Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 123 of 135
Found at i:44596309 original size:22 final size:22
Alignment explanation
Indices: 44596271--44596322 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
44596261 ATTTTGAATA
44596271 AGGGATT-AAAATAAAATTGGT
1 AGGGATTAAAAATAAAATTGGT
*
44596292 AGGGATTAAAAATCAAATTGGT
1 AGGGATTAAAAATAAAATTGGT
44596314 AGGGATTAA
1 AGGGATTAA
44596323 CATGTCTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.46, C:0.02, G:0.25, T:0.27
Consensus pattern (22 bp):
AGGGATTAAAAATAAAATTGGT
Found at i:44596724 original size:12 final size:11
Alignment explanation
Indices: 44596699--44596736 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
44596689 GAAAATGATG
44596699 AATTTTA-ATT
1 AATTTTATATT
44596709 AATTTTATAGTT
1 AATTTTATA-TT
44596721 AATTTT-TATT
1 AATTTTATATT
44596731 AATTTT
1 AATTTT
44596737 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:44599903 original size:33 final size:33
Alignment explanation
Indices: 44599857--44599931 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
44599847 GATAAAATAA
* *
44599857 TAAATAAAATAGTTTAAATTTTTGTAGAACAAT
1 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
44599890 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
1 TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
44599923 TAAATGAAG
1 TAAATGAAG
44599932 CAGTCAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (33 bp):
TAAATGAAGTAGTTTAAATTTTTGTAGAACAAT
Found at i:44600627 original size:24 final size:22
Alignment explanation
Indices: 44600550--44600627 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 22
44600540 ATGTATAATA
*
44600550 AATATAAAAATTAATAATTATTT
1 AATATAAAAATTAA-AATTATAT
*
44600573 AATATTACAAAATTTAAATT-TAAT
1 AATA-TA-AAAATTAAAATTAT-AT
*
44600597 GATTATATAAAATATAAAATTATAT
1 -AATATA-AAAAT-TAAAATTATAT
44600622 AATATA
1 AATATA
44600628 CTAATTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 5 0.12
24 19 0.44
25 18 0.42
26 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
AATATAAAAATTAAAATTATAT
Found at i:44607554 original size:16 final size:16
Alignment explanation
Indices: 44607533--44607563 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44607523 TGAATGTCTA
44607533 GTTGGATTCATGATCG
1 GTTGGATTCATGATCG
44607549 GTTGGATTCATGATC
1 GTTGGATTCATGATC
44607564 CATAAGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (16 bp):
GTTGGATTCATGATCG
Found at i:44608730 original size:34 final size:32
Alignment explanation
Indices: 44608677--44608744 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 32
44608667 TGACGATATT
*
44608677 AAAATAATTTTACAGTAAATTATTAAATTTAA
1 AAAATAATTTTACAGTAAATTATTAAACTTAA
* *
44608709 AAAATAAATTTATATAGTAAATTTTTAAACTTAA
1 AAAAT-AATTT-TACAGTAAATTATTAAACTTAA
44608743 AA
1 AA
44608745 TATATCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 5 0.16
33 5 0.16
34 21 0.68
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
AAAATAATTTTACAGTAAATTATTAAACTTAA
Found at i:44608734 original size:103 final size:103
Alignment explanation
Indices: 44608621--44608826 Score: 387
Period size: 103 Copynumber: 2.0 Consensus size: 103
44608611 ATATATATTA
44608621 AGTAAATTTTTAAACTTAAAATATATCTTTAAAAATTAACTAAGGTTGACGATATTAAAATAATT
1 AGTAAATTTTTAAACTTAAAATATATCTTTAAAAATTAACTAAGGTTGACGATATTAAAATAATT
44608686 TTACAGTAAATTA-TTAAATTTAAAAAATAAATTTATAT
66 TTACAGTAAATTATTTAAA-TTAAAAAATAAATTTATAT
44608724 AGTAAATTTTTAAACTTAAAATATATCTTTAAAAATTAACTAAGGTTGACGATATTAAAATAATT
1 AGTAAATTTTTAAACTTAAAATATATCTTTAAAAATTAACTAAGGTTGACGATATTAAAATAATT
*
44608789 TTACAGTAAATTATTTTAATTAAAAAATAAATTTATAT
66 TTACAGTAAATTATTTAAATTAAAAAATAAATTTATAT
44608827 TTTTCAAATA
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 97 0.96
104 4 0.04
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.40
Consensus pattern (103 bp):
AGTAAATTTTTAAACTTAAAATATATCTTTAAAAATTAACTAAGGTTGACGATATTAAAATAATT
TTACAGTAAATTATTTAAATTAAAAAATAAATTTATAT
Found at i:44613704 original size:14 final size:15
Alignment explanation
Indices: 44613685--44613717 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44613675 GGTATAAAAT
*
44613685 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
44613699 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
44613714 AAAT
1 AAAT
44613718 GCTAGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:44613809 original size:87 final size:88
Alignment explanation
Indices: 44613696--44613877 Score: 348
Period size: 87 Copynumber: 2.1 Consensus size: 88
44613686 AATAAAGTAA
44613696 TAAAAATAAAAGAAATAAAAATGCTAGATGCTTTATGACAAATATAAACATAAGTATTGTGAGAA
1 TAAAAATAAAAGAAATAAAAATGCTAGATGCTTTATGACAAATATAAACATAAGTATTGTGAGAA
44613761 TGATAAAAGAAATGACAAAATAG
66 TGATAAAAGAAATGACAAAATAG
*
44613784 TAAAAATAAGAG-AATAAAAATGCTAGATGCTTTATGACAAATATAAACATAAGTATTGTGAGAA
1 TAAAAATAAAAGAAATAAAAATGCTAGATGCTTTATGACAAATATAAACATAAGTATTGTGAGAA
44613848 TGATAAAAGAAATGACAAAATAG
66 TGATAAAAGAAATGACAAAATAG
44613871 TAAAAAT
1 TAAAAAT
44613878 TAGATAAAAA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 82 0.88
88 11 0.12
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.24
Consensus pattern (88 bp):
TAAAAATAAAAGAAATAAAAATGCTAGATGCTTTATGACAAATATAAACATAAGTATTGTGAGAA
TGATAAAAGAAATGACAAAATAG
Found at i:44615696 original size:45 final size:45
Alignment explanation
Indices: 44615602--44615990 Score: 373
Period size: 44 Copynumber: 8.6 Consensus size: 45
44615592 CTCATCCAAC
* * *
44615602 CCACTGCAACTTCAGGG-GTATAGGAATTG-TAAT-TTCAATCTACT
1 CCACTGCAACTTCAGGGAG-ATAAGATTTGCT-ATCTTCAATCTGCT
* * *
44615646 CCACTGCAACTTTAGAGAAATAAGATTTGCTATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* * * * *
44615691 GCACTGTAACTTCAGGGAGATAAGATTCGTAGCTTGTAGCTTTAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGATT--T-GC---TATCTTCAATCTGCT
* * * *
44615742 TCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* * *
44615787 TCATTGCAACTTCAGGTAGATAAGATTTG-TATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* *
44615831 CCACTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
* *
44615876 CCACTTCAACCTT-AGGGAGA-AGAGATTTG-TAGT-TTTAATCTGCT
1 CCACTGCAA-CTTCAGGGAGATA-AGATTTGCTA-TCTTCAATCTGCT
* * ** *
44615920 CCAATGCAACTTCAGGGGGATAAGATTTG-TGGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
44615964 CCACTGCAACTTCAGGGAGATAAGATT
1 CCACTGCAACTTCAGGGAGATAAGATT
44615991 CTCCACGATG
Statistics
Matches: 286, Mismatches: 43, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.01
44 133 0.47
45 106 0.37
46 3 0.01
47 1 0.00
48 4 0.01
49 1 0.00
51 35 0.12
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCT
Found at i:44615902 original size:89 final size:88
Alignment explanation
Indices: 44615602--44615990 Score: 342
Period size: 89 Copynumber: 4.3 Consensus size: 88
44615592 CTCATCCAAC
* * * * * * * *
44615602 CCACTGCAACTTCAGGG-GTATAGGAATTGTAAT-TTCAATCTACTCCACTGCAACTTTAGAGAA
1 CCACTTCAACTTCAGGGAG-ATAAGATTTGT-ATCTTTAATCTGCTCCACTGCAACTTCAGGGAG
44615665 ATAAGATTTGCTATCTTCAATCTGCT
64 ATAAGATTT-CTATCTTCAATCTGCT
* * * * *
44615691 GCACTGT-AACTTCAGGGAGATAAGATTCGTAGCTTGTAGCTTTAATCTGTTTCACTGCAACTTT
1 CCACT-TCAACTTCAGGGAGATAAGA----T---TTGTATCTTTAATCTGCTCCACTGCAACTTC
* *
44615755 AGGGAAATAAGATTTGCTATCTTCAATCTACT
58 AGGGAGATAAGATTT-CTATCTTCAATCTGCT
* * * *
44615787 TCA-TTGCAACTTCAGGTAGATAAGATTTGTATCTTCAATCTGCTCCACTGCAACTTCAAGGAGA
1 CCACTT-CAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGA
44615851 TAAGATTTACTATCTTCAATCTGCT
65 TAAGATTT-CTATCTTCAATCTGCT
* *
44615876 CCACTTCAACCTT-AGGGAGA-AGAGATTTGTAGT-TTTAATCTGCTCCAATGCAACTTCAGGGG
1 CCACTTCAA-CTTCAGGGAGATA-AGATTTGTA-TCTTTAATCTGCTCCACTGCAACTTCAGGGA
* ** *
44615938 GATAAGATTTGTGGCTTTAATCTGCT
63 GATAAGATTTCTATCTTCAATCTGCT
*
44615964 CCACTGCAACTTCAGGGAGATAAGATT
1 CCACTTCAACTTCAGGGAGATAAGATT
44615991 CTCCACGATG
Statistics
Matches: 249, Mismatches: 33, Indels: 37
0.78 0.10 0.12
Matches are distributed among these distances:
87 3 0.01
88 33 0.13
89 129 0.52
90 7 0.03
92 1 0.00
94 1 0.00
95 2 0.01
96 73 0.29
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (88 bp):
CCACTTCAACTTCAGGGAGATAAGATTTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
AAGATTTCTATCTTCAATCTGCT
Found at i:44620389 original size:24 final size:25
Alignment explanation
Indices: 44620348--44620423 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
44620338 AGCCCGGGCC
44620348 CCCAAACTAAACCTAACCCATCAGA
1 CCCAAACTAAACCTAACCCATCAGA
* *
44620373 CCCAAA-TAAATCAAACCCA-C---
1 CCCAAACTAAACCTAACCCATCAGA
*
44620393 CCCAAACTAAACCTAACCTATCAGA
1 CCCAAACTAAACCTAACCCATCAGA
44620418 CCCAAA
1 CCCAAA
44620424 TACAACCCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 6 0.15
21 10 0.24
22 1 0.02
23 1 0.02
24 11 0.27
25 12 0.29
ACGTcount: A:0.46, C:0.39, G:0.03, T:0.12
Consensus pattern (25 bp):
CCCAAACTAAACCTAACCCATCAGA
Found at i:44622843 original size:16 final size:15
Alignment explanation
Indices: 44622824--44622857 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
44622814 AATAAGCAAG
44622824 TAAATAAATAAATGGA
1 TAAATAAATAAAT-GA
44622840 TAAATAAATAAATGA
1 TAAATAAATAAATGA
44622855 TAA
1 TAA
44622858 TAAGAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAATGA
Found at i:44623757 original size:61 final size:61
Alignment explanation
Indices: 44623682--44623803 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
44623672 GAGAATGGTT
44623682 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
1 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
44623743 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
1 CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
44623804 TCAGCCACTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (61 bp):
CTCTAAGTTTCAAAAACCCGTATGCCCGAAAGATGTGATCTTTCATCGGAGATGGCTGTCC
Found at i:44628790 original size:14 final size:14
Alignment explanation
Indices: 44628760--44628825 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
44628750 CACACATGTA
*
44628760 GTTCACACCT-AGAG
1 GTTCACACATAAG-G
44628774 GTTCACACATAAGG
1 GTTCACACATAAGG
*
44628788 GTTCACTCAAGTAA-G
1 GTTCACAC-A-TAAGG
44628803 G-TCACACAT-AGG
1 GTTCACACATAAGG
44628815 GTTCACACATA
1 GTTCACACATA
44628826 TAGATTTTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 9 0.21
14 22 0.51
15 5 0.12
16 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (14 bp):
GTTCACACATAAGG
Found at i:44628790 original size:41 final size:41
Alignment explanation
Indices: 44628745--44628825 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
44628735 TACATAAGTG
* * *
44628745 GGGTTCACACATGT-AGTTCACACCTAGAGGTTCACACATAA
1 GGGTTCACACAAGTAAGGTCACACATAG-GGTTCACACATAA
*
44628786 GGGTTCACTCAAGTAAGGTCACACATAGGGTTCACACATA
1 GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATA
44628826 TAGATTTTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 24 0.69
42 11 0.31
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
GGGTTCACACAAGTAAGGTCACACATAGGGTTCACACATAA
Found at i:44640655 original size:20 final size:20
Alignment explanation
Indices: 44640622--44640661 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44640612 CTAACCCTCA
*
44640622 AAACTTTTTATTTTCCCCCT
1 AAACTTTTTATTTTCACCCT
44640642 AAAC-TTTTACTTTTCACCCT
1 AAACTTTTTA-TTTTCACCCT
44640662 TTACCCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (20 bp):
AAACTTTTTATTTTCACCCT
Found at i:44643998 original size:18 final size:18
Alignment explanation
Indices: 44643964--44643997 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44643954 AGAATGGGCT
44643964 TAAAAATATTATGAAAAC
1 TAAAAATATTATGAAAAC
44643982 TAAAAATATT-TGAAAA
1 TAAAAATATTATGAAAA
44643998 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAATATTATGAAAAC
Found at i:44644053 original size:24 final size:24
Alignment explanation
Indices: 44644018--44644063 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
44644008 TAAATTAAAA
44644018 AATCAACAAAAATAAAAAAATTTT
1 AATCAACAAAAATAAAAAAATTTT
*
44644042 AATCAA-AGAAAATTAAAAAATT
1 AATCAACA-AAAATAAAAAAATT
44644064 AATGTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
AATCAACAAAAATAAAAAAATTTT
Found at i:44645912 original size:125 final size:124
Alignment explanation
Indices: 44645687--44645964 Score: 425
Period size: 125 Copynumber: 2.2 Consensus size: 124
44645677 TTTCGAGTTC
**
44645687 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTTTACCAGGATGCTATCAGAGAAGAAATTGTGAA
1 ACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTGAA
* * * *
44645751 ATCGTGCCCTCGTGGACGCGATTTTGGTACAATTGGTCATGTAAGAAATAATTTTTTTTG
65 ATCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
44645811 ACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTAT-ATGAGAAGAAATTGTGA
1 ACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAGAAGAAATTGTGA
* *
44645875 AATCGAGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTTTG
64 AATCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
* *
44645936 ACGTTTCTGAGCAAATAGTGTCAAATCGC
1 ACGTTTCTGAGCAAATAGTATAAAATCGC
44645965 GCCCTCGTGG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
124 28 0.20
125 112 0.79
126 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (124 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAGAAGAAATTGTGAAA
TCGAGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAAGAAATAATTATTTTTG
Found at i:44646919 original size:30 final size:30
Alignment explanation
Indices: 44646831--44646948 Score: 152
Period size: 29 Copynumber: 4.0 Consensus size: 30
44646821 TTTATTTTTG
44646831 CATTTTGACCCCTAAACTTTCTC-AAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
** * *
44646860 CATTTCAACACCTAAACTTT-TCTAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
44646889 CATTTTGACCCCTAAACTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
* * *
44646919 CATTTGGA-CCTTAAAATTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTTCTCAAAATTA
44646948 C
1 C
44646949 GTTTCGGCCC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.03
29 60 0.78
30 15 0.19
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTCAAAATTA
Found at i:44646963 original size:29 final size:28
Alignment explanation
Indices: 44646883--44646963 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
44646873 AAACTTTTCT
* *
44646883 AAATTACATTTTGACCCCTAAACTTTCTCA
1 AAATTACA-TTTGGCCCC-AAAATTTCTCA
**
44646913 AAATTACATTTGGACCTTAAAATTTCTCA
1 AAATTACATTTGG-CCCCAAAATTTCTCA
*
44646942 AAATTACGTTTCGGCCCCAAAA
1 AAATTACATTT-GGCCCCAAAA
44646964 GATTTACTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 30 0.71
30 12 0.29
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (28 bp):
AAATTACATTTGGCCCCAAAATTTCTCA
Found at i:44647324 original size:10 final size:10
Alignment explanation
Indices: 44647285--44647351 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
44647275 CCAAGAGGCA
44647285 AAAAAAGAA-
1 AAAAAAGAAG
*
44647294 AAAAAACAAG
1 AAAAAAGAAG
*
44647304 CAAGCAAAAGAGG
1 -AA--AAAAGAAG
44647317 AAAAAAGAAAG
1 AAAAAAG-AAG
**
44647328 AGTAAAGAAG
1 AAAAAAGAAG
44647338 AAAAAAGAAG
1 AAAAAAGAAG
44647348 AAAA
1 AAAA
44647352 GAGAGGAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 8 0.18
10 20 0.44
11 9 0.20
12 2 0.04
13 6 0.13
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:44647468 original size:4 final size:4
Alignment explanation
Indices: 44647461--44647539 Score: 89
Period size: 4 Copynumber: 20.5 Consensus size: 4
44647451 AAAATGGAAG
44647461 AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AAG- AAGAA AAGGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AAGA
44647509 AA-A AAGA AA-A AAGA AA-A AA-A AAGGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA-GA AAGA AA
44647540 AAAATATTCT
Statistics
Matches: 67, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
3 18 0.27
4 40 0.60
5 8 0.12
6 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:44647468 original size:7 final size:7
Alignment explanation
Indices: 44647435--44647538 Score: 72
Period size: 7 Copynumber: 15.0 Consensus size: 7
44647425 GGCTGCTGCT
*
44647435 GAAAGGA
1 GAAAGAA
*
44647442 GAAGGAA
1 GAAAGAA
44647449 GAAA-AA
1 GAAAGAA
*
44647455 TGGAAGAA
1 -GAAAGAA
44647463 GAAAGAA
1 GAAAGAA
*
44647470 -AGA-AA
1 GAAAGAA
44647475 GAAAGAAA
1 GAAAG-AA
44647483 GAAAGAA
1 GAAAGAA
44647490 GAAAGAA
1 GAAAGAA
*
44647497 GAAA-AG
1 GAAAGAA
44647503 GAAAGAA
1 GAAAGAA
*
44647510 AAAAGAA
1 GAAAGAA
*
44647517 AAAAGAA
1 GAAAGAA
* *
44647524 AAAAAAA
1 GAAAGAA
44647531 GGAAAGAA
1 -GAAAGAA
44647539 AAAAATATTC
Statistics
Matches: 77, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
5 2 0.03
6 11 0.14
7 50 0.65
8 14 0.18
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (7 bp):
GAAAGAA
Found at i:44647474 original size:8 final size:8
Alignment explanation
Indices: 44647461--44647539 Score: 89
Period size: 7 Copynumber: 10.2 Consensus size: 8
44647451 AAAATGGAAG
44647461 AAGAAAGA
1 AAGAAAGA
44647469 AAGAAAGA
1 AAGAAAGA
44647477 AAGAAAGA
1 AAGAAAGA
44647485 AAG-AAGA
1 AAGAAAGA
44647492 AAG-AAGAA
1 AAGAAAG-A
44647500 AAGGAAAGA
1 AA-GAAAGA
44647509 AA-AAAGA
1 AAGAAAGA
44647516 AA-AAAGA
1 AAGAAAGA
44647523 AA-AAA-A
1 AAGAAAGA
44647529 AAGGAAAGA
1 AA-GAAAGA
44647538 AA
1 AA
44647540 AAAATATTCT
Statistics
Matches: 65, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
6 3 0.05
7 27 0.42
8 25 0.38
9 7 0.11
10 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGAAAGA
Found at i:44647490 original size:27 final size:27
Alignment explanation
Indices: 44647458--44647539 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
44647448 AGAAAAATGG
44647458 AAGAAGAAAGAAAGAAAGAAAGAAAGA
1 AAGAAGAAAGAAAGAAAGAAAGAAAGA
44647485 AAGAAGAAAG-AAGAAAAGGAAAGAAA-A
1 AAGAAGAAAGAAAG-AAA-GAAAGAAAGA
*
44647512 AAGAAAAAAGAAA-AAA-AAAGGAAAGA
1 AAGAAGAAAGAAAGAAAGAAA-GAAAGA
44647538 AA
1 AA
44647540 AAAATATTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
24 3 0.06
25 4 0.08
26 9 0.18
27 23 0.47
28 10 0.20
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAGAAAGAAAGAAAGAAAGA
Found at i:44647540 original size:11 final size:11
Alignment explanation
Indices: 44647443--44647541 Score: 61
Period size: 11 Copynumber: 9.2 Consensus size: 11
44647433 CTGAAAGGAG
44647443 AAGG-AAGAAA
1 AAGGAAAGAAA
44647453 AATGG-AAGAAGA
1 AA-GGAAAGAA-A
44647465 AA-GAAAGAAA
1 AAGGAAAGAAA
*
44647475 GAAAGAAAGAAA
1 -AAGGAAAGAAA
44647487 GAA-GAAAGAAGAA
1 -AAGGAAAG-A-AA
44647500 AAGGAAAG--A
1 AAGGAAAGAAA
44647509 AA--AAAGAAA
1 AAGGAAAGAAA
* *
44647518 AAAGAAAAAAA
1 AAGGAAAGAAA
44647529 AAGGAAAGAAA
1 AAGGAAAGAAA
44647540 AA
1 AA
44647542 AATATTCTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 23
0.74 0.03 0.23
Matches are distributed among these distances:
7 4 0.05
9 6 0.08
10 4 0.05
11 36 0.49
12 17 0.23
13 7 0.09
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (11 bp):
AAGGAAAGAAA
Found at i:44647843 original size:7 final size:7
Alignment explanation
Indices: 44647817--44647904 Score: 88
Period size: 7 Copynumber: 11.9 Consensus size: 7
44647807 GCAGCCCAGC
44647817 AGAAAAA
1 AGAAAAA
*
44647824 A-AAGAGA
1 AGAA-AAA
*
44647831 AGAAAAC
1 AGAAAAA
44647838 AGAAAAA
1 AGAAAAA
44647845 AGAAAAA
1 AGAAAAA
44647852 GAGAAAAAA
1 -AG-AAAAA
*
44647861 AGGAAAA
1 AGAAAAA
44647868 AGAAAAA
1 AGAAAAA
44647875 AGAAAAAA
1 AG-AAAAA
44647883 AGGAAAAA
1 A-GAAAAA
44647891 AGAGAAAA
1 AGA-AAAA
44647899 AGAAAA
1 AGAAAA
44647905 GAAAATGTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
6 2 0.03
7 35 0.51
8 25 0.37
9 6 0.09
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:44647851 original size:8 final size:8
Alignment explanation
Indices: 44647820--44647904 Score: 84
Period size: 8 Copynumber: 10.5 Consensus size: 8
44647810 GCCCAGCAGA
44647820 AAAAAAAG
1 AAAAAAAG
*
44647828 AGAAGAAAAC
1 A-AA-AAAAG
44647838 AGAAAAAAG
1 A-AAAAAAG
*
44647847 AAAAAGAG
1 AAAAAAAG
44647855 AAAAAAAG
1 AAAAAAAG
*
44647863 -GAAAAAG
1 AAAAAAAG
44647870 -AAAAAAG
1 AAAAAAAG
44647877 AAAAAAAG
1 AAAAAAAG
*
44647885 GAAAAAAG
1 AAAAAAAG
*
44647893 AGAAAAAG
1 AAAAAAAG
44647901 AAAA
1 AAAA
44647905 GAAAATGTCA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
7 12 0.19
8 37 0.58
9 7 0.11
10 8 0.12
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:44647859 original size:23 final size:22
Alignment explanation
Indices: 44647822--44647904 Score: 103
Period size: 23 Copynumber: 3.5 Consensus size: 22
44647812 CCAGCAGAAA
44647822 AAAAAGAGAAGAAAACAGAAAAAAG
1 AAAAA-AGAA-AAAA-AGAAAAAAG
*
44647847 AAAAAGAGAAAAAAAGGAAAAAG
1 AAAAA-AGAAAAAAAGAAAAAAG
44647870 AAAAAAGAAAAAAAGGAAAAAAG
1 AAAAAAGAAAAAAA-GAAAAAAG
44647893 AGAAAAAGAAAA
1 A-AAAAAGAAAA
44647905 GAAAATGTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
22 9 0.17
23 21 0.39
24 14 0.26
25 10 0.19
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAAAGAAAAAAG
Found at i:44648092 original size:22 final size:23
Alignment explanation
Indices: 44648048--44648094 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
44648038 GCATTTTTAT
*
44648048 ATTTTTATTTTTAATTTAATTCA
1 ATTTTTATTTTTAATATAATTCA
44648071 ATTTTTA-TTTTAA-ATAATTTCA
1 ATTTTTATTTTTAATATAA-TTCA
44648093 AT
1 AT
44648095 AAATAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
23 7 0.32
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTATTTTTAATATAATTCA
Found at i:44648483 original size:39 final size:39
Alignment explanation
Indices: 44648430--44648568 Score: 180
Period size: 39 Copynumber: 3.6 Consensus size: 39
44648420 CGTATTTTGA
*
44648430 AAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* *
44648469 AAA-TTTCTGTGTTTTCAAAAAAAA-TTTCTCGTCTTTCAA
1 AAATTTTC-GTGTTTTCAAAAAAAATTTTC-CGTGTTTCAT
**
44648508 AAATTTTCGTGTTTTC--AAAAAATTGACCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
44648545 AAATTTTCGTG-TTTCAAAAAAAAT
1 AAATTTTCGTGTTTTCAAAAAAAAT
44648569 CCTCGTGTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
36 4 0.05
37 25 0.29
38 17 0.20
39 37 0.43
40 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
Found at i:44648543 original size:37 final size:37
Alignment explanation
Indices: 44648364--44648579 Score: 171
Period size: 37 Copynumber: 5.8 Consensus size: 37
44648354 TTAAAAAAAA
*
44648364 TCGTG-TTT-AAAAAATTT-TCGTGTTTCAAAAAAATTCC
1 TCGTGTTTTCAAAAAATTTCTCGTGTTTC--AAAAATT-T
* **
44648401 TCGTGTTTTC-AAAAA-TTCTCGTATTTTGAAAATTT
1 TCGTGTTTTCAAAAAATTTCTCGTGTTTCAAAAATTT
* *
44648436 TCTTGTTTTCAAAAAAAATTT-TCCGTGTTTCATAAA-TT
1 TCGTGTTTTC--AAAAAATTTCT-CGTGTTTCAAAAATTT
*
44648474 TCTGTGTTTTCAAAAAAAATTTCTCGTCTTTCAAAAATTT
1 TC-GTGTTTTC--AAAAAATTTCTCGTGTTTCAAAAATTT
* *
44648514 TCGTGTTTTCAAAAAATTGAC-CGTGTTTCATAAATTT
1 TCGTGTTTTCAAAAAATT-TCTCGTGTTTCAAAAATTT
* *
44648551 TCGTG-TTTCAAAAAAAATCCTCGTGTTTC
1 TCGTGTTTTC-AAAAAATTTCTCGTGTTTC
44648580 GTATTTTATC
Statistics
Matches: 148, Mismatches: 17, Indels: 28
0.77 0.09 0.15
Matches are distributed among these distances:
35 9 0.06
36 11 0.07
37 49 0.33
38 26 0.18
39 48 0.32
40 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (37 bp):
TCGTGTTTTCAAAAAATTTCTCGTGTTTCAAAAATTT
Found at i:44648547 original size:76 final size:76
Alignment explanation
Indices: 44648411--44648568 Score: 214
Period size: 78 Copynumber: 2.1 Consensus size: 76
44648401 TCGTGTTTTC
** * **
44648411 AAAAA-TTCTCGTATTTTGAAAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCATAAA-TT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTC-AAAAAAATTGACCGTGTTTCATAAATTT
44648474 TCTGTGTTTTCAAA
65 TC-GTG-TTTCAAA
*
44648488 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AAAAAATTGACCGTGTTTCATAAATTTT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
44648552 CGTGTTTCAAA
66 CGTGTTTCAAA
44648563 AAAAAT
1 AAAAAT
44648569 CCTCGTGTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
75 13 0.18
76 25 0.34
77 9 0.12
78 26 0.36
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (76 bp):
AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
CGTGTTTCAAA
Found at i:44648651 original size:21 final size:21
Alignment explanation
Indices: 44648634--44648675 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
44648624 TTTAAAAATT
44648634 TTCGTG-TTTCAAAAAAAAAA
1 TTCGTGTTTTCAAAAAAAAAA
44648654 TTCGTGTTTTCAAAAAAGAAAA
1 TTCGTGTTTTCAAAAAA-AAAA
44648676 AGTTGTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (21 bp):
TTCGTGTTTTCAAAAAAAAAA
Found at i:44655721 original size:14 final size:14
Alignment explanation
Indices: 44655704--44655730 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44655694 CTTTTAAGAA
44655704 TTATATTTTTCAAT
1 TTATATTTTTCAAT
44655718 TTATATTTTTCAA
1 TTATATTTTTCAA
44655731 AAAAATCAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTATATTTTTCAAT
Found at i:44656092 original size:77 final size:76
Alignment explanation
Indices: 44655710--44656402 Score: 801
Period size: 77 Copynumber: 9.1 Consensus size: 76
44655700 AGAATTATAT
* * *
44655710 TTTTCAATTTATATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT--
1 TTTTCAATGTCTATTTTTC-AAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCG
* *
44655773 CATGCCGAGGTA
65 CACGCTGAGGTA
* * * ** *
44655785 TTTCTTTTAAATTTCTGTTTTT--TTAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
1 ----TTTTCAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGG
44655848 T--CACGCTGAGGTA
62 TCGCACGCTGAGGTA
* * * * **
44655861 TTTTTTTTAAAATTTCTATTTTT-TAAAAATCAACTCATAATGCGAGAACTGAGTTGAGCCTCGG
1 ----TTTT-CAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGG
44655925 GTCGCACGCTGAGGTA
61 GTCGCACGCTGAGGTA
* * * **
44655941 TTTTCAATGCCTGTTTTTCAAAAAATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCGGGTCAT
1 TTTTCAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGC
44656006 ACGCTGAGGTA
66 ACGCTGAGGTA
* *
44656017 TTCTCAATGTCTATTTTTCAAAAAAATTAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCG
1 TTTTCAATGTCTATTTTTC-AAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCG
*
44656082 CACGCAGAGGTA
65 CACGCTGAGGTA
* * * * *
44656094 TTCTCAATGTCTATTTTTCAAAAAAATTAACTCATAATCCGAGAGATGAGTTGAGCCTCAGGTCA
1 TTTTCAATGTCTATTTTTC-AAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCG
44656159 CACGCTGAGGTA
65 CACGCTGAGGTA
*
44656171 TTTTCAATGTCTATTTTTCAAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCGCGGGTC
1 TTTTCAATGTCTATTTTTC--AAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTC
44656236 GCACGCTGAGGTA
64 GCACGCTGAGGTA
* * * * *
44656249 TTTTCAATTTCTATTTTTC-AAAAATCAACTCATAATCCAATAGGTGAGTTGAGCCTAGGGTCAC
1 TTTTCAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGC
*
44656313 ACGTTGAGGTA
66 ACGCTGAGGTA
* * * * *
44656324 TTTTCAATTTCTATTTTTC-AAAGATCAACTCATAATTCGAGAGGTGGGTTGAGCCTCGAGTCGC
1 TTTTCAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGC
* *
44656388 ACACCGAGGTA
66 ACGCTGAGGTA
44656399 TTTT
1 TTTT
44656403 TAAATTTCAA
Statistics
Matches: 546, Mismatches: 61, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
75 128 0.23
76 127 0.23
77 156 0.29
78 108 0.20
79 15 0.03
80 12 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (76 bp):
TTTTCAATGTCTATTTTTCAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCGC
ACGCTGAGGTA
Found at i:44656131 original size:230 final size:225
Alignment explanation
Indices: 44655721--44656402 Score: 834
Period size: 230 Copynumber: 3.0 Consensus size: 225
44655711 TTTCAATTTA
* *
44655721 TATTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCAT--GCCGAGGT
1 TATTTTTCAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGT
* * ** *
44655784 ATTTCTTTTAAATTTCTGTTTTT-TTAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGG
66 A-TTC---TCAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGG
* * *
44655848 T-CACGCTGAGGTATTTTTTTTAAAATTTCTATTTTTTAAAAATCAACTCATAATGCGAGAACTG
127 TCCACGCTGAGGTA----TTTT-CAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGAA-TG
44655912 AGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATGCC
186 AGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTCAATGCC
* *
44655952 TGTTTTTC-AAAAAATCAACTCATAATTCGAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGT
1 TATTTTTCAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGT
* *
44656016 ATTCTCAATGTCTATTTTTCAAAAAAATTAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTC
66 ATTCTCAATTTCTATTTTTC--AAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTC
* * * *
44656081 GCACGCAGAGGTATTCTCAATGTCTATTTTTCAAAAAAATTAACTCATAATCCGAGAGATGAGTT
129 -CACGCTGAGGTATTTTCAATTTCTATTTTTC--AAAAATCAACTCATAATCCGAGA-ATGAGTT
* * *
44656146 GAGCCTCAGGTCACACGCTGAGGTATTTTCAATGTC
190 GAGCCTCGGGTCGCACGCTGAGGTATTTTCAATGCC
* **
44656182 TATTTTTCAAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCGCGGGTCGCACGCTGAGG
1 TATTTTTC-AAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGG
* * * *
44656247 TATTTTCAATTTCTATTTTTCAAAAATCAACTCATAATCCAATAGGTGAGTTGAGCCTAGGGTCA
65 TATTCTCAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTC-
* * * * *
44656312 CACGTTGAGGTATTTTCAATTTCTATTTTTCAAAGATCAACTCATAATTCGAGAGGTGGGTTGAG
129 CACGCTGAGGTATTTTCAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGA-ATGAGTTGAG
* * *
44656377 CCTCGAGTCGCACACCGAGGTATTTT
193 CCTCGGGTCGCACGCTGAGGTATTTT
44656403 TAAATTTCAA
Statistics
Matches: 393, Mismatches: 46, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
228 74 0.19
229 3 0.01
230 178 0.45
231 49 0.12
232 78 0.20
233 11 0.03
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (225 bp):
TATTTTTCAAAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCATACGCTGAGGT
ATTCTCAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGAGGTGAGTTGAGCCTCGGGTCCA
CGCTGAGGTATTTTCAATTTCTATTTTTCAAAAATCAACTCATAATCCGAGAATGAGTTGAGCCT
CGGGTCGCACGCTGAGGTATTTTCAATGCC
Found at i:44657019 original size:78 final size:79
Alignment explanation
Indices: 44656763--44657649 Score: 1000
Period size: 78 Copynumber: 11.6 Consensus size: 79
44656753 TTATTTTTTT
* * *
44656763 AAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACGCACGCTGAGGTA----TTTTAGA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44656824 TTTCTGTTTTTCAA
66 TTTCTGTTTTTCAA
* *
44656838 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCCGGT--CACGCTGAGGTA----TTTTAGA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44656897 TTTCTGTTTTTCAA
66 TTTCTGTTTTTCAA
*
44656911 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTGAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44656976 TTTCTG-TTTTCAA
66 TTTCTGTTTTTCAA
* *
44656989 ATATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA----TTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44657050 TTTCTGTTTTTCAAA
66 TTTCTGTTTTTC-AA
* * *
44657065 AAATCAACTTATATTGCGAGAGGTGAGTTGAGGCTCGGGTCGTACGCTGAGGTATTTTTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44657130 TTTCTG-TTTTCAA
66 TTTCTGTTTTTCAA
* * * *
44657143 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
* *
44657206 TTTATGATTTTCAA
66 TTTCTGTTTTTCAA
* * *
44657220 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT--CATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
*
44657283 TTTCTATTTTTCAA
66 TTTCTGTTTTTCAA
* * * * * * * *
44657297 AACTCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGAC-TATGCCGAGGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44657360 -TTCATGTTTTTCAA
66 TTTC-TGTTTTTCAA
* * * ** * *
44657374 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACATGCCCAAGTATTTCTTTTAAA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
44657438 TTTCTGTTTTTCAA
66 TTTCTGTTTTTCAA
* * * * *
44657452 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCATTGGGTCACATC-CTGAGGTA---TTTTTCA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCA-CGCTGAGGTATTTTTTTTAA
44657513 ATTTCTGTTTTTTCAAA
65 ATTTCTG-TTTTTC-AA
* * * ** *
44657530 AAATCAACTCATATTTCGAGAGGTGAGTTGAGCATCAGGTAACATC-CTGAGGTA---TTTTTCA
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCA-CGCTGAGGTATTTTTTTTAA
*
44657591 ATATCTAG-TTTTCAA
65 ATTTCT-GTTTTTCAA
* * *
44657606 AAATCAA--C-TATTACGATAGGTGAGTTAAGCCTCGGGTCGCACGC
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGC
44657650 CGAGCTGTTC
Statistics
Matches: 727, Mismatches: 60, Indels: 52
0.87 0.07 0.06
Matches are distributed among these distances:
72 1 0.00
73 99 0.14
74 13 0.02
75 54 0.07
76 101 0.14
77 192 0.26
78 223 0.31
79 31 0.04
80 13 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (79 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAA
TTTCTGTTTTTCAA
Found at i:44657105 original size:154 final size:153
Alignment explanation
Indices: 44656734--44657649 Score: 1031
Period size: 154 Copynumber: 6.0 Consensus size: 153
44656724 TCTCATATGT
*
44656734 CACGCTGAGGTA-TTTTAAATTAT-T-TTTTT---AAATCAACTCATATTGCGAGAAGTGAGTTG
1 CACGCTGAGGTATTTTTAAATT-TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* *
44656793 AGCCTCGGGACGCACGCTGAGGTA----TTTTAGATTTCTGTTTTTCAAAAATCAACTCATATTG
65 AGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCTG-TTTTCAAAAATCAACTCATATTG
*
44656854 CGAGAGGTGAGTTGAGCCTCCGGT-
129 CGAGAGGTGAGTTGAGCCTCGGGTC
*
44656878 CACGCTGAGGTA-TTTTAGATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 CACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* * *
44656942 GCCTCGGGTCGCACGCTGAGGTATTTTTTTTGAATTTCTGTTTTCAAATATCAACTCATATTGTG
66 GCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTGCG
44657007 AGAGGTGAGTTGAGCCTCGGGTC
131 AGAGGTGAGTTGAGCCTCGGGTC
*
44657030 GCACGCTGAGGTA-TTTTAAATTTCTGTTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTT
1 -CACGCTGAGGTATTTTTAAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTT
* *
44657094 GAGGCTCGGGTCGTACGCTGAGGTATTTTTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTG
64 GAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTG
*
44657159 CGAGAGGTGAGTTGAGCCTC-GGAC
129 CGAGAGGTGAGTTGAGCCTCGGGTC
* * * *
44657183 CATGCCGAGGTATTTCTTTTAAATTTATGATTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
1 CACGCTGAGGTA--T-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGT
* * * * * *
44657248 TGAGCCTCGGGT--CATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAACTCAACTTATAT
63 TGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCT-GTTTTCAAAAATCAACTCATAT
* *
44657311 TGCGAGAGGTGAGTTGAGCCT-TGGAC
127 TGCGAGAGGTGAGTTGAGCCTCGGGTC
* * *
44657337 TATGCCGAGGTATTTCTTTTAAA-TTCATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
1 CACGCTGAGGTA--T-TTTTAAATTTC-TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAG
* * * ** * *
44657401 TTGAGCCTC-GGACACATGCCCAAGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATA
62 TTGAGCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCTG-TTTTCAAAAATCAACTCATA
* * *
44657465 ATGCGAGAGGTGAGTTGAGCATTGGGTC
126 TTGCGAGAGGTGAGTTGAGCCTCGGGTC
* *
44657493 ACATC-CTGAGGTATTTTTCAATTTCTGTTTTTTCAAAAAATCAACTCATATTTCGAGAGGTGAG
1 -CA-CGCTGAGGTATTTTTAAATTTCTG-TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAG
* * ** * *
44657557 TTGAGCATCAGGTAACATC-CTGAGGTA---TTTTTCAATATCTAGTTTTCAAAAATCAA--C-T
62 TTGAGCCTCGGGTCGCA-CGCTGAGGTATTTTTTTTAAATTTCT-GTTTTCAAAAATCAACTCAT
* * *
44657615 ATTACGATAGGTGAGTTAAGCCTCGGGTC
125 ATTGCGAGAGGTGAGTTGAGCCTCGGGTC
44657644 GCACGC
1 -CACGC
44657650 CGAGCTGTTC
Statistics
Matches: 676, Mismatches: 64, Indels: 57
0.85 0.08 0.07
Matches are distributed among these distances:
143 1 0.00
144 21 0.03
145 5 0.01
148 52 0.08
150 1 0.00
151 71 0.11
152 22 0.03
153 61 0.09
154 253 0.37
155 115 0.17
156 56 0.08
157 18 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (153 bp):
CACGCTGAGGTATTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
GCCTCGGGTCGCACGCTGAGGTATTTTTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTGCG
AGAGGTGAGTTGAGCCTCGGGTC
Found at i:44657941 original size:30 final size:30
Alignment explanation
Indices: 44657853--44657970 Score: 134
Period size: 29 Copynumber: 4.0 Consensus size: 30
44657843 TTTATTTTTG
*
44657853 CATTTTGACCCCTAAACTTTCT-CAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
** * *
44657882 CATTTCAACCTCTAAACTTT-TATAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
44657911 CATTTTGACCCCTAAACTTTCTAAAAATTA
1 CATTTTGACCCCTAAACTTTCTAAAAATTA
* * *
44657941 CATTTGGACCCTTGAACTTTC-ACAAAATTA
1 CATTTTGACCCCTAAACTTTCTA-AAAATTA
44657971 TGTTTCGGCC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
28 1 0.01
29 41 0.55
30 33 0.44
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTCTAAAAATTA
Found at i:44658354 original size:10 final size:10
Alignment explanation
Indices: 44658315--44658381 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
44658305 CCAAGAGGCA
44658315 AAAAAAGAA-
1 AAAAAAGAAG
*
44658324 AAAAAACAAG
1 AAAAAAGAAG
*
44658334 CAAGCAAAAGAGG
1 -AA--AAAAGAAG
44658347 AAAAAAGAAAG
1 AAAAAAG-AAG
**
44658358 AGTAAAGAAG
1 AAAAAAGAAG
44658368 AAAAAAGAAG
1 AAAAAAGAAG
44658378 AAAA
1 AAAA
44658382 GAGAGGAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 8 0.18
10 20 0.44
11 9 0.20
12 2 0.04
13 6 0.13
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:44658505 original size:4 final size:4
Alignment explanation
Indices: 44658490--44658581 Score: 100
Period size: 4 Copynumber: 22.8 Consensus size: 4
44658480 AAAAGGGAAG
*
44658490 AAGA ATGA AAGA AAGA AAGA AAGA AAGA AAGA AAG- AAGA AAGA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
* *
44658537 AAAA GAAGAA AAGGA AAGA AA-A AAGA AA-A AAGAA AAAA AAGA AAG
1 AAGA -AAG-A AA-GA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAG
44658582 GAAAAAAATA
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
3 9 0.12
4 54 0.72
5 10 0.13
6 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:44658528 original size:27 final size:26
Alignment explanation
Indices: 44658497--44658581 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 26
44658487 AAGAAGAATG
44658497 AAAGAAAGAAAGAAAGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAAAGAAAGAA
44658523 AGAAGAAAGAAAG-AA-AAAG-AAGAA
1 A-AAGAAAGAAAGAAAGAAAGAAAGAA
*
44658547 AAGGAAAGAAA-AAAGAAA-AAAGAA
1 AAAGAAAGAAAGAAAGAAAGAAAGAA
44658571 AAA-AAAGAAAG
1 AAAGAAAGAAAG
44658582 GAAAAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
23 18 0.35
24 16 0.31
25 4 0.08
26 3 0.06
27 11 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (26 bp):
AAAGAAAGAAAGAAAGAAAGAAAGAA
Found at i:44658586 original size:27 final size:29
Alignment explanation
Indices: 44658498--44658588 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 29
44658488 AGAAGAATGA
*
44658498 AAGAAAGAAAGAAAGAAAGAAAGAAAGAAGA
1 AAGAAAG-AAGAAAGAAAGAAA-AAAGAAAA
44658529 AAGAAAGAA-AAAG-AAGAAAAGGAAAGAAAA
1 AAGAAAGAAGAAAGAAAG-AAA--AAAGAAAA
* *
44658559 AAGAAAAAAGAAA-AAA-AAGAAAGGAAAA
1 AAGAAAGAAGAAAGAAAGAA-AAAAGAAAA
44658587 AA
1 AA
44658589 ATATTCTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
28 12 0.23
29 9 0.17
30 19 0.37
31 12 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (29 bp):
AAGAAAGAAGAAAGAAAGAAAAAAGAAAA
Found at i:44658629 original size:10 final size:11
Alignment explanation
Indices: 44658614--44658642 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
44658604 TCGGGTTAAA
44658614 CCGACCCGAC-
1 CCGACCCGACT
44658624 CCGACCCGACT
1 CCGACCCGACT
44658635 CCGACCCG
1 CCGACCCG
44658643 TGACCGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.17, C:0.59, G:0.21, T:0.03
Consensus pattern (11 bp):
CCGACCCGACT
Found at i:44658893 original size:7 final size:7
Alignment explanation
Indices: 44658882--44658958 Score: 79
Period size: 7 Copynumber: 11.0 Consensus size: 7
44658872 ATAAAGAGAG
44658882 AAGAAAA
1 AAGAAAA
*
44658889 CAGAAAA
1 AAGAAAA
44658896 AAGAAAA
1 AAGAAAA
44658903 AGAGAAAAA
1 A-AG-AAAA
*
44658912 AAGGAAA
1 AAGAAAA
44658919 AAGAAAA
1 AAGAAAA
44658926 AAG--AA
1 AAGAAAA
44658931 AAG-AAA
1 AAGAAAA
*
44658937 AGGAAAA
1 AAGAAAA
44658944 AAGAGAAA
1 AAGA-AAA
44658952 AAGAAAA
1 AAGAAAA
44658959 GAAAAGGTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
5 5 0.08
6 4 0.07
7 34 0.58
8 11 0.19
9 5 0.08
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:44658903 original size:8 final size:8
Alignment explanation
Indices: 44658892--44658958 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 8
44658882 AAGAAAACAG
44658892 AAAAAAGA
1 AAAAAAGA
*
44658900 AAAAGAGA
1 AAAAAAGA
44658908 AAAAAAG-
1 AAAAAAGA
*
44658915 GAAAAAG-
1 AAAAAAGA
44658922 AAAAAAGAA
1 AAAAAAG-A
*
44658931 AAGAAAAGG
1 AA-AAAAGA
44658940 AAAAAAGA
1 AAAAAAGA
*
44658948 GAAAAAGA
1 AAAAAAGA
44658956 AAA
1 AAA
44658959 GAAAAGGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
7 12 0.25
8 27 0.56
9 4 0.08
10 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:44658908 original size:15 final size:15
Alignment explanation
Indices: 44658885--44658958 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 15
44658875 AAGAGAGAAG
*
44658885 AAAACAGAAAAAAGA
1 AAAAGAGAAAAAAGA
*
44658900 AAAAGAGAAAAAAAGG
1 AAAAGAG-AAAAAAGA
44658916 AAAA-AGAAAAAAG-
1 AAAAGAGAAAAAAGA
**
44658929 AAAAGA-AAAGGA-A
1 AAAAGAGAAAAAAGA
44658942 AAAAGAG-AAAAAGA
1 AAAAGAGAAAAAAGA
44658956 AAA
1 AAA
44658959 GAAAAGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
13 17 0.35
14 12 0.25
15 8 0.17
16 11 0.23
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAAAGA
Found at i:44658920 original size:18 final size:18
Alignment explanation
Indices: 44658899--44658953 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
44658889 CAGAAAAAAG
*
44658899 AAAAAGAGAAAAAA-AG-G
1 AAAAAG-GAAAAAAGAGAA
44658916 AAAAA-GAAAAAAGA-AA
1 AAAAAGGAAAAAAGAGAA
44658932 AGAAAAGGAAAAAAGAGAA
1 A-AAAAGGAAAAAAGAGAA
44658951 AAA
1 AAA
44658954 GAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 7 0.22
16 2 0.06
17 9 0.28
18 11 0.34
19 3 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAAGAGAA
Found at i:44658945 original size:20 final size:20
Alignment explanation
Indices: 44658894--44658963 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
44658884 GAAAACAGAA
44658894 AAAAGAAAAAGAGAA-AAAAAGG
1 AAAAGAAAAA-A-AAGAAAAA-G
*
44658916 AAAA-AGAAAAAAG-AAAAG
1 AAAAGAAAAAAAAGAAAAAG
*
44658934 AAAAGGAAAAAAGAGAAAAAG
1 AAAA-GAAAAAAAAGAAAAAG
44658955 AAAAGAAAA
1 AAAAGAAAA
44658964 GGTCAATTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
18 5 0.12
19 6 0.15
20 13 0.32
21 13 0.32
22 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAAAAG
Found at i:44658945 original size:26 final size:25
Alignment explanation
Indices: 44658882--44658965 Score: 111
Period size: 26 Copynumber: 3.4 Consensus size: 25
44658872 ATAAAGAGAG
*
44658882 AAGAAAACAGAAAAAAG-AAAAAGAGA
1 AAGAAAA-GGAAAAAAGAAAAAAGA-A
44658908 AA-AAAAGG-AAAAAGAAAAAAGAA
1 AAGAAAAGGAAAAAAGAAAAAAGAA
44658931 AAGAAAAGGAAAAAAGAGAAAAAGAA
1 AAGAAAAGGAAAAAAGA-AAAAAGAA
44658957 AAGAAAAGG
1 AAGAAAAGG
44658966 TCAATTTGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
23 9 0.17
24 14 0.26
25 11 0.21
26 19 0.36
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.00
Consensus pattern (25 bp):
AAGAAAAGGAAAAAAGAAAAAAGAA
Found at i:44659146 original size:22 final size:23
Alignment explanation
Indices: 44659102--44659148 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
44659092 GCATTTTTAT
*
44659102 ATTTTTATTTTTAATTTAATTCA
1 ATTTTTATTTTTAATATAATTCA
44659125 ATTTTTA-TTTTAA-ATAATTTCA
1 ATTTTTATTTTTAATATAA-TTCA
44659147 AT
1 AT
44659149 AAATAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.55
23 7 0.32
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTATTTTTAATATAATTCA
Found at i:44659296 original size:15 final size:16
Alignment explanation
Indices: 44659263--44659298 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
44659253 AAATATTCTA
44659263 AAATTCTCGTGATTTTT
1 AAATTCTCGTGA-TTTT
44659280 AAATTCTCGTG-TTTT
1 AAATTCTCGTGATTTT
44659295 AAAT
1 AAAT
44659299 AGAATCACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
17 11 0.58
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (16 bp):
AAATTCTCGTGATTTT
Found at i:44659523 original size:21 final size:21
Alignment explanation
Indices: 44659497--44659597 Score: 76
Period size: 21 Copynumber: 5.1 Consensus size: 21
44659487 TCGTATTTCG
44659497 AAAATTTTCTTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
*
44659518 AAAATTTTC-CGTGTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
44659536 TAAA-TTTCTGTGTTTTCAAAA
1 AAAATTTTCT-TGTTTTCAAAA
*
44659557 AAAA-TTTCTCGTCTTTC---A
1 AAAATTTTCTTGT-TTTCAAAA
*
44659575 AAAATTTTCGTGTTTTCAAAA
1 AAAATTTTCTTGTTTTCAAAA
44659596 AA
1 AA
44659598 TTGACCGTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.06
18 17 0.27
19 8 0.13
20 4 0.06
21 29 0.47
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.45
Consensus pattern (21 bp):
AAAATTTTCTTGTTTTCAAAA
Found at i:44659535 original size:56 final size:56
Alignment explanation
Indices: 44659414--44659558 Score: 150
Period size: 56 Copynumber: 2.6 Consensus size: 56
44659404 TAAAAAAAAT
* * *
44659414 CGTGTGTCAAAAATTTTCGTGTTTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
1 CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
** * **
44659470 CGTGTTTTCAAAAATTCTCGT-ATTTCGAAAATTTTCTTGTTTTCAAAAAAAATTTTC
1 CGTG-TTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTC-AAAAAAATTCCC
* *
44659527 CGTGTTTCATAAATT-TCTGTGTTTTCAAAAAA
1 CGTGTTTCAAAAATTCTC-GTGATTT-AAAAAA
44659559 AATTTCTCGT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
55 2 0.03
56 35 0.49
57 31 0.43
58 4 0.06
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.43
Consensus pattern (56 bp):
CGTGTTTCAAAAATTCTCGTGATTTAAAAAATTTTCATGTTTTCAAAAAAATTCCC
Found at i:44659551 original size:39 final size:39
Alignment explanation
Indices: 44659498--44659719 Score: 181
Period size: 39 Copynumber: 5.6 Consensus size: 39
44659488 CGTATTTCGA
*
44659498 AAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* *
44659537 AAA-TTTCTGTGTTTTCAAAAAAAA-TTTCTCGTCTTTCAA
1 AAATTTTC-GTGTTTTCAAAAAAAATTTTC-CGTGTTTCAT
**
44659576 AAATTTTCGTGTTTTC--AAAAAATTGACCGTGTTTCAT
1 AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
* * *
44659613 AAATTTTCGTG-TTTCAAAAAAAATCCTCGTGTTTCGTATTTTAT
1 AAATTTTCGTGTTTTCAAAAAAAA---T--T-TTCCGTGTTTCAT
** * *
44659657 CAATATTTTTATGTTTTCAAAAACAAATTTT--GTGTTTTAA
1 -AA-ATTTTCGTGTTTTCAAAAA-AAATTTTCCGTGTTTCAT
44659697 AAATTTTCGTG-TTTCAAAAAAAA
1 AAATTTTCGTGTTTTCAAAAAAAA
44659720 ATTCGTGTTA
Statistics
Matches: 149, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
36 7 0.05
37 34 0.23
38 23 0.15
39 39 0.26
40 11 0.07
41 1 0.01
42 2 0.01
43 2 0.01
44 8 0.05
45 3 0.02
46 7 0.05
47 9 0.06
48 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAAAAATTTTCCGTGTTTCAT
Found at i:44659585 original size:17 final size:17
Alignment explanation
Indices: 44659413--44659632 Score: 127
Period size: 18 Copynumber: 11.8 Consensus size: 17
44659403 TTAAAAAAAA
*
44659413 TCGTGTGTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
44659430 TCGTGTTTTAAAAAATTT
1 TCGTG-TTTCAAAAATTT
* *
44659448 TCATGTTTTCAAAAAAATTCC
1 TCGTG-TTTC--AAAAATT-T
* *
44659469 CCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
* *
44659487 TCGTATTTCGAAAATTT
1 TCGTGTTTCAAAAATTT
*
44659504 TCTTGTTTTCAAAAAAAATTT
1 TCGTG-TTTC---AAAAATTT
*
44659525 TCCGTGTTTCATAAA-TT
1 T-CGTGTTTCAAAAATTT
44659542 TCTGTGTTTTCAAAAAAAATTT
1 TC-GTG-TTTC---AAAAATTT
*
44659564 CTCGTCTTTCAAAAATTT
1 -TCGTGTTTCAAAAATTT
*
44659582 TCGTGTTTTCAAAAAATTGA
1 TCGTG-TTTC-AAAAATT-T
* *
44659602 CCGTGTTTCATAAATTT
1 TCGTGTTTCAAAAATTT
44659619 TCGTGTTTCAAAAA
1 TCGTGTTTCAAAAA
44659633 AAATCCTCGT
Statistics
Matches: 159, Mismatches: 25, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
16 1 0.01
17 40 0.25
18 52 0.33
19 18 0.11
20 11 0.07
21 28 0.18
22 7 0.04
23 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:44659615 original size:76 final size:76
Alignment explanation
Indices: 44659479--44659636 Score: 223
Period size: 78 Copynumber: 2.1 Consensus size: 76
44659469 CCGTGTTTTC
* * **
44659479 AAAAA-TTCTCGTATTTCGAAAATTTTCTTGTTTTCAAAAAAAATTTTCCGTGTTTCATAAA-TT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTC-AAAAAAATTGACCGTGTTTCATAAATTT
44659542 TCTGTGTTTTCAAA
65 TC-GTG-TTTCAAA
*
44659556 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC-AAAAAATTGACCGTGTTTCATAAATTTT
1 AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
44659620 CGTGTTTCAAA
66 CGTGTTTCAAA
44659631 AAAAAT
1 AAAAAT
44659637 CCTCGTGTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
75 13 0.18
76 25 0.34
77 9 0.12
78 27 0.36
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.43
Consensus pattern (76 bp):
AAAAATTTCTCGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTGACCGTGTTTCATAAATTTT
CGTGTTTCAAA
Found at i:44659644 original size:37 final size:38
Alignment explanation
Indices: 44659479--44659647 Score: 188
Period size: 39 Copynumber: 4.4 Consensus size: 38
44659469 CCGTGTTTTC
* *
44659479 AAAAATTCTCGTATTTCGA-AAATTTTCTTGTTTTCAAA
1 AAAAATTCTCGTGTTTC-ATAAATTTTCGTGTTTTCAAA
*
44659517 AAAAATTTTCCGTGTTTCATAAA-TTTCTGTGTTTTCAAA
1 AAAAATTCT-CGTGTTTCATAAATTTTC-GTGTTTTCAAA
* *
44659556 AAAAATTTCTCGTCTTTCAAAAATTTTCGTGTTTTC--A
1 AAAAA-TTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
44659593 AAAAATTGAC-CGTGTTTCATAAATTTTCGTG-TTTCAAA
1 AAAAATT--CTCGTGTTTCATAAATTTTCGTGTTTTCAAA
*
44659631 AAAAATCCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
44659648 GTATTTTATC
Statistics
Matches: 112, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
36 7 0.06
37 33 0.29
38 21 0.19
39 44 0.39
40 7 0.06
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (38 bp):
AAAAATTCTCGTGTTTCATAAATTTTCGTGTTTTCAAA
Found at i:44659702 original size:16 final size:17
Alignment explanation
Indices: 44659681--44659716 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
44659671 TTTCAAAAAC
*
44659681 AAATTTT-GTGTTTTAA
1 AAATTTTCGTGTTTCAA
44659697 AAATTTTCGTGTTTCAA
1 AAATTTTCGTGTTTCAA
44659714 AAA
1 AAA
44659717 AAAATTCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (17 bp):
AAATTTTCGTGTTTCAA
Found at i:44662649 original size:30 final size:29
Alignment explanation
Indices: 44662607--44662719 Score: 156
Period size: 30 Copynumber: 3.9 Consensus size: 29
44662597 NNAAATTAAA
* *
44662607 TTAGGGTTAGGGTTTTTAATTTAATTAGG
1 TTAGGTTTAGGGTTTTTAATTAAATTAGG
44662636 TTATGGTTTAGGGTTTTTAATTAAATTAGG
1 TTA-GGTTTAGGGTTTTTAATTAAATTAGG
**
44662666 TTAGGGTTTAGGGTTTTTAATTAAATTAAA
1 TTA-GGTTTAGGGTTTTTAATTAAATTAGG
*
44662696 TTAGG-TTAGGGTTTTTAATCAAAT
1 TTAGGTTTAGGGTTTTTAATTAAAT
44662720 AATATCAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.23
29 5 0.06
30 54 0.70
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.48
Consensus pattern (29 bp):
TTAGGTTTAGGGTTTTTAATTAAATTAGG
Found at i:44663031 original size:24 final size:24
Alignment explanation
Indices: 44662999--44663054 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
44662989 TGTATGTAGA
44662999 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
*
44663023 GGTGTTTGCATCATGAACGGCGAG
1 GGTGTTTGCATCATGAACGGCGAC
*
44663047 GGAGTTTG
1 GGTGTTTG
44663055 GAAGCCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.27
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGGCGAC
Found at i:44667276 original size:15 final size:15
Alignment explanation
Indices: 44667252--44667287 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
44667242 ATTATAAAGG
44667252 AAGA-AAGAAAAAAA
1 AAGAGAAGAAAAAAA
44667266 AAGAGAAGAAAAAAA
1 AAGAGAAGAAAAAAA
*
44667281 GAGAGAA
1 AAGAGAA
44667288 ATAATGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAGAAGAAAAAAA
Found at i:44670926 original size:21 final size:21
Alignment explanation
Indices: 44670897--44670936 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44670887 TAATGTCATA
44670897 TCAGCATTTTCATCTTGAATT
1 TCAGCATTTTCATCTTGAATT
* *
44670918 TCAGTATTTTCATTTTGAA
1 TCAGCATTTTCATCTTGAA
44670937 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (21 bp):
TCAGCATTTTCATCTTGAATT
Found at i:44674617 original size:3 final size:3
Alignment explanation
Indices: 44674609--44674658 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
44674599 GTAACAACTT
*
44674609 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
44674657 TA
1 TA
44674659 TATTGTTATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:44675130 original size:24 final size:24
Alignment explanation
Indices: 44675103--44675154 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44675093 AATCAAATTC
* *
44675103 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
44675127 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
44675151 AAAT
1 AAAT
44675155 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:44679512 original size:24 final size:24
Alignment explanation
Indices: 44679485--44679531 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44679475 AAACCTAATT
44679485 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
44679509 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
44679532 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:44679547 original size:24 final size:24
Alignment explanation
Indices: 44679497--44679548 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
44679487 AATCAAAGTA
* **
44679497 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
44679521 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
44679545 AAAT
1 AAAT
44679549 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:44692041 original size:25 final size:25
Alignment explanation
Indices: 44692007--44692056 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
44691997 AAATGAACTG
*
44692007 TTGAACAATTTGTTCGATCTTTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
44692032 TTGAACAATTTGTTCGATCTCTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
44692057 CAAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TTGAACAATTTGTTCGATCTCTGCA
Found at i:44693532 original size:4 final size:4
Alignment explanation
Indices: 44693523--44693550 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
44693513 TGAAAGAAGC
44693523 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA
44693551 GTTTGCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:44697246 original size:19 final size:19
Alignment explanation
Indices: 44697222--44697259 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44697212 TCTAGTTTCA
44697222 GATAAAATTTACAGATCTT
1 GATAAAATTTACAGATCTT
*
44697241 GATAAAATTTACGGATCTT
1 GATAAAATTTACAGATCTT
44697260 AATTTGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (19 bp):
GATAAAATTTACAGATCTT
Found at i:44716402 original size:9 final size:9
Alignment explanation
Indices: 44716388--44716427 Score: 71
Period size: 9 Copynumber: 4.4 Consensus size: 9
44716378 GTTAAACAAA
44716388 TCGAGTTAT
1 TCGAGTTAT
44716397 TCGAGTTAT
1 TCGAGTTAT
*
44716406 TCGAGTTAA
1 TCGAGTTAT
44716415 TCGAGTTAT
1 TCGAGTTAT
44716424 TCGA
1 TCGA
44716428 ATCAACTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:44716498 original size:9 final size:9
Alignment explanation
Indices: 44716481--44716517 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44716471 TGAGTTTTCG
44716481 AATTCGAAT
1 AATTCGAAT
*
44716490 AACTCGAAT
1 AATTCGAAT
44716499 AATTCGAAT
1 AATTCGAAT
44716508 AATTCGAAT
1 AATTCGAAT
44716517 A
1 A
44716518 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:44717532 original size:5 final size:5
Alignment explanation
Indices: 44717522--44717547 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44717512 CTCGAAAATT
44717522 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
44717548 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:44722988 original size:3 final size:3
Alignment explanation
Indices: 44722980--44723013 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
44722970 TTAATAACAG
44722980 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
44723014 CAGACCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44723098 original size:3 final size:3
Alignment explanation
Indices: 44723092--44723152 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
44723082 ATTTTTTTGC
44723092 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
44723140 TCT TCT TCT TCT T
1 TCT TCT TCT TCT T
44723153 GACTCTCTTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:44723705 original size:3 final size:3
Alignment explanation
Indices: 44723671--44723743 Score: 69
Period size: 3 Copynumber: 24.7 Consensus size: 3
44723661 CATCTCCATT
* * *
44723671 TTC TCTC TTC TCC TTC TTA TTC TTC TTT TTC TTC TTC TTC TTC -TC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
44723716 CTC TTC TTT TTC TTC TTT TTC -TC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44723744 AAACCCTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:44723728 original size:20 final size:20
Alignment explanation
Indices: 44723671--44723743 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
44723661 CATCTCCATT
* *
44723671 TTCT-CTCTTCTCCTTCTTA
1 TTCTCCTCTTCTTCTTCTTC
* *
44723690 TTCTTCTTTTTCTTCTTCTTC
1 TTC-TCCTCTTCTTCTTCTTC
*
44723711 TTCTCCTCTTCTTTTTCTTC
1 TTCTCCTCTTCTTCTTCTTC
* *
44723731 TTTTTCTCTTCTT
1 TTCTCCTCTTCTT
44723744 AAACCCTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
19 3 0.07
20 26 0.60
21 14 0.33
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCCTCTTCTTCTTCTTC
Found at i:44725110 original size:18 final size:16
Alignment explanation
Indices: 44725068--44725110 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
44725058 TGTCGTTCGT
44725068 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
44725085 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
44725104 TTTCAAA
1 TTTCAAA
44725111 ACCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:44728818 original size:21 final size:22
Alignment explanation
Indices: 44728783--44728830 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
44728773 CAACACACCT
44728783 GTGTGGAAGGAGGCACACGACA
1 GTGTGGAAGGAGGCACACGACA
* *
44728805 GTGTGG-ATGAGGCACACGCCA
1 GTGTGGAAGGAGGCACACGACA
44728826 GTGTG
1 GTGTG
44728831 TGCCAGGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.25, C:0.19, G:0.42, T:0.15
Consensus pattern (22 bp):
GTGTGGAAGGAGGCACACGACA
Found at i:44730610 original size:31 final size:31
Alignment explanation
Indices: 44730575--44730633 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
44730565 ACGTGTATAA
44730575 TTAAATTAAAATTAAAATTTTATATATACAC
1 TTAAATTAAAATTAAAATTTTATATATACAC
* *
44730606 TTAAATTATAATTAAAGTTTTATATATA
1 TTAAATTAAAATTAAAATTTTATATATA
44730634 ATTACACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTAAATTAAAATTAAAATTTTATATATACAC
Found at i:44731654 original size:17 final size:17
Alignment explanation
Indices: 44731616--44731653 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
44731606 GTGGGAGTCG
*
44731616 ATTTTAGAATAATTCTT
1 ATTTTAGAATAATTATT
*
44731633 ATTTTAGCATAATTATT
1 ATTTTAGAATAATTATT
44731650 -TTTT
1 ATTTT
44731654 TTCCACTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTTAGAATAATTATT
Found at i:44736254 original size:80 final size:81
Alignment explanation
Indices: 44736152--44736312 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 81
44736142 TATATGTAAA
44736152 GCAAGCTTCAAAGATTCAAAATCTATACAAAAAAATTGAAAAAAATTTATACGTTAAGCTTGAAA
1 GCAAGCTTCAAAGATTCAAAATCTATACAAAAAAATTGAAAAAAATTTATACGTTAAGCTTGAAA
44736217 TCAAAGGAAAATGATG
66 TCAAAGGAAAATGATG
44736233 GCAAGCTTC-AAGATTCAAAATCTATACAAAAAAATTGAAAAAAATTTATACGTTAAGCTTGAAA
1 GCAAGCTTCAAAGATTCAAAATCTATACAAAAAAATTGAAAAAAATTTATACGTTAAGCTTGAAA
44736297 TCAAAGGAAAATGATG
66 TCAAAGGAAAATGATG
44736313 AAAGGGGTTT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 71 0.89
81 9 0.11
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.25
Consensus pattern (81 bp):
GCAAGCTTCAAAGATTCAAAATCTATACAAAAAAATTGAAAAAAATTTATACGTTAAGCTTGAAA
TCAAAGGAAAATGATG
Found at i:44750407 original size:3 final size:3
Alignment explanation
Indices: 44750399--44750424 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44750389 TTATGTGAAT
44750399 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
44750425 TTGTTCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44752478 original size:2 final size:2
Alignment explanation
Indices: 44752473--44752503 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44752463 CCCCCCCCCA
44752473 AG AG 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 AG AG A
44752504 CCTTTTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44759077 original size:30 final size:30
Alignment explanation
Indices: 44759043--44759256 Score: 224
Period size: 30 Copynumber: 7.9 Consensus size: 30
44759033 ACAAATCCTA
44759043 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
44759073 TCTCAATTTCCTTCCAAAA-----TC---C
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
*
44759095 TCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
44759125 TCTCAATTTCCTTCCAAAA-----TC---C
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
*
44759147 TCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
44759177 TCTCAATTTCCTTCCAAAA-----TC---C
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
*
44759199 TCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATTCTCTCAAAC
*
44759229 TCTCAATTTCCTTCCAAAATCCTCTCAA
1 TCTCAATTTCCTTCCAAAATTCTCTCAA
44759257 TTTCCTTCCA
Statistics
Matches: 153, Mismatches: 7, Indels: 48
0.74 0.03 0.23
Matches are distributed among these distances:
22 60 0.39
25 4 0.03
27 3 0.02
30 86 0.56
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (30 bp):
TCTCAATTTCCTTCCAAAATTCTCTCAAAC
Found at i:44759097 original size:22 final size:22
Alignment explanation
Indices: 44759072--44759119 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
44759062 TTCTCTCAAA
44759072 CTCTCAATTTCCTTCCAAAATC
1 CTCTCAATTTCCTTCCAAAATC
*
44759094 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATC
44759116 CTCT
1 CTCT
44759120 TAAACTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATC
Found at i:44759105 original size:52 final size:52
Alignment explanation
Indices: 44759043--44759275 Score: 448
Period size: 52 Copynumber: 4.5 Consensus size: 52
44759033 ACAAATCCTA
*
44759043 TCTCAATTTCCTTCCAAAATTCTCTCAAACTCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
44759095 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
44759147 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
44759199 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
*
44759251 TCTCAATTTCCTTCCAAAAATCTCT
1 TCTCAATTTCCTTCCAAAATTCTCT
44759276 CAAATCCATA
Statistics
Matches: 179, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 179 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATTCTCTTAAACTCTCAATTTCCTTCCAAAATCC
Found at i:44759152 original size:22 final size:22
Alignment explanation
Indices: 44759124--44759171 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
44759114 TTCTCTTAAA
44759124 CTCTCAATTTCCTTCCAAAATC
1 CTCTCAATTTCCTTCCAAAATC
*
44759146 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATC
44759168 CTCT
1 CTCT
44759172 TAAACTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATC
Found at i:44759204 original size:22 final size:22
Alignment explanation
Indices: 44759176--44759223 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
44759166 TTCTCTTAAA
44759176 CTCTCAATTTCCTTCCAAAATC
1 CTCTCAATTTCCTTCCAAAATC
*
44759198 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATC
44759220 CTCT
1 CTCT
44759224 TAAACTCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.35, G:0.00, T:0.40
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATC
Found at i:44759256 original size:22 final size:22
Alignment explanation
Indices: 44759228--44759278 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
44759218 TTCTCTTAAA
44759228 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCCTTCCAAAAAT
44759249 CCTCTCAATTTCCTTCCAAAAAT
1 -CTCTCAATTTCCTTCCAAAAAT
44759272 CTCTCAA
1 CTCTCAA
44759279 ATCCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAAAT
Found at i:44759349 original size:30 final size:29
Alignment explanation
Indices: 44759313--44759376 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
44759303 CTCAATTTCA
*
44759313 TTTTTTAAAATAATTTTAAATTTTTTATAT
1 TTTTTTAAAAT-AGTTTAAATTTTTTATAT
*
44759343 TTTTTTAAAATAGTTTAAATTTTTTTTAT
1 TTTTTTAAAATAGTTTAAATTTTTTATAT
*
44759372 ATTTT
1 TTTTT
44759377 CATCAATGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTTTAAAATAGTTTAAATTTTTTATAT
Found at i:44759353 original size:20 final size:19
Alignment explanation
Indices: 44759326--44759368 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
44759316 TTTAAAATAA
** *
44759326 TTTTAAATTTTTTATATTT
1 TTTTAAATAGTTTAAATTT
44759345 TTTTAAAATAGTTTAAATTT
1 TTTT-AAATAGTTTAAATTT
44759365 TTTT
1 TTTT
44759369 TATATTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAAATAGTTTAAATTT
Found at i:44762586 original size:273 final size:273
Alignment explanation
Indices: 44762099--44762643 Score: 991
Period size: 273 Copynumber: 2.0 Consensus size: 273
44762089 TTTACCAATC
*
44762099 GCCAGCAACGCATGGCTTTCAAACATCGTCGCCGTTCATGATGCAAACACCTCCACATACACTAT
1 GCCAGCAACGCATGGCTTTCAAACACCGTCGCCGTTCATGATGCAAACACCTCCACATACACTAT
* * *
44762164 TCTTTGAAGGTGGATCATCGTCCCAAGTCCGACAACCAGATGCCAAACTGGAAGAACAACAATCA
66 TCTTTGAAGGTGGATCATCGTCCCAAGTCCGACAACCAGATGACAAACCGAAAGAACAACAATCA
44762229 GCACCGGAGGAAGAACAACCGCCGCCTGAAGCTAGAGGAAGGAGGAATCCAGCGCGTAACCGTCG
131 GCACCGGAGGAAGAACAACCGCCGCCTGAAGCTAGAGGAAGGAGGAATCCAGCGCGTAACCGTCG
*
44762294 ACGGCTGCCATGTGGAACCGAATCCCCCGGGCATAGACATTGATTACCGTATTAAAATTTATTAT
196 ACGGCCGCCATGTGGAACCGAATCCCCCGGGCATAGACATTGATTACCGTATTAAAATTTATTAT
44762359 TTTATGTAATGAT
261 TTTATGTAATGAT
* *
44762372 GCCAGCAACGCATTGCTTTCAAACACCGTCGCTGTTCATGATGCAAACACCTCCACATACACTAT
1 GCCAGCAACGCATGGCTTTCAAACACCGTCGCCGTTCATGATGCAAACACCTCCACATACACTAT
* *
44762437 TCTTTGAAGGTGGATCATCGTCCCAAGTCCGACAACCAGATGACGAACCGAAAGAACAATAATCA
66 TCTTTGAAGGTGGATCATCGTCCCAAGTCCGACAACCAGATGACAAACCGAAAGAACAACAATCA
44762502 GCACCGGAGGAAGAACAACCGCCGCCTGAAGCTAGAGGAAGGAGGAATCCAGCGCGTAACCGTCG
131 GCACCGGAGGAAGAACAACCGCCGCCTGAAGCTAGAGGAAGGAGGAATCCAGCGCGTAACCGTCG
* *
44762567 ACTGCCGCCATGTGGAACCGAATCCCTCGGGCATAGACATTGATTACCGTATTAAAATTTATTAT
196 ACGGCCGCCATGTGGAACCGAATCCCCCGGGCATAGACATTGATTACCGTATTAAAATTTATTAT
44762632 TTTATGTAATGA
261 TTTATGTAATGA
44762644 AATAGAAGTT
Statistics
Matches: 261, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
273 261 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (273 bp):
GCCAGCAACGCATGGCTTTCAAACACCGTCGCCGTTCATGATGCAAACACCTCCACATACACTAT
TCTTTGAAGGTGGATCATCGTCCCAAGTCCGACAACCAGATGACAAACCGAAAGAACAACAATCA
GCACCGGAGGAAGAACAACCGCCGCCTGAAGCTAGAGGAAGGAGGAATCCAGCGCGTAACCGTCG
ACGGCCGCCATGTGGAACCGAATCCCCCGGGCATAGACATTGATTACCGTATTAAAATTTATTAT
TTTATGTAATGAT
Found at i:44762796 original size:23 final size:23
Alignment explanation
Indices: 44762765--44763012 Score: 186
Period size: 23 Copynumber: 10.4 Consensus size: 23
44762755 TAAAAACCCT
*
44762765 AAACACTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
44762788 AAACCCTAACCCTAACCTAACTTAATTAA
1 AAACCCTAA-CCTAA--T---TTAATTAA
** * * *
44762817 AAACCAAAAACTCTAAACCTAAACTAAA
1 AAACC-CTAAC-CT-AA-TTTAA-TTAA
* **
44762845 AAACTCTAATTTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
*
44762868 AAACCCTAAACCCTAA---ACTTAA
1 AAACCCT-AA-CCTAATTTAATTAA
*
44762890 AAACCCTAACCTAATTAAATTAA
1 AAACCCTAACCTAATTTAATTAA
44762913 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
*
44762936 AAACCCTAAACTCTAA---ACTTAA
1 AAACCCT-AAC-CTAATTTAATTAA
44762958 AAACCCTAACCTAA-TTAACTTAA
1 AAACCCTAACCTAATTTAA-TTAA
*
44762981 AAACCCTAACCTAATTAAATTAA
1 AAACCCTAACCTAATTTAATTAA
44763004 AAACCCTAA
1 AAACCCTAA
44763013 ACTTAAAAAC
Statistics
Matches: 181, Mismatches: 23, Indels: 42
0.74 0.09 0.17
Matches are distributed among these distances:
20 9 0.05
21 5 0.03
22 25 0.14
23 82 0.45
24 16 0.09
25 9 0.05
26 2 0.01
27 5 0.03
28 7 0.04
29 14 0.08
30 5 0.03
31 2 0.01
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (23 bp):
AAACCCTAACCTAATTTAATTAA
Found at i:44762803 original size:29 final size:30
Alignment explanation
Indices: 44762744--44762821 Score: 131
Period size: 29 Copynumber: 2.6 Consensus size: 30
44762734 TAATAAAAAT
44762744 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCTAAACACTAA
*
44762774 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACACTAA
*
44762803 CCTAACTTAATTAAAAACC
1 CCTAATTTAATTAAAAACC
44762822 AAAAACTCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 25 0.54
30 21 0.46
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (30 bp):
CCTAATTTAATTAAAAACCCTAAACACTAA
Found at i:44762871 original size:44 final size:44
Alignment explanation
Indices: 44762822--44763062 Score: 205
Period size: 45 Copynumber: 5.5 Consensus size: 44
44762812 ATTAAAAACC
* * ** *
44762822 AAAAACTCTAAACCTAAACTAAAAAACTCTAATTTAATTTAATT
1 AAAAACCCTAAACCTAAACTAAAAAACCCTAACCTAATTAAATT
*
44762866 AAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAAA-CCTAAACTAAAAAACCCTAACCTAATTAAATT
* * * *
44762911 AAAAACCCT-AACCTAATTTAATTAAAAACCCTAAACT--CTAAACTT
1 AAAAACCCTAAACCTAA---ACTAAAAAACCCTAACCTAATTAAA-TT
*
44762956 AAAAACCCT-AACCTAATTAACTTAAAAACCCTAACCTAATTAAATT
1 AAAAACCCTAAACCT-A--AACTAAAAAACCCTAACCTAATTAAATT
* *
44763002 AAAAACCCTAAA-CT----T-AAAAACTCTAACCTAATTTAATT
1 AAAAACCCTAAACCTAAACTAAAAAACCCTAACCTAATTAAATT
*
44763040 AAAAACCCTAAACACTAAGCTAA
1 AAAAACCCTAAAC-CTAAACTAA
44763063 TTTAATTAAA
Statistics
Matches: 165, Mismatches: 14, Indels: 35
0.77 0.07 0.16
Matches are distributed among these distances:
38 33 0.20
39 1 0.01
40 2 0.01
43 5 0.03
44 18 0.11
45 69 0.42
46 30 0.18
47 6 0.04
48 1 0.01
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (44 bp):
AAAAACCCTAAACCTAAACTAAAAAACCCTAACCTAATTAAATT
Found at i:44762937 original size:68 final size:68
Alignment explanation
Indices: 44762856--44763050 Score: 296
Period size: 68 Copynumber: 3.0 Consensus size: 68
44762846 AACTCTAATT
44762856 TAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
1 TAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
44762921 ACC
66 ACC
* *
44762924 TAATTTAATTAAAAACCCTAAACTCTAAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTA
1 TAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
44762989 ACC
66 ACC
* * *
44762992 TAATTAAATT---AA----AAACCCTAAACTTAAAAACTCTAACCTAATTTAATTAAAAACCCTA
1 TAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
44763050 A
66 A
44763051 ACACTAAGCT
Statistics
Matches: 120, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
61 43 0.36
65 2 0.02
68 75 0.62
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (68 bp):
TAATTTAATTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTA
ACC
Found at i:44763102 original size:22 final size:23
Alignment explanation
Indices: 44763060--44763246 Score: 88
Period size: 29 Copynumber: 6.9 Consensus size: 23
44763050 AACACTAAGC
*
44763060 TAATTTAATTAAAAACTCTAACT
1 TAATTTAATTAAAAACCCTAACT
44763083 TAATTTAATT-AAAACCCTAACCCT
1 TAATTTAATTAAAAACCCTAA--CT
44763107 ACCCTAATTTAATTAAAAACCCTAACCCT
1 ----TAATTTAATTAAAAACCCTAA--CT
44763136 AACCTAATTTAATTAAAAACCTTAAACCCTAACT
1 ----TAATTTAATT---AA----AAACCCTAACT
*
44763170 TAATTTAATTAAAAACCCTAACAACC
1 TAATTTAATTAAAAACCCT---AACT
44763196 TAATTTAATTAAAAACCTTAAACCTTAACT
1 TAATTTAATTAAAAA-C-----CC-TAACT
44763226 TAATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
44763247 ACCCTAACCT
Statistics
Matches: 136, Mismatches: 4, Indels: 48
0.72 0.02 0.26
Matches are distributed among these distances:
22 9 0.07
23 20 0.15
24 4 0.03
26 18 0.13
27 3 0.02
28 10 0.07
29 28 0.21
30 28 0.21
32 4 0.03
33 1 0.01
34 2 0.01
36 9 0.07
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACT
Found at i:44763135 original size:29 final size:29
Alignment explanation
Indices: 44763024--44763348 Score: 445
Period size: 30 Copynumber: 11.4 Consensus size: 29
44763014 CTTAAAAACT
*
44763024 CTAACCTAATTTAATTAAAAACCCTAAACA
1 CTAACCTAATTTAATTAAAAACCCT-AACC
*
44763054 CTAAGCTAATTTAATTAAAAA--CT----
1 CTAACCTAATTTAATTAAAAACCCTAACC
*
44763077 CTAACTTAATTTAATT-AAAACCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACC
*
44763105 CTACCCTAATTTAATTAAAAACCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACC
*
44763134 CTAACCTAATTTAATTAAAAACCTTAAACC
1 CTAACCTAATTTAATTAAAAACCCT-AACC
*
44763164 CTAACTTAATTTAATTAAAAACCCTAA--
1 CTAACCTAATTTAATTAAAAACCCTAACC
*
44763191 C-AACCTAATTTAATTAAAAACCTTAAACC
1 CTAACCTAATTTAATTAAAAACCCT-AACC
* *
44763220 TTAACTTAATTTAATTAAAAACCCTAAACC
1 CTAACCTAATTTAATTAAAAACCCT-AACC
44763250 CTAACCTAATTTAATTAAAAACCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACC
*
44763279 CTAACCTAATTTATTTAAAAACCCTAAACC
1 CTAACCTAATTTAATTAAAAACCCT-AACC
44763309 CTAACCTAATTTAATTAAAAACCCTAACC
1 CTAACCTAATTTAATTAAAAACCCTAACC
44763338 CTAACCTAATT
1 CTAACCTAATT
44763349 NNNNNNNNNN
Statistics
Matches: 264, Mismatches: 18, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.02
23 14 0.05
24 2 0.01
26 21 0.08
27 3 0.01
28 16 0.06
29 80 0.30
30 124 0.47
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (29 bp):
CTAACCTAATTTAATTAAAAACCCTAACC
Found at i:44763278 original size:145 final size:137
Alignment explanation
Indices: 44762982--44763348 Score: 475
Period size: 145 Copynumber: 2.5 Consensus size: 137
44762972 TTAACTTAAA
*
44762982 AACCCTAACCTAATTAAATTAAAAACCCTAAACTTAAAAACTCTAACCTAATTTAATTAAAAACC
1 AACCCTAACCTAATTTAATTAAAAACCCTAAAC-------C-CTAACCTAATTTAATTAAAAACC
* *
44763047 CTAAACACTAAGCTAATTTAATTAAAAACTCTAACTTAATTTAATTAAAACCCTAACCCTACCCT
58 CT--A-ACTAACCTAATTTAATTAAAAACTCTAACTTAATTTAATTAAAACCCTAACCCTAACCT
44763112 AATTTAATTAAAAACCCT
120 AATTTAATTAAAAACCCT
* *
44763130 AACCCTAACCTAATTTAATTAAAAACCTTAAACCCTAACTTAATTTAATTAAAAACCCTAAC-AA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACTAA
44763194 CCTAATTTAATTAAAAACCTTAAACCTTAACTTAATTTAATTAAAAACCCTAAACCCTAACCTAA
66 CCTAATTTAATTAAAAA-C-T----C-TAACTTAATTTAATT-AAAACCCT-AACCCTAACCTAA
44763259 TTTAATTAAAAACCCT
122 TTTAATTAAAAACCCT
*
44763275 AACCCTAACCTAATTTATTTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAA--CT
44763340 AACCTAATT
64 AACCTAATT
44763349 NNNNNNNNNN
Statistics
Matches: 199, Mismatches: 8, Indels: 24
0.86 0.03 0.10
Matches are distributed among these distances:
136 18 0.09
137 3 0.02
138 2 0.01
140 24 0.12
141 1 0.01
142 1 0.01
143 15 0.08
144 8 0.04
145 86 0.43
147 1 0.01
148 40 0.20
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (137 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACTAA
CCTAATTTAATTAAAAACTCTAACTTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAA
AAACCCT
Found at i:44775104 original size:18 final size:20
Alignment explanation
Indices: 44775069--44775106 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
44775059 GAAAAATATT
*
44775069 AAATATATATATTATTTTTA
1 AAATATATATAGTATTTTTA
44775089 AAATATA-ATAGT-TTTTTA
1 AAATATATATAGTATTTTTA
44775107 TTTTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATATATATAGTATTTTTA
Found at i:44776601 original size:51 final size:51
Alignment explanation
Indices: 44776542--44776661 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 51
44776532 TTTTCTCTAG
**
44776542 TTAATTTAAATTAATTAAAAGATTGATAATAAAAAATTATATCATCACTAA
1 TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
* * *
44776593 TTAATTTAAACTGATTAAAAGATAAATAATAAAAAATTATATTATCACTAA
1 TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
* * *
44776644 ATAAATTAAATTATTTAA
1 TTAATTTAAATTAATTAA
44776662 GTGATAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (51 bp):
TTAATTTAAATTAATTAAAAGATAAATAATAAAAAATTATATCATCACTAA
Found at i:44777621 original size:13 final size:12
Alignment explanation
Indices: 44777605--44777638 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
44777595 ATTTAGATTT
44777605 TAAAAATAGAAAA
1 TAAAAATA-AAAA
44777618 TAAAAATAAAAA
1 TAAAAATAAAAA
44777630 TAAAGAATA
1 TAAA-AATA
44777639 TAATTGCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:44777628 original size:5 final size:6
Alignment explanation
Indices: 44777605--44777638 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
44777595 ATTTAGATTT
44777605 TAAAAA TAGAAAA TAAAAA TAAAAA TAAAGAA TA
1 TAAAAA TA-AAAA TAAAAA TAAAAA TAAA-AA TA
44777639 TAATTGCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:44781898 original size:3 final size:3
Alignment explanation
Indices: 44781892--44781917 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44781882 CCTTCTTCCC
44781892 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
44781918 ACTCTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:44784830 original size:17 final size:17
Alignment explanation
Indices: 44784784--44784833 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
44784774 TCTCAAATTT
* *
44784784 TGATACCCATATATTTT
1 TGATACCCATATCTTTC
*
44784801 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
44784818 TGATACCCATATCTTT
1 TGATACCCATATCTTT
44784834 GACTTTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.06, T:0.46
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:44793940 original size:22 final size:24
Alignment explanation
Indices: 44793896--44793942 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
44793886 AAAAAACTAG
44793896 AAAAACGTGCTATGATGAGAGCAGAC
1 AAAAACGTGCTATGAT--GAGCAGAC
44793922 AAAAACGTGCTA-GAT-AGCAGA
1 AAAAACGTGCTATGATGAGCAGA
44793943 ATCTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.45, C:0.15, G:0.26, T:0.15
Consensus pattern (24 bp):
AAAAACGTGCTATGATGAGCAGAC
Found at i:44802690 original size:17 final size:18
Alignment explanation
Indices: 44802668--44802701 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44802658 ATAATTGTAA
44802668 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
44802685 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
44802702 CATAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:44811808 original size:21 final size:18
Alignment explanation
Indices: 44811765--44811812 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
44811755 TTTAGGCTAG
*
44811765 ATAATTAAATAATTAGGA
1 ATAATTAAATAATTAGAA
44811783 ATAATTAAATAAAATATAGAA
1 ATAATTAAAT--AAT-TAGAA
44811804 ATAATTAAA
1 ATAATTAAA
44811813 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 10 0.38
20 3 0.12
21 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAATTAAATAATTAGAA
Found at i:44812705 original size:26 final size:25
Alignment explanation
Indices: 44812656--44812736 Score: 62
Period size: 25 Copynumber: 3.3 Consensus size: 25
44812646 TAAAATAAAT
* *
44812656 GAAAGAAAAAGA-ATAGAAAAA-GA
1 GAAAAAAAAAGAGAAAGAAAAAGGA
* * *
44812679 -AAAAACAAAGTAGAACGAAACA-GA
1 GAAAAAAAAAG-AGAAAGAAAAAGGA
*
44812703 GAAGAAAAAGAGAGAAAGAAAAAGGA
1 GAA-AAAAAAAGAGAAAGAAAAAGGA
44812729 GAAAAAAA
1 GAAAAAAA
44812737 TTAGGGTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 8 0.18
23 1 0.02
24 8 0.18
25 16 0.36
26 11 0.25
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.02
Consensus pattern (25 bp):
GAAAAAAAAAGAGAAAGAAAAAGGA
Found at i:44812718 original size:13 final size:13
Alignment explanation
Indices: 44812700--44812736 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
44812690 AGAACGAAAC
44812700 AGAGAAGAAAAAG
1 AGAGAAGAAAAAG
44812713 AGAGAAAGAAAAAG
1 AGAG-AAGAAAAAG
44812727 -GAGAA-AAAAA
1 AGAGAAGAAAAA
44812737 TTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.22
12 2 0.09
13 7 0.30
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AGAGAAGAAAAAG
Found at i:44812723 original size:14 final size:14
Alignment explanation
Indices: 44812700--44812736 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
44812690 AGAACGAAAC
44812700 AGAG-AAGAAAAAG
1 AGAGAAAGAAAAAG
44812713 AGAGAAAGAAAAAG
1 AGAGAAAGAAAAAG
44812727 -GAGAAA-AAAA
1 AGAGAAAGAAAA
44812737 TTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 9 0.39
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAGAAAGAAAAAG
Found at i:44815537 original size:9 final size:9
Alignment explanation
Indices: 44815523--44815558 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
44815513 CTAATTAGGT
*
44815523 GATATTTAG
1 GATATTTTG
44815532 GATATTTTG
1 GATATTTTG
44815541 GATATTTTG
1 GATATTTTG
44815550 GATAATTTT
1 GAT-ATTTT
44815559 ACAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (9 bp):
GATATTTTG
Found at i:44816036 original size:13 final size:13
Alignment explanation
Indices: 44816020--44816054 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
44816010 TCAAACTCAT
*
44816020 AAATATTTATTAG
1 AAATATTTATTAA
44816033 AAATATTTATTAA
1 AAATATTTATTAA
44816046 AAATATTTA
1 AAATATTTA
44816055 CGAGACTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
AAATATTTATTAA
Found at i:44817198 original size:16 final size:16
Alignment explanation
Indices: 44817173--44817206 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44817163 ATGAATATAT
* *
44817173 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
44817189 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
44817205 AT
1 AT
44817207 TGGCTATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:44819495 original size:12 final size:13
Alignment explanation
Indices: 44819470--44819500 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
44819460 GACTCACTGA
44819470 TTTTAAAATGATT
1 TTTTAAAATGATT
44819483 TTTTAAAAT-ATT
1 TTTTAAAATGATT
44819495 TTTTAA
1 TTTTAA
44819501 CTTATATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTTAAAATGATT
Found at i:44828212 original size:44 final size:44
Alignment explanation
Indices: 44828085--44828212 Score: 114
Period size: 49 Copynumber: 2.8 Consensus size: 44
44828075 AACAGATCAG
* *
44828085 TGAAGCTACAATTCCTATACCCTTAAAGTTGCAGTAGGTCGAAA
1 TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGTAGATCGAAA
* * * * * *
44828129 TGAAACTACAATGGTGAATTTATATCCC-TAAAATTGCAGTAGATTGGAT
1 TGAAGCTACAAT--T---CTTATA-CCCTTAAAGTTGCAGTAGATCGAAA
*
44828178 TGAAGCTACAATTCTTATACCCTTGAAGTTGCAGT
1 TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGT
44828213 GGGTCAGAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
43 3 0.05
44 26 0.40
46 1 0.02
47 1 0.02
49 31 0.48
50 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (44 bp):
TGAAGCTACAATTCTTATACCCTTAAAGTTGCAGTAGATCGAAA
Done.