Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 13 of 138
Found at i:3736499 original size:22 final size:22
Alignment explanation
Indices: 3736473--3736515 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3736463 CCACCTTCGT
3736473 AATTTTCTCGGA-AAGCTATCAG
1 AATTTTCT-GGAGAAGCTATCAG
*
3736495 AATTTTCTTGAGAAGCTATCA
1 AATTTTCTGGAGAAGCTATCA
3736516 TTACTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (22 bp):
AATTTTCTGGAGAAGCTATCAG
Found at i:3737481 original size:19 final size:19
Alignment explanation
Indices: 3737437--3737474 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3737427 TGCATGCTAG
*
3737437 ATTTATTTTTAAGTTTTTA
1 ATTTATTTTTAAATTTTTA
3737456 ATTTATTTTTAAATTTTTA
1 ATTTATTTTTAAATTTTTA
3737475 TCTTATTATT
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTATTTTTAAATTTTTA
Found at i:3738240 original size:30 final size:30
Alignment explanation
Indices: 3738206--3738271 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
3738196 TTGATTTTTA
*
3738206 ATTTATATGAAATCATTAAATAAAATTAAT
1 ATTTATATAAAATCATTAAATAAAATTAAT
* * * *
3738236 ATTTATCTAAAATTATTAAATACAATTTAT
1 ATTTATATAAAATCATTAAATAAAATTAAT
*
3738266 AATTAT
1 ATTTAT
3738272 CACGTAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTTATATAAAATCATTAAATAAAATTAAT
Found at i:3738272 original size:30 final size:30
Alignment explanation
Indices: 3738215--3738272 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3738205 AATTTATATG
*
3738215 AAATCATTAAATAAAATTAATATTTATCTA
1 AAATCATTAAATAAAATTAATAATTATCTA
* * *
3738245 AAATTATTAAATACAATTTATAATTATC
1 AAATCATTAAATAAAATTAATAATTATC
3738273 ACGTAAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATCATTAAATAAAATTAATAATTATCTA
Found at i:3739528 original size:3 final size:3
Alignment explanation
Indices: 3739520--3739554 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3739510 AATTTGTATG
3739520 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3739555 TGGTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3742512 original size:5 final size:5
Alignment explanation
Indices: 3742502--3742527 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3742492 AGGACAGAAA
3742502 AAAAG AAAAG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG A
3742528 TCTTGTTGGA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3743533 original size:13 final size:14
Alignment explanation
Indices: 3743515--3743562 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 14
3743505 ATAATCTAAA
3743515 ATATAATAT-AATG
1 ATATAATATAAATG
3743528 ATATAATATGAATATG
1 ATATAATAT-AA-ATG
3743544 ATATAA-ATAAATG
1 ATATAATATAAATG
3743557 ATATAA
1 ATATAA
3743563 AATTGATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 18 0.56
14 2 0.06
15 3 0.09
16 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (14 bp):
ATATAATATAAATG
Found at i:3743557 original size:29 final size:30
Alignment explanation
Indices: 3743515--3743579 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
3743505 ATAATCTAAA
*
3743515 ATAT-AATATAATGATATAATA-TGAATATG
1 ATATAAATATAATGATATAAAATTG-ATATG
3743544 ATATAAATA-AATGATATAAAATTGATATG
1 ATATAAATATAATGATATAAAATTGATATG
*
3743573 ATTTAAA
1 ATATAAA
3743580 ATTTTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (30 bp):
ATATAAATATAATGATATAAAATTGATATG
Found at i:3747807 original size:3 final size:3
Alignment explanation
Indices: 3747799--3747830 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3747789 TAGCAGAATA
3747799 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3747831 AAAAAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3752816 original size:42 final size:42
Alignment explanation
Indices: 3752765--3752847 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
3752755 TTACAAATGT
*
3752765 ATGCTTCCAGCAAACAAATAATTGTTCACTCTATATGTATTA
1 ATGCTTCCAGCAAACAAATAATTGTTCACTCTATAAGTATTA
*
3752807 ATGCTTCCAGCAAACATATAATTGTTCACTCTATAAGTATT
1 ATGCTTCCAGCAAACAAATAATTGTTCACTCTATAAGTATT
3752848 TTTGTGCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (42 bp):
ATGCTTCCAGCAAACAAATAATTGTTCACTCTATAAGTATTA
Found at i:3755144 original size:9 final size:9
Alignment explanation
Indices: 3755132--3755163 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3755122 CATCATCGCA
3755132 TTCATCATC
1 TTCATCATC
*
3755141 TTCATAATC
1 TTCATCATC
3755150 TTCATCATC
1 TTCATCATC
3755159 TTCAT
1 TTCAT
3755164 AGGACTCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (9 bp):
TTCATCATC
Found at i:3764406 original size:6 final size:6
Alignment explanation
Indices: 3764301--3764431 Score: 61
Period size: 6 Copynumber: 20.7 Consensus size: 6
3764291 ATTTTATCTC
* * * ***
3764301 TTTTTA TTTATTT TTTTTAA TTTTAA TTTTTA TATTTA TAAATA TGTTTTA
1 TTTTTA TTT-TTA TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA T-TTTTA
* * *
3764352 TGTTTT- TTTTATA TATCTTTA TTTTTA TCTTTC TTCTTTA -TTCTA TTTTTA
1 T-TTTTA TTTT-TA T-T-TTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
*
3764403 -TTTTA TTTTTA TTTTATC TTATTTA TTTT
1 TTTTTA TTTTTA TTTT-TA TT-TTTA TTTT
3764432 CTTATTATAG
Statistics
Matches: 95, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
5 11 0.12
6 48 0.51
7 28 0.29
8 6 0.06
9 2 0.02
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:3764409 original size:16 final size:15
Alignment explanation
Indices: 3764388--3764431 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3764378 ATCTTTCTTC
3764388 TTTATTCTATTTTTAT
1 TTTATT-TATTTTTAT
*
3764404 TTTATTTTTATTTTAT
1 TTTATTTAT-TTTTAT
*
3764420 CTTATTTATTTT
1 TTTATTTATTTT
3764432 CTTATTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTATTTTTAT
Found at i:3764416 original size:11 final size:11
Alignment explanation
Indices: 3764369--3764431 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
3764359 TTTATATATC
3764369 TTTATTTTTAT
1 TTTATTTTTAT
*
3764380 CTTTCTTCTTTAT
1 -TTTATT-TTTAT
*
3764393 TCTATTTTTAT
1 TTTATTTTTAT
3764404 TTTATTTTTAT
1 TTTATTTTTAT
*
3764415 TTTA-TCTTA-
1 TTTATTTTTAT
3764424 TTTATTTT
1 TTTATTTT
3764432 CTTATTATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 4 0.09
10 6 0.14
11 19 0.44
12 9 0.21
13 5 0.12
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:3766981 original size:20 final size:20
Alignment explanation
Indices: 3766953--3766991 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3766943 CCTATTTTAA
*
3766953 GGTTTATTTATATTTGTTTG
1 GGTTAATTTATATTTGTTTG
*
3766973 GGTTAATTTATGTTTGTTT
1 GGTTAATTTATATTTGTTT
3766992 AAGGTTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.21, T:0.64
Consensus pattern (20 bp):
GGTTAATTTATATTTGTTTG
Found at i:3767034 original size:22 final size:22
Alignment explanation
Indices: 3767006--3767052 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3766996 TTTGTTTAAA
*
3767006 ATTATTTA-ATTATGATTTGTTT
1 ATTATTTAGAATATG-TTTGTTT
3767028 ATTATTTATGAATATGTTTGTTT
1 ATTATTTA-GAATATGTTTGTTT
3767051 AT
1 AT
3767053 ATATATTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.62
Consensus pattern (22 bp):
ATTATTTAGAATATGTTTGTTT
Found at i:3770742 original size:33 final size:34
Alignment explanation
Indices: 3770695--3770780 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 34
3770685 ACATTTTCAA
* * *
3770695 AAAAAAAAAGATAATCAAATTGTATCCAAACAAT-
1 AAAAAATAA-ATAATAAAATTATATCCAAACAATG
* * *
3770729 AAAAAATAAATAATTAAATTATATTCAAATAATG
1 AAAAAATAAATAATAAAATTATATCCAAACAATG
*
3770763 AAATAAT-AATAATAAAAT
1 AAAAAATAAATAATAAAAT
3770781 GGCCACACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 30 0.68
34 14 0.32
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (34 bp):
AAAAAATAAATAATAAAATTATATCCAAACAATG
Found at i:3771804 original size:27 final size:26
Alignment explanation
Indices: 3771772--3771830 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
3771762 GAAAGCAGTC
* *
3771772 GAGCAAGAGATTAAAAGGGAGGCAAA
1 GAGCAAGAGACTAAAAGGGAGACAAA
* *
3771798 GATGCAATAGACTAAGAGGGAGACAAA
1 GA-GCAAGAGACTAAAAGGGAGACAAA
3771825 GAGCAA
1 GAGCAA
3771831 AAATTAGGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.49, C:0.10, G:0.32, T:0.08
Consensus pattern (26 bp):
GAGCAAGAGACTAAAAGGGAGACAAA
Found at i:3776704 original size:93 final size:93
Alignment explanation
Indices: 3776545--3776724 Score: 324
Period size: 93 Copynumber: 1.9 Consensus size: 93
3776535 GACTGTTAGC
* **
3776545 ATATATCATTTCAACTCGTTGCAAAGACATTGAACAGGCATATTTATTCAGTATATTTAAGTTCT
1 ATATATCATTTCAACTCATTGCAAAGACATTGAACAGGCATATTTATTCAGTATATGGAAGTTCT
3776610 TTCTTTTAGGGAACTTTTGCTTTAGCAT
66 TTCTTTTAGGGAACTTTTGCTTTAGCAT
*
3776638 ATATATGATTTCAACTCATTGCAAAGACATTGAACAGGCATATTTATTCAGTATATGGAAGTTCT
1 ATATATCATTTCAACTCATTGCAAAGACATTGAACAGGCATATTTATTCAGTATATGGAAGTTCT
3776703 TTCTTTTAGGGAACTTTTGCTT
66 TTCTTTTAGGGAACTTTTGCTT
3776725 GTGTTTAAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.41
Consensus pattern (93 bp):
ATATATCATTTCAACTCATTGCAAAGACATTGAACAGGCATATTTATTCAGTATATGGAAGTTCT
TTCTTTTAGGGAACTTTTGCTTTAGCAT
Found at i:3778565 original size:32 final size:31
Alignment explanation
Indices: 3778524--3778586 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
3778514 ATAATATAGA
3778524 ATTATATTATTTAATTTAATTTTATTCATAAT
1 ATTATATTATTTAATTTAATTTTA-TCATAAT
* *
3778556 ATTATATTATTTTATTTTATTTTATCATAAT
1 ATTATATTATTTAATTTAATTTTATCATAAT
3778587 TTTGTGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTATATTATTTAATTTAATTTTATCATAAT
Found at i:3779729 original size:16 final size:16
Alignment explanation
Indices: 3779708--3779739 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3779698 CTTAAAAATA
3779708 GACATAAAATAGACTT
1 GACATAAAATAGACTT
*
3779724 GACATAAAGTAGACTT
1 GACATAAAATAGACTT
3779740 AAAGTTGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (16 bp):
GACATAAAATAGACTT
Found at i:3786013 original size:16 final size:16
Alignment explanation
Indices: 3785994--3786077 Score: 114
Period size: 16 Copynumber: 5.2 Consensus size: 16
3785984 TAATGTAGAT
3785994 TTAACATAAAGTAAAC
1 TTAACATAAAGTAAAC
3786010 TTAACATAAAGTAAAC
1 TTAACATAAAGTAAAC
* *
3786026 TTGACATAAAGTAGAC
1 TTAACATAAAGTAAAC
** * *
3786042 TGGACATAAAGTAGAT
1 TTAACATAAAGTAAAC
3786058 TTAACATAAAGTAAAC
1 TTAACATAAAGTAAAC
3786074 TTAA
1 TTAA
3786078 AGCTGATGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (16 bp):
TTAACATAAAGTAAAC
Found at i:3786935 original size:14 final size:14
Alignment explanation
Indices: 3786916--3786950 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3786906 ATAACTCGAC
3786916 ATAAAGTTACTTTA
1 ATAAAGTTACTTTA
3786930 ATAAAGTTACTTTA
1 ATAAAGTTACTTTA
*
3786944 AGAAAGT
1 ATAAAGT
3786951 AGCTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (14 bp):
ATAAAGTTACTTTA
Found at i:3787004 original size:16 final size:16
Alignment explanation
Indices: 3786983--3787032 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
3786973 CTCAAAAGTA
* *
3786983 GACATAAAATAGATTT
1 GACATAAAGTAGACTT
3786999 GACATAAAGTAGACTT
1 GACATAAAGTAGACTT
3787015 GACATAAAGTAGACTT
1 GACATAAAGTAGACTT
3787031 GA
1 GA
3787033 AGTTGATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (16 bp):
GACATAAAGTAGACTT
Found at i:3790268 original size:32 final size:32
Alignment explanation
Indices: 3790225--3790289 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3790215 TACATCAACT
* *
3790225 TTAAGTATACTTTATATCTAGTCTAATTTATG
1 TTAAGTATACTTTATATCAAATCTAATTTATG
* * *
3790257 TTAAGTTTACTTTATGTCAAATCTACTTTATG
1 TTAAGTATACTTTATATCAAATCTAATTTATG
3790289 T
1 T
3790290 CTATTTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (32 bp):
TTAAGTATACTTTATATCAAATCTAATTTATG
Found at i:3790270 original size:16 final size:16
Alignment explanation
Indices: 3790232--3790290 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
3790222 ACTTTAAGTA
* * *
3790232 TACTTTATATCTAGTC
1 TACTTTATGTCAAATC
* * * *
3790248 TAATTTATGTTAAGTT
1 TACTTTATGTCAAATC
3790264 TACTTTATGTCAAATC
1 TACTTTATGTCAAATC
3790280 TACTTTATGTC
1 TACTTTATGTC
3790291 TATTTTTGAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (16 bp):
TACTTTATGTCAAATC
Found at i:3796371 original size:2 final size:2
Alignment explanation
Indices: 3796364--3796398 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3796354 AAGACCATTC
3796364 AG AG 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 AG AG A
3796399 AACAGATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3799033 original size:19 final size:18
Alignment explanation
Indices: 3799005--3799048 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
3798995 GATCAAAATA
*
3799005 TATTAATTTGATTTTATT
1 TATTAATTTGATATTATT
3799023 TATTAATTTTGATATTATT
1 TATTAA-TTTGATATTATT
3799042 TGATTAA
1 T-ATTAA
3799049 AAAAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (18 bp):
TATTAATTTGATATTATT
Found at i:3823313 original size:19 final size:19
Alignment explanation
Indices: 3823289--3823332 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3823279 AGGGAACATA
3823289 TATTAT-TGATTTTGCTGTT
1 TATTATATGATTTTG-TGTT
*
3823308 TATTATATTATTTTGTGTT
1 TATTATATGATTTTGTGTT
3823327 TGATTA
1 T-ATTA
3823333 CTTGCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (19 bp):
TATTATATGATTTTGTGTT
Found at i:3823322 original size:20 final size:21
Alignment explanation
Indices: 3823292--3823332 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3823282 GAACATATAT
3823292 TATTGATTTTGCTGTTT-ATTA
1 TATTGATTTTG-TGTTTGATTA
3823313 TATT-ATTTTGTGTTTGATTA
1 TATTGATTTTGTGTTTGATTA
3823333 CTTGCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (21 bp):
TATTGATTTTGTGTTTGATTA
Found at i:3825804 original size:14 final size:15
Alignment explanation
Indices: 3825764--3825804 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3825754 TCAAAAACAT
*
3825764 ATTAT-TTATAA-AA
1 ATTATATTATAATTA
3825777 ATTATATTATAATTA
1 ATTATATTATAATTA
3825792 ATTA-ATTATAATT
1 ATTATATTATAATT
3825805 TAAAATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 15 0.60
15 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATATTATAATTA
Found at i:3827452 original size:30 final size:30
Alignment explanation
Indices: 3827404--3827471 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 30
3827394 TACCAAATAC
*
3827404 ATTTT-TAGAAAAT-AAAAAAAACAAAAACT
1 ATTTTCTAAAAAATAAAAAAAAACAAAAA-T
3827433 ATTTTCTAAAAAATGAAAAAAAAAACAAAAAT
1 ATTTTCTAAAAAAT--AAAAAAAAACAAAAAT
3827465 ATTTTCT
1 ATTTTCT
3827472 TATAGAGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.15
30 7 0.21
32 8 0.24
33 14 0.41
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (30 bp):
ATTTTCTAAAAAATAAAAAAAAACAAAAAT
Found at i:3827765 original size:28 final size:30
Alignment explanation
Indices: 3827729--3827787 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
3827719 AATTAACAGA
3827729 TTTATAATTAAAATATCATATTAAA-ATTT
1 TTTATAATTAAAATATCATATTAAATATTT
* *
3827758 TTTA-AATTCAAATATTATATTAAATATTT
1 TTTATAATTAAAATATCATATTAAATATTT
3827787 T
1 T
3827788 ATCATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTATAATTAAAATATCATATTAAATATTT
Found at i:3837127 original size:22 final size:22
Alignment explanation
Indices: 3837099--3837145 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3837089 TTTTTGATTA
3837099 TTTGAGAACATTTCA-TTCAGGG
1 TTTGAGAACATTTCACTT-AGGG
**
3837121 TTTGAGAATGTTTCACTTAGGG
1 TTTGAGAACATTTCACTTAGGG
3837143 TTT
1 TTT
3837146 ACGACCTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (22 bp):
TTTGAGAACATTTCACTTAGGG
Found at i:3840172 original size:19 final size:20
Alignment explanation
Indices: 3840152--3840190 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3840142 AATTATACTC
*
3840152 ATAATCAAGTATTACATTCA
1 ATAATCAACTATTACATTCA
3840172 TATAATCAACTATTACATT
1 -ATAATCAACTATTACATT
3840191 ATGAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (20 bp):
ATAATCAACTATTACATTCA
Found at i:3840216 original size:19 final size:18
Alignment explanation
Indices: 3840188--3840226 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
3840178 CAACTATTAC
3840188 ATTATGAATAATAAACTA
1 ATTATGAATAATAAACTA
*
3840206 ATTATTGAATAATTAACTA
1 ATTA-TGAATAATAAACTA
3840225 AT
1 AT
3840227 AAATTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTATGAATAATAAACTA
Found at i:3842950 original size:21 final size:21
Alignment explanation
Indices: 3842925--3842964 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3842915 TTTAAATAAA
3842925 TTTA-TATATAAAACAATTACT
1 TTTATTATATAAAA-AATTACT
*
3842946 TTTATTTTATAAAAAATTA
1 TTTATTATATAAAAAATTA
3842965 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTATTATATAAAAAATTACT
Found at i:3843154 original size:127 final size:127
Alignment explanation
Indices: 3842955--3843212 Score: 457
Period size: 127 Copynumber: 2.0 Consensus size: 127
3842945 TTTTATTTTA
3842955 TAAAAAATTAAAAAATAAAAACTAATAAAAATATATTGGTTGGATTTGATTTTTAAATTTTTACA
1 TAAAAAATTAAAAAATAAAAACTAATAAAAATATATTGGTTGGATTTGATTTTTAAATTTTTACA
3843020 TCCTGATCCGAACTTAATATAAATATTTAATATTTAAATTTAATATAAATCAAATAAAAAAT
66 TCCTGATCCGAACTTAATATAAATATTTAATATTTAAATTTAATATAAATCAAATAAAAAAT
*
3843082 TAAAAAA-TAAAAACTAAAAACTAATAAAAA-ATATTGGTTGGATTTGATTTTTAAAATTTTTTA
1 TAAAAAATTAAAAAATAAAAACTAATAAAAATATATTGGTTGGATTTGATTTTT-AAA-TTTTTA
* *
3843145 CATCTTGATCCGAACTTAATATAAATATTTAATATTTAAATTTAATCTAAATCAAATAAAAAAT
64 CATCCTGATCCGAACTTAATATAAATATTTAATATTTAAATTTAATATAAATCAAATAAAAAAT
3843209 TAAA
1 TAAA
3843213 TTTAATAAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
125 22 0.17
126 25 0.20
127 79 0.63
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (127 bp):
TAAAAAATTAAAAAATAAAAACTAATAAAAATATATTGGTTGGATTTGATTTTTAAATTTTTACA
TCCTGATCCGAACTTAATATAAATATTTAATATTTAAATTTAATATAAATCAAATAAAAAAT
Found at i:3855694 original size:24 final size:24
Alignment explanation
Indices: 3855644--3855710 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
3855634 TTGGTATTAA
* *
3855644 TTCATCTAA-ATTAAAT-AAATTTT
1 TTCA-CTAATATTAAATAAAATATG
3855667 TTCA-TGAATATTAAATAAAATATG
1 TTCACT-AATATTAAATAAAATATG
3855691 TTCACTAATATATAAATAAA
1 TTCACTAATAT-TAAATAAA
3855711 CATAAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 1 0.03
22 2 0.05
23 11 0.30
24 14 0.38
25 9 0.24
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (24 bp):
TTCACTAATATTAAATAAAATATG
Found at i:3858246 original size:9 final size:9
Alignment explanation
Indices: 3858227--3858260 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3858217 TATATAGTTA
3858227 TATATTATAT
1 TATA-TATAT
3858237 TATATATAT
1 TATATATAT
3858246 TATATATAT
1 TATATATAT
3858255 T-TATAT
1 TATATAT
3858261 GTTCACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.21
9 15 0.62
10 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATAT
Found at i:3861495 original size:2 final size:2
Alignment explanation
Indices: 3861488--3861524 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3861478 TCCTCCTAAC
3861488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3861525 AGATCCAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3862535 original size:25 final size:25
Alignment explanation
Indices: 3862503--3862560 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
3862493 GATTCATTTA
**
3862503 ATAA-AATTTTTTTCAATTGTAATT
1 ATAATAATTTTTTTCAATCATAATT
*
3862527 ATAATAATTTTTTTCAATCATAGTT
1 ATAATAATTTTTTTCAATCATAATT
3862552 ATAATAATT
1 ATAATAATT
3862561 ATTATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (25 bp):
ATAATAATTTTTTTCAATCATAATT
Found at i:3863416 original size:56 final size:56
Alignment explanation
Indices: 3863330--3863441 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
3863320 TACTAGCAGT
3863330 GGTGAGAGATAACAATCTATCTTCATTTGCAAGAATAGAATATAAAAAGATTTATA
1 GGTGAGAGATAACAATCTATCTTCATTTGCAAGAATAGAATATAAAAAGATTTATA
3863386 GGTGAGAGATAACAATCTATCTTCATTTGCAAGAATAGAATATAAAAAGATTTATA
1 GGTGAGAGATAACAATCTATCTTCATTTGCAAGAATAGAATATAAAAAGATTTATA
3863442 TTAGTATTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (56 bp):
GGTGAGAGATAACAATCTATCTTCATTTGCAAGAATAGAATATAAAAAGATTTATA
Found at i:3866741 original size:17 final size:17
Alignment explanation
Indices: 3866719--3866754 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3866709 AAGAATTGAA
3866719 TTATTTCTATATATTTG
1 TTATTTCTATATATTTG
3866736 TTATTTCTATATATTTG
1 TTATTTCTATATATTTG
3866753 TT
1 TT
3866755 GTGTAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTATTTCTATATATTTG
Found at i:3868753 original size:2 final size:2
Alignment explanation
Indices: 3868746--3868783 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3868736 GTTTTCTTCA
3868746 AT AT AT AT 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
3868784 GTTGGTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3870481 original size:65 final size:66
Alignment explanation
Indices: 3870363--3870488 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 66
3870353 TTCGCACGGT
* * * * *
3870363 TCTGGGATATGAGCATTTACCCTTTCGACGTTACAGATCAGTCTTTTTATCACGGTTCACAGCGG
1 TCTGGGACATAAGCATTCACCCTTCCGACGTCACAGATCAGTCTTTTTATCACGGTTCACAGCGG
3870428 C
66 C
* *
3870429 TCTGGGACATAAGCATTCACCCTTCCGA-GTCCCAGATCAGTCTTTTTGTCACGGTTCACA
1 TCTGGGACATAAGCATTCACCCTTCCGACGTCACAGATCAGTCTTTTTATCACGGTTCACA
3870489 CTTTTGTGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
65 29 0.55
66 24 0.45
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (66 bp):
TCTGGGACATAAGCATTCACCCTTCCGACGTCACAGATCAGTCTTTTTATCACGGTTCACAGCGG
C
Found at i:3870848 original size:21 final size:22
Alignment explanation
Indices: 3870807--3870848 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3870797 ATTTAGATGA
**
3870807 AATTTTTTATATAAAGTTAATG
1 AATTTTTTATATAAAAATAATG
3870829 AATTTTTTAT-TAAAAATAAT
1 AATTTTTTATATAAAAATAAT
3870849 TAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTTTTTATATAAAAATAATG
Found at i:3871049 original size:14 final size:15
Alignment explanation
Indices: 3871030--3871063 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3871020 TAAATTTGAT
*
3871030 ATATTTTTAA-ATAA
1 ATATTTTTAATAAAA
3871044 ATATTTTTAATAAAA
1 ATATTTTTAATAAAA
3871059 ATATT
1 ATATT
3871064 GGCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTTAATAAAA
Found at i:3871070 original size:100 final size:103
Alignment explanation
Indices: 3870894--3871084 Score: 280
Period size: 100 Copynumber: 1.9 Consensus size: 103
3870884 TAAATTAAGT
*
3870894 ATGTAAAATTTGAAAAAATTTAAAAATATTTTGATATATTTTTTAAATAAATATTTTTAGTAAAA
1 ATGTAAAATTTGAAAAAATTTAAAAATATTTTGATATATTTTTTAAATAAATATTTTTAATAAAA
* * *
3870959 TTGTTAACAAAATTTTTATCATTAAAAAAATCTCAAGA
66 ATATTAACAAAATTTTTATAATTAAAAAAATCTCAAGA
* *
3870997 ATGTAAATTTTGAAAAAATTTAATAA-A-TTTGATATA-TTTTTAAATAAATATTTTTAATAAAA
1 ATGTAAAATTTGAAAAAATTTAAAAATATTTTGATATATTTTTTAAATAAATATTTTTAATAAAA
** *
3871059 ATATTGGCAAAATTTTTGTAATTAAA
66 ATATTAACAAAATTTTTATAATTAAA
3871085 TAAGTATCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 45 0.57
101 9 0.11
102 1 0.01
103 24 0.30
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (103 bp):
ATGTAAAATTTGAAAAAATTTAAAAATATTTTGATATATTTTTTAAATAAATATTTTTAATAAAA
ATATTAACAAAATTTTTATAATTAAAAAAATCTCAAGA
Found at i:3873968 original size:2 final size:2
Alignment explanation
Indices: 3873961--3873997 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3873951 GGTTTGATTT
3873961 AG AG AG 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 AG AG AG A
3873998 AAGGGTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3874031 original size:17 final size:18
Alignment explanation
Indices: 3874005--3874042 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3873995 AGAAAGGGTG
3874005 TTTTTATTTT-CATTTTT
1 TTTTTATTTTGCATTTTT
* *
3874022 TTTTTTTTTTGGATTTTT
1 TTTTTATTTTGCATTTTT
3874040 TTT
1 TTT
3874043 GTTCAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTATTTTGCATTTTT
Found at i:3874752 original size:20 final size:20
Alignment explanation
Indices: 3874727--3874771 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3874717 TTAAAAATTA
3874727 ATAAAAAATTATTTTTAAAT
1 ATAAAAAATTATTTTTAAAT
* *
3874747 ATAAAATATTATTTTTTAAT
1 ATAAAAAATTATTTTTAAAT
3874767 ATAAA
1 ATAAA
3874772 TATAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAAAAATTATTTTTAAAT
Found at i:3876472 original size:12 final size:12
Alignment explanation
Indices: 3876455--3876480 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3876445 TGATAAGATC
3876455 ATATCATGAGCT
1 ATATCATGAGCT
3876467 ATATCATGAGCT
1 ATATCATGAGCT
3876479 AT
1 AT
3876481 GCGGCTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (12 bp):
ATATCATGAGCT
Found at i:3886619 original size:16 final size:16
Alignment explanation
Indices: 3886598--3886654 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3886588 AACTTTTCAG
3886598 AATTTATTTTAGAAAA
1 AATTTATTTTAGAAAA
*
3886614 AATTTATAATTTTA-TAAA
1 AA-TT-T-ATTTTAGAAAA
*
3886632 AATTTATTTTCGAAAA
1 AATTTATTTTAGAAAA
*
3886648 GATTTAT
1 AATTTAT
3886655 AATTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 5 0.15
16 12 0.36
17 4 0.12
18 6 0.18
19 6 0.18
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (16 bp):
AATTTATTTTAGAAAA
Found at i:3886625 original size:19 final size:19
Alignment explanation
Indices: 3886603--3886660 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
3886593 TTCAGAATTT
3886603 ATTTTAGAAAAAATTTATA
1 ATTTTAGAAAAAATTTATA
*
3886622 ATTTTA-TAAAAA-TT-T-
1 ATTTTAGAAAAAATTTATA
* *
3886637 ATTTTCGAAAAGATTTATA
1 ATTTTAGAAAAAATTTATA
3886656 ATTTT
1 ATTTT
3886661 TTTATAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 5 0.16
16 5 0.16
17 4 0.13
18 6 0.19
19 11 0.35
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTTAGAAAAAATTTATA
Found at i:3891793 original size:6 final size:7
Alignment explanation
Indices: 3891778--3891808 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3891768 AAAAAAAAAG
*
3891778 AAATGCA
1 AAATGAA
3891785 AAATGAA
1 AAATGAA
3891792 AAATGAA
1 AAATGAA
3891799 AAATGAA
1 AAATGAA
3891806 AAA
1 AAA
3891809 AATGTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.71, C:0.03, G:0.13, T:0.13
Consensus pattern (7 bp):
AAATGAA
Found at i:3895680 original size:3 final size:3
Alignment explanation
Indices: 3895672--3895714 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3895662 TTCATTATAC
3895672 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 T
3895715 CCTATCCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3897536 original size:12 final size:12
Alignment explanation
Indices: 3897516--3897571 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
3897506 TGTAAGTTTT
3897516 TTATTATTATTG
1 TTATTATTATTG
* *
3897528 TTGTTATTATTA
1 TTATTATTATTG
**
3897540 TTGCTATTATTG
1 TTATTATTATTG
*
3897552 CTATTATTATTG
1 TTATTATTATTG
3897564 TTATTATT
1 TTATTATT
3897572 TTGAAAATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:3897547 original size:9 final size:9
Alignment explanation
Indices: 3897535--3897559 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3897525 TTGTTGTTAT
3897535 TATTATTGC
1 TATTATTGC
3897544 TATTATTGC
1 TATTATTGC
3897553 TATTATT
1 TATTATT
3897560 ATTGTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (9 bp):
TATTATTGC
Found at i:3898780 original size:24 final size:27
Alignment explanation
Indices: 3898753--3898820 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
3898743 AATTCAAAAT
3898753 AAATAAATTATTGATAT-T-A-AA-TTA
1 AAATAAATTATT-ATATCTAATAATTTA
3898777 AAATAAGATATATTATATCTAATAATTTA
1 AAATAA-AT-TATTATATCTAATAATTTA
3898806 AAATAAATTATTATA
1 AAATAAATTATTATA
3898821 AATCATGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
24 6 0.16
25 6 0.16
26 5 0.13
27 8 0.21
28 4 0.11
29 9 0.24
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (27 bp):
AAATAAATTATTATATCTAATAATTTA
Found at i:3907343 original size:20 final size:21
Alignment explanation
Indices: 3907318--3907362 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
3907308 AGAAAAGCTC
*
3907318 TTTTTTTATTTG-AAT-AAAA
1 TTTTTTTTTTTGAAATCAAAA
3907337 TTTTTTTTTTTGAAATCAAAA
1 TTTTTTTTTTTGAAATCAAAA
3907358 TTTTT
1 TTTTT
3907363 GAGTACGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTTTTTTTTGAAATCAAAA
Found at i:3908754 original size:16 final size:17
Alignment explanation
Indices: 3908723--3908756 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
3908713 AAAAATATTT
3908723 TTTATCTTGATTTAAAAA
1 TTTATCTT-ATTTAAAAA
3908741 TTTATCTT-TTTAAAAA
1 TTTATCTTATTTAAAAA
3908757 AAATTTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATCTTATTTAAAAA
Found at i:3909184 original size:21 final size:21
Alignment explanation
Indices: 3909158--3909206 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3909148 TTTTATTATT
*
3909158 TAATTTATCATTT-AATAATA
1 TAATTTATCATTTAAAAAATA
*
3909178 TATATTT-TTATTTAAAAAATA
1 TA-ATTTATCATTTAAAAAATA
3909199 TAATTTAT
1 TAATTTAT
3909207 TTTTATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTTATCATTTAAAAAATA
Found at i:3911755 original size:28 final size:28
Alignment explanation
Indices: 3911713--3911771 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
3911703 ACTGTTGGTG
3911713 CTTAGGCAATAGTTGCCACCAAGTCTTA
1 CTTAGGCAATAGTTGCCACCAAGTCTTA
*
3911741 CTTAGGCAATGGTTGCCACCAAGTCTTA
1 CTTAGGCAATAGTTGCCACCAAGTCTTA
3911769 CTT
1 CTT
3911772 GGATGGGGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (28 bp):
CTTAGGCAATAGTTGCCACCAAGTCTTA
Found at i:3920901 original size:18 final size:18
Alignment explanation
Indices: 3920880--3920917 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3920870 AAAATTTTTG
3920880 TTTAGATAATTATGACAT
1 TTTAGATAATTATGACAT
* *
3920898 TTTATATAATTATGATAT
1 TTTAGATAATTATGACAT
3920916 TT
1 TT
3920918 ATGAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.53
Consensus pattern (18 bp):
TTTAGATAATTATGACAT
Found at i:3920983 original size:42 final size:41
Alignment explanation
Indices: 3920903--3920988 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 41
3920893 GACATTTTAT
*
3920903 ATAATTATGATATTTATGAATAATAATTTATTTATATTCAA
1 ATAATTATGATATTTATCAATAATAATTTATTTATATTCAA
* * *
3920944 ATAATTATGATCATTTGTCATATGATAA-TTATTTTTATTCAA
1 ATAATTATGAT-ATTTATCA-ATAATAATTTATTTATATTCAA
3920986 ATA
1 ATA
3920989 TAATTATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 22 0.56
43 6 0.15
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (41 bp):
ATAATTATGATATTTATCAATAATAATTTATTTATATTCAA
Found at i:3921510 original size:29 final size:29
Alignment explanation
Indices: 3921438--3921511 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 29
3921428 AGAGAGAAGA
* *
3921438 GAAGAAAAAAATGAAGAAGGAAGAGAAAC
1 GAAGAAAAAAAAGAAGAAGGAAAAGAAAC
*
3921467 GAATGAGAAGGAAAAGAAG-AGAGAAAAGAAAC
1 GAA-GA-AA-AAAAAGAAGAAG-GAAAAGAAAC
3921499 GAAGAAAAAAAAG
1 GAAGAAAAAAAAG
3921512 TCTCTGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 8 0.22
30 4 0.11
31 6 0.16
32 19 0.51
ACGTcount: A:0.66, C:0.03, G:0.28, T:0.03
Consensus pattern (29 bp):
GAAGAAAAAAAAGAAGAAGGAAAAGAAAC
Found at i:3923106 original size:20 final size:18
Alignment explanation
Indices: 3923083--3923121 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
3923073 TTGATTCGAT
3923083 TAAAAATATTATTATATTAA
1 TAAAAATATT-TTAT-TTAA
3923103 TAAAAATATTTTATTTAA
1 TAAAAATATTTTATTTAA
3923121 T
1 T
3923122 TTTAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAAAATATTTTATTTAA
Found at i:3924340 original size:28 final size:27
Alignment explanation
Indices: 3924285--3924346 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
3924275 AACTCTTTAA
* *
3924285 TTAAAT-T-GATTTATGATTTTATAGT
1 TTAAATATCGATTTATAATTTTATAAT
* *
3924310 TTAAGTATCGATTTAATAATTTTTTAAT
1 TTAAATATCGATTT-ATAATTTTATAAT
3924338 TTAAATATC
1 TTAAATATC
3924347 AAATCTAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 5 0.17
26 1 0.03
27 5 0.17
28 18 0.62
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (27 bp):
TTAAATATCGATTTATAATTTTATAAT
Found at i:3924615 original size:21 final size:21
Alignment explanation
Indices: 3924586--3924659 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
3924576 TTTTTTGTTA
* *
3924586 TAATTTAATA-ATAGATACTTT
1 TAATATAATATATAAATA-TTT
3924607 TAATATAATATATAAATATTT
1 TAATATAATATATAAATATTT
* *
3924628 TAATAATAA-ATATTACTATTT
1 TAAT-ATAATATATAAATATTT
3924649 TAATATTAATA
1 TAATA-TAATA
3924660 AAAATGATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
20 1 0.02
21 33 0.73
22 11 0.24
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (21 bp):
TAATATAATATATAAATATTT
Found at i:3924638 original size:15 final size:16
Alignment explanation
Indices: 3924612--3924641 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3924602 ACTTTTAATA
3924612 TAATATATAAATATTT
1 TAATATATAAATATTT
3924628 TAATA-ATAAATATT
1 TAATATATAAATATT
3924642 ACTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATATATAAATATTT
Found at i:3924938 original size:15 final size:14
Alignment explanation
Indices: 3924900--3924928 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3924890 AAAAAAATAT
3924900 AAATATTTTTTAAA
1 AAATATTTTTTAAA
3924914 AAATATTTTTTAAA
1 AAATATTTTTTAAA
3924928 A
1 A
3924929 GTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATTTTTTAAA
Found at i:3940291 original size:16 final size:16
Alignment explanation
Indices: 3940270--3940301 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3940260 TTGTAAGCGT
*
3940270 AATGAATGAGAATGGC
1 AATGAATGAAAATGGC
3940286 AATGAATGAAAATGGC
1 AATGAATGAAAATGGC
3940302 CATGTAGCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (16 bp):
AATGAATGAAAATGGC
Found at i:3943645 original size:174 final size:175
Alignment explanation
Indices: 3943455--3943851 Score: 455
Period size: 174 Copynumber: 2.2 Consensus size: 175
3943445 TCCAGTGCAG
3943455 GGAAAATTGATACTTTCAACTTTTTCCCCAAAAATATTTTTTTAAAA-AAAAAATTT-AGAGGAA
1 GGAAAATTGATACTTTCAACTTTTTCCCCAAAAATATTTTTTTAAAACAAAAAATTTCA-AGGAA
* * * * * * **
3943518 AATTGATACTTTCCATTTTTCTTCAAAAATTGATTTTTTTGAAAATTTATTTTTAAGGAAAATTG
65 AATCGATACTTTCAACTTTTCCTCAAAAA--CACTTTTTTGAAAATTTATTTTTAAAAAAAATTG
3943583 ATACTTTCAACTTTTCCCCAAAAATA-TTTTTCGAAAA-AAATTTAAA
128 ATACTTTCAACTTTTCCCCAAAAATATTTTTTCGAAAATAAATTTAAA
* * **** *
3943629 GGAAAATTGATACTTTCAACTTTTT-TCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGGAAA
1 GGAAAATTGATACTTTCAACTTTTTCCCCAAAAATATTTTTTTAAAACAAAAAATTTCAAGGAAA
* * *
3943693 ATCGATATTTTTAACTTTTCCTCAAAAACCCTTTTTTGAAAATTTATTTTTAAAAAAAATTGATA
66 ATCGATACTTTCAACTTTTCCTCAAAAACACTTTTTTGAAAATTTATTTTTAAAAAAAATTGATA
* * ** *
3943758 CTTTCAACTTTTCCTCAAAAATATTTTTTTTTGGAAAATTTTGATTTTTTAA
131 CTTTCAACTTTTCCCCAAAAATA---TTTTTTCGAAAA---T-AAATTTAAA
3943810 GGAAAATTGATACTTTCAAC-TTTTCCCCAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTTCCCCAAAAATATTTTTTT
3943852 GATTTTTATT
Statistics
Matches: 186, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
172 54 0.29
173 19 0.10
174 57 0.31
175 1 0.01
176 10 0.05
180 4 0.02
181 41 0.22
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (175 bp):
GGAAAATTGATACTTTCAACTTTTTCCCCAAAAATATTTTTTTAAAACAAAAAATTTCAAGGAAA
ATCGATACTTTCAACTTTTCCTCAAAAACACTTTTTTGAAAATTTATTTTTAAAAAAAATTGATA
CTTTCAACTTTTCCCCAAAAATATTTTTTCGAAAATAAATTTAAA
Found at i:3943877 original size:5 final size:5
Alignment explanation
Indices: 3943867--3943951 Score: 58
Period size: 5 Copynumber: 17.6 Consensus size: 5
3943857 TTATTTAAAG
*
3943867 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT -AAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAAT
* *
3943915 AAAGA- AAAGT AAAAC AAAA- ATAAA- AAAAT AAAAT AAA
1 AAA-AT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAA
3943952 GGTAAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
3 3 0.05
4 10 0.15
5 45 0.69
6 3 0.05
7 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:3943888 original size:13 final size:13
Alignment explanation
Indices: 3943867--3943951 Score: 61
Period size: 13 Copynumber: 6.6 Consensus size: 13
3943857 TTATTTAAAG
3943867 AAAATAAAATAAT
1 AAAATAAAATAAT
*
3943880 AAAACAAAAT-A-
1 AAAATAAAATAAT
* *
3943891 AAAGTGAAAATAAA
1 AAAAT-AAAATAAT
*
3943905 AAAATAAAATAAAG
1 AAAATAAAAT-AAT
*
3943919 AAAAGTAAAA-CA-
1 AAAA-TAAAATAAT
*
3943931 AAAATAAAAAAAT
1 AAAATAAAATAAT
3943944 AAAATAAA
1 AAAATAAA
3943952 GGTAAAAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
11 8 0.14
12 11 0.19
13 24 0.41
14 10 0.17
15 5 0.09
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:3943901 original size:30 final size:29
Alignment explanation
Indices: 3943866--3943951 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
3943856 TTTATTTAAA
3943866 GAAAATAAAATAATAAAACAAAATAAAAGT
1 GAAAATAAAATAATAAAA-AAAATAAAAGT
* * *
3943896 GAAAATAAAAAAATAAAATAAAGAAAAGT
1 GAAAATAAAATAATAAAAAAAATAAAAGT
* *
3943925 -AAAACAAAAATAAAAAAATAAAATAAA
1 GAAAA-TAAAATAATAAAA-AAAATAAA
3943952 GGTAAAAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 4 0.09
29 19 0.41
30 23 0.50
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (29 bp):
GAAAATAAAATAATAAAAAAAATAAAAGT
Found at i:3943934 original size:21 final size:19
Alignment explanation
Indices: 3943867--3943947 Score: 65
Period size: 22 Copynumber: 3.9 Consensus size: 19
3943857 TTATTTAAAG
*
3943867 AAAATAAAATAATAAAAC-
1 AAAATAAAAAAATAAAACA
*
3943885 AAAATAAAAGTGAAAATAAAAAAA
1 AAAAT-AAA---AAAAT-AAAACA
3943909 TAAAATAAAGAAAAGTAAAACA
1 -AAAATAAA-AAAA-TAAAACA
3943931 AAAATAAAAAAATAAAA
1 AAAATAAAAAAATAAAA
3943948 TAAAGGTAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
18 5 0.10
19 8 0.15
20 4 0.08
21 8 0.15
22 14 0.27
23 5 0.10
24 3 0.06
25 5 0.10
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAATAAAAAAATAAAACA
Found at i:3944113 original size:5 final size:5
Alignment explanation
Indices: 3944103--3944127 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3944093 CTTGAAACCC
3944103 CGGCT CGGCT CGGCT CGGCT CGGCT
1 CGGCT CGGCT CGGCT CGGCT CGGCT
3944128 ATCGGCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
CGGCT
Found at i:3944995 original size:43 final size:44
Alignment explanation
Indices: 3944883--3944996 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 44
3944873 AAAAGCAATA
* *
3944883 ATAATAATAATAATAATAATCAAATAAA-CGAAAAAAAATTAACAG
1 ATAATAAAAATAATAATAAT--AATAAATCCAAAAAAAATTAACAG
* *
3944928 ATAATTAAAAATAA-AATAA-GATAAATCCAAAAAATATT-ACAAG
1 ATAA-TAAAAATAATAATAATAATAAATCCAAAAAAAATTAAC-AG
3944971 ATAA-AAAAATAATAATAATAATAAAT
1 ATAATAAAAATAATAATAATAATAAAT
3944997 TATAATATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
41 8 0.14
42 12 0.20
43 22 0.37
45 9 0.15
46 8 0.14
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.24
Consensus pattern (44 bp):
ATAATAAAAATAATAATAATAATAAATCCAAAAAAAATTAACAG
Found at i:3945003 original size:19 final size:19
Alignment explanation
Indices: 3944979--3945025 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
3944969 AGATAAAAAA
*
3944979 ATAATAATAATAATAAAT-T
1 ATAAT-ATAATAAGAAATAT
3944998 ATAATATAATAAGAAATAT
1 ATAATATAATAAGAAATAT
3945017 ATAACTATA
1 ATAA-TATA
3945026 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
19 10 0.40
20 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAATATAATAAGAAATAT
Found at i:3945028 original size:19 final size:18
Alignment explanation
Indices: 3944977--3945028 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
3944967 CAAGATAAAA
*
3944977 AAATA-ATAATA-ATAAT
1 AAATATATAATATATAAG
3944993 AAAT-TATAATATAATAAG
1 AAATATATAATAT-ATAAG
3945011 AAATATATAACTATATAA
1 AAATATATAA-TATATAA
3945029 ATAAAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 10 0.33
18 8 0.27
19 9 0.30
20 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATATATAATATATAAG
Found at i:3949282 original size:28 final size:28
Alignment explanation
Indices: 3949242--3949307 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
3949232 TTTACGTATT
* *
3949242 TTTTTAATATTTTATATAT-AATATAATA
1 TTTTTATTTTTTTAT-TATGAATATAATA
*
3949270 TTTTTATTTTTTTATTATGAATTTAATA
1 TTTTTATTTTTTTATTATGAATATAATA
* *
3949298 TATTGATTTT
1 TTTTTATTTT
3949308 ATTTTCTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTTTATTTTTTTATTATGAATATAATA
Found at i:3953350 original size:234 final size:234
Alignment explanation
Indices: 3952929--3953579 Score: 1000
Period size: 234 Copynumber: 2.8 Consensus size: 234
3952919 GAGTAGGAGC
* *
3952929 AATGTATGGGCCAGGTGCAACTGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGC
1 AATGTATGGGCCAGGTGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGC
*
3952994 TTGGTGGATATGAGGGTTTAGGGGGTGATGCCTCACTTGGAGGAGTTGGACATGCAGGATGTGGA
66 TTGGTGGATATGAGGGTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGACATGCAGGATGTGGA
* *
3953059 GGGGGCACTGGAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGCGCAGGTGCAGAGTG
131 GGGGGCACTGCAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGTGCAGGTGCAGAGTG
* *
3953124 AGGTGGTGATCCCTTGTAGGGAGTAGGAGGTGCTTTACG
196 AGGTGGTGATCCATTGCAGGGAGTAGGAGGTGCTTTACG
* * * *
3953163 AATGCATGGGCCAGGGGCAGCGGCTGGTGGTGATTTCGGAGGTGGAGTTGGACCTTTACCAGGGC
1 AATGTATGGGCCAGGTGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGC
* * * **
3953228 TTGGTGGATATGAAGGTTTGGGGGGTGATGCCTTACTCGGAGGAGTTGGGGATGCAGGATGTGGA
66 TTGGTGGATATGAGGGTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGACATGCAGGATGTGGA
*
3953293 GGGGGCACTGTAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGTGCAGGTGCAGAGTG
131 GGGGGCACTGCAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGTGCAGGTGCAGAGTG
*
3953358 AGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACG
196 AGGTGGTGATCCATTGCAGGGAGTAGGAGGTGCTTTACG
* *
3953397 GATGTATGGGCCAGGTGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTGCCAGGGC
1 AATGTATGGGCCAGGTGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGC
* * * *
3953462 GTGGCT-GATATGAGGGTTTAGGGCGTGATGCCTTACTTGGAGGAGTT-GCCTTTGCAGGATGTG
66 TTGG-TGGATATGAGGGTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGAC-ATGCAGGATGTG
* * * ** *
3953525 GCGAGGGCGCTGCAACTGGACTAGAAGGGGTACTTGGAGTTGGCTTTGGAGGTGC
129 GAGGGGGCACTGCAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGTGC
3953580 TAAGCAATGT
Statistics
Matches: 378, Mismatches: 37, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
233 1 0.00
234 376 0.99
235 1 0.00
ACGTcount: A:0.18, C:0.13, G:0.43, T:0.26
Consensus pattern (234 bp):
AATGTATGGGCCAGGTGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGC
TTGGTGGATATGAGGGTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGACATGCAGGATGTGGA
GGGGGCACTGCAGGTGGACTAGAAGGGGTACTTGGAGTTGCCTTTGGAGGTGCAGGTGCAGAGTG
AGGTGGTGATCCATTGCAGGGAGTAGGAGGTGCTTTACG
Found at i:3969303 original size:20 final size:20
Alignment explanation
Indices: 3969278--3969334 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
3969268 TTGATAAAAT
*
3969278 ATTATTAAATTTTAATTTTA
1 ATTATTAAAATTTAATTTTA
3969298 ATTATTAAAATTTAA-TTTA
1 ATTATTAAAATTTAATTTTA
* * *
3969317 TTTAATAATATTTAATTT
1 ATTATTAAAATTTAATTT
3969335 ATATGGTAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTATTAAAATTTAATTTTA
Found at i:3972450 original size:234 final size:232
Alignment explanation
Indices: 3972034--3972968 Score: 1391
Period size: 234 Copynumber: 4.0 Consensus size: 232
3972024 TTTTGCTGGT
* * *
3972034 GGTGCAGAGTGAGGTGGTGATCCCTTGTAGGGAGTAGGAGGTGCTTTACCAATGTATGGGCCAGG
1 GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCAGG
*
3972099 TGCAGCTGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATG-AG
66 TGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATGAAG
*
3972163 GGTTAGGGGGTGATGCGCTTACTTGGGAGGAGTTGGGG-TGCAGGATGGTGGAGGGGCA-TGGAG
131 GTTTAGGGGGTGATGC-CTTACTT-GGAGGAGTTGGGGATGCAGGAT-GTGGAGGGGCACTGGAG
* * *
3972226 GTGGATCTAG-GGGGTACTTGGAGTTTGCCTTGGGAGGCGCTA
193 GTGGA-CTAGAGGGGTACTTGGAG-TTGGCTTTGGAGGTGC-A
*
3972268 GGTGCAG-GTGACGGTGGTGATCCATTGGCAGGGAGTAGGAGGTG-TTTACCGATGTATGGGCCA
1 GGTGCAGAGTGA-GGTGGTGATCCATT-GCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCA
*
3972331 GGTGCCAGCTGCTGGTGGTGA-TTTGG-GGTGGAGTTGGACCTTTACCAGGGCCTTGGTGGATAT
64 GGTG-CAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGG-CTTGGTGGATAT
*
3972394 GAAGGTTTAGGGGGTGATGCGCTTACTTGGAGGAGTTGGGGATGCAGGATGTGGAGGGGGCACAG
127 GAAGGTTTAGGGGGTGATGC-CTTACTTGGAGGAGTTGGGGATGCAGGATGTGGA-GGGGCACTG
* *
3972459 TAGGTGGACTAGAGGTGTACTTGGAGTTGGCTTTGGAGGTGCA
190 GAGGTGGACTAGAGGGGTACTTGGAGTTGGCTTTGGAGGTGCA
* *
3972502 GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCGATGTATGGGCCCGG
1 GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCAGG
* *
3972567 TTCAGCCGCTGTTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATGAAG
66 TGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATGAAG
* *
3972632 GTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGGGATGCAGGATGTGGCGGGGGCACTGTAGGT
131 GTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGGGATGCAGGATGTGG-AGGGGCACTGGAGGT
3972697 GGACTAGAAGGGGTACTTGGAGTTGGCTTTGGAGGTGCA
195 GGACTAG-AGGGGTACTTGGAGTTGGCTTTGGAGGTGCA
3972736 GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCAGG
1 GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCAGG
* * * *
3972801 TGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTGCCAGGGCGTGGCGGATATGAGG
66 TGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATGAAG
* **** * **
3972866 GTTTAGGGCGTGATGCCTTACTTGGAGGAGTTGCCTTTGCAGGATGTGGCGAGGGCACTGGAACT
131 GTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGGGATGCAGGATGTGGAG-GGGCACTGGAGGT
3972931 GGACTAGAAGGGGTACTTGGAGTTGGCTTTGGAGGTGC
195 GGACTAG-AGGGGTACTTGGAGTTGGCTTTGGAGGTGC
3972969 TAAGCAATGT
Statistics
Matches: 651, Mismatches: 34, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
233 113 0.17
234 402 0.62
235 116 0.18
236 20 0.03
ACGTcount: A:0.17, C:0.13, G:0.43, T:0.27
Consensus pattern (232 bp):
GGTGCAGAGTGAGGTGGTGATCCATTGCAGGGAGTAGGAGGTGTTTTACCAATGTATGGGCCAGG
TGCAGCCGCTGGTGGTGATTTTGGAGGTGGAGTTGGACCTTTACCAGGGCTTGGTGGATATGAAG
GTTTAGGGGGTGATGCCTTACTTGGAGGAGTTGGGGATGCAGGATGTGGAGGGGCACTGGAGGTG
GACTAGAGGGGTACTTGGAGTTGGCTTTGGAGGTGCA
Found at i:3973861 original size:18 final size:17
Alignment explanation
Indices: 3973836--3973870 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3973826 AAAATATTTT
*
3973836 TTTATGATATTATATAA
1 TTTATGATAATATATAA
3973853 TTTATTGATAATATATAA
1 TTTA-TGATAATATATAA
3973871 AATTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
TTTATGATAATATATAA
Found at i:3979841 original size:148 final size:148
Alignment explanation
Indices: 3979573--3979869 Score: 531
Period size: 148 Copynumber: 2.0 Consensus size: 148
3979563 TAATTGATAA
* *
3979573 AGACATTTAATGCATAAGTCTAAAGTATTCTTTCACATTGATGTCGAAACCTACTTTAGACGGCA
1 AGACATTTAATGCATAAGTCTAAAGTATTCTTTCACATTGATGTCGAAACATACTTCAGACGGCA
*
3979638 GTGGTCCAAACCAGAGCTCCAACTTCGTCAACTAATTAAAACATGAAAGCAGCTTCCATCAAATA
66 GTGGTCCAAACCAGAGCTCCAACTTCGTCAACTAACTAAAACATGAAAGCAGCTTCCATCAAATA
*
3979703 GTGAAGCGCAGAAGGTGG
131 GTGAAGAGCAGAAGGTGG
3979721 AGACATTTAATGCATAAGTCTAAAGTATTCTTTCACATTGATGTCGAAACATACTTCAGACGGCA
1 AGACATTTAATGCATAAGTCTAAAGTATTCTTTCACATTGATGTCGAAACATACTTCAGACGGCA
* * *
3979786 GTGGTCCAAACCAGAGCTCCAACTTTGTCAACTACCTGAAACATGAAAGCAGCTTCCATCAAATA
66 GTGGTCCAAACCAGAGCTCCAACTTCGTCAACTAACTAAAACATGAAAGCAGCTTCCATCAAATA
3979851 GTGAAGAGCAGAAGGTGG
131 GTGAAGAGCAGAAGGTGG
3979869 A
1 A
3979870 TTTTTTTTTT
Statistics
Matches: 142, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 142 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (148 bp):
AGACATTTAATGCATAAGTCTAAAGTATTCTTTCACATTGATGTCGAAACATACTTCAGACGGCA
GTGGTCCAAACCAGAGCTCCAACTTCGTCAACTAACTAAAACATGAAAGCAGCTTCCATCAAATA
GTGAAGAGCAGAAGGTGG
Found at i:3979925 original size:9 final size:8
Alignment explanation
Indices: 3979909--3979957 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 8
3979899 GATTATGAAA
3979909 TAAAATAT
1 TAAAATAT
3979917 TACAAATAT
1 TA-AAATAT
3979926 TAAAAT-T
1 TAAAATAT
3979933 T-AAATAT
1 TAAAATAT
*
3979940 TAAATTTAT
1 TAAA-ATAT
3979949 T-AAATAT
1 TAAAATAT
3979956 TA
1 TA
3979958 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
6 4 0.12
7 8 0.24
8 10 0.29
9 12 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
TAAAATAT
Found at i:3979963 original size:16 final size:16
Alignment explanation
Indices: 3979920--3979957 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
3979910 AAAATATTAC
*
3979920 AAATATTAAA-AT-TT
1 AAATATTAAATTTATT
3979934 AAATATTAAATTTATT
1 AAATATTAAATTTATT
3979950 AAATATTA
1 AAATATTA
3979958 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTAAATTTATT
Found at i:3980883 original size:2 final size:2
Alignment explanation
Indices: 3980842--3980866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3980832 ATCCAAGCAC
3980842 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3980867 ACTTCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3980959 original size:104 final size:104
Alignment explanation
Indices: 3980745--3980949 Score: 401
Period size: 104 Copynumber: 2.0 Consensus size: 104
3980735 TCACCTAAAT
*
3980745 TATATATATATATATATAACTTCCTTAATTATATAGTACAATGGAGTCAAGGACAATCCCTAATT
1 TATATATATATATATATAACTTCCTTAATTATATAGTAAAATGGAGTCAAGGACAATCCCTAATT
3980810 GAATTAGCAATGAAAAAATAAAATCCAAGCACATATATA
66 GAATTAGCAATGAAAAAATAAAATCCAAGCACATATATA
3980849 TATATATATATATATATAACTTCCTTAATTATATAGTAAAATGGAGTCAAGGACAATCCCTAATT
1 TATATATATATATATATAACTTCCTTAATTATATAGTAAAATGGAGTCAAGGACAATCCCTAATT
3980914 GAATTAGCAATGAAAAAATAAAATCCAAGCACATAT
66 GAATTAGCAATGAAAAAATAAAATCCAAGCACATAT
3980950 CCTTCTATAT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (104 bp):
TATATATATATATATATAACTTCCTTAATTATATAGTAAAATGGAGTCAAGGACAATCCCTAATT
GAATTAGCAATGAAAAAATAAAATCCAAGCACATATATA
Found at i:3988562 original size:14 final size:14
Alignment explanation
Indices: 3988517--3988562 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3988507 ATTGGAGAAG
3988517 AAAATAAGTAAAAT
1 AAAATAAGTAAAAT
*
3988531 AAAAT--GTCAAAAGA
1 AAAATAAGT-AAAA-T
3988545 AAAATAAGTAAAAT
1 AAAATAAGTAAAAT
3988559 AAAA
1 AAAA
3988563 GCAATGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 2 0.08
13 4 0.15
14 14 0.54
15 4 0.15
16 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAATAAGTAAAAT
Found at i:3988903 original size:18 final size:18
Alignment explanation
Indices: 3988880--3988915 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3988870 AAATCAGATT
3988880 ATAAAAG-CAAAAGTAAAA
1 ATAAAAGCCAAAAG-AAAA
3988898 ATAAAAGCCAAAAGAAAA
1 ATAAAAGCCAAAAGAAAA
3988916 GATTACTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.08
Consensus pattern (18 bp):
ATAAAAGCCAAAAGAAAA
Found at i:3990266 original size:22 final size:22
Alignment explanation
Indices: 3990228--3990293 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
3990218 TTAAATGTTT
3990228 ATTT-TAATTTTCTTATTTTTTA
1 ATTTATAATTTT-TTATTTTTTA
* **
3990250 ATTTATAATTTTATA-TTTAAA
1 ATTTATAATTTTTTATTTTTTA
3990271 ATTTAATAATTTTTTATTGTTTT
1 ATTT-ATAATTTTTTATT-TTTT
3990294 GGTCTTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 8 0.24
22 16 0.47
23 8 0.24
24 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTATAATTTTTTATTTTTTA
Found at i:3990565 original size:597 final size:604
Alignment explanation
Indices: 3989421--3990611 Score: 1859
Period size: 597 Copynumber: 2.0 Consensus size: 604
3989411 TTAATTTTAT
3989421 AATTAATTTTATTAAAATATAAATTTAAAAATTTGTAATTTTAAAAATGTTTTTAGATAAAATTT
1 AATTAATTTTATTAAAATATAAATTTAAAAATTTGTAATTTTAAAAATGTTTTTAGATAAAATTT
*
3989486 AGTTAGAAGGATTAAGATTTTATAATTGAAAAAAATTAAAAGATAAATAATTTAATATGATATAT
66 AGTTAGAAGGATTAAGAATTTATAATTGAAAAAAATTAAAAGATAAATAATTTAATATGATATAT
* **
3989551 ATATGGATTCTAGATGAAAAATTTTAATAATTTTTTTTTTATATAAGTTAGATGAAAAATAATTA
131 ATAGGGATTCTAGATGAAAAATTTTAATAATAATTTTTTTATATAAGTTAGATGAAAAATAATTA
* * * *
3989616 AAATTAAATATTATATTTTGATTTTGTTATTTATTAATTTATAATTTTATATTTGAAGTTTAATA
196 AAATTAAATATTATATTTTAATTTTCTTATTTATTAATTTATAATTTTATATTTAAAATTTAATA
* * *
3989681 ATATTTTTGTTATTTTGGTATTTATATTGTTGTCAATTCTTTTGCTATTAAATTAATTCTTATTA
261 ATATTTTTATTATTTTGGTATTTATATTGCTGTCAATTCTTTTGCTATTAAATTAATTATTATTA
*
3989746 ATTTATTTTAATTTTTGTGTAATTATTAAATATTCTATTTATTATATAATATATTGAAAGTAATT
326 ATTTATTTTAATTTTTGTGTAATTATTAAAGATTCTATTTATTATATAATATATTGAAAGTAATT
* * * *
3989811 TGTGATAAAATTTTTTTACATCAATTAATGTATCAAAAAGATTAAATTACTTAATAAATTTAATA
391 TGTGATAAAAATTTTTTACATCAATTAATGCATAAAAAAGATTAAATTACTTAATAAATTTAACA
* * *
3989876 TTTTACGATTTATTACTCTTAAGATTAAAAATTACAAAATTACAAAATTTAATGTAGATTTAATT
456 TTTTACAATCTATTACTCTTAAGATTAAAAACTACAAAATTACAAAATTTAATGTAGATTTAATT
* *
3989941 TTTAATGATAGAATAAGTAATATTAATATTTCTAAATATAAG-TTATTTTA-TTTTTATACAAAA
521 TTTAATGATAGAATAAATAACATTAATATTTCTAAATATAAGTTTATTTTATTTTTTATACAAAA
3990004 TAGCAAGCATGCATTTTGC
586 TAGCAAGCATGCATTTTGC
3990023 AATTAATTTTATTAAAATATAAATTTAAAAATTTGTAATTTTAAAAAT-TTTTTAAGATAAAATT
1 AATTAATTTTATTAAAATATAAATTTAAAAATTTGTAATTTTAAAAATGTTTTT-AGATAAAATT
* ** *
3990087 TAGTTAGAGGGATTGTGAATTTATAATTG-AAAAAATTAAGAA-ATTAATAATTTAATATGATAT
65 TAGTTAGAAGGATTAAGAATTTATAATTGAAAAAAATTAA-AAGATAAATAATTTAATATGATAT
* * * *
3990150 ATATGGGGATTTTAGATGAAAAGTTTTAATAA-AATTTTTTTGTATAAGTTAGAT-AAAAATAAT
129 ATATAGGGATTCTAGATGAAAAATTTTAATAATAATTTTTTTATATAAGTTAGATGAAAAATAAT
* *
3990213 TAAAATTAAATGTT-TATTTTAATTTTCTTATTTTTTAATTTATAATTTTATATTTAAAATTTAA
194 TAAAATTAAATATTATATTTTAATTTTCTTATTTATTAATTTATAATTTTATATTTAAAATTTAA
* * *
3990277 TAAT-TTTTTATTGTTTTGGTCTTTATATTGCTGTCAATTCTTTTGCTGTTAAATTAATTATTAT
259 TAATATTTTTATTATTTTGGTATTTATATTGCTGTCAATTCTTTTGCTATTAAATTAATTATTAT
** * *
3990341 TTTTTTATTTTAATTTTTGTGTAATTATTGAAGATTTTATTTATTATATAATATATTGAAAGTAA
324 TAATTTATTTTAATTTTTGTGTAATTATTAAAGATTCTATTTATTATATAATATATTGAAAGTAA
* * * *
3990406 TTTGTGATAAAAAATTTTTTACATTAATTAGTGCATAAAAAAGATTAAGTTACTTAATGAATTTA
389 TTTGTGAT-AAAAATTTTTTACATCAATTAATGCATAAAAAAGATTAAATTACTTAATAAATTTA
3990471 ACATTTTACAATCTATTACT-TTGAAGATTAAAAACTA-AAAATTA-AAATATTTAATGTAGATT
453 ACATTTTACAATCTATTACTCTT-AAGATTAAAAACTACAAAATTACAAA-ATTTAATGTAGATT
3990533 TAATTTTTAATGAT-GAAATAAATAACATTAATATTTCTAAATATAAGTTTATTTTATTTTTTAT
516 TAATTTTTAATGATAG-AATAAATAACATTAATATTTCTAAATATAAGTTTATTTTATTTTTTAT
3990597 ACAAAATAGCAAGCA
580 ACAAAATAGCAAGCA
3990612 AGCCACCACG
Statistics
Matches: 539, Mismatches: 42, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
596 4 0.01
597 188 0.35
598 136 0.25
599 44 0.08
600 19 0.04
601 63 0.12
602 85 0.16
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (604 bp):
AATTAATTTTATTAAAATATAAATTTAAAAATTTGTAATTTTAAAAATGTTTTTAGATAAAATTT
AGTTAGAAGGATTAAGAATTTATAATTGAAAAAAATTAAAAGATAAATAATTTAATATGATATAT
ATAGGGATTCTAGATGAAAAATTTTAATAATAATTTTTTTATATAAGTTAGATGAAAAATAATTA
AAATTAAATATTATATTTTAATTTTCTTATTTATTAATTTATAATTTTATATTTAAAATTTAATA
ATATTTTTATTATTTTGGTATTTATATTGCTGTCAATTCTTTTGCTATTAAATTAATTATTATTA
ATTTATTTTAATTTTTGTGTAATTATTAAAGATTCTATTTATTATATAATATATTGAAAGTAATT
TGTGATAAAAATTTTTTACATCAATTAATGCATAAAAAAGATTAAATTACTTAATAAATTTAACA
TTTTACAATCTATTACTCTTAAGATTAAAAACTACAAAATTACAAAATTTAATGTAGATTTAATT
TTTAATGATAGAATAAATAACATTAATATTTCTAAATATAAGTTTATTTTATTTTTTATACAAAA
TAGCAAGCATGCATTTTGC
Found at i:3999673 original size:22 final size:21
Alignment explanation
Indices: 3999634--3999675 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3999624 ATAAAAAATT
3999634 ATATTATAAATTTCATATAAA
1 ATATTATAAATTTCATATAAA
* *
3999655 ATATTAATATATTTTATATAA
1 ATATT-ATAAATTTCATATAA
3999676 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATAAATTTCATATAAA
Found at i:3999700 original size:14 final size:14
Alignment explanation
Indices: 3999681--3999714 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3999671 TATAATTTTA
3999681 AATTATAAT-TAATT
1 AATTATAATATAA-T
3999695 AATTATAATATAAT
1 AATTATAATATAAT
3999709 AATTAT
1 AATTAT
3999715 TGGTGATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTATAATATAAT
Found at i:3999924 original size:15 final size:15
Alignment explanation
Indices: 3999906--3999943 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3999896 ATTAATAAAA
3999906 AATTTATATT-AAATT
1 AATTT-TATTAAAATT
3999921 AATTTTATTAAAATT
1 AATTTTATTAAAATT
3999936 AATATTTA
1 AAT-TTTA
3999944 AATTCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 13 0.62
16 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTATTAAAATT
Found at i:4000761 original size:19 final size:17
Alignment explanation
Indices: 4000729--4000772 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
4000719 ATATTTCAAC
4000729 ATTTTTCATATTTTATGAT
1 ATTTTT-ATATTTTAT-AT
*
4000748 ATTTTTATATTTTTATTT
1 ATTTTTATA-TTTTATAT
4000766 ATTTTTA
1 ATTTTTA
4000773 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
ATTTTTATATTTTATAT
Found at i:4005471 original size:21 final size:20
Alignment explanation
Indices: 4005432--4005471 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4005422 AATAACAGAT
*
4005432 AAATAAATAAATGACTAAAC
1 AAATAAATAAATGAATAAAC
*
4005452 AAATAAAATAAATTAATAAA
1 AAAT-AAATAAATGAATAAA
4005472 ATGACATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
AAATAAATAAATGAATAAAC
Found at i:4005476 original size:30 final size:29
Alignment explanation
Indices: 4005419--4005490 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
4005409 AAATGTATTT
4005419 AAAAATAACAGATAAATAAATAAATGAC-TA
1 AAAAATAA-A-ATAAATAAATAAATGACATA
*
4005449 AACAAATAAAATAAATTAATAAAATGACATA
1 AA-AAATAAAATAAATAAAT-AAATGACATA
*
4005480 TAAAATAAAAT
1 AAAAATAAAAT
4005491 TACCAGTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 9 0.24
30 19 0.51
31 9 0.24
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (29 bp):
AAAAATAAAATAAATAAATAAATGACATA
Found at i:4005630 original size:41 final size:41
Alignment explanation
Indices: 4005571--4005652 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
4005561 GAACTTGGCT
* * * *
4005571 GAGAAGGTGACTCGGCTCAAGGTGGAAGGAGTTTCGAGTCA
1 GAGAAGGTGACTCAGCTCAAGGTGAAAAGAGCTTCGAGTCA
4005612 GAGAAGGTGACTCAGCTCAAGGTGAAAAGAGCTTCGAGTCA
1 GAGAAGGTGACTCAGCTCAAGGTGAAAAGAGCTTCGAGTCA
4005653 CCAATAGGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.35, T:0.18
Consensus pattern (41 bp):
GAGAAGGTGACTCAGCTCAAGGTGAAAAGAGCTTCGAGTCA
Found at i:4006450 original size:3 final size:3
Alignment explanation
Indices: 4006438--4006476 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
4006428 ACAACACATA
*
4006438 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4006477 TGTTGGGCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4006991 original size:65 final size:65
Alignment explanation
Indices: 4006858--4006998 Score: 151
Period size: 65 Copynumber: 2.2 Consensus size: 65
4006848 GCCGTGAGTC
* * * * * *
4006858 AAAAAAATTAAATAATCCAGACTAAACTAAGACCTAAGATGAATGACCAAGATTGAACCGCAGAT
1 AAAAAAAATAAATAATCCAGACTAAACCAAGACCGAAGATGAATGACCAAGATTAAACAGAAGAT
** * * * *
4006923 AAAAAAAATAAATAATTTAGACTGAACCAAGATCGAAGATGAATGACCTAGATTAAACTATAAG-
1 AAAAAAAATAAATAATCCAGACTAAACCAAGACCGAAGATGAATGACCAAGATTAAAC-AGAAGA
4006987 T
65 T
4006988 -AAAAAAATAAA
1 AAAAAAAATAAA
4006999 ACAACCTGGA
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
64 11 0.17
65 50 0.79
66 2 0.03
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.20
Consensus pattern (65 bp):
AAAAAAAATAAATAATCCAGACTAAACCAAGACCGAAGATGAATGACCAAGATTAAACAGAAGAT
Found at i:4007155 original size:129 final size:129
Alignment explanation
Indices: 4006925--4007164 Score: 318
Period size: 129 Copynumber: 1.9 Consensus size: 129
4006915 CCGCAGATAA
* * * * * *
4006925 AAAAAATAAATAATTTAGACTGAACCAAGATCGAAGATGAATGACCTAGATTAAACTATAAGTAA
1 AAAAAATAAATAATCTAAACTGAACCAAGATCGAAGATGAATGACCAAAATTAAACCACAAGTAA
* *
4006990 AAAAATAAAACAACCTGGACCGAGTCAAAATAAAAAATGAGTGACGGGGTTGCACTGCAAATCC
66 AAAAATAAAACAACATGGACCGAGCCAAAATAAAAAATGAGTGACGGGGTTGCACTGCAAATCC
* * *
4007054 AAAAAATAAATGATCTAAACTGAACCAAGATCGAAGATGAATGACCAAAATTGAACCACATGTTA
1 AAAAAATAAATAATCTAAACTGAACCAAGATCGAAGATGAATGACCAAAATTAAACCACAAG-TA
** ** **
4007119 AAAAAATAAAATGACATGGATTGAGCCAAGGTAAAAAATGAGTGAC
65 AAAAAATAAAACAACATGGACCGAGCCAAAATAAAAAATGAGTGAC
4007165 TTGGATTAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
129 53 0.57
130 40 0.43
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (129 bp):
AAAAAATAAATAATCTAAACTGAACCAAGATCGAAGATGAATGACCAAAATTAAACCACAAGTAA
AAAAATAAAACAACATGGACCGAGCCAAAATAAAAAATGAGTGACGGGGTTGCACTGCAAATCC
Found at i:4007255 original size:131 final size:130
Alignment explanation
Indices: 4007055--4007342 Score: 285
Period size: 130 Copynumber: 2.2 Consensus size: 130
4007045 TGCAAATCCA
* * * * * * *
4007055 AAAAATAAATGATCTAAACTGAACCAAGATCGAAGATGAATGACCAAAATTGAACCACATGTTAA
1 AAAAATAAATAATCTAGACTGAACCAAAATCAAAAATGAATAACCAAAATTGAACCACAAGTTAA
* * * *
4007120 AAAAATAAAATGACATGGATTGAGCCAAGGTAAAAAATGAGTGACTTG-GATTAAATCAC-AGAT
66 AAAAAT-AAATAACATGGACTGAGCCAAGGTAAAAAATAAGTGA-TTGAGACTAAATCACAAG-T
4007183 TAG
128 TAG
* * ***
4007186 AAAAATAAATTATCTAGACTGAACCAAAA-CTAAAAATGAATAACCAGAATTGAATTGCAAGTTA
1 AAAAATAAATAATCTAGACTGAACCAAAATC-AAAAATGAATAACCAAAATTGAACCACAAGTTA
* ** * ** * *
4007250 GAAAAATAAATAATTTGGACTGAGCTAAGGTCGAAAATAAGTGATTGAGACTGAATCGCAAGTTA
65 AAAAAATAAATAACATGGACTGAGCCAAGGTAAAAAATAAGTGATTGAGACTAAATCACAAGTTA
4007315 G
130 G
* *
4007316 AAAAATAAATAACCTAGACTGAGCCAA
1 AAAAATAAATAATCTAGACTGAACCAA
4007343 GGTTGAAAAT
Statistics
Matches: 128, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
129 3 0.02
130 66 0.52
131 59 0.46
ACGTcount: A:0.49, C:0.12, G:0.17, T:0.22
Consensus pattern (130 bp):
AAAAATAAATAATCTAGACTGAACCAAAATCAAAAATGAATAACCAAAATTGAACCACAAGTTAA
AAAAATAAATAACATGGACTGAGCCAAGGTAAAAAATAAGTGATTGAGACTAAATCACAAGTTAG
Found at i:4007287 original size:65 final size:65
Alignment explanation
Indices: 4007182--4007390 Score: 190
Period size: 65 Copynumber: 3.2 Consensus size: 65
4007172 AAATCACAGA
* * * ** * * *
4007182 TTAGAAAAATAAATTATCTAGACTGAACCAA-AACTAAAAATGAA-TAACCAGAATTGAATTGCA
1 TTAGAAAAATAAATAACCTAGACTGAGCCAAGGTC-GAAAAT-AAGTAACTAGAATTGAATCGCA
4007245 AG
64 AG
** * * * * *
4007247 TTAGAAAAATAAATAATTTGGACTGAGCTAAGGTCGAAAATAAGTGA-TTGAGACTGAATCGCAA
1 TTAGAAAAATAAATAACCTAGACTGAGCCAAGGTCGAAAATAAGTAACTAGA-ATTGAATCGCAA
4007311 G
65 G
* * *
4007312 TTAGAAAAATAAATAACCTAGACTGAGCCAAGGTTGAAAATAAGTAACTGGGATTGAATCGCAAG
1 TTAGAAAAATAAATAACCTAGACTGAGCCAAGGTCGAAAATAAGTAACTAGAATTGAATCGCAAG
* *
4007377 TCAAAAAAATAAAT
1 TTAGAAAAATAAAT
4007391 GACTTAGATT
Statistics
Matches: 116, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
64 4 0.03
65 109 0.94
66 3 0.03
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (65 bp):
TTAGAAAAATAAATAACCTAGACTGAGCCAAGGTCGAAAATAAGTAACTAGAATTGAATCGCAAG
Found at i:4007481 original size:65 final size:65
Alignment explanation
Indices: 4007276--4007484 Score: 231
Period size: 65 Copynumber: 3.2 Consensus size: 65
4007266 GGACTGAGCT
* * * * * * *
4007276 AAGGTCGAAAATAAGTGATTGAGACTGAATCGCAAGTTAGAAAAATAAATAACCTAGACTGAGCC
1 AAGGTCGAAAATAAGTGACTGGGACTGAATCGCAAGTCAAAAAAATAAATGACCTAGAATGAACC
* * * * *
4007341 AAGGTTGAAAATAAGTAACTGGGATTGAATCGCAAGTCAAAAAAATAAATGACTTAGATTGAACC
1 AAGGTCGAAAATAAGTGACTGGGACTGAATCGCAAGTCAAAAAAATAAATGACCTAGAATGAACC
* * * * * *
4007406 GAGATAGAAAATAAGTGACTGGGACT-AAACTGCAAGTCAAAAAAATAAATGACCTAAAATAAAC
1 AAGGTCGAAAATAAGTGACTGGGACTGAATC-GCAAGTCAAAAAAATAAATGACCTAGAATGAAC
*
4007470 T
65 C
4007471 AAGGTCGAAAATAA
1 AAGGTCGAAAATAA
4007485 ATTATTGGAC
Statistics
Matches: 118, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
64 3 0.03
65 115 0.97
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (65 bp):
AAGGTCGAAAATAAGTGACTGGGACTGAATCGCAAGTCAAAAAAATAAATGACCTAGAATGAACC
Found at i:4007974 original size:73 final size:73
Alignment explanation
Indices: 4007872--4008009 Score: 206
Period size: 73 Copynumber: 1.9 Consensus size: 73
4007862 ATTCCAAGAC
*
4007872 TCCAAGTTTTACAAAAAAATCGCAAAGATTTCAAAATTCACAAAAAGCCAAGATTTGCAAAGGTT
1 TCCAAGTTTTACAAAAAAATC-CAAAGATTTCAAAATTCACAAAAAGCCAAGATTTACAAAGGTT
4007937 TACAAGAAT
65 TACAAGAAT
* * **
4007946 TCCAAGTTTTGCAAGAAAAAT-CACAGATTTCAAAATTCACAAAAAGTTAAGATTTACAAAGGTT
1 TCCAAGTTTTACAA-AAAAATCCAAAGATTTCAAAATTCACAAAAAGCCAAGATTTACAAAGGTT
4008010 CCAGATTCAC
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
73 39 0.67
74 13 0.22
75 6 0.10
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.26
Consensus pattern (73 bp):
TCCAAGTTTTACAAAAAAATCCAAAGATTTCAAAATTCACAAAAAGCCAAGATTTACAAAGGTTT
ACAAGAAT
Found at i:4008160 original size:17 final size:17
Alignment explanation
Indices: 4008135--4008174 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4008125 AAAGATTCGT
*
4008135 AAGACTTTTAAATTTGC
1 AAGAATTTTAAATTTGC
*
4008152 AAGAATTTTAGATTTGC
1 AAGAATTTTAAATTTGC
4008169 AAGAAT
1 AAGAAT
4008175 GAAAGATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (17 bp):
AAGAATTTTAAATTTGC
Found at i:4009316 original size:21 final size:22
Alignment explanation
Indices: 4009276--4009324 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4009266 TCAGTTTAAG
*
4009276 TTTTTTTTTATCTTCATTTTTC
1 TTTTTTTTTACCTTCATTTTTC
* *
4009298 TTTTTTTTTACCTT-TTTTTTG
1 TTTTTTTTTACCTTCATTTTTC
4009319 TTTTTT
1 TTTTTT
4009325 CAATTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.06, C:0.10, G:0.02, T:0.82
Consensus pattern (22 bp):
TTTTTTTTTACCTTCATTTTTC
Found at i:4012278 original size:16 final size:16
Alignment explanation
Indices: 4012257--4012288 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4012247 AGTAAACATG
*
4012257 ATATATACAAAGAACA
1 ATATATACAAAAAACA
4012273 ATATATACAAAAAACA
1 ATATATACAAAAAACA
4012289 GCATAAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (16 bp):
ATATATACAAAAAACA
Found at i:4013663 original size:2 final size:2
Alignment explanation
Indices: 4013616--4013645 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4013606 TCGTAAGGTT
*
4013616 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4013646 CACACACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4013707 original size:4 final size:4
Alignment explanation
Indices: 4013689--4013739 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
4013679 ATGTATATAA
* * * *
4013689 AAAT -AAT AGAT AAAT AAAT AAAT GACT AAAT AAAT AAAAT AAAT TAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
4013737 AAA
1 AAA
4013740 ATGACATACT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
5 4 0.11
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:4013737 original size:13 final size:13
Alignment explanation
Indices: 4013698--4013741 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
4013688 AAAATAATAG
4013698 ATAAATAAATAAA
1 ATAAATAAATAAA
4013711 TGACTAAATAAATAAA
1 --A-TAAATAAATAAA
*
4013727 ATAAATTAATAAA
1 ATAAATAAATAAA
4013740 AT
1 AT
4013742 GACATACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 13 0.48
14 1 0.04
15 1 0.04
16 12 0.44
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAATAAATAAA
Found at i:4013758 original size:30 final size:29
Alignment explanation
Indices: 4013698--4013758 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
4013688 AAAATAATAG
*
4013698 ATAAATAAATAAATGACTAAATAAATAAA
1 ATAAATAAATAAATGACTAAATAAACAAA
* *
4013727 ATAAATTAATAAAATGAC-ATACTAAACAAA
1 ATAAATAAAT-AAATGACTA-AATAAACAAA
4013757 AT
1 AT
4013759 TACCAACAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.66, C:0.07, G:0.03, T:0.25
Consensus pattern (29 bp):
ATAAATAAATAAATGACTAAATAAACAAA
Found at i:4014678 original size:3 final size:3
Alignment explanation
Indices: 4014672--4014716 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
4014662 CAACACACAA
4014672 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4014717 TGCTGGGCTG
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):
AAT
Found at i:4014981 original size:25 final size:25
Alignment explanation
Indices: 4014946--4014999 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
4014936 TTTATTAAAA
* *
4014946 TTTTTTCAATCACAATTACAATAAT
1 TTTTTTCAATCACAACTACAATAAC
* *
4014971 TTTTTTTAATCATAACTACAATAAC
1 TTTTTTCAATCACAACTACAATAAC
4014996 TTTT
1 TTTT
4015000 ATTACTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTTCAATCACAACTACAATAAC
Found at i:4015853 original size:32 final size:31
Alignment explanation
Indices: 4015812--4015878 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
4015802 TATTTCAACA
* * *
4015812 TTAAGTATTATATTAATTAATAAATTTATAAT
1 TTAAATATTATACTAAATAATAAA-TTATAAT
* *
4015844 TTAAATATTATACTAAATATTATATTATAAT
1 TTAAATATTATACTAAATAATAAATTATAAT
4015875 TTAA
1 TTAA
4015879 GTAGGACATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TTAAATATTATACTAAATAATAAATTATAAT
Done.