Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 139 of 182
Found at i:43383565 original size:21 final size:21
Alignment explanation
Indices: 43383541--43383596 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
43383531 TTAGTATAAA
43383541 ATTATATTTTGATTATTACTT-
1 ATTATATTTTGATTATT-CTTC
** *
43383562 ATTA-ATAAATGTTTATTCTTC
1 ATTATAT-TTTGATTATTCTTC
43383583 ATTATATTTTGATT
1 ATTATATTTTGATT
43383597 TAAAATTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTATATTTTGATTATTCTTC
Found at i:43389589 original size:29 final size:29
Alignment explanation
Indices: 43389557--43389871 Score: 288
Period size: 29 Copynumber: 10.9 Consensus size: 29
43389547 ATTCAGGATC
*
43389557 AAAAATGAAATTTTTGGATA-TTTAGGGGT
1 AAAAATGTAATTTTTGGA-AGTTTAGGGGT
43389586 -AAAATGGTAATTTTTGGAA-TTTAGGGGT
1 AAAAAT-GTAATTTTTGGAAGTTTAGGGGT
* * * * *
43389614 AAAAACGTATTTTTTGGAACTTTCGAGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
* **
43389643 GAAAAATGGAATTTTTGGATA-TTCGGGGGT
1 -AAAAATGTAATTTTTGGA-AGTTTAGGGGT
* **
43389673 -AAAATGGAATTTTTGGATA-TTCGGGGGT
1 AAAAATGTAATTTTTGGA-AGTTTAGGGGT
* * *
43389701 -AAAATAG-AATTTTTGGAAG-TTCGAGCGC
1 AAAAAT-GTAATTTTTGGAAGTTTAG-GGGT
* *
43389729 AAAAATATAATTTTTGGAAGTTTTGGGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
*
43389758 AAAAATGTAATTTTTGGAAGTTTAAGGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
* *
43389787 AAAAATGTAATTTTTGGAAGTTTTGAGGTT
1 AAAAATGTAATTTTTGGAAGTTTAG-GGGT
* **
43389817 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT
43389846 AAAAATGTAATTTTTGGAAGTTTAGG
1 AAAAATGTAATTTTTGGAAGTTTAGG
43389872 ATCCTTTAGA
Statistics
Matches: 242, Mismatches: 32, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.01
28 72 0.30
29 117 0.48
30 49 0.20
31 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:43391005 original size:12 final size:12
Alignment explanation
Indices: 43390988--43391019 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
43390978 ATACTTCAGT
43390988 TATTATTATAAA
1 TATTATTATAAA
*
43391000 TATTATTATTAA
1 TATTATTATAAA
43391012 TATTATTA
1 TATTATTA
43391020 ATGACACCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTATTATAAA
Found at i:43391810 original size:17 final size:17
Alignment explanation
Indices: 43391787--43391874 Score: 108
Period size: 17 Copynumber: 5.3 Consensus size: 17
43391777 TGAACACTTT
*
43391787 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
* *
43391804 TTTTAAATTTAAACTAA
1 ATTTAAATTTAAAATAA
*
43391821 ATTCAAATTT--AATAA
1 ATTTAAATTTAAAATAA
*
43391836 ATTTAAAATTAAAATAA
1 ATTTAAATTTAAAATAA
*
43391853 ATTTAATTTTAAAATAA
1 ATTTAAATTTAAAATAA
43391870 ATTTA
1 ATTTA
43391875 GAATGGTTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
15 12 0.20
17 47 0.80
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:43391839 original size:26 final size:26
Alignment explanation
Indices: 43391807--43391859 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
43391797 ATAATAATTT
*
43391807 TAAATTT-AAACTAAATTCAAATTTAA
1 TAAATTTAAAACTAAAAT-AAATTTAA
*
43391833 TAAATTTAAAATTAAAATAAATTTAA
1 TAAATTTAAAACTAAAATAAATTTAA
43391859 T
1 T
43391860 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAATTTAAAACTAAAATAAATTTAA
Found at i:43391841 original size:32 final size:32
Alignment explanation
Indices: 43391798--43391874 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
43391788 TTTAAATTTA
* * *
43391798 TAATAATTTTAAATTTAAACTAAATTCAAATT
1 TAATAAATTTAAAATTAAAATAAATTCAAATT
* *
43391830 TAATAAATTTAAAATTAAAATAAATTTAATTT
1 TAATAAATTTAAAATTAAAATAAATTCAAATT
43391862 TAAAATAAATTTA
1 T--AATAAATTTA
43391875 GAATGGTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 28 0.74
34 10 0.26
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
TAATAAATTTAAAATTAAAATAAATTCAAATT
Found at i:43392820 original size:92 final size:92
Alignment explanation
Indices: 43392118--43392816 Score: 1193
Period size: 92 Copynumber: 7.6 Consensus size: 92
43392108 AAAATAGGGT
* * *
43392118 TTGATG-TTGAGGCTTCATTTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
43392182 TTTACTGCAACTTCAAGAGGATAAGAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
* *
43392209 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGATTTGTTATCCAAA
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
*
43392274 TTTACTGCAACTTCAAGAGGATAAAAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
* * *
43392301 TTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGCTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
* *
43392366 TTTACTACAACTTCAAGAGGATAGGAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
* *
43392393 TTGATGTTTGATGCTTCATCTTACTATTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
*
43392458 TTTACTGCAACTTCAAGAGGATAAGAT
66 TTTACTGCAACTTCAAGAGGATAAGAA
43392485 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
*
43392550 TTTACTGCAACTTCAAGAGGATAGGAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
43392577 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
* *
43392642 TTTATTGAAACTTCAAGAGGATAAGAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
* *
43392669 TTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAAC
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
*
43392734 TTTACTGCAACTTCAAGAGGATAGGAA
66 TTTACTGCAACTTCAAGAGGATAAGAA
* *
43392761 TTGATGTTTGAAGCTTCATCTTACTCTTGCTACAACTTCAGAGAGGTAAAGACTTG
1 TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTG
43392817 CTATTTTGAT
Statistics
Matches: 570, Mismatches: 37, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
91 6 0.01
92 564 0.99
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (92 bp):
TTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAGATAAAGACTTGTTATCCAAC
TTTACTGCAACTTCAAGAGGATAAGAA
Found at i:43403955 original size:58 final size:58
Alignment explanation
Indices: 43403859--43403993 Score: 135
Period size: 58 Copynumber: 2.3 Consensus size: 58
43403849 GGAAATCTAA
* * * * *
43403859 GGGTAAAACAATAATTTTTAGAAAAATCAAGATCAAAAACAAAATTTTTGGACATTCGG
1 GGGTAAAATAGTAA-TTTTAGAAAAATCAACATAAAAAACAAAATTTTTGGACATCCGG
** ***** *
43403918 GGGTAAAATAGTAATTTTAGAAAAATTGACATAAAAAATGGGTTTTTTGGATATCCGG
1 GGGTAAAATAGTAATTTTAGAAAAATCAACATAAAAAACAAAATTTTTGGACATCCGG
*
43403976 GGGTAAAATGGTAATTTT
1 GGGTAAAATAGTAATTTT
43403994 TGAATTTCGA
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
58 50 0.81
59 12 0.19
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (58 bp):
GGGTAAAATAGTAATTTTAGAAAAATCAACATAAAAAACAAAATTTTTGGACATCCGG
Found at i:43404050 original size:29 final size:30
Alignment explanation
Indices: 43403980--43404291 Score: 237
Period size: 29 Copynumber: 10.7 Consensus size: 30
43403970 ATCCGGGGGT
*
43403980 AAAATGGTAATTTTT-GAA-TTTCGAGGT-A
1 AAAAT-GTAATTTTTGGAAGTTTTGAGGTCA
43404008 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
* *
43404038 AAAATGAAATTTTT-GAA-TATTCTGGGGGT--
1 AAAATGTAATTTTTGGAAGT-TT-T-GAGGTCA
* * * *
43404067 AAAATGGAA-TTTTGGAAGTTTCGGGGTCG
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
* * * *
43404096 AAAATGGAATTTTTAGAAG-TTCGAGGGT-G
1 AAAATGTAATTTTTGGAAGTTTTGA-GGTCA
43404125 AAAATAG-AA-TTTTGGAAGTTTT-AGGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTTGA-GGTCA
* * *
43404154 AAAATGTCATTTTTGGAAGTTTCGAGGTAA
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
*
43404184 AAAATGTAATTTTTGGAAG-TTTG-GGTGTA
1 AAAATGTAATTTTTGGAAGTTTTGAGGT-CA
43404213 AAAATGTAATTTTTGGAAGTTTT-AGGATC-
1 AAAATGTAATTTTTGGAAGTTTTGAGG-TCA
* * *
43404242 AAAATGTAATTTTTTGAAGTTTAGGGGT-A
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
* *
43404271 AAAATATAATTTTTGAAAGTT
1 AAAATGTAATTTTTGGAAGTT
43404292 CAGGGACCTC
Statistics
Matches: 237, Mismatches: 23, Indels: 47
0.77 0.07 0.15
Matches are distributed among these distances:
27 14 0.06
28 30 0.13
29 118 0.50
30 69 0.29
31 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAGTTTTGAGGTCA
Found at i:43404271 original size:88 final size:86
Alignment explanation
Indices: 43403976--43404291 Score: 299
Period size: 88 Copynumber: 3.6 Consensus size: 86
43403966 GGATATCCGG
* *
43403976 GGGT-AAAATGGTAATTTTTGAA-TTTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGT-CA
1 GGGTCAAAAT-GTAATTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAG-TTTGAGGTGTA
*
43404038 AAAATGAAATTTTT-GAA-TATTCTGG
64 AAAATG-AATTTTTGGAAGT-TT-T-A
* * * * * * *
43404063 GGGT-AAAATGGAATTTTGGAAGTTTCGGGGTCGAAAATGGAATTTTTAGAAGTTCGAGG-GTGA
1 GGGTCAAAATGTAATTTTGGAAGTTTCGAGGT-AAAAATGTAATTTTTGGAAGTTTGAGGTGTAA
43404126 AAATAGAA-TTTTGGAAGTTTTA
65 AAAT-GAATTTTTGGAAGTTTTA
*
43404148 GGGTCAAAAATGTCATTTTTGGAAGTTTCGAGGTAAAAAATGTAATTTTTGGAAGTTTG-GGTGT
1 GGGTC-AAAATGT-AATTTTGGAAGTTTCGAGGT-AAAAATGTAATTTTTGGAAGTTTGAGGTGT
43404212 AAAAATGTAATTTTTGGAAGTTTTA
63 AAAAATG-AATTTTTGGAAGTTTTA
* * * * * *
43404237 GGATCAAAATGTAATTTTTTGAAGTTTAGGGGTAAAAATATAATTTTTGAAAGTT
1 GGGTCAAAATGTAA-TTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTT
43404292 CAGGGACCTC
Statistics
Matches: 190, Mismatches: 26, Indels: 26
0.79 0.11 0.11
Matches are distributed among these distances:
85 4 0.02
86 15 0.08
87 65 0.34
88 88 0.46
89 18 0.09
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (86 bp):
GGGTCAAAATGTAATTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTGAGGTGTAAA
AATGAATTTTTGGAAGTTTTA
Found at i:43404274 original size:58 final size:59
Alignment explanation
Indices: 43403980--43404291 Score: 292
Period size: 58 Copynumber: 5.4 Consensus size: 59
43403970 ATCCGGGGGT
* *
43403980 AAAATGGTAATTTTT-GAA-TTTCGAGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCA
1 AAAAT-GTAATTTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTAGGGGTCA
* * * * *
43404038 AAAATGAAATTTTT-GAA-TATTCTGGGGGT-AAAATGGAA-TTTTGGAAGTTTCGGGGTCG
1 AAAATGTAATTTTTGGAAGT-TTC--GAGGTAAAAATGTAATTTTTGGAAGTTTAGGGGTCA
* * *
43404096 AAAATGGAATTTTTAGAAG-TTCGAGGGTGAAAATAG-AA-TTTTGGAAGTTTTA-GGGTCA
1 AAAATGTAATTTTTGGAAGTTTCGA-GGTAAAAAT-GTAATTTTTGGAAG-TTTAGGGGTCA
*
43404154 AAAATGTCATTTTTGGAAGTTTCGAGGTAAAAAATGTAATTTTTGGAAGTTT-GGGTGT-A
1 AAAATGTAATTTTTGGAAGTTTCGAGGT-AAAAATGTAATTTTTGGAAGTTTAGGG-GTCA
* * *
43404213 AAAATGTAATTTTTGGAAGTTT-TAGGATCAAAATGTAATTTTTTGAAGTTTAGGGGT-A
1 AAAATGTAATTTTTGGAAGTTTCGAGG-TAAAAATGTAATTTTTGGAAGTTTAGGGGTCA
* *
43404271 AAAATATAATTTTTGAAAGTT
1 AAAATGTAATTTTTGGAAGTT
43404292 CAGGGACCTC
Statistics
Matches: 217, Mismatches: 20, Indels: 34
0.80 0.07 0.13
Matches are distributed among these distances:
56 1 0.00
57 15 0.07
58 128 0.59
59 58 0.27
60 15 0.07
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTTCGAGGTAAAAATGTAATTTTTGGAAGTTTAGGGGTCA
Found at i:43405449 original size:15 final size:15
Alignment explanation
Indices: 43405429--43405460 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43405419 AATACTTCAG
43405429 TTATTATTATAAATA
1 TTATTATTATAAATA
*
43405444 TTATTATTATTAATA
1 TTATTATTATAAATA
43405459 TT
1 TT
43405461 CACCATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTATAAATA
Found at i:43406256 original size:16 final size:17
Alignment explanation
Indices: 43406225--43406256 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43406215 TAATAATTTT
43406225 AAATTTAAAGTAAATTC
1 AAATTTAAAGTAAATTC
43406242 AAATTTAAA-TAAATT
1 AAATTTAAAGTAAATT
43406257 TAGAATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTAAAGTAAATTC
Found at i:43410401 original size:25 final size:26
Alignment explanation
Indices: 43410373--43410433 Score: 106
Period size: 25 Copynumber: 2.4 Consensus size: 26
43410363 CCTGCTAATT
43410373 ATTCACCAGCTCAAGGC-CGCTATAC
1 ATTCACCAGCTCAAGGCTCGCTATAC
*
43410398 ATTCACCAGCTCAAGGCTTGCTATAC
1 ATTCACCAGCTCAAGGCTCGCTATAC
43410424 ATTCACCAGC
1 ATTCACCAGC
43410434 CTGCTAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (26 bp):
ATTCACCAGCTCAAGGCTCGCTATAC
Found at i:43412295 original size:21 final size:20
Alignment explanation
Indices: 43412269--43412309 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
43412259 GAATCAACGC
43412269 AAAAG-AAGAAAAGGAAAAAGA
1 AAAAGAAAG-AAA-GAAAAAGA
43412290 AAAAGAAAGAAAGAAAAAGA
1 AAAAGAAAGAAAGAAAAAGA
43412310 GCAATACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 8 0.42
22 3 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGAAAGAAAAAGA
Found at i:43413132 original size:60 final size:60
Alignment explanation
Indices: 43413061--43413193 Score: 171
Period size: 60 Copynumber: 2.2 Consensus size: 60
43413051 GACAAAATTG
* * * *
43413061 AATAATTGAGTGATCATTTTGTAACTTTTTATAT-TTGAGTGACCAAAAAAAGAAATTT-TT
1 AATAATTGAGTGATCATTTTGTAACTTTTCAT-TGTTAAATGACCAAAAAAA-AAATTTGCT
* *
43413121 AATAATTGAGTGATTATTTTGTAACTTTTCATTGTTAAATGACCAAAAATAAAATTTGCT
1 AATAATTGAGTGATCATTTTGTAACTTTTCATTGTTAAATGACCAAAAAAAAAATTTGCT
*
43413181 AATAATTGGGTGA
1 AATAATTGAGTGA
43413194 GTACTAGTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
59 7 0.11
60 57 0.89
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (60 bp):
AATAATTGAGTGATCATTTTGTAACTTTTCATTGTTAAATGACCAAAAAAAAAATTTGCT
Found at i:43413958 original size:16 final size:16
Alignment explanation
Indices: 43413915--43413999 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 16
43413905 CATAAAATAA
43413915 ATAAAATCATAAAAATT
1 ATAAAAT-ATAAAAATT
*
43413932 TTAAAATATAAAAATCT
1 ATAAAATATAAAAAT-T
43413949 ATAAAA-AT---AA-T
1 ATAAAATATAAAAATT
43413960 AT-AAATA-AAATAATT
1 ATAAAATATAAA-AATT
43413975 ATATAAATAATAAAAATT
1 ATA-AAAT-ATAAAAATT
43413993 ATTAAAA
1 A-TAAAA
43414000 ATTAATAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 23
0.68 0.03 0.29
Matches are distributed among these distances:
10 3 0.06
11 4 0.07
13 2 0.04
14 2 0.04
15 3 0.06
16 10 0.19
17 16 0.30
18 9 0.17
19 5 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAATATAAAAATT
Found at i:43413980 original size:17 final size:18
Alignment explanation
Indices: 43413949--43413998 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
43413939 ATAAAAATCT
*
43413949 ATAAAAATAATATAAATA
1 ATAAAAATTATATAAATA
*
43413967 A-AATAATTATATAAATA
1 ATAAAAATTATATAAATA
43413984 ATAAAAATTAT-TAAA
1 ATAAAAATTATATAAA
43413999 AATTAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAAAATTATATAAATA
Found at i:43413984 original size:26 final size:27
Alignment explanation
Indices: 43413908--43414001 Score: 79
Period size: 26 Copynumber: 3.5 Consensus size: 27
43413898 TATATATCAT
* * *
43413908 AAAATAAATAAAATC-ATAAAAAT-TTT
1 AAAATATA-AAAATCTATAAAAATAATA
43413934 AAAATATAAAAATCTATAAAAATAATA
1 AAAATATAAAAATCTATAAAAATAATA
* *
43413961 TAAATA-AAATAAT-TATATAAATAATA
1 AAAATATAAA-AATCTATAAAAATAATA
43413987 AAAATTATTAAAAAT
1 AAAA-TA-TAAAAAT
43414002 TAATAATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.11
26 33 0.59
27 11 0.20
28 3 0.05
29 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATATAAAAATCTATAAAAATAATA
Found at i:43416316 original size:19 final size:19
Alignment explanation
Indices: 43416294--43416338 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
43416284 TTTTATTAGG
43416294 ATTTAATATTTAATATAT-T
1 ATTTAATATTTAA-ATATGT
* *
43416313 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
43416332 ATTTAAT
1 ATTTAAT
43416339 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:43416323 original size:26 final size:25
Alignment explanation
Indices: 43416277--43416329 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
43416267 TTTATTTTAA
43416277 AATATATTTTTATTAGGATTTAATATTT
1 AATATATTTTTATT--GATTTAA-ATTT
43416305 AATATATTATTTATT-ATTTAAATTT
1 AATATATT-TTTATTGATTTAAATTT
43416330 GTATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.17
26 6 0.25
28 8 0.33
29 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AATATATTTTTATTGATTTAAATTT
Found at i:43422244 original size:16 final size:16
Alignment explanation
Indices: 43422209--43422242 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
43422199 CTATTTTCTA
43422209 TTTCTTTTAATTCTGT
1 TTTCTTTTAATTCTGT
*
43422225 TTTCTTTT-ATTTTGT
1 TTTCTTTTAATTCTGT
43422240 TTT
1 TTT
43422243 TCCCTAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTCTTTTAATTCTGT
Found at i:43428891 original size:23 final size:23
Alignment explanation
Indices: 43428853--43428914 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
43428843 TAAATTTTGA
*
43428853 TTTTAAA-TTAAGTTTAGATTGG
1 TTTTAAATTTAAATTTAGATTGG
*
43428875 TTTTAAATTTAAATTTAGATTTG
1 TTTTAAATTTAAATTTAGATTGG
43428898 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
43428915 ACTAAATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (23 bp):
TTTTAAATTTAAATTTAGATTGG
Found at i:43430742 original size:59 final size:58
Alignment explanation
Indices: 43430571--43431012 Score: 438
Period size: 59 Copynumber: 7.6 Consensus size: 58
43430561 CCCTAGAGGT
* * *
43430571 CCCT-AAACTATCCAAAAATTACATTTTTACCCCCAAAACTTTCAAAAATTACATTTTTAA
1 CCCTAAAACT-TCCAAAAATTACATTTTTA-CCCCTAAA-TTCCAAAAATTACATTTTTGA
* *
43430631 CCTCGAAAA--TCCTAAAAATTACA-TTTT-CCCCTAAATTTCCAAAAATAACATTTTTGA
1 CC-CTAAAACTTCC-AAAAATTACATTTTTACCCCTAAA-TTCCAAAAATTACATTTTTGA
* *
43430688 -CCTCAAAACTTCTAAAAATTACATTTTTACCCCTAAATATCCAAAAATTACATTTTTAA
1 CCCT-AAAACTTCCAAAAATTACATTTTTACCCCTAAAT-TCCAAAAATTACATTTTTGA
* * * * *
43430747 CCCGAAAACTTCCAAAAATTACATTTTTACCCCTAAACTTCTAAAAATTCCATTATTAA
1 CCCTAAAACTTCCAAAAATTACATTTTTACCCCTAAA-TTCCAAAAATTACATTTTTGA
* * *
43430806 CCCTAAAACTTCTAAAAATTTA-TTTTTTA-CCCTCAAACTTCCAAAAATTATA-TTTTGA
1 CCCTAAAACTTCCAAAAA-TTACATTTTTACCCCT-AAA-TTCCAAAAATTACATTTTTGA
* * * * * * *
43430864 CCGTGAAACTTCCAAACATTATATTTTTACCCCTGAACTTTCAAAAATTCCA-TTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTTACCCCT-AAATTCCAAAAATTACATTTTTGA
* **
43430922 CCCTAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTTTATTTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTTACCCCT-AAATTCCAAAAATTACATTTTTGA
*
43430981 CCCTAAAACTTGCAAAAATTACCA-TTTTACCC
1 CCCTAAAACTTCCAAAAATTA-CATTTTTACCC
43431013 TCGAATGTCT
Statistics
Matches: 324, Mismatches: 41, Indels: 35
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.00
56 5 0.02
57 38 0.12
58 97 0.30
59 159 0.49
60 20 0.06
61 1 0.00
62 3 0.01
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATTACATTTTTACCCCTAAATTCCAAAAATTACATTTTTGA
Found at i:43431013 original size:29 final size:29
Alignment explanation
Indices: 43430571--43431013 Score: 390
Period size: 29 Copynumber: 15.1 Consensus size: 29
43430561 CCCTAGAGGT
43430571 CCCT-AAACTATCCAAAAATTACATTTTTA
1 CCCTAAAACT-TCCAAAAATTACATTTTTA
* *
43430600 CCCCCAAAACTTTCAAAAATTACATTTTTAA
1 -CCCTAAAACTTCCAAAAATTACATTTTT-A
* *
43430631 CCTCGAAAA--TCCTAAAAATTACA-TTTTC
1 CC-CTAAAACTTCC-AAAAATTACATTTTTA
* *
43430659 CCCT-AAATTTCCAAAAATAACATTTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTT-A
*
43430688 -CCTCAAAACTTCTAAAAATTACATTTTTA
1 CCCT-AAAACTTCCAAAAATTACATTTTTA
43430717 CCCCT-AAA-TATCCAAAAATTACATTTTTAA
1 -CCCTAAAACT-TCCAAAAATTACATTTTT-A
*
43430747 CCCGAAAACTTCCAAAAATTACATTTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
* * *
43430776 CCCCT-AAACTTCTAAAAATTCCATTATTAA
1 -CCCTAAAACTTCCAAAAATTACATT-TTTA
* *
43430806 CCCTAAAACTTCTAAAAATTTA-TTTTTTA
1 CCCTAAAACTTCCAAAAA-TTACATTTTTA
* * *
43430835 CCCTCAAACTTCCAAAAATTATATTTTGA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
* * * *
43430864 CCGTGAAACTTCCAAACATTATATTTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
* * * *
43430893 CCCCT-GAACTTTCAAAAATTCCATTTTGA
1 -CCCTAAAACTTCCAAAAATTACATTTTTA
43430922 CCCTAAAACTTCCAAAAATTACATTTTTA
1 CCCTAAAACTTCCAAAAATTACATTTTTA
* **
43430951 CCCCT-GAACTTCCAAAAATTTTATTTTTGA
1 -CCCTAAAACTTCCAAAAATTACATTTTT-A
*
43430981 CCCTAAAACTTGCAAAAATTACCA-TTTTA
1 CCCTAAAACTTCCAAAAATTA-CATTTTTA
43431010 CCCT
1 CCCT
43431014 CGAATGTCTA
Statistics
Matches: 340, Mismatches: 46, Indels: 55
0.77 0.10 0.12
Matches are distributed among these distances:
26 3 0.01
27 10 0.03
28 20 0.06
29 169 0.50
30 120 0.35
31 18 0.05
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTACATTTTTA
Found at i:43431026 original size:29 final size:29
Alignment explanation
Indices: 43430994--43431084 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
43430984 TAAAACTTGC
43430994 AAAAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCTCGAATGTCT
* * ** *
43431023 AAAAACT-CAATTTTTAACCC-AAAACT-TTT
1 AAAAATTACCA-TTTT-ACCCTCGAA-TGTCT
*
43431052 AACAATTACCATTTTACCCTCGAATGTCT
1 AAAAATTACCATTTTACCCTCGAATGTCT
43431081 AAAA
1 AAAA
43431085 TGTCTTTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
28 7 0.16
29 30 0.68
30 7 0.16
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGAATGTCT
Found at i:43431036 original size:59 final size:59
Alignment explanation
Indices: 43430680--43431128 Score: 229
Period size: 58 Copynumber: 7.7 Consensus size: 59
43430670 CAAAAATAAC
* * * * *
43430680 ATTTTTGA-CCTCAAAACTTCTAAAAATTA-CATTTTTACCC-CTAAATATCCAAAAA-TTA
1 ATTTTTGACCCT-AAAACTTCCAAAAATTACCA-TTTTACCCTC-GAATGTCTAAAAACTCA
* * * * *
43430738 CATTTTTAACCCGAAAACTTCCAAAAATTA-CATTTTTACCC-CTAAACT-TCTAAAAATTCC
1 -ATTTTTGACCCTAAAACTTCCAAAAATTACCA-TTTTACCCTC-GAA-TGTCTAAAAACTCA
* * * ** * * *
43430798 ATTATTAACCCTAAAACTTCTAAAAATTTA-TTTTTTACCCTCAAACT-TCCAAAAA-T-T
1 ATTTTTGACCCTAAAACTTCCAAAAA-TTACCATTTTACCCTCGAA-TGTCTAAAAACTCA
* * * * * * *
43430855 ATATTTTGACCGTGAAACTTCCAAACATTA-TATTTTTACCC-CTGAACTTTC-AAAAATTCC
1 AT-TTTTGACCCTAAAACTTCCAAAAATTACCA-TTTTACCCTC-GAA-TGTCTAAAAACTCA
* * **
43430915 A-TTTTGACCCTAAAACTTCCAAAAATTA-CATTTTTACCC-CTGAACT-TCCAAAAATTTT
1 ATTTTTGACCCTAAAACTTCCAAAAATTACCA-TTTTACCCTC-GAA-TGTCTAAAAACTCA
*
43430973 ATTTTTGACCCTAAAACTTGCAAAAATTACCATTTTACCCTCGAATGTCTAAAAACTCA
1 ATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAACTCA
* ** * **
43431032 ATTTTTAACCC-AAAACTTTTAACAATTACCATTTTACCCTCGAATGTCTAAAATGTC-
1 ATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAACTCA
* * ** *
43431089 TTTTTTAACTCC-AAATTTTCCCAAAATTACCATTTTACCC
1 ATTTTTGAC-CCTAAAACTTCCAAAAATTACCATTTTACCC
43431129 CCGAGAGTCC
Statistics
Matches: 327, Mismatches: 46, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
57 17 0.05
58 151 0.46
59 147 0.45
60 12 0.04
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (59 bp):
ATTTTTGACCCTAAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCTAAAAACTCA
Found at i:43431262 original size:21 final size:20
Alignment explanation
Indices: 43431213--43431263 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
43431203 TCCTCATCAA
43431213 TATTTGCATTTATTTTTAAT
1 TATTTGCATTTATTTTTAAT
*
43431233 TATTATGCATTTTTATTTTATAT
1 TATT-TGCATTTAT-TTTTA-AT
43431256 T-TTTGCAT
1 TATTTGCAT
43431264 GTCATTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 7 0.26
23 3 0.11
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (20 bp):
TATTTGCATTTATTTTTAAT
Found at i:43443745 original size:201 final size:201
Alignment explanation
Indices: 43443393--43443828 Score: 685
Period size: 201 Copynumber: 2.2 Consensus size: 201
43443383 CGATTATCCA
** *
43443393 CAAAC-AGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCGAGGCTCATTG
1 CAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTAAAGGCTCAATG
* * * * *
43443457 TGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGCGAAGCAGGTCGAAGTAATAAAATG
66 CGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
43443522 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
131 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
43443587 CGAATT
196 CGAATT
* *
43443593 CAAACAAGTGAGGCGTTCATCTTCCTGATGAGGTATAGAGAAGTATACCAACTAAAGGCTCAATG
1 CAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTAAAGGCTCAATG
** *
43443658 CGAGCAAATCTTCGAACCTTAGCTTCCTAATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATG
66 CGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
* * *
43443723 GTTAGCTTCCTGATGGGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATATAGAGAAG
131 GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
43443788 CGAATT
196 CGAATT
* ** *
43443794 GAAACAAACGACGCGGTCATCTTCCTGATGAGATA
1 CAAACAAGTGAGGCGGTCATCTTCCTGATGAGATA
43443829 CCGAGAAAAA
Statistics
Matches: 213, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
200 5 0.02
201 208 0.98
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (201 bp):
CAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTAAAGGCTCAATG
CGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATG
GTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAG
CGAATT
Found at i:43444231 original size:6 final size:6
Alignment explanation
Indices: 43444210--43444284 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
43444200 TTAGATTGGT
** **
43444210 TTTAAA TTTATT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
43444257 TTTAGA TTT-GT TTTAAA ATTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
43444285 CTAAATTTAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
5 7 0.13
6 46 0.87
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:43444242 original size:23 final size:24
Alignment explanation
Indices: 43444210--43444283 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 24
43444200 TTAGATTGGT
* *
43444210 TTTAAATTTATTTTTAAATTTAAA
1 TTTAGATTTAATTTTAAATTTAAA
* *
43444234 TTT-GTTTTAAATTTAAATTTAAA
1 TTTAGATTTAATTTTAAATTTAAA
* *
43444257 TTTAGATTT-GTTTTAAAATTAAA
1 TTTAGATTTAATTTTAAATTTAAA
43444280 TTTA
1 TTTA
43444284 ACTAAATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 34 0.83
24 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTAGATTTAATTTTAAATTTAAA
Found at i:43444282 original size:29 final size:29
Alignment explanation
Indices: 43444188--43444284 Score: 133
Period size: 29 Copynumber: 3.4 Consensus size: 29
43444178 AAATTTTGAT
* *
43444188 TTTAAA-TTAAGTTTAGATTGGTTTTAAA
1 TTTAAATTTAAATTTAGATTTGTTTTAAA
** *
43444216 TTTATTTTTAAATTTAAATTTGTTTTAAA
1 TTTAAATTTAAATTTAGATTTGTTTTAAA
43444245 TTTAAATTTAAATTTAGATTTGTTTTAAA
1 TTTAAATTTAAATTTAGATTTGTTTTAAA
*
43444274 ATTAAATTTAA
1 TTTAAATTTAA
43444285 CTAAATTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 4 0.07
29 55 0.93
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (29 bp):
TTTAAATTTAAATTTAGATTTGTTTTAAA
Found at i:43451417 original size:29 final size:29
Alignment explanation
Indices: 43451342--43451625 Score: 115
Period size: 29 Copynumber: 9.7 Consensus size: 29
43451332 TTGGTACTCG
* *
43451342 AGGGCAAAATGGTAATCTTTGGTGAAA-TCG
1 AGGGTAAAATGG-AAT-TTTGGTGAAAGTCT
43451372 A-GGTCAAAAATGGAATTTTGG-GAAAGTCT
1 AGGGT--AAAATGGAATTTTGGTGAAAGTCT
* *
43451401 AGGGTAAGATGGTAATTTTTGGTGAAA-TCG
1 AGGGTAAAATGG-AA-TTTTGGTGAAAGTCT
43451431 A-GGTCAATAATGGAATTTT-G-GAAAGT-T
1 AGGGT-AA-AATGGAATTTTGGTGAAAGTCT
*
43451458 AGGGGTAAAAGGGTAATTTTTGGTGAAA-TC-
1 A-GGGTAAAATGG-AA-TTTTGGTGAAAGTCT
*
43451488 GGGGTTAAAAATGGAATTTT-G-GAAAGT-T
1 AGGG-T-AAAATGGAATTTTGGTGAAAGTCT
*
43451516 CAGGGGTAAAATGGTAATTTTGGTGAAA-TCG
1 -A-GGGTAAAATGG-AATTTTGGTGAAAGTCT
*
43451547 A-GATCAAAAATGGAA-TTT--TGAAAGAT-T
1 AGGGT--AAAATGGAATTTTGGTGAAAG-TCT
* *
43451574 AAGGATAAAATGGTAATTTTTGGTGAAA-TCG
1 -AGGGTAAAATGG-AA-TTTTGGTGAAAGTCT
43451605 A-GGTCAAAAATGGAATTTTGG
1 AGGGT--AAAATGGAATTTTGG
43451626 AAAGTTCGGG
Statistics
Matches: 198, Mismatches: 15, Indels: 83
0.67 0.05 0.28
Matches are distributed among these distances:
26 5 0.03
27 20 0.10
28 34 0.17
29 53 0.27
30 45 0.23
31 36 0.18
32 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (29 bp):
AGGGTAAAATGGAATTTTGGTGAAAGTCT
Found at i:43451482 original size:58 final size:59
Alignment explanation
Indices: 43451347--43451712 Score: 503
Period size: 58 Copynumber: 6.2 Consensus size: 59
43451337 ACTCGAGGGC
*
43451347 AAAATGGTAATCTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGGAAAG-TCTA-GGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTT-GGAAAGTTC-AGGGGT
* *
43451406 AAGATGGTAATTTTTGGTGAAATCGAGGTCAATAATGGAATTTTGGAAAGTT-AGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
* * *
43451464 AAAAGGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
* * *
43451523 AAAATGGTAA-TTTTGGTGAAATCGAGATCAAAAATGGAATTTT-GAAAGATT-AAGGAT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG-TTCAGGGGT
*
43451580 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
* * * *
43451639 AAAAATGGTAATTTTTTAGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTCAGGGGT
1 -AAAATGGTAA-TTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
*
43451700 AAAAT-TTAATTTT
1 AAAATGGTAATTTT
43451713 CGACAGTCCA
Statistics
Matches: 274, Mismatches: 24, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
57 20 0.07
58 127 0.46
59 68 0.25
60 15 0.05
61 44 0.16
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGGGGT
Found at i:43451642 original size:29 final size:29
Alignment explanation
Indices: 43451439--43451703 Score: 143
Period size: 29 Copynumber: 9.0 Consensus size: 29
43451429 CGAGGTCAAT
43451439 AATGGAATTTTGGAAAGTT-AGGGGT-AA
1 AATGGAATTTTGGAAAGTTCAGGGGTAAA
*
43451466 AAGGGTAATTTTTGGTGAAA--TC-GGGGTTAAA
1 AATGG-AA-TTTT-G-GAAAGTTCAGGGG-TAAA
43451497 AATGGAATTTTGGAAAGTTCAGGGGT-AA
1 AATGGAATTTTGGAAAGTTCAGGGGTAAA
* *
43451525 AATGGTAATTTTGGTGAAA--TC-GAGATCAAA
1 AATGG-AATTTT-G-GAAAGTTCAGGGGT-AAA
* *
43451555 AATGGAATTTT-GAAAGATT-AAGGAT-AA
1 AATGGAATTTTGGAAAG-TTCAGGGGTAAA
*
43451582 AATGGTAATTTTTGGTGAAA--TC-GAGGTCAAA
1 AATGG-AA-TTTT-G-GAAAGTTCAGGGGT-AAA
*
43451613 AATGGAATTTTGGAAAGTTCGGGGGTAAA
1 AATGGAATTTTGGAAAGTTCAGGGGTAAA
43451642 AATGGTAATTTTTTAGTGAAA--TC-GGGGTTAAA
1 AATGG-AA--TTTT-G-GAAAGTTCAGGGG-TAAA
*
43451674 AATGGAATTTTGGGAAGTTCAGGGGTAAA
1 AATGGAATTTTGGAAAGTTCAGGGGTAAA
43451703 A
1 A
43451704 TTTAATTTTC
Statistics
Matches: 188, Mismatches: 11, Indels: 76
0.68 0.04 0.28
Matches are distributed among these distances:
26 4 0.02
27 22 0.12
28 17 0.09
29 66 0.35
30 28 0.15
31 27 0.14
32 19 0.10
33 1 0.01
34 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.31
Consensus pattern (29 bp):
AATGGAATTTTGGAAAGTTCAGGGGTAAA
Found at i:43452080 original size:162 final size:160
Alignment explanation
Indices: 43451787--43452272 Score: 742
Period size: 162 Copynumber: 3.0 Consensus size: 160
43451777 CATCCAGAAC
* * *
43451787 TCAAAAGACTAATTTAAAATCTCAAAAATTCCT-GAGTCAATTTTGTAATTAAGCAAAAGTTGAT
1 TCAAAGGACTAATTAAAAATCTCAAAAATT-CTAGGGTCAATTTTGTAATTAAGCAAAAGTTGAT
43451851 TTGAGGATTAAATTAAAACAAATTAAACACAACAGGGACTAAATACATAAATAAGCCAAAAAGTG
65 TTGAGGATTAAATTAAAACAAATTAAACACAACAGGGACTAAATACATAAATAAGCCAAAAAGTG
*
43451916 ACACGTGGCAGCCTCTAGTGCAGTAAAACAG
130 ACACGTGGCAGCCTCTAGTGCAGTCAAACAG
43451947 TCAAAGGACTAATTAAAAATCTCAAAAGATTCTAGGGTCAATTTTGTAATTAAGCAAAAGTTGAT
1 TCAAAGGACTAATTAAAAATCTCAAAA-ATTCTAGGGTCAATTTTGTAATTAAGCAAAAGTTGAT
* * *
43452012 TTGAGGATTAAATTAAAAAAAAATTAAACACAACAAGGACTAAATACATAAATAGGCCAAAAAGT
65 TTGAGGATTAAATT-AAAACAAATTAAACACAACAGGGACTAAATACATAAATAAGCCAAAAAGT
*
43452077 GACACGTGGCAACCTCTAGTGCAGTCAAACAG
129 GACACGTGGCAGCCTCTAGTGCAGTCAAACAG
* * * *
43452109 TCAAAGGACTAATTTAAAAATCTTAAAAAATTTCCAAGGTCAATTTTGTAATTAAGAAAAAGTTG
1 TCAAAGGACTAA-TTAAAAATC-TCAAAAA-TTCTAGGGTCAATTTTGTAATTAAGCAAAAGTTG
* * * *
43452174 ATTTGAGGATTAAATCAAAACAAATTAAATAGAACAGGGACTAAATACATAAATAAACCAAAAAG
63 ATTTGAGGATTAAATTAAAACAAATTAAACACAACAGGGACTAAATACATAAATAAGCCAAAAAG
* *
43452239 TGACACGTGGCAG-CTCTGGTGCAGTCACACAG
128 TGACACGTGGCAGCCTCTAGTGCAGTCAAACAG
43452271 TC
1 TC
43452273 GAGGGATTAA
Statistics
Matches: 298, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
160 27 0.09
161 47 0.16
162 108 0.36
163 65 0.22
164 51 0.17
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (160 bp):
TCAAAGGACTAATTAAAAATCTCAAAAATTCTAGGGTCAATTTTGTAATTAAGCAAAAGTTGATT
TGAGGATTAAATTAAAACAAATTAAACACAACAGGGACTAAATACATAAATAAGCCAAAAAGTGA
CACGTGGCAGCCTCTAGTGCAGTCAAACAG
Found at i:43453864 original size:6 final size:6
Alignment explanation
Indices: 43453849--43453907 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
43453839 TTAAATTTGA
* * *
43453849 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT AAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
43453897 ATAAAT TTAAA
1 TTAAAT TTAAA
43453908 ACCCATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:43453883 original size:14 final size:14
Alignment explanation
Indices: 43453864--43453891 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43453854 CTTAAATTTA
43453864 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
43453878 AAGTAAATTTAAAT
1 AAGTAAATTTAAAT
43453892 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AAGTAAATTTAAAT
Found at i:43454842 original size:23 final size:23
Alignment explanation
Indices: 43454816--43454884 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
43454806 CTCATTTAAC
* *
43454816 TTAATCAAACATGTTCACGAATA
1 TTAATCGAACATGTTCACGAACA
*
43454839 TTAAAT-GAACATGTTCATGAACA
1 TT-AATCGAACATGTTCACGAACA
* *
43454862 TTAAACGAACATGTTCAGGAACA
1 TTAATCGAACATGTTCACGAACA
43454885 ATGTTAATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 2 0.05
23 34 0.87
24 3 0.08
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:43454919 original size:22 final size:20
Alignment explanation
Indices: 43454881--43454922 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
43454871 CATGTTCAGG
*
43454881 AACAATGTTAATGAATAATA
1 AACAATGTTAATAAATAATA
43454901 AACAATGTAATAATAAATAATA
1 AACAATGT--TAATAAATAATA
43454923 CATACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (20 bp):
AACAATGTTAATAAATAATA
Found at i:43458874 original size:6 final size:6
Alignment explanation
Indices: 43458856--43458925 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
43458846 TATTTCTAAG
* **
43458856 TTTAAA TTT-AA TTTAAA TTTAAA TTTAAAA TTCATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
43458904 TTT--G TTCTAAA TTTAAA TTTAA
1 TTTAAA TT-TAAA TTTAAA TTTAA
43458926 CTTAAATATG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 36 0.71
7 7 0.14
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:43458878 original size:17 final size:17
Alignment explanation
Indices: 43458856--43458932 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
43458846 TATTTCTAAG
43458856 TTTAAATTT-AATTTAAA
1 TTTAAATTTAAATTT-AA
* *
43458873 TTTAAATTTAAAATTCATT
1 TTTAAATTT-AAATTTA-A
*
43458892 TTTAAATTTAAATTT-G
1 TTTAAATTTAAATTTAA
43458908 TTCTAAATTTAAATTTAA
1 TT-TAAATTTAAATTTAA
*
43458926 CTTAAAT
1 TTTAAAT
43458933 ATGAAATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
16 2 0.04
17 27 0.55
18 7 0.14
19 13 0.27
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:43458903 original size:42 final size:42
Alignment explanation
Indices: 43458841--43458925 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
43458831 GATTTGTTTC
* *
43458841 AAATTTATTTCTAAGTTTAAATTTAATT-TAAATTTAAATTTA
1 AAATTCATTTCTAAATTTAAATTT-ATTCTAAATTTAAATTTA
* *
43458883 AAATTCATTTTTAAATTTAAATTTGTTCTAAATTTAAATTTA
1 AAATTCATTTCTAAATTTAAATTTATTCTAAATTTAAATTTA
43458925 A
1 A
43458926 CTTAAATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (42 bp):
AAATTCATTTCTAAATTTAAATTTATTCTAAATTTAAATTTA
Found at i:43460329 original size:30 final size:28
Alignment explanation
Indices: 43460294--43460572 Score: 123
Period size: 30 Copynumber: 9.5 Consensus size: 28
43460284 ACCCGAGAGC
*
43460294 AAAATGGTAATTTTGGTGAAATCAGGGTT
1 AAAATGG-AATTTTGGTGAAATCAGGGGT
*
43460323 AAAAATGGAATTTT--T-AAGGGT-ACGGGGT
1 -AAAATGGAATTTTGGTGAA--ATCA-GGGGT
*
43460351 AAAATGGTAATTTTTGGTGAAATC-GAGGTT
1 AAAATGG-AA-TTTTGGTGAAATCAG-GGGT
**
43460381 AAAATGGAATTTT-G-GAAAGTTTGGGGGT
1 AAAATGGAATTTTGGTGAAA--TCAGGGGT
43460409 AAAATGGTAATTTTTGGTGAAATC-GGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCAGGGG-T
* *
43460439 AAAAATGGAATTTT--AGAAGGTTC-GAGGGT
1 -AAAATGGAATTTTGGTGAA--ATCAG-GGGT
*
43460468 AAAATGGTAATTTTTGGTGAAACCAGGGGT
1 AAAATGG-AA-TTTTGGTGAAATCAGGGGT
** **
43460498 AAAAATGGAATTTTAGAAGAAGATTTGGGAGT
1 -AAAATGGAATTTT-GGTGAA-ATCAGGG-GT
*
43460530 AAAATGGTAATTTTGGTGAAAT-TGGGGTT
1 AAAATGG-AATTTTGGTGAAATCAGGGG-T
43460559 AAAAATGGAATTTT
1 -AAAATGGAATTTT
43460573 AGAAGGTTCG
Statistics
Matches: 196, Mismatches: 19, Indels: 69
0.69 0.07 0.24
Matches are distributed among these distances:
26 6 0.03
27 13 0.07
28 30 0.15
29 45 0.23
30 53 0.27
31 32 0.16
32 17 0.09
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCAGGGGT
Found at i:43460473 original size:59 final size:59
Alignment explanation
Indices: 43460294--43460725 Score: 538
Period size: 58 Copynumber: 7.3 Consensus size: 59
43460284 ACCCGAGAGC
* * *
43460294 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAATTTTTA-AGGGTAC-GGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTTAGAAGGTTCGGGGGT
* * * *
43460351 AAAATGGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
*
43460409 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
* * *
43460468 AAAATGGTAATTTTTGGTGAAACCAGGGG-TAAAAATGGAATTTTAGAAGAAGATTTGGGAGT
1 AAAATGGTAATTTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTAGAAG--G-TTCGGGGGT
*
43460530 AAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
* * *
43460588 AAAATGGTAATTTTTGGTGAAAGAAACCGGGGTTAAAAATGGAATTTTAGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGT----GAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
* * * * *
43460651 AAAATGGTAATTTCTGGTGAAATCGGAGTT-AAAATGTAATTTTTG-AGAGCTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAG-GTTCGGGGGT
43460709 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
43460726 ACTGTTTGGG
Statistics
Matches: 327, Mismatches: 33, Indels: 29
0.84 0.08 0.07
Matches are distributed among these distances:
56 4 0.01
57 23 0.07
58 105 0.32
59 85 0.26
60 8 0.02
61 32 0.10
62 16 0.05
63 54 0.17
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
Found at i:43460585 original size:29 final size:28
Alignment explanation
Indices: 43460380--43460663 Score: 96
Period size: 30 Copynumber: 9.5 Consensus size: 28
43460370 AAATCGAGGT
* * *
43460380 TAAAATGG-AATTTTGGAAAGTTTGGGGG
1 TAAAATGGTAATTTTAG-AAGGTTCGGGG
* ** **
43460408 TAAAATGGTAATTTTTGGTGAAATCGGGG
1 TAAAATGGTAATTTTAGAAG-GTTCGGGG
43460437 TTAAAAATGG-AATTTTAGAAGGTTCGAGGG
1 -T-AAAATGGTAATTTTAGAAGGTTCG-GGG
* ** ***
43460467 TAAAATGGTAATTTTTGGTGAAACCAGGGG
1 TAAAATGGTAATTTTAGAAG-GTTC-GGGG
*
43460497 TAAAAATGG-AATTTTAGAAGAAGATTTGGGAG
1 T-AAAATGGTAATTTTAGAAG--G-TTCGGG-G
* *
43460529 TAAAATGGTAATTTTGGTGAA-ATT-GGGG
1 TAAAATGGTAATTTT--AGAAGGTTCGGGG
43460557 TTAAAAATGG-AATTTTAGAAGGTTCGGGGG
1 -T-AAAATGGTAATTTTAGAAGGTTC-GGGG
* ***
43460587 TAAAATGGTAATTTTTGGTGAAAGAAACCGGGG
1 TAAAATGGTAA-TTTT--AG-AAG-GTTCGGGG
*
43460620 TTAAAAATGG-AATTTTAGAAAGTTCGAGGG
1 -T-AAAATGGTAATTTTAGAAGGTTCG-GGG
43460650 TAAAATGGTAATTT
1 TAAAATGGTAATTT
43460664 CTGGTGAAAT
Statistics
Matches: 189, Mismatches: 37, Indels: 59
0.66 0.13 0.21
Matches are distributed among these distances:
27 3 0.02
28 33 0.17
29 45 0.24
30 47 0.25
31 27 0.14
32 9 0.05
33 11 0.06
34 7 0.04
35 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.31
Consensus pattern (28 bp):
TAAAATGGTAATTTTAGAAGGTTCGGGG
Found at i:43460718 original size:29 final size:29
Alignment explanation
Indices: 43460294--43460724 Score: 174
Period size: 29 Copynumber: 14.6 Consensus size: 29
43460284 ACCCGAGAGC
* * * * *
43460294 AAAATGGTAATTTTGGTGAAATCAGGGTT
1 AAAATGGTAATTTTTGAGAATTCGGGGGT
* ** *
43460323 AAAAATGG-AATTTTTAAGGGTAC-GGGGT
1 -AAAATGGTAATTTTTGAGAATTCGGGGGT
* * * *
43460351 AAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AAAATGGTAATTTTT-GAGAATTCGGGGGT
* *
43460381 AAAATGG-AATTTTGGA-AAGTTTGGGGGT
1 AAAATGGTAATTTTTGAGAA-TTCGGGGGT
* * *
43460409 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAATTTTT-GAGAATTCGGGGGT
*
43460439 AAAAATGG-AA-TTTT-AGAAGGTTCGAGGGT
1 -AAAATGGTAATTTTTGAGAA--TTCGGGGGT
* ** *
43460468 AAAATGGTAATTTTTGGTGAAACCAGGGGT
1 AAAATGGTAATTTTT-GAGAATTCGGGGGT
* * *
43460498 AAAAATGG-AATTTTAGAAGAAGATTTGGGAGT
1 -AAAATGGTAATTTTTG-AG-A-ATTCGGGGGT
*
43460530 AAAATGGTAATTTTGGTGA-AATT-GGGGTT
1 AAAATGGTAATTTT--TGAGAATTCGGGGGT
43460559 AAAAATGG-AA-TTTT-AGAAGGTTCGGGGGT
1 -AAAATGGTAATTTTTGAGAA--TTCGGGGGT
** *
43460588 AAAATGGTAATTTTTGGTGAAAGAAACCGGGGTT
1 AAAATGGTAA-TTTT--TG--AGAATTCGGGGGT
* *
43460622 AAAAATGG-AATTTTAGA-AAGTTCGAGGGT
1 -AAAATGGTAATTTTTGAGAA-TTCGGGGGT
* * * * *
43460651 AAAATGGTAATTTCTGGTGAAATCGGAGTT
1 AAAATGGTAATTT-TTGAGAATTCGGGGGT
**
43460681 AAAAT-GTAATTTTTGAGAGCTCGGGGGT
1 AAAATGGTAATTTTTGAGAATTCGGGGGT
43460709 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
43460725 GACTGTTTGG
Statistics
Matches: 294, Mismatches: 67, Indels: 81
0.67 0.15 0.18
Matches are distributed among these distances:
25 1 0.00
26 3 0.01
27 12 0.04
28 67 0.23
29 76 0.26
30 64 0.22
31 31 0.11
32 14 0.05
33 6 0.02
34 9 0.03
35 7 0.02
36 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAGAATTCGGGGGT
Found at i:43461349 original size:17 final size:18
Alignment explanation
Indices: 43461317--43461350 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43461307 TGGCGGTTGC
43461317 CCCGGCCACGCTCCGGCT
1 CCCGGCCACGCTCCGGCT
*
43461335 CCCGGCCTC-CTCCGGC
1 CCCGGCCACGCTCCGGC
43461351 CACTTCCGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.03, C:0.59, G:0.26, T:0.12
Consensus pattern (18 bp):
CCCGGCCACGCTCCGGCT
Found at i:43461805 original size:7 final size:7
Alignment explanation
Indices: 43461793--43461817 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43461783 ATTAATACCA
43461793 TATTTAT
1 TATTTAT
43461800 TATTTAT
1 TATTTAT
43461807 TATTTAT
1 TATTTAT
43461814 TATT
1 TATT
43461818 ATAACTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:43461809 original size:3 final size:3
Alignment explanation
Indices: 43461796--43461872 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
43461786 AATACCATAT
* * *
43461796 TTA TTA TTTA TTA TTTA TTA TTA TAA CTA TTA TTA ATA TTCA TTA TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
** * * *
43461844 GGA TTA TTA GTA ATA TTA TGA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43461873 GTCATTGATG
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
3 47 0.84
4 9 0.16
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:43461851 original size:25 final size:25
Alignment explanation
Indices: 43461796--43461860 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
43461786 AATACCATAT
* * *
43461796 TTATTATTTATTATTTATTATTATAA
1 TTATTA-TTAATATTCATTATTAGAA
* *
43461822 CTATTATTAATATTCATTATTAGGA
1 TTATTATTAATATTCATTATTAGAA
*
43461847 TTATTAGTAATATT
1 TTATTATTAATATT
43461861 ATGATTATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (25 bp):
TTATTATTAATATTCATTATTAGAA
Found at i:43462543 original size:6 final size:6
Alignment explanation
Indices: 43462534--43462620 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
43462524 TTAATATCAT
* *
43462534 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
*
43462581 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA -TAAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
43462621 ATAATTTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
4 3 0.05
5 15 0.23
6 42 0.64
7 1 0.02
8 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:43462543 original size:17 final size:17
Alignment explanation
Indices: 43462518--43462620 Score: 117
Period size: 17 Copynumber: 6.3 Consensus size: 17
43462508 TTTTAATATA
* * *
43462518 TTAATTTTAATATCATT
1 TTAAATTTAATATAAAT
43462535 TTAAATTTAAT-TAAAT
1 TTAAATTTAATATAAAT
*
43462551 TTAAATTTAAAATAAAT
1 TTAAATTTAATATAAAT
43462568 TTAAA--TAA-ATAAAT
1 TTAAATTTAATATAAAT
*
43462582 TTAAATTTAAGATAAAT
1 TTAAATTTAATATAAAT
43462599 TTAAATTTAA-ATAAAAT
1 TTAAATTTAATAT-AAAT
43462616 TTAAA
1 TTAAA
43462621 ATAATTTTAA
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
14 11 0.14
15 3 0.04
16 18 0.23
17 45 0.58
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAATATAAAT
Found at i:43462557 original size:11 final size:11
Alignment explanation
Indices: 43462534--43462637 Score: 75
Period size: 11 Copynumber: 9.0 Consensus size: 11
43462524 TTAATATCAT
*
43462534 TTTAAATTTAA
1 TTTAAATTAAA
43462545 -TTAAATTTAAA
1 TTTAAA-TTAAA
*
43462556 TTTAAAATAAA
1 TTTAAATTAAA
43462567 TTTAAATAAATAAA
1 TTTAAAT---TAAA
*
43462581 TTTAAATTTAA
1 TTTAAATTAAA
**
43462592 GATAAATTTAAA
1 TTTAAA-TTAAA
*
43462604 TTTAAATAAAA
1 TTTAAATTAAA
* *
43462615 TTTAAAATAAT
1 TTTAAATTAAA
43462626 TTTAAACTTAAA
1 TTTAAA-TTAAA
43462638 AATCAAATCT
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
10 5 0.07
11 39 0.55
12 16 0.23
14 11 0.15
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:43462959 original size:38 final size:38
Alignment explanation
Indices: 43462908--43463517 Score: 171
Period size: 38 Copynumber: 16.4 Consensus size: 38
43462898 CATCTTGCTC
**
43462908 TTACTTCAATTTCAGAGATAAACACTTGATCCCCAGCT
1 TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* * *
43462946 TTACTTCAATTTCA-AGATAAAGACTTGTTATCCAACT
1 TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* * * * * **
43462983 CTACATCAATTTCAAGGGGATAGACA-ATG--ATCTTGCT
1 TTACTTCAATTTC-A-GAGATAAACACTTGATATCCAGCT
* *
43463020 CTTACTTCAATTTCAGAGATAAAGACTTAATATCCAGCT
1 -TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* **
43463059 TTACTTCAATTTCAAGAGGATGGGAA-AC--G--ATCTTGCT
1 TTACTTCAATTTC-AGA-GAT--AAACACTTGATATCCAGCT
* * * *
43463096 CTTACTTCATTTTC--AGATAAAGAC-TCATTATCCAACT
1 -TTACTTCAATTTCAGAGATAAACACTTGA-TATCCAGCT
* **
43463133 TTACTTCAATTTCAAGAGGAATGAA-A--TG--ATCTTGC-
1 TTACTTCAATTTC-AGA-G-ATAAACACTTGATATCCAGCT
* * * *
43463168 -T-CTTCAATTTCAGAGATAAAGATTTAATATCCAACT
1 TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* ** **
43463204 CTACTTCAATTTCAAGAGGATATGGCA--TG--ATCTTGCT
1 TTACTTCAATTTC-AGA-GATA-AACACTTGATATCCAGCT
* * * *
43463241 CTTACTTCAATTTCAGAGATAAAGATTTAATATCCAACT
1 -TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
** * **
43463280 TCTACTTCAATTTCA-AGA-GGATA--TG--ATCTTGCT
1 T-TACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* *
43463313 CTTACTTCAATTTCAGAGATAAAGACTTAATATCCAGCT
1 -TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
* **
43463352 TTACTTCAATTTCAAGAGGATGGGAA-AC--G--ATCTTGCT
1 TTACTTCAATTTC-AGA-GAT--AAACACTTGATATCCAGCT
* * *
43463389 CTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACT
1 -TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
*** * * *
43463428 TTACTTCAATTTCAAGAGGATAGGGA-ATGATGT--TGCT
1 TTACTTCAATTTC-AGA-GATAAACACTTGATATCCAGCT
* * * *
43463465 CTTACTTCAATTTCAGAGATAAAGATTTAATATCCAACT
1 -TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
*
43463504 CTACTTCAATTTCA
1 TTACTTCAATTTCA
43463518 AGAGGATATG
Statistics
Matches: 415, Mismatches: 95, Indels: 124
0.65 0.15 0.20
Matches are distributed among these distances:
30 4 0.01
31 2 0.00
32 5 0.01
33 31 0.07
34 10 0.02
35 11 0.03
36 36 0.09
37 79 0.19
38 142 0.34
39 58 0.14
40 24 0.06
41 9 0.02
42 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (38 bp):
TTACTTCAATTTCAGAGATAAACACTTGATATCCAGCT
Found at i:43462992 original size:37 final size:37
Alignment explanation
Indices: 43462913--43462998 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
43462903 TGCTCTTACT
* * * *
43462913 TCAATTTCAGAGATAAACACTTGATCCCCAGCTTTACT
1 TCAATTTCA-AGATAAACACTTGATACCCAACTCTACA
* * *
43462951 TCAATTTCAAGATAAAGACTTGTTATCCAACTCTACA
1 TCAATTTCAAGATAAACACTTGATACCCAACTCTACA
43462988 TCAATTTCAAG
1 TCAATTTCAAG
43462999 GGGATAGACA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 32 0.78
38 9 0.22
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (37 bp):
TCAATTTCAAGATAAACACTTGATACCCAACTCTACA
Found at i:43463055 original size:76 final size:76
Alignment explanation
Indices: 43462946--43463768 Score: 1099
Period size: 76 Copynumber: 11.0 Consensus size: 76
43462936 ATCCCCAGCT
* * *
43462946 TTACTTCAATTTCA-AGATAAAGACTTGTTATCCAACTCTACATCAATTTCAAGGGGATA-GACA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGA-A
43463009 ATGATCTTGCTC
65 ATGATCTTGCTC
* * * *
43463021 TTACTTCAATTTCAGAGATAAAGACTTAATATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
*
43463086 CGATCTTGCTC
66 TGATCTTGCTC
* * * *
43463097 TTACTTCATTTTC--AGATAAAGACTCATTATCCAACTTTACTTCAATTTCAAGAGGA-ATGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
43463159 TGATCTTG--C
66 TGATCTTGCTC
* * *
43463168 -T-CTTCAATTTCAGAGATAAAGATTTAATATCCAACTCTACTTCAATTTCAAGAGGATATGG-C
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATA-GGAA
43463230 ATGATCTTGCTC
65 ATGATCTTGCTC
* *
43463242 TTACTTCAATTTCAGAGATAAAGATTTAATATCCAACTTCTACTTCAATTTCAAGAGGAT-----
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAAC-TCTACTTCAATTTCAAGAGGATAGGAA
43463302 ATGATCTTGCTC
65 ATGATCTTGCTC
* * * *
43463314 TTACTTCAATTTCAGAGATAAAGACTTAATATCCAGCTTTACTTCAATTTCAAGAGGATGGGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
*
43463379 CGATCTTGCTC
66 TGATCTTGCTC
* * *
43463390 TTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGGAA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
*
43463455 TGATGTTGCTC
66 TGATCTTGCTC
* * *
43463466 TTACTTCAATTTCAGAGATAAAGATTTAATATCCAACTCTACTTCAATTTCAAGAGGATATGG-C
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATA-GGAA
43463530 ATGATCTTGCTC
65 ATGATCTTGCTC
* * *
43463542 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCACTTCAATTTCAAGAGGATAG
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCA-ACT-C-T-ACTTCAATTTCAAGAGGATAG
43463607 GAAATGATCTTGCTC
62 GAAATGATCTTGCTC
*
43463622 TTACTTCAATTTCAGAGATAAAGA-TGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGAA
1 TTACTTCAATTTCAGAGATAAAGACT-TATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAA
43463685 ATGATCTTGCTC
65 ATGATCTTGCTC
* * * *
43463697 TTACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAAATTCAAGAGGCTAGGAAA
1 TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
43463761 TGATCTTG
66 TGATCTTG
43463769 GTGCGGTCTG
Statistics
Matches: 674, Mismatches: 50, Indels: 48
0.87 0.06 0.06
Matches are distributed among these distances:
69 9 0.01
70 1 0.00
71 61 0.09
72 57 0.08
73 12 0.02
74 41 0.06
75 119 0.18
76 275 0.41
77 29 0.04
78 3 0.00
79 3 0.00
80 64 0.09
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (76 bp):
TTACTTCAATTTCAGAGATAAAGACTTATTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
TGATCTTGCTC
Found at i:43463547 original size:38 final size:38
Alignment explanation
Indices: 43463205--43463710 Score: 236
Period size: 38 Copynumber: 13.3 Consensus size: 38
43463195 TATCCAACTC
*
43463205 TACTTCAATTTCAAGAGGATATGGCATGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATATGGAATGATCTTGCTCT
** * ** ***
43463243 TACTTCAATTTCAGAGATAAAGATTTAAT-ATCCAACT-T
1 TACTTCAATTTCA-AGA-GGATATGGAATGATCTTGCTCT
43463281 CTACTTCAATTTCAAGAGG--AT---ATGATCTTGCTCT
1 -TACTTCAATTTCAAGAGGATATGGAATGATCTTGCTCT
* * **
43463315 TACTTCAATTTC-AGA-GATAAAGACTTAAT-ATCCAGCT-T
1 TACTTCAATTTCAAGAGGAT-ATG---GAATGATCTTGCTCT
* *
43463353 TACTTCAATTTCAAGAGGAT-GGGAAACGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATATGG-AATGATCTTGCTCT
** * ***
43463391 TACTTCAATTTC-AGA-GATAAAGACTTGTTATCCAACT-T
1 TACTTCAATTTCAAGAGGATATGGA-ATG--ATCTTGCTCT
* *
43463429 TACTTCAATTTCAAGAGGATAGGGAATGATGTTGCTCT
1 TACTTCAATTTCAAGAGGATATGGAATGATCTTGCTCT
** * ** ***
43463467 TACTTCAATTTCAGAGATAAAGATTTAAT-ATCCAACTC-
1 TACTTCAATTTCA-AGA-GGATATGGAATGATCTTGCTCT
*
43463505 TACTTCAATTTCAAGAGGATATGGCATGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATATGGAATGATCTTGCTCT
** * *
43463543 TACTTCAATTTC-AGA-GATAAAGACGTGTTATCCACT-CTACT
1 TACTTCAATTTCAAGAGGATATGGA-ATG--AT-C-TTGCT-CT
43463584 TCACTTCAATTTCAAGAGGATA-GGAAATGATCTTGCTCT
1 T-ACTTCAATTTCAAGAGGATATGG-AATGATCTTGCTCT
** * * *
43463623 TACTTCAATTTC-AGA-GATAAAG-ATG-TGTTATCCACT
1 TACTTCAATTTCAAGAGGATATGGAATGAT-CT-TGCTCT
43463659 CTACTTCAATTTCAAGAGGATA-GGAAATGATCTTGCTCT
1 -TACTTCAATTTCAAGAGGATATGG-AATGATCTTGCTCT
43463698 TACTTCAATTTCA
1 TACTTCAATTTCA
43463711 GAGATAAAGA
Statistics
Matches: 347, Mismatches: 71, Indels: 100
0.67 0.14 0.19
Matches are distributed among these distances:
31 1 0.00
32 5 0.01
33 17 0.05
34 3 0.01
35 6 0.02
36 24 0.07
37 45 0.13
38 124 0.36
39 62 0.18
40 31 0.09
41 7 0.02
42 11 0.03
43 6 0.02
44 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (38 bp):
TACTTCAATTTCAAGAGGATATGGAATGATCTTGCTCT
Found at i:43470536 original size:29 final size:30
Alignment explanation
Indices: 43470501--43470581 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
43470491 CCGATTTCAC
*
43470501 CAAAAATTACCATTTTACCCTCGA-ACCTTT
1 CAAAAATTACCATTTTACCCTCGATACC-AT
* * *
43470531 C-AAAATT-TCATTTTTAACCTCGATTCCAT
1 CAAAAATTACCA-TTTTACCCTCGATACCAT
43470560 CAAAAATTACCATTTTATCCCT
1 CAAAAATTACCATTTTA-CCCT
43470582 AAACTTTCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
28 2 0.05
29 19 0.47
30 14 0.35
31 5 0.12
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.37
Consensus pattern (30 bp):
CAAAAATTACCATTTTACCCTCGATACCAT
Found at i:43470565 original size:59 final size:59
Alignment explanation
Indices: 43470473--43470634 Score: 229
Period size: 59 Copynumber: 2.7 Consensus size: 59
43470463 GTGAACTTCT
* * *
43470473 AAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCTCGAACCTTT-C
1 AAAATTTCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTATCCCT--AAACTTTCC
* *
43470532 AAAATTTCATTTTTAACCTCGATTCCATCAAAAATTACCATTTTATCCCTAAACTTTCC
1 AAAATTTCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTATCCCTAAACTTTCC
* *
43470591 AAAATTTCATTTTTGACCTCGATTTTACCAAAAATTACCATTTT
1 AAAATTTCATTTTTAACCTCGATTTCACCAAAAATTACCATTTT
43470635 GCCCCTGGGT
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
58 6 0.07
59 82 0.89
60 4 0.04
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATTTCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTATCCCTAAACTTTCC
Found at i:43473503 original size:21 final size:21
Alignment explanation
Indices: 43473479--43473536 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
43473469 GGAATTGATA
43473479 GTATCAATACTTTTTGAAAAG
1 GTATCAATACTTTTTGAAAAG
*
43473500 GTAT-AGATACTTTTTGAAAAT
1 GTATCA-ATACTTTTTGAAAAG
* *
43473521 GTATCGATATTTTTTG
1 GTATCAATACTTTTTG
43473537 TCCTAGAGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (21 bp):
GTATCAATACTTTTTGAAAAG
Found at i:43476549 original size:21 final size:21
Alignment explanation
Indices: 43476525--43476598 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
43476515 AAAAGGTGTC
43476525 GATACTTTTTGAAAATGTATA
1 GATACTTTTTGAAAATGTATA
* **
43476546 GATATTTTTTGAAACGGTATA
1 GATACTTTTTGAAAATGTATA
*
43476567 GATACTTTTTGAAAATGTATC
1 GATACTTTTTGAAAATGTATA
43476588 GATACTTTTTG
1 GATACTTTTTG
43476599 TCATTGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (21 bp):
GATACTTTTTGAAAATGTATA
Found at i:43478339 original size:29 final size:30
Alignment explanation
Indices: 43478280--43478341 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
43478270 TTGTTGACAG
* * *
43478280 CACACGGTCGTATGCTTAGGTCGTGTGAGC
1 CACACGGTCGTATGCGTAAGTCGTGTAAGC
*
43478310 CACACGGTCGTGTG-GTAAGTCGTGTAAGC
1 CACACGGTCGTATGCGTAAGTCGTGTAAGC
43478339 CAC
1 CAC
43478342 TGACTTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (30 bp):
CACACGGTCGTATGCGTAAGTCGTGTAAGC
Found at i:43478495 original size:41 final size:41
Alignment explanation
Indices: 43478391--43478498 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 41
43478381 GGGGAACCTT
** * *
43478391 TAGCGGCGTTTGGAAAGAAAACGCCGCAAAAGGTAAAGCAA
1 TAGCGGCGTTTATAAAGAAAGCGCCGCAAAAAGTAAAGCAA
* * * *
43478432 TAGCGGCGTTTTTCCATG--AGCGCTGCAAAAAGTAAAGCAA
1 TAGCGGCGTTTAT-AAAGAAAGCGCCGCAAAAAGTAAAGCAA
*
43478472 TAGCGGCGTTTATAGAGAAAGCGCCGC
1 TAGCGGCGTTTATAAAGAAAGCGCCGC
43478499 TAATACTCTA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
39 1 0.02
40 31 0.60
41 18 0.35
42 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (41 bp):
TAGCGGCGTTTATAAAGAAAGCGCCGCAAAAAGTAAAGCAA
Found at i:43478617 original size:82 final size:82
Alignment explanation
Indices: 43478531--43478780 Score: 235
Period size: 82 Copynumber: 3.1 Consensus size: 82
43478521 GTTTATGTCA
* *
43478531 AAGCGCTGCTAAAGGTCACAATATTCACGGCGTTTTCCTATAAGTGTCGTTAAAGGTCAGGACAT
1 AAGCGCTGCTAAAGGTCACAATATTCACGGCGCTTTCCTATAAGTGTCGCTAAAGGTCAGGACAT
* *
43478596 TAGCGACACTTTCCCAT
66 TAGCGGCGCTTTCCCAT
* * * * * * *
43478613 AAGCGCCGCTAAAGGTTAGGC-AT-TAC-CGGTGCTTTCCCATAAGTGCCGCTAAAGGTCAGGTC
1 AAGCGCTGCTAAAGGTCA--CAATATTCACGGCGCTTTCCTATAAGTGTCGCTAAAGGTCAGGAC
43478675 ATTAGCGGCGCTTTCCCAT
64 ATTAGCGGCGCTTTCCCAT
* ** ** *
43478694 CAGCG-TCGCTAAAGGTCA-AGGCATT-AGCGGCGCTTT-CTCATAAGCATTGCTAAAGGTCAGG
1 AAGCGCT-GCTAAAGGTCACA-ATATTCA-CGGCGCTTTCCT-ATAAGTGTCGCTAAAGGTCAGG
*
43478755 GCATTAGCGGCGCTTTCCCAT
62 ACATTAGCGGCGCTTTCCCAT
43478776 AAGCG
1 AAGCG
43478781 TCGCTAATTT
Statistics
Matches: 134, Mismatches: 25, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
81 63 0.47
82 68 0.51
83 2 0.01
84 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (82 bp):
AAGCGCTGCTAAAGGTCACAATATTCACGGCGCTTTCCTATAAGTGTCGCTAAAGGTCAGGACAT
TAGCGGCGCTTTCCCAT
Found at i:43478648 original size:40 final size:40
Alignment explanation
Indices: 43478558--43478787 Score: 280
Period size: 41 Copynumber: 5.7 Consensus size: 40
43478548 ACAATATTCA
* * * *
43478558 CGGCGTTTTCCTATAAGTGTCGTTAAAGGTCAGGACATTAG
1 CGGCGCTTTCCCATAAGCGTCGCTAAAGGTCAGG-CATTAG
* * * * *
43478599 CGACACTTTCCCATAAGCGCCGCTAAAGGTTAGGCATTAC
1 CGGCGCTTTCCCATAAGCGTCGCTAAAGGTCAGGCATTAG
* * *
43478639 CGGTGCTTTCCCATAAGTGCCGCTAAAGGTCAGGTCATTAG
1 CGGCGCTTTCCCATAAGCGTCGCTAAAGGTCAGG-CATTAG
*
43478680 CGGCGCTTTCCCATCAGCGTCGCTAAAGGTCAAGGCATTAG
1 CGGCGCTTTCCCATAAGCGTCGCTAAAGGTC-AGGCATTAG
* * *
43478721 CGGCGCTTTCTCATAAGCATTGCTAAAGGTCAGGGCATTAG
1 CGGCGCTTTCCCATAAGCGTCGCTAAAGGTCA-GGCATTAG
43478762 CGGCGCTTTCCCATAAGCGTCGCTAA
1 CGGCGCTTTCCCATAAGCGTCGCTAA
43478788 TTTATTTAAA
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
40 35 0.22
41 122 0.76
42 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
CGGCGCTTTCCCATAAGCGTCGCTAAAGGTCAGGCATTAG
Found at i:43479608 original size:170 final size:170
Alignment explanation
Indices: 43479321--43479810 Score: 729
Period size: 170 Copynumber: 2.9 Consensus size: 170
43479311 TTGGAATAGT
43479321 AACAATGAAAATGGCGCCCTCTTTAGTGAGA-T-TATATGAACAAATGCCCGAACCTAAATATGT
1 AACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGT
* * *
43479384 TATTGCTATGGGCACGTGTACAATATAGGAGGAGGGATGTTTAATAATGATTCTTATAGTACTGT
66 TATTGCTATGGGCACGTGTACAAT-TA-CAGGAGGGATGTTCAATACTGATTCTTATAGTACTGT
*
43479449 TCGGGGGGTCCATAAGCTAATTCTCGTGCATGTCTATACAGC
129 TCGGGGGGTCGATAAGCTAATTCTCGTGCATGTCTATACAGC
* * *
43479491 AATATTGAAAATGACGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGT
1 AACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGT
** * * *
43479556 TATTGCTATGGGTGCGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTGTAGTACTATAC
66 TATTGCTATGGGCACGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTACTGTTC
* * * *
43479621 GAGGGGTCGATAAGCTAATTCCCGTGGATGTCTATACAGT
131 GGGGGGTCGATAAGCTAATTCTCGTGCATGTCTATACAGC
* *
43479661 AACAATGAGAATGGCACCCTCTTTAGT--GATTATATATGAACAAATGCCCGAACCTAAATATGT
1 AACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGT
* * *
43479724 TATTGCTGTGAGCACGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTATTGTTC
66 TATTGCTATGGGCACGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTACTGTTC
*
43479789 -GGGGGTGGATAAGCTAATTCTC
131 GGGGGGTCGATAAGCTAATTCTC
43479811 ATGAATGTAT
Statistics
Matches: 286, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
167 19 0.07
168 93 0.33
170 118 0.41
171 3 0.01
172 53 0.19
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (170 bp):
AACAATGAAAATGGCGCCCTCTTTAGTGAGATTATATATGAACAAATGCCCGAACCTAAATATGT
TATTGCTATGGGCACGTGTACAATTACAGGAGGGATGTTCAATACTGATTCTTATAGTACTGTTC
GGGGGGTCGATAAGCTAATTCTCGTGCATGTCTATACAGC
Found at i:43479900 original size:29 final size:29
Alignment explanation
Indices: 43479868--43479938 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 29
43479858 AAATAAATTC
* *
43479868 TAAATAGACTAATATAAATAATAACTAAA
1 TAAAAAGAATAATATAAATAATAACTAAA
* * **
43479897 TAAAAATAATAATTTAAATAATATTTAAA
1 TAAAAAGAATAATATAAATAATAACTAAA
*
43479926 T-AAAATAATAATA
1 TAAAAAGAATAATA
43479939 GATAGAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (29 bp):
TAAAAAGAATAATATAAATAATAACTAAA
Found at i:43479904 original size:14 final size:15
Alignment explanation
Indices: 43479869--43479919 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 15
43479859 AATAAATTCT
43479869 AAATAGACTAATATAA
1 AAATA-ACTAATATAA
43479885 ATAATAACTAA-ATAA
1 A-AATAACTAATATAA
*
43479900 AAATAA-TAATTTAA
1 AAATAACTAATATAA
43479914 ATAATA
1 A-AATA
43479920 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 9 0.29
15 9 0.29
16 6 0.19
17 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATAACTAATATAA
Found at i:43479924 original size:11 final size:12
Alignment explanation
Indices: 43479900--43479928 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
43479890 AACTAAATAA
43479900 AAATAATAATTT
1 AAATAATAATTT
43479912 AAATAAT-ATTT
1 AAATAATAATTT
43479923 AAATAA
1 AAATAA
43479929 AATAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATAATTT
Found at i:43479947 original size:15 final size:14
Alignment explanation
Indices: 43479881--43479966 Score: 56
Period size: 15 Copynumber: 6.1 Consensus size: 14
43479871 ATAGACTAAT
*
43479881 ATAAATAATAACTAA
1 ATAAATAATAA-TAG
43479896 ATAAA-AATAATA-
1 ATAAATAATAATAG
* *
43479908 ATTTAAATAATATTTAA
1 A--TAAATAATA-ATAG
43479925 ATAAAATAATAATAG
1 AT-AAATAATAATAG
43479940 ATAGAATAATAA-A-
1 ATA-AATAATAATAG
43479953 ATAAATAAT-ATAG
1 ATAAATAATAATAG
43479966 A
1 A
43479967 AATGTAGATT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
11 1 0.02
12 8 0.14
13 6 0.10
14 11 0.19
15 22 0.37
16 10 0.17
17 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (14 bp):
ATAAATAATAATAG
Found at i:43479947 original size:28 final size:28
Alignment explanation
Indices: 43479877--43479968 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
43479867 CTAAATAGAC
* * *
43479877 TAATATAAATAATAACTAAATAAAAATAA
1 TAATAGAAAGAATAATTAAAT-AAAATAA
** * *
43479906 TAATTTAAATAATATTTAAATAAAATAA
1 TAATAGAAAGAATAATTAAATAAAATAA
* *
43479934 TAATAGATAGAATAATAAAAT-AAATAA
1 TAATAGAAAGAATAATTAAATAAAATAA
43479961 T-ATAGAAA
1 TAATAGAAA
43479969 TGTAGATTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 6 0.11
27 7 0.13
28 22 0.42
29 18 0.34
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
TAATAGAAAGAATAATTAAATAAAATAA
Found at i:43480061 original size:39 final size:39
Alignment explanation
Indices: 43479991--43480065 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
43479981 AATCGAAATA
*
43479991 TATTAATTATTAATATAAATATAATATTAATATAAAGAT
1 TATTAATTATTAATATAAATACAATATTAATATAAAGAT
*
43480030 TATTAATTACTTAATATTAATAGCAA-A-TAATATAAA
1 TATTAATTA-TTAATATAAATA-CAATATTAATATAAA
43480066 TTAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 18 0.56
40 12 0.38
41 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (39 bp):
TATTAATTATTAATATAAATACAATATTAATATAAAGAT
Found at i:43480073 original size:29 final size:28
Alignment explanation
Indices: 43480001--43480074 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
43479991 TATTAATTAT
*
43480001 TAATATAAA-T-ATAATATTAATATAAA
1 TAATATAAATTAATAATATTAATACAAA
* * * *
43480027 GATTATTAATTACTTAATATTAATAGCAAA
1 TAATATAAATTA-ATAATATTAATA-CAAA
43480057 TAATATAAATTAATAATA
1 TAATATAAATTAATAATA
43480075 ATTGATAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
26 6 0.17
27 1 0.03
29 16 0.46
30 12 0.34
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (28 bp):
TAATATAAATTAATAATATTAATACAAA
Found at i:43484054 original size:29 final size:29
Alignment explanation
Indices: 43484022--43484251 Score: 121
Period size: 29 Copynumber: 7.8 Consensus size: 29
43484012 TCAAACATTT
*
43484022 AAAAATCACATTTAACCCCTAAACTTCTC
1 AAAAATTACATTTAACCCCTAAACTTCTC
* * *
43484051 AAAAATTATAATTTTA-CCCTCGAACTTC-C
1 AAAAATTA-CATTTAACCCCT-AAACTTCTC
* * *
43484080 AAAAATAATATTATAACCCCTAAACTTATC
1 AAAAATTACATT-TAACCCCTAAACTTCTC
* * **
43484110 CAAAATTACATTTTGACCCC-ATGCTTCTC
1 AAAAATTACA-TTTAACCCCTAAACTTCTC
* * *
43484139 TAAAATTATATTTAAACCCCTAAACTTTTC
1 AAAAATTACATTT-AACCCCTAAACTTCTC
* ** * *
43484169 TAAAATCCCATTTTAA-CCTTAAACTTTTC
1 AAAAATTACA-TTTAACCCCTAAACTTCTC
* ** *
43484198 CAAAATTATGTTTTGACCCC-AAACTTCTTC
1 AAAAATTA-CATTTAACCCCTAAACTTC-TC
*
43484228 -AAAATTACATTTTGACCCCTAAAC
1 AAAAATTACA-TTTAACCCCTAAAC
43484252 CTTTCTGGAA
Statistics
Matches: 151, Mismatches: 36, Indels: 27
0.71 0.17 0.13
Matches are distributed among these distances:
28 6 0.04
29 88 0.58
30 52 0.34
31 5 0.03
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAATTACATTTAACCCCTAAACTTCTC
Found at i:43484144 original size:59 final size:57
Alignment explanation
Indices: 43484022--43484246 Score: 177
Period size: 59 Copynumber: 3.9 Consensus size: 57
43484012 TCAAACATTT
* * * *
43484022 AAAAATCACATTTAACCCCTAAACTTCTCAAAAATTATAATTTT-ACCCTCGAACTTC-C
1 AAAAATTATATTTAACCCCTAAACTTCTCCAAAATTA-CATTTTGACCC-C-AACTTCTC
* * *
43484080 AAAAATAATATTATAACCCCTAAACTTATCCAAAATTACATTTTGACCCCATGCTTCTC
1 AAAAATTATATT-TAACCCCTAAACTTCTCCAAAATTACATTTTGACCCCA-ACTTCTC
* * * ** * ** *
43484139 TAAAATTATATTTAAACCCCTAAACTTTTCTAAAATCCCATTTTAACCTTAAACTTTTC
1 AAAAATTATATTT-AACCCCTAAACTTCTCCAAAATTACATTTTGACC-CCAACTTCTC
* * * *
43484198 CAAAATTATGTTTTGACCCC-AAACTTCTTCAAAATTACATTTTGACCCC
1 AAAAATTAT-ATTTAACCCCTAAACTTCTCCAAAATTACATTTTGACCCC
43484247 TAAACCTTTC
Statistics
Matches: 132, Mismatches: 28, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
57 1 0.01
58 42 0.32
59 85 0.64
60 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (57 bp):
AAAAATTATATTTAACCCCTAAACTTCTCCAAAATTACATTTTGACCCCAACTTCTC
Found at i:43484165 original size:88 final size:88
Alignment explanation
Indices: 43484076--43484256 Score: 193
Period size: 88 Copynumber: 2.0 Consensus size: 88
43484066 ACCCTCGAAC
* **
43484076 TTCCAAAAATAATATTATAACCCCTAAACTTATCCAAAATTACATTTTGACCCCATGCTTC-TCT
1 TTCCAAAAATAACATTATAA-CCCTAAACTTATCCAAAATTACATTTTGACCCCAAACTTCTTC-
*
43484140 AAAATTATATTTAAACCCCTAAACT
64 AAAATTACATTTAAACCCCTAAACT
* * ** * * * **
43484165 TTTCTAAAATCCCATTTTAACCTTAAACTTTTCCAAAATTATGTTTTGACCCCAAACTTCTTCAA
1 TTCCAAAAATAACATTATAACCCTAAACTTATCCAAAATTACATTTTGACCCCAAACTTCTTCAA
**
43484230 AATTACATTTTGACCCCTAAACCT
66 AATTACATTTAAACCCCTAAA-CT
43484254 TTC
1 TTC
43484257 TGGAATAATG
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
88 54 0.73
89 20 0.27
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (88 bp):
TTCCAAAAATAACATTATAACCCTAAACTTATCCAAAATTACATTTTGACCCCAAACTTCTTCAA
AATTACATTTAAACCCCTAAACT
Found at i:43484251 original size:59 final size:60
Alignment explanation
Indices: 43484095--43484302 Score: 201
Period size: 59 Copynumber: 3.5 Consensus size: 60
43484085 TAATATTATA
* * ** * * **
43484095 ACCCCTAAACTTATCCAAAATTACATTTTGACCCC-ATGCTTCTCTAAAATTATATTTAA
1 ACCCCTAAACTTCTCCAAAATCACATTTTGACCCCTAAACTTTTCTAAAATTATGTTTTG
* * * * * *
43484154 ACCCCTAAACTTTTCTAAAATCCCATTTT-AACCTTAAACTTTTCCAAAATTATGTTTTG
1 ACCCCTAAACTTCTCCAAAATCACATTTTGACCCCTAAACTTTTCTAAAATTATGTTTTG
* * * ** *
43484213 ACCCC-AAACTTCTTCAAAATTACATTTTGACCCCTAAACCTTTCTGGAATAATGTTTTG
1 ACCCCTAAACTTCTCCAAAATCACATTTTGACCCCTAAACTTTTCTAAAATTATGTTTTG
43484272 A--CCTAAACTTCTCCAAAATCACATTTTGACC
1 ACCCCTAAACTTCTCCAAAATCACATTTTGACC
43484303 TCGATTTTCC
Statistics
Matches: 119, Mismatches: 27, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
57 2 0.02
58 46 0.39
59 71 0.60
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (60 bp):
ACCCCTAAACTTCTCCAAAATCACATTTTGACCCCTAAACTTTTCTAAAATTATGTTTTG
Found at i:43488340 original size:14 final size:14
Alignment explanation
Indices: 43488318--43488351 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
43488308 TGAAACCCAA
43488318 GAAAAAAAAGAAAAAG
1 GAAAAAAAAG--AAAG
43488334 GAAAAAAAAGAAAG
1 GAAAAAAAAGAAAG
43488348 GAAA
1 GAAA
43488352 GTCAAGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAG
Found at i:43489210 original size:20 final size:20
Alignment explanation
Indices: 43489181--43489230 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
43489171 GAAGAAAAAT
*
43489181 AAAA-GAAAAAAA-GAAGAAG
1 AAAAGGAAAAAAATG-AGAAA
*
43489200 AAAGGGAAAAAAATGAGAAA
1 AAAAGGAAAAAAATGAGAAA
43489220 AAAAGGAAAAA
1 AAAAGGAAAAA
43489231 GAAAAGGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 22 0.85
21 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (20 bp):
AAAAGGAAAAAAATGAGAAA
Found at i:43490271 original size:50 final size:49
Alignment explanation
Indices: 43490211--43490339 Score: 118
Period size: 48 Copynumber: 2.6 Consensus size: 49
43490201 CGCAATGGCG
* *
43490211 AACCCGGTACCTTAAAAAATGTGATGAGAAGGATTGAGGCCGCAACAGTG
1 AACCCAGTACCTTAAAAAATGTGATGAGAAGG-TTGAGGCCGCAACAGTA
* * * * * * *
43490261 AATCCAGTACCATGAAATATGATGGT-A-AAGGTTGAGGCTGCAACGGTA
1 AACCCAGTACCTTAAAAAATG-TGATGAGAAGGTTGAGGCCGCAACAGTA
* * *
43490309 AACCCAGTACCTTAGAAGATGTGATGGGAAG
1 AACCCAGTACCTTAAAAAATGTGATGAGAAG
43490340 AGGCCACAAC
Statistics
Matches: 60, Mismatches: 16, Indels: 7
0.72 0.19 0.08
Matches are distributed among these distances:
47 3 0.05
48 30 0.50
49 7 0.12
50 17 0.28
51 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (49 bp):
AACCCAGTACCTTAAAAAATGTGATGAGAAGGTTGAGGCCGCAACAGTA
Found at i:43490296 original size:48 final size:48
Alignment explanation
Indices: 43490239--43490550 Score: 185
Period size: 48 Copynumber: 6.5 Consensus size: 48
43490229 ATGTGATGAG
*
43490239 AAGGATTGAGGCCGCAACAGTGAATCCAGTACCATGAA-ATATGATGGTA
1 AAGG-TTGAGGCCGCAACGGTGAATCCAGTACCATGAAGATATGATGG-A
* * * * * *
43490288 AAGGTTGAGGCTGCAACGGTAAACCCAGTACCTTAGAAGATGTGATGGG
1 AAGGTTGAGGCCGCAACGGTGAATCCAGTACCAT-GAAGATATGATGGA
* * *
43490337 AA----GAGGCCACAACGGTGAATCCAGTACTAT-AAAATATGATGGGA
1 AAGGTTGAGGCCGCAACGGTGAATCCAGTACCATGAAGATATGAT-GGA
* ** * * * *
43490381 AAGGTTAAGGCCTTAACGGTGAACCCGGTACCATGAAGATATAAAGAGA
1 AAGGTTGAGGCCGCAACGGTGAATCCAGTACCATGAAGATATGATG-GA
** * * * *
43490430 AAGGTCCAAGACGCAACGGCGAA-CCTAGTACC-TCAGAAGATGTGATGGGA
1 AAGGTTGAGGCCGCAACGGTGAATCC-AGTACCAT--GAAGATATGAT-GGA
* * * *
43490480 AAGATTGAGGCCGTAACGGTGAATCC-GATACCATGAA-ATGTGATCGAA
1 AAGGTTGAGGCCGCAACGGTGAATCCAG-TACCATGAAGATATGAT-GGA
* * *
43490528 AAGGTTAAGGCCACAACAGTGAA
1 AAGGTTGAGGCCGCAACGGTGAA
43490551 CCCGATACCT
Statistics
Matches: 197, Mismatches: 50, Indels: 33
0.70 0.18 0.12
Matches are distributed among these distances:
43 8 0.04
44 4 0.02
45 22 0.11
48 78 0.40
49 43 0.22
50 38 0.19
51 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.18
Consensus pattern (48 bp):
AAGGTTGAGGCCGCAACGGTGAATCCAGTACCATGAAGATATGATGGA
Found at i:43490399 original size:93 final size:92
Alignment explanation
Indices: 43490246--43490420 Score: 235
Period size: 93 Copynumber: 1.9 Consensus size: 92
43490236 GAGAAGGATT
* * * *
43490246 GAGGCCGCAACAGTGAATCCAGTACCATGAAATATGATGGTAAAGGTTGAGGCTGCAACGGTAAA
1 GAGGCCACAACAGTGAATCCAGTACCATAAAATATGATGGGAAAGGTTAAGGCTGCAACGGTAAA
*
43490311 CCCAGTACCTTAGAAGATGTGATGGGAA
66 CCCAGTACCAT-GAAGATGTGATGGGAA
* * * *
43490339 GAGGCCACAACGGTGAATCCAGTACTATAAAATATGATGGGAAAGGTTAAGGCCT-TAACGGTGA
1 GAGGCCACAACAGTGAATCCAGTACCATAAAATATGATGGGAAAGGTTAAGG-CTGCAACGGTAA
*
43490403 ACCCGGTACCATGAAGAT
65 ACCCAGTACCATGAAGAT
43490421 ATAAAGAGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
92 6 0.08
93 63 0.89
94 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (92 bp):
GAGGCCACAACAGTGAATCCAGTACCATAAAATATGATGGGAAAGGTTAAGGCTGCAACGGTAAA
CCCAGTACCATGAAGATGTGATGGGAA
Found at i:43490861 original size:41 final size:41
Alignment explanation
Indices: 43490804--43490895 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
43490794 CATCATTCAG
* *
43490804 TCTTTTACCCATAATCAAGAAGGGTAGATTGAAGATTCCAA
1 TCTTTTACCCATAATCAAGAAGGGTAGAATAAAGATTCCAA
* **
43490845 TCTTTTACCCTTAATCAAGAAGGGTAGAATAAAGATTCTGA
1 TCTTTTACCCATAATCAAGAAGGGTAGAATAAAGATTCCAA
43490886 TCTTTTACCC
1 TCTTTTACCC
43490896 CAAGCCTGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
TCTTTTACCCATAATCAAGAAGGGTAGAATAAAGATTCCAA
Found at i:43491011 original size:39 final size:39
Alignment explanation
Indices: 43490885--43491332 Score: 194
Period size: 39 Copynumber: 11.7 Consensus size: 39
43490875 AAAGATTCTG
* * * * * *
43490885 ATCTTTTACCCCAAGCCTGGGGCAGATCA-TAGTCAGCCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-CCAGTCA
* * **
43490924 ATCTCTTACCCCGAGCCTGAGGTAGAT-TGCAGCCA-TCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-CCAGT-CA
* * * *
43490963 CTCTTTTACCTCGAGCTTGGGGCAGATCACCACCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
* * * ** *
43491002 ATCTGTTACCTCGAGCTTGGGGCAGAT-TGCATCCA-TCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-CCAGTC-A
* * * * * * *
43491041 ATCTCTTA-TCCAAGCCTGGGGAAAATCACTATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
* * * *
43491079 ATC-CTTTACCCCGAGCCTAGGGCATG-TCACGATCAGCCA
1 ATCTC-TTACCCCGAGCCTGGGGCA-GATCACCACCAGTCA
* ** * *
43491118 ATCTTTTACCCCGAGCCTGGGGCAGAT-TGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-CCAGTCA
* ** * *
43491157 ATCTTTTACCTTGAGCTTGGGGTAGAT---CACCA-TC-
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
* * * ** * *
43491191 -TCTTTTACCCCGAGTCTGGGGCAAAT-TGCAGCTA-TAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-CCAGTCA
* *
43491228 GATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 -ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
* * *
43491268 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
*
43491307 ATCTCTTA-CCCGAGCTTGGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
43491333 TGCAACCATT
Statistics
Matches: 313, Mismatches: 74, Indels: 45
0.72 0.17 0.10
Matches are distributed among these distances:
33 20 0.06
35 4 0.01
36 6 0.02
37 3 0.01
38 42 0.13
39 232 0.74
40 6 0.02
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCACCAGTCA
Found at i:43491200 original size:72 final size:72
Alignment explanation
Indices: 43491119--43491262 Score: 198
Period size: 72 Copynumber: 2.0 Consensus size: 72
43491109 GATCAGCCAA
* ** * ** * *
43491119 TCTTTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTTTTACCTTGAGCTTGGGGTAGAT
1 TCTTTTACCCCGAGCCTGGGGCAAATTGCAGCCATAAGATCTCTTACCCCGAGCCTGGGGCAGAT
43491184 CACCATC
66 CACCATC
* *
43491191 TCTTTTACCCCGAGTCTGGGGCAAATTGCAGCTATAAGATCTCTTACCCCGAGCCTGGGGCAGAT
1 TCTTTTACCCCGAGCCTGGGGCAAATTGCAGCCATAAGATCTCTTACCCCGAGCCTGGGGCAGAT
43491256 CACCATC
66 CACCATC
43491263 AGCCAATCTC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (72 bp):
TCTTTTACCCCGAGCCTGGGGCAAATTGCAGCCATAAGATCTCTTACCCCGAGCCTGGGGCAGAT
CACCATC
Found at i:43491393 original size:39 final size:39
Alignment explanation
Indices: 43491229--43491404 Score: 164
Period size: 39 Copynumber: 4.6 Consensus size: 39
43491219 CAGCTATAAG
* *
43491229 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCA
*
43491268 ATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCA
* * * **
43491307 ATCTCTTA-CCCGAGCTTGGGGCAGATTGCAACCATTTG---
1 ATCTCTTACCCCGAGCCTAGGGCA-AAT-C-ACCATCAGCCA
* * * * *
43491345 ATCTTTTACCTCGATCATAGGGCAAATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCA
*
43491384 ATCTCTTACCCCAAGCC-AGGG
1 ATCTCTTACCCCGAGCCTAGGG
43491405 GTAGATTGCA
Statistics
Matches: 109, Mismatches: 21, Indels: 15
0.75 0.14 0.10
Matches are distributed among these distances:
36 5 0.05
37 1 0.01
38 26 0.24
39 70 0.64
40 1 0.01
41 6 0.06
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.22
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAGGGCAAATCACCATCAGCCA
Found at i:43492890 original size:13 final size:14
Alignment explanation
Indices: 43492867--43492895 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43492857 AGTTTCTTTT
43492867 TTTTAAAAAAAAAC
1 TTTTAAAAAAAAAC
43492881 TTTTAAAAAAAAAC
1 TTTTAAAAAAAAAC
43492895 T
1 T
43492896 AAAAAGGAAA
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:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
TTTTAAAAAAAAAC
Found at i:43493837 original size:30 final size:30
Alignment explanation
Indices: 43493803--43493977 Score: 196
Period size: 30 Copynumber: 5.9 Consensus size: 30
43493793 CAAAAATCAT
43493803 ATTTTAACCCTTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* *
43493833 ATTTTAACCCATAAACTTCTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * *
43493863 ATTTTAA-CCTCTAAAATTTT-TAAAATTAT
1 ATTTTAACCCT-TAAACTTTTCCAAAATTAC
43493892 ATTTTAACCCTTAAACTTCTT-CAAAATTAC
1 ATTTTAACCCTTAAACTT-TTCCAAAATTAC
* * *
43493922 ATTTT-ACCCTTTAACTTCTCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
* * * *
43493951 ATTCTGACCCTTAAACCTTCCCAAAAT
1 ATTTTAACCCTTAAACTTTTCCAAAAT
43493978 CATGTTTTGA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
28 1 0.01
29 45 0.37
30 75 0.62
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCCAAAATTAC
Found at i:43493888 original size:59 final size:58
Alignment explanation
Indices: 43493755--43493977 Score: 216
Period size: 59 Copynumber: 3.8 Consensus size: 58
43493745 ACACTGACCC
* * * * * * * *
43493755 CTAAACTTCTTAAAAATATATTTTTACCCCTAAACTTCCAAAAATCATATTTTAACC-
1 CTAAACTTTTTAAAATTACATTTTAACCCTTAAACTTCCCAAAATTACATTTTAACCT
* *
43493812 CTTAAACTTTTCCAAAATTACATTTTAACCCATAAACTTCTCCAAAATTACATTTTAACCT
1 C-TAAACTTTT-TAAAATTACATTTTAACCCTTAAACTTC-CCAAAATTACATTTTAACCT
* * * *
43493873 CTAAAATTTTTAAAATTATATTTTAACCCTTAAACTTCTTCAAAATTACATTTTACCCT
1 CTAAACTTTTTAAAATTACATTTTAACCCTTAAACTTC-CCAAAATTACATTTTAACCT
* * * *
43493932 -TTAACTTCTCTAAAATTACATTCTGACCCTTAAACCTTCCCAAAAT
1 CTAAACTT-TTTAAAATTACATTTTAACCCTTAAA-CTTCCCAAAAT
43493978 CATGTTTTGA
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.01
58 13 0.09
59 95 0.69
60 28 0.20
61 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.39
Consensus pattern (58 bp):
CTAAACTTTTTAAAATTACATTTTAACCCTTAAACTTCCCAAAATTACATTTTAACCT
Found at i:43493947 original size:29 final size:29
Alignment explanation
Indices: 43493751--43493966 Score: 188
Period size: 29 Copynumber: 7.3 Consensus size: 29
43493741 AATCACACTG
* * *
43493751 ACCCCTAAACTTCT-TAAAAATATATTTTT
1 ACCCTTAAACTTCTCTAAAATTACA-TTTT
* * * *
43493780 ACCCCTAAACTTC-CAAAAATCATATTTT
1 ACCCTTAAACTTCTCTAAAATTACATTTT
* *
43493808 AACCCTTAAACTTTTCCAAAATTACATTTT
1 -ACCCTTAAACTTCTCTAAAATTACATTTT
* *
43493838 AACCCATAAACTTCTCCAAAATTACATTTT
1 -ACCCTTAAACTTCTCTAAAATTACATTTT
* * * *
43493868 AACCTCTAAAATT-TTTAAAATTATATTTT
1 ACCCT-TAAACTTCTCTAAAATTACATTTT
43493897 AACCCTTAAACTTCT-TCAAAATTACATTTT
1 -ACCCTTAAACTTCTCT-AAAATTACATTTT
* *
43493927 ACCCTTTAACTTCTCTAAAATTACATTCTG
1 ACCCTTAAACTTCTCTAAAATTACATT-TT
43493957 ACCCTTAAAC
1 ACCCTTAAAC
43493967 CTTCCCAAAA
Statistics
Matches: 156, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.03
29 78 0.50
30 74 0.47
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (29 bp):
ACCCTTAAACTTCTCTAAAATTACATTTT
Found at i:43501607 original size:21 final size:19
Alignment explanation
Indices: 43501563--43501601 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43501553 CTACAACTTA
* *
43501563 AAGCGGAGGCAGTAGTGAG
1 AAGCAGAGGCAGGAGTGAG
43501582 AAGCAGAGGCAGGAGTGAG
1 AAGCAGAGGCAGGAGTGAG
43501601 A
1 A
43501602 GAAGCAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.46, T:0.08
Consensus pattern (19 bp):
AAGCAGAGGCAGGAGTGAG
Found at i:43501974 original size:43 final size:43
Alignment explanation
Indices: 43501925--43502104 Score: 227
Period size: 43 Copynumber: 4.2 Consensus size: 43
43501915 TTATCTATAA
* **
43501925 CGGCGTTTGTGGGGAAA-CAGCCATTAAAGACCATGTTCTTTAG
1 CGGCGTTTGTGGGAAAAGC-GCCGCTAAAGACCATGTTCTTTAG
* **
43501968 CCGCGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAG
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAG
* *
43502011 CGGCGTTTGTGGGGAAAGCGCTGCTAAAGACCATGTTCTTTAG
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAG
* * * *
43502054 CGGCATTTATGGTAAAAGTGCCGCTAAAGACCATGTTCTTTAG
1 CGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAG
*
43502097 CGGTGTTT
1 CGGCGTTT
43502105 TTCCTCATAA
Statistics
Matches: 117, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
43 116 0.99
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAG
Found at i:43502039 original size:86 final size:86
Alignment explanation
Indices: 43501925--43502104 Score: 254
Period size: 86 Copynumber: 2.1 Consensus size: 86
43501915 TTATCTATAA
* * *
43501925 CGGCGTTTGTGGGGAAACAGCCATTAAAGACCATGTTCTTTAGCCGCGTTTGTGAAAAAAGCGCC
1 CGGCGTTTGTGGGGAAACAGCCACTAAAGACCATGTTCTTTAGCCGCATTTATGAAAAAAGCGCC
43501990 GCTAAAGACCATGTTCTTTAG
66 GCTAAAGACCATGTTCTTTAG
** * ** *
43502011 CGGCGTTTGTGGGGAAAGC-GCTGCTAAAGACCATGTTCTTTAGCGGCATTTATGGTAAAAGTGC
1 CGGCGTTTGTGGGGAAA-CAGCCACTAAAGACCATGTTCTTTAGCCGCATTTATGAAAAAAGCGC
43502075 CGCTAAAGACCATGTTCTTTAG
65 CGCTAAAGACCATGTTCTTTAG
*
43502097 CGGTGTTT
1 CGGCGTTT
43502105 TTCCTCATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
86 82 0.99
87 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (86 bp):
CGGCGTTTGTGGGGAAACAGCCACTAAAGACCATGTTCTTTAGCCGCATTTATGAAAAAAGCGCC
GCTAAAGACCATGTTCTTTAG
Found at i:43521855 original size:50 final size:51
Alignment explanation
Indices: 43521743--43522157 Score: 167
Period size: 50 Copynumber: 8.3 Consensus size: 51
43521733 CAGGTTTGAC
* * ** *
43521743 AGGG-AAGGATTGAGG-TCGCAACGGCAAATTCGGTACCTTAAAAGAT-TGA
1 AGGGAAAGG-TTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* * * *
43521792 AGGGAAAGGTTGAGGCT-ATATCATCGAACCCGGTACCTAAAAAGATGTGA
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* ** *
43521842 AGGGAAAGGTTGA-GCTCACAACGGCAAACCCAATACCTAAGAAGATGTGA
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* * * ** * * * *
43521892 TGGGAAAGGTTGAGGC-CTCAACGGTGAACTCAGTACCATGAATAGA--TGA
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACC-TAAAAAGATGTGA
* * * * * * * *
43521941 AGGGAAAGATTGAGGC-CGCGACGGCGAATCCGGTACCTTAGAAGATGTG-
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* * * * * * * *
43521990 ATGGATAGGGAGGTTGAGGCT-GCAATAGCGAACTCGGTACCTCAGAAGATATGA
1 AGGGA-A---AGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* * * * * ** *
43522044 TGGGAAAGATTGAGGC-CACAACAGCGAATCCGATACC-ATGAA-ATATGA
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
* * * * * * * * * *
43522092 TGAGAAAGGTTGAGGCT-GCAACGGTAAACCCAGTACTTTAGAAGATATGA
1 AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
43522142 AGGGAAAGGTTGAGGC
1 AGGGAAAGGTTGAGGC
43522158 CGTAACGACG
Statistics
Matches: 278, Mismatches: 70, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
48 37 0.13
49 75 0.27
50 121 0.44
51 7 0.03
53 35 0.13
54 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (51 bp):
AGGGAAAGGTTGAGGCTCACAACAGCAAACCCGGTACCTAAAAAGATGTGA
Found at i:43522140 original size:98 final size:99
Alignment explanation
Indices: 43521824--43522158 Score: 295
Period size: 98 Copynumber: 3.4 Consensus size: 99
43521814 ATCGAACCCG
* * * * * * * *
43521824 GTACCTAAAAAGATGTGAAGGGAAAGGTTGA-GCTCACAACGGCAAACCCAATACC-TAAGAAGA
1 GTACCTTAGAAGATATGAAGGGAAAGATTGAGGC-CACAACAGCGAATCCGATACCAT-AGAAGA
*
43521887 TGTGATGGGAAAGGTTGAGGCCT-CAACGGTGAACTCA
64 TATGAT-GGAAAGGTTGAGG-CTGCAACGGTGAACTCA
* * * * * * * * *
43521924 GTACCAT-GAATAGATGAAGGGAAAGATTGAGGCCGCGACGGCGAATCCGGTACCTTAGAAGATG
1 GTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCACAACAGCGAATCCGATACCATAGAAGATA
** * *
43521988 TGATGGATAGGGAGGTTGAGGCTGCAATAGCGAACTCG
66 TGATGGA-A---AGGTTGAGGCTGCAACGGTGAACTCA
* *
43522026 GTACCTCAGAAGATATGATGGGAAAGATTGAGGCCACAACAGCGAATCCGATACCAT-GAA-ATA
1 GTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCACAACAGCGAATCCGATACCATAGAAGATA
* *
43522089 TGATGAGAAAGGTTGAGGCTGCAACGGTAAACCCA
66 TGATG-GAAAGGTTGAGGCTGCAACGGTGAACTCA
* *
43522124 GTACTTTAGAAGATATGAAGGGAAAGGTTGAGGCC
1 GTACCTTAGAAGATATGAAGGGAAAGATTGAGGCC
43522159 GTAACGACGA
Statistics
Matches: 188, Mismatches: 38, Indels: 20
0.76 0.15 0.08
Matches are distributed among these distances:
98 54 0.29
99 46 0.24
100 8 0.04
101 10 0.05
102 29 0.15
103 41 0.22
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.18
Consensus pattern (99 bp):
GTACCTTAGAAGATATGAAGGGAAAGATTGAGGCCACAACAGCGAATCCGATACCATAGAAGATA
TGATGGAAAGGTTGAGGCTGCAACGGTGAACTCA
Found at i:43522498 original size:38 final size:37
Alignment explanation
Indices: 43522420--43522520 Score: 130
Period size: 38 Copynumber: 2.6 Consensus size: 37
43522410 CATCATCATT
*
43522420 CAGTCTTTTACCCTTAATCACGAAAGGCAGATTGAAGATTC
1 CAGTCTTTTACCCTTAAT----TAAGGCAGATTGAAGATTC
43522461 CAGTCTTTTACCCTTAATTAAGGACAGATTGAAGATTC
1 CAGTCTTTTACCCTTAATTAAGG-CAGATTGAAGATTC
* *
43522499 CCGTTTTTTACCCTTAATTAAG
1 CAGTCTTTTACCCTTAATTAAG
43522521 AATAGCAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
37 4 0.07
38 34 0.61
41 18 0.32
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (37 bp):
CAGTCTTTTACCCTTAATTAAGGCAGATTGAAGATTC
Found at i:43522586 original size:39 final size:39
Alignment explanation
Indices: 43522542--43522724 Score: 120
Period size: 39 Copynumber: 4.6 Consensus size: 39
43522532 AAAGATTCTG
*
43522542 ATCTCTTACCCCGATCTTGAAGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGATCTTGAGGCAGATCACCATCAGCCA
* * * * * *
43522581 ATCTCTTACCCCAAGCCT-AGGGCAGATTACTATCAGTCA
1 ATCTCTTACCCCGATCTTGA-GGCAGATCACCATCAGCCA
* * * *
43522620 ATCTCTTACCCTGATTTTGGGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGATCTTGAGGCAGATCACCATCAGCCA
* * * * * *
43522659 CCCGATCTCTTGCCTCGA-CGTG-GGCAGATCACAACCATCCA
1 ----ATCTCTTACCCCGATCTTGAGGCAGATCACCATCAGCCA
* * *
43522700 ACCTCTTACCTCGATCATGAGGCAG
1 ATCTCTTACCCCGATCTTGAGGCAG
43522725 GTTACAGTTA
Statistics
Matches: 107, Mismatches: 29, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
37 12 0.11
38 4 0.04
39 63 0.59
41 15 0.14
42 2 0.02
43 11 0.10
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGATCTTGAGGCAGATCACCATCAGCCA
Found at i:43523169 original size:209 final size:208
Alignment explanation
Indices: 43522805--43523381 Score: 649
Period size: 209 Copynumber: 2.7 Consensus size: 208
43522795 TGATGCGGTT
* * * **
43522805 ATCTTCTTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAAC
1 ATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGTGAAAC
* * * * *
43522870 TTCGAACCTCAGCTTCCTGATGAGATATTGAGAAGCAGGTCAATGCAATAAAATGGTCGTCTTCC
66 TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCAA-GCAATAAAATGGTCATCTTCC
* * * * * * *
43522935 TGATAATATACAAAGAAGCGGACCAAATTCATCTTCTTGATGAGATATAGAGAAGTAGATT-G-A
130 TGATGAGATACAGAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAAAGAAGTAGATTAGCA
*
43522998 AATAAGTAATACGCTC
195 AA-AA-TAAGACGCTC
* *
43523014 ATCTTCTTGATGAGATACAAAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGTGAAAC
1 ATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGTGAAAC
* *
43523079 TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCGGGTCGAAGCAATAAAATGGTCTTCTTCC
66 TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTC-AAGCAATAAAATGGTCATCTTCC
*
43523144 TGATGAGATACAGAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAAAGAAGTGGATTAGCA
130 TGATGAGATACAGAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAAAGAAGTAGATTAGCA
* * *
43523209 CAAATGAGACGGTC
195 AAAATAAGACGCTC
* * * * * *
43523223 ATCTTCCTGATTAGATATAGAGAAGTAAAACAAATCAA-GTAAAGCAAAGTTCAGATACGAGTGA
1 ATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCAATG-AAA-CAAAGCTCA-ATATGAGTGA
* * * * * * * *
43523287 AGCTTCAAACCCTTATCTTCTTGATGAGATAC-AGAGAAGTAGGTCTAAGCAATAAAACGATCAT
63 AACTTCGAACCC-CAACTTCCTGATGAGATACTA-AGAAGCAGGTC-AAGCAATAAAATGGTCAT
* * *
43523351 CTTCTTGATGAGATATAGAGAAGTAGACCAA
125 CTTCCTGATGAGATACAGAGAAGTGGACCAA
43523382 GAGATAAAAC
Statistics
Matches: 314, Mismatches: 46, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
208 1 0.00
209 210 0.67
210 13 0.04
211 22 0.07
212 68 0.22
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (208 bp):
ATCTTCTTGATGAGATACAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAATATGAGTGAAAC
TTCGAACCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCAAGCAATAAAATGGTCATCTTCCT
GATGAGATACAGAGAAGTGGACCAAATCCATCTTCTTGATGAGATACAAAGAAGTAGATTAGCAA
AAATAAGACGCTC
Found at i:43530754 original size:13 final size:14
Alignment explanation
Indices: 43530736--43530770 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
43530726 CGGATTCAAT
43530736 GAAGAAAAAAA-AA
1 GAAGAAAAAAAGAA
43530749 GAAGAAAAAAAGAA
1 GAAGAAAAAAAGAA
43530763 -AAGAAAAA
1 GAAGAAAAA
43530771 GGAAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 19 0.90
14 2 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
GAAGAAAAAAAGAA
Found at i:43530775 original size:12 final size:10
Alignment explanation
Indices: 43530737--43530805 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 10
43530727 GGATTCAATG
43530737 AAGAAAAAAA
1 AAGAAAAAAA
43530747 AAGAAGAAAAA
1 AAGAA-AAAAA
43530758 AAGAAAAGAAA
1 AAGAAAA-AAA
43530769 AAGGAAAAAGAAA
1 AA-G-AAAA-AAA
*
43530782 ATAGAAAAAAC
1 A-AGAAAAAAA
* *
43530793 AGGAAAAAGA
1 AAGAAAAAAA
43530803 AAG
1 AAG
43530806 GAGAGACCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
10 15 0.31
11 18 0.37
12 5 0.10
13 10 0.20
14 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:43530782 original size:23 final size:22
Alignment explanation
Indices: 43530737--43530804 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
43530727 GGATTCAATG
43530737 AAGAAAAAAAAA-GAAGAAA-AA
1 AAGAAAAAAAAAGGAA-AAAGAA
43530758 AAGAAAAGAAAAAGGAAAAAGAA
1 AAGAAAA-AAAAAGGAAAAAGAA
* *
43530781 AATAGAAAAAACAGGAAAAAGAA
1 AAGA-AAAAAAAAGGAAAAAGAA
43530804 A
1 A
43530805 GGAGAGACCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.17
22 8 0.20
23 23 0.56
24 3 0.07
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (22 bp):
AAGAAAAAAAAAGGAAAAAGAA
Found at i:43531823 original size:50 final size:50
Alignment explanation
Indices: 43531742--43532130 Score: 272
Period size: 50 Copynumber: 7.9 Consensus size: 50
43531732 ACGACGAATT
* * *
43531742 CGGTACCTTAA-AAGAT-TGAAGGGAAAGGTTGAGCCCGCAATGGTGAACC
1 CGGTACC-TAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* *
43531791 CGGTACCTAAGAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACC
1 CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * *
43531841 CGATACCTAAGAAAATGTGATGGGAAAGGTTGAGGCCGCAATGACGAACC
1 CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * *
43531891 TGATACC-ATGAAGA-GATGAAGAG-AAGGATAGAGGCCGCGACGGCGAACC
1 CGGTACCTAAGAAGATG-TGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACC
* * * * * * ** * *
43531940 TGGTACCTTAGAAGATGTGATGGAAAAAGTTGAGGCCACAATAGTGAACT
1 CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * *
43531990 AGGTACCTCAGAAGATGTGATA-GGAAAGATTAAGGCCGCAACGACGAATC
1 CGGTACCTAAGAAGATGTGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * ***
43532040 TGGTACC-ATGAA-ATGTGATGGGAATGGTTGAGGCCACAACGATAAACC
1 CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
** * * * *
43532088 ATGTACTTTAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACG
1 CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACG
43532131 ATAAACCTGG
Statistics
Matches: 260, Mismatches: 69, Indels: 21
0.74 0.20 0.06
Matches are distributed among these distances:
48 39 0.15
49 51 0.20
50 166 0.64
51 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17
Consensus pattern (50 bp):
CGGTACCTAAGAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
Found at i:43531910 original size:99 final size:100
Alignment explanation
Indices: 43531762--43531981 Score: 255
Period size: 99 Copynumber: 2.2 Consensus size: 100
43531752 AAAGATTGAA
* ** * * * *
43531762 GGGAAAGGTTGAGCCCGCAATGGTGAACCCGGTACCTAAGAAGATATGAAGGGAAAGG-TTGAGG
1 GGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCTAAGAAGAGATGAAGAG-AAGGATAGAGG
43531826 CCGAAACGGCGAACCCGATACCTAAGAAAATGTGAT
65 CCGAAACGGCGAACCCGATACCTAAGAAAATGTGAT
* *
43531862 GGGAAAGGTTGAGGCCGCAATGACGAACCTGATACC-ATGAAGAGATGAAGAGAAGGATAGAGGC
1 GGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCTAAGAAGAGATGAAGAGAAGGATAGAGGC
** * * * *
43531926 CGCGACGGCGAACCTGGTACCTTAGAAGATGTGAT
66 CGAAACGGCGAACCCGATACCTAAGAAAATGTGAT
* * *
43531961 GGAAAAAGTTGAGGCCACAAT
1 GGGAAAGGTTGAGGCCGCAAT
43531982 AGTGAACTAG
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
98 4 0.04
99 66 0.65
100 31 0.31
ACGTcount: A:0.35, C:0.17, G:0.33, T:0.15
Consensus pattern (100 bp):
GGGAAAGGTTGAGGCCGCAATGACGAACCCGATACCTAAGAAGAGATGAAGAGAAGGATAGAGGC
CGAAACGGCGAACCCGATACCTAAGAAAATGTGAT
Found at i:43532101 original size:98 final size:100
Alignment explanation
Indices: 43531787--43532150 Score: 262
Period size: 99 Copynumber: 3.7 Consensus size: 100
43531777 CGCAATGGTG
* * * * * * * *
43531787 AACCCGGTACCTAAGAAGATATGAAGGGAAAGGTTGAGGCCGAAACGGCGAACCCGATACC-TAA
1 AACCAGGTACCTCAGAAGATATGAAGGGAAAGATTAAGGCCGCAACGACGAACCTGGTACCAT-A
* * * *
43531851 GAAAATGTGATGGGAAAGGTTGAGGCCGCAATGACG--
65 GAAGATGTGATGGAAAAAGTTGAGGCCACAA-GA-GTA
* * * * * * * *
43531887 AACCTGATA-C-CATGAAGAGATGAAGAGAAGGA-TAGAGGCCGCGACGGCGAACCTGGTACCTT
1 AACCAGGTACCTCA-GAAGATATGAAGGGAAAGATTA-AGGCCGCAACGACGAACCTGGTACCAT
* *
43531949 AGAAGATGTGATGGAAAAAGTTGAGGCCACAATAGTG
64 AGAAGATGTGATGGAAAAAGTTGAGGCCACAAGAGTA
* * *
43531986 AACTAGGTACCTCAGAAGATGTGATA-GGAAAGATTAAGGCCGCAACGACGAATCTGGTACCAT-
1 AACCAGGTACCTCAGAAGATATGA-AGGGAAAGATTAAGGCCGCAACGACGAACCTGGTACCATA
* **
43532049 GAA-ATGTGATGGGAATGGTTGAGGCCACAACGA-TA
65 GAAGATGTGATGGAAAAAGTTGAGGCCACAA-GAGTA
* * * * * * ** *
43532084 AACCATGTACTTTAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGATAAACCTGGTACCTTAG
1 AACCAGGTACCTCAGAAGATATGAAGGGAAAGATTAAGGCCGCAACGACGAACCTGGTACCATAG
43532149 AA
66 AA
43532151 AACAAGATGC
Statistics
Matches: 207, Mismatches: 45, Indels: 25
0.75 0.16 0.09
Matches are distributed among these distances:
97 2 0.01
98 77 0.37
99 78 0.38
100 45 0.22
101 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (100 bp):
AACCAGGTACCTCAGAAGATATGAAGGGAAAGATTAAGGCCGCAACGACGAACCTGGTACCATAG
AAGATGTGATGGAAAAAGTTGAGGCCACAAGAGTA
Found at i:43532443 original size:41 final size:41
Alignment explanation
Indices: 43532386--43532494 Score: 173
Period size: 41 Copynumber: 2.7 Consensus size: 41
43532376 CATCATCATT
*
43532386 CAGTCTTTTATCCTTAATCAAGAAGGGCAAATTGAAGATTC
1 CAGTCTTTTACCCTTAATCAAGAAGGGCAAATTGAAGATTC
* *
43532427 CAGTCTTTTACCCTTAATTAAGAAGGGCAGATTGAAGATTC
1 CAGTCTTTTACCCTTAATCAAGAAGGGCAAATTGAAGATTC
* *
43532468 AAGTTTTTTACCCTTAATCAAGAAGGG
1 CAGTCTTTTACCCTTAATCAAGAAGGG
43532495 AAGAATAAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (41 bp):
CAGTCTTTTACCCTTAATCAAGAAGGGCAAATTGAAGATTC
Found at i:43532506 original size:41 final size:40
Alignment explanation
Indices: 43532383--43532522 Score: 165
Period size: 41 Copynumber: 3.4 Consensus size: 40
43532373 TTACATCATC
*
43532383 ATTCAGTCTTTTATCCTTAATCAAGAAGGGCAA-ATTGAAG
1 ATTCAGTCTTTTACCCTTAATCAAGAAGGG-AAGATTGAAG
* *
43532423 ATTCCAGTCTTTTACCCTTAATTAAGAAGGGCAGATTGAAG
1 ATT-CAGTCTTTTACCCTTAATCAAGAAGGGAAGATTGAAG
* * *
43532464 ATTCAAGTTTTTTACCCTTAATCAAGAAGGGAAGAATAAAG
1 ATTC-AGTCTTTTACCCTTAATCAAGAAGGGAAGATTGAAG
* *
43532505 ATTCCGATCTCTTACCCT
1 ATTCAG-TCTTTTACCCT
43532523 GATTTTAGAG
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
40 6 0.07
41 79 0.93
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (40 bp):
ATTCAGTCTTTTACCCTTAATCAAGAAGGGAAGATTGAAG
Found at i:43532575 original size:39 final size:38
Alignment explanation
Indices: 43532532--43532627 Score: 122
Period size: 39 Copynumber: 2.5 Consensus size: 38
43532522 TGATTTTAGA
* *
43532532 GCAGATTACCATCAACCAATTTCTTACCCCGAGCTT-GGG
1 GCAGATCACCATCAACCAATCTCTTACCCCGA--TTCGGG
**
43532571 GCAGATCACCATCAGTCAATCTCTTACCCCGATTCCGGG
1 GCAGATCACCATCAACCAATCTCTTACCCCGATT-CGGG
43532610 GCAGATCACCATCAACCA
1 GCAGATCACCATCAACCA
43532628 CCCGATCTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.04
39 47 0.96
ACGTcount: A:0.27, C:0.34, G:0.17, T:0.22
Consensus pattern (38 bp):
GCAGATCACCATCAACCAATCTCTTACCCCGATTCGGG
Found at i:43533091 original size:209 final size:209
Alignment explanation
Indices: 43532725--43533133 Score: 568
Period size: 209 Copynumber: 2.0 Consensus size: 209
43532715 AAAGCGATCT
*
43532725 TCTTCCTGATGAGATACAGAGAAATAAATTAAAACAAGTGATGCGATCATCTTCTTGATGAAATA
1 TCTTCCTGATGAGATACAGAGAAATAAATTAAAACAAGTGATGCGATCATCTTCCTGATGAAATA
* ** * * *
43532790 CTGAGAAGTAAACCAAATCAATGAAACAAAGCTCAATGTGATCGAAACTTCGAACCCCAGCTTCC
66 CAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAACCCAAACTTCC
* ** * *
43532855 TGACAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCGTCTTCCTGATGCGATACAAAGAA
131 TGACAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCACCTTCCTAATGAGATACAAAGAA
43532920 GTGGACCAAATCCA
196 GTGGACCAAATCCA
* * * * * * *
43532934 TCTTCTTGATGAGATACAGAGAAGTAGATTGAAACATGTGATGC-AGTCATCTTCCTGGTGAGAT
1 TCTTCCTGATGAGATACAGAGAAATAAATTAAAACAAGTGATGCGA-TCATCTTCCTGATGAAAT
* *
43532998 ACAGAGAAGTATACCAAATCAATGAAATAAAGCTCAAAATGAGCGAAACTTCGAACCCAAACTTC
65 ACAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAACCCAAACTTC
* ** * *
43533063 TTGATGAGATACTGAGAAGCGGGTCGAAGCAATAAAATGATCACCTTCCTAATGAGATACAGAGA
130 CTGACAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCACCTTCCTAATGAGATACAAAGA
43533128 AGTGGA
195 AGTGGA
43533134 TTAAAACAAA
Statistics
Matches: 173, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
208 1 0.01
209 172 0.99
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (209 bp):
TCTTCCTGATGAGATACAGAGAAATAAATTAAAACAAGTGATGCGATCATCTTCCTGATGAAATA
CAGAGAAGTAAACCAAATCAATGAAACAAAGCTCAAAATGAGCGAAACTTCGAACCCAAACTTCC
TGACAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGATCACCTTCCTAATGAGATACAAAGAA
GTGGACCAAATCCA
Found at i:43545476 original size:17 final size:16
Alignment explanation
Indices: 43545448--43545520 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 16
43545438 GGCTCAACAG
43545448 AATTTATTTAAAATTA
1 AATTTATTTAAAATTA
* *
43545464 AGTTTATTTTAAATTTA
1 AATTTA-TTTAAAATTA
*
43545481 AATTTATTGAAAATTTA
1 AATTTATTTAAAA-TTA
*
43545498 AATTTATTATAAATTTA
1 AATTTATT-TAAAATTA
43545515 AATTTA
1 AATTTA
43545521 AAATACACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
16 10 0.21
17 34 0.72
18 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AATTTATTTAAAATTA
Found at i:43545480 original size:6 final size:6
Alignment explanation
Indices: 43545453--43545522 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
43545443 AACAGAATTT
* * * *
43545453 ATTTAA AATTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTGAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA
43545499 ATTT-- ATTATAA ATTTAA ATTTAA A
1 ATTTAA ATT-TAA ATTTAA ATTTAA A
43545523 ATACACTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
4 6 0.12
5 5 0.10
6 33 0.66
7 6 0.12
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:43545511 original size:34 final size:33
Alignment explanation
Indices: 43545448--43545520 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 33
43545438 GGCTCAACAG
* * *
43545448 AATTTATTTAAAATTAAGTTTATTTTAAATTTA
1 AATTTATTGAAAATTAAATTTATTATAAATTTA
43545481 AATTTATTGAAAATTTAAATTTATTATAAATTTA
1 AATTTATTGAAAA-TTAAATTTATTATAAATTTA
43545515 AATTTA
1 AATTTA
43545521 AAATACACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 12 0.33
34 24 0.67
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
AATTTATTGAAAATTAAATTTATTATAAATTTA
Found at i:43545533 original size:34 final size:33
Alignment explanation
Indices: 43545448--43545534 Score: 79
Period size: 34 Copynumber: 2.6 Consensus size: 33
43545438 GGCTCAACAG
* * *
43545448 AATTTATTTAAAA-TTAAGTTTATTTTAAATTTA
1 AATTTA-TAAAAACTTAAATTTATTATAAATTTA
* *
43545481 AATTTATTGAAAATTTAAATTTATTATAAATTTA
1 AATTTA-TAAAAACTTAAATTTATTATAAATTTA
43545515 AATTTA-AAATACACTTAAAT
1 AATTTATAAA-A-ACTTAAAT
43545535 CATGTCCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.04
33 13 0.28
34 31 0.67
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (33 bp):
AATTTATAAAAACTTAAATTTATTATAAATTTA
Found at i:43546227 original size:10 final size:9
Alignment explanation
Indices: 43546211--43546286 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
43546201 AAATAAAGGC
43546211 ATTAATAAT
1 ATTAATAAT
43546220 AGTTAATAAT
1 A-TTAATAAT
* *
43546230 ATTATTTAT
1 ATTAATAAT
43546239 AATCTAATAAAT
1 -AT-TAAT-AAT
43546251 ATTAATAAT
1 ATTAATAAT
* *
43546260 AATAGTTAAT
1 ATTA-ATAAT
*
43546270 AATAATAAT
1 ATTAATAAT
*
43546279 AATAATAA
1 ATTAATAA
43546287 AGTCAAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
9 25 0.45
10 23 0.42
11 5 0.09
12 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (9 bp):
ATTAATAAT
Found at i:43546261 original size:3 final size:3
Alignment explanation
Indices: 43546243--43546286 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
43546233 ATTTATAATC
* *
43546243 TAA TAAA TAT TAA TAA TAA TAGT TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
43546287 AGTCAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 30 0.86
4 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:43547416 original size:27 final size:26
Alignment explanation
Indices: 43547351--43547451 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 26
43547341 TTAGGAGGTT
43547351 CCTAAACTATCCAGAAATCA-TGTTTTAAAC
1 CCTAAACT-TCCA-AAATCACT-TTTT--AC
43547381 CCTAAACTTTCCAAAATCACTTTTTAC
1 CCTAAAC-TTCCAAAATCACTTTTTAC
*
43547408 CCTAAACTTCCAAAAATTACATTTTTACC
1 CCTAAACTTCC-AAAATCAC-TTTTTA-C
*
43547437 CCTGAACTTCCAAAA
1 CCTAAACTTCCAAAA
43547452 ATTCTATTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.06
27 16 0.25
28 10 0.16
29 21 0.33
30 12 0.19
31 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.32
Consensus pattern (26 bp):
CCTAAACTTCCAAAATCACTTTTTAC
Found at i:43547433 original size:29 final size:28
Alignment explanation
Indices: 43547379--43547788 Score: 167
Period size: 29 Copynumber: 14.2 Consensus size: 28
43547369 CATGTTTTAA
*
43547379 ACCCTAAACTTTCC-AAAATCAC-TTTTT
1 ACCCTAAAC-TTCCAAAAATTACATTTTT
43547406 ACCCTAAACTTCCAAAAATTACATTTTT
1 ACCCTAAACTTCCAAAAATTACATTTTT
*
43547434 ACCCCTGAACTTCCAAAAATT-CTATTTTT
1 A-CCCTAAACTTCCAAAAATTAC-ATTTTT
***
43547463 AACCCTAAAACTTTTGAAAATTACCA-TTTT
1 -ACCCT-AAACTTCCAAAAATTA-CATTTTT
* **
43547493 ACCCCCAAACTTCCAAAAATCCCATTTTT
1 A-CCCTAAACTTCCAAAAATTACATTTTT
* ***
43547522 GACCCCGATTTTTCCAAAAATTACCA-TTTT
1 -A-CCCTAAACTTCCAAAAATTA-CATTTTT
* * * * *
43547552 ACCTTCGAACTTCCTAAAATTCCATTTTA
1 ACCCT-AAACTTCCAAAAATTACATTTTT
* *** *
43547581 ACCCCGATTTTTCCAAAAAATATCA-TTTT
1 A-CCCTAAACTTCCAAAAATTA-CATTTTT
* * *
43547610 ACCCTCGAACTTCCAAAAATTCCCTTTTT
1 ACCCT-AAACTTCCAAAAATTACATTTTT
* * * *
43547639 GACCCTAAATTTTCC-AAGATTCCGTTTTTT
1 -ACCCTAAA-CTTCCAAAAATTAC-ATTTTT
* **
43547669 ACCCTGATTTTCCAAAAATTACATTTTT
1 ACCCTAAACTTCCAAAAATTACATTTTT
* ** *
43547697 ACCCTCGAACTTTCC-AACTTTCCATTTTT
1 ACCCT-AAAC-TTCCAAAAATTACATTTTT
***
43547726 ACCCGCGGA-TGTCCAAAAA-TACATTTTT
1 ACCC-TAAACT-TCCAAAAATTACATTTTT
*
43547754 GACCCTAAAACTTTCAAAAATTACCA-TTTT
1 -ACCCT-AAACTTCCAAAAATTA-CATTTTT
43547784 ACCCT
1 ACCCT
43547789 CGAATATCTA
Statistics
Matches: 283, Mismatches: 68, Indels: 62
0.69 0.16 0.15
Matches are distributed among these distances:
26 4 0.01
27 17 0.06
28 43 0.15
29 145 0.51
30 68 0.24
31 5 0.02
32 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (28 bp):
ACCCTAAACTTCCAAAAATTACATTTTT
Found at i:43547618 original size:58 final size:58
Alignment explanation
Indices: 43547415--43547637 Score: 220
Period size: 59 Copynumber: 3.8 Consensus size: 58
43547405 TACCCTAAAC
* * ** *
43547415 TTCCAAAAATTA-CATTTTTACCC-CTGAACTTCCAAAAATTCTATTTTTAACCCTAAAACTT
1 TTCCAAAAAATACCA-TTTTACCCTC-GAACTTCCAAAAATTCCA-TTTTAACCC--CGATTT
* * * * * *
43547476 TT--GAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCGATTT
1 TTCCAAAAAATACCATTTTACCCTCGAACTTCCAAAAATTCCA-TTTTAACCCCGATTT
* * *
43547533 TTCCAAAAATTACCATTTTACCTTCGAACTTCCTAAAATTCCATTTTAACCCCGATTT
1 TTCCAAAAAATACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCCCGATTT
* *
43547591 TTCCAAAAAATATCATTTTACCCTCGAACTTCCAAAAATTCCCTTTT
1 TTCCAAAAAATACCATTTTACCCTCGAACTTCCAAAAATTCCATTTT
43547638 TGACCCTAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
57 5 0.04
58 56 0.41
59 72 0.52
60 3 0.02
61 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
TTCCAAAAAATACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCCCGATTT
Found at i:43547802 original size:58 final size:57
Alignment explanation
Indices: 43547389--43547904 Score: 281
Period size: 58 Copynumber: 8.9 Consensus size: 57
43547379 ACCCTAAACT
*
43547389 TTCC-AAAAT-CACTTTTT-ACCCT-AAACTTCCAAAAATTA-CATTTTTACCC-CTGAA
1 TTCCAAAAATACA-TTTTTGACCCTCAAACTTTCAAAAATTACCA-TTTTACCCTC-GAA
* * * ** * *
43547443 CTTCCAAAAATTCTATTTTTAACCCTAAAACTTTTGAAAATTACCATTTTACCCCCAAA
1 -TTCCAAAAATAC-ATTTTTGACCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAA
* * ** *
43547502 CTTCCAAAAATCCCATTTTTGACCC-CGATTTTTCCAAAAATTACCATTTTACCTTCGAA
1 -TTCCAAAAAT-ACATTTTTGACCCTCAAACTTT-CAAAAATTACCATTTTACCCTCGAA
* * * * ** * *
43547561 CTTCCTAAAATTCCA-TTTTAACCC-CGATTTTTCCAAAAAATATCATTTTACCCTCGAA
1 -TTCC-AAAAATACATTTTTGACCCTCAAACTTT-CAAAAATTACCATTTTACCCTCGAA
* * * * * * *
43547619 CTTCCAAAAATTCCCTTTTTGACCCT-AAATTTTCCAAGATT-CCGTTTTTTACCCT-GATT
1 -TTCCAAAAA-TACATTTTTGACCCTCAAACTTTCAAAAATTACC--ATTTTACCCTCGA-A
* * * * * *
43547678 TTCCAAAAATTACATTTTT-ACCCTCGAACTTTC-CAACTTTCCATTTTTACCCGCGGA
1 TTCCAAAAA-TACATTTTTGACCCTCAAACTTTCAAAAATTACCA-TTTTACCCTCGAA
*
43547735 TGTCCAAAAATACATTTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCCTCGAA
1 T-TCCAAAAATACATTTTTGACCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAA
* * * * * * * *
43547793 TATCTAAAAACACCATTTTTTATCCTGAATC-TTCCAAAATTACCATTTTACCCTCGGA
1 T-TCCAAAAATA-CATTTTTGACCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAA
* * * *
43547851 TGTCTAAGAATTTCATTTTTGA-CCTCGAACCTTTCAAAAATTACCATTTTACCC
1 T-TCCAA-AAATACATTTTTGACCCTC-AAACTTTCAAAAATTACCATTTTACCC
43547905 CCGAGTGTCT
Statistics
Matches: 368, Mismatches: 66, Indels: 50
0.76 0.14 0.10
Matches are distributed among these distances:
55 4 0.01
56 5 0.01
57 40 0.11
58 172 0.47
59 138 0.38
60 9 0.02
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.37
Consensus pattern (57 bp):
TTCCAAAAATACATTTTTGACCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAA
Found at i:43547946 original size:28 final size:28
Alignment explanation
Indices: 43547887--43547955 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
43547877 GAACCTTTCA
** *
43547887 AAAATTACCATTTTACCCCCGAGTGTCT
1 AAAATTACCATTTTACCCCCGAGCATCC
* *
43547915 AAAATTATCGTTTTACCCCCGAGCATCC
1 AAAATTACCATTTTACCCCCGAGCATCC
*
43547943 AAAATCA-CATTTT
1 AAAATTACCATTTT
43547956 TAACTCCGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.32
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGAGCATCC
Done.