Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 163 of 182
Found at i:49590580 original size:19 final size:19
Alignment explanation
Indices: 49590556--49590593 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
49590546 TATTTTCTAT
* *
49590556 GTTTGATTCATGAAAAATA
1 GTTTGATTAATAAAAAATA
49590575 GTTTGATTAATAAAAAATA
1 GTTTGATTAATAAAAAATA
49590594 ATTTACAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (19 bp):
GTTTGATTAATAAAAAATA
Found at i:49590862 original size:18 final size:18
Alignment explanation
Indices: 49590834--49590874 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
49590824 TTGTTTCTAT
*
49590834 AATTT-TTTTAATATTAA
1 AATTTATTTTAATAATAA
49590851 AATTTATTTTAATAATAA
1 AATTTATTTTAATAATAA
*
49590869 ATTTTA
1 AATTTA
49590875 AAAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTATTTTAATAATAA
Found at i:49590870 original size:17 final size:17
Alignment explanation
Indices: 49590834--49590873 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
49590824 TTGTTTCTAT
*
49590834 AATTTTTTTAATATTAA
1 AATTTTTTTAATAATAA
49590851 AATTTATTTTAATAAT-A
1 AATTT-TTTTAATAATAA
49590868 AATTTT
1 AATTTT
49590874 AAAAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 11 0.52
18 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTTTTAATAATAA
Found at i:49590888 original size:15 final size:16
Alignment explanation
Indices: 49590861--49590891 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49590851 AATTTATTTT
49590861 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
49590877 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
49590892 TTTTAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:49597819 original size:13 final size:13
Alignment explanation
Indices: 49597801--49597827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
49597791 TTTATAATTT
49597801 TTTATAAATTTTA
1 TTTATAAATTTTA
49597814 TTTATAAATTTTA
1 TTTATAAATTTTA
49597827 T
1 T
49597828 GACTTTTTAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATAAATTTTA
Found at i:49598356 original size:3 final size:3
Alignment explanation
Indices: 49598342--49598373 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
49598332 TCTCTTGAAT
49598342 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
49598374 CCCATCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:49598820 original size:29 final size:30
Alignment explanation
Indices: 49598787--49598845 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
49598777 TATCGTCCAA
*
49598787 TGTGTAATTTTATATAT-TAATTTTGATTT
1 TGTGTAATTTTATATATGAAATTTTGATTT
49598816 TGTGTAATTTTATATATGAAATTTTGATTT
1 TGTGTAATTTTATATATGAAATTTTGATTT
49598846 GATCAAATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (30 bp):
TGTGTAATTTTATATATGAAATTTTGATTT
Found at i:49599436 original size:4 final size:4
Alignment explanation
Indices: 49599429--49599458 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
49599419 TTCATTCATT
49599429 CATC CATC CATC CATC CATC CATC CATC CA
1 CATC CATC CATC CATC CATC CATC CATC CA
49599459 AACCCACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (4 bp):
CATC
Found at i:49603702 original size:15 final size:16
Alignment explanation
Indices: 49603659--49603705 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
49603649 ATATTTTAAA
* *
49603659 AAAATTATTTAATATT
1 AAAATAATTTATTATT
49603675 AAAATTAATTTTATTATT
1 AAAA-TAA-TTTATTATT
49603693 -AAATAATTTATTA
1 AAAATAATTTATTA
49603706 AAAATATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.26
16 7 0.26
17 5 0.19
18 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAATAATTTATTATT
Found at i:49604898 original size:24 final size:25
Alignment explanation
Indices: 49604852--49604899 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
49604842 TTTGTTTCAC
*
49604852 TAAAAACAATTTTTAAAAAATATTA
1 TAAAAACAATTTGTAAAAAATATTA
* *
49604877 TAAAAAC-ATTTGTCAAACATATT
1 TAAAAACAATTTGTAAAAAATATT
49604900 TTATGCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAAACAATTTGTAAAAAATATTA
Found at i:49612495 original size:40 final size:39
Alignment explanation
Indices: 49612451--49612583 Score: 92
Period size: 40 Copynumber: 3.3 Consensus size: 39
49612441 CATCTTATAT
49612451 TTTTTTAACAATTTTTTATAGGTTCTGATCATATCTGTTC
1 TTTTTTAACAATTTTTTATA-GTTCTGATCATATCTGTTC
* ** * * * * * *
49612491 TTTTTGACACAATATCTTGAACTA-TCCATAACCCT-CCTATT-
1 TTTTTTA-ACAAT-T-TTTTA-TAGTTC-TGATCATATCTGTTC
*
49612532 TTTTTTAACAATTATTTATAAGTTCTGATCATATCTGTTC
1 TTTTTTAACAATTTTTTAT-AGTTCTGATCATATCTGTTC
49612572 TTTTTTAACAAT
1 TTTTTTAACAAT
49612584 ATTTAGAATT
Statistics
Matches: 65, Mismatches: 19, Indels: 18
0.64 0.19 0.18
Matches are distributed among these distances:
37 1 0.02
38 7 0.11
39 7 0.11
40 23 0.35
41 11 0.17
42 7 0.11
43 7 0.11
44 2 0.03
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (39 bp):
TTTTTTAACAATTTTTTATAGTTCTGATCATATCTGTTC
Found at i:49614192 original size:20 final size:21
Alignment explanation
Indices: 49614147--49614192 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
49614137 AATGAAAACA
*
49614147 AATAA-TTATTTTAGAAAAAT
1 AATAATTTATATTAGAAAAAT
*
49614167 TA-AATTTATATT-GAAAAAT
1 AATAATTTATATTAGAAAAAT
49614186 AATAATT
1 AATAATT
49614193 ACAAAGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
AATAATTTATATTAGAAAAAT
Found at i:49616099 original size:21 final size:21
Alignment explanation
Indices: 49616058--49616111 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
49616048 TCTAATAAAG
**
49616058 ATTTTATATTTTTTTTTATAA
1 ATTTTATATTTTTTTAAATAA
49616079 ATTTTATGA-TTTTTTAAATAA
1 ATTTTAT-ATTTTTTTAAATAA
* *
49616100 TTTTTAAATTTT
1 ATTTTATATTTT
49616112 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTATATTTTTTTAAATAA
Found at i:49618054 original size:124 final size:124
Alignment explanation
Indices: 49617834--49618081 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
49617824 ATCATCAACT
49617834 TCTCTCAACACTAATCACCACCACTATCCAATTAACCAACCACCACAAATAACCACCACTGTCCA
1 TCTCTCAACACTAATCACCACCACTATCCAATTAACCAACCACCACAAATAACCACCACTGTCCA
49617899 CCCTCCACTCTCATCACTGTCAAATCCAAAACCCCTCACAATCACTTCATTTACCATAG
66 CCCTCCACTCTCATCACTGTCAAATCCAAAACCCCTCACAATCACTTCATTTACCATAG
*
49617958 TCTCTCAACACTAATCACCACCACTATCCAATTAACCAACCACCACAACTAACCACCACTGTCCA
1 TCTCTCAACACTAATCACCACCACTATCCAATTAACCAACCACCACAAATAACCACCACTGTCCA
49618023 CCCTCCACTCTCATCACTGTCAAATCCAAAACCCCTCACAATCACTTCATTTACCATAG
66 CCCTCCACTCTCATCACTGTCAAATCCAAAACCCCTCACAATCACTTCATTTACCATAG
49618082 CCACCATAAA
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.34, C:0.42, G:0.02, T:0.22
Consensus pattern (124 bp):
TCTCTCAACACTAATCACCACCACTATCCAATTAACCAACCACCACAAATAACCACCACTGTCCA
CCCTCCACTCTCATCACTGTCAAATCCAAAACCCCTCACAATCACTTCATTTACCATAG
Found at i:49621875 original size:17 final size:16
Alignment explanation
Indices: 49621839--49621877 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
49621829 CATTTTTCGA
49621839 AATTTTTTTTATAAGT
1 AATTTTTTTTATAAGT
49621855 AATTTATTTTTATATAG-
1 AATTT-TTTTTATA-AGT
49621872 AATTTT
1 AATTTT
49621878 ACTTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (16 bp):
AATTTTTTTTATAAGT
Found at i:49622006 original size:22 final size:20
Alignment explanation
Indices: 49621981--49622030 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
49621971 TTATAATGAT
49621981 TAATTATTTATATTTATTAATA
1 TAATTATTTATA-TT-TTAATA
*
49622003 TAATTA-ATATATTTTAATA
1 TAATTATTTATATTTTAATA
49622022 -AATTATTTA
1 TAATTATTTA
49622031 ATAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 2 0.08
21 4 0.16
22 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTATTTATATTTTAATA
Found at i:49622060 original size:13 final size:13
Alignment explanation
Indices: 49622036--49622078 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
49622026 ATTTAATAAC
*
49622036 AAAATTAATTTTA
1 AAAATAAATTTTA
*
49622049 ATAATAAATTTTA
1 AAAATAAATTTTA
49622062 AAAATAATAATTTTA
1 AAAAT-A-AATTTTA
49622077 AA
1 AA
49622079 TTTTAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.60
14 1 0.04
15 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATAAATTTTA
Found at i:49622075 original size:15 final size:16
Alignment explanation
Indices: 49622048--49622078 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
49622038 AATTAATTTT
49622048 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
49622064 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
49622079 TTTTAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:49622416 original size:18 final size:18
Alignment explanation
Indices: 49622393--49622433 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
49622383 ATGATATTAA
49622393 TTATTATAAAAT-ATTATT
1 TTATTATAAAATAATT-TT
49622411 TTATTATAAAATAATTTT
1 TTATTATAAAATAATTTT
49622429 TTATT
1 TTATT
49622434 GTCCAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATAAAATAATTTT
Found at i:49625927 original size:39 final size:39
Alignment explanation
Indices: 49625843--49625976 Score: 97
Period size: 39 Copynumber: 3.4 Consensus size: 39
49625833 ATAGTCCAGT
* * * * **
49625843 AGTGTTTACAGTGTCACTACTACTTCAGTGTGGTGTCGC
1 AGTGTTTACAATGTCACCACCACTTCAGTATGGCATCGC
* * *
49625882 AATGTTTACAATGTCACCACCAGTTCAGTATGGCATTGC
1 AGTGTTTACAATGTCACCACCACTTCAGTATGGCATCGC
* * ** * * ** *
49625921 AGTGTTTACAGTGCCACTGCCAATTTAGTATAACAACGC
1 AGTGTTTACAATGTCACCACCACTTCAGTATGGCATCGC
*
49625960 AGTGTTTACAGTGTCAC
1 AGTGTTTACAATGTCAC
49625977 TGCCGATTCA
Statistics
Matches: 74, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (39 bp):
AGTGTTTACAATGTCACCACCACTTCAGTATGGCATCGC
Found at i:49626023 original size:39 final size:39
Alignment explanation
Indices: 49625919--49626025 Score: 160
Period size: 39 Copynumber: 2.7 Consensus size: 39
49625909 GTATGGCATT
* * * *
49625919 GCAGTGTTTACAGTGCCACTGCCAATTTAGTATAACAAC
1 GCAGTGTTTACAGTGTCACTGCCGATTCAATATAACAAC
49625958 GCAGTGTTTACAGTGTCACTGCCGATTCAATATAACAAC
1 GCAGTGTTTACAGTGTCACTGCCGATTCAATATAACAAC
**
49625997 GCAGTGTTTACAGTGTCACTATCGATTCA
1 GCAGTGTTTACAGTGTCACTGCCGATTCA
49626026 TTACACTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (39 bp):
GCAGTGTTTACAGTGTCACTGCCGATTCAATATAACAAC
Found at i:49631843 original size:22 final size:22
Alignment explanation
Indices: 49631815--49631857 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
49631805 AGTGTTTAAT
49631815 TCATGCAGAAGGAAATATATTG
1 TCATGCAGAAGGAAATATATTG
49631837 TCATGCAGAAGGAAATATATT
1 TCATGCAGAAGGAAATATATT
49631858 ATATTGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (22 bp):
TCATGCAGAAGGAAATATATTG
Found at i:49634633 original size:20 final size:21
Alignment explanation
Indices: 49634594--49634639 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
49634584 ATTTTAATGT
49634594 TAAGTTTTATATTCAAAAAAA
1 TAAGTTTTATATTCAAAAAAA
*
49634615 TAAGTTTTA-ATTTAAAAAAA
1 TAAGTTTTATATTCAAAAAAA
*
49634635 AAAGT
1 TAAGT
49634640 CTAAATAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
TAAGTTTTATATTCAAAAAAA
Found at i:49636347 original size:3 final size:3
Alignment explanation
Indices: 49636339--49636369 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
49636329 AAACTATCTC
49636339 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
49636370 TGTGAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:49640320 original size:17 final size:18
Alignment explanation
Indices: 49640280--49640322 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
49640270 TATTATAATC
* *
49640280 ATTATTTTGGTTACTTTA
1 ATTATTTTGGTCAATTTA
*
49640298 AATATTTT-GTCAATTTA
1 ATTATTTTGGTCAATTTA
49640315 ATTATTTT
1 ATTATTTT
49640323 AATTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTATTTTGGTCAATTTA
Found at i:49641364 original size:47 final size:47
Alignment explanation
Indices: 49641310--49641444 Score: 177
Period size: 45 Copynumber: 2.9 Consensus size: 47
49641300 TTTATGATTT
* * * * *
49641310 TTTACCAATATAATACAAAAATAATAATTAAATATCAAAATGGGTTA
1 TTTACCAAAATGATACAAAAATAATATTTATATACCAAAATGGGTTA
* *
49641357 TTTACCAAAATGGTAC-AAAA-AATATTTATATACCAAAATGAGTTA
1 TTTACCAAAATGATACAAAAATAATATTTATATACCAAAATGGGTTA
49641402 TTTACCAAAATGATA-AAAAATAAATATTTATATACCAAAATGG
1 TTTACCAAAATGATACAAAAAT-AATATTTATATACCAAAATGG
49641445 TATCCACACT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
45 39 0.51
46 4 0.05
47 33 0.43
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (47 bp):
TTTACCAAAATGATACAAAAATAATATTTATATACCAAAATGGGTTA
Found at i:49641402 original size:17 final size:17
Alignment explanation
Indices: 49641382--49641414 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49641372 CAAAAAATAT
49641382 TTATATACCAAAATGAG
1 TTATATACCAAAATGAG
*
49641399 TTATTTACCAAAATGA
1 TTATATACCAAAATGA
49641415 TAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (17 bp):
TTATATACCAAAATGAG
Found at i:49642632 original size:28 final size:28
Alignment explanation
Indices: 49642532--49642633 Score: 66
Period size: 28 Copynumber: 3.5 Consensus size: 28
49642522 GTCCGGGGAC
* *
49642532 AAAATGGTAATTTTGGACT-TTTGAGGGC
1 AAAATGGTAATTTTGGA-TATTCGAGGGT
* * * *
49642560 AAAATGGTAATTTTTAGAAAAATCGA-GAT
1 AAAATGGTAA-TTTT-GGATATTCGAGGGT
*
49642589 AAAAAATGAG-ATTTTTGGATATTCGAGGGT
1 --AAAATG-GTAATTTTGGATATTCGAGGGT
49642619 AAAATGGTAATTTTG
1 AAAATGGTAATTTTG
49642634 AGTGTTTTGA
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
27 1 0.02
28 22 0.41
29 12 0.22
30 11 0.20
31 7 0.13
32 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTGGATATTCGAGGGT
Found at i:49642689 original size:58 final size:59
Alignment explanation
Indices: 49642590--49642934 Score: 227
Period size: 58 Copynumber: 5.9 Consensus size: 59
49642580 AATCGAGATA
* *
49642590 AAAAAT-GAGATTTTTGGATA-TTCGAGGGT--AAAATGGTAATTTTGAG-TGTTTTGAGGTC
1 AAAAATGGA-ATTTTTGGA-AGTTCG-GGGTCAAAAAT-GAAATTTTGAGAAGTTTTGAGGTC
*
49642648 AAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAAATTTTTG-GAAG-TTTG-GGGC
1 AAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAAA-TTTTGAGAAGTTTTGAGGTC
* * * *
49642705 AAAAATGTAATTTTTGGAAGTTCAGAGG-C-AAAATGTAATTTTTG-GAAGTTTT-AGGGTT
1 AAAAATGGAATTTTTGGAAGTTC-GGGGTCAAAAATG-AAATTTTGAGAAGTTTTGA-GGTC
* ** * * * *
49642763 AAAAATGAAATTTTTTTAAGTTTAGGGGT-AAAAATGTAATTTTTAGAAG-TTTAAGGGT-
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAATGAAATTTTGAGAAGTTTTGA-GGTC
* ** * ** *
49642821 AAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGTAATTTTTTGAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAATGAAATTTTGAGAAGTTTTGAGGTC
* ** *
49642881 AAAAATAGAATTTTTGGAAGTTTCAAGGTCAAAATAT-AATTTTTGGAGAAGTTT
1 AAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAA-ATGAAATTTT-GAGAAGTTT
49642935 AGGGACCTCC
Statistics
Matches: 234, Mismatches: 32, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
56 15 0.06
57 36 0.15
58 84 0.36
59 52 0.22
60 38 0.16
61 9 0.04
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAAATTTTGAGAAGTTTTGAGGTC
Found at i:49642710 original size:87 final size:85
Alignment explanation
Indices: 49642526--49642927 Score: 280
Period size: 87 Copynumber: 4.6 Consensus size: 85
49642516 TTGGATGTCC
* * * *** *
49642526 GGGGACAAAATGGTAATTTTGG-ACTTTTGAGGGCAAAATGGTAATTTTTAGAAAAATC-GAGAT
1 GGGGA-AAAAT-GTAATTTTGGAAGTTTTGAGGTCAAAATGG-AATTTTTGGAAGTTTCAG-GGT
* * *
49642589 AAAAAATGAGATTTTTGGATA-TTC
62 CAAAAATGAAATTTTTGGA-AGTTT
* * *
49642613 GAGGGTAAAATGGTAATTTT-GAGTGTTTTGAGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGT
1 G-GGGAAAAAT-GTAATTTTGGA-AGTTTTGAGGTC-AAAATGGAATTTTTGGAAGTTTCAGGGT
49642676 CAAAAATGAAATTTTTGGAAGTTT
62 CAAAAATGAAATTTTTGGAAGTTT
** * * *
49642700 GGGGCAAAAATGTAATTTTTGGAAGTTCAGAGG-CAAAATGTAATTTTTGGAAGTTTTAGGGTTA
1 GGGG-AAAAATGTAA-TTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTTCAGGGTCA
**
49642764 AAAATGAAATTTTTTTAAGTTT
64 AAAATGAAATTTTTGGAAGTTT
* * * * *
49642786 AGGGGTAAAAATGTAATTTTTAGAAG-TTTAAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGT
1 -GGGG-AAAAATGTAA-TTTTGGAAGTTTTGA-GGTCAAAATGGAATTTTTGGAAGTTTCAGGGT
* *
49642850 CAAAAATGTAATTTTTTGAAGTTT
62 CAAAAATGAAATTTTTGGAAGTTT
* ** **
49642874 CGAGGTCAAAAATAG-AATTTTTGGAAGTTTCAAGGTCAAAATATAATTTTTGGA
1 -G-GG-GAAAAAT-GTAA-TTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGGA
49642928 GAAGTTTAGG
Statistics
Matches: 262, Mismatches: 36, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
85 18 0.07
86 39 0.15
87 80 0.31
88 75 0.29
89 45 0.17
90 5 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (85 bp):
GGGGAAAAATGTAATTTTGGAAGTTTTGAGGTCAAAATGGAATTTTTGGAAGTTTCAGGGTCAAA
AATGAAATTTTTGGAAGTTT
Found at i:49642775 original size:30 final size:29
Alignment explanation
Indices: 49642644--49642938 Score: 316
Period size: 29 Copynumber: 10.1 Consensus size: 29
49642634 AGTGTTTTGA
* **
49642644 GGTCAAAAATGGAATTTTTGGAAGTTCGG
1 GGTCAAAAATGTAATTTTTGGAAGTTTAG
*
49642673 GGTCAAAAATGAAATTTTTGGAAGTTT-G
1 GGTCAAAAATGTAATTTTTGGAAGTTTAG
* *
49642701 GGGCAAAAATGTAATTTTTGGAAGTTCAG
1 GGTCAAAAATGTAATTTTTGGAAGTTTAG
49642730 AGG-C-AAAATGTAATTTTTGGAAGTTTTAG
1 -GGTCAAAAATGTAATTTTTGGAAG-TTTAG
* * **
49642759 GGTTAAAAATGAAATTTTTTTAAGTTTAGG
1 GGTCAAAAATGTAATTTTTGGAAGTTTA-G
*
49642789 GGT-AAAAATGTAATTTTTAGAAGTTTAAG
1 GGTCAAAAATGTAATTTTTGGAAGTTT-AG
49642818 GGT-AAAAATGTAATTTTTGGAAGTTTTAG
1 GGTCAAAAATGTAATTTTTGGAAG-TTTAG
* *
49642847 GGTCAAAAATGTAATTTTTTGAAGTTTCG
1 GGTCAAAAATGTAATTTTTGGAAGTTTAG
*
49642876 AGGTCAAAAATAG-AATTTTTGGAAGTTTCAA
1 -GGTCAAAAAT-GTAATTTTTGGAAGTTT-AG
*
49642907 GGTC-AAAATATAATTTTTGGAGAAGTTTAG
1 GGTCAAAAATGTAATTTTT-G-GAAGTTTAG
49642937 GG
1 GG
49642939 ACCTCCAGGG
Statistics
Matches: 230, Mismatches: 21, Indels: 29
0.82 0.08 0.10
Matches are distributed among these distances:
28 46 0.20
29 99 0.43
30 77 0.33
31 8 0.03
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
GGTCAAAAATGTAATTTTTGGAAGTTTAG
Found at i:49642915 original size:59 final size:58
Alignment explanation
Indices: 49642639--49642927 Score: 313
Period size: 59 Copynumber: 5.0 Consensus size: 58
49642629 TTTTGAGTGT
* * *
49642639 TTTGAGGTCAAAAATGGAATTTTTGGAAG-TTCGGGGTCAAAAATGAAATTTTTGGAAG
1 TTTGAGGTCAAAAATGTAATTTTTGGAAGTTTCAGGGTC-AAAATGTAATTTTTGGAAG
*
49642697 TTTG-GGGCAAAAATGTAATTTTTGGAAG-TTCAGAGG-CAAAATGTAATTTTTGGAAG
1 TTTGAGGTCAAAAATGTAATTTTTGGAAGTTTCAG-GGTCAAAATGTAATTTTTGGAAG
* * * ** * *
49642753 TTTTAGGGTTAAAAATGAAATTTTTTTAAGTTT-AGGGGTAAAAATGTAATTTTTAGAAG
1 TTTGA-GGTCAAAAATGTAATTTTTGGAAGTTTCA-GGGTCAAAATGTAATTTTTGGAAG
* * *
49642812 TTTAAGGGT-AAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGTAATTTTTTGAAG
1 TTTGA-GGTCAAAAATGTAATTTTTGGAAGTTTCAGGGTC-AAAATGTAATTTTTGGAAG
* *
49642871 TTTCGAGGTCAAAAATAG-AATTTTTGGAAGTTTCAAGGTCAAAATATAATTTTTGGA
1 TTT-GAGGTCAAAAAT-GTAATTTTTGGAAGTTTCAGGGTCAAAATGTAATTTTTGGA
49642928 GAAGTTTAGG
Statistics
Matches: 197, Mismatches: 23, Indels: 21
0.82 0.10 0.09
Matches are distributed among these distances:
56 21 0.11
57 27 0.14
58 52 0.26
59 69 0.35
60 27 0.14
61 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (58 bp):
TTTGAGGTCAAAAATGTAATTTTTGGAAGTTTCAGGGTCAAAATGTAATTTTTGGAAG
Found at i:49643981 original size:12 final size:12
Alignment explanation
Indices: 49643949--49644002 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
49643939 AAACAATTAT
*
49643949 TTAATGTTATAA
1 TTAATATTATAA
*
49643961 TTAATTATTATCA
1 TTAA-TATTATAA
49643974 TTAATA-T-T-A
1 TTAATATTATAA
*
49643983 TTAATAATATAA
1 TTAATATTATAA
49643995 TTAATATT
1 TTAATATT
49644003 CACATTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 2 0.06
12 14 0.40
13 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTAATATTATAA
Found at i:49644681 original size:14 final size:15
Alignment explanation
Indices: 49644662--49644695 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
49644652 CTTTGTAATC
49644662 ATTTTGGACTTTTT-
1 ATTTTGGACTTTTTA
*
49644676 ATTTTGGGCTTTTTA
1 ATTTTGGACTTTTTA
49644691 ATTTT
1 ATTTT
49644696 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.65
Consensus pattern (15 bp):
ATTTTGGACTTTTTA
Found at i:49644704 original size:6 final size:6
Alignment explanation
Indices: 49644687--49644756 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
49644677 TTTTGGGCTT
* * *
49644687 TTTAAT TTTAAA TTTAAAA ATT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
49644734 TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
49644757 ATTGACCCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 31 0.61
7 9 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:49644736 original size:17 final size:17
Alignment explanation
Indices: 49644693--49644758 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
49644683 GCTTTTTAAT
*
49644693 TTTAAATTTAAAA-ATTA
1 TTTAAATTTAAAATA-AA
*
49644710 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
49644728 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
49644745 TTTAAATTTAAAAT
1 TTTAAATTTAAAAT
49644759 TGACCCAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 30 0.68
18 13 0.30
19 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:49645647 original size:3 final size:3
Alignment explanation
Indices: 49645639--49645686 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
49645629 AATAGTATAA
*
49645639 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49645687 TTTGTAGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:49647118 original size:27 final size:27
Alignment explanation
Indices: 49647088--49647139 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
49647078 AATACCCTTT
*
49647088 GGTGCCACCACTTGATATCCCTCCAAG
1 GGTGCCACCACTTAATATCCCTCCAAG
*
49647115 GGTGCCGCCACTTAATATCCCTCCA
1 GGTGCCACCACTTAATATCCCTCCA
49647140 CTAATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (27 bp):
GGTGCCACCACTTAATATCCCTCCAAG
Found at i:49654135 original size:28 final size:29
Alignment explanation
Indices: 49654102--49654202 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 29
49654092 AATCGGGGTT
49654102 TAAAATGG-AATTTT-AGAAAGTTCAAGGG
1 TAAAATGGTAATTTTGA-AAAGTTCAAGGG
49654130 TAAAATGGTAATTTTGGTAAAA-TT-AA-GG
1 TAAAATGGTAATTTT-G-AAAAGTTCAAGGG
* *
49654158 TAAAAAATGG-AGTTTTGAAAAGTTCGAGGG
1 T--AAAATGGTAATTTTGAAAAGTTCAAGGG
49654188 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
49654203 TTGGTAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
27 4 0.07
28 21 0.35
29 19 0.32
30 12 0.20
31 3 0.05
32 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
TAAAATGGTAATTTTGAAAAGTTCAAGGG
Found at i:49654137 original size:59 final size:59
Alignment explanation
Indices: 49654073--49654377 Score: 323
Period size: 58 Copynumber: 5.2 Consensus size: 59
49654063 TTTCGGGGGG
* ** *
49654073 AAATGGTAATTTTTGTTGAAATCGGGGTTTAAAATGGAATTTTAGAAAGTTCAAGGGTA
1 AAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGTA
* * * * *
49654132 AAATGGTAA-TTTTGGTAAAATTAAGGTAAAAAATGGAGTTTT-GAAAAGTTCGAGGGTA
1 AAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAG-AAAGTTCAAGGGTA
* * * * * * * *
49654190 AAATGGTAATTTTTTGGTAAAATCAGGGCTAAAAATGAAATTTTGGAAAGTTTAGGGGCA
1 AAATGGTAA-TTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGTA
* * * * *
49654250 AAATTGTAATTTTTGGTGAAATCGAGGTTAAAAATAGAATTTTAAAAAGTTCGAGGGTA
1 AAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGTA
* * *
49654309 AAATGGTAA-TTTTGGTGAAATCAAGGTTAAAAATAGAATTTTAGAAAATT-TAGGGTCA
1 AAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGT-A
49654367 AAAT-GTAATTT
1 AAATGGTAATTT
49654378 CAAAAAGTCT
Statistics
Matches: 203, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
57 10 0.05
58 92 0.45
59 55 0.27
60 45 0.22
61 1 0.00
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (59 bp):
AAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGAAAGTTCAAGGGTA
Found at i:49654348 original size:29 final size:29
Alignment explanation
Indices: 49654260--49654350 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 29
49654250 AAATTGTAAT
49654260 TTTTGGTGAAATCGAGGTTAAAAATAGAA
1 TTTTGGTGAAATCGAGGTTAAAAATAGAA
** * *
49654289 TTTT--AAAAAGTTCGAGGGT-AAAATGGTAA
1 TTTTGGTGAAA--TCGAGGTTAAAAATAG-AA
*
49654318 TTTTGGTGAAATCAAGGTTAAAAATAGAA
1 TTTTGGTGAAATCGAGGTTAAAAATAGAA
49654347 TTTT
1 TTTT
49654351 AGAAAATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
27 3 0.06
28 6 0.13
29 29 0.62
30 6 0.13
31 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (29 bp):
TTTTGGTGAAATCGAGGTTAAAAATAGAA
Found at i:49654429 original size:30 final size:30
Alignment explanation
Indices: 49654357--49654586 Score: 198
Period size: 30 Copynumber: 7.8 Consensus size: 30
49654347 TTTTAGAAAA
* *
49654357 TTTAGGGTCAAAATGTAA-TTTCAAAAAGT
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
* * *
49654386 CTTGGGGTCAAAATATAATTTTTAAAAAGC
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
* * * * ***
49654416 ATTAGGGTTAAAATGTAAGTTTGGTAAAG-
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
* * *
49654445 TTTAAGGTTAAAATATAATTTTCAAAAAGT
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
*
49654475 TTTGGGGTCAAAATATAA-TTTTAGAAAAGT
1 TTTAGGGTCAAAATATAATTTTTA-AAAAGT
* * * *
49654505 TTTAAGGTCAAAATGTAATTTTTAGAAATT
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
**
49654535 TTTAGGGTCAAAATATAA-TTTGGAAAAGT
1 TTTAGGGTCAAAATATAATTTTTAAAAAGT
** *
49654564 TTGGGGGTCAAAATGTAATTTTT
1 TTTAGGGTCAAAATATAATTTTT
49654587 GGATAGTACA
Statistics
Matches: 157, Mismatches: 39, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
29 63 0.40
30 89 0.57
31 5 0.03
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (30 bp):
TTTAGGGTCAAAATATAATTTTTAAAAAGT
Found at i:49654458 original size:59 final size:58
Alignment explanation
Indices: 49654357--49654586 Score: 235
Period size: 59 Copynumber: 3.9 Consensus size: 58
49654347 TTTTAGAAAA
* ** ** *
49654357 TTTAGGGTCAAAATGTAATTTCAAAAAGTCTTGGGGTCAAAATATAATTTTTAAAAAGC
1 TTTAGGGTCAAAATATAATTTGGAAAAGT-TTAAGGTCAAAATATAATTTTTAAAAAGT
* * * * * *
49654416 ATTAGGGTTAAAATGTAAGTTTGGTAAAGTTTAAGGTTAAAATATAATTTTCAAAAAGT
1 TTTAGGGTCAAAATATAA-TTTGGAAAAGTTTAAGGTCAAAATATAATTTTTAAAAAGT
* * * * *
49654475 TTTGGGGTCAAAATATAATTTTAGAAAAGTTTTAAGGTCAAAATGTAATTTTTAGAAATT
1 TTTAGGGTCAAAATATAA-TTTGGAAAAG-TTTAAGGTCAAAATATAATTTTTAAAAAGT
** *
49654535 TTTAGGGTCAAAATATAATTTGGAAAAGTTTGGGGGTCAAAATGTAATTTTT
1 TTTAGGGTCAAAATATAATTTGGAAAAGTTT-AAGGTCAAAATATAATTTTT
49654587 GGATAGTACA
Statistics
Matches: 142, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
58 3 0.02
59 89 0.63
60 50 0.35
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (58 bp):
TTTAGGGTCAAAATATAATTTGGAAAAGTTTAAGGTCAAAATATAATTTTTAAAAAGT
Found at i:49654483 original size:89 final size:90
Alignment explanation
Indices: 49654348--49654586 Score: 281
Period size: 89 Copynumber: 2.7 Consensus size: 90
49654338 AAAATAGAAT
* * *
49654348 TTTAGAAA-ATTTAGGGTCAAAATGTAATTTCAAAAAGTCTTGGGGTCAAAATATAATTTTTA-A
1 TTTAGAAATGTTTAGGGTCAAAATATAATTTCAAAAAGTTTTGGGGTCAAAATATAATTTTTAGA
* *
49654411 AAAGCATTAGGGTTAAAATGTAA-G
66 AAAGCATTAAGGTCAAAATGTAATG
* * *
49654435 TTTGGTAAA-GTTTAAGGTTAAAATATAATTTTCAAAAAGTTTTGGGGTCAAAATATAA-TTTTA
1 TTTAG-AAATGTTTAGGGTCAAAATATAA-TTTCAAAAAGTTTTGGGGTCAAAATATAATTTTTA
** *
49654498 GAAAAGTTTTAAGGTCAAAATGTAATT
64 GAAAAGCATTAAGGTCAAAATGTAATG
* ** * *
49654525 TTTAGAAATTTTTAGGGTCAAAATATAATTTGGAAAAGTTTGGGGGTCAAAATGTAATTTTT
1 TTTAGAAATGTTTAGGGTCAAAATATAATTTCAAAAAGTTTTGGGGTCAAAATATAATTTTT
49654587 GGATAGTACA
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
87 4 0.03
88 23 0.18
89 76 0.60
90 24 0.19
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37
Consensus pattern (90 bp):
TTTAGAAATGTTTAGGGTCAAAATATAATTTCAAAAAGTTTTGGGGTCAAAATATAATTTTTAGA
AAAGCATTAAGGTCAAAATGTAATG
Found at i:49655781 original size:17 final size:17
Alignment explanation
Indices: 49655756--49655799 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
49655746 TTTTTTTATT
*
49655756 ATTTAATTATTATTAAA
1 ATTTTATTATTATTAAA
49655773 ATTTTATTATTATTAAA
1 ATTTTATTATTATTAAA
49655790 ATTATTATTA
1 ATT-TTATTA
49655800 AATATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTATTATTATTAAA
Found at i:49655800 original size:29 final size:29
Alignment explanation
Indices: 49655746--49655807 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
49655736 TTTCAGTTTC
* *
49655746 TTTTTTTATTATTTAATTATTATTAAA-A
1 TTTTATTATTATTAAATTATTATTAAATA
49655774 TTTTATTATTATTAAAATTATTATTAAATA
1 TTTTATTATTATT-AAATTATTATTAAATA
49655804 TTTT
1 TTTT
49655808 TAATGAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 12 0.40
29 13 0.43
30 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTATTATTATTAAATTATTATTAAATA
Found at i:49656638 original size:16 final size:16
Alignment explanation
Indices: 49656617--49656671 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
49656607 TTAAAACCAT
*
49656617 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
49656633 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
49656650 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
49656666 TCTAAA
1 TTTAAA
49656672 ATCAATTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:49657201 original size:91 final size:91
Alignment explanation
Indices: 49656969--49658092 Score: 1557
Period size: 91 Copynumber: 12.3 Consensus size: 91
49656959 TGATGTCGGG
*
49656969 GCTTCATCTTA-CTCTTACTACAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAAC
1 GCTTCATC-TAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAAC
* * *
49657033 TTCAAGAGGATAGGGATTGACGTTTGAT
65 TTCAAGAGGATAGGAAATGATG-TTGAT
*
49657061 TCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
49657126 TCAAGAGGATAGGAAATGATATTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
* *
49657152 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTATTATAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
49657217 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
49657243 GCTTCATCTTA-CTCTTACTACAACTTCAGAGAGATACAA-ACTTGCTATCCAACTTTACTACAA
1 GCTTCATC-TAGCTCTTACTACAACTTCAGAGAGATA-AAGACTTGCTATCCAACTTTACTACAA
*
49657306 CTTCAAGAGGATAGGAAATGATGTTGGT
64 CTTCAAGAGGATAGGAAATGATGTTGAT
* * * *
49657334 GCTTCATCTAGCTCTTACTACAACTTCAAAGAGATAAAGGCTTGCTATCCAGCTTTACTACTACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
49657399 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
* * *
49657425 GCTTCATCTAGCTCTTACTACAACTTCAAAGAGATAAAGACTTGTTATCCAGCTTTACTACAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* *
49657490 TCAAGAGGAAAGGTAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
49657516 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
*
49657581 TCAAGAGGATAGGAAATGAGGTTTGAT
66 TCAAGAGGATAGGAAATGATG-TTGAT
*
49657608 GCTTCATCTAACTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
49657673 TCAAGAGGATAGGAAATGATGTTGAT
66 TCAAGAGGATAGGAAATGATGTTGAT
49657699 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
* * *
49657764 TCAAGAGGATAAGAATTGACAT-TTGAA
66 TCAAGAGGATAGGAAATG--ATGTTGAT
* * * * *
49657791 GCTTCATCTTGCTCTTACTATAACTTTAGAGAGATAAAGA-TT-CATTATCCAACTTTGCTATAA
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGC--TATCCAACTTTACTACAA
* * * *
49657854 CTTTAAGAGGATAAGAATTGACAT-TTGAA
64 CTTCAAGAGGATAGGAAATG--ATGTTGAT
* * * * * * *
49657883 ACTTCATCTTGCTCTTAATATAACTTTAGAGAGATAAAGA-TTCGTTATCCAACTTTACTATAAC
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTT-GCTATCCAACTTTACTACAAC
* * * * *
49657947 TTAAAGAGGATAAGAATTGACGTTTGAA
65 TTCAAGAGGATAGGAAATGATG-TTGAT
* * * *
49657975 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGA-TTCGTTATCCAACTTTACTATAAC
1 GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTT-GCTATCCAACTTTACTACAAC
* * *
49658039 TTCAAGAGGATAAGAATTGACAT-TTGAA
65 TTCAAGAGGATAGGAAATG--ATGTTGAT
* *
49658067 GCTTTATCTTGCTCTTACTACAACTT
1 GCTTCATCTAGCTCTTACTACAACTT
49658093 TTTCCCTTTC
Statistics
Matches: 962, Mismatches: 54, Indels: 32
0.92 0.05 0.03
Matches are distributed among these distances:
90 6 0.01
91 509 0.53
92 444 0.46
93 2 0.00
94 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (91 bp):
GCTTCATCTAGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAGGAAATGATGTTGAT
Found at i:49657959 original size:40 final size:40
Alignment explanation
Indices: 49657901--49658051 Score: 110
Period size: 40 Copynumber: 3.5 Consensus size: 40
49657891 TTGCTCTTAA
*
49657901 TATAACTTTAGAGAGATAAAGATTCGTTATCCAACTTTAC
1 TATAACTTAAGAGAGATAAAGATTCGTTATCCAACTTTAC
**
49657941 TATAACTTAA-AGAGGAT-AAGAATTGACGTTTGAAGCTTCATCTTGCTCTTAC
1 TATAACTTAAGAGA-GATAAAG-ATT--CG-TT--A---TC--C-AACT-TTAC
*
49657993 TATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTAC
1 TATAACTTAAGAGAGATAAAGATTCGTTATCCAACTTTAC
49658033 TATAACTTCAAGAG-GATAA
1 TATAACTT-AAGAGAGATAA
49658052 GAATTGACAT
Statistics
Matches: 87, Mismatches: 7, Indels: 34
0.68 0.05 0.27
Matches are distributed among these distances:
39 6 0.07
40 32 0.37
41 6 0.07
42 3 0.03
43 2 0.02
44 2 0.02
45 1 0.01
47 1 0.01
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
52 19 0.22
53 6 0.07
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (40 bp):
TATAACTTAAGAGAGATAAAGATTCGTTATCCAACTTTAC
Found at i:49657999 original size:52 final size:51
Alignment explanation
Indices: 49657937--49658092 Score: 131
Period size: 52 Copynumber: 3.2 Consensus size: 51
49657927 TTATCCAACT
49657937 TTACTATAACTTAAAGAGGATAAGAATTGACGTTTGAAGCTTCATCTTGCTC
1 TTACTATAACTT-AAGAGGATAAGAATTGACGTTTGAAGCTTCATCTTGCTC
* **
49657989 TTACTATAACTTCAGAGAGATAA-AGATT--CG-TT--A---TC--C-AACT-
1 TTACTATAACTTAAGAG-GATAAGA-ATTGACGTTTGAAGCTTCATCTTGCTC
* *
49658029 TTACTATAACTTCAAGAGGATAAGAATTGACATTTGAAGCTTTATCTTGCTC
1 TTACTATAACTT-AAGAGGATAAGAATTGACGTTTGAAGCTTCATCTTGCTC
*
49658081 TTACTACAACTT
1 TTACTATAACTT
49658093 TTTCCCTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 32
0.66 0.08 0.27
Matches are distributed among these distances:
40 20 0.25
41 7 0.09
42 2 0.03
43 2 0.03
44 2 0.03
45 1 0.01
47 1 0.01
48 1 0.01
49 2 0.03
50 3 0.04
51 7 0.09
52 31 0.39
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (51 bp):
TTACTATAACTTAAGAGGATAAGAATTGACGTTTGAAGCTTCATCTTGCTC
Found at i:49658253 original size:51 final size:51
Alignment explanation
Indices: 49658186--49658405 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
49658176 ATTATTGCAA
* * *
49658186 CTTAGACCTTTCCCTTTTCTTTTTTTGCGATACTGAATCTGCCATTGCGGT
1 CTTAGATCTTTCCCTTTTCTGTTTTTGCGATACTGGATCTGCCATTGCGGT
* * * ** * * * * *
49658237 CTTAAATCTTTCCC-TTTCATGCTTCTAAGGTACACGG-TCCGCCGTTGC-GA
1 CTTAGATCTTTCCCTTTTC-TGTTTTTGCGATAC-TGGATCTGCCATTGCGGT
* * * * *
49658287 CTTAGACCTTTCCCTTTTGTGTTTTGGCGGTACTGGATCTACCATTGCGGT
1 CTTAGATCTTTCCCTTTTCTGTTTTTGCGATACTGGATCTGCCATTGCGGT
*
49658338 CTTAGATCTTTCCCTTTTGTGTTTTTGC-AGTACTGGATCTGCCATTGCGGT
1 CTTAGATCTTTCCCTTTTCTGTTTTTGCGA-TACTGGATCTGCCATTGCGGT
49658389 CTTAGATCTTTCCCTTT
1 CTTAGATCTTTCCCTTT
49658406 CATGTTTCTA
Statistics
Matches: 133, Mismatches: 30, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
49 2 0.02
50 34 0.26
51 96 0.72
52 1 0.01
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (51 bp):
CTTAGATCTTTCCCTTTTCTGTTTTTGCGATACTGGATCTGCCATTGCGGT
Found at i:49658386 original size:101 final size:101
Alignment explanation
Indices: 49658093--49658405 Score: 308
Period size: 101 Copynumber: 3.1 Consensus size: 101
49658083 ACTACAACTT
* * * *
49658093 TTTCCCTTTCGTCTTTTTACGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCC-GTTGTGT
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGATCTTTCCCTTTTGTGT
* * * *** *
49658157 CTTTTGAGGAACACGACCCATTATTGCAACTTAGACC
66 -TTTTGAGGTACAGGATCCGCCATTGCGACTTAGACC
* * * * * ** *
49658194 TTTCCCTTTTCTTTTTTTGCGATACTGAATCTGCCATTGCGGTCTTAAATCTTTCCCTTTCATGC
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGATCTTTCCCTTTTGTGT
* * *
49658259 TTCTAAGGTACACGG-TCCGCCGTTGCGACTTAGACC
66 TTTTGAGGTACA-GGATCCGCCATTGCGACTTAGACC
* * *
49658295 TTTCCCTTTTGTGTTTTGGCGGTACTGGATCTACCATTGCGGTCTTAGATCTTTCCCTTTTGTGT
1 TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGATCTTTCCCTTTTGTGT
* * * *
49658360 TTTTGCA-GTACTGGATCTGCCATTGCGGTCTTAGATC
66 TTTTG-AGGTACAGGATCCGCCATTGC-GACTTAGACC
49658397 TTTCCCTTT
1 TTTCCCTTT
49658406 CATGTTTCTA
Statistics
Matches: 168, Mismatches: 39, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
100 2 0.01
101 144 0.86
102 22 0.13
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (101 bp):
TTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCATTGCGGTCTTAGATCTTTCCCTTTTGTGT
TTTTGAGGTACAGGATCCGCCATTGCGACTTAGACC
Found at i:49665540 original size:59 final size:58
Alignment explanation
Indices: 49665477--49665767 Score: 329
Period size: 59 Copynumber: 5.0 Consensus size: 58
49665467 ATTTTGGACT
* *
49665477 TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGGGGTTTAAAATGGAATTTTAGAAAG
1 TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGAGG-TAAAAATGGAATTTTAGAAAG
* * *
49665536 TTC-GGGGGAAAATGGTAA-TTTTGGTAAAATTAAGGTAAAAATGGAGTTTT-GAAAAG
1 TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGAGGTAAAAATGGAATTTTAG-AAAG
* * * * * *
49665592 TTCGAGGGTAAAATGGTAATTTTTTGGTAAAATCGAGGCTAAAAATGAAATTTTGGAAAG
1 TTCGGGGGGAAAATGGTAA-TTTTTGGTGAAATTGAGG-TAAAAATGGAATTTTAGAAAG
* * * *
49665652 TTTGGGGGCAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGAAATTTTAGAAAG
1 TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGAGG-TAAAAATGGAATTTTAGAAAG
* * * *
49665711 TTTAGGGGGTAAAATGGTAA-TTTTGGTGAAATTAAGGTTAAAATGGAATTTTAGAAA
1 -TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGAGGTAAAAATGGAATTTTAGAAA
49665768 ATTTAGGGTC
Statistics
Matches: 200, Mismatches: 25, Indels: 15
0.83 0.10 0.06
Matches are distributed among these distances:
55 1 0.00
56 20 0.10
57 27 0.14
58 33 0.17
59 68 0.34
60 50 0.25
61 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (58 bp):
TTCGGGGGGAAAATGGTAATTTTTGGTGAAATTGAGGTAAAAATGGAATTTTAGAAAG
Found at i:49665614 original size:29 final size:29
Alignment explanation
Indices: 49665516--49665674 Score: 86
Period size: 29 Copynumber: 5.5 Consensus size: 29
49665506 AATTGGGGTT
49665516 TAAAATGG-AATTTT-AGAAAGTTCG-GGG
1 TAAAATGGTAATTTTGA-AAAGTTCGAGGG
* *
49665543 GAAAATGGTAATTTTGGTAAAA-TT--AAGG
1 TAAAATGGTAATTTT-G-AAAAGTTCGAGGG
*
49665571 TAAAAATGG-AGTTTTGAAAAGTTCGAGGG
1 T-AAAATGGTAATTTTGAAAAGTTCGAGGG
*
49665600 TAAAATGGTAATTTTTTGGTAAAA--TCGAGGC
1 TAAAATGGTAA--TTTT-G-AAAAGTTCGAGGG
* * * *
49665631 TAAAAAT-GAAATTTTGGAAAGTTTGGGGG
1 T-AAAATGGTAATTTTGAAAAGTTCGAGGG
*
49665660 CAAAATGGTAATTTT
1 TAAAATGGTAATTTT
49665675 TGGTGAAATT
Statistics
Matches: 100, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
26 4 0.04
27 13 0.13
28 26 0.26
29 29 0.29
30 3 0.03
31 15 0.15
32 6 0.06
33 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (29 bp):
TAAAATGGTAATTTTGAAAAGTTCGAGGG
Found at i:49665725 original size:29 final size:29
Alignment explanation
Indices: 49665633--49666027 Score: 210
Period size: 30 Copynumber: 13.4 Consensus size: 29
49665623 ATCGAGGCTA
* *
49665633 AAAATGAAATTTTGGAAAGTTT-GGGGGC
1 AAAATGAAATTTTAGAAAGTTTAGGGGTC
* * *
49665661 AAAATGGTAATTTTTGGTGAAA--TT-GGGGTTA
1 AAAAT-G-AAATTTT--AGAAAGTTTAGGGG-TC
49665692 AAAATGAAATTTTAGAAAGTTTAGGGGGT-
1 AAAATGAAATTTTAGAAAGTTTA-GGGGTC
* * * *
49665721 AAAATGGTAATTTTGGTGAAA--TTA-AGGTT
1 AAAAT-GAAATTTT--AGAAAGTTTAGGGGTC
* *
49665750 AAAATGGAATTTTAGAAAATTTA-GGGTC
1 AAAATGAAATTTTAGAAAGTTTAGGGGTC
* * *
49665778 AAAATGTAATTTCAAAAAGTCTTA-GGGTC
1 AAAATGAAATTTTAGAAAGT-TTAGGGGTC
*
49665807 AAAAT-ATAATTTTTAGAAAGTATTA-GGGTT
1 AAAATGA-AA-TTTTAGAAAGT-TTAGGGGTC
*
49665837 AAAATGAAAATTTAGAAAAGTTTA-GGGTC
1 AAAATGAAATTTTAG-AAAGTTTAGGGGTC
* **
49665866 AAAAT-ATAATTTTCAAAAAGTTTTTGGGTC
1 AAAATGA-AATTTT-AGAAAGTTTAGGGGTC
* *
49665896 AAAAT-ATAATTTTGGAAAAGTTAAGGGGTC
1 AAAATGA-AATTTTAG-AAAGTTTAGGGGTC
* * *
49665926 AAAATGTAATTTTCAAAAAGTTTTGGGGTC
1 AAAATGAAATTTT-AGAAAGTTTAGGGGTC
* * *
49665956 AAAATGTAATTTTTAGAAATTTTTGGGGTC
1 AAAATG-AAATTTTAGAAAGTTTAGGGGTC
** *
49665986 AAAATTTAA-TTTGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTTAG-AAAGTTTAGGGGTC
*
49666015 AAAATGTAATTTT
1 AAAATGAAATTTT
49666028 TGGATAGTTC
Statistics
Matches: 290, Mismatches: 48, Indels: 56
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.01
27 4 0.01
28 42 0.14
29 84 0.29
30 133 0.46
31 15 0.05
32 8 0.03
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (29 bp):
AAAATGAAATTTTAGAAAGTTTAGGGGTC
Found at i:49666000 original size:89 final size:87
Alignment explanation
Indices: 49665750--49666027 Score: 330
Period size: 89 Copynumber: 3.1 Consensus size: 87
49665740 AATTAAGGTT
* * *
49665750 AAAATGGAATTTTAGAAAA-TTTAGGGTCAAAATGTAA-TTTCAAAAAGTCTTAGGGTCAAAATA
1 AAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTCAAAAA-TTTTTGGGTCAAAATA
** *
49665813 TAATTTTTAGAAAGTATTA-GGGTT
65 TAATTTGGA-AAAGT-TTAGGGGTC
* * *
49665837 AAAATGAAAATTTAGAAAAGTTTAGGGTCAAAATATAATTTTCAAAAAGTTTTTGGGTCAAAATA
1 AAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTCAAAAA-TTTTTGGGTCAAAATA
*
49665902 TAATTTTGGAAAAGTTAAGGGGTC
65 TAA-TTTGGAAAAGTTTAGGGGTC
* * *
49665926 AAAATGTAATTTTCA-AAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAATTTTTGGGGTCAAAA
1 AAAATGTAATTTT-AGAAAAG-TTTAGGGTCAAAATGTAATTTTCAAAAATTTTT-GGGTCAAAA
*
49665990 TTTAATTTGGAAAAGTTTAGGGGTC
63 TATAATTTGGAAAAGTTTAGGGGTC
49666015 AAAATGTAATTTT
1 AAAATGTAATTTT
49666028 TGGATAGTTC
Statistics
Matches: 167, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
87 17 0.10
88 19 0.11
89 89 0.53
90 42 0.25
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (87 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGTCAAAATGTAATTTTCAAAAATTTTTGGGTCAAAATAT
AATTTGGAAAAGTTTAGGGGTC
Found at i:49666028 original size:59 final size:58
Alignment explanation
Indices: 49665757--49666027 Score: 255
Period size: 59 Copynumber: 4.6 Consensus size: 58
49665747 GTTAAAATGG
* * *
49665757 AATTTT-AGAAAA-TTTAGGGTCAAAATGTAATTTCAAAAAGTCTTAGGGTCAAAATAT
1 AATTTTCA-AAAAGTTTAGGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATAT
* * * * *
49665814 AATTTTTAGAAAGTATTAGGGTTAAAATGAAAATTTAGAAAAG-TTTAGGGTCAAAATAT
1 AATTTTCAAAAAGT-TTAGGGTCAAAATGTAATTTTAG-AAAGTTTTAGGGTCAAAATAT
* * * * *
49665873 AATTTTCAAAAAGTTTTTGGGTCAAAATATAATTTTGGAAAAG-TTAAGGGGTCAAAATGT
1 AATTTTCAAAAAG-TTTAGGGTCAAAATGTAATTTTAG-AAAGTTTTA-GGGTCAAAATAT
* * * *
49665933 AATTTTCAAAAAGTTTTGGGGTCAAAATGTAATTTTTAGAAATTTTTGGGGTCAAAATTT
1 AATTTTCAAAAAG-TTTAGGGTCAAAATGTAA-TTTTAGAAAGTTTTAGGGTCAAAATAT
**
49665993 AA-TTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT
1 AATTTTCAAAAAGTTTA-GGGTCAAAATGTAATTTT
49666028 TGGATAGTTC
Statistics
Matches: 178, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
57 9 0.05
58 9 0.05
59 91 0.51
60 62 0.35
61 7 0.04
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (58 bp):
AATTTTCAAAAAGTTTAGGGTCAAAATGTAATTTTAGAAAGTTTTAGGGTCAAAATAT
Found at i:49667222 original size:17 final size:15
Alignment explanation
Indices: 49667200--49667238 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
49667190 TTATTATTTA
49667200 ATTATTATTAAAATGTT
1 ATTATTATTAAAA--TT
49667217 ATTATTATTAAAATT
1 ATTATTATTAAAATT
49667232 ATTATTA
1 ATTATTA
49667239 AATATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
ATTATTATTAAAATT
Found at i:49668078 original size:16 final size:16
Alignment explanation
Indices: 49668057--49668111 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
49668047 TTAAAACCAT
*
49668057 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
49668073 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
49668090 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
49668106 TCTAAA
1 TTTAAA
49668112 ATCATTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:49672164 original size:48 final size:47
Alignment explanation
Indices: 49672106--49672253 Score: 111
Period size: 48 Copynumber: 3.1 Consensus size: 47
49672096 TTTTTTTATT
*
49672106 CAATTAATCATTTAAGAAAAAAAATATTTATCATAAAAATACTAAATC
1 CAATCAATCATTTAAGAAAAAAAATATTTA-CATAAAAATACTAAATC
* * ** * * * * ** * * *
49672154 CAATCAATCATATT--TAATAAAGTTGTCTAAATTAATTTATTATTTATT
1 CAATCAATCAT-TTAAGAAAAAAAATATTTACATAAAAATACTA--AATC
49672202 CAATCAATCATTTAAGAAAAAAAATATTTACCATAAAAATACTAAATC
1 CAATCAATCATTTAAGAAAAAAAATATTTA-CATAAAAATACTAAATC
49672250 CAAT
1 CAAT
49672254 ATTGGATTTA
Statistics
Matches: 67, Mismatches: 27, Indels: 12
0.63 0.25 0.11
Matches are distributed among these distances:
46 8 0.12
47 11 0.16
48 29 0.43
49 11 0.16
50 8 0.12
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (47 bp):
CAATCAATCATTTAAGAAAAAAAATATTTACATAAAAATACTAAATC
Found at i:49673016 original size:7 final size:7
Alignment explanation
Indices: 49672994--49673031 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
49672984 ACAAAATATC
49672994 TCTATAA
1 TCTATAA
*
49673001 TTTAT-A
1 TCTATAA
49673007 TCTATAA
1 TCTATAA
49673014 TCTATAA
1 TCTATAA
49673021 TCTATAA
1 TCTATAA
49673028 TCTA
1 TCTA
49673032 GAATACCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (7 bp):
TCTATAA
Found at i:49682514 original size:24 final size:24
Alignment explanation
Indices: 49682487--49682577 Score: 62
Period size: 23 Copynumber: 3.9 Consensus size: 24
49682477 CAACATTAAA
*
49682487 AACAATAAAAACAACAATAAAAAT
1 AACAATAAAAACAACAAAAAAAAT
** * **
49682511 AACAGCAAAAATAAC-ACGAAAAT
1 AACAATAAAAACAACAAAAAAAAT
* * *
49682534 AGCAATCAAAACAATAAAAAAAAT
1 AACAATAAAAACAACAAAAAAAAT
*
49682558 AAC--TCAAAAACAGCAAAAAA
1 AACAAT-AAAAACAACAAAAAA
49682578 TCAACCAAAA
Statistics
Matches: 48, Mismatches: 17, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
22 1 0.02
23 27 0.56
24 20 0.42
ACGTcount: A:0.70, C:0.15, G:0.04, T:0.10
Consensus pattern (24 bp):
AACAATAAAAACAACAAAAAAAAT
Found at i:49682598 original size:21 final size:21
Alignment explanation
Indices: 49682540--49682609 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 21
49682530 AAATAGCAAT
*
49682540 CAAAACAATAAAAAAAAT-AAC
1 CAAAACAGT-AAAAAAATCAAC
*
49682561 TCAAAAACAG-CAAAAAATCAAC
1 -C-AAAACAGTAAAAAAATCAAC
*
49682583 CAAAACAGTAAAAAAAGC-AC
1 CAAAACAGTAAAAAAATCAAC
49682603 CAAAACA
1 CAAAACA
49682610 ATAATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 16 0.39
21 15 0.37
22 4 0.10
23 6 0.15
ACGTcount: A:0.69, C:0.20, G:0.04, T:0.07
Consensus pattern (21 bp):
CAAAACAGTAAAAAAATCAAC
Found at i:49684689 original size:24 final size:23
Alignment explanation
Indices: 49684662--49684714 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
49684652 CGCTTCATTA
49684662 TCACCCTTT-TTCGAATCCTCACCT
1 TCACCCTTTCTTC--ATCCTCACCT
49684686 TCA-CCTTTACCTTCATCCTCACCT
1 TCACCCTTT--CTTCATCCTCACCT
49684710 TCACC
1 TCACC
49684715 TTTACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 1 0.04
26 3 0.12
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (23 bp):
TCACCCTTTCTTCATCCTCACCT
Found at i:49684699 original size:12 final size:12
Alignment explanation
Indices: 49684682--49684720 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49684672 TCGAATCCTC
49684682 ACCTTCACCTTT
1 ACCTTCACCTTT
*
49684694 ACCTTCATCC-TC
1 ACCTTCA-CCTTT
49684706 ACCTTCACCTTT
1 ACCTTCACCTTT
49684718 ACC
1 ACC
49684721 CTCATCCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTTCACCTTT
Found at i:49684715 original size:24 final size:24
Alignment explanation
Indices: 49684676--49684729 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
49684666 CCTTTTTCGA
*
49684676 ATCCTCACCTTCACCTTTACCTTC
1 ATCCTCACCTTCACCTTTACCCTC
49684700 ATCCTCACCTTCACCTTTACCCTC
1 ATCCTCACCTTCACCTTTACCCTC
49684724 ATCCTC
1 ATCCTC
49684730 GCCCCCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCCTCACCTTCACCTTTACCCTC
Found at i:49684723 original size:18 final size:18
Alignment explanation
Indices: 49684680--49684724 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49684670 TTTCGAATCC
* *
49684680 TCACCTTCACCTTTACCT
1 TCACCCTCACCTTCACCT
*
49684698 TCATCCTCACCTTCACCT
1 TCACCCTCACCTTCACCT
*
49684716 TTACCCTCA
1 TCACCCTCA
49684725 TCCTCGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACCCTCACCTTCACCT
Found at i:49687404 original size:12 final size:12
Alignment explanation
Indices: 49687361--49687499 Score: 71
Period size: 12 Copynumber: 12.2 Consensus size: 12
49687351 ATAACATCCA
49687361 AACAA-AAAAAT
1 AACAACAAAAAT
* *
49687372 AGCAACCAAAAT
1 AACAACAAAAAT
** *
49687384 AGGAGCAAAAAT
1 AACAACAAAAAT
49687396 AACAAC---AA-
1 AACAACAAAAAT
*
49687404 AACAACATTAAA-
1 AACAACA-AAAAT
49687416 AACAACAAAAAT
1 AACAACAAAAAT
* *
49687428 AGCAATAAAAAT
1 AACAACAAAAAT
**
49687440 AGGAA-AAAAAT
1 AACAACAAAAAT
*
49687451 AACAGCAAAAAT
1 AACAACAAAAAT
49687463 AAC-ACAAAAAT
1 AACAACAAAAAT
* **
49687474 AGCAATGAAAAT
1 AACAACAAAAAT
*
49687486 AATAA-AAAAAT
1 AACAACAAAAAT
49687497 AAC
1 AAC
49687500 TCCTAAACAG
Statistics
Matches: 97, Mismatches: 23, Indels: 16
0.71 0.17 0.12
Matches are distributed among these distances:
8 6 0.06
9 2 0.02
11 31 0.32
12 58 0.60
ACGTcount: A:0.69, C:0.13, G:0.07, T:0.11
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:49687484 original size:23 final size:23
Alignment explanation
Indices: 49687390--49687497 Score: 85
Period size: 23 Copynumber: 4.8 Consensus size: 23
49687380 AAATAGGAGC
* * * *
49687390 AAAAATAACAACAAAACAACATT
1 AAAAATAACAAAAAAATAGCAAT
*
49687413 AAAAACAAC--AAAAATAGCAAT
1 AAAAATAACAAAAAAATAGCAAT
** * **
49687434 AAAAATAGGAAAAAAATAACAGC
1 AAAAATAACAAAAAAATAGCAAT
*
49687457 AAAAATAACACAAAAATAGCAAT
1 AAAAATAACAAAAAAATAGCAAT
* *
49687480 GAAAATAATAAAAAAATA
1 AAAAATAACAAAAAAATA
49687498 ACTCCTAAAC
Statistics
Matches: 63, Mismatches: 20, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
21 14 0.22
23 49 0.78
ACGTcount: A:0.71, C:0.11, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAATAACAAAAAAATAGCAAT
Found at i:49695336 original size:24 final size:24
Alignment explanation
Indices: 49695304--49695353 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
49695294 TATGAAGAGA
*
49695304 CTTAGTAGCTCATTCAACTTTGTG
1 CTTAATAGCTCATTCAACTTTGTG
49695328 CTTAATAGCTCATTCAACTTTGTG
1 CTTAATAGCTCATTCAACTTTGTG
49695352 CT
1 CT
49695354 GTGGATGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (24 bp):
CTTAATAGCTCATTCAACTTTGTG
Found at i:49698293 original size:12 final size:12
Alignment explanation
Indices: 49698278--49698340 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
49698268 TAAAAACAAC
49698278 AAAATAGCAATA
1 AAAATAGCAATA
*
49698290 AAAACAGCAATA
1 AAAATAGCAATA
* **
49698302 AAAATAACAGCA
1 AAAATAGCAATA
* **
49698314 AAAATAAC-ACG
1 AAAATAGCAATA
49698325 AAAATAGCAATA
1 AAAATAGCAATA
49698337 AAAA
1 AAAA
49698341 CAATAAAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 8 0.20
12 32 0.80
ACGTcount: A:0.68, C:0.13, G:0.08, T:0.11
Consensus pattern (12 bp):
AAAATAGCAATA
Found at i:49698361 original size:21 final size:21
Alignment explanation
Indices: 49698337--49698404 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
49698327 AATAGCAATA
49698337 AAAACAATAAAAAAAT-AACTC
1 AAAACAATAAAAAAATCAAC-C
**
49698358 AAAA-ACAGCAAAAAATCAACC
1 AAAACA-ATAAAAAAATCAACC
* *
49698379 AAAACAGT-AAAAAAGC-ACC
1 AAAACAATAAAAAAATCAACC
49698398 AAAACAA
1 AAAACAA
49698405 CAATATAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.21
21 17 0.45
22 4 0.11
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.07
Consensus pattern (21 bp):
AAAACAATAAAAAAATCAACC
Found at i:49698370 original size:22 final size:22
Alignment explanation
Indices: 49698336--49698392 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
49698326 AAATAGCAAT
*
49698336 AAAAACAATAAAAAAAT-AACTC
1 AAAAACAGTAAAAAAATCAAC-C
*
49698358 AAAAACAG-CAAAAAATCAACC
1 AAAAACAGTAAAAAAATCAACC
49698379 -AAAACAGTAAAAAA
1 AAAAACAGTAAAAAA
49698393 GCACCAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.23
21 13 0.43
22 10 0.33
ACGTcount: A:0.72, C:0.16, G:0.04, T:0.09
Consensus pattern (22 bp):
AAAAACAGTAAAAAAATCAACC
Found at i:49698382 original size:20 final size:20
Alignment explanation
Indices: 49698346--49698403 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
49698336 AAAAACAATA
49698346 AAAAAAT-AACTCAAAAACAGC
1 AAAAAATCAAC-C-AAAACAGC
*
49698367 AAAAAATCAACCAAAACAGT
1 AAAAAATCAACCAAAACAGC
*
49698387 AAAAAAGC-ACCAAAACA
1 AAAAAATCAACCAAAACA
49698404 ACAATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.26
20 14 0.41
21 8 0.24
22 3 0.09
ACGTcount: A:0.67, C:0.21, G:0.05, T:0.07
Consensus pattern (20 bp):
AAAAAATCAACCAAAACAGC
Found at i:49702394 original size:24 final size:23
Alignment explanation
Indices: 49702367--49702419 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
49702357 CGCTTCATTA
49702367 TCACCCTTT-TTCGAATCCTCACCT
1 TCACCCTTTCTTC--ATCCTCACCT
49702391 TCA-CCTTTACCTTCATCCTCACCT
1 TCACCCTTT--CTTCATCCTCACCT
49702415 TCACC
1 TCACC
49702420 TTTACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 1 0.04
26 3 0.12
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (23 bp):
TCACCCTTTCTTCATCCTCACCT
Found at i:49702404 original size:12 final size:12
Alignment explanation
Indices: 49702387--49702425 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49702377 TCGAATCCTC
49702387 ACCTTCACCTTT
1 ACCTTCACCTTT
*
49702399 ACCTTCATCC-TC
1 ACCTTCA-CCTTT
49702411 ACCTTCACCTTT
1 ACCTTCACCTTT
49702423 ACC
1 ACC
49702426 CTCATCCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTTCACCTTT
Found at i:49702420 original size:24 final size:24
Alignment explanation
Indices: 49702381--49702434 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
49702371 CCTTTTTCGA
*
49702381 ATCCTCACCTTCACCTTTACCTTC
1 ATCCTCACCTTCACCTTTACCCTC
49702405 ATCCTCACCTTCACCTTTACCCTC
1 ATCCTCACCTTCACCTTTACCCTC
49702429 ATCCTC
1 ATCCTC
49702435 GCCCCCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCCTCACCTTCACCTTTACCCTC
Found at i:49702428 original size:18 final size:18
Alignment explanation
Indices: 49702385--49702429 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49702375 TTTCGAATCC
* *
49702385 TCACCTTCACCTTTACCT
1 TCACCCTCACCTTCACCT
*
49702403 TCATCCTCACCTTCACCT
1 TCACCCTCACCTTCACCT
*
49702421 TTACCCTCA
1 TCACCCTCA
49702430 TCCTCGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACCCTCACCTTCACCT
Found at i:49705200 original size:34 final size:35
Alignment explanation
Indices: 49705121--49705209 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 35
49705111 AGATAGTAAT
*
49705121 AAAAACAGCAATAAAAATAACAACAAAAATAACAC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
* ** * * *
49705156 GAAATTAGCAATCAAAACAATAA-AAAAATAACTC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
*
49705190 AAAAACAGCAA-AAAATCAAC
1 AAAAACAGCAATAAAAACAAC
49705210 CAAAACAGTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
33 6 0.15
34 18 0.44
35 17 0.41
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.11
Consensus pattern (35 bp):
AAAAACAGCAATAAAAACAACAACAAAAATAACAC
Found at i:49705224 original size:21 final size:20
Alignment explanation
Indices: 49705168--49705236 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
49705158 AATTAGCAAT
*
49705168 CAAAACAATAAAAAAAT-AAC
1 CAAAACAGT-AAAAAATCAAC
*
49705188 TCAAAAACAGCAAAAAATCAAC
1 -C-AAAACAGTAAAAAATCAAC
*
49705210 CAAAACAGTAGAAAAAGC-AC
1 CAAAACAGTA-AAAAATCAAC
49705230 CAAAACA
1 CAAAACA
49705237 ACAATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (20 bp):
CAAAACAGTAAAAAATCAAC
Found at i:49709224 original size:24 final size:23
Alignment explanation
Indices: 49709197--49709249 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
49709187 CGCTTCATTA
49709197 TCACCCTTT-TTCGAATCCTCACCT
1 TCACCCTTTCTTC--ATCCTCACCT
49709221 TCA-CCTTTACCTTCATCCTCACCT
1 TCACCCTTT--CTTCATCCTCACCT
49709245 TCACC
1 TCACC
49709250 TTTACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 1 0.04
26 3 0.12
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (23 bp):
TCACCCTTTCTTCATCCTCACCT
Found at i:49709234 original size:12 final size:12
Alignment explanation
Indices: 49709217--49709255 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49709207 TCGAATCCTC
49709217 ACCTTCACCTTT
1 ACCTTCACCTTT
*
49709229 ACCTTCATCC-TC
1 ACCTTCA-CCTTT
49709241 ACCTTCACCTTT
1 ACCTTCACCTTT
49709253 ACC
1 ACC
49709256 CTCATCCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTTCACCTTT
Found at i:49709250 original size:24 final size:24
Alignment explanation
Indices: 49709211--49709264 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
49709201 CCTTTTTCGA
*
49709211 ATCCTCACCTTCACCTTTACCTTC
1 ATCCTCACCTTCACCTTTACCCTC
49709235 ATCCTCACCTTCACCTTTACCCTC
1 ATCCTCACCTTCACCTTTACCCTC
49709259 ATCCTC
1 ATCCTC
49709265 GCCCCCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCCTCACCTTCACCTTTACCCTC
Found at i:49709258 original size:18 final size:18
Alignment explanation
Indices: 49709215--49709259 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49709205 TTTCGAATCC
* *
49709215 TCACCTTCACCTTTACCT
1 TCACCCTCACCTTCACCT
*
49709233 TCATCCTCACCTTCACCT
1 TCACCCTCACCTTCACCT
*
49709251 TTACCCTCA
1 TCACCCTCA
49709260 TCCTCGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACCCTCACCTTCACCT
Found at i:49712031 original size:34 final size:35
Alignment explanation
Indices: 49711952--49712040 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 35
49711942 AGATAGTAAT
*
49711952 AAAAACAGCAATAAAAATAACAACAAAAATAACAC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
* ** * * *
49711987 GAAATTAGCAATCAAAACAATAA-AAAAATAACTC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
*
49712021 AAAAACAGCAA-AAAATCAAC
1 AAAAACAGCAATAAAAACAAC
49712041 CAAAACAGTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
33 6 0.15
34 18 0.44
35 17 0.41
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.11
Consensus pattern (35 bp):
AAAAACAGCAATAAAAACAACAACAAAAATAACAC
Found at i:49712055 original size:21 final size:20
Alignment explanation
Indices: 49711999--49712067 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
49711989 AATTAGCAAT
*
49711999 CAAAACAATAAAAAAAT-AAC
1 CAAAACAGT-AAAAAATCAAC
*
49712019 TCAAAAACAGCAAAAAATCAAC
1 -C-AAAACAGTAAAAAATCAAC
*
49712041 CAAAACAGTAGAAAAAGC-AC
1 CAAAACAGTA-AAAAATCAAC
49712061 CAAAACA
1 CAAAACA
49712068 ACAATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (20 bp):
CAAAACAGTAAAAAATCAAC
Found at i:49716055 original size:24 final size:23
Alignment explanation
Indices: 49716028--49716080 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
49716018 CCCTTCATTA
49716028 TCACCCTTT-TTCGAATCCTCACCT
1 TCACCCTTTCTTC--ATCCTCACCT
49716052 TCA-CCTTTACCTTCATCCTCACCT
1 TCACCCTTT--CTTCATCCTCACCT
49716076 TCACC
1 TCACC
49716081 TTTACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 1 0.04
26 3 0.12
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (23 bp):
TCACCCTTTCTTCATCCTCACCT
Found at i:49716065 original size:12 final size:12
Alignment explanation
Indices: 49716048--49716086 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49716038 TCGAATCCTC
49716048 ACCTTCACCTTT
1 ACCTTCACCTTT
*
49716060 ACCTTCATCC-TC
1 ACCTTCA-CCTTT
49716072 ACCTTCACCTTT
1 ACCTTCACCTTT
49716084 ACC
1 ACC
49716087 CTCATCCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTTCACCTTT
Found at i:49716081 original size:24 final size:24
Alignment explanation
Indices: 49716042--49716095 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
49716032 CCTTTTTCGA
*
49716042 ATCCTCACCTTCACCTTTACCTTC
1 ATCCTCACCTTCACCTTTACCCTC
49716066 ATCCTCACCTTCACCTTTACCCTC
1 ATCCTCACCTTCACCTTTACCCTC
49716090 ATCCTC
1 ATCCTC
49716096 GCCCCCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCCTCACCTTCACCTTTACCCTC
Found at i:49716089 original size:18 final size:18
Alignment explanation
Indices: 49716046--49716090 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49716036 TTTCGAATCC
* *
49716046 TCACCTTCACCTTTACCT
1 TCACCCTCACCTTCACCT
*
49716064 TCATCCTCACCTTCACCT
1 TCACCCTCACCTTCACCT
*
49716082 TTACCCTCA
1 TCACCCTCA
49716091 TCCTCGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACCCTCACCTTCACCT
Found at i:49718861 original size:34 final size:35
Alignment explanation
Indices: 49718782--49718870 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 35
49718772 AGATAGTAAT
*
49718782 AAAAACAGCAATAAAAATAACAACAAAAATAACAC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
* ** * * *
49718817 GAAATTAGCAATCAAAACAATAA-AAAAATAACTC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
*
49718851 AAAAACAGCAA-AAAATCAAC
1 AAAAACAGCAATAAAAACAAC
49718871 CAAAACAGTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
33 6 0.15
34 18 0.44
35 17 0.41
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.11
Consensus pattern (35 bp):
AAAAACAGCAATAAAAACAACAACAAAAATAACAC
Found at i:49718885 original size:21 final size:20
Alignment explanation
Indices: 49718829--49718897 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
49718819 AATTAGCAAT
*
49718829 CAAAACAATAAAAAAAT-AAC
1 CAAAACAGT-AAAAAATCAAC
*
49718849 TCAAAAACAGCAAAAAATCAAC
1 -C-AAAACAGTAAAAAATCAAC
*
49718871 CAAAACAGTAGAAAAAGC-AC
1 CAAAACAGTA-AAAAATCAAC
49718891 CAAAACA
1 CAAAACA
49718898 ACAATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (20 bp):
CAAAACAGTAAAAAATCAAC
Found at i:49722884 original size:24 final size:23
Alignment explanation
Indices: 49722857--49722909 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 23
49722847 CGCTTCATTA
49722857 TCACCCTTT-TTCGAATCCTCACCT
1 TCACCCTTTCTTC--ATCCTCACCT
49722881 TCA-CCTTTACCTTCATCCTCACCT
1 TCACCCTTT--CTTCATCCTCACCT
49722905 TCACC
1 TCACC
49722910 TTTACCCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.20
24 16 0.64
25 1 0.04
26 3 0.12
ACGTcount: A:0.17, C:0.45, G:0.02, T:0.36
Consensus pattern (23 bp):
TCACCCTTTCTTCATCCTCACCT
Found at i:49722894 original size:12 final size:12
Alignment explanation
Indices: 49722877--49722915 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
49722867 TCGAATCCTC
49722877 ACCTTCACCTTT
1 ACCTTCACCTTT
*
49722889 ACCTTCATCC-TC
1 ACCTTCA-CCTTT
49722901 ACCTTCACCTTT
1 ACCTTCACCTTT
49722913 ACC
1 ACC
49722916 CTCATCCTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 19 0.83
13 2 0.09
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTTCACCTTT
Found at i:49722910 original size:24 final size:24
Alignment explanation
Indices: 49722871--49722924 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
49722861 CCTTTTTCGA
*
49722871 ATCCTCACCTTCACCTTTACCTTC
1 ATCCTCACCTTCACCTTTACCCTC
49722895 ATCCTCACCTTCACCTTTACCCTC
1 ATCCTCACCTTCACCTTTACCCTC
49722919 ATCCTC
1 ATCCTC
49722925 GCCCCCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.00, T:0.35
Consensus pattern (24 bp):
ATCCTCACCTTCACCTTTACCCTC
Found at i:49722918 original size:18 final size:18
Alignment explanation
Indices: 49722875--49722919 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
49722865 TTTCGAATCC
* *
49722875 TCACCTTCACCTTTACCT
1 TCACCCTCACCTTCACCT
*
49722893 TCATCCTCACCTTCACCT
1 TCACCCTCACCTTCACCT
*
49722911 TTACCCTCA
1 TCACCCTCA
49722920 TCCTCGCCCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.47, G:0.00, T:0.36
Consensus pattern (18 bp):
TCACCCTCACCTTCACCT
Found at i:49725692 original size:34 final size:35
Alignment explanation
Indices: 49725613--49725701 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 35
49725603 AGATAGTAAT
*
49725613 AAAAACAGCAATAAAAATAACAACAAAAATAACAC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
* ** * * *
49725648 GAAATTAGCAATCAAAACAATAA-AAAAATAACTC
1 AAAAACAGCAATAAAAACAACAACAAAAATAACAC
*
49725682 AAAAACAGCAA-AAAATCAAC
1 AAAAACAGCAATAAAAACAAC
49725702 CAAAACAGTA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
33 6 0.15
34 18 0.44
35 17 0.41
ACGTcount: A:0.67, C:0.17, G:0.04, T:0.11
Consensus pattern (35 bp):
AAAAACAGCAATAAAAACAACAACAAAAATAACAC
Found at i:49725716 original size:21 final size:20
Alignment explanation
Indices: 49725660--49725728 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
49725650 AATTAGCAAT
*
49725660 CAAAACAATAAAAAAAT-AAC
1 CAAAACAGT-AAAAAATCAAC
*
49725680 TCAAAAACAGCAAAAAATCAAC
1 -C-AAAACAGTAAAAAATCAAC
*
49725702 CAAAACAGTAGAAAAAGC-AC
1 CAAAACAGTA-AAAAATCAAC
49725722 CAAAACA
1 CAAAACA
49725729 ACAATATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.41
21 15 0.37
22 9 0.22
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (20 bp):
CAAAACAGTAAAAAATCAAC
Found at i:49733876 original size:30 final size:30
Alignment explanation
Indices: 49733822--49733880 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
49733812 TTTGAGATTT
*
49733822 GGGCTTGTAAATGAATTTCCCAAATTAAAC
1 GGGCTTGTAAATGAACTTCCCAAATTAAAC
* **
49733852 GGGCTTGTAAATGGACTTGTCAAATTAAA
1 GGGCTTGTAAATGAACTTCCCAAATTAAA
49733881 TTTAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (30 bp):
GGGCTTGTAAATGAACTTCCCAAATTAAAC
Found at i:49746819 original size:19 final size:20
Alignment explanation
Indices: 49746789--49746843 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
49746779 TTTCAACATA
*
49746789 ATACCAATATTTTTAAC-GG
1 ATACCAAAATTTTTAACAGG
* * *
49746808 ATGCCAAAATTTCTAACATG
1 ATACCAAAATTTTTAACAGG
*
49746828 ATACTAAAATTTTTAA
1 ATACCAAAATTTTTAA
49746844 GCAAAAACCA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (20 bp):
ATACCAAAATTTTTAACAGG
Found at i:49753844 original size:19 final size:21
Alignment explanation
Indices: 49753805--49753844 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49753795 GATTTGCCTC
49753805 TCATATAAGTCCATGTTTCCT
1 TCATATAAGTCCATGTTTCCT
*
49753826 TCATTTAAG-CCAT-TTTCCT
1 TCATATAAGTCCATGTTTCCT
49753845 GAAGACTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (21 bp):
TCATATAAGTCCATGTTTCCT
Found at i:49763930 original size:19 final size:20
Alignment explanation
Indices: 49763900--49763954 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
49763890 TTTCAACATA
*
49763900 ATACCAATATTTTTAAC-GG
1 ATACCAAAATTTTTAACAGG
* * *
49763919 ATGCCAAAATTTCTAACATG
1 ATACCAAAATTTTTAACAGG
*
49763939 ATACTAAAATTTTTAA
1 ATACCAAAATTTTTAA
49763955 GCAAAAACCA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (20 bp):
ATACCAAAATTTTTAACAGG
Found at i:49772450 original size:24 final size:26
Alignment explanation
Indices: 49772423--49772470 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
49772413 ATTATTAATA
49772423 TTAAAAACA-TTAAAATA-AATATTT
1 TTAAAAACATTTAAAATATAATATTT
*
49772447 TTAAAAATATTTAAAATATAATAT
1 TTAAAAACATTTAAAATATAATAT
49772471 GGACAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAAAAACATTTAAAATATAATATTT
Found at i:49780130 original size:155 final size:155
Alignment explanation
Indices: 49779848--49780148 Score: 505
Period size: 155 Copynumber: 1.9 Consensus size: 155
49779838 AGACATCTCA
* *
49779848 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATTAAACTGTCTGGAGATGTGCCACAAATT
1 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGTGCCACAAATT
* *
49779913 TCACATGTGTTTGTCACCGATGACCTTCTTCTCTTCTATAAAGCGGGCATGAAACAAGGTGAAGT
66 TCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCTATAAAGCGGCCATGAAACAAGGTGAAGT
*
49779978 CCGAAGAATCCTACAAATTTCACAT
131 CCAAAGAATCCTACAAATTTCACAT
49780003 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGAT-TGGCCACAAAT
1 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGT-GCCACAAAT
* * *
49780067 TTCACATTTGTTTGTCACCGATAACTTTCTTCTCTTCTATAAAGTGGCCATGAAACAAGGTGAAG
65 TTCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCTATAAAGCGGCCATGAAACAAGGTGAAG
*
49780132 TCCAAAGAATTCTACAA
130 TCCAAAGAATCCTACAA
49780149 GAACATAGCA
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
154 1 0.01
155 135 0.99
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (155 bp):
TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGTGCCACAAATT
TCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCTATAAAGCGGCCATGAAACAAGGTGAAGT
CCAAAGAATCCTACAAATTTCACAT
Found at i:49792752 original size:19 final size:18
Alignment explanation
Indices: 49792728--49792771 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
49792718 TGTTTTTATG
49792728 AATAAAATAATTTTGTAAA
1 AATAAAATAATTTTG-AAA
* *
49792747 AATAAATTACTTTTGAAA
1 AATAAAATAATTTTGAAA
*
49792765 TATAAAA
1 AATAAAA
49792772 GTTTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AATAAAATAATTTTGAAA
Found at i:49798248 original size:27 final size:27
Alignment explanation
Indices: 49798188--49798248 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
49798178 TCGGATCTCG
* * *
49798188 AGGTTTAAGGTTTGGGTTTAAGATTTA
1 AGGTTCAAGATTTGGGTTTAAGATTCA
* * *
49798215 AGATTCAAGATTTGGGTTTACGGTTCA
1 AGGTTCAAGATTTGGGTTTAAGATTCA
49798242 AGGTTCA
1 AGGTTCA
49798249 TTCATGTTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (27 bp):
AGGTTCAAGATTTGGGTTTAAGATTCA
Found at i:49807854 original size:16 final size:16
Alignment explanation
Indices: 49807833--49807867 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
49807823 AAGCATCAGC
49807833 TTGGAA-CTGGAACAAG
1 TTGGAACCT-GAACAAG
49807849 TTGGAACCTGAACAAG
1 TTGGAACCTGAACAAG
49807865 TTG
1 TTG
49807868 TTGATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (16 bp):
TTGGAACCTGAACAAG
Found at i:49810913 original size:19 final size:20
Alignment explanation
Indices: 49810867--49810918 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
49810857 TGGTCTTTGC
* * *
49810867 TTAAAAATTTTAGTATCATG
1 TTAAAAATTTTGGCATCACG
*
49810887 TTAGAAATTTTGGCATC-CG
1 TTAAAAATTTTGGCATCACG
*
49810906 TTAAAAATATTGG
1 TTAAAAATTTTGG
49810919 TATTATGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (20 bp):
TTAAAAATTTTGGCATCACG
Found at i:49822672 original size:19 final size:18
Alignment explanation
Indices: 49822631--49822674 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
49822621 TAAATAAAAC
*
49822631 TTTTATATTTCAAAAGTA
1 TTTTATTTTTCAAAAGTA
* *
49822649 ATTTATTTTTACAAAATTA
1 TTTTATTTTT-CAAAAGTA
49822668 TTTTATT
1 TTTTATT
49822675 CATAAAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTATTTTTCAAAAGTA
Found at i:49835537 original size:155 final size:155
Alignment explanation
Indices: 49835255--49835555 Score: 505
Period size: 155 Copynumber: 1.9 Consensus size: 155
49835245 TGCTATGTTC
* * *
49835255 TTGTAGAATTCTTTGGACTTCACCTTGTTTCATGGCCACTTTATAGAAGAGAAGAAAGTTATCGG
1 TTGTAGAATTCTTCGGACTTCACCTTGTTTCATGCCCACTTTATAGAAGAGAAGAAAGTCATCGG
* *
49835320 TGACAAACAAATGTGAAATTTGTGGCCAATCTCTAGACAGTTTGATGGGCTTTCATTTGTCACCT
66 TGACAAACAAATGTGAAATTTGTGGCCAATCTCCAGACAGTTTAATGGGCTTTCATTTGTCACCT
49835385 TTAAGCACTTCATCAAATGTGAAAT
131 TTAAGCACTTCATCAAATGTGAAAT
* * *
49835410 TTGTAGGATTCTTCGGACTTCACCTTGTTTCATGCCCGCTTTATAGAAGAGAAGAAGGTCATCGG
1 TTGTAGAATTCTTCGGACTTCACCTTGTTTCATGCCCACTTTATAGAAGAGAAGAAAGTCATCGG
*
49835475 TGACAAACACATGTGAAATTTGTGG-CACATCTCCAGACAGTTTAATGGGCTTTCATTTGTCACC
66 TGACAAACAAATGTGAAATTTGTGGCCA-ATCTCCAGACAGTTTAATGGGCTTTCATTTGTCACC
49835539 TTTAAGCACTTCATCAA
130 TTTAAGCACTTCATCAA
49835556 TGAGATGTCT
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
154 2 0.01
155 134 0.99
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (155 bp):
TTGTAGAATTCTTCGGACTTCACCTTGTTTCATGCCCACTTTATAGAAGAGAAGAAAGTCATCGG
TGACAAACAAATGTGAAATTTGTGGCCAATCTCCAGACAGTTTAATGGGCTTTCATTTGTCACCT
TTAAGCACTTCATCAAATGTGAAAT
Found at i:49837553 original size:155 final size:155
Alignment explanation
Indices: 49837271--49837571 Score: 505
Period size: 155 Copynumber: 1.9 Consensus size: 155
49837261 AGACATCTCA
*
49837271 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTGGAGATGTGCCACAAATT
1 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGTGCCACAAATT
* *
49837336 TCACATGTGTTTGTCACCGATGACCTTCTTCTCTTCCATAAAGCGGGCATGAAACAAGGTGAAGT
66 TCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCCATAAAGCGGCCATGAAACAAGGTGAAGT
*
49837401 CCGAAGAATCCTACAAATTTCACAT
131 CCAAAGAATCCTACAAATTTCACAT
49837426 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGAT-TGGCCACAAAT
1 TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGT-GCCACAAAT
* * * *
49837490 TTCACATTTGTTTGTCACCGATAACTTTCTTCTCTTCTATAAAGTGGCCATGAAACAAGGTGAAG
65 TTCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCCATAAAGCGGCCATGAAACAAGGTGAAG
*
49837555 TCCAAAGAATTCTACAA
130 TCCAAAGAATCCTACAA
49837572 GAACATAGCA
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
154 1 0.01
155 135 0.99
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (155 bp):
TTGATGAAGTGCTTAAAGGTGACAAATGAAAGCCCATCAAACTGTCTAGAGATGTGCCACAAATT
TCACATGTGTTTGTCACCGATAACCTTCTTCTCTTCCATAAAGCGGCCATGAAACAAGGTGAAGT
CCAAAGAATCCTACAAATTTCACAT
Found at i:49850193 original size:19 final size:18
Alignment explanation
Indices: 49850169--49850212 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
49850159 TGTTTTTATG
49850169 AATAAAATAATTTTGTAAA
1 AATAAAATAATTTTG-AAA
* *
49850188 AATAAATTACTTTTGAAA
1 AATAAAATAATTTTGAAA
*
49850206 TATAAAA
1 AATAAAA
49850213 GTTTTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
AATAAAATAATTTTGAAA
Found at i:49854662 original size:7 final size:7
Alignment explanation
Indices: 49854640--49854677 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
49854630 ACAAAATATC
49854640 TCTATAA
1 TCTATAA
*
49854647 TTTAT-A
1 TCTATAA
49854653 TCTATAA
1 TCTATAA
49854660 TCTATAA
1 TCTATAA
49854667 TCTATAA
1 TCTATAA
49854674 TCTA
1 TCTA
49854678 GAATACCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (7 bp):
TCTATAA
Found at i:49857553 original size:19 final size:19
Alignment explanation
Indices: 49857517--49857554 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49857507 TATTTCGAGG
*
49857517 TTATAATTATAATTAAAAT
1 TTATAATTATAATCAAAAT
49857536 TTATAATTGAT-ATCAAAAT
1 TTATAATT-ATAATCAAAAT
49857555 CTCTAACAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (19 bp):
TTATAATTATAATCAAAAT
Found at i:49858355 original size:6 final size:6
Alignment explanation
Indices: 49858327--49858434 Score: 80
Period size: 6 Copynumber: 18.2 Consensus size: 6
49858317 CTTTTCGTTT
* * *
49858327 AATTTA AAGTTA AA-TTG ATTTTA AATTT- -ATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * ** *
49858372 AATTTA ATTATTTA AATTT- ACTTTG AATTTA AATTTA AATAAA AATTAA
1 AATTTA A--ATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
49858421 AACATTA AATTTA A
1 AA-TTTA AATTTA A
49858435 CATTAAAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
4 4 0.05
5 7 0.09
6 60 0.74
7 4 0.05
8 6 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:49858389 original size:26 final size:25
Alignment explanation
Indices: 49858353--49858411 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
49858343 GATTTTAAAT
49858353 TTATTTAAATTTAAATTTAAATTTAA
1 TTATTTAAATTT-AATTTAAATTTAA
* *
49858379 TTATTTAAATTTACTTTGAATTTAA
1 TTATTTAAATTTAATTTAAATTTAA
49858404 --ATTTAAAT
1 TTATTTAAAT
49858412 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 8 0.26
25 11 0.35
26 12 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTATTTAAATTTAATTTAAATTTAA
Found at i:49860232 original size:30 final size:30
Alignment explanation
Indices: 49860196--49860550 Score: 462
Period size: 30 Copynumber: 11.9 Consensus size: 30
49860186 AAATTGTCCA
49860196 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
49860226 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
49860256 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
** *
49860286 AAAATTATGTTTTGACCCTAAAAATTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
49860316 AAAATTACATCTTGACCCCAAAATTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
49860346 AAAATTATATTTTTACCCTGAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
49860376 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* *
49860406 AAAATTACATATTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * *
49860436 ATAATTACATTTTGACCCCAAAACTTTTCA
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* * * *
49860466 AAAAGTACATTTTAACCATAAAACTTTTCT
1 AAAATTACATTTTGACCCTAAAACTTTTCC
* ** *
49860496 AAAATTATATTTTGACCCCGAAAC-TTTCA
1 AAAATTACATTTTGACCCTAAAACTTTTCC
*
49860525 AAAATTACCATTTT-ACCCTTAAACTT
1 AAAATTA-CATTTTGACCCTAAAACTT
49860551 CCCTAAATCC
Statistics
Matches: 284, Mismatches: 39, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
29 19 0.07
30 265 0.93
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTAAAACTTTTCC
Found at i:49860586 original size:59 final size:58
Alignment explanation
Indices: 49860523--49860718 Score: 189
Period size: 59 Copynumber: 3.3 Consensus size: 58
49860513 CCGAAACTTT
* * *
49860523 CAAAAATTACCATTTTACCCTTAAACTTCCCTAAATCCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCTCAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * * * * * ** * **
49860582 CAAAACTTATCGTTTTA-CCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTGC
1 CAAAAATTACCATTTTACCCT-CAAACTTTCC-AAATTCCATTTTTAACCCCGATTTCAC
* * *
49860641 CAAAATTTACCATTTTATTCCTCAAACTTTCCAAATTCCATTTTTAGCCCCGATTTCA-
1 CAAAAATTACCATTTTA-CCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
49860699 CAAAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
49860719 CTAAAAACCC
Statistics
Matches: 105, Mismatches: 29, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
57 2 0.02
58 19 0.18
59 72 0.69
60 9 0.09
61 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTCAAACTTTCCAAATTCCATTTTTAACCCCGATTTCAC
Found at i:49860627 original size:118 final size:116
Alignment explanation
Indices: 49860505--49860717 Score: 250
Period size: 118 Copynumber: 1.8 Consensus size: 116
49860495 TAAAATTATA
*
49860505 TTTTGACCCCGAAACTTT-CAAAAATTACCATTTTA-CCCTTAAACTTCCCTAAATCCCATTTTT
1 TTTTGACCCCG--ACTTTCCAAAAATTACCATTTTATCCCTCAAACTTCCC-AAATCCCATTTTT
* * *
49860568 AACCCCGATTTCACCAAAACTTATCGTTTTACCTCCGAACTTTCCAAAATTTCAT
63 AACCCCGATTTCA-CAAAAATTACCATTTTACCTCCGAACTTTCCAAAATTTCAT
** ** * * * * *
49860623 TTTTGACCTTGTTTTTGCCAAAATTTACCATTTTATTCCTCAAACTTTCCAAATTCCATTTTTAG
1 TTTTGACCCCGACTTT-CCAAAAATTACCATTTTATCCCTCAAACTTCCCAAATCCCATTTTTAA
49860688 CCCCGATTTCACAAAAATTACCATTTTACC
65 CCCCGATTTCACAAAAATTACCATTTTACC
49860718 CCTAAAAACC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
116 3 0.04
117 16 0.20
118 49 0.62
119 11 0.14
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.38
Consensus pattern (116 bp):
TTTTGACCCCGACTTTCCAAAAATTACCATTTTATCCCTCAAACTTCCCAAATCCCATTTTTAAC
CCCGATTTCACAAAAATTACCATTTTACCTCCGAACTTTCCAAAATTTCAT
Found at i:49872523 original size:31 final size:31
Alignment explanation
Indices: 49872481--49872803 Score: 204
Period size: 31 Copynumber: 9.7 Consensus size: 31
49872471 TAACACGTCT
49872481 TCAT-CTC-TGAAATTGAAGTAAGAGCAACG
1 TCATCCTCTTGAAATTGAAGTAAGAGCAACG
* * **
49872510 TCATCCCCTTGAAATCGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ACG
*
49872546 CTTTAT-CTC-TGAAATTGAAGTAAGAGCAACG
1 --TCATCCTCTTGAAATTGAAGTAAGAGCAACG
* *
49872577 TCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG
1 TCATCCTCTTGAAATTGAAGTA-AG--AG-CAAC--G
* * *
49872614 TCTTCATCTCTGAAATTGAAGTAAGAGCAATG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
* *
49872646 TCATCCCCTTGAAATTGAAGTAGAGAGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-AGA-G--CA-ACG
* **
49872682 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
**
49872714 TCATCCTCTTGAAATTGAAGTAGAGTGGATAACACG
1 TCATCCTCTTGAAATTGAAGTA-A---GAGCA-ACG
* **
49872750 TCTTTATCTCTGAAATTGAAGTAAGAGCAACG
1 TCATCCTCT-TGAAATTGAAGTAAGAGCAACG
49872782 TCATCCTCTTGAAATTGAAGTA
1 TCATCCTCTTGAAATTGAAGTA
49872804 GAGTTGGATA
Statistics
Matches: 224, Mismatches: 40, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
29 7 0.03
30 5 0.02
31 67 0.30
32 35 0.16
33 5 0.02
34 3 0.01
35 13 0.06
36 35 0.16
37 38 0.17
38 16 0.07
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (31 bp):
TCATCCTCTTGAAATTGAAGTAAGAGCAACG
Done.