Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 54 of 141
Found at i:16249193 original size:10 final size:10
Alignment explanation
Indices: 16249169--16249211 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
16249159 TTTCTTCTTC
*
16249169 CTTCTTCTTT
1 CTTCTTTTTT
16249179 CTTCTTTTTT
1 CTTCTTTTTT
*
16249189 TTTC-TTTTT
1 CTTCTTTTTT
16249198 -TTCTTTTTT
1 CTTCTTTTTT
16249207 CTTCT
1 CTTCT
16249212 CCTTCGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 3 0.10
9 10 0.34
10 16 0.55
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTCTTTTTT
Found at i:16249193 original size:17 final size:17
Alignment explanation
Indices: 16249158--16249209 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
16249148 TCTTTCCCCC
* *
16249158 CTTTCTTCTTCCTTCTT
1 CTTTCTTCTTCTTTTTT
*
16249175 CTTTCTTCTTTTTTTTT
1 CTTTCTTCTTCTTTTTT
16249192 CTTT-TT-TTCTTTTTT
1 CTTTCTTCTTCTTTTTT
16249207 CTT
1 CTT
16249210 CTCCTTCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 11 0.35
16 2 0.06
17 18 0.58
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
CTTTCTTCTTCTTTTTT
Found at i:16249728 original size:30 final size:30
Alignment explanation
Indices: 16249692--16249858 Score: 164
Period size: 30 Copynumber: 5.7 Consensus size: 30
16249682 AAATGTAGCA
* *
16249692 AAATTTTTGGGG-CAAAAGTGTAATTTTGAG
1 AAATTTTAGGGGTCAAAA-TGTAATTTTAAG
*
16249722 AAATTTTAGGGGTTAAAATGTAATTTTAAG
1 AAATTTTAGGGGTCAAAATGTAATTTTAAG
* *
16249752 GAAGTTTAGGGGTCAAAATGTAA-TTTAA-
1 AAATTTTAGGGGTCAAAATGTAATTTTAAG
* ** *
16249780 AAATTTTA-GTGTTGAAATGTAATTTTGAG
1 AAATTTTAGGGGTCAAAATGTAATTTTAAG
* * *
16249809 AAAGTTTAGTGGTCAAAATGCAATTTT-AG
1 AAATTTTAGGGGTCAAAATGTAATTTTAAG
*
16249838 AAAAGTTTAGGGGTCAAAATG
1 -AAATTTTAGGGGTCAAAATG
16249859 GAAAAAAAAT
Statistics
Matches: 113, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
27 11 0.10
28 10 0.09
29 14 0.12
30 74 0.65
31 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (30 bp):
AAATTTTAGGGGTCAAAATGTAATTTTAAG
Found at i:16252394 original size:30 final size:30
Alignment explanation
Indices: 16252337--16252398 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
16252327 GCTTTTTGAA
* * *
16252337 AATATTTACAAAAATAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
16252367 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
16252397 AA
1 AA
16252399 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:16258265 original size:15 final size:15
Alignment explanation
Indices: 16258245--16258280 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
16258235 CAATCGCAAG
16258245 AAGTAATAAAGTGAC
1 AAGTAATAAAGTGAC
16258260 AAGTAATAAAGTGAC
1 AAGTAATAAAGTGAC
16258275 AAGTAA
1 AAGTAA
16258281 ATGTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AAGTAATAAAGTGAC
Found at i:16262928 original size:15 final size:15
Alignment explanation
Indices: 16262908--16262943 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
16262898 CAATCGCAAG
16262908 AAGTAATAAAGTGAC
1 AAGTAATAAAGTGAC
16262923 AAGTAATAAAGTGAC
1 AAGTAATAAAGTGAC
16262938 AAGTAA
1 AAGTAA
16262944 ATGTCGAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AAGTAATAAAGTGAC
Found at i:16263868 original size:103 final size:103
Alignment explanation
Indices: 16263753--16263958 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
16263743 AATTAAATTC
16263753 AAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGATATGTTCAGCATAACA
1 AAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGATATGTTCAGCATAACA
*
16263818 ACAACAAAAATTAAAGAGATAGGGAACAAGAATCAAAT
66 ACAACAAAAATTAAAGAGATAGAGAACAAGAATCAAAT
16263856 AAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGATATGTTCAGCATAACA
1 AAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGATATGTTCAGCATAACA
* * *
16263921 ATAACAAAAATTAAAGAGGTAGAGAATAAGAATCAAAT
66 ACAACAAAAATTAAAGAGATAGAGAACAAGAATCAAAT
16263959 CCGGTGTTTT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (103 bp):
AAGCTAAATTGATTAAATTAACCATTCCAACAACATAAATATTCATAGATATGTTCAGCATAACA
ACAACAAAAATTAAAGAGATAGAGAACAAGAATCAAAT
Found at i:16271825 original size:23 final size:22
Alignment explanation
Indices: 16271782--16271825 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
16271772 TTCTAAGTTG
16271782 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
16271805 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
16271826 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:16272027 original size:51 final size:50
Alignment explanation
Indices: 16271969--16272155 Score: 250
Period size: 51 Copynumber: 3.7 Consensus size: 50
16271959 TCAGTTCACA
* *
16271969 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTACACG
* * * * *
16272020 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTACACG
* * *
16272071 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTACACG
16272121 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
16272156 CACTTTCACT
Statistics
Matches: 116, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 41 0.35
51 71 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTACACG
Found at i:16272144 original size:101 final size:101
Alignment explanation
Indices: 16271967--16272151 Score: 318
Period size: 101 Copynumber: 1.8 Consensus size: 101
16271957 GTTCAGTTCA
*
16271967 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
16272032 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* *
16272069 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCTGCA
16272133 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
16272152 CCATCACTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.52
102 34 0.43
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:16273786 original size:25 final size:25
Alignment explanation
Indices: 16273758--16273805 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
16273748 GGATAGGATT
16273758 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
16273783 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
16273806 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:16275313 original size:20 final size:21
Alignment explanation
Indices: 16275290--16275330 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16275280 AATTTCCCAT
16275290 ATTTATATAT-ATTATATTAA
1 ATTTATATATGATTATATTAA
* *
16275310 ATTTGTATATGATTATTTTAA
1 ATTTATATATGATTATATTAA
16275331 CTTGCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTATATATGATTATATTAA
Found at i:16275391 original size:27 final size:25
Alignment explanation
Indices: 16275321--16275391 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
16275311 TTTGTATATG
*
16275321 ATTATTTTAACTTGCTTTATAGAAT
1 ATTATTTTAAGTTGCTTTATAGAAT
* *
16275346 ATTATTTTAAGTTACTTTATATGTCAT
1 ATTATTTTAAGTTGCTTTATA-G-AAT
* *
16275373 TTTATTTTAAGTTGTTTTA
1 ATTATTTTAAGTTGCTTTA
16275392 CATATTACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 19 0.50
26 1 0.03
27 18 0.47
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (25 bp):
ATTATTTTAAGTTGCTTTATAGAAT
Found at i:16282412 original size:15 final size:14
Alignment explanation
Indices: 16282391--16282433 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
16282381 TTAAATCAAA
16282391 ATAATTTTATTTTT
1 ATAATTTTATTTTT
*
16282405 ATTAATTTAAATTTTT
1 A-TAATTT-TATTTTT
*
16282421 AAAATTTTATTTT
1 ATAATTTTATTTT
16282434 GGTGAGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATAATTTTATTTTT
Found at i:16288459 original size:31 final size:31
Alignment explanation
Indices: 16288390--16288459 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
16288380 TTTGGCCTAC
16288390 TTCAATCCCTAATGTTATCAGACATTCTCAA
1 TTCAATCCCTAATGTTATCAGACATTCTCAA
* * *
16288421 TTTAATCCCTAATGTTATTAGACATT-TCTAG
1 TTCAATCCCTAATGTTATCAGACATTCTC-AA
16288452 TTCAATCC
1 TTCAATCC
16288460 TTTGGATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
TTCAATCCCTAATGTTATCAGACATTCTCAA
Found at i:16288563 original size:12 final size:12
Alignment explanation
Indices: 16288546--16288570 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16288536 CTTTGAAATC
16288546 TTTAAAAATTAT
1 TTTAAAAATTAT
16288558 TTTAAAAATTAT
1 TTTAAAAATTAT
16288570 T
1 T
16288571 AAAATTACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAAATTAT
Found at i:16288623 original size:22 final size:21
Alignment explanation
Indices: 16288598--16288638 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16288588 GAAAAAATAT
16288598 ATATAAATTTATAAAAATTACA
1 ATATAAATTTA-AAAAATTACA
**
16288620 ATATTTATTTAAAAAATTA
1 ATATAAATTTAAAAAATTA
16288639 AAAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATAAATTTAAAAAATTACA
Found at i:16288808 original size:27 final size:27
Alignment explanation
Indices: 16288772--16288831 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
16288762 TTTTATAAAA
*
16288772 TTTTAATAAAATTTATTTCTTTTTA-AT
1 TTTTAATAAAATTTAGTT-TTTTTATAT
* *
16288799 TTTTAGTAAATTTTAGTTTTTTTATAT
1 TTTTAATAAAATTTAGTTTTTTTATAT
16288826 TTTTAA
1 TTTTAA
16288832 AATGTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTAATAAAATTTAGTTTTTTTATAT
Found at i:16288929 original size:24 final size:25
Alignment explanation
Indices: 16288873--16288929 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
16288863 AATAATTTCA
*
16288873 ATAATTTTAATTTTTATATAATTTT
1 ATAATTTTAATTTTTATACAATTTT
*
16288898 ATAGTTTT-A-TTTTATAACAATTTT
1 ATAATTTTAATTTTTAT-ACAATTTT
*
16288922 TTAATTTT
1 ATAATTTT
16288930 TTAAATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 6 0.22
24 14 0.52
25 7 0.26
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATAATTTTAATTTTTATACAATTTT
Found at i:16290449 original size:21 final size:21
Alignment explanation
Indices: 16290420--16290511 Score: 130
Period size: 21 Copynumber: 4.4 Consensus size: 21
16290410 TTTTGCTCTG
* *
16290420 CTCTGCTTCTCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16290441 CTTTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16290462 CTCTGCTTCCCTCGCTGCAAC
1 CTCTGCTTCCCTCGCTGCAGC
* *
16290483 CGCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
16290504 CTCTGCTT
1 CTCTGCTT
16290512 TAAGTTGTAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.04, C:0.45, G:0.18, T:0.33
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:16293608 original size:9 final size:9
Alignment explanation
Indices: 16293344--16293639 Score: 218
Period size: 9 Copynumber: 31.4 Consensus size: 9
16293334 TTAAAACGCC
*
16293344 AGTTATTTA
1 AGTTATGTA
* *
16293353 ATTTGTGTA
1 AGTTATGTA
*
16293362 ATTTATGTA
1 AGTTATGTA
16293371 AGTTATGTA
1 AGTTATGTA
*
16293380 AGATATTATGTT
1 AG---TTATGTA
16293392 A-TTATGTA
1 AGTTATGTA
*
16293400 AGTTATGCA
1 AGTTATGTA
*
16293409 AGTTTATATATA
1 AG--T-TATGTA
*
16293421 AGCTTGTAGATA
1 AG-TTAT-G-TA
*
16293433 ACTTATGTA
1 AGTTATGTA
16293442 AGTTAATATGTA
1 AG-T--TATGTA
*
16293454 AGTTATTTA
1 AGTTATGTA
*
16293463 ATTTATGTA
1 AGTTATGTA
*
16293472 AATTATGTA
1 AGTTATGTA
*
16293481 AGTTATTTA
1 AGTTATGTA
*
16293490 ATTTATGTA
1 AGTTATGTA
16293499 AGTTATGTA
1 AGTTATGTA
*
16293508 AGTTATTTA
1 AGTTATGTA
*
16293517 ATTTATGTA
1 AGTTATGTA
16293526 AGTTATGTA
1 AGTTATGTA
*
16293535 AGTTATTTA
1 AGTTATGTA
*
16293544 AGTTATTTA
1 AGTTATGTA
*
16293553 ATTTATGTA
1 AGTTATGTA
16293562 AGTTATGTA
1 AGTTATGTA
*
16293571 AGTTATTTA
1 AGTTATGTA
*
16293580 ATTTATGTA
1 AGTTATGTA
*
16293589 ATTTATGTA
1 AGTTATGTA
16293598 AGTTATGTA
1 AGTTATGTA
*
16293607 AGATAT-TA
1 AGTTATGTA
*
16293615 CGTTACTGAGTA
1 AGTTA-T--GTA
*
16293627 AGTTATGCA
1 AGTTATGTA
16293636 AGTT
1 AGTT
16293640 TATATATAAG
Statistics
Matches: 229, Mismatches: 42, Indels: 32
0.76 0.14 0.11
Matches are distributed among these distances:
8 12 0.05
9 176 0.77
10 4 0.02
11 7 0.03
12 30 0.13
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Found at i:16298147 original size:103 final size:103
Alignment explanation
Indices: 16298039--16298280 Score: 355
Period size: 103 Copynumber: 2.3 Consensus size: 103
16298029 TTACCATAAT
*
16298039 CCTAAACCCTAAAATATAAAATTTAAACCCTAATCCATATA-CCCTATTAACCCATATACCCTAT
1 CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATA-AGCCCTATTAACCCATATACCCTAT
16298103 GCCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
65 GCCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
* * *
16298142 CCTAAACCTTAAAATATAAAATTTAAACCCTAAACCATAAGCCTTCTTAACCCATATACCCTATG
1 CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATAAGCCCTATTAACCCATATACCCTATG
*
16298207 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTGAAC
66 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
* ** *
16298245 TCTAAAATCT-AAATAATAAACA-ATAAACCCTAAACC
1 CCTAAACCCTAAAAT-ATAAA-ATTTAAACCCTAAACC
16298281 CTACACCCTA
Statistics
Matches: 126, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
102 5 0.04
103 120 0.95
104 1 0.01
ACGTcount: A:0.41, C:0.29, G:0.04, T:0.26
Consensus pattern (103 bp):
CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATAAGCCCTATTAACCCATATACCCTATG
CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
Found at i:16298278 original size:7 final size:7
Alignment explanation
Indices: 16298268--16298391 Score: 65
Period size: 7 Copynumber: 17.9 Consensus size: 7
16298258 TAATAAACAA
16298268 TAAACCC
1 TAAACCC
16298275 TAAACCC
1 TAAACCC
*
16298282 TACACCC
1 TAAACCC
*
16298289 TAAACCA
1 TAAACCC
*
16298296 TAAACTC
1 TAAACCC
*
16298303 TAAACTC
1 TAAACCC
* *
16298310 TTAACAC
1 TAAACCC
* *
16298317 TAAATCA
1 TAAACCC
*
16298324 TAAACTGC
1 TAAAC-CC
*
16298332 -ATA-CC
1 TAAACCC
*
16298337 TAAAACCA
1 T-AAACCC
16298345 TAAA-CC
1 TAAACCC
* *
16298351 TACACCA
1 TAAACCC
16298358 TAAACCC
1 TAAACCC
*
16298365 TAAACCG
1 TAAACCC
*
16298372 TAAACAC
1 TAAACCC
*
16298379 TAAACCG
1 TAAACCC
16298386 TAAACC
1 TAAACC
16298392 AATAACCCTT
Statistics
Matches: 84, Mismatches: 28, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
5 1 0.01
6 4 0.05
7 77 0.92
8 2 0.02
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:16298278 original size:14 final size:14
Alignment explanation
Indices: 16298261--16298391 Score: 77
Period size: 14 Copynumber: 8.9 Consensus size: 14
16298251 ATCTAAATAA
*
16298261 TAAACAATAAACCC
1 TAAACCATAAACCC
* *
16298275 TAAACCCTACACCC
1 TAAACCATAAACCC
*
16298289 TAAACCATAAACTC
1 TAAACCATAAACCC
* *
16298303 TAAACTC-TTAACAC
1 TAAAC-CATAAACCC
*
16298317 TAAATCATAAACTGCATACC
1 TAAACCATAAA---C---CC
16298337 TAAAACCATAAA-CC
1 T-AAACCATAAACCC
*
16298351 TACACCATAAACCC
1 TAAACCATAAACCC
* *
16298365 TAAACCGTAAACAC
1 TAAACCATAAACCC
*
16298379 TAAACCGTAAACC
1 TAAACCATAAACC
16298392 AATAACCCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
13 10 0.11
14 67 0.74
15 1 0.01
17 1 0.01
20 2 0.02
21 9 0.10
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.18
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:16298319 original size:28 final size:28
Alignment explanation
Indices: 16298242--16298329 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
16298232 CTACTAGCTG
* * * * *
16298242 AACTCTAAAATCTAAATAATAAACAATA
1 AACTCTAAACTCTTAACACTAAACCATA
* * *
16298270 AACCCTAAAC-CCTACACCCTAAACCATA
1 AACTCTAAACTCTTA-ACACTAAACCATA
*
16298298 AACTCTAAACTCTTAACACTAAATCATA
1 AACTCTAAACTCTTAACACTAAACCATA
16298326 AACT
1 AACT
16298330 GCATACCTAA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
27 2 0.04
28 41 0.89
29 3 0.07
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (28 bp):
AACTCTAAACTCTTAACACTAAACCATA
Found at i:16298384 original size:21 final size:19
Alignment explanation
Indices: 16298268--16298440 Score: 62
Period size: 21 Copynumber: 8.3 Consensus size: 19
16298258 TAATAAACAA
*
16298268 TAAACCCTAAACCCTACACCC
1 TAAA-CCTAAACCCTA-AACC
*
16298289 TAAACCATAAACTCTAAACTC
1 TAAACC-TAAACCCTAAAC-C
* * *
16298310 TTAACACTAAATCATAAA-C
1 TAAAC-CTAAACCCTAAACC
* *
16298329 TGCATACCTAAAACCATAAACC
1 T--AAACCT-AAACCCTAAACC
*
16298351 TACACCATAAACCCTAAACC
1 TAAACC-TAAACCCTAAACC
*
16298371 GTAAACACTAAACCGTAAACC
1 -TAAAC-CTAAACCCTAAACC
* *
16298392 AATAACCCTTAGACCCTAAGA-C
1 --TAAACC-TAAACCCTAA-ACC
*
16298414 GATAACCTAAACCCTTAAACC
1 TA-AACCTAAACCC-TAAACC
16298435 TTAAAC
1 -TAAAC
16298441 TTTTAAATCT
Statistics
Matches: 114, Mismatches: 21, Indels: 34
0.67 0.12 0.20
Matches are distributed among these distances:
19 2 0.02
20 29 0.25
21 64 0.56
22 18 0.16
23 1 0.01
ACGTcount: A:0.45, C:0.32, G:0.03, T:0.19
Consensus pattern (19 bp):
TAAACCTAAACCCTAAACC
Found at i:16298561 original size:22 final size:22
Alignment explanation
Indices: 16298504--16298571 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
16298494 TCTTATTAAA
16298504 CCCTAAACCATAAG-CCATTAAC
1 CCCTAAACCATAAGCCCA-TAAC
* * *
16298526 CCATAGACCCTAAGCCCATAAC
1 CCCTAAACCATAAGCCCATAAC
16298548 CCCTAAACCATAAGCTCC-TAAC
1 CCCTAAACCATAAGC-CCATAAC
16298570 CC
1 CC
16298572 TTACACACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 33 0.87
23 5 0.13
ACGTcount: A:0.37, C:0.41, G:0.06, T:0.16
Consensus pattern (22 bp):
CCCTAAACCATAAGCCCATAAC
Found at i:16298758 original size:12 final size:12
Alignment explanation
Indices: 16298741--16298771 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
16298731 TAATTTTTTC
16298741 ATTTTAACAAAT
1 ATTTTAACAAAT
16298753 ATTTTAACAAAT
1 ATTTTAACAAAT
16298765 ATTTTAA
1 ATTTTAA
16298772 ACTATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTTAACAAAT
Found at i:16298779 original size:10 final size:10
Alignment explanation
Indices: 16298764--16298788 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
16298754 TTTTAACAAA
16298764 TATTTTAAAC
1 TATTTTAAAC
16298774 TATTTTAAAC
1 TATTTTAAAC
16298784 TATTT
1 TATTT
16298789 GAGCATTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTTAAAC
Found at i:16299000 original size:72 final size:73
Alignment explanation
Indices: 16298916--16299153 Score: 273
Period size: 73 Copynumber: 3.3 Consensus size: 73
16298906 CATTAGCGAT
* ** * * * **
16298916 GCTTTCCTAAAAACACCGCTGTATCCATGAAAGCTCAAAAAACGACATTGTTTCGTTTAGG-TTT
1 GCTTTCCCAAAAATGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAGGTTTT
*
16298980 TTAGCGGC
66 TTTGCGGC
* * * * * *
16298988 GCTTTCCCAAAAATGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTTGGGTTTAGGTTTT
1 GCTTTCCCAAAAATGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAGGTTTT
16299053 TTTGCGGC
66 TTTGCGGC
** * * *
16299061 GCTTTCTTAAAAATGCCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTAGGTTTT
1 GCTTTCCCAAAAATGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAGGTTTT
16299126 TTTGCGGC
66 TTTGCGGC
*
16299134 GCTTTCCC-AAAACGCCGCTA
1 GCTTTCCCAAAAATGCCGCTA
16299154 AAGCCCTCGC
Statistics
Matches: 135, Mismatches: 30, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
72 57 0.42
73 78 0.58
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (73 bp):
GCTTTCCCAAAAATGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAGGTTTT
TTTGCGGC
Found at i:16299336 original size:114 final size:112
Alignment explanation
Indices: 16299056--16299380 Score: 347
Period size: 112 Copynumber: 2.9 Consensus size: 112
16299046 AGGTTTTTTT
* * * * * * *
16299056 GCGGCGCTTT-CTTAAAAATGCCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTA
1 GCGGCGCTTTAC-TAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
*
16299120 GGTTTTTTTGCGGCGCTTTCCCA-AAACGCCGCTAAAGCCCTCGCATTA
65 GG-TTTTTTGCGGCGCTTTCTCAGAAACGCCGCTAAAGCCCTCGCATTA
*
16299168 GCGGCGCTTTACTAAAAACGCCGCTAAATCCCTAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
1 GCGGCGCTTTACTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
* * *
16299233 GTTTGTTTGCGGCGCTTTCTCAGAAACGCCGCTAAAG-CCTTGATCTTTT
66 GTTT-TTTGCGGCGCTTTCTCAGAAACGCCGCTAAAGCCCTCG--CATTA
* * * * * *
16299282 GGGGTGCTTT-CTTGAAAACGCCGCTAAAATCCCCGAAA-CTCCGAAAACGACGTCGTTGGGCTT
1 GCGGCGCTTTAC-TAAAAACGCCGCT-AAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * *
16299345 AGATTTTTAGCGGCGCTTTCT-GGAAATCGCCGCTAA
64 AGGTTTTTTGCGGCGCTTTCTCAGAAA-CGCCGCTAA
16299381 TGTTTATTTT
Statistics
Matches: 183, Mismatches: 22, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
111 3 0.02
112 80 0.44
113 39 0.21
114 51 0.28
115 10 0.05
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (112 bp):
GCGGCGCTTTACTAAAAACGCCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTTGCGGCGCTTTCTCAGAAACGCCGCTAAAGCCCTCGCATTA
Found at i:16299748 original size:30 final size:27
Alignment explanation
Indices: 16299706--16299765 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
16299696 TCTGTTAAAA
* *
16299706 TATTATAGAAGAATTTACTGATAAAATTT
1 TATTATAAAAGAAGTTAC-GA-AAAATTT
*
16299735 TATTGATAAAAGAAGTTACGAAGAATTT
1 TATT-ATAAAAGAAGTTACGAAAAATTT
16299763 TAT
1 TAT
16299766 AATATTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.33
29 6 0.22
30 12 0.44
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (27 bp):
TATTATAAAAGAAGTTACGAAAAATTT
Found at i:16301144 original size:24 final size:23
Alignment explanation
Indices: 16301112--16301158 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
16301102 AAGGGGTTAC
*
16301112 AAGGAGATGAAAGGTGAAGAGTT
1 AAGGAGATGAAAGGTGAAAAGTT
*
16301135 AAGGAAGATGATAGGTGAAAAGTT
1 AAGG-AGATGAAAGGTGAAAAGTT
16301159 GATTATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (23 bp):
AAGGAGATGAAAGGTGAAAAGTT
Found at i:16314074 original size:16 final size:16
Alignment explanation
Indices: 16314053--16314103 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
16314043 TGGTTGGGGG
*
16314053 AATGGAATAAATCTGT
1 AATGGAATAAAGCTGT
16314069 AATGGAATAAAGCTGT
1 AATGGAATAAAGCTGT
** *
16314085 AACAGAATAGAGCTGT
1 AATGGAATAAAGCTGT
16314101 AAT
1 AAT
16314104 AGTATTATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.25
Consensus pattern (16 bp):
AATGGAATAAAGCTGT
Found at i:16314247 original size:26 final size:24
Alignment explanation
Indices: 16314215--16314300 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 24
16314205 GTTATTAAAT
16314215 TTTAATAGGATTATTATTAAATATAA
1 TTTAATA--ATTATTATTAAATATAA
* * *
16314241 TTTAATAATAAATAATTTAATCATAA
1 TTTAATAAT-TATTATTAAAT-ATAA
*
16314267 TTTTAACATAATTATTATTAAATACAA
1 -TTT-A-ATAATTATTATTAAATATAA
16314294 TTTAATA
1 TTTAATA
16314301 CAAATAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
24 5 0.10
25 9 0.19
26 14 0.29
27 6 0.12
28 9 0.19
29 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (24 bp):
TTTAATAATTATTATTAAATATAA
Found at i:16314257 original size:15 final size:15
Alignment explanation
Indices: 16314237--16314266 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16314227 ATTATTAAAT
16314237 ATAATTTAATAATAA
1 ATAATTTAATAATAA
*
16314252 ATAATTTAATCATAA
1 ATAATTTAATAATAA
16314267 TTTTAACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTTAATAATAA
Found at i:16314681 original size:46 final size:46
Alignment explanation
Indices: 16314614--16314710 Score: 194
Period size: 46 Copynumber: 2.1 Consensus size: 46
16314604 TGGTTGATGT
16314614 TAAGTAAAATAATTATCTAGATGCAAAATGATCCCTAATGCAATCC
1 TAAGTAAAATAATTATCTAGATGCAAAATGATCCCTAATGCAATCC
16314660 TAAGTAAAATAATTATCTAGATGCAAAATGATCCCTAATGCAATCC
1 TAAGTAAAATAATTATCTAGATGCAAAATGATCCCTAATGCAATCC
16314706 TAAGT
1 TAAGT
16314711 GCAATTTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.29
Consensus pattern (46 bp):
TAAGTAAAATAATTATCTAGATGCAAAATGATCCCTAATGCAATCC
Found at i:16318335 original size:20 final size:21
Alignment explanation
Indices: 16318297--16318336 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16318287 CTATCATGAG
16318297 TATTGATACTTGGGGTAGAGA
1 TATTGATACTTGGGGTAGAGA
*
16318318 TATTGATACTT-TGGTAGAG
1 TATTGATACTTGGGGTAGAG
16318337 GTATCAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.05, G:0.30, T:0.38
Consensus pattern (21 bp):
TATTGATACTTGGGGTAGAGA
Found at i:16341238 original size:20 final size:20
Alignment explanation
Indices: 16341215--16341274 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
16341205 AATCATGCCT
16341215 ATTATCGTAATATCAACAAA
1 ATTATCGTAATATCAACAAA
* **
16341235 ATTAT--TAA-ATCATGC-CT
1 ATTATCGTAATATCA-ACAAA
16341252 ATTATCGTAATATCAACAAA
1 ATTATCGTAATATCAACAAA
16341272 ATT
1 ATT
16341275 CACCCAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
19 4 0.14
20 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTATCGTAATATCAACAAA
Found at i:16341249 original size:37 final size:37
Alignment explanation
Indices: 16341199--16341274 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
16341189 ATTGCATACT
16341199 TTATTAAATCATGCCTATTATCGTAATATCAACAAAA
1 TTATTAAATCATGCCTATTATCGTAATATCAACAAAA
16341236 TTATTAAATCATGCCTATTATCGTAATATCAACAAAA
1 TTATTAAATCATGCCTATTATCGTAATATCAACAAAA
16341273 TT
1 TT
16341275 CACCCAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (37 bp):
TTATTAAATCATGCCTATTATCGTAATATCAACAAAA
Found at i:16342924 original size:40 final size:40
Alignment explanation
Indices: 16342880--16343065 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
16342870 GCTCCTCGTT
*
16342880 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
16342920 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
16342960 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
16343000 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
16343041 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16343066 CAGCATTCAA
Statistics
Matches: 133, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 3 0.02
40 117 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:16351771 original size:40 final size:39
Alignment explanation
Indices: 16351734--16351825 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
16351724 GCTACTCGTT
*
16351734 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
16351774 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
16351813 CAAATGCCTTCGG
1 CAAATGCCTTCGG
16351826 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:16351805 original size:39 final size:40
Alignment explanation
Indices: 16351715--16351878 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
16351705 CGGAATTTAA
** *
16351715 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
16351755 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16351794 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
16351834 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
16351874 CCGGA
1 CCGGA
16351879 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:16360245 original size:21 final size:21
Alignment explanation
Indices: 16360184--16360250 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
16360174 TTAGGGTTAA
16360184 GGTTTCGTTAAAATAATTTAG
1 GGTTTCGTTAAAATAATTTAG
** *** **
16360205 GGTTAGGTTTGTATGGTTTAG
1 GGTTTCGTTAAAATAATTTAG
*
16360226 GGTTTTGTTAAAATAATTTAG
1 GGTTTCGTTAAAATAATTTAG
16360247 GGTT
1 GGTT
16360251 CTAGGTTTTA
Statistics
Matches: 32, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.01, G:0.27, T:0.46
Consensus pattern (21 bp):
GGTTTCGTTAAAATAATTTAG
Found at i:16360394 original size:34 final size:33
Alignment explanation
Indices: 16360301--16360405 Score: 138
Period size: 34 Copynumber: 3.1 Consensus size: 33
16360291 GTTCTTTTTC
* * *
16360301 AAAAATTAATTAAATTAGGGTTTAGGGGTTTAA
1 AAAAATTAATTAAATTTGGGTTTAGTGTTTTAA
16360334 AATAAATTAATTAAATTTGGGTTTAGTGTTTTAGA
1 AA-AAATTAATTAAATTTGGGTTTAGTGTTTTA-A
* * *
16360369 GAAAATTAATTAAATTTGGGTTTAGTTTTTTTA
1 AAAAATTAATTAAATTTGGGTTTAGTGTTTTAA
16360402 AAAA
1 AAAA
16360406 TAATATTGTG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
33 6 0.10
34 55 0.87
35 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (33 bp):
AAAAATTAATTAAATTTGGGTTTAGTGTTTTAA
Found at i:16360810 original size:125 final size:126
Alignment explanation
Indices: 16360474--16360987 Score: 755
Period size: 126 Copynumber: 4.1 Consensus size: 126
16360464 TTTTTTATTG
* * * *
16360474 CAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAATGCTTCA
1 CAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTCA
* ** *
16360539 AGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCTTACGTGAACACTCTTTTTCTA
66 AGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
* * * *
16360600 CAGTAGTTCTTAAAAATATAATTTTAAGAAGACGATTCTGAACAAATAGTGTCAAAAACACTTCA
1 CAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTCA
*
16360665 AGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACACTCTTTTTCTA
66 AGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
*
16360726 CAGTAGTTCCTAAAAAAACAATTTTGAGAAGAC-ATTCTGAACAAATAGTGTCAAAAACGCTTCA
1 CAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTCA
* * * *
16360790 AGAAGGATGCACTATTAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
66 AGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
* *
16360851 CAGTAGTTCCTGAAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCTT
1 CAGTAGTTCCT--AAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTT
* * * *
16360916 CAAGTAGGATGCATTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTTTTTTTCTA
64 CAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
16360979 CAGTAGTTC
1 CAGTAGTTC
16360988 ATGTTTGGCC
Statistics
Matches: 352, Mismatches: 31, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
125 97 0.28
126 140 0.40
127 23 0.07
128 92 0.26
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
CAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGAACAAATAGTGTCAAAAACGCTTCA
AGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
Found at i:16360937 original size:253 final size:252
Alignment explanation
Indices: 16360474--16360987 Score: 755
Period size: 253 Copynumber: 2.0 Consensus size: 252
16360464 TTTTTTATTG
* * *
16360474 CAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAATGCTTCA
1 CAGTAGTTCCTAAAAAAACAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAACGCTTCA
* * * **
16360539 AGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCTTACGTGAACACTCTTTTTCTACAGT
66 AGAAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGAACACTCTTTTTCTACAGT
* *
16360604 AGTTCTTAAAAATATAATTTTAAGAAGACGATTCTGAACAAATAGTGTCAAAAACACTTCAAGCA
131 AGTTCTAAAAAAAATAATTTTAAGAAGACGATTCTGAACAAATAGTGTCAAAAACACTTCAAGCA
*
16360669 GGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTGGACACTCTTTTTCTA
196 GGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
* *
16360726 CAGTAGTTCCTAAAAAAACAATTTTGAGAAGAC-ATTCTGAACAAATAGTGTCAAAAACGCTTCA
1 CAGTAGTTCCTAAAAAAACAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAACGCTTCA
* * *
16360790 AGAAGGATGCACTATTAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACAG
66 AGAAGGATGCACTATCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGAACACTCTTTTTCTACAG
* * **
16360854 TAGTTCCTGAAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAATGCTTCAA
130 TAGTT-CT-AAAAAAAATAATTTTAAGAAGACGATTCTGAACAAATAGTGTCAAAAACACTTCAA
* * * *
16360919 GTAGGATGCATTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTTTTTTTCTA
193 GCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
16360979 CAGTAGTTC
1 CAGTAGTTC
16360988 ATGTTTGGCC
Statistics
Matches: 234, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
251 87 0.37
252 35 0.15
253 112 0.48
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (252 bp):
CAGTAGTTCCTAAAAAAACAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAACGCTTCA
AGAAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGAACACTCTTTTTCTACAGT
AGTTCTAAAAAAAATAATTTTAAGAAGACGATTCTGAACAAATAGTGTCAAAAACACTTCAAGCA
GGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACACTCTTTTTCTA
Found at i:16364103 original size:24 final size:23
Alignment explanation
Indices: 16364047--16364103 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
16364037 AAGAACTTCT
16364047 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAATA
16364070 ATTTACTATT-AAAATATTAAAAATAA
1 ATTT--TATTAAAAATA-TAAAAAT-A
16364096 ATTTTATT
1 ATTTTATT
16364104 TTATTAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.13
24 10 0.33
25 11 0.37
26 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAATA
Found at i:16364258 original size:21 final size:21
Alignment explanation
Indices: 16364233--16364272 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16364223 TGGTTCAGCT
16364233 TCCAACGGAGGTTGTGGTTAC
1 TCCAACGGAGGTTGTGGTTAC
*
16364254 TCCAACGGGGGTTGTGGTT
1 TCCAACGGAGGTTGTGGTT
16364273 GCACAGGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.38, T:0.30
Consensus pattern (21 bp):
TCCAACGGAGGTTGTGGTTAC
Found at i:16365833 original size:15 final size:15
Alignment explanation
Indices: 16365813--16365848 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
16365803 CAGATTGAAC
16365813 GGACCCGGTGAGTGT
1 GGACCCGGTGAGTGT
16365828 GGACCCGGTGAGTGT
1 GGACCCGGTGAGTGT
16365843 GGACCC
1 GGACCC
16365849 ATCTACTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.44, T:0.17
Consensus pattern (15 bp):
GGACCCGGTGAGTGT
Found at i:16366368 original size:30 final size:30
Alignment explanation
Indices: 16366334--16366402 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
16366324 ATTAATTAAA
*
16366334 GAGAGTTTTGAGAAATTTAAAAAGAATTTT
1 GAGAGTTTTGAGAAATTTAAAAAGAAATTT
* * *
16366364 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAAAGAAATTT
16366394 GAGAGTTTT
1 GAGAGTTTT
16366403 TTGATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAAAAGAAATTT
Found at i:16370036 original size:22 final size:22
Alignment explanation
Indices: 16370011--16370053 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
16370001 TTGATTGATA
16370011 GATTTT-TTATGTTAGGTTTTAG
1 GATTTTATTATGTTA-GTTTTAG
16370033 GATTTTCATTATGTTAGTTTT
1 GATTTT-ATTATGTTAGTTTT
16370054 GTAATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (22 bp):
GATTTTATTATGTTAGTTTTAG
Found at i:16371149 original size:2 final size:2
Alignment explanation
Indices: 16371142--16371166 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16371132 TAGCTTCTCT
16371142 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 T
16371167 TCTTTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16372714 original size:8 final size:9
Alignment explanation
Indices: 16372691--16372731 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
16372681 AACCATTCCA
16372691 ATAAATAATT
1 ATAAA-AATT
16372701 -TAAAAATT
1 ATAAAAATT
*
16372709 ATAAAAATA
1 ATAAAAATT
16372718 ATAAAAATT
1 ATAAAAATT
16372727 -TAAAA
1 ATAAAA
16372732 TCCAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 9 0.32
9 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:16376533 original size:24 final size:24
Alignment explanation
Indices: 16376501--16376559 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
16376491 CCAAAATAGA
16376501 AACTGTGGCTAAAGTAGTGTTTGG
1 AACTGTGGCTAAAGTAGTGTTTGG
16376525 AACTGTGGCTAAAGTAGTGTTTGG
1 AACTGTGGCTAAAGTAGTGTTTGG
16376549 AACTGTGGCTA
1 AACTGTGGCTA
16376560 CGATTTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.32
Consensus pattern (24 bp):
AACTGTGGCTAAAGTAGTGTTTGG
Found at i:16377470 original size:63 final size:63
Alignment explanation
Indices: 16377371--16377546 Score: 185
Period size: 63 Copynumber: 2.8 Consensus size: 63
16377361 CTAACCTAGT
* * * ** *
16377371 TTATTTAACACAAGCATCACATCACACACAATCATTCCCTGTATCAACAC-TT-AAAACTCTAGC
1 TTATTTTACACAAGCAACACAACATGCACAATCATTCCCTGCATCAACACATTCAAAAC-C-AGC
* * * * ** *
16377434 TTATTTTACATAAGCAACACAACATGTACAATCATTCCATGCATTAACACATTCAGCACCAGT
1 TTATTTTACACAAGCAACACAACATGCACAATCATTCCCTGCATCAACACATTCAAAACCAGC
* *
16377497 TTATTTTACACAAGCACCACAACATGCACAATCATTCCCTACATCAACAC
1 TTATTTTACACAAGCAACACAACATGCACAATCATTCCCTGCATCAACAC
16377547 CTTCTCTAGG
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
63 86 0.93
64 3 0.03
65 3 0.03
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.27
Consensus pattern (63 bp):
TTATTTTACACAAGCAACACAACATGCACAATCATTCCCTGCATCAACACATTCAAAACCAGC
Found at i:16380587 original size:43 final size:43
Alignment explanation
Indices: 16380526--16380618 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
16380516 TGATGTTAAT
* * *
16380526 GCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCCGA-AAAC
1 GCCGCTAAAGGCCATGTTCTTTAGCGACGCTTCTCCC-ACAAAC
16380569 GCCGCTAAAGGCCATGTTCTTTAGCGACGCTTCTCCCACAAAC
1 GCCGCTAAAGGCCATGTTCTTTAGCGACGCTTCTCCCACAAAC
16380612 GCCGCTA
1 GCCGCTA
16380619 TTGTTTGGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (43 bp):
GCCGCTAAAGGCCATGTTCTTTAGCGACGCTTCTCCCACAAAC
Found at i:16381174 original size:25 final size:26
Alignment explanation
Indices: 16381123--16381184 Score: 90
Period size: 25 Copynumber: 2.4 Consensus size: 26
16381113 TTTTACAATG
* *
16381123 ATTAAGTTATGTAAATAATATGAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
*
16381149 ATTAAGTTATGCATAT-ATATAAGTT
1 ATTAAGTTATGCAAATAATATAAGTT
16381174 ATTAAGTTATG
1 ATTAAGTTATG
16381185 TAAGTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.44
Consensus pattern (26 bp):
ATTAAGTTATGCAAATAATATAAGTT
Found at i:16381188 original size:17 final size:17
Alignment explanation
Indices: 16381123--16381194 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
16381113 TTTTACAATG
* *
16381123 ATTAAGTTATGTAAATA
1 ATTAAGTTATGTAAGTT
*
16381140 ATATGAGTTAT-TAAGTT
1 AT-TAAGTTATGTAAGTT
** *
16381157 ATGCA-TATATATAAGTT
1 ATTAAGT-TATGTAAGTT
16381174 ATTAAGTTATGTAAGTT
1 ATTAAGTTATGTAAGTT
16381191 ATTA
1 ATTA
16381195 TGTGAGTTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (17 bp):
ATTAAGTTATGTAAGTT
Found at i:16381309 original size:17 final size:17
Alignment explanation
Indices: 16381287--16381346 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
16381277 ATATATTTTA
16381287 AAATTATTAAGTTATGT
1 AAATTATTAAGTTATGT
* *
16381304 AAATTATGTGAGTTGT-T
1 AAATTAT-TAAGTTATGT
*
16381321 AAGTTATTAAGTTATGT
1 AAATTATTAAGTTATGT
*
16381338 AAGTTATTA
1 AAATTATTA
16381347 TGTGAATTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 6 0.17
17 24 0.67
18 6 0.17
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (17 bp):
AAATTATTAAGTTATGT
Found at i:16381342 original size:9 final size:8
Alignment explanation
Indices: 16381290--16381346 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 8
16381280 TATTTTAAAA
16381290 TTATTAAG
1 TTATTAAG
*
16381298 TTATGTAAA
1 TTAT-TAAG
*
16381307 TTATGTGAG
1 TTAT-TAAG
*
16381316 TTGTTAAG
1 TTATTAAG
16381324 TTATTAAG
1 TTATTAAG
16381332 TTATGTAAG
1 TTAT-TAAG
16381341 TTATTA
1 TTATTA
16381347 TGTGAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 20 0.49
9 21 0.51
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (8 bp):
TTATTAAG
Found at i:16381369 original size:46 final size:46
Alignment explanation
Indices: 16381298--16381470 Score: 159
Period size: 46 Copynumber: 3.6 Consensus size: 46
16381288 AATTATTAAG
* * *
16381298 TTATGTAAATTATGTGAGTTGTTAAGTTATTAAGTTATGTAAGTTA
1 TTATGTAAATTATATAAGTTATTAAGTTATTAAGTTATGTAAGTTA
* * * *
16381344 TTATGTGAATTATATAAGTTATTAAGTTA-TATGGTATGACATATATATATGTA
1 TTATGTAAATTATATAAGTTATTAAGTTATTA-AGT-T---ATGTA-A-GT-TA
* * * *
16381397 TTATGTAAATTATGTGAGTTGTTAAGTTGTTAAGTTATGTAAGTTA
1 TTATGTAAATTATATAAGTTATTAAGTTATTAAGTTATGTAAGTTA
*
16381443 TTATGTGAATTATATAAGTTATTAAGTT
1 TTATGTAAATTATATAAGTTATTAAGTT
16381471 GGACATTTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
45 2 0.02
46 53 0.54
47 2 0.02
48 1 0.01
49 4 0.04
50 4 0.04
51 1 0.01
52 2 0.02
53 28 0.28
54 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (46 bp):
TTATGTAAATTATATAAGTTATTAAGTTATTAAGTTATGTAAGTTA
Found at i:16381375 original size:17 final size:17
Alignment explanation
Indices: 16381290--16381375 Score: 66
Period size: 17 Copynumber: 4.8 Consensus size: 17
16381280 TATTTTAAAA
* *
16381290 TTATTAAGTTATGTAAA
1 TTATTAAGTTATATAAG
* *
16381307 TTATGTGAGTTGT-TAAG
1 TTAT-TAAGTTATATAAG
*
16381324 TTATTAAGTTATGTAAG
1 TTATTAAGTTATATAAG
*
16381341 TTATTATGTGAATTATATAAG
1 TTATTA----AGTTATATAAG
16381362 TTATTAAGTTATAT
1 TTATTAAGTTATAT
16381376 GGTATGACAT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
16 6 0.11
17 28 0.51
18 6 0.11
21 15 0.27
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (17 bp):
TTATTAAGTTATATAAG
Found at i:16381448 original size:53 final size:54
Alignment explanation
Indices: 16381314--16381470 Score: 128
Period size: 53 Copynumber: 2.9 Consensus size: 54
16381304 AAATTATGTG
* * *
16381314 AGTTGTTAAGTTAT-TAAGTTATGTAAGTTATTATGTGAATTATATAAGTTATTA
1 AGTTGTTAAGTTATGTAAGTTATATATG-TATTATGTAAATTATATAAGTTATTA
* * * * * *
16381368 AGTT-ATATGGTATG-ACA-TATATATATGTATTATGTAAATTATGTGAGTTGTTA
1 AGTTGTTAAGTTATGTA-AGT-TATATATGTATTATGTAAATTATATAAGTTATTA
* *
16381421 AGTTGTTAAGTTATGTAAGTTAT-TATGTGAATTATATAAGTTAT-TAAGTT
1 AGTTGTTAAGTTATGTAAGTTATATATGT--ATTATGTAAATTATATAAGTT
16381471 GGACATTTTT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
53 39 0.49
54 27 0.34
55 14 0.17
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (54 bp):
AGTTGTTAAGTTATGTAAGTTATATATGTATTATGTAAATTATATAAGTTATTA
Found at i:16382115 original size:21 final size:21
Alignment explanation
Indices: 16382091--16382137 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
16382081 TTAACTATTT
* *
16382091 AAATTAGTTAATGATATTGTA
1 AAATTAGATAATGAAATTGTA
* *
16382112 AAATTAGATGATTAAATTGTA
1 AAATTAGATAATGAAATTGTA
16382133 AAATT
1 AAATT
16382138 TCAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
AAATTAGATAATGAAATTGTA
Found at i:16384238 original size:2 final size:2
Alignment explanation
Indices: 16384231--16384257 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16384221 AACAGTAAAA
16384231 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
16384258 TGGAGAAGAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16384740 original size:199 final size:199
Alignment explanation
Indices: 16384386--16385137 Score: 1193
Period size: 199 Copynumber: 3.8 Consensus size: 199
16384376 ATAGATATAT
* * * * **
16384386 AAACTGAGAACAGAACTTTGTGGTGTTTGTTCCTTAGCGCCGCTAATGACCATATTTAGCGGCGT
1 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
* ** * *
16384451 TTTTACCTTAGTGCCGCAAAACCCATTAAATTCGTAGCCAAAAATTGCATCGTTTTGTCTTTATT
66 TTTTACCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCATCGTTTTGTCTTCATT
* * **
16384516 ATTAAGAACATTTTT-CGGTGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACTGTTT
131 ATTAAGAA-TTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACCATTT
16384580 TACGA
195 TACGA
*
16384585 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCAT
1 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
* *
16384650 TTTTCCCTTAGCGCCGCAAAACCCATTAAAGTCACAGCCAAAAACTGCATCGTTTTGTCTTCATT
66 TTTTACCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCATCGTTTTGTCTTCATT
*
16384715 ATTAAGAATTTTTTGTGGCGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACCATTTT
131 ATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACCATTTT
16384780 ACGA
196 ACGA
16384784 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
1 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
* * * * *
16384849 TTTTCCCTTAGAGCCGTAAAACCCATTAAATTCACAGCCAAAAATTGCACCGTTTTGTCTTCATT
66 TTTTACCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCATCGTTTTGTCTTCATT
* *
16384914 ATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGGCAAAATGACACCATTTT
131 ATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACCATTTT
*
16384979 ATGA
196 ACGA
*
16384983 AAACTGAGAACAGAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
1 AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
*
16385048 TTTTACCTTAGCGCCGCAAAACCCATTAAATTCGCAGCCAAAAACTGCA-CTGTTTTGTCTTCAT
66 TTTTACCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCATC-GTTTTGTCTTCAT
* *
16385112 TATTAAGAATATTTTGTGGCGTTTTT
130 TATTAAGAATTTTTTGCGGCGTTTTT
16385138 AACAAAAACG
Statistics
Matches: 514, Mismatches: 37, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
198 6 0.01
199 508 0.99
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (199 bp):
AAACTGAGAACAAAACTTTGCGGCGTTTTTTCCTTAGCGCCGCTAATGACCACCTTTAGCGGCGT
TTTTACCTTAGCGCCGCAAAACCCATTAAATTCACAGCCAAAAACTGCATCGTTTTGTCTTCATT
ATTAAGAATTTTTTGCGGCGTTTTTTAGTAGCGCCACTAATGCCCAGCCAAAACGACACCATTTT
ACGA
Found at i:16385346 original size:19 final size:19
Alignment explanation
Indices: 16385324--16385366 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
16385314 TTTTATTTTT
*
16385324 ATTTTTTATAATTTTTACA
1 ATTTTTTACAATTTTTACA
16385343 ATTTTTTACAATTTTTACA
1 ATTTTTTACAATTTTTACA
16385362 ATTTT
1 ATTTT
16385367 AAATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTACAATTTTTACA
Found at i:16385346 original size:30 final size:30
Alignment explanation
Indices: 16385289--16385347 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16385279 AATTTTAGTG
* *
16385289 TTTTTATTTCTTTTTAATTTTTTAATTTTA
1 TTTTTATTTCTTTATAATTTTTCAATTTTA
16385319 TTTTTATTT-TTTATAATTTTTACAATTTT
1 TTTTTATTTCTTTATAATTTTT-CAATTTT
16385348 TTACAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTTATTTCTTTATAATTTTTCAATTTTA
Found at i:16385357 original size:9 final size:9
Alignment explanation
Indices: 16385326--16385366 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
16385316 TTATTTTTAT
*
16385326 TTTTTATAA
1 TTTTTACAA
16385335 TTTTTACAA
1 TTTTTACAA
16385344 TTTTTTACAA
1 -TTTTTACAA
16385354 TTTTTACAA
1 TTTTTACAA
16385363 TTTT
1 TTTT
16385367 AAATTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.70
10 9 0.30
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTTACAA
Found at i:16385565 original size:88 final size:89
Alignment explanation
Indices: 16385463--16385636 Score: 242
Period size: 88 Copynumber: 2.0 Consensus size: 89
16385453 TATAAAGAAC
* * * * **
16385463 TTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTTAAACCCTAACCTGACCCCAAA
1 TTATTTAATATATAAATTAAAAAATACTAATTAATCCAAACCCTAAACCATAACCCAACCCCAAA
16385528 TCCCTAACCC-TAACCCCTAAACT
66 TCCCTAACCCTTAACCCCTAAACT
* * * **
16385551 TTATTTAATATATAAATTAAAAAATAGTAATTAATCTAAACCCTAAACCATAACCCAATCCTGAA
1 TTATTTAATATATAAATTAAAAAATACTAATTAATCCAAACCCTAAACCATAACCCAACCCCAAA
16385616 TCCCTAACCCTTAACCCCTAA
66 TCCCTAACCCTTAACCCCTAA
16385637 CCCCTAACCC
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
88 64 0.86
89 10 0.14
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (89 bp):
TTATTTAATATATAAATTAAAAAATACTAATTAATCCAAACCCTAAACCATAACCCAACCCCAAA
TCCCTAACCCTTAACCCCTAAACT
Found at i:16385636 original size:14 final size:14
Alignment explanation
Indices: 16385617--16385656 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
16385607 AATCCTGAAT
16385617 CCCTAACCCTTAAC
1 CCCTAACCCTTAAC
*
16385631 CCCTAACCCCTAAC
1 CCCTAACCCTTAAC
*
16385645 CCCTAAACCTTA
1 CCCTAACCCTTA
16385657 TTTAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.50, G:0.00, T:0.20
Consensus pattern (14 bp):
CCCTAACCCTTAAC
Found at i:16385653 original size:8 final size:7
Alignment explanation
Indices: 16385617--16385650 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
16385607 AATCCTGAAT
16385617 CCCTAAC
1 CCCTAAC
*
16385624 CCTTAAC
1 CCCTAAC
16385631 CCCTAAC
1 CCCTAAC
16385638 CCCTAAC
1 CCCTAAC
16385645 CCCTAA
1 CCCTAA
16385651 ACCTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAC
Found at i:16386145 original size:114 final size:113
Alignment explanation
Indices: 16385941--16386181 Score: 302
Period size: 114 Copynumber: 2.1 Consensus size: 113
16385931 AACCGCCGCT
* * * *
16385941 AAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTACCTAAAAACGCTACTAAATCCCCAAAA
1 AAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTACCTAAAAACACCACAAAATCCCCAAAA
* * * * *
16386006 GCTCAGAAGACAGCGTCGTTAGGCTTAGATTTTTTTGTGGCGCTTTCTC
66 GCTCAGAAAACAGCGCCGTTAGGCTTAG-GTATTTTGCGGCGCTTTCTC
* * * * *
16386055 AAAAACGCCGCTAAAGCCCTGAACATTAGCGGCGCTTTCTTAAAAACACCGCAAAATCCCCGAAA
1 AAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTACCTAAAAACACCACAAAATCCCCAAAA
* * * *
16386120 GCTCCGAAAACGGCGCCGTTGGGCTTAGGTATTTTGCGGCGCTTTCTG
66 GCTCAGAAAACAGCGCCGTTAGGCTTAGGTATTTTGCGGCGCTTTCTC
*
16386168 GAAAACGCCGCTAA
1 AAAAACGCCGCTAA
16386182 TGCTTATTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
113 29 0.27
114 79 0.73
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (113 bp):
AAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTACCTAAAAACACCACAAAATCCCCAAAA
GCTCAGAAAACAGCGCCGTTAGGCTTAGGTATTTTGCGGCGCTTTCTC
Found at i:16388453 original size:15 final size:15
Alignment explanation
Indices: 16388430--16388471 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
16388420 CATACAAATT
*
16388430 AAAGAATTATTAGAA
1 AAAGAATTAATAGAA
*
16388445 AAAGGATTAATAGAA
1 AAAGAATTAATAGAA
*
16388460 AAA-AAATAATAG
1 AAAGAATTAATAG
16388472 TTCACATTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (15 bp):
AAAGAATTAATAGAA
Found at i:16390553 original size:24 final size:22
Alignment explanation
Indices: 16390526--16390570 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16390516 ACAGTTCAAA
16390526 ATTTTTCTTTCCATTTATTAAAAG
1 ATTTTTC--TCCATTTATTAAAAG
*
16390550 ATTTTTCTGCATTTATTAAAA
1 ATTTTTCTCCATTTATTAAAA
16390571 CTATGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTTCTCCATTTATTAAAAG
Found at i:16391177 original size:42 final size:42
Alignment explanation
Indices: 16391130--16391224 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
16391120 TAAAAATATC
* * * *
16391130 AAGGAAACAACATGGGAAAGCAACATCCATG-TCTAGACAAAA
1 AAGGAAGCAACATGGGAAAACAACATACAGGTTC-AGACAAAA
*
16391172 AAGGAAGCAACTTGGGAAAACAACATACAGGTTCAGACAAAA
1 AAGGAAGCAACATGGGAAAACAACATACAGGTTCAGACAAAA
16391214 AAGGAAGCAAC
1 AAGGAAGCAAC
16391225 GTAGAAGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.11
Consensus pattern (42 bp):
AAGGAAGCAACATGGGAAAACAACATACAGGTTCAGACAAAA
Found at i:16400938 original size:216 final size:215
Alignment explanation
Indices: 16400558--16400992 Score: 789
Period size: 216 Copynumber: 2.0 Consensus size: 215
16400548 AGACAATATA
* * *
16400558 CAAAGTGTTAATGTAATTCATGAATAATTTTATTAACCCATCCATTTGAAAAAATTACAAGTGTA
1 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCATTTGAAAAAATTACAAATGTA
*
16400623 CTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTTCTATTTGCCCTAGTGAAGTG
66 CTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
16400688 GATGAGTCATGTTTTGCATTCCTATCATCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
131 GATGAGTCATGTTTTGCATTCCTATCATCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
*
16400753 GTCTTGGTAAAACAAATCCC
196 GTCTTGGTAAAAAAAATCCC
*
16400773 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAAATTACAAATGT
1 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCATTTG-AAAAAATTACAAATGT
16400838 ACTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGT
65 ACTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGT
* *
16400903 GGATGAGTCATGTTTTGCATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGTTAGTAA
130 GGATGAGTCATGTTTTGCATTCCTATCATCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAA
16400968 AGTCTTGGTAAAAAAAATCCC
195 AGTCTTGGTAAAAAAAATCCC
16400989 CAAA
1 CAAA
16400993 CTATATCCTC
Statistics
Matches: 211, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
215 45 0.21
216 166 0.79
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (215 bp):
CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCATTTGAAAAAATTACAAATGTA
CTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
GATGAGTCATGTTTTGCATTCCTATCATCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
GTCTTGGTAAAAAAAATCCC
Found at i:16409736 original size:38 final size:38
Alignment explanation
Indices: 16409679--16409763 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 38
16409669 TAGCACCTAG
*
16409679 TTTA-ATATATGTATGTATATATTATTTAGTTTAAATTGT
1 TTTATATATATGTA-GTATATATTATTTAGTATAAATT-T
*
16409718 TTTTTATATATGTA-TATATATTATTTAGTATAAATTT
1 TTTATATATATGTAGTATATATTATTTAGTATAAATTT
16409755 TTTATATAT
1 TTTATATAT
16409764 TATTTCAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
37 9 0.21
38 21 0.50
39 3 0.07
40 9 0.21
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (38 bp):
TTTATATATATGTAGTATATATTATTTAGTATAAATTT
Found at i:16413991 original size:12 final size:12
Alignment explanation
Indices: 16413970--16414033 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
16413960 GATCCAATTA
*
16413970 AAAAATCAAAAT
1 AAAAAGCAAAAT
* *
16413982 CAAAAGCAAAAG
1 AAAAAGCAAAAT
16413994 AAAAAGCAAAA-
1 AAAAAGCAAAAT
16414005 AAGAAAG-AAAAT
1 AA-AAAGCAAAAT
* * *
16414017 CAAAATCAAAGT
1 AAAAAGCAAAAT
16414029 AAAAA
1 AAAAA
16414034 AAATGAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
11 9 0.22
12 32 0.78
ACGTcount: A:0.73, C:0.09, G:0.09, T:0.08
Consensus pattern (12 bp):
AAAAAGCAAAAT
Found at i:16416335 original size:88 final size:87
Alignment explanation
Indices: 16416172--16416338 Score: 228
Period size: 87 Copynumber: 1.9 Consensus size: 87
16416162 GTGAAAATAA
* * *
16416172 CAGATCTTGCCTTCTTGCATCGACGGCGAAGCAGATCGAAAATAAAGCCTTGCCTCCCTCGGTTG
1 CAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTG
*
16416237 TAGTGGAGCAGGTTAAAGATAG
66 CAGTGGAGCAGGTTAAAGATAG
* * * * *
16416259 CAGATCTTGTCTTCCTGCATTGACAGTGAAGCAGATCGAAGATACTAGCCTTGCCTCCAAT-GGT
1 CAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAATA-AAGCCTTGCCTCC-ATCGGT
16416323 TGCAGTGGAGCAGGTT
64 TGCAGTGGAGCAGGTT
16416339 GATGGTAGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 38 0.55
88 30 0.43
89 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (87 bp):
CAGATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAAATAAAGCCTTGCCTCCATCGGTTG
CAGTGGAGCAGGTTAAAGATAG
Found at i:16416576 original size:132 final size:132
Alignment explanation
Indices: 16416346--16417000 Score: 1051
Period size: 132 Copynumber: 5.0 Consensus size: 132
16416336 GTTGATGGTA
* * ***
16416346 GATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGC
1 GATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
* *
16416411 TGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGG
66 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
*
16416476 CA
131 CG
* * * *
16416478 GATTTTACCTCATTGTGGTTACAGTGGATTACATTGAAGCCAGTAATTTTATCTCCCTAGTTGGC
1 GATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
16416543 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
66 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
16416608 CG
131 CG
* * *
16416610 GATTTTACCTCCTTATGGTTACAGTGGAGTGCATTGAAGCCAGTAATTTTATCTCCCTGGTTGGC
1 GATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
16416675 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
66 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
16416740 CG
131 CG
* *
16416742 GATTTTACTTCACTT-TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGGTTGG
1 GATTTTACCTC-CTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGG
* * *
16416806 CAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGAAGTAGATCGAAGATG
65 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
*
16416871 GTG
130 GCG
* *
16416874 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
1 GATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
* * * *
16416939 AGTGGAGTAGATTGAAAATTACAGATCTTATCTGCCTAAGCAGTAGTGGAGCAGATCGAAGA
66 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
16417001 CCCCAACCTT
Statistics
Matches: 487, Mismatches: 34, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 482 0.99
133 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (132 bp):
GATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGGC
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
CG
Found at i:16416862 original size:44 final size:44
Alignment explanation
Indices: 16416807--16417146 Score: 169
Period size: 44 Copynumber: 7.8 Consensus size: 44
16416797 TCTGGTTGGC
*
16416807 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * **** * * *
16416851 AGTGAAGTAGATCGAAGATGGTGGATTTTACCTCCCTGAG--GTT
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG-T
* * * * ** *
16416894 ACAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCT-GGTTGGC
1 --AGTGGAGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAG-CAGT
* *
16416939 AGTGGAGTAGATTGAAAATTACAGATCTTATCTGCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * *** * * *
16416983 AGTGGAGCAGATCGAAGACCCCA-ACCTTATCTCCTTAAGCAGC
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * *
16417026 AGTGGACTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
* * * * * ** *
16417070 AGTGGAGCAGATCGTAGA-AACCA-ATCCTATCTCCCTGAAGTTGC
1 AGTGGAGTAGATTGAAGATTA-CAGATCTTATCTCCCT-AAGCAGT
* * *
16417114 AGTGGAGCAGATT-AAAATCACAGATCTTATCTC
1 AGTGGAGTAGATTGAAGATTACAGATCTTATCTC
16417147 TCTGAAGTTG
Statistics
Matches: 211, Mismatches: 68, Indels: 34
0.67 0.22 0.11
Matches are distributed among these distances:
41 3 0.01
42 2 0.01
43 67 0.32
44 121 0.57
45 16 0.08
46 1 0.00
47 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
Found at i:16416944 original size:43 final size:44
Alignment explanation
Indices: 16416763--16416954 Score: 126
Period size: 44 Copynumber: 4.4 Consensus size: 44
16416753 ACTTTGGTTA
* *
16416763 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCT-GGTTGG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTAGGTTGG
* * * * **
16416806 CAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAG-CAG
1 CAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TATCTCCCTAGGTTGG
* * * *** * * * *
16416850 TAGTGAAGTAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT-A
1 CAGTGGAGTAGATTGAAGCCAGT-AATTCTATCTCCCT-AGGTTGG
*
16416895 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT-GGTTGG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTAGGTTGG
16416938 CAGTGGAGTAGATTGAA
1 CAGTGGAGTAGATTGAA
16416955 AATTACAGAT
Statistics
Matches: 106, Mismatches: 33, Indels: 20
0.67 0.21 0.13
Matches are distributed among these distances:
41 3 0.03
42 5 0.05
43 34 0.32
44 42 0.40
45 20 0.19
46 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTAGGTTGG
Found at i:16417029 original size:87 final size:88
Alignment explanation
Indices: 16416937--16417146 Score: 291
Period size: 87 Copynumber: 2.4 Consensus size: 88
16416927 TCCCTGGTTG
* *
16416937 GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTGCCTAAGCAGTAGTGGAGCAGATCGAAGAC
1 GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAA
* *
16417002 CCCAA-CCTTATCT-CCTTAAGCA
66 ACCAATCC-TATCTCCCTGAAGCA
* * *
16417024 GCAGTGGACTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGTAGAA
1 GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAA
**
16417089 ACCAATCCTATCTCCCTGAAGTT
66 ACCAATCCTATCTCCCTGAAGCA
* *
16417112 GCAGTGGAGCAGATT-AAAATCACAGATCTTATCTC
1 GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTC
16417147 TCTGAAGTTG
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
87 88 0.81
88 20 0.19
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (88 bp):
GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAA
ACCAATCCTATCTCCCTGAAGCA
Found at i:16417152 original size:44 final size:43
Alignment explanation
Indices: 16416937--16417170 Score: 140
Period size: 44 Copynumber: 5.3 Consensus size: 43
16416927 TCCCTGGTTG
* * **
16416937 GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTGCCT-AAGCA
1 GCAGTGGAGCAGATT-AAAATCACAGATCTTATCT-CCTGAAGTT
* * * * * * * **
16416981 GTAGTGGAGCAGATCGAAGACCCCA-ACCTTATCTCCTTAAGCA
1 GCAGTGGAGCAGAT-TAAAATCACAGATCTTATCTCCTGAAGTT
* * **
16417024 GCAGTGGA-CTAGGTTGAAAATTACAGATCTTATCTCCCT-AAGCA
1 GCAGTGGAGC-AGATT-AAAATCACAGATCTTATCT-CCTGAAGTT
* *
16417068 GTAGTGGAGCAGATCGTAGAAA-C-CA-ATCCTATCTCCCTGAAGTT
1 GCAGTGGAGCAGAT--TA-AAATCACAGATCTTATCT-CCTGAAGTT
16417112 GCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTT
1 GCAGTGGAGCAGATTAAAATCACAGATCTTATCTC-CTGAAGTT
*
16417156 GCAGTAGAGCAGATT
1 GCAGTGGAGCAGATT
16417171 GCATTTAGTC
Statistics
Matches: 150, Mismatches: 25, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
41 3 0.02
42 7 0.05
43 43 0.29
44 88 0.59
45 5 0.03
46 4 0.03
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (43 bp):
GCAGTGGAGCAGATTAAAATCACAGATCTTATCTCCTGAAGTT
Found at i:16419090 original size:25 final size:25
Alignment explanation
Indices: 16419040--16419090 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
16419030 TACTTTGCAA
*
16419040 ATGATTTATTTTAAGTTATTTATAT
1 ATGATTTATTTTAAGTTACTTATAT
* *
16419065 ATGATTTTATTTTTAGTTGCTT-TAT
1 ATGA-TTTATTTTAAGTTACTTATAT
16419090 A
1 A
16419091 CATAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (25 bp):
ATGATTTATTTTAAGTTACTTATAT
Found at i:16419331 original size:14 final size:15
Alignment explanation
Indices: 16419302--16419334 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16419292 TGCCTTGTAT
16419302 TATTTAATCTATTCA
1 TATTTAATCTATTCA
16419317 TATTTAATC-ATTCA
1 TATTTAATCTATTCA
16419331 TATT
1 TATT
16419335 ATTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTAATCTATTCA
Found at i:16420914 original size:13 final size:13
Alignment explanation
Indices: 16420892--16420958 Score: 89
Period size: 13 Copynumber: 5.2 Consensus size: 13
16420882 CATCTATTAC
*
16420892 CATATAACCAATT
1 CATATAACCATTT
*
16420905 CATTTAACCATTT
1 CATATAACCATTT
* *
16420918 CATGTAGCCATTT
1 CATATAACCATTT
16420931 CATATAACCATTT
1 CATATAACCATTT
*
16420944 CGTATAACCATTT
1 CATATAACCATTT
16420957 CA
1 CA
16420959 ACAAAACTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (13 bp):
CATATAACCATTT
Found at i:16421309 original size:45 final size:45
Alignment explanation
Indices: 16421250--16421358 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
16421240 TGTCATTGCT
* *
16421250 TCTTTCAACCATGGTCTTACTCACTCCCTTCATGATGCCATAGAG
1 TCTTTCAACTATGGTCTTACTCACTCCCATCATGATGCCATAGAG
* * *** * *
16421295 TCTTGT-AGCTATGGTCTTATTTGTTTCCATCATGATGCTATAGAG
1 TCTT-TCAACTATGGTCTTACTCACTCCCATCATGATGCCATAGAG
16421340 TCTTTCAACTATGGTCTTA
1 TCTTTCAACTATGGTCTTA
16421359 TTTGTTTCTG
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 1 0.02
45 50 0.96
46 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (45 bp):
TCTTTCAACTATGGTCTTACTCACTCCCATCATGATGCCATAGAG
Found at i:16421375 original size:45 final size:45
Alignment explanation
Indices: 16421279--16421366 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
16421269 CTCACTCCCT
*
16421279 TCATGATGCCATAGAGTCTTGTAGCTATGGTCTTATTTGTTTCCA
1 TCATGATGCCATAGAGTCTTGTAACTATGGTCTTATTTGTTTCCA
*
16421324 TCATGATGCTATAGAGTCTT-TCAACTATGGTCTTATTTGTTTC
1 TCATGATGCCATAGAGTCTTGT-AACTATGGTCTTATTTGTTTC
16421367 TGTTATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (45 bp):
TCATGATGCCATAGAGTCTTGTAACTATGGTCTTATTTGTTTCCA
Found at i:16421393 original size:16 final size:16
Alignment explanation
Indices: 16421374--16421406 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16421364 TTCTGTTATG
16421374 ATTTACTATA-ACATAT
1 ATTTA-TATACACATAT
16421390 ATTTATATACACATAT
1 ATTTATATACACATAT
16421406 A
1 A
16421407 GATAAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATATACACATAT
Found at i:16422801 original size:85 final size:84
Alignment explanation
Indices: 16422658--16422821 Score: 274
Period size: 85 Copynumber: 1.9 Consensus size: 84
16422648 GGGCTGTTAC
* * *
16422658 ATTTGCAGTTATTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAACTGCCACTT
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGATTAAACAAACTGCCAC-T
*
16422723 GGTTCATGATCGAACCACAT
65 GGTTCATAATCGAACCACAT
*
16422743 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGATTAAACAAACTGCCGCTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGATTAAACAAACTGCCACTG
16422808 GTTCATAATCGAAC
66 GTTCATAATCGAAC
16422822 TACACTGTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 15 0.20
85 59 0.80
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (84 bp):
ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTACAGATTAAACAAACTGCCACTG
GTTCATAATCGAACCACAT
Found at i:16423372 original size:28 final size:28
Alignment explanation
Indices: 16423340--16423447 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
16423330 AAATTTTGGA
16423340 CAAAATTGTAAAATCTAAAAAATAGAGG
1 CAAAATTGTAAAATCTAAAAAATAGAGG
*
16423368 CAAAACTGTAAAATCTAAAAAATA-AGGG
1 CAAAATTGTAAAATCTAAAAAATAGA-GG
* * ** *
16423396 CAAAATTATAAAATTTTGAAAATAGGGG
1 CAAAATTGTAAAATCTAAAAAATAGAGG
*
16423424 ACAAAATTGTAAAATTTTAAAAAA
1 -CAAAATTGTAAAA-TCTAAAAAA
16423448 AGGGAATACA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
27 1 0.02
28 46 0.70
29 12 0.18
30 7 0.11
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24
Consensus pattern (28 bp):
CAAAATTGTAAAATCTAAAAAATAGAGG
Found at i:16428601 original size:37 final size:38
Alignment explanation
Indices: 16428549--16428629 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 38
16428539 AAAAAATTTT
* *
16428549 AAAAGAGTATTTTAAAAATATTTTAATATAA-AAAAAG
1 AAAAAAGTATTTTAAAAATATTTTAAAATAATAAAAAG
*
16428586 AAAAAAGTATTTTAAAAATATTTTAAAATAATAAAAAT
1 AAAAAAGTATTTTAAAAATATTTTAAAATAATAAAAAG
16428624 AAAAAA
1 AAAAAA
16428630 TAAAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 29 0.73
38 11 0.28
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (38 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATAATAAAAAG
Found at i:16428615 original size:10 final size:11
Alignment explanation
Indices: 16428535--16428574 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
16428525 TATTTTAAAA
*
16428535 TTTAAAAAAAT
1 TTTAAAAATAT
16428546 TTTAAAAGAGTAT
1 TTTAAAA-A-TAT
16428559 TTTAAAAATAT
1 TTTAAAAATAT
16428570 TTTAA
1 TTTAA
16428575 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
12 2 0.08
13 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:16430204 original size:16 final size:15
Alignment explanation
Indices: 16430169--16430201 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
16430159 AAAAATTACT
16430169 TAATTATTTTAAATA
1 TAATTATTTTAAATA
16430184 TAATTAATTTT-AATA
1 TAATT-ATTTTAAATA
16430199 TAA
1 TAA
16430202 ATTTTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATTTTAAATA
Found at i:16431259 original size:24 final size:26
Alignment explanation
Indices: 16431217--16431266 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
16431207 CCTTCAAATT
* *
16431217 AATTTTTTTTTCAATTAGGTA-TTAA
1 AATTCTTTTTTCAACTAGGTACTTAA
16431242 AATTCTTTTTT-AACTAGGTACTTAA
1 AATTCTTTTTTCAACTAGGTACTTAA
16431267 TCTATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (26 bp):
AATTCTTTTTTCAACTAGGTACTTAA
Found at i:16432737 original size:43 final size:43
Alignment explanation
Indices: 16432666--16432969 Score: 402
Period size: 43 Copynumber: 7.2 Consensus size: 43
16432656 TTTTAGAAAT
* *
16432666 AAACGCCGCTATAGACCATGACC-TTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* **
16432708 AAACGCCGCTATAGATCAGGACCTTTAGCGGCG-TTTTTGCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
*
16432750 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCACAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
16432793 AAACACCACTATAGCTCAAGACCTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
16432836 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCCTTTT-CCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCG-CTTTTCCCAC
** *
16432879 AAACGCCGCTATATCTCAAGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
16432922 AAACG-CGCTATAGAACAA-ACCTTTAGCGACGCTTCTCGCAA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
16432963 AAACGCC
1 AAACGCC
16432970 ACTAAAAACA
Statistics
Matches: 230, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
41 23 0.10
42 76 0.33
43 126 0.55
44 5 0.02
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16435459 original size:25 final size:25
Alignment explanation
Indices: 16435431--16435480 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16435421 TTAGATAAAA
* *
16435431 TTATTTTAGTGTTTTTATTTCATTT
1 TTATTTTAGTATTTTAATTTCATTT
* *
16435456 TTATTTTTGTATTTTAATTTTATTT
1 TTATTTTAGTATTTTAATTTCATTT
16435481 CCTATAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (25 bp):
TTATTTTAGTATTTTAATTTCATTT
Found at i:16435468 original size:19 final size:18
Alignment explanation
Indices: 16435442--16435480 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16435432 TATTTTAGTG
*
16435442 TTTTTATTTCATTTTTAT
1 TTTTTATTTCAATTTTAT
*
16435460 TTTTGTATTTTAATTTTAT
1 TTTT-TATTTCAATTTTAT
16435479 TT
1 TT
16435481 CCTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTATTTCAATTTTAT
Found at i:16435973 original size:48 final size:47
Alignment explanation
Indices: 16435918--16436022 Score: 183
Period size: 47 Copynumber: 2.2 Consensus size: 47
16435908 TTTTAATACA
* *
16435918 TAGTTTTTTAATTTATATTTATAAAAATTAGATAAAATTAAAAATTT
1 TAGTTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
16435965 TAGTTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
1 TAGTTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
16436012 TAGTGTTTTTA
1 TAGT-TTTTTA
16436023 TTTCATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
47 49 0.89
48 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (47 bp):
TAGTTTTTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTT
Found at i:16436036 original size:25 final size:26
Alignment explanation
Indices: 16436008--16436060 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
16435998 AAAATTAAAA
* *
16436008 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTAATTTCATTTCTT
* *
16436033 ATTTTGGTATTTTAATTTTATTTCTT
1 ATTTTAGTATTTTAATTTCATTTCTT
16436059 AT
1 AT
16436061 AATTTGGTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.19, C:0.04, G:0.08, T:0.70
Consensus pattern (26 bp):
ATTTTAGTATTTTAATTTCATTTCTT
Found at i:16436486 original size:15 final size:15
Alignment explanation
Indices: 16436428--16436493 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
16436418 GCCTTTAAAA
*
16436428 CCCTAAAC-CCTAAAT
1 CCCTAAACTCCT-AAC
*
16436443 CCCT-AACTCTTAAC
1 CCCTAAACTCCTAAC
* **
16436457 CACTAATGT-CTAAC
1 CCCTAAACTCCTAAC
16436471 CCCTAAACTCCTAAC
1 CCCTAAACTCCTAAC
16436486 CCCTAAAC
1 CCCTAAAC
16436494 CTTAAATCCC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 18 0.46
15 21 0.54
ACGTcount: A:0.35, C:0.41, G:0.02, T:0.23
Consensus pattern (15 bp):
CCCTAAACTCCTAAC
Found at i:16436861 original size:15 final size:15
Alignment explanation
Indices: 16436825--16436863 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
16436815 CAACCATTAA
16436825 TTAAA-CCATAATCC
1 TTAAATCCATAATCC
*
16436839 CT-AATCCATAATCC
1 TTAAATCCATAATCC
16436853 TTAAATCCATA
1 TTAAATCCATA
16436864 TATACGCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.41, C:0.28, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAATCCATAATCC
Found at i:16437488 original size:41 final size:40
Alignment explanation
Indices: 16437435--16437564 Score: 134
Period size: 41 Copynumber: 3.2 Consensus size: 40
16437425 AGCGCTAATA
* *
16437435 CAAAAACACCGCTAAAGACCTGAGCATTAGCAGCGATTCCT
1 CAAAAACGCCGCTAAAG-CCTGGGCATTAGCAGCGATTCCT
* * * * *
16437476 TAGAAACGCCGCTAAAGCCCTGGGAATTAGCGGCGCTTCCT
1 CAAAAACGCCGCTAAAG-CCTGGGCATTAGCAGCGATTCCT
* ** *
16437517 CAAAAACGCCACTAAAGCCTTGGGCATTAGTGGCGCTTCCT
1 CAAAAACGCCGCTAAAGCC-TGGGCATTAGCAGCGATTCCT
16437558 CAAAAAC
1 CAAAAAC
16437565 ACTGCTAATG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
40 2 0.03
41 73 0.97
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (40 bp):
CAAAAACGCCGCTAAAGCCTGGGCATTAGCAGCGATTCCT
Found at i:16437716 original size:39 final size:39
Alignment explanation
Indices: 16437673--16437787 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 39
16437663 GCTTTTTTGG
*
16437673 AAAGCGCCGCTAATGCTTATTTTTAGCGGCGTTTTCC-A
1 AAAGCGCCGCTAATGCTTATCTTTAGCGGCGTTTTCCGA
*
16437711 TAAAGCGCCGCTAATG-TTCGATCTTTAGCGGCATTTTCCGA
1 -AAAGCGCCGCTAATGCTT--ATCTTTAGCGGCGTTTTCCGA
* *
16437752 AAAGCGCCGCTAATACTCGATCTTTAGCGGCGTTTT
1 AAAGCGCCGCTAATGCT-TATCTTTAGCGGCGTTTT
16437788 TTATCCAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
38 2 0.03
39 15 0.23
40 47 0.71
41 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (39 bp):
AAAGCGCCGCTAATGCTTATCTTTAGCGGCGTTTTCCGA
Found at i:16440902 original size:43 final size:43
Alignment explanation
Indices: 16440835--16441061 Score: 314
Period size: 43 Copynumber: 5.3 Consensus size: 43
16440825 GCTTCGGAAA
* * *
16440835 AAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * *
16440878 AAACGCCGCTAAAAACCACA-ACCTTTAACGACGCTTTTCCCGC
1 AAACGCCGCTAAAGACCA-AGACCTTTAGCGGCGCTTTTCCCAC
* * *
16440921 AATCGCCGCTAAAGACTAAGACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
16440964 AAACGCCGCT-AAGACCAAGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
16441006 AAACGCCGCTAAAGACCAAAACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
16441049 AAACGCCACTAAA
1 AAACGCCGCTAAA
16441062 AACATGACTT
Statistics
Matches: 162, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 40 0.25
43 121 0.75
44 1 0.01
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:16441031 original size:85 final size:85
Alignment explanation
Indices: 16440835--16441062 Score: 314
Period size: 85 Copynumber: 2.7 Consensus size: 85
16440825 GCTTCGGAAA
* * *
16440835 AAACGCTGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCGCAAACGCCGCTAAAAACCACAAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCT-AAAACCACAAC
*
16440900 CTTTAACGACGCTTTTCCCGC
65 CTTTAACGACGCTTTTCCCAC
* * * *
16440921 AATCGCCGCTAAAGACTAAGACCTTTAGCGGCACTTTTCCCACAAACGCCGCTAAGACCA-AGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAACCACA-AC
* * *
16440985 CTTTAGCGGCGCTTTTCTCAC
65 CTTTAACGACGCTTTTCCCAC
* *
16441006 AAACGCCGCTAAAGACCAAAACCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAA
16441063 ACATGACTTA
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 76 0.61
86 47 0.38
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (85 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAACCACAACC
TTTAACGACGCTTTTCCCAC
Found at i:16441259 original size:18 final size:18
Alignment explanation
Indices: 16441236--16441295 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
16441226 ATAAAACAAG
16441236 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
*** * *
16441254 TTACATAAGAAAATT-G-T
1 TTACAT-TCTATATTAGAA
16441271 TTACATTCTATATTAGAA
1 TTACATTCTATATTAGAA
16441289 TTACATT
1 TTACATT
16441296 AGAATACATA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 14 0.48
19 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (18 bp):
TTACATTCTATATTAGAA
Found at i:16446439 original size:24 final size:24
Alignment explanation
Indices: 16446411--16446462 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16446401 TTCGTAGGTC
* *
16446411 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
16446435 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
16446459 AAAT
1 AAAT
16446463 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:16447989 original size:34 final size:35
Alignment explanation
Indices: 16447951--16448017 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16447941 AAGTAGAATG
*
16447951 TTTTCCGGAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGGAAAATGATTTACTGGAAAATATTTTAC
* *
16447985 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGGAAAATGATTTACTGGAAAATATTTT
16448018 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGGAAAATGATTTACTGGAAAATATTTTAC
Found at i:16447991 original size:20 final size:20
Alignment explanation
Indices: 16447966--16448005 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16447956 CGGAAAATGA
*
16447966 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
16447986 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16448006 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16448117 original size:20 final size:20
Alignment explanation
Indices: 16448092--16448168 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
16448082 TCCGGAAAAG
16448092 TTGTTTTTACATATATTAAA
1 TTGTTTTTACATATATTAAA
*
16448112 TTGTTTTTACATATATATTAA
1 TTGTTTTTACATATAT-TAAA
** *
16448133 TAAATTTTT--ATATTTTAAA
1 T-TGTTTTTACATATATTAAA
16448152 TTGTTTTTACATATATT
1 TTGTTTTTACATATATT
16448169 GCAATGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.11
19 4 0.09
20 27 0.60
21 4 0.09
22 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TTGTTTTTACATATATTAAA
Found at i:16450842 original size:15 final size:13
Alignment explanation
Indices: 16450813--16450839 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16450803 CCAGAAACTG
16450813 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
16450826 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
16450839 A
1 A
16450840 CATCTACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:16451065 original size:24 final size:24
Alignment explanation
Indices: 16451030--16451075 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
16451020 GGTGAAGAGA
*
16451030 GTGAAGAGAGGAGCTGTGGAAAGG
1 GTGAAGAAAGGAGCTGTGGAAAGG
16451054 GTGAAGAAAGGAGCTGTGGAAA
1 GTGAAGAAAGGAGCTGTGGAAA
16451076 TGGTTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (24 bp):
GTGAAGAAAGGAGCTGTGGAAAGG
Found at i:16461568 original size:22 final size:20
Alignment explanation
Indices: 16461527--16461568 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16461517 AAAAAATAAG
*
16461527 AATTTAAAAATCGTAACTAT
1 AATTTAAAAATCCTAACTAT
16461547 AATTTAAAAATTTCCTAACTAT
1 AATTTAAAAA--TCCTAACTAT
16461569 CCTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTTAAAAATCCTAACTAT
Found at i:16466910 original size:35 final size:38
Alignment explanation
Indices: 16466844--16466936 Score: 120
Period size: 35 Copynumber: 2.4 Consensus size: 38
16466834 AAGAATTAGT
16466844 TAAAAATATTAATATGTGTACATGCATATGCATATGTATAG
1 TAAAAATATTAATATGTGTA-A-GCA-ATGCATATGTATAG
16466885 TAAAAATATTAATATGTGT-A-C-ATGCATATGTATAG
1 TAAAAATATTAATATGTGTAAGCAATGCATATGTATAG
16466920 TAAAAATAATTACATAT
1 TAAAAAT-ATTA-ATAT
16466937 AAATAAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
35 21 0.42
36 4 0.08
37 5 0.10
39 1 0.02
41 19 0.38
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (38 bp):
TAAAAATATTAATATGTGTAAGCAATGCATATGTATAG
Found at i:16467010 original size:21 final size:21
Alignment explanation
Indices: 16466971--16467011 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16466961 TTATACTACA
* *
16466971 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
16466992 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
16467012 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:16467048 original size:24 final size:24
Alignment explanation
Indices: 16467020--16467076 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
16467010 ATATTTTTTA
16467020 AAAAATAACTAAAT-ATAAAAAGAAT
1 AAAAA-AACTAAATAATAAAAA-AAT
*
16467045 AAAAAAACTAATTAATAAAAAAAT
1 AAAAAAACTAAATAATAAAAAAAT
16467069 AAAGAAAA
1 AAA-AAAA
16467077 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (24 bp):
AAAAAAACTAAATAATAAAAAAAT
Done.