Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 54 of 322
Found at i:16960760 original size:20 final size:19
Alignment explanation
Indices: 16960737--16960795 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
16960727 TAATTTTATT
16960737 TTAATAGTTTTAATATTAAA
1 TTAATA-TTTTAATATTAAA
* * *
16960757 TTAAATATCTTGATAGTAAA
1 TT-AATATTTTAATATTAAA
* *
16960777 TTATTAATTTAATATTAAA
1 TTAATATTTTAATATTAAA
16960796 GTGATTACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 12 0.40
20 14 0.47
21 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAATATTTTAATATTAAA
Found at i:16965429 original size:15 final size:15
Alignment explanation
Indices: 16965409--16965441 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
16965399 ATTCTCTCAA
16965409 ATGGTATCATACTTT
1 ATGGTATCATACTTT
16965424 ATGGTATCATACTTT
1 ATGGTATCATACTTT
16965439 ATG
1 ATG
16965442 ATATGGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (15 bp):
ATGGTATCATACTTT
Found at i:16966476 original size:16 final size:17
Alignment explanation
Indices: 16966455--16966486 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
16966445 ACGATAATGA
16966455 TAAAAATAT-TTTATAT
1 TAAAAATATATTTATAT
16966471 TAAAAATATATTTATA
1 TAAAAATATATTTATA
16966487 AAAATGGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAAATATATTTATAT
Found at i:16966933 original size:72 final size:72
Alignment explanation
Indices: 16966816--16966958 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
16966806 CTTTCAAGTT
16966816 GGTCTCCCTAATGGGTAACAATTCTTCTTTTCTTTTCAAGCTTTATGAATTAATCTCTAAAACAT
1 GGTCTCCCTAATGGGTAACAATTCTTCTTTTCTTTTCAAGCTTTATGAATTAATCTCTAAAACAT
16966881 TAGAATC
66 TAGAATC
* * *
16966888 GGTCTCCCTAATTGGTAACAATTCTTCTTTTCTTTTCAAGCTTTATGGATTAATCTCTAGAACAT
1 GGTCTCCCTAATGGGTAACAATTCTTCTTTTCTTTTCAAGCTTTATGAATTAATCTCTAAAACAT
16966953 TAGAAT
66 TAGAAT
16966959 TGTGACTTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (72 bp):
GGTCTCCCTAATGGGTAACAATTCTTCTTTTCTTTTCAAGCTTTATGAATTAATCTCTAAAACAT
TAGAATC
Found at i:16967548 original size:106 final size:105
Alignment explanation
Indices: 16967423--16967634 Score: 379
Period size: 106 Copynumber: 2.0 Consensus size: 105
16967413 AACCAATATG
16967423 GAAAAAAAGTCAAACAAGTCAAGTTTAGCATTTAAATCCTTCTAGTCACTCAATGATTTAGAGCT
1 GAAAAAAAGTCAAACAAGTCAAGTTTAGCATTTAAATCCTTCTAGTCACTCAATGATTTAGAGCT
16967488 AAGATTACAAATTATCATCCAAATAATAGAGATAATATAA
66 AAGATTACAAATTATCATCCAAATAATAGAGATAATATAA
* * *
16967528 GAAAAAAATGTCAAATAAGTCAAGTTTAGCCTTTAAATCCTTCTAGTCATTCAATGATTTAGAGC
1 GAAAAAAA-GTCAAACAAGTCAAGTTTAGCATTTAAATCCTTCTAGTCACTCAATGATTTAGAGC
*
16967593 TAAGATTACAAATTATCATCCAAATGATAGAGATAATATAA
65 TAAGATTACAAATTATCATCCAAATAATAGAGATAATATAA
16967634 G
1 G
16967635 TAAAGCATAT
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
105 8 0.08
106 94 0.92
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (105 bp):
GAAAAAAAGTCAAACAAGTCAAGTTTAGCATTTAAATCCTTCTAGTCACTCAATGATTTAGAGCT
AAGATTACAAATTATCATCCAAATAATAGAGATAATATAA
Found at i:16971112 original size:79 final size:79
Alignment explanation
Indices: 16970981--16971211 Score: 354
Period size: 79 Copynumber: 2.9 Consensus size: 79
16970971 TCACATGCAC
16970981 GGTTATAAATCAGAATCAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
1 GGTTATAAATCAGAATCAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
16971046 AAAGTAACGTAGAG
66 AAAGTAACGTAGAG
* *
16971060 GGTTATAAATTAGAATTAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
1 GGTTATAAATCAGAATCAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
16971125 AAAGTAACGTAGAG
66 AAAGTAACGTAGAG
* * * ** * * * *
16971139 GGTTATAAATCAGAATCAATAATAATCAATCTAACATAATCATATATCACATATTCTTTATCAAC
1 GGTTATAAATCAGAATCAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
*
16971204 AGAGTAAC
66 AAAGTAAC
16971212 ATAAAGTCAT
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 138 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.29
Consensus pattern (79 bp):
GGTTATAAATCAGAATCAGTAACAATCAGTCTAACATGTTCAGATATCGCATATTCCTCATCAAC
AAAGTAACGTAGAG
Found at i:16972959 original size:22 final size:22
Alignment explanation
Indices: 16972924--16972965 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16972914 TTTATATGAA
** *
16972924 ATATGATATGCTCTGTTATGGG
1 ATATGATAACCTCTGATATGGG
16972946 ATATGATAACCTCTGATATG
1 ATATGATAACCTCTGATATG
16972966 TTATAAGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (22 bp):
ATATGATAACCTCTGATATGGG
Found at i:16973736 original size:21 final size:20
Alignment explanation
Indices: 16973712--16973757 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16973702 ATGTATAAAA
* *
16973712 AAAAGTGTACCAAAAAAATTT
1 AAAA-TGTACAAAAAAAAGTT
*
16973733 AAAATGTATAAAAAAAAGTT
1 AAAATGTACAAAAAAAAGTT
16973753 AAAAT
1 AAAAT
16973758 AAAGCTTGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (20 bp):
AAAATGTACAAAAAAAAGTT
Found at i:16974140 original size:14 final size:15
Alignment explanation
Indices: 16974123--16974164 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
16974113 ATGAAATGTA
16974123 AAAAAATAAATTA-T
1 AAAAAATAAATTAGT
16974137 AAAAAATAAATTAGT
1 AAAAAATAAATTAGT
16974152 ACAAAAATTAAAT
1 A-AAAAA-TAAAT
16974165 CTTGCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.52
15 2 0.08
16 5 0.20
17 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAAAATAAATTAGT
Found at i:16977719 original size:3 final size:3
Alignment explanation
Indices: 16977700--16977738 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
16977690 GATTCAGGAA
* *
16977700 ATG ACG ATG ATG GTG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
16977739 GTGGTGGTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:16982106 original size:50 final size:48
Alignment explanation
Indices: 16981995--16982112 Score: 137
Period size: 48 Copynumber: 2.4 Consensus size: 48
16981985 TATGAGAGTC
* * ** *
16981995 AGTGTAAGTCCATGTCTGGAACATGGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGACGAAAGCT
* * * *
16982043 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAG--ACGAAAGCT
16982093 AGTGTAAGACCATGTCTGGG
1 AGTGTAAGACCATGTCTGGG
16982113 GCAGTGTAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 33 0.57
50 25 0.43
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGAGACGAAAGCT
Found at i:16982121 original size:22 final size:22
Alignment explanation
Indices: 16982093--16982134 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16982083 TATGAAAGCT
16982093 AGTGTAAGACCATGTCTGGGGC
1 AGTGTAAGACCATGTCTGGGGC
* *
16982115 AGTGTAAGGCCATGTTTGGG
1 AGTGTAAGACCATGTCTGGG
16982135 ACATGGCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.26
Consensus pattern (22 bp):
AGTGTAAGACCATGTCTGGGGC
Found at i:16982160 original size:72 final size:72
Alignment explanation
Indices: 16982043--16982187 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
16982033 GACGAGAGCT
16982043 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGT
1 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGT
16982108 CTGGGGC
66 CTGGGGC
16982115 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGT
1 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGT
16982180 CTGGGGC
66 CTGGGGC
16982187 A
1 A
16982188 TGGCATCAGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (72 bp):
AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGT
CTGGGGC
Found at i:16982190 original size:50 final size:50
Alignment explanation
Indices: 16982115--16982295 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 50
16982105 TGTCTGGGGC
* *
16982115 AGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGACATATGAAAGCT
* * * * * * *
16982165 AGTGTAAGACCATGTCTGGGGCATGGCATCAGCACCGACAGATGTAAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGACATATGAAAGCT
* * * * *
16982215 AGTGTAAGACCATGTTTGGGACATGGCTTCGGCCTCGATATATGAGAGTT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGACATATGAAAGCT
*
16982265 AGTGTAAGAGCATGTTTGGGACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
16982296 ACTTTGATGT
Statistics
Matches: 108, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (50 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGACATATGAAAGCT
Found at i:16982219 original size:122 final size:120
Alignment explanation
Indices: 16981994--16982234 Score: 302
Period size: 122 Copynumber: 2.0 Consensus size: 120
16981984 TTATGAGAGT
* ** * * *
16981994 CAGTGTAAGTCCATGTCTGGAACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGGCCATGTT
1 CAGTGTAAGGCCATGTCTGGAACATGGCATCGGCACCGAGACGAAAGCTAGTGTAAGACCATGTC
* * * * *
16982059 TGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATGTCTGGGG
66 TGGGACATGGCATCAGCACCGACAGATGAAAGCCAGTGTAAGACCATGTCTGGGG
* * * *
16982114 CAGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATG
1 CAGTGTAAGGCCATGTCTGGAACATGGCATCGGCACCGAG--ACGAAAGCTAGTGTAAGACCATG
* * *
16982179 TCTGGGGCATGGCATCAGCACCGACAGATGTAAGCCAGTGTAAGACCATGTTTGGG
64 TCTGGGACATGGCATCAGCACCGACAGATGAAAGCCAGTGTAAGACCATGTCTGGG
16982235 ACATGGCTTC
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
120 34 0.34
122 67 0.66
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (120 bp):
CAGTGTAAGGCCATGTCTGGAACATGGCATCGGCACCGAGACGAAAGCTAGTGTAAGACCATGTC
TGGGACATGGCATCAGCACCGACAGATGAAAGCCAGTGTAAGACCATGTCTGGGG
Found at i:16982290 original size:100 final size:100
Alignment explanation
Indices: 16982114--16982294 Score: 281
Period size: 100 Copynumber: 1.8 Consensus size: 100
16982104 ATGTCTGGGG
*
16982114 CAGTGTAAGGCCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATG
*
16982179 TCTGGGGCATGGCATCAGCACCGACAGATGTAAGC
66 TCTGGGACATGGCATCAGCACCGACAGATGTAAGC
* * * * * *
16982214 CAGTGTAAGACCATGTTTGGGACATGGCTTCGGCCTCGATATATGAGAGTTAGTGTAAGAGCATG
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATG
*
16982279 TTTGGGACATGGCATC
66 TCTGGGACATGGCATC
16982295 GACTTTGATG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 72 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (100 bp):
CAGTGTAAGACCATGTTTGGGACATGGCATCGGCCCCGAGATATGAAAGCTAGTGTAAGACCATG
TCTGGGACATGGCATCAGCACCGACAGATGTAAGC
Found at i:16989344 original size:20 final size:21
Alignment explanation
Indices: 16989321--16989359 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16989311 TTTCATCTTC
*
16989321 AACAACTT-CTTTTCTTCAGT
1 AACAACTTCCTCTTCTTCAGT
16989341 AACAACTTCCTCTTCTTCA
1 AACAACTTCCTCTTCTTCA
16989360 ATAATAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.41
Consensus pattern (21 bp):
AACAACTTCCTCTTCTTCAGT
Found at i:16998250 original size:42 final size:43
Alignment explanation
Indices: 16998138--16998255 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
16998128 AATGCCTTAC
* **
16998138 CCCAGATATGGTCTTGCATGTAATCTCATATCGATGCCAATAG
1 CCCAGATATGGTCTTACACATAATCTCATATCGATGCCAATAG
* * * *
16998181 CCCAGCTATGGTCTTACACGA-AGTCTCATATCGATG-CGATAT
1 CCCAGATATGGTCTTACAC-ATAATCTCATATCGATGCCAATAG
*
16998223 CTCAGATATGGTCTTACACATAATCTCAGTATC
1 CCCAGATATGGTCTTACACATAATCTCA-TATC
16998256 CCTAATGTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.02
42 27 0.44
43 34 0.55
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (43 bp):
CCCAGATATGGTCTTACACATAATCTCATATCGATGCCAATAG
Found at i:17004769 original size:42 final size:42
Alignment explanation
Indices: 17004656--17004775 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 42
17004646 AGTATCGTAC
* *
17004656 CAATGCCATATCGCAGATATGGTCTTACATATAATCTCATAT
1 CAATGCCATATCCCAGATATGGTCTTACACATAATCTCATAT
* * *
17004698 CGATGCCAATAACCCAGCTATGGTCTTACACA-AAGTCTCATAT
1 CAATGCC-ATATCCCAGATATGGTCTTACACATAA-TCTCATAT
* *
17004741 CAATGCCATATCCCAGGTATGGTCTTACACGTAAT
1 CAATGCCATATCCCAGATATGGTCTTACACATAAT
17004776 ATTAGTAACC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
42 30 0.45
43 36 0.55
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACATAATCTCATAT
Found at i:17012739 original size:30 final size:30
Alignment explanation
Indices: 17012705--17012772 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
17012695 AATCTGATAA
*
17012705 ATAAAAACTAAATTATTAAA-AATAAAAAAT
1 ATAAAAACTAAATT-TTAAATAACAAAAAAT
* *
17012735 ATAAAAATTAAATTTTAAATTTACAAAAAAT
1 ATAAAAACTAAATTTTAAA-TAACAAAAAAT
17012766 ATAAAAA
1 ATAAAAA
17012773 ATTATAGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 13 0.39
31 15 0.45
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
ATAAAAACTAAATTTTAAATAACAAAAAAT
Found at i:17015044 original size:36 final size:36
Alignment explanation
Indices: 17014972--17015044 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
17014962 TCGTCCACTC
** **
17014972 AATCAACTTAATATGAAGACCTAGGATGTGTTAAAG
1 AATCAACTTAATATGAAGACCTAGGACATGCAAAAG
* * *
17015008 AATCAAGTTTATATGAAGACTTAGGACATGCAAAAG
1 AATCAACTTAATATGAAGACCTAGGACATGCAAAAG
17015044 A
1 A
17015045 CCTAATTTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (36 bp):
AATCAACTTAATATGAAGACCTAGGACATGCAAAAG
Found at i:17018074 original size:30 final size:30
Alignment explanation
Indices: 17018040--17018100 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
17018030 TCCTTAACTC
17018040 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
17018070 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
17018100 A
1 A
17018101 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:17019375 original size:17 final size:17
Alignment explanation
Indices: 17019353--17019389 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
17019343 TTATCCTTTG
*
17019353 TTTATTTTCCTTATTTA
1 TTTATTTTCATTATTTA
17019370 TTTATTTTCATTATTTA
1 TTTATTTTCATTATTTA
17019387 TTT
1 TTT
17019390 TTATCTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTCATTATTTA
Found at i:17019401 original size:19 final size:16
Alignment explanation
Indices: 17019357--17019414 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
17019347 CCTTTGTTTA
*
17019357 TTTTCCTTATTTATTT
1 TTTTCATTATTTATTT
17019373 ATTTTCATTATTTATTT
1 -TTTTCATTATTTATTT
*
17019390 TTATCTCAATTATCTATTT
1 TT-T-TC-ATTATTTATTT
17019409 TTTTCA
1 TTTTCA
17019415 CATCCCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.08
17 18 0.50
18 3 0.08
19 12 0.33
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCATTATTTATTT
Found at i:17022477 original size:24 final size:24
Alignment explanation
Indices: 17022441--17022574 Score: 110
Period size: 24 Copynumber: 5.6 Consensus size: 24
17022431 AAGTGTAGGA
* *
17022441 TCTGTAACTGTATCTACATCTATG
1 TCTGTATCAGTATCTACATCTATG
* * *
17022465 TCTGTATCAGTATCTATATATGTG
1 TCTGTATCAGTATCTACATCTATG
* * * *
17022489 TTTGTATCAGTACCTACAACTATA
1 TCTGTATCAGTATCTACATCTATG
* * * *
17022513 TTTGTAATC-GTATTTGCATCTGTG
1 TCTGT-ATCAGTATCTACATCTATG
* *
17022537 -CTGTATCAGTATCTGCATCTAAG
1 TCTGTATCAGTATCTACATCTATG
17022560 TCTGTATCAGTATCT
1 TCTGTATCAGTATCT
17022575 GCAACTGTAT
Statistics
Matches: 85, Mismatches: 22, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
22 3 0.04
23 15 0.18
24 64 0.75
25 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (24 bp):
TCTGTATCAGTATCTACATCTATG
Found at i:17022589 original size:24 final size:24
Alignment explanation
Indices: 17022467--17022591 Score: 78
Period size: 24 Copynumber: 5.2 Consensus size: 24
17022457 CATCTATGTC
** *
17022467 TGTATCAGTATCTATATA-TGTGTT
1 TGTATCAGTATCTGCA-ACTGTATT
* * *
17022491 TGTATCAGTACCTACAACTATATT
1 TGTATCAGTATCTGCAACTGTATT
* * **
17022515 TGTAATC-GTATTTGCATCTGT-GC
1 TGT-ATCAGTATCTGCAACTGTATT
* * *
17022538 TGTATCAGTATCTGCATCT-AAGTC
1 TGTATCAGTATCTGCAACTGTA-TT
17022562 TGTATCAGTATCTGCAACTGTATT
1 TGTATCAGTATCTGCAACTGTATT
17022586 TGTATC
1 TGTATC
17022592 TGAACTGCAT
Statistics
Matches: 78, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
22 3 0.04
23 15 0.19
24 56 0.72
25 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (24 bp):
TGTATCAGTATCTGCAACTGTATT
Found at i:17024580 original size:33 final size:33
Alignment explanation
Indices: 17024535--17024628 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
17024525 AACACAGTGT
* *
17024535 CAGTACAATCTGGGCCAAAGCCCTATTCAGTAA
1 CAGTACAGTCTGGGCCTAAGCCCTATTCAGTAA
*
17024568 CAGTACAGTCTGGGCCTTAGCCC--TT-A--AA
1 CAGTACAGTCTGGGCCTAAGCCCTATTCAGTAA
*
17024596 CAGTAGCAGTATGGGCCTAAGCCCTAATTCAGT
1 CAGTA-CAGTCTGGGCCTAAGCCCT-ATTCAGT
17024629 CTCGACATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
28 7 0.14
29 16 0.33
30 1 0.02
31 2 0.04
32 2 0.04
33 21 0.43
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (33 bp):
CAGTACAGTCTGGGCCTAAGCCCTATTCAGTAA
Found at i:17024628 original size:29 final size:28
Alignment explanation
Indices: 17024566--17024620 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
17024556 CCTATTCAGT
* *
17024566 AACAGTACAGTCTGGGCCTTAGCCCTTA
1 AACAGTACAGTATGGGCCTAAGCCCTTA
17024594 AACAGTAGCAGTATGGGCCTAAGCCCT
1 AACAGTA-CAGTATGGGCCTAAGCCCT
17024621 AATTCAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (28 bp):
AACAGTACAGTATGGGCCTAAGCCCTTA
Found at i:17024677 original size:31 final size:31
Alignment explanation
Indices: 17024639--17024717 Score: 158
Period size: 31 Copynumber: 2.5 Consensus size: 31
17024629 CTCGACATTT
17024639 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
17024670 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
17024701 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
17024718 ATTGTAAACG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:17024804 original size:42 final size:42
Alignment explanation
Indices: 17024745--17024832 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
17024735 CCATAGGCCT
*
17024745 ATTTCAATAACACATGAAATATCAATGAATGTATGCAAGCCC
1 ATTTCAATAACACATGAAATACCAATGAATGTATGCAAGCCC
* * *
17024787 ATTTCAATATCATATGAAATACCATTGAATGTATGCAAGCCC
1 ATTTCAATAACACATGAAATACCAATGAATGTATGCAAGCCC
17024829 ATTT
1 ATTT
17024833 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (42 bp):
ATTTCAATAACACATGAAATACCAATGAATGTATGCAAGCCC
Found at i:17025031 original size:26 final size:26
Alignment explanation
Indices: 17024983--17025082 Score: 166
Period size: 26 Copynumber: 3.9 Consensus size: 26
17024973 CGCTTTTCGG
17024983 TAAACTGGGGCA-AAGCCCTTTTCAA
1 TAAACTGGGGCATAAGCCCTTTTCAA
* **
17025008 TAAACTGGGGCATAAGCCATTTTCGG
1 TAAACTGGGGCATAAGCCCTTTTCAA
17025034 TAAACTGGGGCATAAGCCCTTTTCAA
1 TAAACTGGGGCATAAGCCCTTTTCAA
17025060 TAAACTGGGGCATAAGCCCTTTT
1 TAAACTGGGGCATAAGCCCTTTT
17025083 GCACTTCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 12 0.18
26 56 0.82
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (26 bp):
TAAACTGGGGCATAAGCCCTTTTCAA
Found at i:17025065 original size:52 final size:51
Alignment explanation
Indices: 17024976--17025082 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 51
17024966 GTCAAAGCGC
17024976 TTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCA
1 TTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCA
*
17025027 TTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCC
1 TTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATAAACTGGGGCATAAGCCA
17025079 TTTT
1 TTTT
17025083 GCACTTCCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 19 0.35
52 35 0.65
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (51 bp):
TTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTGGGGCATAAGCCA
Found at i:17025195 original size:20 final size:20
Alignment explanation
Indices: 17025131--17025187 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
17025121 TTATGAATAC
17025131 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* **
17025151 ATCATGTGCATTTTTTACAT
1 ATCATGTGCATATCATACAT
17025171 ATCATGTGCATATCATA
1 ATCATGTGCATATCATA
17025188 TCAATCATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:17025967 original size:27 final size:27
Alignment explanation
Indices: 17025906--17025969 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
17025896 GGCGTATTCA
17025906 TCATTTTACCATACAAGGGTATTACGG
1 TCATTTTACCATACAAGGGTATTACGG
* * *
17025933 TCACTTTACCCTACAGGGGCT-TTACGG
1 TCATTTTACCATACAAGGG-TATTACGG
*
17025960 TCTTTTTACC
1 TCATTTTACC
17025970 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (27 bp):
TCATTTTACCATACAAGGGTATTACGG
Found at i:17026053 original size:27 final size:27
Alignment explanation
Indices: 17026023--17026130 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
17026013 GTAAATCTAC
17026023 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
*
17026050 AAACCAATGGTATTTCTA-TAATTTT-T
1 AAACCAAGGGTATTTC-AGTAATTTTGT
* *
17026076 AGAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
17026106 AAATCAGGGGTATTTTGGTAATTTT
1 AAACCAAGGGTATTTCAGTAATTTT
17026131 ACAAATTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
26 1 0.01
27 41 0.60
28 7 0.10
29 18 0.26
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:17026128 original size:56 final size:54
Alignment explanation
Indices: 17026020--17026189 Score: 175
Period size: 54 Copynumber: 3.1 Consensus size: 54
17026010 TTGGTAAATC
* * *
17026020 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTT
1 TACAAATCAAGGGTATTTC-GTAATTTTGTAAACCAGTGGTATTT-TGGTAATTTT
* * *
17026075 TAGAAAGTCAAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAA-TTT
1 TACAAA-TCAAGGGTATTTC-GTAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
** ***
17026130 TACAAATTGAGGGTATTTCGATAATTTCACAAACCAGTGGTATTTTGGTAA-TTT
1 TACAAATCAAGGGTATTTCG-TAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
17026184 TACAAA
1 TACAAA
17026190 CTAGGGGTAT
Statistics
Matches: 97, Mismatches: 15, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
53 1 0.01
54 45 0.46
55 14 0.14
56 37 0.38
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
TACAAATCAAGGGTATTTCGTAATTTTGTAAACCAGTGGTATTTTGGTAATTTT
Found at i:17026136 original size:27 final size:27
Alignment explanation
Indices: 17026072--17026251 Score: 136
Period size: 27 Copynumber: 6.7 Consensus size: 27
17026062 TTTCTATAAT
* *
17026072 TTTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTTACAAA-TCAGGGGTATTT-TGGTAA
**
17026100 TTTTGTAAATCAGGGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
* * *
17026127 TTTTACAAAT-TGAGGGTATTTCGATAA
1 TTTTACAAATCAG-GGGTATTTTGGTAA
* * *
17026154 TTTCACAAACCAGTGGTATTTTGGTAA
1 TTTTACAAATCAGGGGTATTTTGGTAA
17026181 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTACAAATC-AGGGGTATTTTGGTAA
* ** *
17026208 TTCTATCCTA-CAGGGGTATTTTAGTAA
1 TTTTA-CAAATCAGGGGTATTTTGGTAA
* *
17026235 TTTCAC-AATCAAGGGTA
1 TTTTACAAATCAGGGGTA
17026252 AAACGGTAAT
Statistics
Matches: 122, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
25 1 0.01
26 11 0.09
27 99 0.81
28 11 0.09
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
TTTTACAAATCAGGGGTATTTTGGTAA
Found at i:17026316 original size:54 final size:54
Alignment explanation
Indices: 17026245--17026370 Score: 182
Period size: 54 Copynumber: 2.3 Consensus size: 54
17026235 TTTCACAATC
* * *
17026245 AAGGGTAAAACGGTAATTTTATAAA-CTGATGGTAAAATGGTAATTTTGTAAATT
1 AAGGGTAAAACGGTAATTTTATAAATC-GAGGGTAAAATGGTAATTCTATAAATT
* *
17026299 AAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAAATT
1 AAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTATAAATT
*
17026353 GAGGGTAAAACGGTAATT
1 AAGGGTAAAACGGTAATT
17026371 CCATGCCTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
54 63 0.98
55 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (54 bp):
AAGGGTAAAACGGTAATTTTATAAATCGAGGGTAAAATGGTAATTCTATAAATT
Found at i:17026371 original size:27 final size:27
Alignment explanation
Indices: 17026246--17026370 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
17026236 TTCACAATCA
*
17026246 AGGGTAAAACGGTAATTTTATAAACTG
1 AGGGTAAAACGGTAATTTTATAAATTG
* * * *
17026273 ATGGTAAAATGGTAATTTTGTAAATTA
1 AGGGTAAAACGGTAATTTTATAAATTG
* * *
17026300 AGGGTAAAACGATAATTTTGTAAATCG
1 AGGGTAAAACGGTAATTTTATAAATTG
* *
17026327 AGGGTAAAATGGTAATTCTATAAATTG
1 AGGGTAAAACGGTAATTTTATAAATTG
17026354 AGGGTAAAACGGTAATT
1 AGGGTAAAACGGTAATT
17026371 CCATGCCTCC
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (27 bp):
AGGGTAAAACGGTAATTTTATAAATTG
Found at i:17030666 original size:12 final size:12
Alignment explanation
Indices: 17030649--17030684 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
17030639 TAGGTTTCCC
17030649 AAAATGGAAATG
1 AAAATGGAAATG
*
17030661 AAAATGAAAATG
1 AAAATGGAAATG
17030673 AAAATGGAAATG
1 AAAATGGAAATG
17030685 GAATCTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:17030687 original size:6 final size:6
Alignment explanation
Indices: 17030649--17030684 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
17030639 TAGGTTTCCC
* *
17030649 AAAATG GAAATG AAAATG AAAATG AAAATG GAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
17030685 GAATCTTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:17035781 original size:20 final size:20
Alignment explanation
Indices: 17035740--17035786 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
17035730 CGGCAATGTT
*
17035740 TAAGTTGTGAAAGACTATGG
1 TAAGTTGTGAAAGACTAAGG
*
17035760 TATGTTGTGAAAGA-TCAAGG
1 TAAGTTGTGAAAGACT-AAGG
17035780 TAAGTTG
1 TAAGTTG
17035787 CAAGTTGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (20 bp):
TAAGTTGTGAAAGACTAAGG
Found at i:17040743 original size:27 final size:27
Alignment explanation
Indices: 17040702--17040785 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
17040692 AAGAAGCGTC
*
17040702 CTGGTGGCTATGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGTT
*
17040729 CTGGTGGCTCGGCCACA-ATTATCTGTT
1 CTGGTGGCTCTGCCACATA-TATCTGTT
* *
17040756 CTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGTT
17040782 CTGG
1 CTGG
17040786 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 13 0.26
27 37 0.74
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGTT
Found at i:17047095 original size:24 final size:24
Alignment explanation
Indices: 17047068--17047128 Score: 104
Period size: 24 Copynumber: 2.5 Consensus size: 24
17047058 GTAAGGAGGG
*
17047068 GATAAGTGAGAAGATTTAGGAGCT
1 GATAAGGGAGAAGATTTAGGAGCT
17047092 GATAAGGGAGAAGATTTAGGAGCT
1 GATAAGGGAGAAGATTTAGGAGCT
17047116 GATAAGGGGAGAA
1 GATAA-GGGAGAA
17047129 AATAAAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 28 0.80
25 7 0.20
ACGTcount: A:0.39, C:0.03, G:0.38, T:0.20
Consensus pattern (24 bp):
GATAAGGGAGAAGATTTAGGAGCT
Found at i:17048617 original size:27 final size:27
Alignment explanation
Indices: 17048579--17048689 Score: 118
Period size: 27 Copynumber: 4.1 Consensus size: 27
17048569 AGGAAGCGTC
*
17048579 CTGGTGGCTATGCCACAATTCTCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
*
17048606 CTGGTGGCTATGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
* **
17048633 CTGGTGGCTCTGCCACAATTATCTCTT
1 CTGGTGGCTATGCCACAATTATCTGAT
* * * *
17048660 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGAT
17048686 CTGG
1 CTGG
17048690 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 15 0.20
27 58 0.77
28 2 0.03
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:17048663 original size:54 final size:53
Alignment explanation
Indices: 17048579--17048689 Score: 150
Period size: 54 Copynumber: 2.1 Consensus size: 53
17048569 AGGAAGCGTC
* * *
17048579 CTGGTGGCTATGCCACAATTCTCTGATCTGGTGGCTATGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTCATCTGGTGACTATGCCACAT-TATCTGTT
* * * *
17048633 CTGGTGGCTCTGCCACAATTATCTCTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTCATCTGGTGACTATGCCACATTATCTGTT
17048686 CTGG
1 CTGG
17048690 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 12 0.24
54 38 0.76
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTCATCTGGTGACTATGCCACATTATCTGTT
Found at i:17063874 original size:12 final size:12
Alignment explanation
Indices: 17063857--17063881 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17063847 TTTTAATAAG
17063857 ATTTAATATTAA
1 ATTTAATATTAA
17063869 ATTTAATATTAA
1 ATTTAATATTAA
17063881 A
1 A
17063882 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:17067001 original size:11 final size:11
Alignment explanation
Indices: 17066987--17067032 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
17066977 GTCCTCTCAC
17066987 AATTCTCTCTA
1 AATTCTCTCTA
*
17066998 AATTCTTTCTA
1 AATTCTCTCTA
*
17067009 AATTCCCTC-A
1 AATTCTCTCTA
*
17067019 AATT-TCTCTC
1 AATTCTCTCTA
17067029 AATT
1 AATT
17067033 TTTGTCAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
9 3 0.10
10 9 0.31
11 17 0.59
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTCTCTCTA
Found at i:17067040 original size:21 final size:22
Alignment explanation
Indices: 17067016--17067059 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
17067006 CTAAATTCCC
17067016 TCAAA-TT-TCTCTCAATTTTTG
1 TCAAAGTTGTCTCT-AATTTTTG
17067037 TCAAAGTTGTCTCTAATTTTTG
1 TCAAAGTTGTCTCTAATTTTTG
17067059 T
1 T
17067060 AAAAAAGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (22 bp):
TCAAAGTTGTCTCTAATTTTTG
Found at i:17068218 original size:7 final size:7
Alignment explanation
Indices: 17068198--17068240 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
17068188 CATAATAAAA
17068198 TAGTCATT
1 TAGT-ATT
*
17068206 TCGTATT
1 TAGTATT
17068213 TAGTATT
1 TAGTATT
17068220 TAGTATT
1 TAGTATT
17068227 TAGTATT
1 TAGTATT
17068234 TAGTATT
1 TAGTATT
17068241 ACCTATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 30 0.91
8 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.56
Consensus pattern (7 bp):
TAGTATT
Found at i:17069179 original size:21 final size:22
Alignment explanation
Indices: 17069133--17069183 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
17069123 CCAACACCCA
*
17069133 CAACCA-AATCCCCTGCCGAAG
1 CAACCACAATCCCCTACCGAAG
* *
17069154 GAACCACAATCCCC-ACCGGAG
1 CAACCACAATCCCCTACCGAAG
17069175 CAACCACAA
1 CAACCACAA
17069184 CCCTTGCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.37, C:0.43, G:0.14, T:0.06
Consensus pattern (22 bp):
CAACCACAATCCCCTACCGAAG
Found at i:17069533 original size:128 final size:127
Alignment explanation
Indices: 17069300--17069674 Score: 576
Period size: 128 Copynumber: 2.9 Consensus size: 127
17069290 GTAGAAACTT
* *
17069300 TTTTTATATAG-TTTCATATAATAAAATAAAAGTTAT-TTTTAATATTTTAATTGTACGTTACTT
1 TTTTTATATAGTTTTAAT-TAATAAAATAAAA-TT-TGTTTTAATATTTTAATTGTACTTTACTT
17069363 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
63 TTTTTTAATTTTATT-AAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTT
17069428 A
127 A
*
17069429 CTTTTTATATAGTTTTAATTAATAAAATAAAATTTGTTTTAATATTTTAATTGTACTTTAC-CTT
1 -TTTTTATATAGTTTTAATTAATAAAATAAAATTTGTTTTAATATTTTAATTGTACTTTACTTTT
*
17069493 TTTTAATTTTATTGAAATAAATGTTCTTTTAAATTGGCCAATATTTTTATTATTTTTATATTTA
65 TTTTAATTTTATT-AAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
*
17069557 TTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTT
1 TTTTTATATAGTTTTAATTAATAAAATAAAATTTG-TTTTAATATTTTAATTGTACTTTACTTTT
* * *
17069622 TTTTCATTTTAATACAATACATGTTCTTTTAAATTAGCCAATATTTTTTATTA
65 TTTTAATTTTATTA-AATAAATGTTCTTTTAAATTAGCCAATA-TTTTTATTA
17069675 AAATAAATGT
Statistics
Matches: 228, Mismatches: 11, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
127 34 0.15
128 91 0.40
129 65 0.29
130 33 0.14
131 5 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.56
Consensus pattern (127 bp):
TTTTTATATAGTTTTAATTAATAAAATAAAATTTGTTTTAATATTTTAATTGTACTTTACTTTTT
TTTAATTTTATTAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATATTTA
Found at i:17069685 original size:39 final size:39
Alignment explanation
Indices: 17069628--17069712 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
17069618 TTTTTTTTCA
* * *
17069628 TTTTAATACAATACATGTTCTTTTAAATTA-GCCAATATT
1 TTTTAATAAAATAAATGTTATTTTAAA-TACGCCAATATT
* * *
17069667 TTTTATTAAAATAAATGTTATTTTGAATACGGCAATA-T
1 TTTTAATAAAATAAATGTTATTTTAAATACGCCAATATT
17069705 TTTTAATA
1 TTTTAATA
17069713 TTTTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
38 10 0.26
39 28 0.74
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (39 bp):
TTTTAATAAAATAAATGTTATTTTAAATACGCCAATATT
Found at i:17069716 original size:8 final size:9
Alignment explanation
Indices: 17069700--17069729 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17069690 TGAATACGGC
17069700 AATATTTTT
1 AATATTTTT
17069709 AATATTTTT
1 AATATTTTT
17069718 -ATATTTTT
1 AATATTTTT
17069726 AATA
1 AATA
17069730 AAATATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:17072973 original size:126 final size:126
Alignment explanation
Indices: 17072748--17073055 Score: 483
Period size: 126 Copynumber: 2.5 Consensus size: 126
17072738 AGTCTAAGGC
* * *
17072748 TTTTTTAGATACTACTGTAGCAAAAGGGTGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTGAT
1 TTTTTTAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTTCGTAATTTTGCTGAT
* *
17072813 AGTGCATCCTTCTTAAAGAGTTTTTGACACTATTTGTTCAAAAACATCTTTTCAAAATTAT
66 AGTGCATCCTTCTTAAAGAGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTAT
*
17072874 TTTTTTAGATACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTTTCGTAATTTTGCTGAT
1 TTTTTTAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTTCGTAATTTTGCTGAT
* * * *
17072939 AGTGCATCCTTCTTGAAGCGTTTTTAACACTATTTGTTCAGAAACATCTTCTCATAATTAT
66 AGTGCATCCTTCTTAAAGAGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTAT
* * * *
17073000 TTTTTCAAATACTACTGTAGTAAAAGAGCGTCCACATGGGAGC-TTTTTTCGTAATT
1 TTTTTTAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTTCGTAATT
17073056 AACAGTTAAT
Statistics
Matches: 167, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
125 13 0.08
126 154 0.92
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (126 bp):
TTTTTTAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTTCGTAATTTTGCTGAT
AGTGCATCCTTCTTAAAGAGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTAT
Found at i:17073240 original size:15 final size:16
Alignment explanation
Indices: 17073220--17073252 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
17073210 TAAAACAATC
17073220 AAAAACCCT-AACCCT
1 AAAAACCCTGAACCCT
17073235 AAAAACCCTGAACCCT
1 AAAAACCCTGAACCCT
17073251 AA
1 AA
17073253 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.36, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAACCCTGAACCCT
Found at i:17073355 original size:15 final size:15
Alignment explanation
Indices: 17073331--17073387 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
17073321 TTCCCTTAAA
*
17073331 AAACACTAAAACCCT
1 AAACCCTAAAACCCT
* *
17073346 AAACCTTAAAAACCTT
1 AAACCCT-AAAACCCT
17073362 AAACCACT-AAACCCT
1 AAACC-CTAAAACCCT
17073377 -AACCCTAAAAC
1 AAACCCTAAAAC
17073388 AATCAAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.06
14 8 0.24
15 11 0.32
16 12 0.35
17 1 0.03
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAAAACCCT
Found at i:17073364 original size:24 final size:25
Alignment explanation
Indices: 17073324--17073374 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
17073314 TTAATTTTTC
17073324 CCTTAAAAAACACTAAAACC-CTAAA
1 CCTTAAAAAACACT-AAACCACTAAA
17073349 CCTT-AAAAAC-CTTAAACCACTAAA
1 CCTTAAAAAACAC-TAAACCACTAAA
17073373 CC
1 CC
17073375 CTAACCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.25
24 14 0.58
25 4 0.17
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (25 bp):
CCTTAAAAAACACTAAACCACTAAA
Found at i:17073480 original size:173 final size:173
Alignment explanation
Indices: 17073182--17073585 Score: 661
Period size: 173 Copynumber: 2.3 Consensus size: 173
17073172 AAAAAACACC
* * *
17073182 AAAACCCTAAACCACTAAATCCTAACCCTAAAACAATCAAAAACCCTAACCCT-AAAAACCCTGA
1 AAAAACCTAAACCACTAAACCCTAACCCTAAAACAATCAAAAACCCTAACCCTAAAAAACCCTAA
** *
17073246 ACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATTAATTCTCAACTCTAATT
66 ACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATTAACCCTAAACTCTAATT
*
17073311 AAATTAA-TTTTTCCCTTAAAAAACACTAAAACCCTAAA-CCTT
131 AAATTAACTTTTTCCCTT-AAAAACACTAAAACCCTAAAGCCTA
**
17073353 AAAAACCTTAAACCACTAAACCCTAACCCTAAAACAATCAAAAACCCTAACCCTAAAAAACTTTA
1 AAAAACC-TAAACCACTAAACCCTAACCCTAAAACAATCAAAAACCCTAACCCTAAAAAACCCTA
17073418 AACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATTAACCCTAAACTCTAAT
65 AACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATTAACCCTAAACTCTAAT
17073483 TAAATTAACTTTTTCCCTTAAAAACACTAAAACCCTAAAGCCTA
130 TAAATTAACTTTTTCCCTTAAAAACACTAAAACCCTAAAGCCTA
** *
17073527 AAAAACCTAAACCACTAAACTTTAACCCTAAAATAATCAAAAACCCTAACCCTAAAAAA
1 AAAAACCTAAACCACTAAACCCTAACCCTAAAACAATCAAAAACCCTAACCCTAAAAAA
17073586 GGGGCAAAAC
Statistics
Matches: 217, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
171 6 0.03
172 45 0.21
173 146 0.67
174 20 0.09
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.29
Consensus pattern (173 bp):
AAAAACCTAAACCACTAAACCCTAACCCTAAAACAATCAAAAACCCTAACCCTAAAAAACCCTAA
ACCCTAATTTAATTGATTTTTTTAATTTCATAGTTAATTTAATTAATTAACCCTAAACTCTAATT
AAATTAACTTTTTCCCTTAAAAACACTAAAACCCTAAAGCCTA
Found at i:17076688 original size:22 final size:22
Alignment explanation
Indices: 17076663--17076718 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
17076653 CTCGTATGAG
* * *
17076663 CTTACTGTTTAGCTCGATAGAA
1 CTTACTGTTCAACTCAATAGAA
* *
17076685 CTTACCGATTCAACTCAATAGAG
1 CTTACTG-TTCAACTCAATAGAA
17076708 CTTACTGTTCA
1 CTTACTGTTCA
17076719 TCAGCTTAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (22 bp):
CTTACTGTTCAACTCAATAGAA
Found at i:17076690 original size:45 final size:45
Alignment explanation
Indices: 17076602--17076716 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 45
17076592 TTACGATATA
* *
17076602 TCAACTCGTAAGAGCTTACTGTTTTTAGCACATTAGAGCTTACC-ATT
1 TCAACTCGTATGAGCTTACTG--TTTAGCACATTAGAACTTACCGA-T
* *
17076649 TCAGCTCGTATGAGCTTACTGTTTAGCTCGA-TAGAACTTACCGAT
1 TCAACTCGTATGAGCTTACTGTTTAGCAC-ATTAGAACTTACCGAT
*
17076694 TCAACTC-AATAGAGCTTACTGTT
1 TCAACTCGTAT-GAGCTTACTGTT
17076717 CATCAGCTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
44 2 0.03
45 36 0.61
46 2 0.03
47 19 0.32
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (45 bp):
TCAACTCGTATGAGCTTACTGTTTAGCACATTAGAACTTACCGAT
Found at i:17079323 original size:13 final size:13
Alignment explanation
Indices: 17079305--17079329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17079295 GTAAGTGATT
17079305 TTGATGATTTTTC
1 TTGATGATTTTTC
17079318 TTGATGATTTTT
1 TTGATGATTTTT
17079330 TGCATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:17080105 original size:47 final size:47
Alignment explanation
Indices: 17080037--17080438 Score: 457
Period size: 47 Copynumber: 8.6 Consensus size: 47
17080027 TTTGTGTGCT
* **
17080037 AGTGTAAGA-CATGTCTAGGACAT-GCATCGACCACATTATGA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCA-TA-GATGAGCC
* * * *
17080083 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TTCATA-GATGAGCC
* * *
17080131 AGTGTAAGA-CATGTCTGGGACAT-GCATC-AGCCTC-GAGATGTAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CTTCATAGATG--AGCC
* * * * * * *
17080177 AGTGTACGA-CATATCTGGGACAT-GCATCGGCTACA-AAATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
*
17080221 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATAGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
* * *
17080268 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
*
17080315 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATAGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
*
17080362 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATAGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
17080409 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
17080439 AGCATTATAC
Statistics
Matches: 312, Mismatches: 32, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
43 2 0.01
44 12 0.04
45 14 0.04
46 60 0.19
47 200 0.64
48 23 0.07
49 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTTCATAGATGAGCC
Found at i:17080389 original size:141 final size:139
Alignment explanation
Indices: 17080034--17080440 Score: 533
Period size: 141 Copynumber: 2.9 Consensus size: 139
17080024 TTATTTGTGT
* *
17080034 GCTAGTGTAAGACATGTCTAGGACATGCATCGACCACATTATGA-GAGCCAGTGTAAGACCATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACTACA-TA-GATGAGCCAGTGTAAGACCATGT
* * *
17080098 CTGGGACATGGCATCGGCATTGAGACGA-GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCA
64 CTGGGACATGGCATCGAC-TTGATA-GATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCA
*
17080160 GCCTCGAGATGTAA
127 GACTCGAGATGT-A
* * * * * *
17080174 GCTAGTGTACGACATATCTGGGACATGCATCGGCTACA-AAATGTGTCAGTGTAAGACCATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACTACATAGATGAGCCAGTGTAAGACCATGTCT
17080238 GGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACT
66 GGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGACT
*
17080302 TGATAGATGT-
131 CG--AGATGTA
**
17080312 G-TCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATG
1 GCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACATAGATGAGCCAGTGTAAGACCATG
17080376 TCTGGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG
63 TCTGGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG
17080441 CATTATACCC
Statistics
Matches: 235, Mismatches: 21, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
136 2 0.01
137 20 0.09
138 63 0.27
139 18 0.08
140 48 0.20
141 83 0.35
142 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (139 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACTACATAGATGAGCCAGTGTAAGACCATGTCT
GGGACATGGCATCGACTTGATAGATGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGACT
CGAGATGTA
Found at i:17083009 original size:716 final size:716
Alignment explanation
Indices: 17081562--17082994 Score: 2821
Period size: 716 Copynumber: 2.0 Consensus size: 716
17081552 GGCATTTTAA
17081562 TCAAATAAAATGGGAAAAATAAGCCAAAAATCAGCTTATTGTTTCATGTTGCTGCCGAAAATTTG
1 TCAAATAAAATGGGAAAAATAAGCCAAAAATCAGCTTATTGTTTCATGTTGCTGCCGAAAATTTG
17081627 GGGTTCTCCATAGCTAGGGTTTTCAAGCTTTTCAAGCTCAATAGTAAGTACTCTCAAGCCCCGTT
66 GGGTTCTCCATAGCTAGGGTTTTCAAGCTTTTCAAGCTCAATAGTAAGTACTCTCAAGCCCCGTT
17081692 TTTAATGTTCTTTATATTTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCAT
131 TTTAATGTTCTTTATATTTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCAT
17081757 GCTAGGGTTCATTTTTAGAAATTTACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGA
196 GCTAGGGTTCATTTTTAGAAATTTACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGA
17081822 ATATGAAGGTTGGATGTGTGTTAAACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAG
261 ATATGAAGGTTGGATGTGTGTTAAACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAG
*
17081887 GACCTTTTTGCAAAAGGTGTAAAGTATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTTC
326 GACCTTTTTGCAAAAGGTGTAAAGTATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGC
* *
17081952 CATAAGAGGGAAAAGTGTTCGACTAGGCTTGGGTAAGGTAGAAATAGCATGCATTTCATTATATG
391 CATAAGAGGGAAAAGTGTTCGACTAGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACG
17082017 AGCCTAGGGACTAAAACGTAAAAATGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGT
456 AGCCTAGGGACTAAAACGTAAAAATGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGT
17082082 GAAATTTAGACTTGAAAAGGTATAATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTC
521 GAAATTTAGACTTGAAAAGGTATAATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTC
17082147 GAGGAATAAATTTCAGAGTAAGATCGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTC
586 GAGGAATAAATTTCAGAGTAAGATCGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTC
17082212 CGAGACAAATTTCAGGTAAGTTCGAATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGAT
651 CGAGACAAATTTCAGGTAAGTTCGAATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGAT
17082277 T
716 T
17082278 TCAAATAAAATGGGAAAAATAAGCCAAAAATCAGCTTATTGTTTCATGTTGCTGCCGAAAATTTG
1 TCAAATAAAATGGGAAAAATAAGCCAAAAATCAGCTTATTGTTTCATGTTGCTGCCGAAAATTTG
17082343 GGGTTCTCCATAGCTAGGGTTTTCAAGCTTTTCAAGCTCAATAGTAAGTACTCTCAAGCCCCGTT
66 GGGTTCTCCATAGCTAGGGTTTTCAAGCTTTTCAAGCTCAATAGTAAGTACTCTCAAGCCCCGTT
17082408 TTTAATGTTCTTTATATTTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCAT
131 TTTAATGTTCTTTATATTTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCAT
17082473 GCTAGGGTTCATTTTTAGAAATTTACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGA
196 GCTAGGGTTCATTTTTAGAAATTTACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGA
17082538 ATATGAAGGTTGGATGTGTGTTAAACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAG
261 ATATGAAGGTTGGATGTGTGTTAAACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAG
17082603 GACCTTTTTGCAAAAGGTGTAAAGTATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGC
326 GACCTTTTTGCAAAAGGTGTAAAGTATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGC
* *
17082668 CATAAGAGGGAAAAGTGTTTGGCTAGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACG
391 CATAAGAGGGAAAAGTGTTCGACTAGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACG
17082733 AGCCTAGGGACTAAAACGTAAAAATGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGT
456 AGCCTAGGGACTAAAACGTAAAAATGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGT
17082798 GAAATTTAGACTTGAAAAGGTATAATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTC
521 GAAATTTAGACTTGAAAAGGTATAATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTC
17082863 GAGGAATAAATTTCAGAGTAAGATCGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTC
586 GAGGAATAAATTTCAGAGTAAGATCGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTC
17082928 CGAGACAAATTTCAGGTAAGTTCGAATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGAT
651 CGAGACAAATTTCAGGTAAGTTCGAATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGAT
17082993 T
716 T
17082994 T
1 T
17082995 ATGAATGTAT
Statistics
Matches: 712, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
716 712 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.32
Consensus pattern (716 bp):
TCAAATAAAATGGGAAAAATAAGCCAAAAATCAGCTTATTGTTTCATGTTGCTGCCGAAAATTTG
GGGTTCTCCATAGCTAGGGTTTTCAAGCTTTTCAAGCTCAATAGTAAGTACTCTCAAGCCCCGTT
TTTAATGTTCTTTATATTTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCAT
GCTAGGGTTCATTTTTAGAAATTTACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGA
ATATGAAGGTTGGATGTGTGTTAAACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAG
GACCTTTTTGCAAAAGGTGTAAAGTATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGC
CATAAGAGGGAAAAGTGTTCGACTAGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACG
AGCCTAGGGACTAAAACGTAAAAATGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGT
GAAATTTAGACTTGAAAAGGTATAATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTC
GAGGAATAAATTTCAGAGTAAGATCGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTC
CGAGACAAATTTCAGGTAAGTTCGAATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGAT
T
Found at i:17083425 original size:84 final size:84
Alignment explanation
Indices: 17083284--17083451 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
17083274 TATTTTTGAA
17083284 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAAAAATTT
1 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAAAAATTT
17083349 ACCCATGCATTAGTTACTT
66 ACCCATGCATTAGTTACTT
*
17083368 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
1 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAAAAATTT
17083433 ACCCATGCATTAGTTACTT
66 ACCCATGCATTAGTTACTT
17083452 GTATTTTGAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (84 bp):
ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAAAAATTT
ACCCATGCATTAGTTACTT
Found at i:17083771 original size:936 final size:936
Alignment explanation
Indices: 17082432--17084185 Score: 3481
Period size: 936 Copynumber: 1.9 Consensus size: 936
17082422 TATTTTTGAA
17082432 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
1 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
17082497 ACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGAATATGAAGGTTGGATGTGTGTTAA
66 ACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGAATATGAAGGTTGGATGTGTGTTAA
17082562 ACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAGGACCTTTTTGCAAAAGGTGTAAAG
131 ACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAGGACCTTTTTGCAAAAGGTGTAAAG
* *
17082627 TATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGCCATAAGAGGGAAAAGTGTTTGGCT
196 TATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGCCATAAGAGGGAAAAGTGTTCGACT
17082692 AGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACGAGCCTAGGGACTAAAACGTAAAAA
261 AGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACGAGCCTAGGGACTAAAACGTAAAAA
17082757 TGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGTGAAATTTAGACTTGAAAAGGTATA
326 TGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGTGAAATTTAGACTTGAAAAGGTATA
17082822 ATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTCGAGGAATAAATTTCAGAGTAAGAT
391 ATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTCGAGGAATAAATTTCAGAGTAAGAT
17082887 CGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTCCGAGACAAATTTCAGGTAAGTTCG
456 CGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTCCGAGACAAATTTCAGGTAAGTTCG
17082952 AATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGATTTATGAATGTATGGGAATTGCATT
521 AATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGATTTATGAATGTATGGGAATTGCATT
17083017 TGATGATGGCATGAAAATTTATGAAATATATCCTTAATAATGACATGTTGATAAATGTCCCGATT
586 TGATGATGGCATGAAAATTTATGAAATATATCCTTAATAATGACATGTTGATAAATGTCCCGATT
17083082 GAGGTTGGAAAGGAAATCTGATGGATAAACCATAGCTTCAATGACTTGAGATCCTGCATGTGTTG
651 GAGGTTGGAAAGGAAATCTGATGGATAAACCATAGCTTCAATGACTTGAGATCCTGCATGTGTTG
17083147 CAGAAAGGATTCAGCCAGGACAGGTAATCTGTTGATCTCAAATATAAAAAGGATCTAGCCCGAAT
716 CAGAAAGGATTCAGCCAGGACAGGTAATCTGTTGATCTCAAATATAAAAAGGATCTAGCCCGAAT
17083212 GGGTGTTCCTTGAGTGATCGAGCCTCCCGAAGAATATCAAGCCCCGTTTTTAATGTTCTTTATAT
781 GGGTGTTCCTTGAGTGATCGAGCCTCCCGAAGAATATCAAGCCCCGTTTTTAATGTTCTTTATAT
17083277 TTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTA
846 TTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTA
17083342 AAAATTTACCCATGCATTAGTTACTT
911 AAAATTTACCCATGCATTAGTTACTT
17083368 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
1 ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
17083433 ACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGAATATGAAGGTTGGATGTGTGTTAA
66 ACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGAATATGAAGGTTGGATGTGTGTTAA
17083498 ACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAGGACCTTTTTGCAAAAGGTGTAAAG
131 ACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAGGACCTTTTTGCAAAAGGTGTAAAG
17083563 TATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGCCATAAGAGGGAAAAGTGTTCGACT
196 TATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGCCATAAGAGGGAAAAGTGTTCGACT
*
17083628 AGGCTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACGAGCCTAGGGACTAAAACGTAAAAA
261 AGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACGAGCCTAGGGACTAAAACGTAAAAA
17083693 TGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGTGAAATTTAGACTTGAAAAGGTATA
326 TGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGTGAAATTTAGACTTGAAAAGGTATA
17083758 ATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTCGAGGAATAAATTTCAGAGTAAGAT
391 ATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTCGAGGAATAAATTTCAGAGTAAGAT
17083823 CGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTCCGAGACAAATTTCAGGTAAGTTCG
456 CGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTCCGAGACAAATTTCAGGTAAGTTCG
17083888 AATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGATTTATGAATGTATGGGAATTGCATT
521 AATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGATTTATGAATGTATGGGAATTGCATT
17083953 TGATGATGGCATGAAAATTTATGAAATATATCCTTAATAATGACATGTTGATAAATGTCCCGATT
586 TGATGATGGCATGAAAATTTATGAAATATATCCTTAATAATGACATGTTGATAAATGTCCCGATT
17084018 GAGGTTGGAAAGGAAATCTGATGGATAAACCATAGCTTCAATGACTTGAGATCCTGCATGTGTTG
651 GAGGTTGGAAAGGAAATCTGATGGATAAACCATAGCTTCAATGACTTGAGATCCTGCATGTGTTG
17084083 CAGAAAGGATTCAGCCAGGACAGGTAATCTGTTGATCTCAAATATAAAAAGGATCTAGCCCGAAT
716 CAGAAAGGATTCAGCCAGGACAGGTAATCTGTTGATCTCAAATATAAAAAGGATCTAGCCCGAAT
17084148 GGGTGTTCCTTGAGTGATCGAGCCTCCCGAAGAATATC
781 GGGTGTTCCTTGAGTGATCGAGCCTCCCGAAGAATATC
17084186 TGTGCATTGT
Statistics
Matches: 815, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
936 815 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (936 bp):
ATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTAGAAATTT
ACCCATGCATTAGTTACTTGTATTTTGATGTTTATGGAGGAATATGAAGGTTGGATGTGTGTTAA
ACATCTTTTCCTAGGTGATTTTCATGAAAAACCCCTAAAAGGACCTTTTTGCAAAAGGTGTAAAG
TATGAGGTAGAAATGTGACATAATGGAAAAATGTGGGCTGCCATAAGAGGGAAAAGTGTTCGACT
AGACTTGGGTAAGGTAGAAATAGCATGCATTTCATTATACGAGCCTAGGGACTAAAACGTAAAAA
TGTGAAAGGTTAGGGGTAAAACGGTCATTTGGACCAGGGGTGAAATTTAGACTTGAAAAGGTATA
ATGTGAGGTGTTAGTAATTTAATTTTATTATTATAGACCTCGAGGAATAAATTTCAGAGTAAGAT
CGAGGAAAACGAAAAGTTTCAGAATAACTGAAACACGATTCCGAGACAAATTTCAGGTAAGTTCG
AATAACTTAAAGTAAACTCATAGTATGCTTAATTGCATGATTTATGAATGTATGGGAATTGCATT
TGATGATGGCATGAAAATTTATGAAATATATCCTTAATAATGACATGTTGATAAATGTCCCGATT
GAGGTTGGAAAGGAAATCTGATGGATAAACCATAGCTTCAATGACTTGAGATCCTGCATGTGTTG
CAGAAAGGATTCAGCCAGGACAGGTAATCTGTTGATCTCAAATATAAAAAGGATCTAGCCCGAAT
GGGTGTTCCTTGAGTGATCGAGCCTCCCGAAGAATATCAAGCCCCGTTTTTAATGTTCTTTATAT
TTTTGAAATCCTGGTAGCTTACTCTCTCTATTTCTACCCATATTTCATGCTAGGGTTCATTTTTA
AAAATTTACCCATGCATTAGTTACTT
Found at i:17092338 original size:47 final size:44
Alignment explanation
Indices: 17092222--17092347 Score: 128
Period size: 47 Copynumber: 2.7 Consensus size: 44
17092212 TTATTTGTGT
* * *
17092222 GCTAGTGTAAGACATGTCTGAGACATGCATTGGCCACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTACGAGA
* * *
17092268 GCCAGTGTAAAACCATGTATGGGACATGGCATCGG-CATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATT---ACGAGA
17092316 GCTAGTGTAAGACATGTCTGGGACATGCATCG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCG
17092348 ACTACAAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
45 4 0.06
46 16 0.24
47 25 0.38
48 21 0.32
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.23
Consensus pattern (44 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTACGAGA
Found at i:17092429 original size:50 final size:48
Alignment explanation
Indices: 17092270--17092489 Score: 140
Period size: 47 Copynumber: 4.6 Consensus size: 48
17092260 TTATGAGAGC
* * * * *
17092270 CAGTGTAAAACCATGTATGGGACATGGCATCGGCATTGAGA-CGA-GAGCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ATCG-GATAGATGAGGT
* *
17092319 -AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTAC--A-AAATG-TGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGA-T-CGGATAGATGAGGT
* *
17092362 CAATGTAAGACCATGTCTGGGACATGGGATCAGCA-CGGATATG-TGAGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATC-G-ATCGGATA-GATGAG-GT
** ** *
17092412 CAGTGTAAGACCATGTCTAAGACATGGCATCGATTTGATAGATGAGCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGATCGGATAGATGAGGT
*
17092460 -AGTGTAAGACCATGTCTGGGACATGACATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
17092490 AACATTATAC
Statistics
Matches: 134, Mismatches: 21, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
43 3 0.02
44 10 0.07
45 17 0.13
46 9 0.07
47 42 0.31
48 15 0.11
49 9 0.07
50 29 0.22
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGATCGGATAGATGAGGT
Found at i:17093232 original size:16 final size:16
Alignment explanation
Indices: 17093211--17093241 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17093201 GCCGTGTGTG
17093211 ACACACGGCCAGCCCA
1 ACACACGGCCAGCCCA
17093227 ACACACGGCCAGCCC
1 ACACACGGCCAGCCC
17093242 CATGGGCGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.52, G:0.19, T:0.00
Consensus pattern (16 bp):
ACACACGGCCAGCCCA
Found at i:17100261 original size:21 final size:22
Alignment explanation
Indices: 17100237--17100283 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
17100227 GTCCCTGCAC
*
17100237 CACACGGACGTGTGCC-TCTGT
1 CACACGGACGTGTGCCACCTGT
* *
17100258 CACATGGCCGTGTGCCACCTGT
1 CACACGGACGTGTGCCACCTGT
17100280 CACA
1 CACA
17100284 TGGGCGTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.21
Consensus pattern (22 bp):
CACACGGACGTGTGCCACCTGT
Found at i:17100282 original size:22 final size:21
Alignment explanation
Indices: 17100245--17100286 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
17100235 ACCACACGGA
*
17100245 CGTGTGCCTCTGTCACATGGC
1 CGTGTGCCCCTGTCACATGGC
17100266 CGTGTGCCACCTGTCACATGG
1 CGTGTGCC-CCTGTCACATGG
17100287 GCGTTTCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.12, C:0.33, G:0.29, T:0.26
Consensus pattern (21 bp):
CGTGTGCCCCTGTCACATGGC
Found at i:17104110 original size:26 final size:29
Alignment explanation
Indices: 17104081--17104144 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
17104071 AATCAATAAA
17104081 ATAATATT-ATA-ATATATAACTATTA-C
1 ATAATATTAATACATATATAACTATTATC
*
17104107 ATAAAATATTAATACATATATAACTATTATT
1 AT--AATATTAATACATATATAACTATTATC
17104138 ATAATAT
1 ATAATAT
17104145 AGATTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 2 0.06
28 6 0.19
29 8 0.25
30 14 0.44
31 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATATTAATACATATATAACTATTATC
Found at i:17104111 original size:31 final size:30
Alignment explanation
Indices: 17104059--17104135 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
17104049 TATAATAAAT
* * *
17104059 TAATATATTACTAAT-CAATAAAATAATATTA
1 TAATATATAACTATTACAATAAAAT-AT-TAA
17104090 TAATATATAACTATTAC-ATAAAATATTAA
1 TAATATATAACTATTACAATAAAATATTAA
17104119 TACATATATAACTATTA
1 TA-ATATATAACTATTA
17104136 TTATAATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.10
30 16 0.39
31 20 0.49
32 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATATATAACTATTACAATAAAATATTAA
Found at i:17104243 original size:16 final size:15
Alignment explanation
Indices: 17104200--17104248 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
17104190 ATCATCGATG
*
17104200 TATATATATAAATTA
1 TATATATATATATTA
*
17104215 TAAATATATTATATTA
1 TATATATA-TATATTA
*
17104231 TATATATCATATAATA
1 TATATAT-ATATATTA
17104247 TA
1 TA
17104249 ATAGGAGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 7 0.25
16 20 0.71
17 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATATTA
Found at i:17104585 original size:17 final size:17
Alignment explanation
Indices: 17104563--17104599 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
17104553 AGAATAAAAA
17104563 AATAATACATAATATAT
1 AATAATACATAATATAT
**
17104580 AATAATATGTAATATAT
1 AATAATACATAATATAT
17104597 AAT
1 AAT
17104600 GTATTACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AATAATACATAATATAT
Found at i:17105811 original size:34 final size:34
Alignment explanation
Indices: 17105724--17105847 Score: 176
Period size: 34 Copynumber: 3.6 Consensus size: 34
17105714 TATTTATGGC
*
17105724 AGGTACATGCGAACTGTATATGTGTGCAAACCCT
1 AGGTACATGCGAACTGTATATGTGTGCGAACCCT
* * *
17105758 AGGTGACATGTGAATTGTATATGTGTGCGAACTCT
1 AGGT-ACATGCGAACTGTATATGTGTGCGAACCCT
* *
17105793 AGGTACATGTGAACTGTATATGTGTACGAACCCT
1 AGGTACATGCGAACTGTATATGTGTGCGAACCCT
*
17105827 AGGTATATGCGAACTGTATAT
1 AGGTACATGCGAACTGTATAT
17105848 ATATATGTGA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
34 50 0.62
35 30 0.38
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (34 bp):
AGGTACATGCGAACTGTATATGTGTGCGAACCCT
Found at i:17105860 original size:36 final size:34
Alignment explanation
Indices: 17105724--17105877 Score: 137
Period size: 34 Copynumber: 4.4 Consensus size: 34
17105714 TATTTATGGC
* * * * *
17105724 AGGTACATGCGAACTGTATATGTGTGCAAACCCT
1 AGGTACATGTGAACTGTATATATATACGAACCCT
* * * * *
17105758 AGGTGACATGTGAATTGTATATGTGTGCGAACTCT
1 AGGT-ACATGTGAACTGTATATATATACGAACCCT
* *
17105793 AGGTACATGTGAACTGTATATGTGTACGAACCCT
1 AGGTACATGTGAACTGTATATATATACGAACCCT
* * *
17105827 AGGTATATGCGAACTGTATATATATATGTGAACCCT
1 AGGTACATGTGAACTGTATATATATA--CGAACCCT
*
17105863 ATGTACATGTGAACT
1 AGGTACATGTGAACT
17105878 ATGCAAAACC
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
34 53 0.52
35 30 0.29
36 19 0.19
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (34 bp):
AGGTACATGTGAACTGTATATATATACGAACCCT
Found at i:17106196 original size:34 final size:34
Alignment explanation
Indices: 17106158--17106316 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 34
17106148 TATTTATGGC
*
17106158 AGGTACATGCAAACTGTATATGTATGCGAACCCT
1 AGGTACATGCAAACTGTATATGTGTGCGAACCCT
** * **
17106192 AGGTAACATGTGAATTGTATATGTGTATGAACCCT
1 AGGT-ACATGCAAACTGTATATGTGTGCGAACCCT
***
17106227 AGGTAACATGTGGACTGTATATGTGTGCGAACCCT
1 AGGT-ACATGCAAACTGTATATGTGTGCGAACCCT
*
17106262 AGGTATATGCAAACTGTATATGTGTGCGAACCCT
1 AGGTACATGCAAACTGTATATGTGTGCGAACCCT
* * * *
17106296 AGATATATGCTAACTATATAT
1 AGGTACATGCAAACTGTATAT
17106317 ATATATGTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 48 0.45
35 59 0.55
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (34 bp):
AGGTACATGCAAACTGTATATGTGTGCGAACCCT
Found at i:17106211 original size:35 final size:35
Alignment explanation
Indices: 17106169--17106297 Score: 179
Period size: 35 Copynumber: 3.7 Consensus size: 35
17106159 GGTACATGCA
*
17106169 AACTGTATATGTATGCGAACCCTAGGTAACATGTG
1 AACTGTATATGTGTGCGAACCCTAGGTAACATGTG
* **
17106204 AATTGTATATGTGTATGAACCCTAGGTAACATGTG
1 AACTGTATATGTGTGCGAACCCTAGGTAACATGTG
* * **
17106239 GACTGTATATGTGTGCGAACCCTAGGT-ATATGCA
1 AACTGTATATGTGTGCGAACCCTAGGTAACATGTG
17106273 AACTGTATATGTGTGCGAACCCTAG
1 AACTGTATATGTGTGCGAACCCTAG
17106298 ATATATGCTA
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
34 28 0.34
35 54 0.66
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (35 bp):
AACTGTATATGTGTGCGAACCCTAGGTAACATGTG
Found at i:17107782 original size:55 final size:55
Alignment explanation
Indices: 17107715--17107825 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
17107705 ATATATATAA
*
17107715 ATTGTTAATATATTTTATACTATATGATATGATATAACATTATAGTAGAAGAGTT
1 ATTGTTAATATATTATATACTATATGATATGATATAACATTATAGTAGAAGAGTT
* *
17107770 ATTGTTAATATATTATATATTATATGATATGATATAACATTATAGTAGAAGGGTT
1 ATTGTTAATATATTATATACTATATGATATGATATAACATTATAGTAGAAGAGTT
17107825 A
1 A
17107826 ACTTCCAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (55 bp):
ATTGTTAATATATTATATACTATATGATATGATATAACATTATAGTAGAAGAGTT
Found at i:17108106 original size:8 final size:8
Alignment explanation
Indices: 17108088--17108117 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
17108078 AAATATATAA
17108088 AATATTATT
1 AATA-TATT
17108097 AATATATT
1 AATATATT
17108105 AATATATT
1 AATATATT
17108113 AATAT
1 AATAT
17108118 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATATATT
Found at i:17114304 original size:32 final size:32
Alignment explanation
Indices: 17114268--17114333 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
17114258 AAATATTAAT
17114268 TTATTGGGAAAAAGAAAAAGAAAAAATAGAAG
1 TTATTGGGAAAAAGAAAAAGAAAAAATAGAAG
17114300 TTATTGGGAAAAAGAAAAAGAAAAAATAGAAG
1 TTATTGGGAAAAAGAAAAAGAAAAAATAGAAG
17114332 TT
1 TT
17114334 GGAAAATTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.21, T:0.18
Consensus pattern (32 bp):
TTATTGGGAAAAAGAAAAAGAAAAAATAGAAG
Found at i:17117568 original size:17 final size:17
Alignment explanation
Indices: 17117546--17117581 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
17117536 AGTTGAATAA
17117546 TTCAATAAAGTAAGATT
1 TTCAATAAAGTAAGATT
17117563 TTCAATAAAGTAAGATT
1 TTCAATAAAGTAAGATT
17117580 TT
1 TT
17117582 AAAAGACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (17 bp):
TTCAATAAAGTAAGATT
Found at i:17120866 original size:8 final size:8
Alignment explanation
Indices: 17120832--17120898 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
17120822 TCTCTTTTTC
17120832 TTTTATTT
1 TTTTATTT
**
17120840 TCATATTT
1 TTTTATTT
*
17120848 CTTTTGTTTT
1 -TTTT-ATTT
17120858 TTTTATTT
1 TTTTATTT
*
17120866 TCTTATTT
1 TTTTATTT
17120874 CTTTT-TTT
1 -TTTTATTT
*
17120882 TTTTACTT
1 TTTTATTT
17120890 TTTTATTT
1 TTTTATTT
17120898 T
1 T
17120899 GTTCCTTAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
7 4 0.09
8 29 0.64
9 9 0.20
10 3 0.07
ACGTcount: A:0.10, C:0.07, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:17120867 original size:26 final size:25
Alignment explanation
Indices: 17120821--17120885 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 25
17120811 GCCTCACACG
* *
17120821 TTCTCTTTTTCTTTTATTTTCATAT
1 TTCTTTTTTTTTTTTATTTTCATAT
*
17120846 TTCTTTTGTTTTTTTTATTTTCTTAT
1 TTCTTTT-TTTTTTTTATTTTCATAT
17120872 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
17120886 ACTTTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 13 0.36
26 23 0.64
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTTTTTTTTTATTTTCATAT
Found at i:17120955 original size:24 final size:24
Alignment explanation
Indices: 17120918--17120978 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
17120908 TAAATTGTCT
* * *
17120918 TTTTATTTTTTTTCCTTTT-TTGA
1 TTTTGTTTTATTTCATTTTGTTGA
* *
17120941 TTTTTTTCTTATTTCATTTTGTTTA
1 TTTTGTT-TTATTTCATTTTGTTGA
17120966 TTTTGTTTTATTT
1 TTTTGTTTTATTT
17120979 TTTATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.19
24 16 0.52
25 9 0.29
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.79
Consensus pattern (24 bp):
TTTTGTTTTATTTCATTTTGTTGA
Found at i:17121194 original size:13 final size:13
Alignment explanation
Indices: 17121176--17121200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17121166 TTAAATAAAC
17121176 AAAATAATATAAG
1 AAAATAATATAAG
17121189 AAAATAATATAA
1 AAAATAATATAA
17121201 AACTTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAATAATATAAG
Found at i:17121229 original size:19 final size:20
Alignment explanation
Indices: 17121205--17121260 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
17121195 ATATAAAACT
17121205 TAAAAAAGAAAAAAAATTAA
1 TAAAAAAGAAAAAAAATTAA
* * *
17121225 -GAAAAAG-ACAAAATTTAA
1 TAAAAAAGAAAAAAAATTAA
17121243 TAAAAAAGTAAAAAAAAT
1 TAAAAAAG-AAAAAAAAT
17121261 AAGGGTGGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
21 6 0.22
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (20 bp):
TAAAAAAGAAAAAAAATTAA
Found at i:17121336 original size:20 final size:21
Alignment explanation
Indices: 17121304--17121343 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
17121294 TGACTCCACC
17121304 AAAAAAAAGTTAAA-AAATTT
1 AAAAAAAAGTTAAAGAAATTT
17121324 AAAAAGAAA-TTAAAGAAATT
1 AAAAA-AAAGTTAAAGAAATT
17121344 GTATTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAAAAAGTTAAAGAAATTT
Found at i:17121577 original size:18 final size:18
Alignment explanation
Indices: 17121554--17121607 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
17121544 ACAAATTTTT
*
17121554 TTAAATTAATAATATAAA
1 TTAAATAAATAATATAAA
* *
17121572 TTAAATAAACAAAATAAA
1 TTAAATAAATAATATAAA
* *
17121590 ATAAAAAAATAATATAAA
1 TTAAATAAATAATATAAA
17121608 ACTTAAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TTAAATAAATAATATAAA
Found at i:17121586 original size:14 final size:13
Alignment explanation
Indices: 17121569--17121608 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17121559 TTAATAATAT
*
17121569 AAATTAAATAAACA
1 AAATAAAATAAA-A
17121583 AAATAAAATAAAA
1 AAATAAAATAAAA
*
17121596 AAATAATATAAAA
1 AAATAAAATAAAA
17121609 CTTAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:17121627 original size:36 final size:38
Alignment explanation
Indices: 17121561--17121636 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
17121551 TTTTTAAATT
17121561 AATAATATAAATTAAATAAACAAAATAAAA-TAA-AAA
1 AATAATATAAATTAAATAAACAAAATAAAATTAAGAAA
*
17121597 AATAATATAAAACTTAAA-AAAGAAAA-AAAATTAAGAAA
1 AATAATAT-AAA-TTAAATAAACAAAATAAAATTAAGAAA
17121635 AA
1 AA
17121637 GACAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 12 0.34
37 13 0.37
38 10 0.29
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (38 bp):
AATAATATAAATTAAATAAACAAAATAAAATTAAGAAA
Found at i:17121771 original size:20 final size:19
Alignment explanation
Indices: 17121740--17121786 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
17121730 CCAACTTTTT
17121740 AAAAATTTAAAA-AAAGTTA
1 AAAAATTTAAAAGAAA-TTA
17121759 AAAAATTTAAAAAGAAATTA
1 AAAAATTT-AAAAGAAATTA
17121779 AAGAAATT
1 AA-AAATT
17121787 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 9 0.36
21 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAAGAAATTA
Found at i:17121857 original size:14 final size:14
Alignment explanation
Indices: 17121838--17121864 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17121828 AAAAATATGG
17121838 TTAATATTTAAAAA
1 TTAATATTTAAAAA
17121852 TTAATATTTAAAA
1 TTAATATTTAAAA
17121865 TTTTCAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:17121990 original size:21 final size:23
Alignment explanation
Indices: 17121943--17122000 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
17121933 TAAAGTTAAA
17121943 AAAACATTTTTAAAAATAATAATT
1 AAAACA-TTTTAAAAATAATAATT
*
17121967 -AAA-ATTTTAAAAA-AATATTAT
1 AAAACATTTTAAAAATAATAAT-T
17121988 AAAACATTTTAAA
1 AAAACATTTTAAA
17122001 TATACATTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 5 0.17
21 10 0.33
22 4 0.13
23 11 0.37
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAACATTTTAAAAATAATAATT
Found at i:17122009 original size:23 final size:22
Alignment explanation
Indices: 17121943--17122009 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
17121933 TAAAGTTAAA
*
17121943 AAAACATTTTTAAAAATAATAAT
1 AAAACA-TTTTAAAAATAATTAT
* *
17121966 TAAA-ATTTTAAAAAAATATTAT
1 AAAACATTTTAAAAATA-ATTAT
*
17121988 AAAACATTTTAAATATACATTA
1 AAAACATTTTAAAAATA-ATTA
17122010 CAAATTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.29
22 8 0.23
23 17 0.49
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAACATTTTAAAAATAATTAT
Found at i:17122078 original size:17 final size:17
Alignment explanation
Indices: 17122032--17122088 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
17122022 AGTTAATAAT
* *
17122032 AAAAAATAAAACAAAATG
1 AAAAAAGAAAA-AAAATC
*
17122050 AAATAAGAAAAAAAATC
1 AAAAAAGAAAAAAAATC
17122067 AAAAAAGGAAAAAAAAT-
1 AAAAAA-GAAAAAAAATC
17122084 AAAAA
1 AAAAA
17122089 GACAATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 15 0.44
18 19 0.56
ACGTcount: A:0.81, C:0.04, G:0.07, T:0.09
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATC
Found at i:17122128 original size:16 final size:16
Alignment explanation
Indices: 17122107--17122177 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
17122097 ATTAAGGAAC
17122107 AAAATAA-AAAAGTAAA
1 AAAATAAGAAAA-TAAA
17122123 AAAATAAGAAAATAAA
1 AAAATAAGAAAATAAA
*
17122139 AGAAA-AA-AACA-AAA
1 A-AAATAAGAAAATAAA
* *
17122153 GAAATATGAAAATAAA
1 AAAATAAGAAAATAAA
17122169 AAAA-AAGAA
1 AAAATAAGAA
17122178 CGTGTCAGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 10 0.23
16 20 0.45
17 7 0.16
ACGTcount: A:0.80, C:0.01, G:0.08, T:0.10
Consensus pattern (16 bp):
AAAATAAGAAAATAAA
Found at i:17122145 original size:22 final size:24
Alignment explanation
Indices: 17122114--17122174 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
17122104 AACAAAATAA
* *
17122114 AAAAGTAAAAAAATAAGAAA-AT-
1 AAAAGAAAAAAAAAAAGAAATATG
17122136 AAAAGAAAAAAACAAAAGAAATATG
1 AAAAGAAAAAAA-AAAAGAAATATG
*
17122161 AAAATAAAAAAAAA
1 AAAAGAAAAAAAAA
17122175 GAACGTGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 11 0.33
23 7 0.21
24 4 0.12
25 11 0.33
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (24 bp):
AAAAGAAAAAAAAAAAGAAATATG
Found at i:17122172 original size:8 final size:8
Alignment explanation
Indices: 17122107--17122172 Score: 55
Period size: 8 Copynumber: 8.5 Consensus size: 8
17122097 ATTAAGGAAC
17122107 AAAATAAA
1 AAAATAAA
*
17122115 AAAGTAAA
1 AAAATAAA
*
17122123 AAAATAAG
1 AAAATAAA
17122131 AAAATAAA
1 AAAATAAA
*
17122139 AGAA-AAA
1 AAAATAAA
*
17122146 AACA-AAA
1 AAAATAAA
* **
17122153 GAAATATG
1 AAAATAAA
17122161 AAAATAAA
1 AAAATAAA
17122169 AAAA
1 AAAA
17122173 AAGAACGTGT
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
7 10 0.23
8 33 0.77
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:17122175 original size:22 final size:21
Alignment explanation
Indices: 17122107--17122177 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 21
17122097 ATTAAGGAAC
17122107 AAAATAAAAAAGTAAAAAAATAAG
1 AAAAT-AAAAA-TAAAAAAA-AAG
*
17122131 AAAATAAAAGAAAAAAACAAAAG
1 AAAATAAAA-ATAAAAA-AAAAG
*
17122154 AAATATGAAAATAAAAAAAAAG
1 AAA-ATAAAAATAAAAAAAAAG
17122176 AA
1 AA
17122178 CGTGTCAGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.17
23 21 0.51
24 13 0.32
ACGTcount: A:0.80, C:0.01, G:0.08, T:0.10
Consensus pattern (21 bp):
AAAATAAAAATAAAAAAAAAG
Found at i:17122537 original size:42 final size:44
Alignment explanation
Indices: 17122490--17122582 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
17122480 TAAAAAAGCC
17122490 AATAAAATTA-CA-ATATAAATTTATCTTTTTCATTTTTTATCA
1 AATAAAATTATCATATATAAATTTATCTTTTTCATTTTTTATCA
*
17122532 AATAAAATTATTATATATAAATTTATCTTTTTCATTTTTTATCA
1 AATAAAATTATCATATATAAATTTATCTTTTTCATTTTTTATCA
17122576 AATAAAA
1 AATAAAA
17122583 ATTCATTAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 10 0.21
43 1 0.02
44 37 0.77
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (44 bp):
AATAAAATTATCATATATAAATTTATCTTTTTCATTTTTTATCA
Found at i:17125798 original size:22 final size:24
Alignment explanation
Indices: 17125771--17125816 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
17125761 GATGTGAATG
17125771 AAAAAATTG-TATAAAAAT-ATAA
1 AAAAAATTGATATAAAAATCATAA
*
17125793 AAAAAATTGATATCAAAATCATAA
1 AAAAAATTGATATAAAAATCATAA
17125817 TAGATGTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAAATTGATATAAAAATCATAA
Found at i:17129179 original size:37 final size:37
Alignment explanation
Indices: 17129129--17129205 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
17129119 GTCACATTAT
17129129 GACTTCCTTCTGCTTAGGTCCATTCTTGATATTTTTA
1 GACTTCCTTCTGCTTAGGTCCATTCTTGATATTTTTA
17129166 GACTTCCTTCTGCTTAGGTCCATTCTTGATATTTTTA
1 GACTTCCTTCTGCTTAGGTCCATTCTTGATATTTTTA
17129203 GAC
1 GAC
17129206 CTTGTGTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (37 bp):
GACTTCCTTCTGCTTAGGTCCATTCTTGATATTTTTA
Found at i:17129296 original size:13 final size:13
Alignment explanation
Indices: 17129278--17129309 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
17129268 AAATTATACT
17129278 AGTAATTTTATTA
1 AGTAATTTTATTA
17129291 AGTAATTTTATTA
1 AGTAATTTTATTA
*
17129304 AATAAT
1 AGTAAT
17129310 ACATTAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
AGTAATTTTATTA
Found at i:17130128 original size:6 final size:6
Alignment explanation
Indices: 17130110--17130150 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
17130100 TAATATTGGA
* * *
17130110 GGAGAT GGGGAT GGAGAT GGAGAT GGGGAT GAAGAT GGAGA
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGAGA
17130151 GGAAAGCTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGAGAT
Found at i:17130133 original size:18 final size:18
Alignment explanation
Indices: 17130110--17130150 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
17130100 TAATATTGGA
*
17130110 GGAGATGGGGATGGAGAT
1 GGAGATGGGGATGAAGAT
17130128 GGAGATGGGGATGAAGAT
1 GGAGATGGGGATGAAGAT
17130146 GGAGA
1 GGAGA
17130151 GGAAAGCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.15
Consensus pattern (18 bp):
GGAGATGGGGATGAAGAT
Found at i:17131129 original size:18 final size:19
Alignment explanation
Indices: 17131101--17131145 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
17131091 TATCAAATAA
*
17131101 ATTTATTAAATATAAATTC
1 ATTTATTAAATAAAAATTC
17131120 ATTT-TTAAATAAAAATT-
1 ATTTATTAAATAAAAATTC
17131137 ATTATATTA
1 ATT-TATTA
17131146 TAACACTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTATTAAATAAAAATTC
Found at i:17139382 original size:9 final size:9
Alignment explanation
Indices: 17139368--17139401 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
17139358 GGGTGTTTTA
17139368 TTTTTTCTC
1 TTTTTTCTC
*
17139377 TTTTTTCTT
1 TTTTTTCTC
17139386 TTTTTTCTC
1 TTTTTTCTC
17139395 TTTTTTC
1 TTTTTTC
17139402 CCTTGTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:17146087 original size:10 final size:11
Alignment explanation
Indices: 17146074--17146119 Score: 69
Period size: 10 Copynumber: 4.4 Consensus size: 11
17146064 TTTTTTCTTC
17146074 TTTTCAATTTT
1 TTTTCAATTTT
*
17146085 TTTT-GATTTT
1 TTTTCAATTTT
17146095 TTTTCAATTTT
1 TTTTCAATTTT
17146106 TTTTC-ATTTT
1 TTTTCAATTTT
17146116 TTTT
1 TTTT
17146120 AAATATCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 14 0.44
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTCAATTTT
Found at i:17146098 original size:21 final size:21
Alignment explanation
Indices: 17146074--17146119 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
17146064 TTTTTTCTTC
*
17146074 TTTTCAATTTTTTTTGATTTT
1 TTTTCAATTTTTTTTCATTTT
17146095 TTTTCAATTTTTTTTCATTTT
1 TTTTCAATTTTTTTTCATTTT
17146116 TTTT
1 TTTT
17146120 AAATATCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTTCAATTTTTTTTCATTTT
Found at i:17147365 original size:31 final size:32
Alignment explanation
Indices: 17147320--17147386 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 32
17147310 ACATGCATCC
*
17147320 ACCTTGCTAAAATGAATCTCCA-A-ATTCGGCTA
1 ACCTTGCTAAAATG-ATC-CCATACATTCGGCCA
*
17147352 ACCTTG-TTAAATGATCCCATACATTCGGCCA
1 ACCTTGCTAAAATGATCCCATACATTCGGCCA
17147383 ACCT
1 ACCT
17147387 ATATAAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 3 0.10
30 4 0.13
31 18 0.58
32 6 0.19
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (32 bp):
ACCTTGCTAAAATGATCCCATACATTCGGCCA
Found at i:17152097 original size:13 final size:13
Alignment explanation
Indices: 17152079--17152103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17152069 TGGTCATCAT
17152079 GGTGTGAACACAA
1 GGTGTGAACACAA
17152092 GGTGTGAACACA
1 GGTGTGAACACA
17152104 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:17154398 original size:53 final size:53
Alignment explanation
Indices: 17154335--17154440 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
17154325 GTTTAATTTT
17154335 ATTAGTTACTTATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCA
1 ATTAGTTACTTATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCA
17154388 ATTAGTTACTTATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCA
1 ATTAGTTACTTATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCA
17154441 GCCACCCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (53 bp):
ATTAGTTACTTATGAGATTAGGATTTGTTGGAGGCCTATATAAGCATTGGCCA
Found at i:17156595 original size:13 final size:13
Alignment explanation
Indices: 17156577--17156601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17156567 GACATGAACA
17156577 CATTTAATCATAT
1 CATTTAATCATAT
17156590 CATTTAATCATA
1 CATTTAATCATA
17156602 ATTAAACAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
CATTTAATCATAT
Found at i:17158684 original size:30 final size:30
Alignment explanation
Indices: 17158582--17158684 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 30
17158572 TCAAGTTAAA
*
17158582 CTAAA-ATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGATTTAGCTCGTGAG
* * * * * *
17158611 CTAAAGT-TAAGCTGAGATTAAACTCCTAAG
1 CTAAA-TATGAGCTAAGATTTAGCTCGTGAG
* ** *
17158641 CTGAAGCTGAGCTAAGGTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGATTTAGCTCGTGAG
17158671 CTAAATATGAGCTA
1 CTAAATATGAGCTA
17158685 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 19, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
29 5 0.10
30 47 0.90
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (30 bp):
CTAAATATGAGCTAAGATTTAGCTCGTGAG
Found at i:17159321 original size:6 final size:5
Alignment explanation
Indices: 17159297--17159359 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
17159287 AAGGGAAAAC
*
17159297 AAAGA AAAGA AAAGAA AAAGCA AAAGCA AAAGA AGA-A AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA
17159345 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
17159360 GAGGCAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 25 0.50
6 20 0.40
7 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:17159327 original size:12 final size:10
Alignment explanation
Indices: 17159297--17159359 Score: 58
Period size: 11 Copynumber: 6.0 Consensus size: 10
17159287 AAGGGAAAAC
17159297 AAAGAAAAGA
1 AAAGAAAAGA
17159307 AAAGAAAAAGCA
1 AAAG-AAAAG-A
17159319 AAAGCAAAAGA
1 AAAG-AAAAGA
*
17159330 AGA-AAAAGA
1 AAAGAAAAGA
17159339 AAATGAAATA-A
1 AAA-GAAA-AGA
17159350 AAAGAAAAGA
1 AAAGAAAAGA
17159360 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:17159463 original size:30 final size:31
Alignment explanation
Indices: 17159427--17159508 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
17159417 TTTTGAAATC
* * *
17159427 AAAAAGAAAAAGAAAAAGAAA-ATGAGATTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
*
17159457 AAAAAGAGAATG-AAAAGAAATTTGAGAGTG
1 AAAAAGAGAATGAAAAAGAAATATGAGAGTG
*
17159487 AAAAAGAGGATGAAAAAGAAAT
1 AAAAAGAGAATGAAAAAGAAAT
17159509 TGAAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.18
30 28 0.62
31 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12
Consensus pattern (31 bp):
AAAAAGAGAATGAAAAAGAAATATGAGAGTG
Done.