Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 11 of 106
Found at i:5231431 original size:25 final size:26
Alignment explanation
Indices: 5231403--5231498 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 26
5231393 ATTTTCATTA
5231403 ATTTAATTTAATTT-TTATATTATAT
1 ATTTAATTTAATTTCTTATATTATAT
* *
5231428 ATTTATTTTAATTTCTTTTACTTATATT
1 ATTTAATTTAATTTCTTATA-TTATA-T
* * *
5231456 ATGTAAATTTTAATTTCGTATATTTTAT
1 AT-TTAA-TTTAATTTCTTATATTATAT
*
5231484 -TTTATTTTAATTTCT
1 ATTTAATTTAATTTCT
5231499 AATTCTTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
25 22 0.39
26 6 0.11
27 6 0.11
28 4 0.07
29 6 0.11
30 12 0.21
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTAATTTAATTTCTTATATTATAT
Found at i:5231490 original size:55 final size:55
Alignment explanation
Indices: 5231409--5231512 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
5231399 ATTAATTTAA
* *
5231409 TTTAATTTTTATATTATATATTTATTTTAATTTCT-TTTACTTATATTATGTAAAT
1 TTTAATTTGTATATTATATATTTATTTTAATTTCTAATT-CTTATATTATGTAAAT
*
5231464 TTTAATTTCGTATATTTTAT-TTTATTTTAATTTCTAATTCTTATATTAT
1 TTTAATTT-GTATATTATATATTTATTTTAATTTCTAATTCTTATATTAT
5231513 ATATTTTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
55 33 0.75
56 11 0.25
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (55 bp):
TTTAATTTGTATATTATATATTTATTTTAATTTCTAATTCTTATATTATGTAAAT
Found at i:5248072 original size:29 final size:29
Alignment explanation
Indices: 5248006--5248078 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
5247996 AAAAAAACTT
5248006 AAATTAATATTTA-ATTTTCTATTATAATC
1 AAATTAAT-TTTATATTTTCTATTATAATC
* *
5248035 AATTTAATTTTATATTTT-TATTTTAAATC
1 AAATTAATTTTATATTTTCTATTAT-AATC
*
5248064 AAATAAATTCTTATA
1 AAATTAATT-TTATA
5248079 ACTAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 9 0.24
29 23 0.62
30 5 0.14
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATTAATTTTATATTTTCTATTATAATC
Found at i:5254608 original size:27 final size:27
Alignment explanation
Indices: 5254569--5254626 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
5254559 AAGAGTTTTA
*
5254569 AGTTACGTGGCCTCATTC-GAGATGAGG
1 AGTTACGTAGCCTCATTCAG-GATGAGG
*
5254596 AGTTACGTAGCCTCGTTCAGGATGAGG
1 AGTTACGTAGCCTCATTCAGGATGAGG
5254623 AGTT
1 AGTT
5254627 TTAAGTTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (27 bp):
AGTTACGTAGCCTCATTCAGGATGAGG
Found at i:5254652 original size:61 final size:61
Alignment explanation
Indices: 5254547--5254835 Score: 380
Period size: 61 Copynumber: 4.7 Consensus size: 61
5254537 TTGTAAAACT
* *** *
5254547 TCATTCAAGATGAAGAGTTTTAAGTTACGTGGCCTCATTCGAGATGAGGAGTTACGTAGCC
1 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
* * * * * *
5254608 TCGTTCAGGATGAGGAGTTTTAAGTTACGAAACCTCATTTGAGATGAGGAGTTATGTACCC
1 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
* * * * ** *
5254669 TAATTCAAAATAAGGAATTTTAAGTTACGAAACCTCATTCGAGATAAAAAGTTACGTAGTC
1 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
5254730 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
1 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
* ** *
5254791 TCATTCAAGATAAATAGTTTTAAGTTACGAAACCTCATTCAAGAT
1 TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGAT
5254836 TAGAAGTTTT
Statistics
Matches: 195, Mismatches: 33, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 195 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (61 bp):
TCATTCAAGATGAGGAGTTTTAAGTTACGAAACCTCATTCGAGATAAGGAGTTACGTAGCC
Found at i:5254654 original size:34 final size:34
Alignment explanation
Indices: 5254596--5254880 Score: 162
Period size: 34 Copynumber: 9.0 Consensus size: 34
5254586 CGAGATGAGG
* * * *
5254596 AGTTACGTAGCCTCGTTCAGGATGAGGAGTTTTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
**
5254630 AGTTACGAAACCTCATTTGAGATGAGGAG--TTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* * * * *
5254662 TG-TAC----CCTAATTCAAAATAAGGAATTTTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* *
5254691 AGTTACGAAACCTCATTCGAGAT-A--A----AA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* **
5254718 AGTTACGTAGTCTCATTCAAGATGAGGAGTTTTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* *
5254752 AGTTACGAAACCTCATTCGAGATAAGGAG--TTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* * **
5254784 CG-TA-G---CCTCATTCAAGATAAATAGTTTTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* *
5254813 AGTTACGAAACCTCATTCAAGATTAGAAGTTTTA
1 AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
* * * *
5254847 AGTTAAGTAACCTAATTCCAGATGAGGAGCTTTT
1 AGTTACGAAACCTCATTCAAGATGAGGAG-TTTT
5254881 TCCTTTTATA
Statistics
Matches: 187, Mismatches: 42, Indels: 43
0.69 0.15 0.16
Matches are distributed among these distances:
27 49 0.26
28 1 0.01
29 8 0.04
30 7 0.04
31 7 0.04
32 8 0.04
33 1 0.01
34 102 0.55
35 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (34 bp):
AGTTACGAAACCTCATTCAAGATGAGGAGTTTTA
Found at i:5254785 original size:27 final size:27
Alignment explanation
Indices: 5254752--5254803 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5254742 AGGAGTTTTA
*
5254752 AGTTACGAAACCTCATTCGAGATAAGG
1 AGTTACGAAACCTCATTCAAGATAAGG
* *
5254779 AGTTACGTAGCCTCATTCAAGATAA
1 AGTTACGAAACCTCATTCAAGATAA
5254804 ATAGTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
AGTTACGAAACCTCATTCAAGATAAGG
Found at i:5254809 original size:27 final size:27
Alignment explanation
Indices: 5254752--5254809 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5254742 AGGAGTTTTA
* *
5254752 AGTTACGAAACCTCATTCGAGATAAGG
1 AGTTACGAAACCTCATTCAAGATAAAG
* * *
5254779 AGTTACGTAGCCTCATTCAAGATAAAT
1 AGTTACGAAACCTCATTCAAGATAAAG
5254806 AGTT
1 AGTT
5254810 TTAAGTTACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (27 bp):
AGTTACGAAACCTCATTCAAGATAAAG
Found at i:5262107 original size:19 final size:19
Alignment explanation
Indices: 5262083--5262120 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5262073 AAACCCCCTC
5262083 GATGGACGATATGTTCACA
1 GATGGACGATATGTTCACA
*
5262102 GATGGAGGATATGTTCACA
1 GATGGACGATATGTTCACA
5262121 ATGTTTTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (19 bp):
GATGGACGATATGTTCACA
Found at i:5274063 original size:20 final size:21
Alignment explanation
Indices: 5274035--5274077 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
5274025 GAAGTAACTC
5274035 TTGCACTTTAATT-AC-TTATT
1 TTGCACTTT-ATTAACTTTATT
*
5274055 TTGCTCTTTATTAACTTTATT
1 TTGCACTTTATTAACTTTATT
5274076 TT
1 TT
5274078 TCTCAAGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 10 0.50
21 7 0.35
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (21 bp):
TTGCACTTTATTAACTTTATT
Found at i:5275587 original size:19 final size:19
Alignment explanation
Indices: 5275546--5275585 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
5275536 TTTTTGAATA
5275546 TTTTGTGATTTTTATTTTG
1 TTTTGTGATTTTTATTTTG
*
5275565 TTTTG-GATTTTT-TTTTC
1 TTTTGTGATTTTTATTTTG
5275582 TTTT
1 TTTT
5275586 TTATAGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.07, C:0.03, G:0.12, T:0.78
Consensus pattern (19 bp):
TTTTGTGATTTTTATTTTG
Found at i:5277676 original size:13 final size:13
Alignment explanation
Indices: 5277645--5277699 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
5277635 AGTATATTTT
5277645 TTAAA-TAATTAA
1 TTAAATTAATTAA
5277657 -TATAATTAATTAA
1 TTA-AATTAATTAA
**
5277670 TTAAATTTTTTAA
1 TTAAATTAATTAA
*
5277683 TTTAAATAAATTAA
1 -TTAAATTAATTAA
5277697 TTA
1 TTA
5277700 TCACATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 2 0.06
12 2 0.06
13 18 0.53
14 12 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TTAAATTAATTAA
Found at i:5279412 original size:108 final size:109
Alignment explanation
Indices: 5279209--5279420 Score: 311
Period size: 108 Copynumber: 1.9 Consensus size: 109
5279199 TAAAATGACT
* * * * *
5279209 AAATATATTGATTTAGTTACAAATTTCACAATTTACAAATACACTTTTTTTTTTGAAATTATTCA
1 AAATATATTAATTTAGTTACAAATTTCACAATTTACAAATAAAC-TATTCTTTTGAAATTAGTCA
*
5279274 ACTTTTACTCAATTTACCTTTTATTAAAATTTACTCAAATTAGTA
65 ACTCTTACTCAATTTACCTTTTATTAAAATTTACTCAAATTAGTA
* *
5279319 AAATATGTTAATTTAGTTACAACTTTCACAATTTACAAATAAAC-ATTCTTTTGAAATTAGTCAA
1 AAATATATTAATTTAGTTACAAATTTCACAATTTACAAATAAACTATTCTTTTGAAATTAGTCAA
*
5279383 CTCTTA-TCCAATTTACCTTTTATTTAAATTTACTCAAA
66 CTCTTACT-CAATTTACCTTTTATTAAAATTTACTCAAA
5279421 ATTTCTTATA
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
107 1 0.01
108 51 0.55
110 40 0.43
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (109 bp):
AAATATATTAATTTAGTTACAAATTTCACAATTTACAAATAAACTATTCTTTTGAAATTAGTCAA
CTCTTACTCAATTTACCTTTTATTAAAATTTACTCAAATTAGTA
Found at i:5286173 original size:28 final size:28
Alignment explanation
Indices: 5286115--5286205 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 28
5286105 AGCGCTACTA
* *
5286115 CGCTTGGAATACCC-CTAGG-CGCTTCTG
1 CGCTTGGAATGCCCTCT-GGACACTTCTG
5286142 CGCTTGGAATGCCCTCTGGACACTTCTG
1 CGCTTGGAATGCCCTCTGGACACTTCTG
* * *
5286170 CGCTTAGAATG-TCTTTGGACACTTCTG
1 CGCTTGGAATGCCCTCTGGACACTTCTG
**
5286197 TACTTGGAA
1 CGCTTGGAA
5286206 CACCCTTAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 35 0.65
28 19 0.35
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (28 bp):
CGCTTGGAATGCCCTCTGGACACTTCTG
Found at i:5286196 original size:27 final size:28
Alignment explanation
Indices: 5286136--5286196 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
5286126 CCCCTAGGCG
*
5286136 CTTCTGCGCTTGGAATGCCCTCTGGACA
1 CTTCTGCGCTTAGAATGCCCTCTGGACA
* *
5286164 CTTCTGCGCTTAGAATG-TCTTTGGACA
1 CTTCTGCGCTTAGAATGCCCTCTGGACA
5286191 CTTCTG
1 CTTCTG
5286197 TACTTGGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.15, C:0.28, G:0.23, T:0.34
Consensus pattern (28 bp):
CTTCTGCGCTTAGAATGCCCTCTGGACA
Found at i:5286219 original size:27 final size:27
Alignment explanation
Indices: 5286189--5286282 Score: 91
Period size: 27 Copynumber: 3.5 Consensus size: 27
5286179 TGTCTTTGGA
5286189 CACTTCTGTACTTGGAACACCCTTAAG
1 CACTTCTGTACTTGGAACACCCTTAAG
* * **
5286216 CACTTCTATACTTGGAACACCTTTGTG
1 CACTTCTGTACTTGGAACACCCTTAAG
* ** * *
5286243 CCCTTCTGCGCTTAGAACACCC-TAGG
1 CACTTCTGTACTTGGAACACCCTTAAG
*
5286269 CGCTTCTGTACTTG
1 CACTTCTGTACTTG
5286283 AAATGCCCTT
Statistics
Matches: 51, Mismatches: 16, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
26 12 0.24
27 39 0.76
ACGTcount: A:0.20, C:0.31, G:0.17, T:0.32
Consensus pattern (27 bp):
CACTTCTGTACTTGGAACACCCTTAAG
Found at i:5291514 original size:16 final size:17
Alignment explanation
Indices: 5291476--5291517 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5291466 TTTTTTTTGT
5291476 AAATAAATGTATCAAAA
1 AAATAAATGTATCAAAA
5291493 ATAATAAATG-AGT-AAAA
1 A-AATAAATGTA-TCAAAA
5291510 AAATAAAT
1 AAATAAAT
5291518 AACAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (17 bp):
AAATAAATGTATCAAAA
Found at i:5294155 original size:6 final size:6
Alignment explanation
Indices: 5294131--5294236 Score: 95
Period size: 6 Copynumber: 17.7 Consensus size: 6
5294121 TGGAGGTGGT
* * * * * * *
5294131 GGCGGC GGAGGG GGAGGC GGCGGC GGCGGT GGCGGT GGGGGA GGCGGC
1 GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC
* * * * * *
5294179 GGCGGC GGTGGC GGGGGC GGAGGC GGCGGC GGCGGT GGGGGA GGCGGC
1 GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC GGCGGC
5294227 GGCGGC GGCG
1 GGCGGC GGCG
5294237 ACGGTGGGGG
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.05, C:0.21, G:0.71, T:0.04
Consensus pattern (6 bp):
GGCGGC
Found at i:5294170 original size:27 final size:27
Alignment explanation
Indices: 5294134--5294243 Score: 159
Period size: 27 Copynumber: 4.1 Consensus size: 27
5294124 AGGTGGTGGC
5294134 GGCGGAGGGGGAGGCGGCGGCGGCGGT
1 GGCGGAGGGGGAGGCGGCGGCGGCGGT
*
5294161 GGCGGTGGGGGAGGCGGCGGCGGCGGT
1 GGCGGAGGGGGAGGCGGCGGCGGCGGT
5294188 GGCGG-GGGCGGAGGCGGCGGCGGCGGT
1 GGCGGAGGG-GGAGGCGGCGGCGGCGGT
* * * *
5294215 GGGGGAGGCGGCGGCGGCGGCGACGGT
1 GGCGGAGGGGGAGGCGGCGGCGGCGGT
5294242 GG
1 GG
5294244 GGGTGGACAT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
26 3 0.04
27 71 0.93
28 2 0.03
ACGTcount: A:0.05, C:0.20, G:0.70, T:0.05
Consensus pattern (27 bp):
GGCGGAGGGGGAGGCGGCGGCGGCGGT
Found at i:5294176 original size:21 final size:21
Alignment explanation
Indices: 5294152--5294234 Score: 103
Period size: 21 Copynumber: 3.7 Consensus size: 21
5294142 GGGAGGCGGC
*
5294152 GGCGGCGGTGGCGGTGGGGGA
1 GGCGGCGGCGGCGGTGGGGGA
5294173 GGCGGCGGCGGCGGTGGCGGGGGCGGA
1 GGCGGCGGCGGCGGT-----GGG-GGA
5294200 GGCGGCGGCGGCGGTGGGGGA
1 GGCGGCGGCGGCGGTGGGGGA
5294221 GGCGGCGGCGGCGG
1 GGCGGCGGCGGCGG
5294235 CGACGGTGGG
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
21 31 0.56
22 3 0.05
26 3 0.05
27 18 0.33
ACGTcount: A:0.04, C:0.20, G:0.71, T:0.05
Consensus pattern (21 bp):
GGCGGCGGCGGCGGTGGGGGA
Found at i:5297959 original size:10 final size:11
Alignment explanation
Indices: 5297919--5297968 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
5297909 AGTTAATGTT
5297919 ACAAAAAAT-A
1 ACAAAAAATCA
*
5297929 AGCATAAAATCA
1 A-CAAAAAATCA
5297941 ACAAAAAATCA
1 ACAAAAAATCA
*
5297952 A-AAGAAATCA
1 ACAAAAAATCA
*
5297962 AGAAAAA
1 ACAAAAA
5297969 TTATGCTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 10 0.30
11 21 0.64
12 2 0.06
ACGTcount: A:0.72, C:0.12, G:0.06, T:0.10
Consensus pattern (11 bp):
ACAAAAAATCA
Found at i:5298078 original size:50 final size:50
Alignment explanation
Indices: 5298024--5298126 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
5298014 TTCAATCAGA
*
5298024 TTAATAATAAAATTTGAAAAATAAAACTAAGTCAAATAAAGTTAACAAAC
1 TTAATAATAAAAATTGAAAAATAAAACTAAGTCAAATAAAGTTAACAAAC
* * *
5298074 TTAATAATAAAAATTGAAAAATAAGACTAAGTCAGATAAAGTTAACAGAC
1 TTAATAATAAAAATTGAAAAATAAAACTAAGTCAAATAAAGTTAACAAAC
5298124 TTA
1 TTA
5298127 GTCATTAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (50 bp):
TTAATAATAAAAATTGAAAAATAAAACTAAGTCAAATAAAGTTAACAAAC
Found at i:5299492 original size:2 final size:2
Alignment explanation
Indices: 5299485--5299543 Score: 95
Period size: 2 Copynumber: 30.0 Consensus size: 2
5299475 TAAACAGTAC
5299485 AT AT AT AT AT AT AT -T AT AT AT AT AT A- 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
5299525 AT AT ACT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT
5299544 TTTTAAGAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 50 0.93
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5299504 original size:13 final size:12
Alignment explanation
Indices: 5299485--5299543 Score: 95
Period size: 11 Copynumber: 5.0 Consensus size: 12
5299475 TAAACAGTAC
5299485 ATATATATATAT
1 ATATATATATAT
5299497 AT-TATATATAT
1 ATATATATATAT
5299508 ATA-ATATATAT
1 ATATATATATAT
5299519 ATATATATATACT
1 ATATATATATA-T
5299532 ATATATATATAT
1 ATATATATATAT
5299544 TTTTAAGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
11 22 0.50
12 10 0.23
13 12 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATATATATAT
Found at i:5299505 original size:15 final size:15
Alignment explanation
Indices: 5299485--5299543 Score: 91
Period size: 15 Copynumber: 3.8 Consensus size: 15
5299475 TAAACAGTAC
5299485 ATATATATATATATT
1 ATATATATATATATT
5299500 ATATATATATAATATAT
1 ATATATATAT-ATAT-T
*
5299517 ATATATATATATACT
1 ATATATATATATATT
5299532 ATATATATATAT
1 ATATATATATAT
5299544 TTTTAAGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
15 23 0.56
16 7 0.17
17 11 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:5311012 original size:2 final size:2
Alignment explanation
Indices: 5310993--5311035 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
5310983 ATTGTGCTCC
5310993 TA TA T- TA TA T- TGA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5311033 TA T
1 TA T
5311036 TGTATGATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 3 0.08
2 33 0.89
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5311162 original size:36 final size:35
Alignment explanation
Indices: 5311117--5311185 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
5311107 GAATGATGAT
* *
5311117 ATTACCTGTGTGTGATGTGGGGGTGCACATGATGGC
1 ATTACCTGTGCGCGATGT-GGGGTGCACATGATGGC
*
5311153 ATTAGCTGTGCGCGATGTGGGGTGCACATGATG
1 ATTACCTGTGCGCGATGTGGGGTGCACATGATG
5311186 ACTCTGACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.17, C:0.14, G:0.39, T:0.29
Consensus pattern (35 bp):
ATTACCTGTGCGCGATGTGGGGTGCACATGATGGC
Found at i:5313318 original size:63 final size:64
Alignment explanation
Indices: 5313185--5313306 Score: 183
Period size: 63 Copynumber: 1.9 Consensus size: 64
5313175 AGTAATAACA
* * *
5313185 GGTTTTTTTTTTTTACAACTTAACTTTTGCCTAAGTTGCCCTTTTATGGATTTTCAACTCAACG
1 GGTTTTTTTTTTCTACAACTTAACTTTTGCCTAAGTTGCCCTGTTAAGGATTTTCAACTCAACG
** *
5313249 GGTTTTTTTTTTCTA-GTCTTAACTTTTGCCTAAGTTGTCCTGTTAAGGATTTTCAACT
1 GGTTTTTTTTTTCTACAACTTAACTTTTGCCTAAGTTGCCCTGTTAAGGATTTTCAACT
5313307 TTGTGGGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 38 0.73
64 14 0.27
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (64 bp):
GGTTTTTTTTTTCTACAACTTAACTTTTGCCTAAGTTGCCCTGTTAAGGATTTTCAACTCAACG
Found at i:5316837 original size:445 final size:443
Alignment explanation
Indices: 5315816--5317132 Score: 1096
Period size: 445 Copynumber: 3.0 Consensus size: 443
5315806 AGTTGTTCTA
* * * * * * * *
5315816 TTAAGGATTTTCGACCTAGCGGATTTTCTTTTTAAGGGCAATTTAGGCTTTTATTGAAGAGCAAT
1 TTAAGGATTTTCAACTTAGTGG-TCTT-TTTTTAAAGGCAATTTAGGCTCTTATTGAAAAGTAAT
* * ** *** * * ** * * *
5315881 TGATCTTTAAGCATAGTAATGTTTCAAGAATTTACCT-TTGATTGGGTTGATTGTGAAGAGTAAA
64 TAATCTTCAAATATAGTAACACTTCAAGAATTT-GCTATTGATTGGATCAATTATAAAGAATAAA
* * * * ** * * *
5315945 TCTTAACAATAAGTCTTCTTTGCTTCACTTGCAATTTGATAGTTTGAACTTCTTGAATTTTCGAC
128 CCCTAGCAATAAGTCTTATTCACTTCACTTGCTATTTGATAGTTTGAACTTCTTTAATTTTCGAA
* * ** * * *
5316010 GTCAACTTT-GTAGTTTAAACGTCGTAAAGATTTGAATTATCTTTAATCAAAGAGACTTTTTCTT
193 ATCAA-TTTAGTAGTTTAAATGTCACAAAGATTTAAATTATCTTTAATCGAAGAGATTTTTTCTT
* * * * * * * ** * * *
5316074 -TCTTTTTT-G-TTGACTAAACTTGGCAATTAGATCAAACTACCTATGTAACTTTTCATATAAAG
257 ATTTTTTTTAGATTGACTGAACTTGACAATGAAACCAAGCTACCTACATACCTTCTAATATAAAG
* * * * *** ** * *
5316136 GATCAAGTCATTACGTAGTT-TTTT-T-TTTAAC-ATCTTAACTTTTGTATAAGTTATCTTTTTA
322 GATCAAGCCATAACGTAGTTCTTTTATGTTTTACGATC-GAACTTTTACCTAAGTCGTCCTTTGA
* * * * * * * ** *
5316197 TGGATTTTCAACTTAAC-GAGTTTTTTTT-TAAGTCTTAAGTTTTGCATTAGCTATCCTAG
386 AGAATTTTCAACTTAACTG-GTTTTTTTTCAAAGTCCTAACTTTTGC-TAAACCGT-CTTG
** * * * * ** * * ** *
5316256 -TAAGGATTTTTGACTTATTAAG-CTTTTTTTTATAA-GTAGTTTAATCTTTTATCGAGGAGCAA
1 TTAAGGATTTTCAACTTAGT-GGTC-TTTTTTTA-AAGGCAATTTAGGCTCTTATTGAAAAGTAA
* * * ** *
5316318 TTGAT-TTCCAAGTATAGTAACGCTTCAAGAATTTGCTATTGATTGGATTGATTATAAAGAGTAA
63 TTAATCTT-CAAATATAGTAACACTTCAAGAATTTGCTATTGATTGGATCAATTATAAAGAATAA
*
5316382 ACCCTAGCAAT-AGATCTTATTCACTTCACTTGCTATTTGATAGTTTGAACTTCTTTAATTTTTG
127 ACCCTAGCAATAAG-TCTTATTCACTTCACTTGCTATTTGATAGTTTGAACTTCTTTAATTTTCG
* *
5316446 AGAAT-AATTTAGTAGTTTAAATGTCACAAAGATTTGAATTATCTTTAATTGAAGAG-TGTTTTT
191 A-AATCAATTTAGTAGTTTAAATGTCACAAAGATTTAAATTATCTTTAATCGAAGAGAT-TTTTT
* * *
5316509 CTTATTTTTTTTATG-TTGACTGAACTTGACAATGAGAA-TAAGTTGCCTACATACCTTCTAATA
254 CTTATTTTTTTTA-GATTGACTGAACTTGACAATGA-AACCAAGCTACCTACATACCTTCTAATA
* * * ** * * * * *
5316572 TGAAA-GATCAAGTCATAACGTAGTTCTTTTTTTTTTTGTGGTTGAACTTTTGCCTTAGTTGTCC
317 T-AAAGGATCAAGCCATAACGTAGTTCTTTTATGTTTTACGATCGAACTTTTACCTAAGTCGTCC
*
5316636 TTTGAAGGATTCTTCAACTTAAAC-GGCTTTTATTTT-AAAGTCCTAACTTTTGCTAAACCGTCT
381 TTTGAAGAATT-TTCAACTT-AACTGG-TTTT-TTTTCAAAGTCCTAACTTTTGCTAAACCGTCT
5316699 TG
442 TG
5316701 TTAAGGATTTTCAACTTAGTGGTCTTTTTTTAAAGGCAATTTAGGCTCTTATTGAAAAGTAATTA
1 TTAAGGATTTTCAACTTAGTGGTCTTTTTTTAAAGGCAATTTAGGCTCTTATTGAAAAGTAATTA
* * * **
5316766 ATCTTCAAATATAGTAACACTTCAAGAATTTGCTATTGATTGGGTCAATTGTGAAGAATAGGCCC
66 ATCTTCAAATATAGTAACACTTCAAGAATTTGCTATTGATTGGATCAATTATAAAGAATAAACCC
* ** * *
5316831 TAGCAATAAGTCTTCTTTGCTTCACTTGTTATTTGATAGTTTGAACTTCTTTAATTTTCGAAGTC
131 TAGCAATAAGTCTTATTCACTTCACTTGCTATTTGATAGTTTGAACTTCTTTAATTTTCGAAATC
* * ** * *
5316896 TATTTGGTAGTTTGTATGTCGCAAAGATTTAAATTATCTTTAATCGAAGAGACTTTTTTTTTATT
196 AATTTAGTAGTTTAAATGTCACAAAGATTTAAATTATCTTTAATCGAAGAGA-TTTTTTCTTATT
* * * * *
5316961 TTTTTTAGATTGATTGAACTTGGCAATGAAACCAAGCTACTTACGTACCTTTTAATATAAAGGAT
260 TTTTTTAGATTGACTGAACTTGACAATGAAACCAAGCTACCTACATACCTTCTAATATAAAGGAT
* *
5317026 CAAGCCATAACGTAGTTCTTTTATGTTTTACGATCGAACTTTTACCTAAGTCGTCTTTTTAAGAA
325 CAAGCCATAACGTAGTTCTTTTATGTTTTACGATCGAACTTTTACCTAAGTCGTCCTTTGAAGAA
5317091 TTTTCAACTTAACTGGTTTTTTTTCAAAGTCCTAACTTTTGC
390 TTTTCAACTTAACTGGTTTTTTTTCAAAGTCCTAACTTTTGC
5317133 CGAAGCATTT
Statistics
Matches: 709, Mismatches: 133, Indels: 66
0.78 0.15 0.07
Matches are distributed among these distances:
437 9 0.01
438 180 0.25
439 26 0.04
440 1 0.00
441 54 0.08
442 8 0.01
443 5 0.01
444 55 0.08
445 207 0.29
446 145 0.20
447 19 0.03
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (443 bp):
TTAAGGATTTTCAACTTAGTGGTCTTTTTTTAAAGGCAATTTAGGCTCTTATTGAAAAGTAATTA
ATCTTCAAATATAGTAACACTTCAAGAATTTGCTATTGATTGGATCAATTATAAAGAATAAACCC
TAGCAATAAGTCTTATTCACTTCACTTGCTATTTGATAGTTTGAACTTCTTTAATTTTCGAAATC
AATTTAGTAGTTTAAATGTCACAAAGATTTAAATTATCTTTAATCGAAGAGATTTTTTCTTATTT
TTTTTAGATTGACTGAACTTGACAATGAAACCAAGCTACCTACATACCTTCTAATATAAAGGATC
AAGCCATAACGTAGTTCTTTTATGTTTTACGATCGAACTTTTACCTAAGTCGTCCTTTGAAGAAT
TTTCAACTTAACTGGTTTTTTTTCAAAGTCCTAACTTTTGCTAAACCGTCTTG
Found at i:5326775 original size:22 final size:23
Alignment explanation
Indices: 5326737--5326785 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5326727 ATATATAATA
*
5326737 CATTTTTATTATATTCACTTCTT
1 CATTTTTATTATATTCAATTCTT
*
5326760 CATTTTTATT-TTTTCAATTCTT
1 CATTTTTATTATATTCAATTCTT
5326782 -ATTT
1 CATTT
5326786 GTTTATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 10 0.42
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.65
Consensus pattern (23 bp):
CATTTTTATTATATTCAATTCTT
Found at i:5326790 original size:23 final size:23
Alignment explanation
Indices: 5326764--5326823 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
5326754 CTTCTTCATT
5326764 TTTAT-TTTTTCAATT-CTTATTTG
1 TTTATCTTTTT-AATTCCTT-TTTG
5326787 TTTATCTTTTTAATTCCTTTTTG
1 TTTATCTTTTTAATTCCTTTTTG
*
5326810 TTTATACATTTTAA
1 TTTAT-CTTTTTAA
5326824 AGATGTCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (23 bp):
TTTATCTTTTTAATTCCTTTTTG
Found at i:5331404 original size:2 final size:2
Alignment explanation
Indices: 5331397--5331427 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5331387 TTAATTTGAA
*
5331397 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5331428 AAGGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5341865 original size:27 final size:27
Alignment explanation
Indices: 5341814--5341867 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5341804 AGCTGCTTAT
* *
5341814 CCTCCCCCACCTTCTGCGTACCCTCCA
1 CCTCCCCCACCTTCAGCATACCCTCCA
*
5341841 CCTCCCCCACCTTCAGCATATCCTCCA
1 CCTCCCCCACCTTCAGCATACCCTCCA
5341868 GCTACATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.15, C:0.57, G:0.06, T:0.22
Consensus pattern (27 bp):
CCTCCCCCACCTTCAGCATACCCTCCA
Found at i:5345134 original size:21 final size:22
Alignment explanation
Indices: 5345102--5345143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5345092 ATCAATGTCA
* *
5345102 TAATTCCAACTGTTTTTAAATG
1 TAATTCCAACTGCTTTCAAATG
5345124 TAATT-CAACTGCTTTCAAAT
1 TAATTCCAACTGCTTTCAAAT
5345144 ACCTTAGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (22 bp):
TAATTCCAACTGCTTTCAAATG
Found at i:5355459 original size:2 final size:2
Alignment explanation
Indices: 5355454--5355488 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5355444 AACACACAAC
*
5355454 AT AT AT AT AT AT AT AT AT GT 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 A
5355489 CACACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5356052 original size:2 final size:2
Alignment explanation
Indices: 5356045--5356077 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5356035 TTGTAGGAAA
5356045 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5356078 TTTTAGAATG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5357306 original size:23 final size:23
Alignment explanation
Indices: 5357262--5357307 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5357252 AGTCATGCTA
**
5357262 CCTATCTTTATATGTTTTTTTTT
1 CCTATCTTTATATGTTGATTTTT
5357285 CCTATCTTTATATGTTGATTTTT
1 CCTATCTTTATATGTTGATTTTT
5357308 GTGGGTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.13, G:0.07, T:0.65
Consensus pattern (23 bp):
CCTATCTTTATATGTTGATTTTT
Found at i:5365371 original size:2 final size:2
Alignment explanation
Indices: 5365364--5365402 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5365354 AACACTTAAA
5365364 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
5365403 AAGGGATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5373482 original size:42 final size:42
Alignment explanation
Indices: 5373436--5373577 Score: 121
Period size: 42 Copynumber: 3.4 Consensus size: 42
5373426 TGACTGAGTG
*
5373436 GGAGATGGTGGGGATGCAGGAGGATTCTGTGATTCTGTTGGA
1 GGAGATGGTGGAGATGCAGGAGGATTCTGTGATTCTGTTGGA
* * * * ** *
5373478 GGAGATGGAGGAG-TGTA--AGTAGTT-GGTGGAGTTGGAGTGGGA
1 GGAGATGGTGGAGATGCAGGAGGA-TTCTGT-GA-TT-CTGTTGGA
* *
5373520 GGAGATGGTGGTGATGGAGGAGGATTCTGTGATTCTGTTGGA
1 GGAGATGGTGGAGATGCAGGAGGATTCTGTGATTCTGTTGGA
*
5373562 GGAGACGGTGGAGATG
1 GGAGATGGTGGAGATG
5373578 TTGATGGAGG
Statistics
Matches: 74, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
39 5 0.07
40 4 0.05
41 5 0.07
42 46 0.62
43 5 0.07
44 4 0.05
45 5 0.07
ACGTcount: A:0.21, C:0.04, G:0.49, T:0.26
Consensus pattern (42 bp):
GGAGATGGTGGAGATGCAGGAGGATTCTGTGATTCTGTTGGA
Found at i:5373592 original size:99 final size:99
Alignment explanation
Indices: 5373481--5373664 Score: 325
Period size: 99 Copynumber: 1.9 Consensus size: 99
5373471 TGTTGGAGGA
* **
5373481 GATGGAGGAGTGTAAGTAGTTGGTGGAGTTGGAGTGGGAGGAGATGGTG-GTGATGGAGGAGGAT
1 GATGGAGGAGTGTAAGTAGTTGATGGAACTGGAGTGGGAGGAGATGGTGAG-GATGGAGGAGGAT
5373545 TCTGTGATTCTGTTGGAGGAGACGGTGGAGATGTT
65 TCTGTGATTCTGTTGGAGGAGACGGTGGAGATGTT
5373580 GATGGAGGAGTGTAAGTAGTTGATGGAACTGGAGTGGGAGGAGATGGTGAGGATGGAGGAGGATT
1 GATGGAGGAGTGTAAGTAGTTGATGGAACTGGAGTGGGAGGAGATGGTGAGGATGGAGGAGGATT
5373645 CTGTGATTCTGTTGGAGGAG
66 CTGTGATTCTGTTGGAGGAG
5373665 TATAAGTAGT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
99 80 0.99
100 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.48, T:0.26
Consensus pattern (99 bp):
GATGGAGGAGTGTAAGTAGTTGATGGAACTGGAGTGGGAGGAGATGGTGAGGATGGAGGAGGATT
CTGTGATTCTGTTGGAGGAGACGGTGGAGATGTT
Found at i:5386235 original size:15 final size:15
Alignment explanation
Indices: 5386217--5386385 Score: 54
Period size: 15 Copynumber: 11.4 Consensus size: 15
5386207 ATGTTTTATT
5386217 TATTAAATATTAATA
1 TATTAAATATTAATA
5386232 TATTAAAT-TT--T-
1 TATTAAATATTAATA
* * *
5386243 TATTGAGTATAAATAA
1 TATTAAATATTAAT-A
* **
5386259 AAAAAAATTATTAATA
1 TATTAAAT-ATTAATA
* *
5386275 T-TTTAATAATAATA
1 TATTAAATATTAATA
5386289 TTATTAAAT-TATAA-A
1 -TATTAAATAT-TAATA
*
5386304 -ATAAAATATTAATA
1 TATTAAATATTAATA
*
5386318 T-TTAAAAAATTAATA
1 TATT-AAATATTAATA
*
5386333 -ATTAAATTATGCTAAAA
1 TATTAAA-TAT--TAATA
*
5386350 TATT-AATATTTAAAA
1 TATTAAATA-TTAATA
*
5386365 TATTAATTATTAATA
1 TATTAAATATTAATA
*
5386380 TTTTAA
1 TATTAA
5386386 TTAATTTATA
Statistics
Matches: 110, Mismatches: 24, Indels: 40
0.63 0.14 0.23
Matches are distributed among these distances:
11 6 0.05
12 2 0.02
13 9 0.08
14 15 0.14
15 46 0.42
16 17 0.15
17 12 0.11
18 3 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (15 bp):
TATTAAATATTAATA
Found at i:5386292 original size:23 final size:21
Alignment explanation
Indices: 5386258--5386385 Score: 86
Period size: 22 Copynumber: 6.1 Consensus size: 21
5386248 AGTATAAATA
*
5386258 AAAAAAAATTATTAATATTTT
1 AAAATAAATTATTAATATTTT
*
5386279 AATAATAATATTATTAA-ATTAT
1 AA-AATAA-ATTATTAATATTTT
*
5386301 AAAATAAAATATTAATA-TTT
1 AAAATAAATTATTAATATTTT
* **
5386321 -AAA-AAATTAATAATTAAATT
1 AAAATAAATTATTAA-TATTTT
*** *
5386341 ATGCTAAAATATTAATA-TTT
1 AAAATAAATTATTAATATTTT
5386361 AAAATATTAATTATTAATATTTT
1 AAAATA--AATTATTAATATTTT
5386384 AA
1 AA
5386386 TTAATTTATA
Statistics
Matches: 80, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
18 8 0.10
19 5 0.06
20 16 0.20
21 10 0.12
22 28 0.35
23 13 0.16
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (21 bp):
AAAATAAATTATTAATATTTT
Found at i:5386470 original size:16 final size:17
Alignment explanation
Indices: 5386451--5386485 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5386441 ATAAAAGATA
5386451 TTTTTA-TCTTTTTATT
1 TTTTTATTCTTTTTATT
*
5386467 TTTTTATTTTTTTTATT
1 TTTTTATTCTTTTTATT
5386484 TT
1 TT
5386486 CAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTATTCTTTTTATT
Found at i:5386479 original size:8 final size:8
Alignment explanation
Indices: 5386451--5386485 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5386441 ATAAAAGATA
*
5386451 TTTTTATC
1 TTTTTATT
5386459 TTTTTATT
1 TTTTTATT
5386467 TTTTTATTT
1 TTTTTA-TT
5386476 TTTTTATT
1 TTTTTATT
5386484 TT
1 TT
5386486 CAAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:5386610 original size:22 final size:22
Alignment explanation
Indices: 5386583--5386637 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5386573 TGTTCTTATC
*
5386583 TTATTTTATTTTCACGTAATAA
1 TTATTTTATTTTCACATAATAA
5386605 TTATTTTATTTTCACATAATAA
1 TTATTTTATTTTCACATAATAA
5386627 TTATTTTATTT
1 TTATTTTATTT
5386638 CATTCTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTTTATTTTCACATAATAA
Found at i:5386615 original size:43 final size:42
Alignment explanation
Indices: 5386533--5386616 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
5386523 ATAATAATTA
* *
5386533 TTCTTGTCTTATTTCATTCATCGTAATAGTTATTCTATTTTG
1 TTCTTATCTTATTTCATTCATCGTAATAATTATTCTATTTTG
* *
5386575 TTCTTATCTTATTTTATTTTCA-CGTAATAATTATTTTATTTT
1 TTCTTATCTTATTTCA--TTCATCGTAATAATTATTCTATTTT
5386617 CACATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 14 0.39
43 18 0.50
44 4 0.11
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (42 bp):
TTCTTATCTTATTTCATTCATCGTAATAATTATTCTATTTTG
Found at i:5388523 original size:19 final size:18
Alignment explanation
Indices: 5388488--5388523 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5388478 ATAAATTTTT
*
5388488 TATTTTTTTATTTATATA
1 TATTTATTTATTTATATA
5388506 TATTTATTTATGTTATAT
1 TATTTATTTAT-TTATAT
5388524 TTTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTATTTATTTATATA
Found at i:5389870 original size:24 final size:23
Alignment explanation
Indices: 5389821--5389881 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
5389811 ACCTATTACG
5389821 TTTAATTAATAATTTTTTATTATA-
1 TTTAATT-A-AATTTTTTATTATAT
*
5389845 TTTAATTAAATTTTTATATTTTTAT
1 TTTAATTAAATTTTT-TA-TTATAT
5389870 TTTAAATTAAAT
1 TTT-AATTAAAT
5389882 AAAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.22
23 3 0.09
24 11 0.34
25 3 0.09
26 8 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAATTAAATTTTTTATTATAT
Found at i:5393132 original size:27 final size:27
Alignment explanation
Indices: 5393102--5393182 Score: 69
Period size: 27 Copynumber: 3.1 Consensus size: 27
5393092 ATTTTTGTTT
5393102 GCAAAAGCAATGCTATCAGAGTGGTTA
1 GCAAAAGCAATGCTATCAGAGTGGTTA
* * * *** * *
5393129 GC--AAG-ATTCCTATTATTTTTGTTT
1 GCAAAAGCAATGCTATCAGAGTGGTTA
5393153 GCAAAAGCAATGCTATCAGAGTGGTTA
1 GCAAAAGCAATGCTATCAGAGTGGTTA
5393180 GCA
1 GCA
5393183 CTCTTAATTT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
24 13 0.37
25 3 0.09
26 3 0.09
27 16 0.46
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (27 bp):
GCAAAAGCAATGCTATCAGAGTGGTTA
Found at i:5393154 original size:51 final size:51
Alignment explanation
Indices: 5393078--5393182 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
5393068 GAGAAGATTT
5393078 GCAAGATTCCTATTATTTTTGTTTGCAAAAGCAATGCTATCAGAGTGGTTA
1 GCAAGATTCCTATTATTTTTGTTTGCAAAAGCAATGCTATCAGAGTGGTTA
5393129 GCAAGATTCCTATTATTTTTGTTTGCAAAAGCAATGCTATCAGAGTGGTTA
1 GCAAGATTCCTATTATTTTTGTTTGCAAAAGCAATGCTATCAGAGTGGTTA
5393180 GCA
1 GCA
5393183 CTCTTAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (51 bp):
GCAAGATTCCTATTATTTTTGTTTGCAAAAGCAATGCTATCAGAGTGGTTA
Found at i:5393156 original size:24 final size:24
Alignment explanation
Indices: 5393075--5393156 Score: 65
Period size: 24 Copynumber: 3.3 Consensus size: 24
5393065 CATGAGAAGA
5393075 TTTGCAAGATTCCTATTATTTTTG
1 TTTGCAAGATTCCTATTATTTTTG
* * * *** *
5393099 TTTGCAAAAGCAATGCTATCAGAGTGG
1 TTTGC--AAG-ATTCCTATTATTTTTG
*
5393126 TTAGCAAGATTCCTATTATTTTTG
1 TTTGCAAGATTCCTATTATTTTTG
5393150 TTTGCAA
1 TTTGCAA
5393157 AAGCAATGCT
Statistics
Matches: 39, Mismatches: 16, Indels: 6
0.64 0.26 0.10
Matches are distributed among these distances:
24 20 0.51
25 3 0.08
26 3 0.08
27 13 0.33
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (24 bp):
TTTGCAAGATTCCTATTATTTTTG
Found at i:5393936 original size:16 final size:17
Alignment explanation
Indices: 5393906--5393940 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5393896 GATATAGTAA
5393906 TATTTTTTAAATAATTT
1 TATTTTTTAAATAATTT
*
5393923 TATTTTTT-ATTAATTT
1 TATTTTTTAAATAATTT
5393939 TA
1 TA
5393941 AAAATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTTAAATAATTT
Found at i:5415882 original size:16 final size:18
Alignment explanation
Indices: 5415856--5415889 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5415846 AAAGTTTTTT
5415856 TAAATTTA-TTTTTAAAA
1 TAAATTTATTTTTTAAAA
5415873 TAAA-TTATTTTTTAAAA
1 TAAATTTATTTTTTAAAA
5415890 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAAATTTATTTTTTAAAA
Found at i:5438984 original size:17 final size:16
Alignment explanation
Indices: 5438958--5438990 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5438948 TGTTTATGAT
5438958 TTATATAATTATATCA
1 TTATATAATTATATCA
5438974 TTATGATAATTATATCA
1 TTAT-ATAATTATATCA
5438991 AGTACAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
TTATATAATTATATCA
Found at i:5442193 original size:37 final size:37
Alignment explanation
Indices: 5442143--5442237 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
5442133 GAGTTGGGTC
* *
5442143 TACTCTGATACCACTTGTCACAAA-CTTACATTGGATT
1 TACTCTGATACCACTTGTCACAAATC-CACATTGAATT
5442180 TACTCTGATACCACTTGTCACAAATCCACATTGAATT
1 TACTCTGATACCACTTGTCACAAATCCACATTGAATT
*
5442217 TACTTTGATACCACTTGTCAC
1 TACTCTGATACCACTTGTCAC
5442238 CAGCCCATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 53 0.98
38 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.35
Consensus pattern (37 bp):
TACTCTGATACCACTTGTCACAAATCCACATTGAATT
Found at i:5442948 original size:17 final size:18
Alignment explanation
Indices: 5442931--5442964 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5442921 TATTTACAAT
5442931 TTAT-ATAATTAT-TTAA
1 TTATGATAATTATGTTAA
5442947 TTATGATAATTATGTTAA
1 TTATGATAATTATGTTAA
5442965 GTATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TTATGATAATTATGTTAA
Found at i:5445273 original size:531 final size:528
Alignment explanation
Indices: 5443883--5445519 Score: 1606
Period size: 530 Copynumber: 3.1 Consensus size: 528
5443873 AATAAGGTAC
* * * * * * * * * * *
5443883 TTATAACATAACAATAATCTAAAATAATAAATGTACCACACA-AACAAACAAATATAGTAAATTG
1 TTATAACATAACAATAATTTAAGACACTGAATGTACCGCACACAA-AAATAAATCTAATACATTC
** * ** * *
5443947 TAAACATTATAATTCAGTACTCAGAGTCATCAAGTCCAAAATTTAAAAAAAATCAAAAAAAATAC
65 TAAACATTATGCTTAAACACTCAAAGTCATCAAGTCC--AATTTAAAAAAAAT--AAAAAAATAA
* * * * * *
5444012 TTTACTTGCTATAGCACACAAGTATTATATCTTGTGGCATTATTAAATTAAAAGTAATGAGTCAT
126 TTTACTTGCCACATCACACAAGTATTATATCTTGTAGCATAATTAAATTAAAAGTAA-G-TTC-T
* * * * *
5444077 CATTTTTTTTTACATTTCATCTTAGCAATTTATAGTTTCCAATGATTGTATCATGAAAATTCGAA
188 CA--TTTATTTACATTTCATCTTAACAATTTGTAGTTTCTAATGATTGTATCATGAAAATTCAAA
* *
5444142 TTCAAATTAACATTTCATCTATTACGAGATTTTATCTTATTT-AAGATTTATGTAATTATTTTAT
251 TTCAAATTAACATTTCATC---TACGAGATTTTACCTTATTTGCA-ATTTATGTAATTATTTTAT
* *
5444206 TATGATAATTATGTCAAGTACATGTCACAAAACATATATCATTGACTAAAAATGACTAAATTCAA
312 TATGATAATTATGTCAAGTACATGTCACAAAACAGATATCATTGACT-CAAATGACTAAATTCAA
** * * * * *
5444271 ACCTTTTTACTCCCAAAATCATATTTTAACAAAAAATAAATTTATATTATATCAAGTAAACATC-
376 A-CTTTTTACT--TTAAATAATATTTTAAAAAAAAATAAATGTATATTAT-GCAAGTACACATCA
* * *
5444335 GAATTATTAGGTAAAGATAAATACTAAGCACAAATGTTGAACTTTCACTTTATAAGGAAAGTTTG
437 G-ATTATTAGGTAAAGATAAATACTAAGTACAAATGTTG-ACTTTCACTTTATAAGAAAATTTTG
* ** * *
5444400 GATACATA-TCCCTTATCTGGATATGATAT
500 GATATATATTTAC-TATCTAGATACGATAT
* *
5444429 TTATAACATAACAATAATTTAAGACATTGAATGTACCGCACACAAAAATAAATCTAGTACATTCT
1 TTATAACATAACAATAATTTAAGACACTGAATGTACCGCACACAAAAATAAATCTAATACATTCT
* * * * *
5444494 AAATATTATGCTTAAATACTCAAAGTCACCAAGTCCAA-TT-CAAAAAAT----AATTAA-TT-C
66 AAACATTATGCTTAAACACTCAAAGTCATCAAGTCCAATTTAAAAAAAATAAAAAAATAATTTAC
* * * * * * * *
5444551 --ACCGCATCACACAAGTTTTATATCTTATAGCACAATTAAATTGAAAGTAATGAGTCCTCGTTT
131 TTGCCACATCACACAAGTATTATATCTTGTAGCATAATTAAATTAAAAGT-A--AGTTCTCATTT
* * **
5444614 ATTTACAATTCATCTTAACAATTTGTAGTTT-TCAATGATTGTAAT-GTGGGAATTCAAATTCAA
193 ATTTACATTTCATCTTAACAATTTGTAGTTTCT-AATGATTGT-ATCATGAAAATTCAAATTCAA
* * * * * * ** *
5444677 TTTGACATTTTATCTACGAGATTTTACTTTATTTGCGATTTATGTATTTATTTCGTTACGATAAT
256 ATTAACATTTCATCTACGAGATTTTACCTTATTTGCAATTTATGTAATTATTTTATTATGATAAT
* * * *
5444742 TATGTCAAATATATGTTACAAAACAGATATCATTGACTCAAATGACTAAATTCAAATTTTCTTAC
321 TATGTCAAGTACATGTCACAAAACAGATATCATTGACTCAAATGACTAAATTCAAACTTT-TTAC
* ** * *
5444807 TTTGAAATTATATTTTAATTGAAAAA-ACATGTAGATTATGCAAAGTACACATCAGATTATTAGG
385 TTT-AAATAATATTTTAA-AAAAAAATAAATGTATATTATGC-AAGTACACATCAGATTATTAGG
* * * *
5444871 TAAAGATAAATACTAAGTACGAATGTTAGACTTTAATTTTACAAGAAAATTTTGGATATATATTT
447 TAAAGATAAATACTAAGTACAAATGTT-GACTTTCACTTTATAAGAAAATTTTGGATATATATTT
* *
5444936 ACTATCTCTGATACAATAT
511 ACTATCT-AGATACGATAT
* * * * * * *
5444955 TTATAACAAAACACTAATTTAATAAACTGAATGT-CC-TACACAAAATTAAATCTAATACATTGT
1 TTATAACATAACAATAATTTAAGACACTGAATGTACCGCACACAAAAATAAATCTAATACATTCT
* *
5445018 AAACATTATGCTTAGACACTTAAAGTCATCAAGTCCAATTTAAAAAAAATAAAAAAATAATTTAC
66 AAACATTATGCTTAAACACTCAAAGTCATCAAGTCCAATTTAAAAAAAATAAAAAAATAATTTAC
*
5445083 TTGCCACATCACACAAGTATTATATCTTGTAGCATAATTAAATTAAAAGTAAGTTCTCATTTGTT
131 TTGCCACATCACACAAGTATTATATCTTGTAGCATAATTAAATTAAAAGTAAGTTCTCATTTATT
** * **
5445148 TATGTTTCATCTTAACAGTTTGTAGTTTCTAATGATCATATCATGAAAATTCAAATTCAAATTAA
196 TACATTTCATCTTAACAATTTGTAGTTTCTAATGATTGTATCATGAAAATTCAAATTCAAATTAA
* *
5445213 CATTTCATCTACAAGATTTTACCTTATTTGCAATTTGTGTAATTATTTTATTATGATAATTATGT
261 CATTTCATCTACGAGATTTTACCTTATTTGCAATTTATGTAATTATTTTATTATGATAATTATGT
* * * * * *
5445278 -AAGGTGCAGGTCACAAAACTGATATTATTGACTCAAATAACTAAATTCAAACATTTTACTTCTA
326 CAA-GTACATGTCACAAAACAGATATCATTGACTCAAATGACTAAATTCAAACTTTTTACTT-TA
* * * * *
5445342 AA-AATATTTTGACAAAAAAATATATGTATATTATGTCAAGTACACGTCAAATTATAAGGTAAAG
389 AATAATATTTT-AAAAAAAAATAAATGTATATTATG-CAAGTACACATCAGATTATTAGGTAAAG
* * * * * * *
5445406 ATAAATACCAAGTATAAATATTGAGCTTTCACTTTATAAGAAAATTTTAGATATGTATATATTAT
452 ATAAATACTAAGTACAAATGTTGA-CTTTCACTTTATAAGAAAATTTTGGATATATATTTACTAT
* *
5445471 CTAAGGTACGGTAT
516 CT-AGATACGATAT
* *
5445485 TTATAATATAACAGTAATTTAAGACACTGAATGTA
1 TTATAACATAACAATAATTTAAGACACTGAATGTA
5445520 ACATAAAAAC
Statistics
Matches: 889, Mismatches: 168, Indels: 83
0.78 0.15 0.07
Matches are distributed among these distances:
524 57 0.06
525 106 0.12
526 75 0.08
527 76 0.09
529 14 0.02
530 208 0.23
531 164 0.18
532 41 0.05
533 3 0.00
534 44 0.05
535 3 0.00
536 4 0.00
542 7 0.01
543 2 0.00
544 2 0.00
546 81 0.09
547 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (528 bp):
TTATAACATAACAATAATTTAAGACACTGAATGTACCGCACACAAAAATAAATCTAATACATTCT
AAACATTATGCTTAAACACTCAAAGTCATCAAGTCCAATTTAAAAAAAATAAAAAAATAATTTAC
TTGCCACATCACACAAGTATTATATCTTGTAGCATAATTAAATTAAAAGTAAGTTCTCATTTATT
TACATTTCATCTTAACAATTTGTAGTTTCTAATGATTGTATCATGAAAATTCAAATTCAAATTAA
CATTTCATCTACGAGATTTTACCTTATTTGCAATTTATGTAATTATTTTATTATGATAATTATGT
CAAGTACATGTCACAAAACAGATATCATTGACTCAAATGACTAAATTCAAACTTTTTACTTTAAA
TAATATTTTAAAAAAAAATAAATGTATATTATGCAAGTACACATCAGATTATTAGGTAAAGATAA
ATACTAAGTACAAATGTTGACTTTCACTTTATAAGAAAATTTTGGATATATATTTACTATCTAGA
TACGATAT
Found at i:5448556 original size:34 final size:34
Alignment explanation
Indices: 5448513--5448580 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
5448503 GAACTTTGAT
*
5448513 TACCAGCCAACAAAGACAACAAAATTATACAGTG
1 TACCAGCCAACAAAGAAAACAAAATTATACAGTG
*
5448547 TACCAGCCAACAAAGAAAACAAAATTATTCAGTG
1 TACCAGCCAACAAAGAAAACAAAATTATACAGTG
5448581 GAAATTCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (34 bp):
TACCAGCCAACAAAGAAAACAAAATTATACAGTG
Found at i:5459921 original size:21 final size:21
Alignment explanation
Indices: 5459890--5459937 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5459880 TATAATTTAT
* *
5459890 AATAAATTTTATTATATATATA
1 AATATATTTAATT-TATATATA
*
5459912 CATATATTTAATTTATATATA
1 AATATATTTAATTTATATATA
5459933 AATAT
1 AATAT
5459938 TAGTATAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATTTAATTTATATATA
Found at i:5462199 original size:19 final size:19
Alignment explanation
Indices: 5462171--5462207 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5462161 TAAGTGTCCA
5462171 ATGGACTTACCAACAAATC
1 ATGGACTTACCAACAAATC
*
5462190 ATGGATTTACCAACAAAT
1 ATGGACTTACCAACAAAT
5462208 AATGATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (19 bp):
ATGGACTTACCAACAAATC
Found at i:5470712 original size:35 final size:35
Alignment explanation
Indices: 5470635--5470712 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
5470625 CTTCGTATAG
* * * *
5470635 AATAACTAGAATAAGTGAAGCATTACTTCACGCAA
1 AATAATTAGAATAAGTGAAACACTACTTCACACAA
* * **
5470670 AACAATTAGAATAAGTGAAACACTATTTCACATGA
1 AATAATTAGAATAAGTGAAACACTACTTCACACAA
5470705 AATAATTA
1 AATAATTA
5470713 ATAAAAGTAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.26
Consensus pattern (35 bp):
AATAATTAGAATAAGTGAAACACTACTTCACACAA
Found at i:5470959 original size:29 final size:29
Alignment explanation
Indices: 5470933--5471025 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
5470923 TCGTATACTA
5470933 ATTCACATACA-CTTTCTTTTCTTATACCT
1 ATTCACATACAGC-TTCTTTTCTTATACCT
* * * *
5470962 ATTTACATACAGCTTCTTTTATTGTACTT
1 ATTCACATACAGCTTCTTTTCTTATACCT
* * * *
5470991 GA-TCACGTATAGTTTCTTCTCTTATACCT
1 -ATTCACATACAGCTTCTTTTCTTATACCT
*
5471020 TTTCAC
1 ATTCAC
5471026 GTATACATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.05, T:0.48
Consensus pattern (29 bp):
ATTCACATACAGCTTCTTTTCTTATACCT
Found at i:5477749 original size:6 final size:6
Alignment explanation
Indices: 5477740--5477791 Score: 68
Period size: 6 Copynumber: 8.0 Consensus size: 6
5477730 AACAAAAAAG
5477740 AAGAGA AAGAGAA AAGAAGA AAGAGA AAGAGA TAAGAAGA AAGAGA AAGAGA
1 AAGAGA AAGAG-A AAG-AGA AAGAGA AAGAGA -AAG-AGA AAGAGA AAGAGA
5477792 TGTAGAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
6 23 0.55
7 14 0.33
8 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (6 bp):
AAGAGA
Found at i:5477762 original size:14 final size:13
Alignment explanation
Indices: 5477740--5477791 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 13
5477730 AACAAAAAAG
5477740 AAGAGAAAGAGAA
1 AAGAGAAAGAGAA
5477753 AAGAAGAAAGAG-A
1 AAG-AGAAAGAGAA
5477766 AAGAGATAAGA-AGA
1 AAGAGA-AAGAGA-A
5477780 AAGAGAAAGAGA
1 AAGAGAAAGAGA
5477792 TGTAGAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.09
13 15 0.44
14 16 0.47
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (13 bp):
AAGAGAAAGAGAA
Found at i:5477801 original size:20 final size:20
Alignment explanation
Indices: 5477740--5477792 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
5477730 AACAAAAAAG
*
5477740 AAGAGAAAGAGAAAAGAAGA
1 AAGAGAAAGAGATAAGAAGA
5477760 AAGAGAAAGAGATAAGAAGA
1 AAGAGAAAGAGATAAGAAGA
5477780 AAGAGAAAGAGAT
1 AAGAGAAAGAGAT
5477793 GTAGAGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (20 bp):
AAGAGAAAGAGATAAGAAGA
Found at i:5477963 original size:15 final size:16
Alignment explanation
Indices: 5477943--5477981 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
5477933 CTCTTGATTA
5477943 AATATATATA-TATAT
1 AATATATATACTATAT
5477958 AATATAT-TACTATAT
1 AATATATATACTATAT
*
5477973 TATATATAT
1 AATATATAT
5477982 GAAATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.86
16 1 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AATATATATACTATAT
Found at i:5478884 original size:2 final size:2
Alignment explanation
Indices: 5478877--5478903 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5478867 AGACATTTTG
5478877 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5478904 TTACTAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5490250 original size:24 final size:24
Alignment explanation
Indices: 5490223--5490269 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5490213 TTATATCATT
*
5490223 GTAACGTG-ATTACAATGAGAGAAG
1 GTAA-GTGCATTACAATAAGAGAAG
*
5490247 GTAATTGCATTACAATAAGAGAA
1 GTAAGTGCATTACAATAAGAGAA
5490270 TGGAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (24 bp):
GTAAGTGCATTACAATAAGAGAAG
Found at i:5517502 original size:2 final size:2
Alignment explanation
Indices: 5517489--5517538 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
5517479 ATAAATTAAC
*
5517489 AT AT AC 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
5517531 AT AT AT AT
1 AT AT AT AT
5517539 CAATCTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5530061 original size:35 final size:35
Alignment explanation
Indices: 5530010--5530078 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
5530000 GAACAACCTG
*
5530010 AACAAGTGAAAAGCTACTTCACGCAGAATAACTAA
1 AACAAGTGAAAAGCTACTTCACGCAGAACAACTAA
**
5530045 AACAAGTGAAGCGCTACTTCACGCAGAACAACTA
1 AACAAGTGAAAAGCTACTTCACGCAGAACAACTA
5530079 GAATAAGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.45, C:0.23, G:0.16, T:0.16
Consensus pattern (35 bp):
AACAAGTGAAAAGCTACTTCACGCAGAACAACTAA
Found at i:5530097 original size:35 final size:35
Alignment explanation
Indices: 5530010--5530097 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
5530000 GAACAACCTG
* *
5530010 AACAAGTGAA-AAGCTACTTCACGCAGAATAACTAA
1 AACAAGTGAAGCA-CTACTTCACGCAGAACAACTAA
* *
5530045 AACAAGTGAAGCGCTACTTCACGCAGAACAACTAG
1 AACAAGTGAAGCACTACTTCACGCAGAACAACTAA
*
5530080 AATAAGT-AGAGCACTACT
1 AACAAGTGA-AGCACTACT
5530098 CCATATGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 1 0.02
35 44 0.98
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (35 bp):
AACAAGTGAAGCACTACTTCACGCAGAACAACTAA
Found at i:5530373 original size:29 final size:29
Alignment explanation
Indices: 5530341--5530399 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
5530331 CCTATTCTCA
5530341 TACAACTTCTTCTCTTATA-CTTGTTCACG
1 TACAACTTCTTCTCTTATATCTT-TTCACG
** *
5530370 TACAGTTTCTTCTTTTATATCTTTTCACG
1 TACAACTTCTTCTCTTATATCTTTTCACG
5530399 T
1 T
5530400 GTACCTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.19, C:0.24, G:0.07, T:0.51
Consensus pattern (29 bp):
TACAACTTCTTCTCTTATATCTTTTCACG
Found at i:5533638 original size:16 final size:16
Alignment explanation
Indices: 5533617--5533660 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 16
5533607 GAACTCCATG
5533617 TTCTTTTTTCTCTTTC
1 TTCTTTTTTCTCTTTC
5533633 TTCTTTTTT-TCTTTC
1 TTCTTTTTTCTCTTTC
*
5533648 TTTTTTTTTCTCT
1 TTCTTTTTTCTCT
5533661 CCTTGCTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTTTCTCTTTC
Found at i:5533645 original size:15 final size:15
Alignment explanation
Indices: 5533617--5533658 Score: 68
Period size: 14 Copynumber: 2.8 Consensus size: 15
5533607 GAACTCCATG
5533617 TTCTTTTTTCTCTTTC
1 TTCTTTTTT-TCTTTC
5533633 TTCTTTTTTTCTTTC
1 TTCTTTTTTTCTTTC
5533648 TT-TTTTTTTCT
1 TTCTTTTTTTCT
5533659 CTCCTTGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 9 0.35
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTCTTTTTTTCTTTC
Found at i:5534868 original size:2 final size:2
Alignment explanation
Indices: 5534861--5534890 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5534851 ATGATAATGG
5534861 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
5534891 CAATTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5558699 original size:22 final size:22
Alignment explanation
Indices: 5558671--5558725 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
5558661 CACCGTAGTG
*
5558671 GCCAGATCTGGCCACATGGTGT
1 GCCAGATCTGGCCACATGCTGT
*
5558693 GCCAGATCTGGCCATATGCTGT
1 GCCAGATCTGGCCACATGCTGT
5558715 GCCAGAT-TGGC
1 GCCAGATCTGGC
5558726 GTTTTGTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (22 bp):
GCCAGATCTGGCCACATGCTGT
Found at i:5558919 original size:15 final size:15
Alignment explanation
Indices: 5558890--5558923 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5558880 AATTATAAAA
*
5558890 TAAAATATTATTAAT
1 TAAAATATTAGTAAT
5558905 TAAAATATTAGTAAT
1 TAAAATATTAGTAAT
5558920 TAAA
1 TAAA
5558924 TTATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATATTAGTAAT
Found at i:5558935 original size:25 final size:25
Alignment explanation
Indices: 5558899--5558952 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5558889 ATAAAATATT
5558899 ATTA-ATTAAAATATT-AGTAATTAA
1 ATTATATTAAAATATTGA-TAATTAA
*
5558923 ATTATATTAAAATATTGATATTTAA
1 ATTATATTAAAATATTGATAATTAA
5558948 ATTAT
1 ATTAT
5558953 TAATTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 22 0.81
26 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
ATTATATTAAAATATTGATAATTAA
Found at i:5558962 original size:15 final size:15
Alignment explanation
Indices: 5558850--5558989 Score: 52
Period size: 15 Copynumber: 9.6 Consensus size: 15
5558840 TAATTTAAAC
5558850 ATTATTAA-TATTAA
1 ATTATTAATTATTAA
* *
5558864 TATGATTAAAATATTAA
1 -ATTATT-AATTATTAA
*
5558881 ATTA-TAA--AATAA
1 ATTATTAATTATTAA
*
5558893 AATATT-ATTAATTAA
1 ATTATTAATT-ATTAA
* * *
5558908 AATATTAGTAATTAA
1 ATTATTAATTATTAA
5558923 ATTA-T-ATTA--AA
1 ATTATTAATTATTAA
*
5558934 A-TATTGA-TATTTAA
1 ATTATTAATTA-TTAA
5558948 ATTATTAATTATTAA
1 ATTATTAATTATTAA
5558963 TATT-TTAATTAATTATAA
1 -ATTATTAATT-A-T-TAA
5558981 ATTATTAAT
1 ATTATTAAT
5558990 ATTTAAAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 35
0.67 0.08 0.25
Matches are distributed among these distances:
10 2 0.02
11 6 0.06
12 9 0.09
13 3 0.03
14 6 0.06
15 39 0.41
16 12 0.13
17 10 0.11
18 8 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
ATTATTAATTATTAA
Found at i:5558962 original size:40 final size:41
Alignment explanation
Indices: 5558875--5558962 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 41
5558865 ATGATTAAAA
*
5558875 TATTAAATTATAAAATAAAATATTATTAATTAAAATATTAGT
1 TATTAAATTAT-AAATAAAATATTATTAATTAAAATATTAAT
* * * *
5558917 AATTAAATTAT-ATTAAAATATTGA-TATTTAAATTATTAAT
1 TATTAAATTATAAATAAAATATT-ATTAATTAAAATATTAAT
5558957 TATTAA
1 TATTAA
5558963 TATTTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 28 0.72
41 1 0.03
42 10 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (41 bp):
TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
Found at i:5559006 original size:26 final size:26
Alignment explanation
Indices: 5558954--5559008 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5558944 TTAAATTATT
** *
5558954 AATTATTAATATTTTAATTAATTATA
1 AATTATTAATATTTTAAAAAATAATA
5558980 AATTATTAATA-TTTAAAAAATAAATA
1 AATTATTAATATTTTAAAAAAT-AATA
5559006 AAT
1 AAT
5559009 AATAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATTATTAATATTTTAAAAAATAATA
Found at i:5563048 original size:14 final size:14
Alignment explanation
Indices: 5562994--5563050 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 14
5562984 TTTTAGAAAT
*
5562994 TTTTTATAAAATATA
1 TTTTTATTAAATA-A
5563009 TATTTT-TT-AATAA
1 T-TTTTATTAAATAA
5563022 TTTCTTA--AAATAA
1 TTT-TTATTAAATAA
5563035 TTTTTATTAAATAA
1 TTTTTATTAAATAA
5563049 TT
1 TT
5563051 AATATAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
12 5 0.14
13 12 0.34
14 12 0.34
15 2 0.06
16 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTATTAAATAA
Found at i:5563413 original size:15 final size:16
Alignment explanation
Indices: 5563393--5563422 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5563383 CTGTTATGCA
5563393 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
5563408 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
5563423 AAAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:5593318 original size:25 final size:25
Alignment explanation
Indices: 5593276--5593325 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5593266 TTTAAGCCCT
*
5593276 ATCTGCAATTAAAGATTAGATTAAG
1 ATCTGCAATTAAAGATTAGAGTAAG
*
5593301 ATCTGCACTTCAAA-ATTAGAGTAAG
1 ATCTGCAATT-AAAGATTAGAGTAAG
5593326 CATTTATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (25 bp):
ATCTGCAATTAAAGATTAGAGTAAG
Found at i:5604996 original size:2 final size:2
Alignment explanation
Indices: 5604989--5605033 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5604979 AATAGTCATC
*
5604989 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5605031 TA T
1 TA T
5605034 TAGTTGAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5617812 original size:20 final size:20
Alignment explanation
Indices: 5617787--5617824 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5617777 GAAATTGGCA
5617787 AATTGCTGAATTTAGTTTGG
1 AATTGCTGAATTTAGTTTGG
*
5617807 AATTGCTGATTTTAGTTT
1 AATTGCTGAATTTAGTTT
5617825 AAGTATTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (20 bp):
AATTGCTGAATTTAGTTTGG
Found at i:5633039 original size:13 final size:12
Alignment explanation
Indices: 5632996--5633049 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
5632986 AAGGTTTAAG
*
5632996 TTTTAATTAATA
1 TTTTAATTAAAA
5633008 TTTTAAACTTAAAA
1 TTTT-AA-TTAAAA
* *
5633022 ATTAAATTAAAA
1 TTTTAATTAAAA
5633034 TTTTAATTATAAA
1 TTTTAATTA-AAA
5633047 TTT
1 TTT
5633050 ATTTATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 17 0.50
13 10 0.29
14 7 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTTAATTAAAA
Found at i:5633726 original size:21 final size:21
Alignment explanation
Indices: 5633697--5633776 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
5633687 TCCAACTTTC
*
5633697 AATAAAATATTAATATTTTAA
1 AATATAATATTAATATTTTAA
*
5633718 AATATAATATTAAAATTATT-A
1 AATATAATATTAATATT-TTAA
*
5633739 AATACACATATTAATA-TTTAA
1 AATATA-ATATTAATATTTTAA
*
5633760 ATTATCAATTATTAATA
1 AATAT-AA-TATTAATA
5633777 AAAAAAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.04
21 27 0.56
22 19 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATAATATTAATATTTTAA
Found at i:5633727 original size:15 final size:16
Alignment explanation
Indices: 5633699--5633728 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5633689 CAACTTTCAA
5633699 TAAAATATTAATATTT
1 TAAAATATTAATATTT
5633715 TAAAATA-TAATATT
1 TAAAATATTAATATT
5633729 AAAATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:5633822 original size:16 final size:16
Alignment explanation
Indices: 5633801--5633832 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5633791 TTATTCCTAT
5633801 TTAAAAACAAAATAAA
1 TTAAAAACAAAATAAA
*
5633817 TTAAAAATAAAATAAA
1 TTAAAAACAAAATAAA
5633833 ATAATATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
TTAAAAACAAAATAAA
Found at i:5633873 original size:113 final size:106
Alignment explanation
Indices: 5633735--5634001 Score: 277
Period size: 113 Copynumber: 2.4 Consensus size: 106
5633725 TATTAAAATT
* * **
5633735 ATTAAATACACATATTAATATTTAAATTATCAATTATTAATA-AAAAAAATTATAAATTATTCCT
1 ATTAAATA-AAATATTAATATTTAAATTATCAATTATTAATATAAAAAAATTACAAATTATTAAT
*
5633799 ATTTAAAAACAAAATAAATTAAAAATAAAAT-AAAATAATATCATTTAA
65 ATTT-AAAA-AAAA-AAATAAAAAAT-AAATCAAAATAA-A--ATTTAA
* * * * *
5633847 ATTAGATAAACAATATTAATAATTAAATCATCAATTATTAATATTTAAATAAATTACCAATTATT
1 ATTAAAT-AA-AATATTAATATTTAAATTATCAATTATTAATA--TAAAAAAATTACAAATTATT
* * *
5633912 AATATTTAAAAAATAAAATAAAAAATTAATCATAATAAAATTTAA
62 AATATTTAAAAAAAAAAATAAAAAATAAATCAAAATAAAATTTAA
* *
5633957 ATTAAATAAAATATTAATATTTAAATTATCTATTATTAANATAAA
1 ATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATAAA
5634002 TTAATTTTTG
Statistics
Matches: 131, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
106 4 0.03
108 28 0.21
109 2 0.02
110 12 0.09
112 11 0.08
113 46 0.35
114 3 0.02
115 4 0.03
116 21 0.16
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.37
Consensus pattern (106 bp):
ATTAAATAAAATATTAATATTTAAATTATCAATTATTAATATAAAAAAATTACAAATTATTAATA
TTTAAAAAAAAAAATAAAAAATAAATCAAAATAAAATTTAA
Found at i:5633899 original size:26 final size:26
Alignment explanation
Indices: 5633870--5633925 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
5633860 TATTAATAAT
*
5633870 TAAATCATCAATTATTAATATTTAAA
1 TAAATCACCAATTATTAATATTTAAA
*
5633896 TAAATTACCAATTATTAATATTTAAA
1 TAAATCACCAATTATTAATATTTAAA
5633922 -AAAT
1 TAAAT
5633926 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAATCACCAATTATTAATATTTAAA
Found at i:5633902 original size:19 final size:21
Alignment explanation
Indices: 5633856--5633896 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5633846 AATTAGATAA
5633856 ACAA-TATTAATAATTAAATC
1 ACAATTATTAATAATTAAATC
*
5633876 ATCAATTATTAATATTTAAAT
1 A-CAATTATTAATAATTAAAT
5633897 AAATTACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 3 0.17
22 14 0.78
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
ACAATTATTAATAATTAAATC
Found at i:5634167 original size:23 final size:23
Alignment explanation
Indices: 5634137--5634197 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
5634127 TTAATCATAA
5634137 TAATATTTAAATTAAAAAAATAT
1 TAATATTTAAATTAAAAAAATAT
** *
5634160 TAATATTTAAATT-ATTAATTAT
1 TAATATTTAAATTAAAAAAATAT
*
5634182 TAATATTTTAATTAAA
1 TAATATTTAAATTAAA
5634198 TTCTAGATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATATTTAAATTAAAAAAATAT
Found at i:5634184 original size:15 final size:17
Alignment explanation
Indices: 5634157--5634195 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5634147 ATTAAAAAAA
5634157 TATTAA-TATTTAA-AT
1 TATTAATTATTTAATAT
5634172 TATTAATTA-TTAATAT
1 TATTAATTATTTAATAT
5634188 T-TTAATTA
1 TATTAATTA
5634196 AATTCTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAATTATTTAATAT
Found at i:5634195 original size:45 final size:43
Alignment explanation
Indices: 5634078--5634197 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 43
5634068 ATTGATATTT
*
5634078 TAAATAAATTATCAATTATTAATATTTT--TT-AAAAAATAAA
1 TAAATAAATTATTAATTATTAATATTTTAATTAAAAAAATAAA
* *
5634118 TAAATAAA--ATTAATCATAATAATATTTAAATTAAAAAAATATTAA
1 TAAATAAATTATTAAT--TATTAATATTTTAATTAAAAAAATA--AA
**
5634163 TATTTAAATTATTAATTATTAATATTTTAATTAAA
1 TAAATAAATTATTAATTATTAATATTTTAATTAAA
5634198 TTCTAGATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
38 5 0.08
40 18 0.28
42 2 0.03
43 8 0.12
45 25 0.39
47 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (43 bp):
TAAATAAATTATTAATTATTAATATTTTAATTAAAAAAATAAA
Found at i:5634226 original size:24 final size:26
Alignment explanation
Indices: 5634177--5634226 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
5634167 TAAATTATTA
*
5634177 ATTATTAATATTTTAATTAAATTCTAG
1 ATTATTAATATTTTAA-TAAAATCTAG
5634204 ATTATTAAT-TTTTAA-AAAATCTA
1 ATTATTAATATTTTAATAAAATCTA
5634227 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
26 6 0.27
27 9 0.41
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
ATTATTAATATTTTAATAAAATCTAG
Found at i:5634235 original size:112 final size:113
Alignment explanation
Indices: 5634015--5634239 Score: 259
Period size: 112 Copynumber: 2.0 Consensus size: 113
5634005 ATTTTTGACA
*
5634015 AATCTAATAAATTAAATTATAAATAAATAATCATAATATTGAAATGATCAATTATTGATATTTTA
1 AATCTAATAAATTAAATTATAAATAAATAAT-ATAATATTGAAATGATCAATTATTAATATTTTA
*
5634080 AATAAATTATCAATTATTAATATTTTTTAAAAAATAAATAAATAAAATT
65 AATAAATTATCAATTATTAATATTTTTTAAAAAATAAAAAAATAAAATT
* * *
5634129 AATCATAATAATATTTAAATTA-AAA-AAAT-AT-TAATATTTAAATTATTAATTATTAATATTT
1 AATC-TAATAA-A-TTAAATTATAAATAAATAATATAATATTGAAATGATCAATTATTAATATTT
* *
5634190 TAATTAAATTCT-AGATTATT-A-A-TTTTTAAAAAATCTAATAAAAATAAAAT
63 TAAATAAATTATCA-ATTATTAATATTTTTTAAAAAA--TAA-AAAAATAAAAT
5634240 GTCATATAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
109 11 0.11
110 1 0.01
111 5 0.05
112 52 0.54
114 6 0.06
115 10 0.10
116 4 0.04
117 8 0.08
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (113 bp):
AATCTAATAAATTAAATTATAAATAAATAATATAATATTGAAATGATCAATTATTAATATTTTAA
ATAAATTATCAATTATTAATATTTTTTAAAAAATAAAAAAATAAAATT
Found at i:5643222 original size:104 final size:104
Alignment explanation
Indices: 5643042--5643244 Score: 318
Period size: 104 Copynumber: 2.0 Consensus size: 104
5643032 ACATTCAGGC
* * *
5643042 ATCTCCGGATTGTACAACAACATACACTCATTCAGGCTTCAGTTATAATTGAAATACTGCCCAAA
1 ATCTCCGGATTGTACAACAACATACACTCACTCAGGCTTCAGTTATAATAGAAACACTGCCCAAA
*
5643107 TAAAAGTTAGCAGATCCTAAAATGTGAATCTTTGGAAGT
66 TAAAAGTTAGCAGATCCTAAAATGCGAATCTTTGGAAGT
* *
5643146 ATCTCCGGATTGTACAACAGCATACACTTACTCAGGCTTCAGTTATAATAGAAACACTG-CCAAA
1 ATCTCCGGATTGTACAACAACATACACTCACTCAGGCTTCAGTTATAATAGAAACACTGCCCAAA
* *
5643210 CTAAAAGTTAGCAGATCTTAAAATGCGAATGTTTG
66 -TAAAAGTTAGCAGATCCTAAAATGCGAATCTTTG
5643245 AATTACTTCC
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
103 5 0.06
104 85 0.94
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (104 bp):
ATCTCCGGATTGTACAACAACATACACTCACTCAGGCTTCAGTTATAATAGAAACACTGCCCAAA
TAAAAGTTAGCAGATCCTAAAATGCGAATCTTTGGAAGT
Found at i:5653541 original size:2 final size:2
Alignment explanation
Indices: 5653534--5653561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5653524 AATAACTAGA
5653534 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
5653562 TTATTTATTT
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:5656513 original size:18 final size:19
Alignment explanation
Indices: 5656492--5656530 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5656482 TCATATTTAT
5656492 TTAATTTAAA-ATATAATA
1 TTAATTTAAATATATAATA
*
5656510 TTAATTTAAATATATCATA
1 TTAATTTAAATATATAATA
5656529 TT
1 TT
5656531 TTAATTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATTTAAATATATAATA
Found at i:5657584 original size:3 final size:3
Alignment explanation
Indices: 5657576--5657602 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5657566 TATTGATATA
5657576 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
5657603 AAGAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5666924 original size:30 final size:30
Alignment explanation
Indices: 5666890--5666978 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 30
5666880 TGAGGTTGCT
* * *
5666890 GGAGGAGGAGTTGCCGGTGGGGGAGTAGCA
1 GGAGGAGGAGTAGCAGGTGGGGGAGAAGCA
* * *
5666920 GGAGGAGGAGAAGCAGGTGGTGGAGAAGCC
1 GGAGGAGGAGTAGCAGGTGGGGGAGAAGCA
* * * *
5666950 GGTGGAGGAGTGGCGGGAGGGGGAGAAGC
1 GGAGGAGGAGTAGCAGGTGGGGGAGAAGC
5666979 CGGTGGTGGA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.09, G:0.58, T:0.09
Consensus pattern (30 bp):
GGAGGAGGAGTAGCAGGTGGGGGAGAAGCA
Found at i:5666953 original size:45 final size:44
Alignment explanation
Indices: 5666902--5667037 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 44
5666892 AGGAGGAGTT
5666902 GCCGGTGGGGGAGTAGCAGGAGGAGGAGAAGCAGGTGGTGGAGAA
1 GCCGGTGGGGGAGTAGCAGGAGGAGGAGAAGCAGGTGGTGGAG-A
* * * * *
5666947 GCCGGTGGAGGAGTGGCGGGAGGGGGAGAAGCCGGTGGTGGAGA
1 GCCGGTGGGGGAGTAGCAGGAGGAGGAGAAGCAGGTGGTGGAGA
* * *
5666991 GCTAACGGGTGGGGGAGTTGCTGGAGGAGGAG-AGCTAGGTGGAGGAG
1 GC---C-GGTGGGGGAGTAGCAGGAGGAGGAGAAGC-AGGTGGTGGAG
5667038 TTGAAACTGG
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
44 3 0.04
45 38 0.51
47 4 0.05
48 30 0.40
ACGTcount: A:0.22, C:0.10, G:0.57, T:0.11
Consensus pattern (44 bp):
GCCGGTGGGGGAGTAGCAGGAGGAGGAGAAGCAGGTGGTGGAGA
Found at i:5666989 original size:15 final size:15
Alignment explanation
Indices: 5666902--5666990 Score: 70
Period size: 15 Copynumber: 5.9 Consensus size: 15
5666892 AGGAGGAGTT
* *
5666902 GCCGGTGGGGGAGTA
1 GCCGGTGGAGGAGAA
* *
5666917 GCAGGAGGAGGAGAA
1 GCCGGTGGAGGAGAA
* *
5666932 GCAGGTGGTGGAGAA
1 GCCGGTGGAGGAGAA
**
5666947 GCCGGTGGAGGAGTG
1 GCCGGTGGAGGAGAA
* * *
5666962 GCGGGAGGGGGAGAA
1 GCCGGTGGAGGAGAA
*
5666977 GCCGGTGGTGGAGA
1 GCCGGTGGAGGAGA
5666991 GCTAACGGGT
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 56 1.00
ACGTcount: A:0.22, C:0.10, G:0.58, T:0.09
Consensus pattern (15 bp):
GCCGGTGGAGGAGAA
Found at i:5667056 original size:33 final size:32
Alignment explanation
Indices: 5666980--5667056 Score: 77
Period size: 33 Copynumber: 2.3 Consensus size: 32
5666970 GGGAGAAGCC
*
5666980 GGTGGTGGAGAGCTAACGGGTGGGGGAGTTGCT
1 GGTGGTGGAGAGCTAAC-GGTGGAGGAGTTGCT
* *
5667013 GGAGGAGGAGAGCT-A-GGTGGAGGAGTTGAAACT
1 GGTGGTGGAGAGCTAACGGTGGAGGAGTTG---CT
5667046 GGTGGTGGAGA
1 GGTGGTGGAGA
5667057 AGCCGTCACT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
30 12 0.33
32 1 0.03
33 23 0.64
ACGTcount: A:0.22, C:0.06, G:0.53, T:0.18
Consensus pattern (32 bp):
GGTGGTGGAGAGCTAACGGTGGAGGAGTTGCT
Found at i:5668649 original size:2 final size:2
Alignment explanation
Indices: 5668591--5668630 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5668581 TATTACTACA
5668591 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
5668631 TCTTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5668778 original size:42 final size:40
Alignment explanation
Indices: 5668719--5668805 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 40
5668709 AATACACTAG
*
5668719 TGATTTAAGTAAGTACTT-ACCTTCATTATTTTGCTTCCCTAC
1 TGATTTAAGTAAGTACTTCA-CTTCATTA-TATGCTT-CCTAC
*
5668761 TGATTTAAGTAAGTACTTCATTTCATTATATGCTTCCTAC
1 TGATTTAAGTAAGTACTTCACTTCATTATATGCTTCCTAC
5668801 TGATT
1 TGATT
5668806 ATTTCCTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.24
41 6 0.14
42 25 0.60
43 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.46
Consensus pattern (40 bp):
TGATTTAAGTAAGTACTTCACTTCATTATATGCTTCCTAC
Found at i:5681228 original size:25 final size:26
Alignment explanation
Indices: 5681200--5681266 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
5681190 TTAAGAATTT
*
5681200 ATTTAATTTAAAATAAAAATATAA-A
1 ATTTAATTTAAAATAAAAAAATAATA
*
5681225 ATTTAATTTAACATAATAAAAAAATAATG
1 ATTTAATTT-A-A-AATAAAAAAATAATA
5681254 ATTT-ATTTAAAAT
1 ATTTAATTTAAAAT
5681267 TTTTAAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 12 0.33
26 2 0.06
27 2 0.06
28 16 0.44
29 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (26 bp):
ATTTAATTTAAAATAAAAAAATAATA
Found at i:5692844 original size:29 final size:29
Alignment explanation
Indices: 5692799--5692891 Score: 132
Period size: 29 Copynumber: 3.2 Consensus size: 29
5692789 GTACATGAGC
* * *
5692799 ACAAGAGAGGAAACTGTATGTGAATAGGT
1 ACAAGAAAAGAAACTGTACGTGAATAGGT
* *
5692828 ACAAGAAAAGAAGCTGTACATGAATAGGT
1 ACAAGAAAAGAAACTGTACGTGAATAGGT
*
5692857 ACAAAAAAAGAAACTGTACGTGAATAGGT
1 ACAAGAAAAGAAACTGTACGTGAATAGGT
5692886 ACAAGA
1 ACAAGA
5692892 GAACAAAGTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (29 bp):
ACAAGAAAAGAAACTGTACGTGAATAGGT
Found at i:5694130 original size:272 final size:268
Alignment explanation
Indices: 5693590--5694128 Score: 1035
Period size: 272 Copynumber: 2.0 Consensus size: 268
5693580 TTTGCAAATC
5693590 TTTTTGAGCAAGTAAGTTCTTTTTTTTTTTAAATAGAATTTCTTGTTTGATTTTTTTTACTTGTA
1 TTTTTGAGCAAGTAAGTTCTTTTTTTTTTTAAATAGAATTTCTTGTTTGATTTTTTTTACTTGTA
5693655 TTTTTCTTTTTTTTTCAAAAAAATTTGAATTCTCTTGCTTGTTGCTGCCTGCATGAAATTTTTTT
66 TTTTTCTTTTTTTTTCAAAAAAATTTGAATTCTCTTGCTTGTTGCTGCCTGCATGAAATTTTTTT
5693720 TAATTGAAATATGAAGAAAAAAATTTCATACATGAGATGATGCTTCTTTTTTTTATGTGTGTGTT
131 TAATTGAAATATGAAGAAAAAAATTTCATACATGAGATGATGCTTCTTTTTTTTA-GTGTGTGTT
5693785 CAAACAAATAAATAAATTATTTGATTTTAAAATAAAATCACAAAGCAAGAATATTTGTGTTCAAA
195 CAAACAAATAAATAAATTATTTGATTTTAAAATAAAATCACAAAGCAAGAATATTTGTGTTCAAA
5693850 AAAAAAAAA
260 AAAAAAAAA
5693859 NTTTTTGAGCAAGTAAGTTCTTTTTTTTTTTTTAAATAGAATTTCTTGTTTGATTTTTTTTACTT
1 -TTTTTGAGCAAGTAAGTTC--TTTTTTTTTTTAAATAGAATTTCTTGTTTGATTTTTTTTACTT
5693924 GTATTTTTCTTTTTTTTTCAAAAAAATTTGAATTCTCTTGCTTGTTGCTGCCTGCATGAAATTTT
63 GTATTTTTCTTTTTTTTTCAAAAAAATTTGAATTCTCTTGCTTGTTGCTGCCTGCATGAAATTTT
5693989 TTTTAATTGAAATATGAAGAAAAAAATTTCATACATGAGATGATGCTTCTTTTTTTTA-TGTGTG
128 TTTTAATTGAAATATGAAGAAAAAAATTTCATACATGAGATGATGCTTCTTTTTTTTAGTGTGTG
5694053 TTCAAACAAATAAATAAATTATTTGATTTTAAAATAAAATCACAAAGCAAGAATATTTGTGTTCA
193 TTCAAACAAATAAATAAATTATTTGATTTTAAAATAAAATCACAAAGCAAGAATATTTGTGTTCA
5694118 AAAAAAAAAAA
258 AAAAAAAAAAA
5694129 AAAACTAACT
Statistics
Matches: 267, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
270 101 0.38
272 166 0.62
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (268 bp):
TTTTTGAGCAAGTAAGTTCTTTTTTTTTTTAAATAGAATTTCTTGTTTGATTTTTTTTACTTGTA
TTTTTCTTTTTTTTTCAAAAAAATTTGAATTCTCTTGCTTGTTGCTGCCTGCATGAAATTTTTTT
TAATTGAAATATGAAGAAAAAAATTTCATACATGAGATGATGCTTCTTTTTTTTAGTGTGTGTTC
AAACAAATAAATAAATTATTTGATTTTAAAATAAAATCACAAAGCAAGAATATTTGTGTTCAAAA
AAAAAAAA
Found at i:5694672 original size:144 final size:137
Alignment explanation
Indices: 5694432--5694711 Score: 357
Period size: 144 Copynumber: 2.0 Consensus size: 137
5694422 ACAGAAGTAA
* * ** *
5694432 ATAAAGGCTGAAGTAAAAGAAGCAAATAAAGGTTGATTAACTTGTCTATTTTTTTTCTCTGACTT
1 ATAAAGGCTGAAGAAAAAGAAGCAAATAAAGCTTGACAAACTTGTCAATTTTTTTTCTCTGACTT
* * *
5694497 GTTGGCAGCAAAGCTGCAAGTTGCAGTTTTTTTGTTTTTTTTGCTTGTATAAAGAAAATGGCTTT
66 GTTGGCAGCAAAGCTGCAAGTTGCAG----TTT-TTTTTATT--TTATATAAAGAAAAGGGCTTT
5694562 TTACTTTGGAGCTC
124 TTACTTTGGAGCTC
* *
5694576 ATAAAGGCTGAAGAAAAAGTAA-CAAATAAAGCTTGACAAACTTGTCAAATTTTTTTTCTTTGAT
1 ATAAAGGCTGAAGAAAAAG-AAGCAAATAAAGCTTGACAAACTTGTC-AATTTTTTTTCTCTGAC
*
5694640 TTGTTGGCAGCAAAAGCTGTAAGTTGCA-TTTTTTTTATTTTATATAAAGAAAAGGGCTTTTTAC
64 TTGTTGGCAGC-AAAGCTGCAAGTTGCAGTTTTTTTTATTTTATATAAAGAAAAGGGCTTTTTAC
5694704 TTTGGAGC
128 TTTGGAGC
5694712 CGCAAGCTCT
Statistics
Matches: 122, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
138 31 0.25
140 7 0.06
141 3 0.02
144 39 0.32
145 27 0.22
146 15 0.12
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (137 bp):
ATAAAGGCTGAAGAAAAAGAAGCAAATAAAGCTTGACAAACTTGTCAATTTTTTTTCTCTGACTT
GTTGGCAGCAAAGCTGCAAGTTGCAGTTTTTTTTATTTTATATAAAGAAAAGGGCTTTTTACTTT
GGAGCTC
Found at i:5696926 original size:18 final size:18
Alignment explanation
Indices: 5696905--5696958 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
5696895 TTCTATATTT
*
5696905 TTTTATTTCCTCATTTTG
1 TTTTATTTTCTCATTTTG
* *
5696923 TTTT-TTTTCT-A-TATA
1 TTTTATTTTCTCATTTTG
5696938 TTTTATTTTCTCATTTTG
1 TTTTATTTTCTCATTTTG
5696956 TTT
1 TTT
5696959 GTTTTCTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.21
16 7 0.25
17 6 0.21
18 9 0.32
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTATTTTCTCATTTTG
Found at i:5696951 original size:33 final size:34
Alignment explanation
Indices: 5696888--5696965 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 34
5696878 AAGTTTATCT
*
5696888 TTTTTTGTTCTATATTTTTTTATTTCCTCATTTTG
1 TTTTTT-TTCTATATTATTTTATTTCCTCATTTTG
*
5696923 TTTTTTTTCTATA-TATTTTATTTTCTCATTTTG
1 TTTTTTTTCTATATTATTTTATTTCCTCATTTTG
*
5696956 TTTGTTTTCT
1 TTTTTTTTCT
5696966 TTTTTAGGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 27 0.68
34 7 0.17
35 6 0.15
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.73
Consensus pattern (34 bp):
TTTTTTTTCTATATTATTTTATTTCCTCATTTTG
Found at i:5696963 original size:17 final size:16
Alignment explanation
Indices: 5696901--5696965 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
5696891 TTTGTTCTAT
*
5696901 ATTTTTTTATTTCCTC
1 ATTTTTTTATTTTCTC
*
5696917 ATTTTGTTTTTTTTCT-
1 ATTTT-TTTATTTTCTC
*
5696933 ATATATTTTATTTTCTC
1 AT-TTTTTTATTTTCTC
*
5696950 ATTTTGTTTGTTTTCT
1 ATTTT-TTTATTTTCT
5696966 TTTTTAGGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
16 18 0.46
17 21 0.54
ACGTcount: A:0.12, C:0.11, G:0.05, T:0.72
Consensus pattern (16 bp):
ATTTTTTTATTTTCTC
Found at i:5703927 original size:29 final size:29
Alignment explanation
Indices: 5703852--5703967 Score: 146
Period size: 29 Copynumber: 4.0 Consensus size: 29
5703842 GAGCTAATAA
*
5703852 AGAAG-AGCTATACATGAGTAGGTACAAG
1 AGAAGAAGCTATACATGAATAGGTACAAG
* * * *
5703880 AGAGGAAACTGTACGTGAATAAGG-ACAAG
1 AGAAGAAGCTATACATGAAT-AGGTACAAG
5703909 AGAAGAAGCTATACATGAATAGGTACAAG
1 AGAAGAAGCTATACATGAATAGGTACAAG
* *
5703938 AGAAGAAGCTGTACGTGAATAGGTACAAG
1 AGAAGAAGCTATACATGAATAGGTACAAG
5703967 A
1 A
5703968 TAACAAGGTA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.09
29 64 0.86
30 3 0.04
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.16
Consensus pattern (29 bp):
AGAAGAAGCTATACATGAATAGGTACAAG
Found at i:5703950 original size:58 final size:57
Alignment explanation
Indices: 5703852--5703967 Score: 180
Period size: 58 Copynumber: 2.0 Consensus size: 57
5703842 GAGCTAATAA
* *
5703852 AGAAGAGCTATACATGAGTAGGTACAAGAGAGGAAACTGTACGTGAATAAGG-ACAAG
1 AGAAGAGCTATACATGAATAGGTACAAGAGAAGAAACTGTACGTGAAT-AGGTACAAG
*
5703909 AGAAGAAGCTATACATGAATAGGTACAAGAGAAGAAGCTGTACGTGAATAGGTACAAG
1 AGAAG-AGCTATACATGAATAGGTACAAGAGAAGAAACTGTACGTGAATAGGTACAAG
5703967 A
1 A
5703968 TAACAAGGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 8 0.15
58 46 0.85
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.16
Consensus pattern (57 bp):
AGAAGAGCTATACATGAATAGGTACAAGAGAAGAAACTGTACGTGAATAGGTACAAG
Found at i:5706888 original size:10 final size:10
Alignment explanation
Indices: 5706873--5706908 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5706863 CCTAATGGTT
5706873 TTTTTATTTA
1 TTTTTATTTA
*
5706883 TTTTTATTGA
1 TTTTTATTTA
5706893 TTTTTATTGTA
1 TTTTTATT-TA
5706904 TTTTT
1 TTTTT
5706909 TTCTTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:5710595 original size:37 final size:37
Alignment explanation
Indices: 5710474--5710595 Score: 192
Period size: 37 Copynumber: 3.3 Consensus size: 37
5710464 TGATGATGGC
* * *
5710474 TGATGATGTTGAGGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGATGAAGTGTGCGAGTAAGGAGTGCACACA
5710511 TGATGATGATTG-AGTGTGCGAGTAAGGAGTGCACACA
1 TGATGATGA-TGAAGTGTGCGAGTAAGGAGTGCACACA
*
5710548 TGACGATGATGAAGTGTGCGAGTAAGGAGTGCACACA
1 TGATGATGATGAAGTGTGCGAGTAAGGAGTGCACACA
5710585 TGATGATGATG
1 TGATGATGATG
5710596 TATGTATATG
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
36 2 0.03
37 74 0.95
38 2 0.03
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.24
Consensus pattern (37 bp):
TGATGATGATGAAGTGTGCGAGTAAGGAGTGCACACA
Found at i:5711058 original size:22 final size:22
Alignment explanation
Indices: 5711030--5711080 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
5711020 TCAAGTGTCA
5711030 CTGCAGCAAAAACT-CATTCCCG
1 CTGCAGCAAAAA-TGCATTCCCG
* *
5711052 CTGCAGCAAGAATGCCTTCCCG
1 CTGCAGCAAAAATGCATTCCCG
5711074 CTGCAGC
1 CTGCAGC
5711081 GAGAACCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.25, C:0.37, G:0.20, T:0.18
Consensus pattern (22 bp):
CTGCAGCAAAAATGCATTCCCG
Done.