alignment explanation
Indices: 6358151--6358223 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
6358141 ATACTTTACA
*
6358151 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
** * *
6358174 ATATAAATGATACATATTACATT
1 ATATAAGCGCTACCTATTACATT
*
6358197 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
6358220 ATAT
1 ATAT
6358224 TTTTACCTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:6358612 original size:23 final size:23
Alignment explanation
Indices: 6358586--6358648 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6358576 ATATAACCAC
*
6358586 TACCTATTACATTATATAAATGA
1 TACCTATTACATTATATAAACGA
*
6358609 TACCTATTACATTATATAAACGC
1 TACCTATTACATTATATAAACGA
*
6358632 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6358649 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6359006 original size:430 final size:431
Alignment explanation
Indices: 6357555--6359281 Score: 3152
Period size: 430 Copynumber: 4.0 Consensus size: 431
6357545 ATGTTTATTG
*
6357555 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACTCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
6357620 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
6357685 TATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
* * *
6357750 ACGCTACTTATTACATTATATAAGCGCTATCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
6357815 TGTCCATACTTTTTATAAAAAGGATCGATACTTCT-TTTAAAATTATGTAATTTATGTTTCAA-T
261 TGTCCATACTTTTTATAAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
*
6357878 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
325 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
6357943 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
390 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
6357985 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
6358050 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
6358115 TATAGACACTTTTATAAAGAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
* *
6358180 ATGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
6358245 TGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
* *
6358310 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAC
326 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
6358375 TTATTTGATTGTTTTGATATTTTAT--AA-AATATTTAGAA
391 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
6358413 TTTTTAA-TT--TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
* *
6358475 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAA
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
6358540 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
* *
6358605 ATGATACCTATTACATTATATAAACGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
6358670 TGTCCATACTTTTTATAAAAAGGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAA-T
261 TGTCCATACTTTTTATAAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
6358733 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
325 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
*
6358798 ATTATTTGATTGTTTTGATATTTGATAAAATAATATTTAGAA
390 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
* *
6358840 TTTTTAATTTAATAATAATATATATCATAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
6358905 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
6358970 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
6359035 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
6359100 TGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
6359165 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
326 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
6359230 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
391 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
*
6359271 -TTTAAATTTAA
1 TTTTTAATTTAA
6359282 CAACATTAAC
Statistics
Matches: 1258, Mismatches: 28, Indels: 22
0.96 0.02 0.02
Matches are distributed among these distances:
424 89 0.07
425 301 0.24
426 3 0.00
427 20 0.02
428 20 0.02
429 4 0.00
430 623 0.50
431 198 0.16
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (431 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:6359042 original size:23 final size:23
Alignment explanation
Indices: 6359016--6359078 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6359006 ATATAACCAC
6359016 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6359039 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6359062 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6359079 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6359217 original size:855 final size:855
Alignment explanation
Indices: 6357567--6359260 Score: 3190
Period size: 855 Copynumber: 2.0 Consensus size: 855
6357557 TTTAATTTAA
*
6357567 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACTCCTATAATTACTAAATTAATATCT
1 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
* * *
6357632 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
66 TAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAATATAGACACTTT
* * *
6357697 TATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACTTATT
131 TATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
* *
6357762 ACATTATATAAGCGCTATCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
196 ACATTATATAAACGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
6357827 TTATAAAAAGGATCGATACTTCTTTTAAAATTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
261 TTATAAAAAGGATCGATACTTCTTTTAAAATTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
*
6357892 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTT
326 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
* *
6357957 TTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAA
391 TTGATATTTGATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCATAACGTAAAA
*
6358022 AATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
456 AAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
*
6358087 AAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAGAGGATAGATACTTTACAA
521 AAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAA
* *
6358152 TATAAGCACTACCTATTACATTATATAAATGATACATATTACATTATATAAGCGCTACCTATTAC
586 TATAACCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCTACCTATTAC
*
6358217 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTT
651 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTT
6358282 TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
716 TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
* *
6358347 AATTTAATAATTTCATTTGCACAAAAACTTATTTGATTGTTTTGATATTTTATAAAATATTTAGA
781 AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTTAGA
6358412 ATTTTTAATT
846 ATTTTTAATT
6358422 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
1 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
6358487 TAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAATATAGACACTTT
66 TAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAATATAGACACTTT
*
6358552 TATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAATGATACCTATT
131 TATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
6358617 ACATTATATAAACGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
196 ACATTATATAAACGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
*
6358682 TTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
261 TTATAAAAAGGATCGATACTTCTTTTAAAATTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
6358747 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
326 TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
6358812 TTGATATTTGATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCATAACGTAAAA
391 TTGATATTTGATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCATAACGTAAAA
6358877 AAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
456 AAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
6358942 AAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAA
521 AAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAA
*
6359007 TATAACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTAC
586 TATAACCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCTACCTATTAC
6359072 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTT
651 ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTT
6359137 TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
716 TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
6359202 AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATA
781 AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATA
6359261 ATATTTAGAA
Statistics
Matches: 817, Mismatches: 22, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
855 817 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (855 bp):
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
TAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAATATAGACACTTT
TATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
ACATTATATAAACGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTT
TTATAAAAAGGATCGATACTTCTTTTAAAATTATGTAATTTATGTTTCAATTTTTTTAATAGTGT
TTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTT
TTGATATTTGATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCATAACGTAAAA
AAGAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTT
AAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAA
TATAACCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCTACCTATTAC
ATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTT
TAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATT
AATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTTAGA
ATTTTTAATT
Found at i:6362462 original size:23 final size:23
Alignment explanation
Indices: 6362436--6362498 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
6362426 ATATAACCAC
6362436 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
6362459 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
6362482 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6362499 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:6362888 original size:16 final size:16
Alignment explanation
Indices: 6362859--6362892 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6362849 ATCTATTACA
*
6362859 TTTTTCAATCGACACT
1 TTTTTAAATCGACACT
*
6362875 TTTTTAAATGGACACT
1 TTTTTAAATCGACACT
6362891 TT
1 TT
6362893 GTTGTGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47
Consensus pattern (16 bp):
TTTTTAAATCGACACT
Found at i:6364093 original size:3 final size:3
Alignment explanation
Indices: 6364085--6364156 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
6364075 ACTTGTTTGG
* * * * *
6364085 ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
6364133 GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
6364157 GTCAGCTTCA
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:6364139 original size:36 final size:36
Alignment explanation
Indices: 6364092--6364173 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 36
6364082 TGGATCATCA
*
6364092 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
6364128 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
*
6364164 TCATCTTCAT
1 TCATCATCAT
6364174 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:6364157 original size:12 final size:12
Alignment explanation
Indices: 6364086--6364173 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
6364076 CTTGTTTGGA
* *
6364086 TCATCATCATCA
1 TCATCTTCATCG
* * *
6364098 TCATCATCGTCA
1 TCATCTTCATCG
6364110 TCATCTTCATCG
1 TCATCTTCATCG
*
6364122 TCAGCTTCATCG
1 TCATCTTCATCG
*
6364134 TCATCATCATCG
1 TCATCTTCATCG
6364146 TCATCTTCATCG
1 TCATCTTCATCG
* *
6364158 TCAGCTTCATCT
1 TCATCTTCATCG
6364170 TCAT
1 TCAT
6364174 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:6364182 original size:18 final size:18
Alignment explanation
Indices: 6364110--6364173 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
6364100 ATCATCGTCA
*
6364110 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * *
6364128 TCATCGTCATC-ATCATCG
1 TCATCTTCATCGA-CAGCT
*
6364146 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
6364164 TCATCTTCAT
1 TCATCTTCAT
6364174 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:6366768 original size:33 final size:33
Alignment explanation
Indices: 6366731--6366796 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
6366721 CATCTTAATA
* *
6366731 TCACCCCTTAACACCCCAATTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
6366764 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
6366797 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:6366854 original size:19 final size:19
Alignment explanation
Indices: 6366830--6366871 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
6366820 CCCCTTATGC
6366830 CTCTCAAGTGTATCTTCGA
1 CTCTCAAGTGTATCTTCGA
* *
6366849 CTCTCAAGTTTCTCTTCGA
1 CTCTCAAGTGTATCTTCGA
6366868 CTCT
1 CTCT
6366872 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40
Consensus pattern (19 bp):
CTCTCAAGTGTATCTTCGA
Found at i:6368927 original size:24 final size:24
Alignment explanation
Indices: 6368899--6368952 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
6368889 CCATTCTATC
6368899 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
6368923 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
6368947 TATTTT
1 TATTTT
6368953 AATCGATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:6369324 original size:20 final size:19
Alignment explanation
Indices: 6369278--6369324 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
6369268 TCCGGTAACC
*
6369278 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
6369297 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
6369318 TTTTACC
1 TTTTACC
6369325 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:6369368 original size:181 final size:182
Alignment explanation
Indices: 6369064--6369537 Score: 693
Period size: 181 Copynumber: 2.6 Consensus size: 182
6369054 CGTACTTACG
* * * * *
6369064 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGATTT
* * *
6369129 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
6369194 AGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
6369245 AAAGTATCGACACTTTTAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGATTT
* *
6369310 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
6369375 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * *
6369427 AAAGTACCGACACTTTAAATGTATCCGGTAGCGC-TTTACCGGTTTTATCATTTCT-ATACCGGT
1 AAAGTATCGACACTTTAAATATATCCGGTAAC-CTTTTACCGGTTTTATCATTT-TGATACC-GA
* * *
6369490 TTTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
63 TTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
6369538 AATTTGGATC
Statistics
Matches: 265, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
181 165 0.62
182 53 0.20
183 47 0.18
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGATTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:6373262 original size:244 final size:247
Alignment explanation
Indices: 6372829--6373319 Score: 763
Period size: 244 Copynumber: 2.0 Consensus size: 247
6372819 ACGCTGGACA
*
6372829 GGATAGCGATTATCCTGCAGGCTAGTTCCAACAAATGACTCACATGAGAAAATTCACCCAAAACC
1 GGATAGCGATTATCCTGCAGGCTAGTTCC-ACAAATGACTCACAGGAGAAAATTCACCCAAAACC
* *
6372894 AGAGAAAAAAGTCTCTAGGGTTTAACGAAATATTATAAAATCAAACAATGCCCAAAATCAGTCCA
65 AGAGAAAAAAGTCTATAGGGTTTAACGAAATATTATAAAATCAAACAATGCCCAAAATCAATCCA
* *
6372959 CAAGCCAGACTGTTATAGCAAAAAATCGTGTTTATCCTAATTTTGCCAAAAATAGAAAAATCTCA
130 CAAGCCAGACTGTTATAGCAAAAAATCGTATTTATCCGAATTTTGCCAAAAATAGAAAAATCTCA
* *
6373024 GAAATTACTCTAAATTGAAATTTGAAATAAAATAAGCAATCTGCAAAAAATCT
195 GAAATCACTCTAAATTGAAATTCGAAATAAAATAAGCAATCTGCAAAAAATCT
* * *
6373077 GGATAGCGATTATCCTGCGGGCTAGTT-C-CAGATGATTCACAGGAGAAAATTC-CCCAAAACCA
1 GGATAGCGATTATCCTGCAGGCTAGTTCCACAAATGACTCACAGGAGAAAATTCACCCAAAACCA
* *
6373139 GAGAAAAAAGTCTATAGGGTTTAACGGAATATTATAAAATCAAACAGTGCCCAAAATCAATCCAC
66 GAGAAAAAAGTCTATAGGGTTTAACGAAATATTATAAAATCAAACAATGCCCAAAATCAATCCAC
* ** * * * * **
6373204 CAGCTGGACTTTTATAGCCAAAAATCTTATTTATTCGAATTTTGCCAAAAATAGAAAAATCTTGG
131 AAGCCAGACTGTTATAGCAAAAAATCGTATTTATCCGAATTTTGCCAAAAATAGAAAAATCTCAG
6373269 AAATCACTCTAAATTGAAATTCGAAATAAAATAAGCAATCTGCAAAAAATC
196 AAATCACTCTAAATTGAAATTCGAAATAAAATAAGCAATCTGCAAAAAATC
6373320 GTCCCAAATC
Statistics
Matches: 222, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
244 174 0.78
245 21 0.09
247 1 0.00
248 26 0.12
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (247 bp):
GGATAGCGATTATCCTGCAGGCTAGTTCCACAAATGACTCACAGGAGAAAATTCACCCAAAACCA
GAGAAAAAAGTCTATAGGGTTTAACGAAATATTATAAAATCAAACAATGCCCAAAATCAATCCAC
AAGCCAGACTGTTATAGCAAAAAATCGTATTTATCCGAATTTTGCCAAAAATAGAAAAATCTCAG
AAATCACTCTAAATTGAAATTCGAAATAAAATAAGCAATCTGCAAAAAATCT
Found at i:6386571 original size:21 final size:21
Alignment explanation
Indices: 6386537--6386581 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6386527 CTACACCCGT
6386537 AATAGCGCCCGCGACAGCCAC
1 AATAGCGCCCGCGACAGCCAC
* * **
6386558 AATAGTGCCTGCGATGGCCAC
1 AATAGCGCCCGCGACAGCCAC
6386579 AAT
1 AAT
6386582 CACGATAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.33, G:0.24, T:0.13
Consensus pattern (21 bp):
AATAGCGCCCGCGACAGCCAC
Found at i:6391063 original size:15 final size:15
Alignment explanation
Indices: 6391043--6391072 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6391033 TATCTTAGCG
6391043 AGAAGAGGAGCAGGA
1 AGAAGAGGAGCAGGA
6391058 AGAAGAGGAGCAGGA
1 AGAAGAGGAGCAGGA
6391073 TGGAGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.47, T:0.00
Consensus pattern (15 bp):
AGAAGAGGAGCAGGA
Found at i:6391845 original size:32 final size:32
Alignment explanation
Indices: 6391804--6391867 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
6391794 CTTTTTCATC
6391804 GATGTGAAGAATTAACTTTTGTTGAATTTGGG
1 GATGTGAAGAATTAACTTTTGTTGAATTTGGG
6391836 GATGTGAAGAATTAACTTTTGTTGAATTTGGG
1 GATGTGAAGAATTAACTTTTGTTGAATTTGGG
6391868 TGTGTAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (32 bp):
GATGTGAAGAATTAACTTTTGTTGAATTTGGG
Found at i:6394772 original size:6 final size:6
Alignment explanation
Indices: 6394761--6394785 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6394751 GAATGTAAAT
6394761 ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA A
6394786 AAATATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:6398540 original size:3 final size:3
Alignment explanation
Indices: 6398532--6398615 Score: 159
Period size: 3 Copynumber: 27.7 Consensus size: 3
6398522 AAATAAATGT
6398532 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
6398581 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6398616 TTTAAAACTT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 77 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.