Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 81 of 125
Found at i:16252102 original size:59 final size:60
Alignment explanation
Indices: 16251986--16252104 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
16251976 TCCCCATAAA
16251986 TGAGGCTTTAAAACTTTTGAAAAATAAAATGCTCCCTCATAACTAAGGTTTTGAAACTTT
1 TGAGGCTTTAAAACTTTTGAAAAATAAAATGCTCCCTCATAACTAAGGTTTTGAAACTTT
* *
16252046 TGAGGCTTTGAAACTTTTG-AAAATAAAATGCTCCCCTCA-AACTGAGGATTTT-AAACTTT
1 TGAGGCTTTAAAACTTTTGAAAAATAAAATGCT-CCCTCATAACTAAGG-TTTTGAAACTTT
16252105 AAAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
59 27 0.49
60 28 0.51
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (60 bp):
TGAGGCTTTAAAACTTTTGAAAAATAAAATGCTCCCTCATAACTAAGGTTTTGAAACTTT
Found at i:16252321 original size:91 final size:86
Alignment explanation
Indices: 16252046--16252350 Score: 286
Period size: 84 Copynumber: 3.5 Consensus size: 86
16252036 TTGAAACTTT
* * * *
16252046 TGAGGCTTTGAAACTTTTG-AAAATAAAATGCTC-CCCTCAAACTGAGGATTTTA-AA-CTTTAA
1 TGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCAC-AATTGAGG-CTTTAGAATTTTTAA
** *
16252107 AAAATAAAATGCT-TCCCTTTAGC
64 AAAATAAAATGCTCTCCC-ACAAC
* * * * * *
16252130 TAAGGCTCTGAAACTTTTG-AAAATAAAATGCTCAT-CGACAACTAAGGCTTTAGAATTTTTGAA
1 TGAGGCTTTGAAACTTTTGAAAAATAAAATGCTC-TCCCACAATTGAGGCTTTAGAATTTTTAAA
*
16252193 AAATAAAATGCTCTCCCACAAT
65 AAATAAAATGCTCTCCCACAAC
* * *
16252215 TGAGGCTTTGGAACTTTTGAAAAATAAAATGCTCTCCCATAATTGAGGCTTTGGAATTTTTAAAA
1 TGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAATTGAGGCTTTAGAATTTTT---A
16252280 AATTAAATAAAATGCTC-CCTCACAAC
63 AA--AAATAAAATGCTCTCC-CACAAC
* *
16252306 TGAGGCTTTGAAAC-TTTGAAAAATAAAATGGTCTCTCACAATTGA
1 TGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAATTGA
16252351 ATCTTTAAAA
Statistics
Matches: 182, Mismatches: 26, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
83 4 0.02
84 40 0.22
85 37 0.20
86 38 0.21
89 2 0.01
90 30 0.16
91 31 0.17
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (86 bp):
TGAGGCTTTGAAACTTTTGAAAAATAAAATGCTCTCCCACAATTGAGGCTTTAGAATTTTTAAAA
AATAAAATGCTCTCCCACAAC
Found at i:16252344 original size:42 final size:42
Alignment explanation
Indices: 16252046--16252364 Score: 225
Period size: 42 Copynumber: 7.4 Consensus size: 42
16252036 TTGAAACTTT
*
16252046 TGAGGCTTTGAAACTTTTG-AAAATAAAATGCTCCCCTCA-AAC
1 TGAGGCTTTGAAAC-TTTGAAAAATAAAATGCT-CTCTCACAAC
* * * * ** *
16252088 TGAGGATTTTAAACTTTAAAAAATAAAATGCT-TCCCTTTAGC
1 TGAGGCTTTGAAACTTTGAAAAATAAAATGCTCTCTC-ACAAC
* * *
16252130 TAAGGCTCTGAAACTTTTG-AAAATAAAATGCTCATC-GACAAC
1 TGAGGCTTTGAAAC-TTTGAAAAATAAAATGCTC-TCTCACAAC
* ** * *
16252172 TAAGGCTTTAGAATTTTTGAAAAATAAAATGCTCTCCCACAAT
1 TGAGGCTTT-GAAACTTTGAAAAATAAAATGCTCTCTCACAAC
* * * *
16252215 TGAGGCTTTGGAACTTTTGAAAAATAAAATGCTCTCCCATAAT
1 TGAGGCTTTGAAAC-TTTGAAAAATAAAATGCTCTCTCACAAC
** * *
16252258 TGAGGCTTTGGAATTTTTAAAAAATTAAATAAAATGCTCCCTCACAAC
1 TGAGGCTTT-GAAACTTT---GAA--AAATAAAATGCTCTCTCACAAC
* *
16252306 TGAGGCTTTGAAACTTTGAAAAATAAAATGGTCTCTCACAAT
1 TGAGGCTTTGAAACTTTGAAAAATAAAATGCTCTCTCACAAC
** *
16252348 TGAATCTTTAAAACTTT
1 TGAGGCTTTGAAACTTT
16252365 TGCAAAACAA
Statistics
Matches: 218, Mismatches: 43, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 101 0.46
43 71 0.33
44 6 0.03
46 2 0.01
47 6 0.03
48 27 0.12
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (42 bp):
TGAGGCTTTGAAACTTTGAAAAATAAAATGCTCTCTCACAAC
Found at i:16258105 original size:29 final size:29
Alignment explanation
Indices: 16258063--16258124 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
16258053 CCCAATTATC
16258063 AAGTAGATGGCTTGGTGAAATTGTGTTAA
1 AAGTAGATGGCTTGGTGAAATTGTGTTAA
16258092 AAGTAGATGGCTTGGTGAAATTGTGTTAA
1 AAGTAGATGGCTTGGTGAAATTGTGTTAA
16258121 AAGT
1 AAGT
16258125 TAAATGGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
AAGTAGATGGCTTGGTGAAATTGTGTTAA
Found at i:16258723 original size:14 final size:14
Alignment explanation
Indices: 16258704--16258753 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
16258694 TCAAAAATTC
*
16258704 TTTTTTTGTTTTTG
1 TTTTTTTATTTTTG
* *
16258718 TTTTTTTATTATTA
1 TTTTTTTATTTTTG
*
16258732 TTTTTTTAATTTTGG
1 TTTTTTT-ATTTTTG
16258747 TTTTTTT
1 TTTTTTT
16258754 TGAAAGGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (14 bp):
TTTTTTTATTTTTG
Found at i:16259075 original size:35 final size:35
Alignment explanation
Indices: 16259046--16259128 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
16259036 GCAAGTTGAG
*
16259046 AAATAGGGATGACTAGGACTAAGTCGCAAGTCAAA
1 AAATAAGGATGACTAGGACTAAGTCGCAAGTCAAA
* * **
16259081 AAATAAGGATGACTGGGACTAAATCATAAGTTC-AA
1 AAATAAGGATGACTAGGACTAAGTCGCAAG-TCAAA
*
16259116 AAATAAAGATGAC
1 AAATAAGGATGAC
16259129 AGAAACTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 39 0.95
36 2 0.05
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (35 bp):
AAATAAGGATGACTAGGACTAAGTCGCAAGTCAAA
Found at i:16259137 original size:35 final size:35
Alignment explanation
Indices: 16259063--16259157 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
16259053 GATGACTAGG
* * * * * **
16259063 ACTAAGTCGCAAGTCAAAAAATAAGGATGACTGGG
1 ACTAAATCACAAGTTAAAAAATAAAGATGACAGAA
* *
16259098 ACTAAATCATAAGTTCAAAAATAAAGATGACAGAA
1 ACTAAATCACAAGTTAAAAAATAAAGATGACAGAA
*
16259133 ACTAAATCACAATTTAAAAAATAAA
1 ACTAAATCACAAGTTAAAAAATAAA
16259158 AGCAACTGAG
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.54, C:0.13, G:0.14, T:0.20
Consensus pattern (35 bp):
ACTAAATCACAAGTTAAAAAATAAAGATGACAGAA
Found at i:16259286 original size:35 final size:35
Alignment explanation
Indices: 16259223--16259336 Score: 133
Period size: 35 Copynumber: 3.3 Consensus size: 35
16259213 CACAAGTTAG
* *
16259223 GAAATAAAAA-GACTAGGAATGAATCGTAAGTCAA
1 GAAATAAAAATGACTAGGATTGAACCGTAAGTCAA
* *
16259257 GAAATAAAAATGATTAGGATTGAGCCGTAAGTCAA
1 GAAATAAAAATGACTAGGATTGAACCGTAAGTCAA
* * * *
16259292 -AAATTAAAAATGACTGGGACTGAACCGTAAGTTAG
1 GAAA-TAAAAATGACTAGGATTGAACCGTAAGTCAA
16259327 GAAATAAAAA
1 GAAATAAAAA
16259337 CAAATTAGGA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 13 0.19
35 51 0.76
36 3 0.04
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (35 bp):
GAAATAAAAATGACTAGGATTGAACCGTAAGTCAA
Found at i:16259430 original size:35 final size:35
Alignment explanation
Indices: 16259391--16259481 Score: 82
Period size: 35 Copynumber: 2.6 Consensus size: 35
16259381 ACCAAAGTCG
* *
16259391 CAAGTCAAGAAATAAAGATGATTGAAACTAAA-TT
1 CAAGTCAAGAAATAAAGATGATCGAAACTAAACCT
**
16259425 CCAAGT-TGGAAAATGAAA-ATGATCGAAACTAAACCT
1 -CAAGTCAAG-AAAT-AAAGATGATCGAAACTAAACCT
16259461 CAAGTCAA-AGAATAAAGATGA
1 CAAGTCAAGA-AATAAAGATGA
16259482 CATGAACTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
34 5 0.11
35 35 0.80
36 4 0.09
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (35 bp):
CAAGTCAAGAAATAAAGATGATCGAAACTAAACCT
Found at i:16259964 original size:35 final size:33
Alignment explanation
Indices: 16259924--16260015 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 33
16259914 CCGCGAGTTG
* *
16259924 AAAAATAAAGATGATCTGGACTAAAGCGTAAGTC
1 AAAAATAAA-ATGATCGGGACTAAACCGTAAGTC
*
16259958 AGAAAATAAAAGTG-GCAGGGACTAAACCGTAAGTC
1 A-AAAATAAAA-TGATC-GGGACTAAACCGTAAGTC
16259993 AAAAAGTAAAAATGATCGGGACT
1 AAAAA-T-AAAATGATCGGGACT
16260016 GAGTCACAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
34 7 0.15
35 36 0.75
36 5 0.10
ACGTcount: A:0.48, C:0.12, G:0.23, T:0.17
Consensus pattern (33 bp):
AAAAATAAAATGATCGGGACTAAACCGTAAGTC
Found at i:16260096 original size:70 final size:70
Alignment explanation
Indices: 16259978--16260110 Score: 155
Period size: 70 Copynumber: 1.9 Consensus size: 70
16259968 AGTGGCAGGG
* **
16259978 ACTAAACCGTAAGTCAAAAAGTAAAAATGATCGGGACTGAGTCACAAGTTAA-AAAATAAAAATA
1 ACTAAACCGTAAGTCAAAAAGTAAAAATGACCAAGACTGAGTCACAAG-TAAGAAAATAAAAATA
16260042 ACCATA
65 ACCATA
* * * *
16260048 ACTAAACTGTAAGTTAAGAAA-TAAAAATGACCAAGACTGAG-CTGCAAGTAAGGAAATAAAAAT
1 ACTAAACCGTAAGTCAA-AAAGTAAAAATGACCAAGACTGAGTC-ACAAGTAAGAAAATAAAAAT
16260111 GGCTGAGACT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
69 4 0.08
70 46 0.87
71 3 0.06
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.19
Consensus pattern (70 bp):
ACTAAACCGTAAGTCAAAAAGTAAAAATGACCAAGACTGAGTCACAAGTAAGAAAATAAAAATAA
CCATA
Found at i:16260104 original size:35 final size:35
Alignment explanation
Indices: 16260022--16260111 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 35
16260012 GACTGAGTCA
* *
16260022 CAAGTTAAAAAATAAAAATAACCATAACTAAACTG
1 CAAGTTAAGAAATAAAAATGACCATAACTAAACTG
* * *
16260057 TAAGTTAAGAAATAAAAATGACCA-AGACTGAGCTG
1 CAAGTTAAGAAATAAAAATGACCATA-ACTAAACTG
16260092 CAAG-TAAGGAAATAAAAATG
1 CAAGTTAA-GAAATAAAAATG
16260112 GCTGAGACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 4 0.09
35 43 0.91
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (35 bp):
CAAGTTAAGAAATAAAAATGACCATAACTAAACTG
Found at i:16261331 original size:45 final size:45
Alignment explanation
Indices: 16261282--16261378 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
16261272 TTAAACTACT
16261282 AGCTAATCT-AGACTTGAGTGCTAGCCAATCTGAGATTAAAATGCC
1 AGCTAATCTAAG-CTTGAGTGCTAGCCAATCTGAGATTAAAATGCC
* * * *
16261327 AGCTAATCTAAGCTTGGGTGCTAGCTAATCTGAGTTTAAAATGCT
1 AGCTAATCTAAGCTTGAGTGCTAGCCAATCTGAGATTAAAATGCC
16261372 AGCTAAT
1 AGCTAAT
16261379 TTGGGGTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
45 45 0.96
46 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (45 bp):
AGCTAATCTAAGCTTGAGTGCTAGCCAATCTGAGATTAAAATGCC
Found at i:16261375 original size:23 final size:23
Alignment explanation
Indices: 16261261--16261378 Score: 82
Period size: 23 Copynumber: 5.2 Consensus size: 23
16261251 TGGATGTCAA
* *
16261261 CTAATCTGA-ACTTAAACTACTAG
1 CTAATCTGAGA-TTAAAATGCTAG
* *
16261284 CTAATCT-AGACTT-GAGTGCTAG
1 CTAATCTGAGA-TTAAAATGCTAG
* *
16261306 CCAATCTGAGATTAAAATGCCAG
1 CTAATCTGAGATTAAAATGCTAG
* * ***
16261329 CTAATCTAAGCTT-GGGTGCTAG
1 CTAATCTGAGATTAAAATGCTAG
*
16261351 CTAATCTGAGTTTAAAATGCTAG
1 CTAATCTGAGATTAAAATGCTAG
16261374 CTAAT
1 CTAAT
16261379 TTGGGGTTAA
Statistics
Matches: 72, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
22 31 0.43
23 41 0.57
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (23 bp):
CTAATCTGAGATTAAAATGCTAG
Found at i:16261388 original size:23 final size:23
Alignment explanation
Indices: 16261345--16261406 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
16261335 TAAGCTTGGG
* * *
16261345 TGCTAGCTAATCTGAGTTTAAAA
1 TGCTAGCTAATTTGGGGTTAAAA
*
16261368 TGCTAGCTAATTTGGGGTTAAAG
1 TGCTAGCTAATTTGGGGTTAAAA
* *
16261391 TGCCAACTAATTTGGG
1 TGCTAGCTAATTTGGG
16261407 CTTGGGTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (23 bp):
TGCTAGCTAATTTGGGGTTAAAA
Found at i:16261801 original size:33 final size:32
Alignment explanation
Indices: 16261743--16261805 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
16261733 TTTTTTCTTT
16261743 CTTTTTTTTTTTGTTATTTTTCTCTTAACAAA
1 CTTTTTTTTTTTGTTATTTTTCTCTTAACAAA
16261775 CTTTATTTTTCTTT-TT-TTTTTCCTCTTAACA
1 CTTT-TTTTT-TTTGTTATTTTT-CTCTTAACA
16261806 GATTTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 9 0.32
33 16 0.57
34 3 0.11
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.67
Consensus pattern (32 bp):
CTTTTTTTTTTTGTTATTTTTCTCTTAACAAA
Found at i:16268651 original size:9 final size:8
Alignment explanation
Indices: 16268601--16268724 Score: 90
Period size: 8 Copynumber: 15.4 Consensus size: 8
16268591 TAGGGTCTCA
16268601 TTTTAGGG
1 TTTTAGGG
*
16268609 TTTTGGGG
1 TTTTAGGG
*
16268617 TTTTAAGG
1 TTTTAGGG
*
16268625 TCTTAGGG
1 TTTTAGGG
16268633 ATTTTA-GG
1 -TTTTAGGG
16268641 TTGTTAGGG
1 TT-TTAGGG
*
16268650 TTTTAAGG
1 TTTTAGGG
*
16268658 -TTTAGTG
1 TTTTAGGG
**
16268665 TTTTAGTA
1 TTTTAGGG
*
16268673 TTTTGGGG
1 TTTTAGGG
* *
16268681 TTTCAAGG
1 TTTTAGGG
16268689 TTTTAGAGG
1 TTTTAG-GG
*
16268698 TTTTAAGG
1 TTTTAGGG
* *
16268706 TTTCAAGG
1 TTTTAGGG
16268714 TTTTAGGG
1 TTTTAGGG
16268722 TTT
1 TTT
16268725 CGGGGTTTTT
Statistics
Matches: 89, Mismatches: 22, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
7 7 0.08
8 67 0.75
9 15 0.17
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.49
Consensus pattern (8 bp):
TTTTAGGG
Found at i:16268651 original size:33 final size:31
Alignment explanation
Indices: 16268600--16268733 Score: 101
Period size: 33 Copynumber: 4.2 Consensus size: 31
16268590 TTAGGGTCTC
*
16268600 ATTTTAGGGTTTTGGGGTTTTAAGGTCTTAGGG
1 ATTTTA-GGTTTTAGGGTTTTAAGGT-TTAGGG
*
16268633 ATTTTAGGTTGTTAGGGTTTTAAGGTTTAGTG
1 ATTTTAGGTT-TTAGGGTTTTAAGGTTTAGGG
* * *
16268665 -TTTTAGTATTTTGGGGTTTCAAGGTTTTAGAGG
1 ATTTTAG-GTTTTAGGGTTTTAAGG-TTTAG-GG
* * * *
16268698 -TTTTAAGGTTTCAAGGTTTTAGGGTTTCGGG
1 ATTTT-AGGTTTTAGGGTTTTAAGGTTTAGGG
*
16268729 GTTTT
1 ATTTT
16268734 TTATCTATGC
Statistics
Matches: 82, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
31 20 0.24
32 24 0.29
33 36 0.44
34 2 0.02
ACGTcount: A:0.16, C:0.03, G:0.32, T:0.49
Consensus pattern (31 bp):
ATTTTAGGTTTTAGGGTTTTAAGGTTTAGGG
Found at i:16268682 original size:31 final size:32
Alignment explanation
Indices: 16268600--16268708 Score: 107
Period size: 33 Copynumber: 3.3 Consensus size: 32
16268590 TTAGGGTCTC
*
16268600 ATTTTAGGGTTTTGGGGTTTTAAGGTCTTAGGG
1 ATTTTAGGTTTTTGGGGTTTTAAGGT-TTAGGG
* * *
16268633 ATTTTAGGTTGTTAGGGTTTTAAGGTTTAGTG
1 ATTTTAGGTTTTTGGGGTTTTAAGGTTTAGGG
*
16268665 -TTTTA-GTATTTTGGGGTTTCAAGGTTTTAGAGG
1 ATTTTAGGT-TTTTGGGGTTTTAAGG-TTTAG-GG
16268698 -TTTTAAGGTTT
1 ATTTT-AGGTTT
16268709 CAAGGTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
30 2 0.03
31 18 0.29
32 10 0.16
33 28 0.44
34 3 0.05
35 2 0.03
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (32 bp):
ATTTTAGGTTTTTGGGGTTTTAAGGTTTAGGG
Found at i:16268707 original size:25 final size:24
Alignment explanation
Indices: 16268638--16268724 Score: 97
Period size: 25 Copynumber: 3.6 Consensus size: 24
16268628 TAGGGATTTT
16268638 AGGTTGTTAGGGTTTTAAGGTTT--
1 AGGTT-TTAGGGTTTTAAGGTTTCA
** **
16268661 AGTGTTTTAGTATTTTGGGGTTTCA
1 AG-GTTTTAGGGTTTTAAGGTTTCA
16268686 AGGTTTTAGAGGTTTTAAGGTTTCA
1 AGGTTTTAG-GGTTTTAAGGTTTCA
16268711 AGGTTTTAGGGTTT
1 AGGTTTTAGGGTTT
16268725 CGGGGTTTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
23 15 0.29
24 15 0.29
25 22 0.42
ACGTcount: A:0.18, C:0.02, G:0.31, T:0.48
Consensus pattern (24 bp):
AGGTTTTAGGGTTTTAAGGTTTCA
Found at i:16270835 original size:16 final size:15
Alignment explanation
Indices: 16270794--16270839 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
16270784 ATCTTTTGTA
16270794 AATTTCTTTTTTT-TT
1 AATTT-TTTTTTTATT
*
16270809 AATTTTCTTTTTATT
1 AATTTTTTTTTTATT
16270824 AATCTTTTTTTTTATT
1 AAT-TTTTTTTTTATT
16270840 TTTTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 10 0.37
16 11 0.41
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTTTTTTTTTATT
Found at i:16271677 original size:18 final size:18
Alignment explanation
Indices: 16271635--16271699 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
16271625 AAATTATATG
16271635 TAATAAA-ATTT-TAAAT
1 TAATAAATATTTATAAAT
* *
16271651 TATTTAATATTTATAAAT
1 TAATAAATATTTATAAAT
*
16271669 TAATAAATAATTGA-AAAT
1 TAATAAAT-ATTTATAAAT
*
16271687 TATTAAATTATTT
1 TAATAAA-TATTT
16271700 GTTAATAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 5 0.13
17 4 0.11
18 24 0.63
19 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
TAATAAATATTTATAAAT
Found at i:16271750 original size:29 final size:29
Alignment explanation
Indices: 16271718--16271786 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
16271708 ATAATTAACT
16271718 TTTATTTATTAATTTACCATATAATAAAA
1 TTTATTTATTAATTTACCATATAATAAAA
** *
16271747 TTTATTTATTAATTTATTATATAATGAAA
1 TTTATTTATTAATTTACCATATAATAAAA
16271776 TTTATTTATTA
1 TTTATTTATTA
16271787 TATTAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTATTTATTAATTTACCATATAATAAAA
Found at i:16271778 original size:25 final size:26
Alignment explanation
Indices: 16271750--16271814 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
16271740 AATAAAATTT
* *
16271750 ATTTATTAATTTATTATA-TAATGAA
1 ATTTATTAATTTATTAAATTAATAAA
*
16271775 ATTTATTTATTATATTAAATTAATAAA
1 ATTTATTAATT-TATTAAATTAATAAA
*
16271802 ATTTTTATAATTT
1 ATTTAT-TAATTT
16271815 TAAATAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 10 0.31
26 6 0.19
27 12 0.38
28 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTATTAATTTATTAAATTAATAAA
Found at i:16271808 original size:29 final size:29
Alignment explanation
Indices: 16271717--16271809 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
16271707 AATAATTAAC
*
16271717 TTTTATTTATTA-ATTTACCATATAATAAAATT
1 TTTTATTTATTATA-TTA-AAT-TAATAAAA-T
* * *
16271749 TATTTATTAATT-TATTATA-TAATGAAA-
1 T-TTTATTTATTATATTAAATTAATAAAAT
16271776 -TTTATTTATTATATTAAATTAATAAAAT
1 TTTTATTTATTATATTAAATTAATAAAAT
16271804 TTTTAT
1 TTTTAT
16271810 AATTTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
25 9 0.18
26 6 0.12
27 7 0.14
29 12 0.24
31 1 0.02
32 4 0.08
33 10 0.20
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTTATTTATTATATTAAATTAATAAAAT
Found at i:16272386 original size:16 final size:15
Alignment explanation
Indices: 16272367--16272408 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
16272357 GCCAACCAAC
*
16272367 TTTTTTGCTTTGATT
1 TTTTTTTCTTTGATT
*
16272382 TTTTTTTCTTTGGTT
1 TTTTTTTCTTTGATT
16272397 TTTATTTTCTTT
1 TTT-TTTTCTTT
16272409 TTAGTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.05, C:0.07, G:0.10, T:0.79
Consensus pattern (15 bp):
TTTTTTTCTTTGATT
Found at i:16272586 original size:11 final size:10
Alignment explanation
Indices: 16272551--16272583 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
16272541 GACAAATAAA
16272551 TTTATAATTT
1 TTTATAATTT
16272561 TTTATAATTT
1 TTTATAATTT
16272571 TTTATAATTT
1 TTTATAATTT
16272581 TTT
1 TTT
16272584 TATTTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTATAATTT
Found at i:16274098 original size:4 final size:4
Alignment explanation
Indices: 16274089--16274113 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16274079 CAACCAAGAA
16274089 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
16274114 GACTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:16275439 original size:21 final size:21
Alignment explanation
Indices: 16275389--16275441 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
16275379 CTATTATTAT
*
16275389 TAAAAATAACAT-GTTGAAGA
1 TAAAAATAACATAGATGAAGA
*
16275409 TAAATA-AACATAGAATGAA-A
1 TAAAAATAACATAG-ATGAAGA
16275429 TAAAAATAACATA
1 TAAAAATAACATA
16275442 TAATTTATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 10 0.37
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (21 bp):
TAAAAATAACATAGATGAAGA
Found at i:16276516 original size:99 final size:98
Alignment explanation
Indices: 16276214--16276518 Score: 382
Period size: 101 Copynumber: 3.1 Consensus size: 98
16276204 TTATTTTAAG
* * * * *
16276214 AAAATTCATTAAG-CTTTCTAATAGTTTCGTAAGATCTAATTCAATATTTAAATCCTCCAATAGT
1 AAAATTCATTAAGTC-CTCTAATAATTTGGTAAGAT-TAATTCAAAATTTAAATCTTCCAATAGT
*
16276278 TTGATAGGATTGAAAATTTTATTATTATTTTTTACAA
64 TTG-TAGGATTGAAAATTTTATTATTATTTTTTTC-A
* * * *
16276315 AAAATTCATTAAGTCCTCTAATATTTTGATAAGATTTAATTCAAGATTTAAAT-TCTCTAATAGT
1 AAAATTCATTAAGTCCTCTAATAATTTGGTAAGA-TTAATTCAAAATTTAAATCT-TCCAATAGT
* * * *
16276379 TTAGTAGGACTAAAAATTTTATTATTA-TTATTTAA
64 TT-GTAGGATTGAAAATTTTATTATTATTTTTTTCA
*
16276414 AAAATTCATTAAGTCCTCCAATAATTTGGTAAGACTTAATTCAAAATTTAAATCTTCCAATAGTT
1 AAAATTCATTAAGTCCTCTAATAATTTGGTAAGA-TTAATTCAAAATTTAAATCTTCCAATAGTT
16276479 TGTAGGATTGAAAATTTTATTATTATTTTTTTCA
65 TGTAGGATTGAAAATTTTATTATTATTTTTTTCA
16276513 AAAATT
1 AAAATT
16276519 TTATTATGAA
Statistics
Matches: 176, Mismatches: 22, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
98 22 0.12
99 71 0.40
100 5 0.03
101 75 0.43
102 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.44
Consensus pattern (98 bp):
AAAATTCATTAAGTCCTCTAATAATTTGGTAAGATTAATTCAAAATTTAAATCTTCCAATAGTTT
GTAGGATTGAAAATTTTATTATTATTTTTTTCA
Found at i:16276668 original size:16 final size:17
Alignment explanation
Indices: 16276649--16276681 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16276639 AAAAAGTGAA
*
16276649 ATAAATGAA-AAAATAT
1 ATAAATAAACAAAATAT
16276665 ATAAATAAACAAAATAT
1 ATAAATAAACAAAATAT
16276682 GAAAATTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAAATAAACAAAATAT
Found at i:16277444 original size:14 final size:14
Alignment explanation
Indices: 16277425--16277462 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
16277415 TTATTCAAAT
16277425 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
16277439 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
16277453 TTTTT-TTTTT
1 TTTTTGTTTTT
16277463 CCCTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:16277469 original size:18 final size:17
Alignment explanation
Indices: 16277448--16277497 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
16277438 GTTTTTGTTT
16277448 TTTTGTTTTTTTTTTCCC
1 TTTTGTTTTTTTTTT-CC
16277466 TTTT-TTTATTTTTTTCC
1 TTTTGTTT-TTTTTTTCC
16277483 -TTTGTTTTGTTTTTT
1 TTTTGTTTT-TTTTTT
16277498 TTTAAAGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.14
17 14 0.48
18 11 0.38
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTGTTTTTTTTTTCC
Found at i:16277470 original size:34 final size:35
Alignment explanation
Indices: 16277431--16277497 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
16277421 AAATTTTTTG
* **
16277431 TTTTTTTGTTTTTGTTTTTTTGTTTT-TTTTTTCCC
1 TTTTTTTATTTTT-TTCCTTTGTTTTGTTTTTTCCC
16277466 TTTTTTTATTTTTTTCCTTTGTTTTGTTTTTT
1 TTTTTTTATTTTTTTCCTTTGTTTTGTTTTTT
16277498 TTTAAAGGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.01, C:0.07, G:0.07, T:0.84
Consensus pattern (35 bp):
TTTTTTTATTTTTTTCCTTTGTTTTGTTTTTTCCC
Found at i:16277498 original size:8 final size:8
Alignment explanation
Indices: 16277424--16277459 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
16277414 ATTATTCAAA
16277424 TTTTTTGT
1 TTTTTTGT
16277432 TTTTTTG-
1 TTTTTTGT
16277439 -TTTTTGT
1 TTTTTTGT
16277446 TTTTTTGT
1 TTTTTTGT
16277454 TTTTTT
1 TTTTTT
16277460 TTTCCCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTGT
Found at i:16277498 original size:18 final size:18
Alignment explanation
Indices: 16277434--16277498 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
16277424 TTTTTTGTTT
**
16277434 TTTTGTTTTTGTTTTTTTG
1 TTTTGTTTTT-TTCCTTTG
*
16277453 TTTT-TTTTTTCCCTTT-
1 TTTTGTTTTTTTCCTTTG
*
16277469 TTTTATTTTTTTCCTTTG
1 TTTTGTTTTTTTCCTTTG
16277487 TTTTGTTTTTTT
1 TTTTGTTTTTTT
16277499 TTAAAGGCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.10
17 15 0.38
18 16 0.41
19 4 0.10
ACGTcount: A:0.02, C:0.08, G:0.08, T:0.83
Consensus pattern (18 bp):
TTTTGTTTTTTTCCTTTG
Found at i:16277835 original size:84 final size:83
Alignment explanation
Indices: 16277657--16277913 Score: 273
Period size: 84 Copynumber: 3.0 Consensus size: 83
16277647 AAACTAAAAA
* * ** * * *
16277657 ATTATACCTAGAGATCTTACAAATTATTGACTCTAAAATAGATT-TAGCTCGAAAGACTTGTGAA
1 ATTATACCTAGAGATCTTACAAA-TATTGACTATAAAATAGATTCAATTTCG-AATATTTATGAA
** * * *
16277721 TCTTATTCAAAGGACATGGAA
64 TCTTACCCAAA-GACTTAGAG
* * *
16277742 ATTACACCTAGAGATCTTACAAATATTGACTATGAAATAGATTCAATTTCGAATATTTCTGAATC
1 ATTATACCTAGAGATCTTACAAATATTGACTATAAAATAGATTCAATTTCGAATATTTATGAATC
16277807 TTACCCAGAAGACTTAGAG
66 TTACCCA-AAGACTTAGAG
* * * *
16277826 ATTATACCTAGAGGTTTTACAAATATTAACTATAAAATAGATTCAATTTGGAATATTTATGAATC
1 ATTATACCTAGAGATCTTACAAATATTGACTATAAAATAGATTCAATTTCGAATATTTATGAATC
* *
16277891 TTGCCTATAAGACTTAGAG
66 TTACCCA-AAGACTTAGAG
16277910 ATTA
1 ATTA
16277914 CGTCCAGAGG
Statistics
Matches: 146, Mismatches: 24, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
84 118 0.81
85 28 0.19
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (83 bp):
ATTATACCTAGAGATCTTACAAATATTGACTATAAAATAGATTCAATTTCGAATATTTATGAATC
TTACCCAAAGACTTAGAG
Found at i:16277923 original size:84 final size:84
Alignment explanation
Indices: 16277657--16277948 Score: 259
Period size: 84 Copynumber: 3.5 Consensus size: 84
16277647 AAACTAAAAA
* * * * ** * * *
16277657 ATTATACCTAGAGATCTTACAAATTATTGACTCTAAAATAGATT-TAGCTCGAAAGACTTGTGAA
1 ATTATACCTAGAGGTCTTACAAA-TATTAACTATAAAATAGATTCAATTTCG-AATATTTATGAA
** * * *
16277721 TCTTATTCA-AAGGACATGGAA
64 TCTTACCCAGAA-GACTTAGAG
* * * * *
16277742 ATTACACCTAGAGATCTTACAAATATTGACTATGAAATAGATTCAATTTCGAATATTTCTGAATC
1 ATTATACCTAGAGGTCTTACAAATATTAACTATAAAATAGATTCAATTTCGAATATTTATGAATC
16277807 TTACCCAGAAGACTTAGAG
66 TTACCCAGAAGACTTAGAG
* *
16277826 ATTATACCTAGAGGTTTTACAAATATTAACTATAAAATAGATTCAATTTGGAATATTTATGAATC
1 ATTATACCTAGAGGTCTTACAAATATTAACTATAAAATAGATTCAATTTCGAATATTTATGAATC
* * *
16277891 TTGCCTATAAGACTTAGAG
66 TTACCCAGAAGACTTAGAG
* * * *
16277910 ATTACGT-CC-AGAGGTCTTATAAATCTCAACTTTAAAATA
1 ATTA--TACCTAGAGGTCTTACAAATATTAACTATAAAATA
16277949 AATTTAGTTC
Statistics
Matches: 174, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
84 143 0.82
85 30 0.17
86 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (84 bp):
ATTATACCTAGAGGTCTTACAAATATTAACTATAAAATAGATTCAATTTCGAATATTTATGAATC
TTACCCAGAAGACTTAGAG
Found at i:16284659 original size:99 final size:99
Alignment explanation
Indices: 16284415--16284700 Score: 324
Period size: 99 Copynumber: 2.8 Consensus size: 99
16284405 TAAACTTTTT
* * * * * *
16284415 AATAGTTTAGTAAGATTTAATTTAATATTTAAATCCTCTAATAGTTTGGTAGGATTGAAAATTTT
1 AATAGTTTGGTAAGACTTAATTCAAAATTTAAATCCTCCAATAGTTTGGTAGGATTAAAAATTTT
* * *
16284480 ATTATTATTTTTTTACAAAAAAATTCATTAAGTCTTCC
66 ATTATTA--TTTTT--AAAAAAATTCATCAAGTCCTCA
* * * * *
16284518 AATATTTTGATAAGACTTAATTCAAGATTTAAATCCTTCAATAGTTTGGTGGGATTAAAAATTTT
1 AATAGTTTGGTAAGACTTAATTCAAAATTTAAATCCTCCAATAGTTTGGTAGGATTAAAAATTTT
16284583 ATTATTATTATTT-AAAAAATTCATCAAGTCCTCA
66 ATTATTATT-TTTAAAAAAATTCATCAAGTCCTCA
* * * * * *
16284617 AATAGTTTGGTAAAACTTAATTGAAAATTTAAGTCCTCCAATAGTTTAGTAAGACTAAAAATTTT
1 AATAGTTTGGTAAGACTTAATTCAAAATTTAAATCCTCCAATAGTTTGGTAGGATTAAAAATTTT
16284682 ATTA-TATTTTTCAAAAAAA
66 ATTATTATTTTT-AAAAAAA
16284701 AAAATCATTA
Statistics
Matches: 156, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
97 3 0.02
98 4 0.03
99 82 0.53
101 2 0.01
102 3 0.02
103 62 0.40
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (99 bp):
AATAGTTTGGTAAGACTTAATTCAAAATTTAAATCCTCCAATAGTTTGGTAGGATTAAAAATTTT
ATTATTATTTTTAAAAAAATTCATCAAGTCCTCA
Found at i:16287201 original size:11 final size:11
Alignment explanation
Indices: 16287179--16287207 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
16287169 ATTACGTGAG
16287179 ATTTAT-TAAA
1 ATTTATATAAA
16287189 ATTTATATAAA
1 ATTTATATAAA
16287200 ATTTATAT
1 ATTTATAT
16287208 TGTAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTATATAAA
Found at i:16288302 original size:11 final size:12
Alignment explanation
Indices: 16288280--16288308 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
16288270 ATTGAAATTT
16288280 TTTTATGTTTTA
1 TTTTATGTTTTA
16288292 TTTTA-GTTTTA
1 TTTTATGTTTTA
16288303 TTTTAT
1 TTTTAT
16288309 TTATCTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTATGTTTTA
Found at i:16288575 original size:3 final size:3
Alignment explanation
Indices: 16288567--16288612 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16288557 TTTGATGCCT
16288567 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16288613 ATTTAAACCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16289425 original size:16 final size:17
Alignment explanation
Indices: 16289385--16289425 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
16289375 TTTTTAGAAA
*
16289385 ATAATATTTAATAATTT
1 ATAATTTTTAATAATTT
*
16289402 -TAAATTTTAAT-ATTT
1 ATAATTTTTAATAATTT
16289417 ATAATTTTT
1 ATAATTTTT
16289426 TTATCCTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATAATTTTTAATAATTT
Found at i:16289608 original size:6 final size:6
Alignment explanation
Indices: 16289597--16289630 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
16289587 AATATATCTT
16289597 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATT
16289631 ATTGATTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:16292450 original size:114 final size:113
Alignment explanation
Indices: 16292088--16292559 Score: 307
Period size: 115 Copynumber: 4.2 Consensus size: 113
16292078 AAAACATAGT
* * * * *
16292088 TTTTATTAAAAATAT-AAAAAATATATTTTTTAAAATTTAACAAAGATGACATTTTTAAAAT-AA
1 TTTTGTTAAAAATATGAAAAAATATATTTTTCAAAATTCAAAAAAGATGACATTTCTAAAATGAA
* * * * * *
16292151 AAAATGGAATGTTTGTTGAAAAGATGACACTTT-AAAGATAAAAACATAGT--
66 AACA--GAGTTTTTGTTGAAAAAATGAC-TTTTCTAAGATAAAAA-AT-GTCA
* * ** * *
16292201 TTTTGTTAAAAATAAGAAAACAA-ATATTTTTCAAAATTCAACAAAAAAAAACGTTTCTAATATA
1 TTTTGTTAAAAATATGAAAA-AATATATTTTTCAAAATTCAA-AAAAGATGACATTTCTAAAAT-
* * * * *
16292265 GAAAACATAGCTTTTGTTGAAAAAA-CAATGTTTCTAATAT-AAAAATG-CAA
63 GAAAACAGAGTTTTTGTTGAAAAAATGACT-TTTCTAAGATAAAAAATGTC-A
* * * * * * *
16292315 TTTTTATTTAAAATGTGGAAAAAATATATTTTTCAAAATTCAATAGAGATGACATTTCCAAGATG
1 -TTTTGTTAAAAATAT-GAAAAAATATATTTTTCAAAATTCAAAAAAGATGACATTTCTAAAATG
16292380 AAAACAGAGTTTTTGTTGAAAAAATGACTTTTCTAAGATAAAAAATGTCA
64 AAAACAGAGTTTTTGTTGAAAAAATGACTTTTCTAAGATAAAAAATGTCA
* * ** *
16292430 TCTTTGTTGAAAATATGAAAAAA-A-A--TTTCAGAATT-AAAAAA-ATGATGTTTCTAAGAT-A
1 T-TTTGTTAAAAATATGAAAAAATATATTTTTCAAAATTCAAAAAAGATGACATTTCTAAAATGA
* * * * *
16292488 AAAAAGTAGTCTTTGTTGAAAAGATGA-TTCTTATAAAATAAAAACATAGT--
65 AAACAG-AGTTTTTGTTGAAAAAATGACTT-TTCTAAGATAAAAA-AT-GTCA
16292538 TTTTGTTAAAAATATGAAAAAA
1 TTTTGTTAAAAATATGAAAAAA
16292560 ATAGAACATA
Statistics
Matches: 284, Mismatches: 54, Indels: 48
0.74 0.14 0.12
Matches are distributed among these distances:
107 28 0.10
108 44 0.15
109 6 0.02
110 11 0.04
112 2 0.01
113 16 0.06
114 68 0.24
115 80 0.28
116 24 0.08
117 5 0.02
ACGTcount: A:0.49, C:0.07, G:0.11, T:0.34
Consensus pattern (113 bp):
TTTTGTTAAAAATATGAAAAAATATATTTTTCAAAATTCAAAAAAGATGACATTTCTAAAATGAA
AACAGAGTTTTTGTTGAAAAAATGACTTTTCTAAGATAAAAAATGTCA
Found at i:16292515 original size:40 final size:40
Alignment explanation
Indices: 16292463--16292554 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
16292453 AATTTCAGAA
* *
16292463 TTAAAAAAATGATGT-TTCTAAGATAAAAA-AGTAGTCTTTG
1 TTAAAAAAATGAT-TCTTATAAAATAAAAACA-TAGTCTTTG
* * *
16292503 TTGAAAAGATGATTCTTATAAAATAAAAACATAGTTTTTG
1 TTAAAAAAATGATTCTTATAAAATAAAAACATAGTCTTTG
*
16292543 TTAAAAATATGA
1 TTAAAAAAATGA
16292555 AAAAAATAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.02
40 41 0.95
41 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (40 bp):
TTAAAAAAATGATTCTTATAAAATAAAAACATAGTCTTTG
Found at i:16292622 original size:37 final size:37
Alignment explanation
Indices: 16292568--16292642 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
16292558 AAATAGAACA
* * *
16292568 TAAAATATCTTTACTTAATGTTATTACATATAAAATT
1 TAAAATATCTTTACTTAATATTATTAAACATAAAATT
*
16292605 TAAAATA-CATTTTCTTAATATTATTAAACATAAAATT
1 TAAAATATC-TTTACTTAATATTATTAAACATAAAATT
16292642 T
1 T
16292643 GTTTTGTGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 1 0.03
37 32 0.97
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (37 bp):
TAAAATATCTTTACTTAATATTATTAAACATAAAATT
Found at i:16293061 original size:16 final size:17
Alignment explanation
Indices: 16293024--16293065 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
16293014 GAATCACATA
*
16293024 TTTCCCTTTAATATCTC
1 TTTCCCTTTAATATCAC
16293041 TTTCCCTTTAA-ATCAC
1 TTTCCCTTTAATATCAC
16293057 TTTCCCTTT
1 TTTCCCTTT
16293066 CGAAATCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTCCCTTTAATATCAC
Found at i:16298143 original size:3 final size:3
Alignment explanation
Indices: 16298124--16298219 Score: 73
Period size: 3 Copynumber: 34.3 Consensus size: 3
16298114 AGTATGGTAA
* * *
16298124 TAT TCT TAT TCT TAT TAT TAT TAT TAT TA- CAT TA- TATT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* * *
16298167 TAC TA- TAG TA- TAT TA- TAT TAG TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16298211 TAT T-T TAT T
1 TAT TAT TAT T
16298220 TTCTTCTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
2 15 0.20
3 59 0.78
4 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:16299115 original size:21 final size:20
Alignment explanation
Indices: 16299065--16299116 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
16299055 TTCATTTTAC
*
16299065 TTTTTATTTTATTTTTTAAA
1 TTTTTATTTTATTTCTTAAA
*
16299085 TTATTTATTTTATTATCTTAAG
1 TT-TTTATTTTATT-TCTTAAA
*
16299107 TTTTAATTTT
1 TTTTTATTTT
16299117 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 18 0.67
22 7 0.26
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTATTTTATTTCTTAAA
Found at i:16309803 original size:12 final size:12
Alignment explanation
Indices: 16309786--16309810 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16309776 AGGCAGCTTG
16309786 AACAAAAAAAAA
1 AACAAAAAAAAA
16309798 AACAAAAAAAAA
1 AACAAAAAAAAA
16309810 A
1 A
16309811 GAGAAGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AACAAAAAAAAA
Found at i:16311240 original size:35 final size:37
Alignment explanation
Indices: 16311158--16311241 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 37
16311148 ATTTTCTTTA
* * *
16311158 TAGTATGCTATTATTATTATTATATATTATAATAATAT
1 TAGTATG-TAGTATTATTATTAGATATTATAACAATAT
*
16311196 TAGTA--TAGTATTATTATTAGA-ATTATTACAAT-T
1 TAGTATGTAGTATTATTATTAGATATTATAACAATAT
16311229 TAGTATGTAGTAT
1 TAGTATGTAGTAT
16311242 AGTATATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
33 6 0.15
34 9 0.22
35 20 0.50
38 5 0.12
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (37 bp):
TAGTATGTAGTATTATTATTAGATATTATAACAATAT
Found at i:16311284 original size:3 final size:3
Alignment explanation
Indices: 16311276--16311413 Score: 112
Period size: 3 Copynumber: 48.3 Consensus size: 3
16311266 TAGATGGTAC
* * * *
16311276 TAT TAT TAT TCT TAT TAT TAT TAT TAT CAT TA- CAC TA- TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* * * * * *
16311320 TA- TAC TA- TAG TA- TAT TA- TAT CAA TAC TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
16311364 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TA- TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16311410 TAT T
1 TAT T
16311414 TTCTTTCTTC
Statistics
Matches: 111, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
2 15 0.14
3 94 0.85
4 2 0.02
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:16311917 original size:14 final size:15
Alignment explanation
Indices: 16311898--16311927 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16311888 TTGAACATTT
16311898 AAATTTTTT-GGTGA
1 AAATTTTTTCGGTGA
16311912 AAATTTTTTCGGTGA
1 AAATTTTTTCGGTGA
16311927 A
1 A
16311928 TGTTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (15 bp):
AAATTTTTTCGGTGA
Found at i:16312288 original size:22 final size:21
Alignment explanation
Indices: 16312263--16312316 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
16312253 TTTTTCATTT
* *
16312263 TTTTTAATTTTATTCTTCTTAAT
1 TTTTT-ATTTTATT-ATCTTAAG
16312286 TTTTTATTTTATTATCTTAAG
1 TTTTTATTTTATTATCTTAAG
16312307 TTTTTATTTT
1 TTTTTATTTT
16312317 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.55
22 8 0.28
23 5 0.17
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTATTTTATTATCTTAAG
Found at i:16313682 original size:20 final size:21
Alignment explanation
Indices: 16313645--16313689 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
16313635 TAAAATACGT
16313645 TAAATCTTAAACACTAAA-CC
1 TAAATCTTAAACACTAAACCC
*
16313665 TAAATCTTAGAC-CATAAACCC
1 TAAATCTTAAACAC-TAAACCC
16313686 TAAA
1 TAAA
16313690 GTCAACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATCTTAAACACTAAACCC
Found at i:16313702 original size:18 final size:19
Alignment explanation
Indices: 16313679--16313726 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
16313669 TCTTAGACCA
* *
16313679 TAAACCCTAAAGTCAA-CC
1 TAAACCCTAAAATAAATCC
* *
16313697 TAAACCTTAAAATAAATCT
1 TAAACCCTAAAATAAATCC
16313716 TAAACCCTAAA
1 TAAACCCTAAA
16313727 CATTAAACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAACCCTAAAATAAATCC
Found at i:16315391 original size:17 final size:17
Alignment explanation
Indices: 16315369--16315421 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
16315359 AAATTAATTT
*
16315369 AACAAAAAAGGAATAAA
1 AACAAAAAAGAAATAAA
*
16315386 AACAAAAAACAAA-AAA
1 AACAAAAAAGAAATAAA
*
16315402 ATCAAAAAAGAAAATAAA
1 AACAAAAAAG-AAATAAA
16315420 AA
1 AA
16315422 AATGAAAAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 11 0.38
17 14 0.48
18 4 0.14
ACGTcount: A:0.81, C:0.08, G:0.06, T:0.06
Consensus pattern (17 bp):
AACAAAAAAGAAATAAA
Found at i:16315402 original size:16 final size:16
Alignment explanation
Indices: 16315369--16315420 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
16315359 AAATTAATTT
*
16315369 AACAAAAAAGGAATAAA
1 AACAAAAAA-GAAAAAA
*
16315386 AACAAAAAACAAAAAA
1 AACAAAAAAGAAAAAA
*
16315402 ATCAAAAAAGAAAATAA
1 AACAAAAAAGAAAA-AA
16315419 AA
1 AA
16315421 AAATGAAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.81, C:0.08, G:0.06, T:0.06
Consensus pattern (16 bp):
AACAAAAAAGAAAAAA
Found at i:16316265 original size:14 final size:13
Alignment explanation
Indices: 16316245--16316282 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
16316235 TAACAAAAAC
16316245 AAAAAAAAAGTTG
1 AAAAAAAAAGTTG
16316258 ACAAAAAAAA-TTG
1 A-AAAAAAAAGTTG
16316271 AAGAAAAAAAGT
1 AA-AAAAAAAGT
16316283 AAAAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 12 0.55
14 9 0.41
ACGTcount: A:0.71, C:0.03, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAAAAAAAGTTG
Found at i:16316423 original size:31 final size:31
Alignment explanation
Indices: 16316384--16316454 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
16316374 AATTATTAAT
*
16316384 TATATAAATAAAGTATTTTTATTAA-ACTAAGA
1 TATATAAATAAA-TAATTTTATTAATA-TAAGA
*
16316416 TAT-TAAAT-AATAATTTTATTAATATAATA
1 TATATAAATAAATAATTTTATTAATATAAGA
16316445 TATATAAATA
1 TATATAAATA
16316455 TAAAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
29 18 0.53
30 8 0.24
31 5 0.15
32 3 0.09
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (31 bp):
TATATAAATAAATAATTTTATTAATATAAGA
Found at i:16316457 original size:29 final size:29
Alignment explanation
Indices: 16316376--16316457 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
16316366 GATGGATGAA
*
16316376 TTATTAAT-T-ATATAAATAAAGTAT--TT
1 TTATTAATATAATATATATAAA-TATAATT
*
16316402 TTATTAA-ACTAAGATAT-TAAATAATAATT
1 TTATTAATA-TAATATATATAAAT-ATAATT
16316431 TTATTAATATAATATATATAAATATAA
1 TTATTAATATAATATATATAAATATAA
16316458 AAATGAAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
26 8 0.18
27 7 0.16
28 4 0.09
29 20 0.44
30 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATTAATATAATATATATAAATATAATT
Found at i:16317511 original size:20 final size:20
Alignment explanation
Indices: 16317486--16317539 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
16317476 ATAATGGATC
16317486 GATCCATTTTTATAGCGATA
1 GATCCATTTTTATAGCGATA
* *
16317506 GATCCATTTTTATAGGGATT
1 GATCCATTTTTATAGCGATA
* *
16317526 GATCTATTCTTATA
1 GATCCATTTTTATA
16317540 ATGGGTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
GATCCATTTTTATAGCGATA
Found at i:16320152 original size:138 final size:138
Alignment explanation
Indices: 16319904--16320182 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 138
16319894 TCAATTTAAG
16319904 ACATGGGATAAAATGCTTGATACCAATAACATCAAGAGTATTTTGAATGCATGTAATCAAGTATA
1 ACATGGGATAAAATGCTTGATACCAATAACATCAAGAGTATTTTGAATGCATGTAATCAAGTATA
16319969 ATATGCACAATGAAGTTCACATACATGTATTCAAGCACAAAACCATAAGTGTATCCAATTAAGAT
66 ATATGCACAATGAAGTTCACATACATGTATTCAAGCACAAAACCATAAGTGTATCCAATTAAGAT
16320034 GTTATAGC
131 GTTATAGC
* *
16320042 ACATGGGATACAATGCTTGATACCAATAATATCAAGAGTATTTTGAATGCATGTAATCAAGTATA
1 ACATGGGATAAAATGCTTGATACCAATAACATCAAGAGTATTTTGAATGCATGTAATCAAGTATA
16320107 ATATGCACAATGAAGTTCACATACATGTATTCAAGCACAAAACCATAAGTGTATCCAATTAAGAT
66 ATATGCACAATGAAGTTCACATACATGTATTCAAGCACAAAACCATAAGTGTATCCAATTAAGAT
16320172 GTTATAGC
131 GTTATAGC
16320180 ACA
1 ACA
16320183 AAATCATTCA
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (138 bp):
ACATGGGATAAAATGCTTGATACCAATAACATCAAGAGTATTTTGAATGCATGTAATCAAGTATA
ATATGCACAATGAAGTTCACATACATGTATTCAAGCACAAAACCATAAGTGTATCCAATTAAGAT
GTTATAGC
Found at i:16322184 original size:20 final size:20
Alignment explanation
Indices: 16322159--16322198 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16322149 ATCAATTGAG
16322159 CACAAAAATAA-AAAATATTT
1 CACAAAAATAATAAAA-ATTT
*
16322179 CACAAAATTAATAAAAATTT
1 CACAAAAATAATAAAAATTT
16322199 AAGCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
CACAAAAATAATAAAAATTT
Found at i:16326837 original size:9 final size:9
Alignment explanation
Indices: 16326817--16326862 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
16326807 AAAAAAGAAT
*
16326817 AAGATAAAA
1 AAGACAAAA
*
16326826 AAAACTAAAA
1 AAGAC-AAAA
16326836 AAGACAAAA
1 AAGACAAAA
16326845 AAG-C-AAA
1 AAGACAAAA
16326852 AAGACAAAA
1 AAGACAAAA
16326861 AA
1 AA
16326863 CAACAAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 15 0.48
10 8 0.26
ACGTcount: A:0.78, C:0.09, G:0.09, T:0.04
Consensus pattern (9 bp):
AAGACAAAA
Found at i:16326844 original size:16 final size:16
Alignment explanation
Indices: 16326784--16326875 Score: 55
Period size: 16 Copynumber: 5.8 Consensus size: 16
16326774 ATTTTAATTT
*
16326784 AAAAAA-ACTAAAAA-
1 AAAAAAGACAAAAAAG
* *
16326798 AAAATAGAGAAAAAAG
1 AAAAAAGACAAAAAAG
* * * *
16326814 AATAAGATAAAAAAAACT
1 AA-AAAAGACAAAAAA-G
16326832 AAAAAAGACAAAAAAG
1 AAAAAAGACAAAAAAG
* *
16326848 CAAAAAGACAAAAAAC
1 AAAAAAGACAAAAAAG
*
16326864 AACAAAGA-AAAA
1 AAAAAAGACAAAA
16326876 TAATGAGTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
14 5 0.08
15 10 0.17
16 22 0.37
17 20 0.34
18 2 0.03
ACGTcount: A:0.78, C:0.08, G:0.09, T:0.05
Consensus pattern (16 bp):
AAAAAAGACAAAAAAG
Found at i:16326956 original size:10 final size:10
Alignment explanation
Indices: 16326941--16326976 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
16326931 TATTATGGAT
16326941 TTAAAAAAAA
1 TTAAAAAAAA
*
16326951 TTAAAAAAGA
1 TTAAAAAAAA
16326961 TTAAAAAAAAA
1 TT-AAAAAAAA
16326972 TTAAA
1 TTAAA
16326977 TCTAGATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (10 bp):
TTAAAAAAAA
Found at i:16366869 original size:12 final size:14
Alignment explanation
Indices: 16366846--16366877 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
16366836 CTTAAACTTC
16366846 AAACTCTCATT-GA
1 AAACTCTCATTGGA
16366859 AAACT-TCATTGGA
1 AAACTCTCATTGGA
16366872 AAACTC
1 AAACTC
16366878 ATGTGTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (14 bp):
AAACTCTCATTGGA
Found at i:16367367 original size:3 final size:3
Alignment explanation
Indices: 16367359--16367403 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
16367349 GGAAAGCAGG
16367359 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16367404 TAAGATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16369442 original size:2 final size:2
Alignment explanation
Indices: 16369429--16369466 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16369419 AATTCCACCA
*
16369429 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16369467 TGACTGCTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:16369563 original size:21 final size:21
Alignment explanation
Indices: 16369539--16369582 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16369529 CCCACCGTTC
*
16369539 CTCATCCAACTTCAATTGGAG
1 CTCATCCAACTTCAACTGGAG
* *
16369560 CTCATCCACCTTCCACTGGAG
1 CTCATCCAACTTCAACTGGAG
16369581 CT
1 CT
16369583 GCTCTTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (21 bp):
CTCATCCAACTTCAACTGGAG
Found at i:16374997 original size:11 final size:11
Alignment explanation
Indices: 16374951--16374997 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
16374941 TTAAATATAA
16374951 AATATAAAATAT
1 AATATAAAA-AT
*
16374963 AATACAAAAAT
1 AATATAAAAAT
*
16374974 GATAT-AAAA-
1 AATATAAAAAT
16374983 AATATAAAAAT
1 AATATAAAAAT
16374994 AATA
1 AATA
16374998 CGAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.14
10 8 0.28
11 9 0.31
12 8 0.28
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:16375170 original size:42 final size:44
Alignment explanation
Indices: 16375088--16375177 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
16375078 GAATTTTGAT
** *
16375088 ATATAATTTTTTTATAAAACATGATATAAATATACAAATTA-TA
1 ATATAATTTTCATATAAAACATAATATAAATATACAAATTATTA
*
16375131 ATATAATTTTCATATAAAA-ATAATATAAATATATAAATTATTA
1 ATATAATTTTCATATAAAACATAATATAAATATACAAATTATTA
16375174 ATAT
1 ATAT
16375178 TTTACAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 19 0.45
43 23 0.55
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (44 bp):
ATATAATTTTCATATAAAACATAATATAAATATACAAATTATTA
Found at i:16375194 original size:42 final size:41
Alignment explanation
Indices: 16375101--16375194 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 41
16375091 TAATTTTTTT
* * *
16375101 ATAAAACATGATATAAATATACAAATTATAATATAATTTTCAT
1 ATAAAA-ATAATATAAATATACAAATTATAATAT-ATTTACAA
*
16375144 ATAAAAATAATATAAATATATAAATTATTAATAT-TTTACAAA
1 ATAAAAATAATATAAATATACAAATTA-TAATATATTTAC-AA
*
16375186 ATATAAATA
1 ATAAAAATA
16375195 CGCGAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
41 4 0.09
42 28 0.64
43 12 0.27
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (41 bp):
ATAAAAATAATATAAATATACAAATTATAATATATTTACAA
Found at i:16383434 original size:6 final size:6
Alignment explanation
Indices: 16383425--16383449 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16383415 TGATTTTTTT
16383425 ACAATA ACAATA ACAATA ACAATA A
1 ACAATA ACAATA ACAATA ACAATA A
16383450 AAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
ACAATA
Found at i:16385104 original size:21 final size:22
Alignment explanation
Indices: 16385067--16385119 Score: 81
Period size: 21 Copynumber: 2.4 Consensus size: 22
16385057 CCCAAAATTA
16385067 ATAAAATATTAATTTTTAAAAT
1 ATAAAATATTAATTTTTAAAAT
*
16385089 ATAAAATATT-ATTTTTTAAAT
1 ATAAAATATTAATTTTTAAAAT
16385110 ATAAATATAT
1 ATAAA-ATAT
16385120 AAATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTAATTTTTAAAAT
Found at i:16387020 original size:30 final size:30
Alignment explanation
Indices: 16386986--16387047 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
16386976 CCTAGCAACG
*
16386986 GCCCTTGAGTAGCTAATTGCCCTACCAATT
1 GCCCTTGAGTAGCTAACTGCCCTACCAATT
* *
16387016 GCCCTTGAGTAGCTGACTGCCCTAGCAATT
1 GCCCTTGAGTAGCTAACTGCCCTACCAATT
16387046 GC
1 GC
16387048 TAATGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (30 bp):
GCCCTTGAGTAGCTAACTGCCCTACCAATT
Found at i:16388016 original size:21 final size:21
Alignment explanation
Indices: 16387991--16388032 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16387981 TGATAACTAA
16387991 AAACAAATTAATTAAGGATTT
1 AAACAAATTAATTAAGGATTT
*
16388012 AAACAGATTAATTAAGGATTT
1 AAACAAATTAATTAAGGATTT
16388033 TTCTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (21 bp):
AAACAAATTAATTAAGGATTT
Found at i:16388913 original size:4 final size:4
Alignment explanation
Indices: 16388904--16388929 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16388894 TTTTGAATTA
16388904 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
16388930 TAGTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:16391317 original size:3 final size:3
Alignment explanation
Indices: 16391311--16391361 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
16391301 TAAATAAATA
* *
16391311 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16391359 AAT
1 AAT
16391362 TAAAAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16391764 original size:50 final size:49
Alignment explanation
Indices: 16391542--16391921 Score: 366
Period size: 49 Copynumber: 7.9 Consensus size: 49
16391532 TTGAAAATTT
* * * *
16391542 AAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTTTAAAATTTTTATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAAC-TTTAAAATTCTCATCTTG
*
16391592 AAAATAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAGAA-TCTTATCTTG
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAA-AATTCTCATCTTG
* ** *
16391642 AAAAAGCTTCTCTCAATAGAGGCTCAATAACTTTAAAA-----ATCTT-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
* * * * *
16391685 AAAAAACTCCTCTCAGTAGAGGCTTAATAACTTTAAAATTCTCATATTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
* * * *
16391734 AAAAAGGTTCATCTCAGTAGAGGCTCAATAACTTTAAAATT-T--TCTTG
1 AAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
* *
16391781 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAGATTCTCATTTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
* * * * * * *
16391830 GAAAAGCTCATCTGAGCAAAGGCTTAACAACTTTAAAATTTTCATTTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
* * **
16391879 GAAAAGCTCCTCTCAACAGAGTTTCAACAACTTTTAAAATTCT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAAC-TTTAAAATTCT
16391922 TTCTGTTCTC
Statistics
Matches: 279, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
43 34 0.12
44 5 0.02
46 30 0.11
47 10 0.04
48 6 0.02
49 104 0.37
50 63 0.23
51 27 0.10
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (49 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCATCTTG
Found at i:16391908 original size:98 final size:96
Alignment explanation
Indices: 16391542--16391921 Score: 351
Period size: 96 Copynumber: 3.9 Consensus size: 96
16391532 TTGAAAATTT
* * *
16391542 AAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTTTAAAATTTTTATCTTGAAAATAGCTCCTCTC
1 AAAAGGCTCATCTCAGCAAAGGCTCAACAAC-TTTAAAA--TTT-TCTTGAAAA-AGCTCCTCTC
* * *
16391607 AGCAGAGGCTCAACAACTTTAAGAA-TCTTATCTTGA
61 AACAGAGGCTCAACAACTTTAA-AATTCTCATATTGA
** * * * * **
16391643 AAAA-GCTTC-TCTCAATAGAGGCTCAATAACTTTAAAA--ATCTT-AAAAAACTCCTCTCAGTA
1 AAAAGGC-TCATCTCAGCAAAGGCTCAACAACTTTAAAATTTTCTTGAAAAAGCTCCTCTCAACA
* *
16391703 GAGGCTTAATAACTTTAAAATTCTCATATTGA
65 GAGGCTCAACAACTTTAAAATTCTCATATTGA
* * * * *
16391735 AAAAGGTTCATCTCAGTAGAGGCTCAATAACTTTAAAATTTTCTTGAAAAAGCTCCTCTCAGCAG
1 AAAAGGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATTTTCTTGAAAAAGCTCCTCTCAACAG
* * *
16391800 AGGCTCAACAACTTTAAGATTCTCATTTTGG
66 AGGCTCAACAACTTTAAAATTCTCATATTGA
* * *
16391831 AAAA-GCTCATCTGAGCAAAGGCTTAACAACTTTAAAATTTTCATTTTGGAAAAGCTCCTCTCAA
1 AAAAGGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATTTTC---TTGAAAAAGCTCCTCTCAA
**
16391895 CAGAGTTTCAACAACTTTTAAAATTCT
63 CAGAGGCTCAACAAC-TTTAAAATTCT
16391922 TTCTGTTCTC
Statistics
Matches: 236, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
91 2 0.01
92 43 0.18
93 32 0.14
94 4 0.02
95 36 0.15
96 47 0.20
98 30 0.13
99 17 0.07
100 19 0.08
101 6 0.03
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (96 bp):
AAAAGGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATTTTCTTGAAAAAGCTCCTCTCAACAG
AGGCTCAACAACTTTAAAATTCTCATATTGA
Found at i:16403455 original size:18 final size:17
Alignment explanation
Indices: 16403418--16403474 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
16403408 AAGAAGAAAA
* *
16403418 AAAAAGAAGGAAAGATAG
1 AAAAAGAA-AAAAAATAG
16403436 AAGAAAGAAAAAAAATAG
1 AA-AAAGAAAAAAAATAG
* *
16403454 AAAACGAAAAAAGA-AG
1 AAAAAGAAAAAAAATAG
16403470 AAAAA
1 AAAAA
16403475 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 6 0.18
17 10 0.30
18 11 0.33
19 6 0.18
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAAGAAAAAAAATAG
Found at i:16403471 original size:16 final size:15
Alignment explanation
Indices: 16403404--16403473 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 15
16403394 GGATAAGGAA
16403404 AAAAAAGAAG-AAA-
1 AAAAAAGAAGAAAAG
*
16403417 AAAAAAGAAGGAAAG
1 AAAAAAGAAGAAAAG
*
16403432 ---ATAGAAG-AAAG
1 AAAAAAGAAGAAAAG
*
16403443 AAAAAAAATAGAAAACG
1 AAAAAAGA-AGAAAA-G
16403460 AAAAAAGAAGAAAA
1 AAAAAAGAAGAAAA
16403474 AATTAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
11 4 0.09
12 6 0.13
13 10 0.22
14 6 0.13
15 2 0.04
16 9 0.20
17 8 0.18
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAGAAAAG
Found at i:16404888 original size:23 final size:23
Alignment explanation
Indices: 16404861--16404905 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16404851 TAAGATCCCA
16404861 TTTTTATTTTTATTCCTTTGTTG
1 TTTTTATTTTTATTCCTTTGTTG
*
16404884 TTTTTATTTTTATTCTTTTGTT
1 TTTTTATTTTTATTCCTTTGTT
16404906 TAATCTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (23 bp):
TTTTTATTTTTATTCCTTTGTTG
Found at i:16405322 original size:33 final size:30
Alignment explanation
Indices: 16405284--16405353 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
16405274 GGTTTTAAGG
*
16405284 TTTAGGATTAAATTTAAGGTTTAGGGTTTTGGT
1 TTTAGGATTAAAGTT-AGGTTTAGGG-TTT-GT
* *
16405317 TTTAGGGTTTAAGGTTAGGTTTAGGGTTTGT
1 TTTA-GGATTAAAGTTAGGTTTAGGGTTTGT
16405348 TTTAGG
1 TTTAGG
16405354 GTTTAGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 6 0.18
32 3 0.09
33 14 0.42
34 8 0.24
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (30 bp):
TTTAGGATTAAAGTTAGGTTTAGGGTTTGT
Found at i:16405337 original size:52 final size:52
Alignment explanation
Indices: 16405281--16405384 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
16405271 GTTGGTTTTA
* *
16405281 AGGTTTAGGATTAAATTTAAGGTTTAGGGTTTTGGTTTTAGGGTTTAAGGTT
1 AGGTTTAGGATTAAATTTAAGGTTTAGGATTTTGGTTTTAAGGTTTAAGGTT
* *** *
16405333 AGGTTTAGGGTTTGTTTTAGGGTTTAGGATTTTGGTTTTAAGGTTTAAGGTT
1 AGGTTTAGGATTAAATTTAAGGTTTAGGATTTTGGTTTTAAGGTTTAAGGTT
16405385 TTGGTTAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (52 bp):
AGGTTTAGGATTAAATTTAAGGTTTAGGATTTTGGTTTTAAGGTTTAAGGTT
Found at i:16405345 original size:40 final size:41
Alignment explanation
Indices: 16405204--16405345 Score: 123
Period size: 40 Copynumber: 3.6 Consensus size: 41
16405194 TACAATTGGT
* * * *
16405204 TTTAAGGTTTAGGGTTA-GATTTAGGATTTTAGTTTTAGGG
1 TTTAAGGATTAGGTTTAGGGTTTAGGATTTTGGTTTTAGGG
** * * *
16405244 TTTAAAGTTTTAGTTTTAGGGTTT--GATGTTGGTTTTAAGG
1 TTT-AAGGATTAGGTTTAGGGTTTAGGATTTTGGTTTTAGGG
** * *
16405284 TTT-AGGATTAAATTTAAGGTTTAGGGTTTTGGTTTTAGGG
1 TTTAAGGATTAGGTTTAGGGTTTAGGATTTTGGTTTTAGGG
16405324 TTTAAGG-TTAGGTTTAGGGTTT
1 TTTAAGGATTAGGTTTAGGGTTT
16405346 GTTTTAGGGT
Statistics
Matches: 79, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
38 14 0.18
40 47 0.59
41 14 0.18
42 4 0.05
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (41 bp):
TTTAAGGATTAGGTTTAGGGTTTAGGATTTTGGTTTTAGGG
Found at i:16405352 original size:45 final size:46
Alignment explanation
Indices: 16405253--16405501 Score: 172
Period size: 45 Copynumber: 5.5 Consensus size: 46
16405243 GTTTAAAGTT
* * * * * **
16405253 TTAGTTTTAGGG-TTTGATGTT-GGTTTTAAGGTTTAGGATTAAAT
1 TTAGTTTTAGGGTTTTGGTTTTAGGGTTTAAGGTTAAGGTTTAAGG
* *
16405297 TTAAGGTTTAGGGTTTTGGTTTTAGGGTTTAAGGTT-AGGTTTAGGG
1 TT-AGTTTTAGGGTTTTGGTTTTAGGGTTTAAGGTTAAGGTTTAAGG
* * * *
16405343 TTTGTTTTAGGGTTTAGGATTTT-GGTTTTAAGGTTTAAGGTTT-TGG
1 TTAGTTTTAGGGTTTTGG-TTTTAGGGTTTAAGG-TTAAGGTTTAAGG
** ** * * *
16405389 TTAGTTTTAGGG-TTTGGAGTTAGGGCGTCAGTTTAGGGTTTAAGG
1 TTAGTTTTAGGGTTTTGGTTTTAGGGTTTAAGGTTAAGGTTTAAGG
* * * *
16405434 TTAGGTTTAGAGTTTAGGTTTTAGGGTTT--GTTTTAAGGTTTAAGG
1 TTAGTTTTAGGGTTTTGGTTTTAGGGTTTAAG-GTTAAGGTTTAAGG
16405479 TTAGTGTTTAGGGTTTATGGTTT
1 TTAGT-TTTAGGGTTT-TGGTTT
16405502 GTTTTAAGGC
Statistics
Matches: 158, Mismatches: 35, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
44 13 0.08
45 69 0.44
46 54 0.34
47 22 0.14
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.49
Consensus pattern (46 bp):
TTAGTTTTAGGGTTTTGGTTTTAGGGTTTAAGGTTAAGGTTTAAGG
Found at i:16405377 original size:21 final size:20
Alignment explanation
Indices: 16405223--16405390 Score: 79
Period size: 21 Copynumber: 8.7 Consensus size: 20
16405213 TAGGGTTAGA
* *
16405223 TTTAGGATTTTAGTTTTAGGG
1 TTTAGG-TTTTGGTTTTAAGG
* * *
16405244 TTTAAAGTTTTAGTTTTAGGG
1 TTT-AGGTTTTGGTTTTAAGG
* *
16405265 TTT-GATGTTGGTTTTAAGG
1 TTTAGGTTTTGGTTTTAAGG
* ***
16405284 TTTAGG-ATTAAATTTAAGG
1 TTTAGGTTTTGGTTTTAAGG
*
16405303 TTTAGGGTTTTGGTTTTAGGG
1 TTTA-GGTTTTGGTTTTAAGG
*
16405324 TTTA-----AGG--TT-AGG
1 TTTAGGTTTTGGTTTTAAGG
* *
16405336 TTTAGGGTTT-GTTTTAGGG
1 TTTAGGTTTTGGTTTTAAGG
16405355 TTTAGGATTTTGGTTTTAAGG
1 TTTAGG-TTTTGGTTTTAAGG
16405376 TTTAAGGTTTTGGTT
1 TTT-AGGTTTTGGTT
16405391 AGTTTTAGGG
Statistics
Matches: 110, Mismatches: 22, Indels: 30
0.68 0.14 0.19
Matches are distributed among these distances:
12 6 0.05
13 2 0.02
15 2 0.02
16 1 0.01
18 2 0.02
19 35 0.32
20 6 0.05
21 51 0.46
22 5 0.05
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (20 bp):
TTTAGGTTTTGGTTTTAAGG
Found at i:16405488 original size:39 final size:38
Alignment explanation
Indices: 16405427--16405520 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 38
16405417 CAGTTTAGGG
*
16405427 TTTAAGGTT-AGGTTTAGAGTTTAGGTTTTAGGGTTTGT
1 TTTAAGGTTAAGG-TTAGAGTTTAGGGTTTAGGGTTTGT
* *
16405465 TTTAAGGTTTAAGGTTAGTGTTTAGGGTTTATGGTTTGT
1 TTTAAGG-TTAAGGTTAGAGTTTAGGGTTTAGGGTTTGT
*
16405504 TTTAAGGCTTAGGGTTA
1 TTTAAGG-TTAAGGTTA
16405521 ATTCTAAGGT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 7 0.14
39 39 0.80
40 3 0.06
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (38 bp):
TTTAAGGTTAAGGTTAGAGTTTAGGGTTTAGGGTTTGT
Found at i:16405519 original size:19 final size:19
Alignment explanation
Indices: 16405453--16405519 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
16405443 GAGTTTAGGT
16405453 TTTAGGGTTTGTTTTAAGG
1 TTTAGGGTTTGTTTTAAGG
* * *
16405472 TTTAAGGTTAGTGTTTAGGG
1 TTTAGGGTTTGT-TTTAAGG
*
16405492 TTTATGGTTTGTTTTAAGG
1 TTTAGGGTTTGTTTTAAGG
*
16405511 CTTAGGGTT
1 TTTAGGGTT
16405520 AATTCTAAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.16, C:0.01, G:0.31, T:0.51
Consensus pattern (19 bp):
TTTAGGGTTTGTTTTAAGG
Found at i:16409053 original size:16 final size:18
Alignment explanation
Indices: 16409022--16409055 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16409012 TCAAAATTAA
16409022 AAAAATAAATAAAAAAGT
1 AAAAATAAATAAAAAAGT
16409040 AAAAA-AAA-AAAAAAGT
1 AAAAATAAATAAAAAAGT
16409056 CAGTCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAAATAAATAAAAAAGT
Found at i:16410048 original size:12 final size:12
Alignment explanation
Indices: 16410031--16410059 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16410021 CTAACCTCTC
16410031 TTTTTTTTTCTT
1 TTTTTTTTTCTT
16410043 TTTTTTTTTCTT
1 TTTTTTTTTCTT
16410055 TTTTT
1 TTTTT
16410060 ATAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:16412134 original size:240 final size:239
Alignment explanation
Indices: 16411712--16412175 Score: 820
Period size: 240 Copynumber: 1.9 Consensus size: 239
16411702 TCAAGTTCTT
* *
16411712 ATATATATATTCTATTTTTTCTTTTAACAAAACTGTTATTGTCAAAATAAATAAATAAATAAAAA
1 ATATATATATTATATTTTTTCTTTTAACAAAACTATTATTGTCAAAATAAATAAATAAATAAAAA
* *
16411777 TTCAACATTGTTTCCGACAAAACAAATTCTCTTCCATAGCACATAACGGCTTAGTTGGGATATTA
66 TTCAACATTGTTGCCGACAAAACAAATTCTCTTCCATAGCACATAACGGCTTAGTTAGGATATTA
*
16411842 ATCCTCCTGCTCGAGTTGTCTGAATAATTGTCAACTTGGAAATCAAGCTATGCACCAGTATGACT
131 ATCCTCCTGCTCGAGTTGTCTGAATAATTGACAACTTGGAAATCAAGCTATGCACCAGTATGACT
16411907 AAGATTTAACTTTCTTCTCCACATTTCAACGGTCCTTTCCCAGC
196 AAGATTTAACTTTCTTCTCCACATTTCAACGGTCCTTTCCCAGC
16411951 ATATATATATTATATTTTTTCTTTTAACAAAACTATTATTGTCCAAAATAAATAAATAAATAAAA
1 ATATATATATTATATTTTTTCTTTTAACAAAACTATTATTGT-CAAAATAAATAAATAAATAAAA
* * *
16412016 ATTCAACATTGTTGCCGACGAAACAAATTCTCTTCCGTAGCATATAACGGCTTAGTTAGGATATT
65 ATTCAACATTGTTGCCGACAAAACAAATTCTCTTCCATAGCACATAACGGCTTAGTTAGGATATT
* *
16412081 AATCCTCTTGCTTGAGTTGTCTGAATAATTGACAACTTGGAAATCAAGCTATGCACCAGTATGAC
130 AATCCTCCTGCTCGAGTTGTCTGAATAATTGACAACTTGGAAATCAAGCTATGCACCAGTATGAC
*
16412146 TAGGATTTAACTTTCTTCTCCACATTTCAA
195 TAAGATTTAACTTTCTTCTCCACATTTCAA
16412176 TAGTCCCTTC
Statistics
Matches: 213, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
239 40 0.19
240 173 0.81
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (239 bp):
ATATATATATTATATTTTTTCTTTTAACAAAACTATTATTGTCAAAATAAATAAATAAATAAAAA
TTCAACATTGTTGCCGACAAAACAAATTCTCTTCCATAGCACATAACGGCTTAGTTAGGATATTA
ATCCTCCTGCTCGAGTTGTCTGAATAATTGACAACTTGGAAATCAAGCTATGCACCAGTATGACT
AAGATTTAACTTTCTTCTCCACATTTCAACGGTCCTTTCCCAGC
Found at i:16419050 original size:20 final size:20
Alignment explanation
Indices: 16419025--16419075 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
16419015 AAACCCAAAA
*
16419025 AAAAACTCAAAAAAGTCTAG
1 AAAAACTCAAAAAAGTCCAG
* *
16419045 AAAAAC-CTAAAAATTCCAG
1 AAAAACTCAAAAAAGTCCAG
16419064 AAAAACCTCAAA
1 AAAAA-CTCAAA
16419076 CCTTCCCGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 15 0.60
20 7 0.28
21 3 0.12
ACGTcount: A:0.61, C:0.20, G:0.06, T:0.14
Consensus pattern (20 bp):
AAAAACTCAAAAAAGTCCAG
Found at i:16419482 original size:3 final size:3
Alignment explanation
Indices: 16419466--16419627 Score: 90
Period size: 3 Copynumber: 54.3 Consensus size: 3
16419456 AAATAAAAAA
* * *
16419466 AAT AAA AAT GAT AAT AAT AAT AAT AAT AAT -AT AGT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
16419512 AAT AGT AAT -AT AAT AA- AAGT AAT -AT AA- GAT ACT -AT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT A-AT
** * *
16419554 AAT AAT GGT AAT AAAT ATAT AAT AAT -AT AAT ATAT AAC AAA AAT AAAT
1 AAT AAT AAT AAT -AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT
*
16419602 ATAT AAT ATAT ACT -AT AAT AAT AAT A
1 A-AT AAT A-AT AAT AAT AAT AAT AAT A
16419628 TCTAATATAT
Statistics
Matches: 121, Mismatches: 21, Indels: 34
0.69 0.12 0.19
Matches are distributed among these distances:
2 15 0.12
3 83 0.69
4 23 0.19
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16419505 original size:17 final size:17
Alignment explanation
Indices: 16419483--16419628 Score: 75
Period size: 17 Copynumber: 8.9 Consensus size: 17
16419473 ATGATAATAA
16419483 TAATAATAATAATATAG
1 TAATAATAATAATATAG
16419500 TAATAAT-ATAATAATAG
1 TAATAATAATAAT-ATAG
16419517 TAAT-ATAATAA-A-AG
1 TAATAATAATAATATAG
*
16419531 TAAT-ATAA-GATACTA-
1 TAATAATAATAATA-TAG
* *
16419546 TAATATATAATAATGGTAA
1 TAATA-ATAATAAT-ATAG
*
16419565 TAAATATATAATAATATAA
1 T-AATA-ATAATAATATAG
*
16419584 TATATAACAA-AA-ATA-
1 TA-ATAATAATAATATAG
*
16419599 -AATATATAAT-ATATAC
1 TAATA-ATAATAATATAG
16419615 T-ATAATAATAATAT
1 TAATAATAATAATAT
16419629 CTAATATATA
Statistics
Matches: 105, Mismatches: 6, Indels: 37
0.71 0.04 0.25
Matches are distributed among these distances:
13 4 0.04
14 16 0.15
15 13 0.12
16 18 0.17
17 25 0.24
18 8 0.08
19 8 0.08
20 13 0.12
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (17 bp):
TAATAATAATAATATAG
Found at i:16419525 original size:45 final size:44
Alignment explanation
Indices: 16419476--16419638 Score: 141
Period size: 45 Copynumber: 3.8 Consensus size: 44
16419466 AATAAAAATG
16419476 ATAATA-ATAATAATAATAATATAGTAATAATATAATAATAGTAAT
1 ATAATATATAATAAT-ATAATATA-TAATAATATAATAATAGTAAT
*
16419521 ATAATA-A-AAGTAATATAAGATACTATAAT-ATATAATAATGGTAAT
1 ATAATATATAA-TAATAT-A-ATA-TATAATAATATAATAATAGTAAT
*
16419566 A-AATATATAATAATATAATATATAACAA-A-AATAA-A-T-AT
1 ATAATATATAATAATATAATATATAATAATATAATAATAGTAAT
*
16419604 ATAATATATACTATAATAATAATATCTAAT-ATATA
1 ATAATATATA--ATAAT-ATAATATATAATAATATA
16419639 GTATACTCAT
Statistics
Matches: 100, Mismatches: 5, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
38 3 0.03
39 9 0.09
41 11 0.11
42 17 0.17
43 5 0.05
44 9 0.09
45 35 0.35
46 9 0.09
47 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (44 bp):
ATAATATATAATAATATAATATATAATAATATAATAATAGTAAT
Found at i:16421430 original size:92 final size:90
Alignment explanation
Indices: 16421235--16421431 Score: 205
Period size: 92 Copynumber: 2.1 Consensus size: 90
16421225 AGCCATCTTT
** *
16421235 CTGAACTTTTTCTTTTTAGTTCAAGTTGCCATTTCGAGTTCTCAACTCAAATTTTCTCTTTGGGT
1 CTGAACTTTTT-TTTTTAGTTCAAGTCACCATTTCAAGTTCTCAACTCAAATTTTCTCTTTGGGT
* * * *
16421300 CTAAGCTGCCCTATTAGGTTTTCAAC
65 CCAAGCTACCCTATCAGGTTTTAAAC
* * * * * * *
16421326 CTAAACTTTTTTTTTTTAGGTTCAAGTCACCTTTTCAATTTTTCAACTCAAACTTTTTTTTTTTG
1 CTGAAC-TTTTTTTTTTA-GTTCAAGTCACCATTTCAAGTTCTCAACTCAAA-TTTTCTCTTTGG
*
16421391 GTCCAAGCTACCCTATCGGGTTTTAAAC
63 GTCCAAGCTACCCTATCAGGTTTTAAAC
* *
16421419 TTGAACCTTTTTT
1 CTGAACTTTTTTT
16421432 GTGTTATTTT
Statistics
Matches: 85, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
91 11 0.13
92 38 0.45
93 36 0.42
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (90 bp):
CTGAACTTTTTTTTTTAGTTCAAGTCACCATTTCAAGTTCTCAACTCAAATTTTCTCTTTGGGTC
CAAGCTACCCTATCAGGTTTTAAAC
Found at i:16421449 original size:11 final size:10
Alignment explanation
Indices: 16421435--16421469 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
16421425 CTTTTTTGTG
16421435 TTATTTTTATT
1 TTATTTTT-TT
16421446 TTATTTTGTTT
1 TTATTTT-TTT
16421457 TTATTTTTTT
1 TTATTTTTTT
16421467 TTA
1 TTA
16421470 AGTTCAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 16 0.70
12 1 0.04
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (10 bp):
TTATTTTTTT
Found at i:16421452 original size:21 final size:21
Alignment explanation
Indices: 16421428--16421469 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16421418 CTTGAACCTT
16421428 TTTTG-TGTTATTTTTATTTTA
1 TTTTGTTGTTATTTTT-TTTTA
*
16421449 TTTTGTTTTTATTTTTTTTTA
1 TTTTGTTGTTATTTTTTTTTA
16421470 AGTTCAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (21 bp):
TTTTGTTGTTATTTTTTTTTA
Found at i:16421468 original size:16 final size:16
Alignment explanation
Indices: 16421438--16421467 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16421428 TTTTGTGTTA
16421438 TTTTTATTTTATTTTG
1 TTTTTATTTTATTTTG
16421454 TTTTTATTTT-TTTT
1 TTTTTATTTTATTTT
16421468 TAAGTTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTTATTTTATTTTG
Found at i:16424321 original size:47 final size:46
Alignment explanation
Indices: 16424170--16424773 Score: 720
Period size: 47 Copynumber: 12.9 Consensus size: 46
16424160 TGAAAGTTTA
*
16424170 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTCATG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTG
** * * *
16424215 AAAAACCTCCTTTCAGTAGAGGCTCAACGACTTTAAAATCTCATCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTG
* * *
16424263 AAAAGGTTCCTCTCAGCAGAGGCTTAACAACTTTAAAAATTTTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTG
* *
16424310 AAAAGGCTCCTCTCAGCAGAGGCTTAACGACTTTAAAATTCTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTG
* *
16424356 AAAAAGCTCCTCTCAGCA-AGGCTCAACGACTTTAAAA-TCTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTG
* *
16424400 AAAAGGTTCCTCTCAGCAGAGGCTCAACAACTTAAAAAATTCTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTT-TAAAATTCTCTTG
*
16424447 AAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATTCTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTG
* *
16424494 AAAAGGCTTCTCTCAGTAGAGGCTCAACAACTTTAAAATCTCATCTTGG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTT-G
* *
16424543 AAAA-GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATCTCATCTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTG
* * *
16424590 AAAA-GCTCCTCTCAACAGAGGTTCAATAACTTTAAAA-TCTCATATG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC-T-TG
* * *
16424636 AAAA-ACTCCTCTCAGCAGAGGCTCCACAACTTTAAAATCTCATCTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTG
* * *
16424683 AAAA-GCTCCCCTCAACAGAGGCTCCACAACTTTAAAAAAATTCTCTTG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT---AAAATTCTCTTG
* *
16424731 AAAAGGCTCCTCTCAACAGAGGCTCAATAACTTTAAAATTCTC
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC
16424774 ATCTGTTTTC
Statistics
Matches: 488, Mismatches: 51, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
44 25 0.05
45 67 0.14
46 79 0.16
47 187 0.38
48 85 0.17
49 40 0.08
50 5 0.01
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (46 bp):
AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTG
Found at i:16424573 original size:95 final size:92
Alignment explanation
Indices: 16424170--16424773 Score: 720
Period size: 93 Copynumber: 6.5 Consensus size: 92
16424160 TGAAAGTTTA
* ** * *
16424170 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTCATGAAAAACCTCCTTTCAGTAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAGGCTCCTCTCAGCAG
*
16424234 AGGCTCAACGACTTTAAAATCTCATCTTG
66 AGGCTCAACAACTTTAAAAT-TC-TCTTG
* * *
16424263 AAAAGGTTCCTCTCAGCAGAGGCTTAACAACTTTAAAAATTTTCTTGAAAAGGCTCCTCTCAGCA
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTGAAAAGGCTCCTCTCAGCA
* *
16424328 GAGGCTTAACGACTTTAAAATTCTCTTG
65 GAGGCTCAACAACTTTAAAATTCTCTTG
* * *
16424356 AAAAAGCTCCTCTCAGCA-AGGCTCAACGACTTTAAAA-TCTCTTGAAAAGGTTCCTCTCAGCAG
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAGGCTCCTCTCAGCAG
*
16424419 AGGCTCAACAACTTAAAAAATTCTCTTG
66 AGGCTCAACAACTT-TAAAATTCTCTTG
* * *
16424447 AAAAGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAAATTCTCTTGAAAAGGCTTCTCTCAGTA
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTGAAAAGGCTCCTCTCAGCA
16424512 GAGGCTCAACAACTTTAAAATCTCATCTTGG
65 GAGGCTCAACAACTTTAAAAT-TC-TCTT-G
* * *
16424543 AAAA-GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATCTCATCTAGAAAA-GCTCCTCTCAAC
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTGAAAAGGCTCCTCTCAGC
* *
16424606 AGAGGTTCAATAACTTTAAAA-TCTCATATG
64 AGAGGCTCAACAACTTTAAAATTCTC-T-TG
* * * * *
16424636 AAAA-ACTCCTCTCAGCAGAGGCTCCACAACTTTAAAATCTCATCTAGAAAA-GCTCCCCTCAAC
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TC-TCTTGAAAAGGCTCCTCTCAGC
*
16424699 AGAGGCTCCACAACTTTAAAAAAATTCTCTTG
64 AGAGGCTCAACAACTTT---AAAATTCTCTTG
* *
16424731 AAAAGGCTCCTCTCAACAGAGGCTCAATAACTTTAAAATTCTC
1 AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC
16424774 ATCTGTTTTC
Statistics
Matches: 451, Mismatches: 42, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
90 36 0.08
91 32 0.07
92 29 0.06
93 141 0.31
94 53 0.12
95 108 0.24
96 48 0.11
97 4 0.01
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.26
Consensus pattern (92 bp):
AAAAGGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAGGCTCCTCTCAGCAG
AGGCTCAACAACTTTAAAATTCTCTTG
Found at i:16428869 original size:60 final size:60
Alignment explanation
Indices: 16428540--16428982 Score: 521
Period size: 59 Copynumber: 7.3 Consensus size: 60
16428530 NNNNNNNNNN
* * *
16428540 TTTCAACTTTTCCCCAAAAAAT--TTTTTTGGGAAATTTTCATTTTCAAGGAAAATCTGATAC
1 TTTCAACTTTTCCTC-AAAAATCCTTTTTT-GAAAATTTTGATTTTCAAGGAAAAT-TGATAC
* *
16428601 TTTCAACTTTTCCTCAAAAATCTTTTTTTGAAAA-TTT-ATTTTTAAGGAAAATTGATAC
1 TTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
* *
16428659 TTTCAATTTTTCC-CTAAAAAT-ATTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
1 TTTCAACTTTTCCTC-AAAAATCCTTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
* ** * *
16428718 TTTCAACTTTTCCCCAAAAATCCTTTGTTTTTGAAAATTTATTTTTTTTAAGGAAAATTCATAC
1 TTTCAACTTTTCCTCAAAAATCC--T-TTTTTGAAAATTT-TGATTTTCAAGGAAAATTGATAC
* *
16428782 TTTCAACTTTTTCCT-AAAAAT-ATTTTTTGAAAATTTTGATTTTCAAAGAAAATTGATAC
1 TTTCAAC-TTTTCCTCAAAAATCCTTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
*
16428841 TTTCAACTTTTCCTCAAAAATCCTTTTTTTGGAAATTTTGATTTTCAAGGAAAATTGATAC
1 TTTCAACTTTTCCTCAAAAATCC-TTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
* * * *
16428902 TTTCAACTTTTCCTCAAGAACCTCTTTTTTG-AAATTTT-ATTTTTAAAGAAAAATTGATAC
1 TTTCAACTTTTCCTCAAAAATC-CTTTTTTGAAAATTTTGA-TTTTCAAGGAAAATTGATAC
16428962 TTTCAACTTTTCC-CTAAAAAT
1 TTTCAACTTTTCCTC-AAAAAT
16428983 ATATTTTTTT
Statistics
Matches: 336, Mismatches: 28, Indels: 37
0.84 0.07 0.09
Matches are distributed among these distances:
57 12 0.04
58 34 0.10
59 85 0.25
60 65 0.19
61 81 0.24
62 8 0.02
63 13 0.04
64 32 0.10
65 6 0.02
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (60 bp):
TTTCAACTTTTCCTCAAAAATCCTTTTTTGAAAATTTTGATTTTCAAGGAAAATTGATAC
Found at i:16429040 original size:15 final size:15
Alignment explanation
Indices: 16428999--16429063 Score: 69
Period size: 15 Copynumber: 4.2 Consensus size: 15
16428989 TTTTTATTTT
16428999 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
*
16429014 T-AAAAGTGAAAAAAA
1 TAAAAAAT-AAAAAAA
*
16429029 TAAAAAATAAAAAAG
1 TAAAAAATAAAAAAA
*
16429044 TAAAACAAAAATAAAAA
1 TAAAA-AATAA-AAAAA
16429061 TAA
1 TAA
16429064 GATAAAGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
14 5 0.12
15 20 0.49
16 9 0.22
17 7 0.17
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (15 bp):
TAAAAAATAAAAAAA
Found at i:16429961 original size:6 final size:6
Alignment explanation
Indices: 16429952--16430112 Score: 54
Period size: 6 Copynumber: 26.2 Consensus size: 6
16429942 GAAAACAAAA
16429952 AATAAT AATAAT AAT-AT AATAAT AATAA- ATATAACT ATATAAAT AA-AAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT A-ATAA-T A-AT-AAT AATAAT
* * * *
16430001 ACAT-AT AAATATT AATAGA- AAAAAA AATAA- AGAT-AT ACAT-AT ATTAAT
1 A-ATAAT -AATAAT AATA-AT AATAAT AATAAT A-ATAAT A-ATAAT AATAAT
* * *
16430049 ACATAAT AATAAT AAATAAAT AATAA- AATACAT AA-AAT ACAAAAG AATAAA
1 A-ATAAT AATAAT -AAT-AAT AATAAT AATA-AT AATAAT A-ATAAT AATAAT
*
16430100 AATAAA AATAAT A
1 AATAAT AATAAT A
16430113 CAAAATAAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 42
0.70 0.06 0.24
Matches are distributed among these distances:
5 21 0.17
6 72 0.59
7 19 0.15
8 9 0.07
9 2 0.02
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (6 bp):
AATAAT
Found at i:16430087 original size:17 final size:17
Alignment explanation
Indices: 16429952--16430084 Score: 63
Period size: 17 Copynumber: 7.9 Consensus size: 17
16429942 GAAAACAAAA
16429952 AATAATAAT-AAT-AAT
1 AATAATAATAAATAAAT
16429967 -ATAATAAT-AATAAAT
1 AATAATAATAAATAAAT
16429982 -ATAACTATATAAAT-AA-
1 AATAA-TA-ATAAATAAAT
16429998 AATACAT-ATAAATATTAAT
1 AATA-ATAATAAATA--AAT
* *
16430017 AGA-AA-AAAAAATAAAG
1 A-ATAATAATAAATAAAT
* *
16430033 ATATACATATATTAATACAT
1 A-ATA-ATA-ATAAATAAAT
16430053 AATAATAATAAATAAAT
1 AATAATAATAAATAAAT
*
16430070 AATAA-AATACATAAA
1 AATAATAATAAATAAA
16430085 ATACAAAAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
14 11 0.12
15 13 0.14
16 15 0.16
17 22 0.24
18 17 0.18
19 6 0.07
20 8 0.09
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
AATAATAATAAATAAAT
Found at i:16430092 original size:16 final size:15
Alignment explanation
Indices: 16430053--16430124 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 15
16430043 ATTAATACAT
*
16430053 AATAATAATAAATAAA
1 AATAAAAAT-AATAAA
16430069 TAAT-AAAATACAT-AA
1 -AATAAAAATA-ATAAA
*
16430084 AATACAAAAGAATAAA
1 AATA-AAAATAATAAA
16430100 AATAAAAATAATACAA
1 AATAAAAATAATA-AA
16430116 AATAAAAAT
1 AATAAAAAT
16430125 TGAATTGGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 3 0.06
15 13 0.28
16 28 0.60
17 3 0.06
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:16430454 original size:41 final size:41
Alignment explanation
Indices: 16430320--16430613 Score: 457
Period size: 41 Copynumber: 7.1 Consensus size: 41
16430310 TTTTACCAAA
* * *
16430320 GCTCTTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-ATAAATT
*
16430363 GCTCCTCTAAACAGAGGCATCACGACTTT-GAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
* *
16430403 GCTCCTCTAAACAGAGGCATCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
* *
16430444 GCTCCTCTAAACAGAGACACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
16430485 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAACTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA-TAAATT
*
16430526 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
*
16430567 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
16430608 GCTCCT
1 GCTCCT
16430614 TGACAGTTGA
Statistics
Matches: 236, Mismatches: 12, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
40 40 0.17
41 167 0.71
42 4 0.02
43 25 0.11
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
Found at i:16431872 original size:22 final size:22
Alignment explanation
Indices: 16431847--16431889 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16431837 TTTCTCATTT
*
16431847 TTTTTTCTTTTTTTTCA-CCATC
1 TTTTTT-TTATTTTTCATCCATC
16431869 TTTTTTTTATTTTTCATCCAT
1 TTTTTTTTATTTTTCATCCAT
16431890 TGTTGATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTTTTATTTTTCATCCATC
Found at i:16436085 original size:59 final size:57
Alignment explanation
Indices: 16435805--16436307 Score: 647
Period size: 58 Copynumber: 8.6 Consensus size: 57
16435795 TTGTGTAGGG
* * * *
16435805 AAAATTGATACTTTCAACTTTTCCCCAAAATTATTTTTTTG-AAATTTATTTTTTTAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAAATTTA-TTTTTAAGA
*
16435863 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTATTTTTAAGA
*
16435920 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAAT-ATTTTTTGAAAATTTATTTTTAAGA
*
16435978 AAAATTGATACTTTCAA-TTTTCCCTAAAAATATTTTTTGAAAATTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAA-TTT-ATTTTTAAGA
* * * *
16436036 AAAATTGATACTTTCAACTTTTCCCTAAAAGTATTTTTTGAAAATTTTGACTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAA-TTT-ATTTTTAAGA
* *
16436095 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCCTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAAT--ATTTTTTGAAAATTTATTTTTAAGA
*
16436154 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGAAAA-TTT-ATTTTTAAGA
* * * *
16436214 AAAATTGATACTTTTAACTTTT-CCTCAAGAACCTCTTTTTTGAAATTTTATTTTTAAAGA
1 AAAATTGATACTTTCAACTTTTCCCT-AA-AA-ATATTTTTTGAAAATTTATTTTT-AAGA
16436274 AAAATTGATACTTTCAACTTTTCCCTAAAAATAT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATAT
16436308 ATATATTTTT
Statistics
Matches: 400, Mismatches: 26, Indels: 38
0.86 0.06 0.08
Matches are distributed among these distances:
56 14 0.04
57 55 0.14
58 123 0.31
59 114 0.28
60 67 0.17
61 26 0.06
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTATTTTTAAGA
Found at i:16436363 original size:16 final size:15
Alignment explanation
Indices: 16436322--16436382 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 15
16436312 ATTTTTTTAA
16436322 AAAAATAAAAAAAAT
1 AAAAATAAAAAAAAT
*
16436337 AAAAGTGAAAAAAAAT
1 AAAAAT-AAAAAAAAT
16436353 AAAAAATAAAAATAAGAT
1 -AAAAATAAAAA-AA-AT
*
16436371 AAAGATAAAAAA
1 AAAAATAAAAAA
16436383 TATTAAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.13
16 15 0.38
17 17 0.44
18 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:16436378 original size:24 final size:23
Alignment explanation
Indices: 16436320--16436384 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
16436310 ATATTTTTTT
* *
16436320 AAAAAAATAAAAAAAATAAAAGTG
1 AAAAAAA-ATAAAAAATAAAAATG
16436344 AAAAAAAATAAAAAATAAAAAT-
1 AAAAAAAATAAAAAATAAAAATG
*
16436366 AAGATAAAGATAAAAAATA
1 AA-A-AAAAATAAAAAATA
16436385 TTAAATAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 20 0.56
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAAAATAAAAAATAAAAATG
Found at i:16436429 original size:9 final size:9
Alignment explanation
Indices: 16436412--16436441 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16436402 AATAAATGAA
*
16436412 AAAATAAAT
1 AAAACAAAT
16436421 AAAACAAAT
1 AAAACAAAT
16436430 AAAACAAAT
1 AAAACAAAT
16436439 AAA
1 AAA
16436442 TAAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACAAAT
Found at i:16437296 original size:17 final size:17
Alignment explanation
Indices: 16437270--16437319 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 17
16437260 AAAAAAAAAT
16437270 ATAATAATAATATAAT-A
1 ATAA-AATAATATAATAA
16437287 ATAAAGATAACTAT-ATAA
1 ATAAA-ATAA-TATAATAA
16437305 ATAAAATACATATAA
1 ATAAAATA-ATATAA
16437320 ATATTAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.04
17 16 0.57
18 11 0.39
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (17 bp):
ATAAAATAATATAATAA
Found at i:16437417 original size:37 final size:38
Alignment explanation
Indices: 16437308--16437419 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 38
16437298 TATATAAATA
* * *
16437308 AAATACATATAAATATTAACAGAAAAAAAATAAATAAAG
1 AAATACATATAAATA-CAAAAGAATAAAAATAAATAAAG
* * * *
16437347 ATATACATATATTAATACATAATAATAATAAATAAATAATG
1 AAATACATATA--AATACAAAAGAATAA-AAATAAATAAAG
16437388 AAATACATA-AAATACAAAAGAATAAAAATAAA
1 AAATACATATAAATACAAAAGAATAAAAATAAA
16437420 AATAATACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
37 7 0.12
38 13 0.22
39 10 0.17
40 7 0.12
41 23 0.38
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.24
Consensus pattern (38 bp):
AAATACATATAAATACAAAAGAATAAAAATAAATAAAG
Found at i:16437438 original size:16 final size:15
Alignment explanation
Indices: 16437365--16437438 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 15
16437355 ATATTAATAC
*
16437365 ATAATAATAATAAATAA
1 ATAAAAATAAT-AA-AA
16437382 ATAATGAAATACAT-AAA
1 ATAA--AAATA-ATAAAA
*
16437399 ATACAAAAGAATAAAA
1 ATA-AAAATAATAAAA
16437415 ATAAAAATAATACAAA
1 ATAAAAATAATA-AAA
16437431 ATAAAAAT
1 ATAAAAAT
16437439 TGAATTGGGC
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 10 0.21
16 21 0.44
17 9 0.19
18 2 0.04
19 4 0.08
20 2 0.04
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.22
Consensus pattern (15 bp):
ATAAAAATAATAAAA
Done.