Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 66 of 208
Found at i:19197694 original size:101 final size:100
Alignment explanation
Indices: 19197425--19197856 Score: 476
Period size: 102 Copynumber: 4.2 Consensus size: 100
19197415 TGGTTTAATT
* * * * * *
19197425 TTTTTTATGAATGTAAATTTTTTTTATAATTATTTTAAAATTATTTTTTTAGTAA--TATGATTA
1 TTTTTTATGAATGT-AA-TTTTTTAAAAATTATTTTATAGTTATTTTGTTAATAATTTATGATTA
* *
19197488 TGTTATAATTTGTTTGTGTTTTAGTTTAGTGTTTTGTGA
64 GGTTATAAATTG-TTGTG-TTTAGTTTAGTGTTTTGTGA
* * * * * * *
19197527 -ATTTCATGTAAATTTTTTTTATTTTTT-TAAATTATTTTATAGTTATTTTGTTAATAACTTAAG
1 TTTTTTATG--AA----TGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAATAATTTATG
* *
19197590 ATTAGGTCATAAATTGTTGTGCTTAGTTTAGTGTTTTGTGA
60 ATTAGGTTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGA
* * *
19197631 TTTTTTATTAATGTAATTTTTTAAAAGATTATTTTATAGTTATTTTGCTAGTAATTTATGATTAG
1 TTTTTTATGAATGTAATTTTTTAAAA-ATTATTTTATAGTTATTTTGTTAATAATTTATGATTAG
* * *
19197696 GTTATAAATTGATAGTGTTTAGTTTAGCGTTTTGTAA
65 GTTATAAATTG-TTGTGTTTAGTTTAGTGTTTTGTGA
* *
19197733 TTTTTTATGAATGTAAATTTTTTAAAATTTATTTTATAGTTATTTTGTTATTAATTTATGATTAG
1 TTTTTTATGAATGT-AATTTTTTAAAAATTATTTTATAGTTATTTTGTTAATAATTTATGATTAG
19197798 GTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
65 GTTATAAATTGTT-GTGTTTAGTTTAGTGTTTTGTGA
*
19197835 TTTTTTATGAAAGTAATTTTTT
1 TTTTTTATGAATGTAATTTTTT
19197857 TATAATGTAA
Statistics
Matches: 278, Mismatches: 38, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
99 9 0.03
100 2 0.01
101 59 0.21
102 114 0.41
103 16 0.06
104 43 0.15
105 16 0.06
106 17 0.06
107 2 0.01
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (100 bp):
TTTTTTATGAATGTAATTTTTTAAAAATTATTTTATAGTTATTTTGTTAATAATTTATGATTAGG
TTATAAATTGTTGTGTTTAGTTTAGTGTTTTGTGA
Found at i:19197857 original size:17 final size:16
Alignment explanation
Indices: 19197835--19197870 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19197825 TGTTTTGTGA
19197835 TTTTTTATGAAAGTAAT
1 TTTTTTAT-AAAGTAAT
*
19197852 TTTTTTATAATGTAAT
1 TTTTTTATAAAGTAAT
19197868 TTT
1 TTT
19197871 ATTTGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTTTTATAAAGTAAT
Found at i:19204207 original size:24 final size:26
Alignment explanation
Indices: 19204180--19204228 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
19204170 ATAAACATTA
*
19204180 AACTAAC-AAATAA-TTTATAATAAT
1 AACTAACAAAATAACTTTAAAATAAT
19204204 AACTAACAAAATAACTTTAAAATAA
1 AACTAACAAAATAACTTTAAAATAA
19204229 ATTAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (26 bp):
AACTAACAAAATAACTTTAAAATAAT
Found at i:19204365 original size:4 final size:4
Alignment explanation
Indices: 19204341--19204378 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
19204331 TACATTATTC
19204341 TTCT TT-T TTCT TCTCCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT T-T-CT TTCT TTCT TTCT TTCT TTCT T
19204379 CTTCCTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 3 0.10
4 23 0.74
5 2 0.06
6 3 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:19207534 original size:6 final size:6
Alignment explanation
Indices: 19207525--19207552 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
19207515 TCCAACTCAA
19207525 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAA
19207553 CTGAAACCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.14
Consensus pattern (6 bp):
CAAAAT
Found at i:19207612 original size:6 final size:6
Alignment explanation
Indices: 19207601--19207634 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
19207591 AGAGCAATTT
*
19207601 AAAAGA AAAAGA AAAGGA AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA
19207635 AGAACTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:19209734 original size:124 final size:123
Alignment explanation
Indices: 19209428--19209769 Score: 558
Period size: 123 Copynumber: 2.8 Consensus size: 123
19209418 TTATTTCGAG
* *
19209428 TTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* * *
19209493 AAATCGCGCCCTTGTGGACGCGATTTTACTACAGTAGGTCATGTAAGAAGTAATTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
* * * * *
19209551 TTAATGTTTCTAAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTCAGAAGAAATCGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
19209616 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTT
*
19209675 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
19209740 AAATCGCGCCCTCGTGGACGCGATTTTGCT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCT
19209770 GCAGCAGCAA
Statistics
Matches: 199, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
123 106 0.53
124 93 0.47
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTT
Found at i:19212076 original size:30 final size:29
Alignment explanation
Indices: 19212038--19212306 Score: 363
Period size: 29 Copynumber: 9.3 Consensus size: 29
19212028 CAGTGGTGTC
*
19212038 AGGTTAGGGCAATGGGTTTTTAATTAAATT
1 AGGTTAGGGTAA-GGGTTTTTAATTAAATT
*
19212068 ATGTTAGGGTTAA-GGTTTTTAATTAAATT
1 AGGTTAGGG-TAAGGGTTTTTAATTAAATT
19212097 AGG-T----T-AGGGTTTTTAATTAAATT
1 AGGTTAGGGTAAGGGTTTTTAATTAAATT
* *
19212120 AGGTTAGGGCAGTGGGTTTTTAATTAAATT
1 AGGTTAGGGTA-AGGGTTTTTAATTAAATT
19212150 AGGTTAGGGTTAAGGGTTTTTAATTAAATT
1 AGGTTAGGG-TAAGGGTTTTTAATTAAATT
19212180 AGGTTAGGGTTAAGGGTTTTTAATTAAATT
1 AGGTTAGGG-TAAGGGTTTTTAATTAAATT
*
19212210 AGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTAAGGGTTTTTAATTAAATT
* * *
19212239 AGGTTAGGATTAGGATTTTTAATTAAATT
1 AGGTTAGGGTAAGGGTTTTTAATTAAATT
*
19212268 AGGTTAGGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTAAGGGTTTTTAATTAAATT
19212297 AGGTTAGGGT
1 AGGTTAGGGT
19212307 TTTTAATTAA
Statistics
Matches: 217, Mismatches: 12, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
22 1 0.00
23 20 0.09
24 1 0.00
28 1 0.00
29 101 0.47
30 90 0.41
31 3 0.01
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (29 bp):
AGGTTAGGGTAAGGGTTTTTAATTAAATT
Found at i:19212107 original size:23 final size:23
Alignment explanation
Indices: 19212075--19212322 Score: 136
Period size: 30 Copynumber: 9.1 Consensus size: 23
19212065 ATTATGTTAG
*
19212075 GGTTAAGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
19212098 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
19212121 GGTTAGGGCAGTGGGTTTTTAATTAAATTAGGTTA
1 GGTT-----A--GGGTTTTTAATT-AA--A--TTA
19212156 GGGTTAAGGGTTTTTAATTAAATTAGGTTA
1 -GGTT-AGGGTTTTTAATTAA---A--TTA
19212186 GGGTTAAGGGTTTTTAATTAAATTAGGTTA
1 -GGTT-AGGGTTTTTAATTAA---A--TTA
19212216 GGGTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
19212240 GGTTAGGATTAGGATTTTTAATTAAATTAGGTTA
1 GGTTA-G----GG-TTTTTAATT-AA--A--TTA
19212274 GGGTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGGTTTTTAATTAAATTA
19212298 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
19212321 GG
1 GG
19212323 GTTTTTATTA
Statistics
Matches: 197, Mismatches: 2, Indels: 52
0.78 0.01 0.21
Matches are distributed among these distances:
23 56 0.28
24 7 0.04
26 2 0.01
28 5 0.03
29 35 0.18
30 71 0.36
31 2 0.01
32 2 0.01
33 1 0.01
34 4 0.02
35 8 0.04
36 4 0.02
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.44
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:19212314 original size:18 final size:18
Alignment explanation
Indices: 19212277--19212329 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
19212267 TAGGTTAGGG
19212277 TTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATT-AA--A
19212298 GGTTAGGGTTTTTAATTAAA
1 --TTAGGGTTTTTAATTAAA
19212318 TTAGGGTTTTTA
1 TTAGGGTTTTTA
19212330 TTACATCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 12 0.40
20 1 0.03
22 2 0.07
23 15 0.50
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:19212432 original size:71 final size:71
Alignment explanation
Indices: 19212328--19212512 Score: 307
Period size: 71 Copynumber: 2.6 Consensus size: 71
19212318 TTAGGGTTTT
* * *
19212328 TATTACATCAAATAGAACTTATATTTTATTATATCAAATAATATCAAGATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTT
19212393 CTATGCC
65 CTATGCC
*
19212400 TATTATATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
*
19212465 TATGCG
66 TATGCC
*
19212471 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATA
19212513 AATTTAAATA
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 93 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAACTTC
TATGCC
Found at i:19212505 original size:25 final size:25
Alignment explanation
Indices: 19212400--19212510 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
19212390 TTTCTATGCC
*
19212400 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
* *
19212425 TATTATATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * **
19212446 AATAAC-TCGAAA-AAACTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
19212471 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
19212496 TATTACATCAAATAA
1 TATTACATCAAATAA
19212511 TAAATTTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
20 2 0.03
21 10 0.15
22 2 0.03
23 2 0.03
24 4 0.06
25 35 0.52
26 12 0.18
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:19212941 original size:18 final size:18
Alignment explanation
Indices: 19212914--19212948 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19212904 CGGAAAAGGA
* *
19212914 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
19212932 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
19212949 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:19214735 original size:11 final size:10
Alignment explanation
Indices: 19214705--19214770 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
19214695 GCCATTGATG
*
19214705 AAAATATAAA
1 AAAATTTAAA
19214715 AAAATTTAAA
1 AAAATTTAAA
* *
19214725 ATTATTTTAAA
1 A-AAATTTAAA
*
19214736 AAAATATAAA
1 AAAATTTAAA
19214746 AAAATTTAAA
1 AAAATTTAAA
** *
19214756 ATTATTTTAA
1 AAAATTTAAA
19214766 AAAAT
1 AAAAT
19214771 GAAATTGAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 35 0.81
11 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:19214740 original size:31 final size:31
Alignment explanation
Indices: 19214705--19214769 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
19214695 GCCATTGATG
19214705 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
19214736 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
19214767 AAA
1 AAA
19214770 TGAAATTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:19214752 original size:21 final size:20
Alignment explanation
Indices: 19214705--19214756 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
19214695 GCCATTGATG
* *
19214705 AAAATATAAAAAAATTTAAA
1 AAAATTTAAAAAAATATAAA
* *
19214725 ATTATTTTAAAAAAATATAAA
1 A-AAATTTAAAAAAATATAAA
19214746 AAAATTTAAAA
1 AAAATTTAAAA
19214757 TTATTTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTTAAAAAAATATAAA
Found at i:19214825 original size:40 final size:40
Alignment explanation
Indices: 19214781--19214867 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 40
19214771 GAAATTGAGG
*
19214781 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTAGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
* *
19214821 GGAAATTGAAATTAAATATGGGTTTGAGAGAAATTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
19214861 GGAAATT
1 GGAAATT
19214868 TGGAAGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.44, C:0.00, G:0.25, T:0.31
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTGAGAGAAATTTAGAA
Found at i:19214867 original size:12 final size:12
Alignment explanation
Indices: 19214850--19214875 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19214840 GGGTTTGAGA
19214850 GAAATTTGGAAG
1 GAAATTTGGAAG
19214862 GAAATTTGGAAG
1 GAAATTTGGAAG
19214874 GA
1 GA
19214876 TTAGAGAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GAAATTTGGAAG
Found at i:19215783 original size:13 final size:13
Alignment explanation
Indices: 19215765--19215796 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
19215755 ATGTACCTGG
19215765 ATTTAATAGAGAA
1 ATTTAATAGAGAA
19215778 ATTTAATAGAGAA
1 ATTTAATAGAGAA
*
19215791 TTTTAA
1 ATTTAA
19215797 CAGTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (13 bp):
ATTTAATAGAGAA
Found at i:19217387 original size:13 final size:13
Alignment explanation
Indices: 19217369--19217401 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19217359 AATGGCATAA
19217369 AAATAATATAAAC-
1 AAATAA-ATAAACG
19217382 AAATAAATAAACG
1 AAATAAATAAACG
19217395 AAATAAA
1 AAATAAA
19217402 AAAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAATAAACG
Found at i:19217834 original size:17 final size:19
Alignment explanation
Indices: 19217799--19217839 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
19217789 ATATGTGTAT
*
19217799 ATATATAAATATGAGAAAA
1 ATATATAAATATGAAAAAA
19217818 ATAT-TAAAT-TGAAAAAA
1 ATATATAAATATGAAAAAA
19217835 ATATA
1 ATATA
19217840 ATATGTACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.29
Consensus pattern (19 bp):
ATATATAAATATGAAAAAA
Found at i:19217874 original size:26 final size:27
Alignment explanation
Indices: 19217829--19217880 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
19217819 TATTAAATTG
*
19217829 AAAAAAATATAATATGTACATATATAT
1 AAAAAAATATAATATATACATATATAT
*
19217856 AAAAAAATA-ATTATATACATATATA
1 AAAAAAATATAATATATACATATATA
19217881 GATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAAAAATATAATATATACATATATAT
Found at i:19226060 original size:27 final size:27
Alignment explanation
Indices: 19226024--19226075 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19226014 CGTTTTACAA
* * * *
19226024 TTCATTATTAGGGTTCGTGGTTACCCT
1 TTCATGATTAAGGTTCATGGCTACCCT
19226051 TTCATGATTAAGGTTCATGGCTACC
1 TTCATGATTAAGGTTCATGGCTACC
19226076 ATTCCTAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
TTCATGATTAAGGTTCATGGCTACCCT
Found at i:19229286 original size:46 final size:46
Alignment explanation
Indices: 19229210--19229326 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 46
19229200 TACGTATGAT
* * *
19229210 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
19229254 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
19229300 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
19229327 AGTACTCAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 10 0.15
45 5 0.07
46 53 0.78
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:19230173 original size:28 final size:28
Alignment explanation
Indices: 19230138--19230196 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
19230128 CAGAATTTGG
*
19230138 ATAATATTCTCGTTTATTTATTTTGAAA
1 ATAATATTCTCATTTATTTATTTTGAAA
19230166 ATAATATTCTCATTTATTTATTTTGAAA
1 ATAATATTCTCATTTATTTATTTTGAAA
19230194 ATA
1 ATA
19230197 GACTCATTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.53
Consensus pattern (28 bp):
ATAATATTCTCATTTATTTATTTTGAAA
Found at i:19230202 original size:25 final size:27
Alignment explanation
Indices: 19230145--19230204 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
19230135 TGGATAATAT
* *
19230145 TCTCGTTTATTTATTTTGAAAATAATA
1 TCTCATTTATTTATTTTGAAAATAAGA
19230172 TTCTCATTTATTTATTTTGAAAAT-AGA
1 -TCTCATTTATTTATTTTGAAAATAAGA
19230199 -CTCATT
1 TCTCATT
19230205 CAAGATTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
27 2 0.07
28 22 0.73
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.52
Consensus pattern (27 bp):
TCTCATTTATTTATTTTGAAAATAAGA
Found at i:19235443 original size:20 final size:20
Alignment explanation
Indices: 19235415--19235458 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
19235405 TAAGGTAATA
*
19235415 AAATTGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
19235435 AAATAGTAAGTTCATACTTG
1 AAATAGTAAGTTCATACTTG
19235455 AAAT
1 AAAT
19235459 GGAAAGTGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (20 bp):
AAATAGTAAGTTCATACTTG
Found at i:19235465 original size:20 final size:20
Alignment explanation
Indices: 19235422--19235465 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
19235412 ATAAAATTGT
*
19235422 AAGTTCATACTTGAAATAGT
1 AAGTTCATACTTGAAATAGA
*
19235442 AAGTTCATACTTGAAATGGA
1 AAGTTCATACTTGAAATAGA
19235462 AAGT
1 AAGT
19235466 GATGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
AAGTTCATACTTGAAATAGA
Found at i:19242438 original size:15 final size:16
Alignment explanation
Indices: 19242412--19242441 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19242402 TTTCTTAATA
19242412 TATTACTTTATTTTAT
1 TATTACTTTATTTTAT
19242428 TATTA-TTTATTTTA
1 TATTACTTTATTTTA
19242442 ACATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTACTTTATTTTAT
Found at i:19251117 original size:17 final size:17
Alignment explanation
Indices: 19251095--19251136 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
19251085 ATGTTGAATG
19251095 TGGAAATAAATATGTTT
1 TGGAAATAAATATGTTT
*
19251112 TGGAAAGAAATATGTTT
1 TGGAAATAAATATGTTT
19251129 TGGAAATA
1 TGGAAATA
19251137 CTACTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (17 bp):
TGGAAATAAATATGTTT
Found at i:19251312 original size:24 final size:24
Alignment explanation
Indices: 19251280--19251328 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
19251270 TTATGATGCA
*
19251280 AAAAATAATTGAGAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
19251304 AAAAATAATTGAAAATTCAATTGG
1 AAAAATAATTGAAAATTCAATTGG
19251328 A
1 A
19251329 CACCCATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (24 bp):
AAAAATAATTGAAAATTCAATTGG
Found at i:19252353 original size:21 final size:21
Alignment explanation
Indices: 19252329--19252377 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
19252319 AGCATAGAAG
19252329 ACTGTTATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
*
19252350 ACTGATATCCCAATAGGGCAA
1 ACTGTTATCCCAATAGGGCAA
19252371 ACTGTTA
1 ACTGTTA
19252378 GTGCAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (21 bp):
ACTGTTATCCCAATAGGGCAA
Found at i:19253107 original size:18 final size:18
Alignment explanation
Indices: 19253093--19253135 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
19253083 GAAAATCCTT
19253093 GAAGGATTTAAAATCCCA
1 GAAGGATTTAAAATCCCA
19253111 GAAGGATTTAAAATCCCA
1 GAAGGATTTAAAATCCCA
19253129 GAAGGAT
1 GAAGGAT
19253136 ATAGAGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (18 bp):
GAAGGATTTAAAATCCCA
Found at i:19254379 original size:145 final size:145
Alignment explanation
Indices: 19254116--19254407 Score: 487
Period size: 145 Copynumber: 2.0 Consensus size: 145
19254106 ATCAAAGGTG
* * *
19254116 ACAGAACGAAATGTATTTTACCAAAATTATTCTTTACCCATGATCTTGAGAAAAGAGGTGATATA
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
* *
19254181 AATGTTCAAAAAATTCGTTTTAGTGAGAATTTAGTAGATTTTTTTACTAAGGCATTGCCAACTTC
66 AATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
*
19254246 AACCTTTGAAAGACT
131 AACATTTGAAAGACT
*
19254261 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCTATGATCTTGCA-AAAAGAGGTGATAT
1 ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTG-AGAAAAGAGGTGATAT
* *
19254325 AAATGTTCAACAAATTTGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTT
65 AAATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTT
19254390 CAACATTTGAAAGACT
130 CAACATTTGAAAGACT
19254406 AC
1 AC
19254408 TACACAAGAT
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
145 136 0.99
146 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (145 bp):
ACAGAACGAAACGTATTTCACCAAAATTATTCTTCACCCATGATCTTGAGAAAAGAGGTGATATA
AATGTTCAAAAAATTCGTTCTAGTGAGAATTTAGTAGATCTTTTTACTAAGGCATTGCCAACTTC
AACATTTGAAAGACT
Found at i:19255190 original size:17 final size:17
Alignment explanation
Indices: 19255168--19255220 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
19255158 TTGTTGAAGA
19255168 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
*
19255185 ATCTGTTT-G--TTT-A
1 ATCTGTTTGGATTTTGC
19255198 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
19255215 ATCTGT
1 ATCTGT
19255221 CTGTTGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.27
14 4 0.13
16 4 0.13
17 14 0.47
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (17 bp):
ATCTGTTTGGATTTTGC
Found at i:19255202 original size:30 final size:30
Alignment explanation
Indices: 19255167--19255225 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
19255157 TTTGTTGAAG
*
19255167 AATCTGTTTGGATTTTGCATCTGTTTGTTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTTT
19255197 AATCTGTTTGGATTTTGCATCTGTCTGTT
1 AATCTGTTTGGATTTTGCATCTGTCTGTT
19255226 GAAGAATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.54
Consensus pattern (30 bp):
AATCTGTTTGGATTTTGCATCTGTCTGTTT
Found at i:19258398 original size:18 final size:19
Alignment explanation
Indices: 19258361--19258412 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
19258351 AATATGGGAA
*
19258361 ATGTATGTGTATTCTAAAAT
1 ATGTATGTATATT-TAAAAT
19258381 ATGTATGTATATTT-AAAT
1 ATGTATGTATATTTAAAAT
* *
19258399 ATATATGTACATTT
1 ATGTATGTATATTT
19258413 GTAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.55
19 1 0.03
20 12 0.41
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (19 bp):
ATGTATGTATATTTAAAAT
Found at i:19258543 original size:3 final size:3
Alignment explanation
Indices: 19258535--19258635 Score: 150
Period size: 3 Copynumber: 33.7 Consensus size: 3
19258525 TGTACATGAA
* *
19258535 AAT AAT AAT TAC AAT -AT CAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
19258580 AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19258628 AAT AAT AA
1 AAT AAT AA
19258636 GGAGAAAATA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 84 0.95
4 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19260981 original size:32 final size:32
Alignment explanation
Indices: 19260942--19261034 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
19260932 TTAGATATTG
19260942 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
19260974 ATTATGTTTTAAGCTTGTTGGATATTCAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
19261006 ATTATGTTTTAAGCTTGTTAGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
19261035 ATGATTGACA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:19262442 original size:19 final size:19
Alignment explanation
Indices: 19262396--19262444 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
19262386 CATCCAAACA
19262396 CCAGAAAAGTAAATCATTTT
1 CCAGAAAA-TAAATCATTTT
** *
19262416 AAAAAAAATAAATCATTTT
1 CCAGAAAATAAATCATTTT
19262435 CCAGAAAATA
1 CCAGAAAATA
19262445 TTTCACTAGC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (19 bp):
CCAGAAAATAAATCATTTT
Found at i:19266460 original size:22 final size:22
Alignment explanation
Indices: 19266428--19266474 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
19266418 GTCTCTATCT
19266428 TGAGGTATTTCAATTTTTTGAC
1 TGAGGTATTTCAATTTTTTGAC
*
19266450 TGAGGTTTTTCAATTTTTTGAC
1 TGAGGTATTTCAATTTTTTGAC
19266472 TGA
1 TGA
19266475 ATGCTAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (22 bp):
TGAGGTATTTCAATTTTTTGAC
Found at i:19269631 original size:72 final size:72
Alignment explanation
Indices: 19269514--19269659 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 72
19269504 TGGGGATTTG
* *
19269514 ATCTTTCAAATTAGTACACAAAATTTCAGAGAATATTTACTTTCTTTCCTAAGGAT-GGATATTA
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTT-CTAAGGATGGGATATTA
19269578 GAAAAGAT
65 GAAAAGAT
* *
19269586 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATGTTTGCTTTCTTTCTAAGGATGGGATATTAG
1 ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
19269651 AAAAGAT
66 AAAAGAT
19269658 AT
1 AT
19269660 TTTGTGTGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 8 0.12
72 61 0.88
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (72 bp):
ATCTTCCAAATTAGCACACAAAATTTCAGAGAATATTTACTTTCTTTCTAAGGATGGGATATTAG
AAAAGAT
Found at i:19278017 original size:48 final size:48
Alignment explanation
Indices: 19277946--19278042 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
19277936 TACCTTCAAA
*
19277946 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCTATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
*
19277994 GCACACACCACCACTACTATTCAATTTAAATCTAGTTGCCTTTCCATT
1 GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
19278042 G
1 G
19278043 TTCAATTTGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (48 bp):
GCACACACCACCACTACTATTCAATTTAAATCTACTTGCCTTTCCATT
Found at i:19285095 original size:19 final size:19
Alignment explanation
Indices: 19285061--19285101 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
19285051 ATACATTTAT
*
19285061 AAACATGAAAACAAATATTA
1 AAACAAGAAAACAAATA-TA
19285081 AAACAAGAAAA-AAATATA
1 AAACAAGAAAACAAATATA
19285099 AAA
1 AAA
19285102 TGATACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 5 0.25
20 10 0.50
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (19 bp):
AAACAAGAAAACAAATATA
Found at i:19285363 original size:23 final size:24
Alignment explanation
Indices: 19285308--19285382 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 24
19285298 AAGTAGCACC
* *
19285308 AAAATAGCATAAAAACAACATAAA
1 AAAATAGCATACAAACAACACAAA
* *
19285332 AATACAGCA-ACAAACAACACAAA
1 AAAATAGCATACAAACAACACAAA
* *
19285355 AAAATAGCATCACTAACAACACCAA
1 AAAATAGCAT-ACAAACAACACAAA
19285380 AAA
1 AAA
19285383 CCTGCAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 19 0.46
24 7 0.17
25 15 0.37
ACGTcount: A:0.65, C:0.21, G:0.04, T:0.09
Consensus pattern (24 bp):
AAAATAGCATACAAACAACACAAA
Found at i:19285427 original size:24 final size:23
Alignment explanation
Indices: 19285391--19285437 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
19285381 AACCTGCAAA
19285391 ATATAATCAACCAACCAAAATAT
1 ATATAATCAACCAACCAAAATAT
* * *
19285414 ATATACATTAACCAATCAACATAT
1 ATATA-ATCAACCAACCAAAATAT
19285438 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (23 bp):
ATATAATCAACCAACCAAAATAT
Found at i:19290658 original size:29 final size:29
Alignment explanation
Indices: 19290626--19290695 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
19290616 GAACAAACCA
* *
19290626 AAACAAAATAGAGTACAACAACACATTTC
1 AAACAAAATAGAGCACAACAACACAATTC
* * *
19290655 AAACAGAACAGAGCAGAACAACACAATTC
1 AAACAAAATAGAGCACAACAACACAATTC
19290684 AAACAAAATAGA
1 AAACAAAATAGA
19290696 ACCGAATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.11
Consensus pattern (29 bp):
AAACAAAATAGAGCACAACAACACAATTC
Found at i:19294719 original size:29 final size:29
Alignment explanation
Indices: 19294661--19294752 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 29
19294651 TGTATAGCTG
* *
19294661 GCCCGTATGACTCCACACAGTCC-AACACAC
1 GCCCGTATGTC-CCACACAG-CCTGACACAC
* * *
19294691 GCCCGTATGTCCCACACTGCTTGAGACAC
1 GCCCGTATGTCCCACACAGCCTGACACAC
*
19294720 GCCCGTGTGTCCCACACAGCCTGACACAC
1 GCCCGTATGTCCCACACAGCCTGACACAC
19294749 GCCC
1 GCCC
19294753 ATGTCACCTG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.02
29 41 0.79
30 10 0.19
ACGTcount: A:0.23, C:0.43, G:0.18, T:0.15
Consensus pattern (29 bp):
GCCCGTATGTCCCACACAGCCTGACACAC
Found at i:19302810 original size:25 final size:25
Alignment explanation
Indices: 19302768--19302822 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19302758 ACGAGCTGTT
* *
19302768 ATATACAGAAAACTCCACAAATGCA
1 ATATACAGAAAACGCCACAAAGGCA
**
19302793 ATATACAGAGTACGCCACAAAGGCA
1 ATATACAGAAAACGCCACAAAGGCA
19302818 ATATA
1 ATATA
19302823 ATGCCACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (25 bp):
ATATACAGAAAACGCCACAAAGGCA
Found at i:19302830 original size:19 final size:20
Alignment explanation
Indices: 19302806--19302891 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
19302796 TACAGAGTAC
* *
19302806 GCCACAAAGGC-AATATAAT
1 GCCACAAAGGCTAACAAAAT
*
19302825 GCCACAATGGCTAACAAAAT
1 GCCACAAAGGCTAACAAAAT
*
19302845 GTCACAAAGGCCTAATCAAAAT
1 GCCACAAAGG-CTAA-CAAAAT
* *
19302867 ACGCCATAAAGACTAACAAAAT
1 --GCCACAAAGGCTAACAAAAT
19302889 GCC
1 GCC
19302892 CCCAAGCACC
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.19
20 17 0.31
21 4 0.07
22 12 0.22
23 4 0.07
24 7 0.13
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.15
Consensus pattern (20 bp):
GCCACAAAGGCTAACAAAAT
Found at i:19306725 original size:88 final size:88
Alignment explanation
Indices: 19306630--19306810 Score: 362
Period size: 88 Copynumber: 2.1 Consensus size: 88
19306620 CTCTCAATGA
19306630 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
1 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
19306695 CTAACTAGCAAAGCAAACCTACT
66 CTAACTAGCAAAGCAAACCTACT
19306718 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
1 GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
19306783 CTAACTAGCAAAGCAAACCTACT
66 CTAACTAGCAAAGCAAACCTACT
19306806 GGTAA
1 GGTAA
19306811 AACTAATTCA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 93 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (88 bp):
GGTAAGAATTAATCTTGTGAGTCTTTTAAAAATGTTTATATCAACCAATCAAAATGTGTAAGAAT
CTAACTAGCAAAGCAAACCTACT
Found at i:19313303 original size:17 final size:17
Alignment explanation
Indices: 19313263--19313303 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
19313253 TCAACCCACA
19313263 ATTTTTTTTAATTTTCT
1 ATTTTTTTTAATTTTCT
19313280 -TTCTTTTTT-ATATTTCT
1 ATT-TTTTTTAAT-TTTCT
19313297 ATTTTTT
1 ATTTTTT
19313304 ATTTTTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.19
17 15 0.71
18 2 0.10
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTTTAATTTTCT
Found at i:19314090 original size:18 final size:18
Alignment explanation
Indices: 19314067--19314101 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19314057 TAGGCTAACT
19314067 AAGTATATTGAAACTCTC
1 AAGTATATTGAAACTCTC
19314085 AAGTATATTGAAACTCT
1 AAGTATATTGAAACTCT
19314102 AATTAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (18 bp):
AAGTATATTGAAACTCTC
Found at i:19318159 original size:91 final size:89
Alignment explanation
Indices: 19317972--19318143 Score: 231
Period size: 91 Copynumber: 1.9 Consensus size: 89
19317962 ATTAAGCCCC
* * * * *
19317972 TTTTTTTTCACTCAATTGGATAGTTGAATTTTCAAAATGCATCAAAAAAGCTCTCAAACTTTTTC
1 TTTTTTTACACTCAATTGGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTTC
*
19318037 AAAAAAAAAACAATTAAGCCTTTATT
66 --AAAAAAAACAATTAAGCCTTTATG
* *
19318063 TTTTTTTACACTCAATTAGG-TACTTGAACTGTCAAAATGCATAAAAAAAGTTCTCAAAGTTTTT
1 TTTTTTTACACTCAATT-GGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTT
19318127 C-AAAAAAACAATTAAGC
65 CAAAAAAAACAATTAAGC
19318144 TCATGCTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
88 16 0.22
91 55 0.75
92 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (89 bp):
TTTTTTTACACTCAATTGGATACTTGAACTGTCAAAATGCATAAAAAAAGCTCTCAAACTTTTTC
AAAAAAAACAATTAAGCCTTTATG
Found at i:19318318 original size:10 final size:10
Alignment explanation
Indices: 19318305--19318351 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
19318295 AGAAAATTTG
19318305 TAAAAATTAA
1 TAAAAATTAA
**
19318315 TAAATTTTAA
1 TAAAAATTAA
19318325 TAAAAATTAGA
1 TAAAAATTA-A
*
19318336 -AAAAATTTA
1 TAAAAATTAA
19318345 TAAAAAT
1 TAAAAAT
19318352 CATAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 1 0.03
10 28 0.93
11 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:19318356 original size:29 final size:29
Alignment explanation
Indices: 19318324--19318397 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
19318314 ATAAATTTTA
19318324 ATAAAAATTAGAAAAAATTTATAAAAATC
1 ATAAAAATTAGAAAAAATTTATAAAAATC
* ** *
19318353 ATAAAAAAATA-TTAAATTTTATAAAAATC
1 AT-AAAAATTAGAAAAAATTTATAAAAATC
19318382 ATAAAATATATAGAAA
1 ATAAAA-AT-TAGAAA
19318398 TGTATAGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
28 4 0.12
29 20 0.59
30 9 0.26
31 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
ATAAAAATTAGAAAAAATTTATAAAAATC
Found at i:19318358 original size:20 final size:20
Alignment explanation
Indices: 19318285--19318360 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
19318275 AATGATAAAA
*
19318285 ATAAAAATCA-AGAAAATTT
1 ATAAAAATCATAAAAAATTT
* *
19318304 GTAAAAAT--TAATAAATTTT
1 ATAAAAATCATAA-AAAATTT
* *
19318323 AATAAAAATTAGAAAAAATTT
1 -ATAAAAATCATAAAAAATTT
19318344 ATAAAAATCATAAAAAA
1 ATAAAAATCATAAAAAA
19318361 ATATTAAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 22 0.50
21 6 0.14
22 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAAAAATCATAAAAAATTT
Found at i:19318403 original size:28 final size:29
Alignment explanation
Indices: 19318337--19318437 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
19318327 AAAATTAGAA
19318337 AAAATTTATAAAAATCATAAAAAAATATT
1 AAAATTTATAAAAATCATAAAAAAATATT
* *
19318366 AAATTTTATAAAAATCAT-AAAATATA-T
1 AAAATTTATAAAAATCATAAAAAAATATT
* *
19318393 AGAAATGTATAGAAAT-ATAGAAAAGAATATAT
1 A-AAATTTATAAAAATCATA-AAAA-AATAT-T
19318425 AAAATTTTATAAA
1 AAAA-TTTATAAA
19318438 GTCGTAAGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
27 4 0.07
28 18 0.32
29 21 0.37
30 3 0.05
31 3 0.05
32 8 0.14
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAATTTATAAAAATCATAAAAAAATATT
Found at i:19318462 original size:11 final size:11
Alignment explanation
Indices: 19318446--19318498 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 11
19318436 AAGTCGTAAG
19318446 AAAATGATAAA
1 AAAATGATAAA
19318457 AAAATG-TAAA
1 AAAATGATAAA
19318467 AAAAT-AT-AA
1 AAAATGATAAA
* *
19318476 AATACG-TAAA
1 AAAATGATAAA
*
19318486 AAAATTATAAA
1 AAAATGATAAA
19318497 AA
1 AA
19318499 TTATCATACC
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
9 6 0.18
10 15 0.45
11 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.21
Consensus pattern (11 bp):
AAAATGATAAA
Found at i:19318466 original size:10 final size:10
Alignment explanation
Indices: 19318441--19318499 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
19318431 TTATAAAGTC
*
19318441 GTAAGAAAAT
1 GTAAAAAAAT
19318451 GATAAAAAAAT
1 G-TAAAAAAAT
19318462 GTAAAAAAAT
1 GTAAAAAAAT
* * *
19318472 AT-AAAATAC
1 GTAAAAAAAT
19318481 GTAAAAAAAT
1 GTAAAAAAAT
*
19318491 -TATAAAAAT
1 GTAAAAAAAT
19318500 TATCATACCA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
GTAAAAAAAT
Found at i:19318475 original size:20 final size:20
Alignment explanation
Indices: 19318440--19318498 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
19318430 TTTATAAAGT
*
19318440 CGTAAGAAAATGATAAAAAAA
1 CGTAAAAAAAT-ATAAAAAAA
* *
19318461 TGTAAAAAAATAT-AAAATA
1 CGTAAAAAAATATAAAAAAA
19318480 CGTAAAAAAATTATAAAAA
1 CGTAAAAAAA-TATAAAAA
19318499 TTATCATACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 14 0.44
20 5 0.16
21 13 0.41
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.20
Consensus pattern (20 bp):
CGTAAAAAAATATAAAAAAA
Found at i:19318723 original size:20 final size:20
Alignment explanation
Indices: 19318700--19318738 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19318690 TTTTTTATGA
19318700 TTTTCATAAAATTTTACAAC
1 TTTTCATAAAATTTTACAAC
* * *
19318720 TTTTTATATATTTTTACAA
1 TTTTCATAAAATTTTACAA
19318739 TTGATATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTCATAAAATTTTACAAC
Found at i:19318796 original size:19 final size:19
Alignment explanation
Indices: 19318759--19318824 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
19318749 TTCTAATTTT
*
19318759 TAATTTTTATTAAAATTTAA
1 TAATTTTTA-TAAATTTTAA
*
19318779 TAATTTTTATAAATTTTAT
1 TAATTTTTATAAATTTTAA
* * * * *
19318798 TGATTATTATTATTTTTTA
1 TAATTTTTATAAATTTTAA
19318817 TAATTTTT
1 TAATTTTT
19318825 GTTACACGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 27 0.75
20 9 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TAATTTTTATAAATTTTAA
Found at i:19320564 original size:96 final size:96
Alignment explanation
Indices: 19320190--19320544 Score: 586
Period size: 96 Copynumber: 3.7 Consensus size: 96
19320180 GCCTTATCCT
* * * *
19320190 ACAACGGAACCCCAATACTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
19320255 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
19320286 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
19320351 CAGGCTTGACATGGGGCTTTCTGGTTGTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
*
19320382 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACATGGAAGATTCTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
*
19320447 CAGGCTTGACGTGGGGCTTTCTGG-CGCTGAA
66 CAGGCTTGACGTGGGGCTTTCTGGTTG-TGAA
* * * * *
19320478 ACAAAGGAACGTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATATAGGGAAAATTTTGAGAC
1 ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
19320543 CA
66 CA
19320545 AGTTTGATGT
Statistics
Matches: 245, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
95 1 0.00
96 244 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (96 bp):
ACAAAGGAACCTCAGTATTGTTCTCTTAATGAAGTGTCCTATGAATACACGGAAGATTCTGAGAC
CAGGCTTGACGTGGGGCTTTCTGGTTGTGAA
Found at i:19326960 original size:30 final size:30
Alignment explanation
Indices: 19326924--19326983 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19326914 TATTTTATTA
19326924 TTAATTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
*
19326954 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
19326984 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:19327139 original size:12 final size:12
Alignment explanation
Indices: 19327110--19327141 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
19327100 ATATATTTTT
19327110 AAATT-ATATAA
1 AAATTAATATAA
19327121 AAA-TAATATAA
1 AAATTAATATAA
19327132 AAATTAATAT
1 AAATTAATAT
19327142 GGGCAGGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 12 0.63
12 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:19332092 original size:43 final size:42
Alignment explanation
Indices: 19332042--19332140 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
19332032 TCCCAGACGT
* * *
19332042 GGTCTTACATGTAATCAAATAACGATGCCACTGTCCCAAACAG
1 GGTCTTACAAGTAATCAAAT-ACGACGCCAATGTCCCAAACAG
* * * * *
19332085 GGTCTTACACGTAATCATATACGGCGCCAATGTCCCAGACAT
1 GGTCTTACAAGTAATCAAATACGACGCCAATGTCCCAAACAG
19332127 GGTCTTACAAGTAA
1 GGTCTTACAAGTAA
19332141 ATCTCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 30 0.62
43 18 0.38
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (42 bp):
GGTCTTACAAGTAATCAAATACGACGCCAATGTCCCAAACAG
Found at i:19332132 original size:42 final size:43
Alignment explanation
Indices: 19332026--19332179 Score: 134
Period size: 43 Copynumber: 3.6 Consensus size: 43
19332016 TCGTACAACA
* * * *
19332026 CCAACGTCCCAGACGTGGTCTTACATGTAATCAAATAACGATG
1 CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
* * * * * *
19332069 CCACTGTCCCAAACAGGGTCTTACACGTAATCATAT-ACGGCG
1 CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
* *
19332111 CCAATGTCCCAGACATGGTCTTACAAGTAAATCTCAAAT--TGATG
1 CCAATGTCCCAGACATGGTCTTACAAGT-AA--TCAAATAACGACG
* *
19332155 CCAACGTCCCAGACGTGGTCTTACA
1 CCAATGTCCCAGACATGGTCTTACA
19332180 CGATATCACA
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
42 28 0.31
43 31 0.35
44 25 0.28
45 5 0.06
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (43 bp):
CCAATGTCCCAGACATGGTCTTACAAGTAATCAAATAACGACG
Found at i:19334293 original size:2 final size:2
Alignment explanation
Indices: 19334288--19334329 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19334278 TTATACAAAT
19334288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19334330 GTAANNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19334441 original size:2 final size:2
Alignment explanation
Indices: 19334434--19334499 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
19334424 NNNNNNNNNN
19334434 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19334475 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19334500 TGAAAGTAGG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19343765 original size:44 final size:44
Alignment explanation
Indices: 19343702--19343794 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
19343692 AGAAATATCC
*
19343702 AAGACCACAGAGAATGAAAGCTTTTCTTGGTTAGCCTTTAAGTA
1 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
19343746 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
1 AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
19343790 AAGAC
1 AAGAC
19343795 TTCTTACAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGACCACAGAGAATGAAAGCTTTTCTTGGTAAGCCTTTAAGTA
Found at i:19346186 original size:23 final size:22
Alignment explanation
Indices: 19346143--19346186 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
19346133 TTTCAAGTCA
19346143 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
19346166 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
19346187 TTAATCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:19346418 original size:51 final size:50
Alignment explanation
Indices: 19346360--19346499 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 50
19346350 CCGGTTCACA
*
19346360 TAGTAGCCTACACATAGTACTACACATGTGACCATCACTATCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACT-TCTGATACACG
* * *
19346411 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-TTTTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACC-ATCACTTCTGATACACG
* *
19346461 TAGTAGCCTGCACAT-GTACTACACACGTAACCATCACTT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTT
19346500 TCACTTTCAC
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
48 4 0.05
49 16 0.20
50 24 0.30
51 32 0.40
52 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTTCTGATACACG
Found at i:19361263 original size:15 final size:15
Alignment explanation
Indices: 19361243--19361301 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
19361233 AAAATATTTG
19361243 AAATATTTTAATATA
1 AAATATTTTAATATA
*
19361258 AAATA-TTTAATTTCA
1 AAATATTTTAATAT-A
*
19361273 AAATATAATTTAAAATA
1 AAATAT--TTTAATATA
19361290 AAATATTTTAAT
1 AAATATTTTAAT
19361302 TAATTTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 7 0.19
15 16 0.44
17 7 0.19
18 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTTAATATA
Found at i:19361362 original size:24 final size:24
Alignment explanation
Indices: 19361335--19361419 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 24
19361325 ATTAACAATA
19361335 TTATTAAATTATATATTATTATTT
1 TTATTAAATTATATATTATTATTT
* *
19361359 TTATTAAATTATAT-TTAATAATT
1 TTATTAAATTATATATTATTATTT
* *
19361382 ATATTAAA--ATATGATTAAATTGTTTT
1 TTATTAAATTATAT-ATT--ATT-ATTT
19361408 TTATTAAATTAT
1 TTATTAAATTAT
19361420 TTTTAATAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
21 4 0.09
23 16 0.34
24 14 0.30
25 2 0.04
26 9 0.19
28 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTATTAAATTATATATTATTATTT
Found at i:19365541 original size:70 final size:71
Alignment explanation
Indices: 19365433--19365586 Score: 204
Period size: 70 Copynumber: 2.2 Consensus size: 71
19365423 AGAGTATCCT
* * * * * * * *
19365433 GATATCAACACCTTGGAATTGCGATACCTTTAATAGTATTGAAGAATGGAGACA-TCTTTAGTGG
1 GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
19365497 TATCGC
66 TATCGC
* *
19365503 GATATCCACACTTTGGAATCGTGATACCTCTAACAGTATTGAAGAATGGGGACACCCTTCAATGG
1 GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
19365568 TATCGC
66 TATCGC
19365574 GATATCCAC-CTTT
1 GATATCCACACTTT
19365587 CCAAAAAGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 51 0.70
71 22 0.30
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (71 bp):
GATATCCACACTTTGGAATCGCGATACCTCTAACAGTATTGAAGAATGGAGACACCCTTCAATGG
TATCGC
Found at i:19365672 original size:22 final size:22
Alignment explanation
Indices: 19365619--19365673 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
19365609 CACTGCCTAA
*
19365619 GGTATCGTGATATCCTCTTATG
1 GGTATCGCGATATCCTCTTATG
*** * *
19365641 AAAATTGCGATATCTTCTTATG
1 GGTATCGCGATATCCTCTTATG
19365663 GGTATCGCGAT
1 GGTATCGCGAT
19365674 GTAACAACCC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (22 bp):
GGTATCGCGATATCCTCTTATG
Found at i:19368311 original size:13 final size:13
Alignment explanation
Indices: 19368293--19368317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19368283 TAACTTATAT
19368293 GTGTGAAAATTTC
1 GTGTGAAAATTTC
19368306 GTGTGAAAATTT
1 GTGTGAAAATTT
19368318 TATCGTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:19369535 original size:43 final size:44
Alignment explanation
Indices: 19369433--19369549 Score: 118
Period size: 43 Copynumber: 2.7 Consensus size: 44
19369423 TGAGTTATCG
* *
19369433 TGTAAGACCACGTCT-GGG-ATGTTGGCATGGAATTGAGATTTACG
1 TGTAAGACCACGTCTGGGGCA-G-TGGCATTGAATTGAGATTTACA
*
19369477 TGTAAGACC-CTGTCTGGGGCAGTGGCATTGATATT-TGA-TTACA
1 TGTAAGACCAC-GTCTGGGGCAGTGGCATTGA-ATTGAGATTTACA
* *
19369520 TGTAAGACCACGTCTGGGACATTGGCATTG
1 TGTAAGACCACGTCTGGGGCAGTGGCATTG
19369550 TACGAGCTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
43 31 0.49
44 24 0.38
45 7 0.11
46 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGGCAGTGGCATTGAATTGAGATTTACA
Found at i:19384352 original size:26 final size:25
Alignment explanation
Indices: 19384323--19384394 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
19384313 AACACGTCAG
19384323 AAAAGGAAGCCATTGTGGCATAATAC
1 AAAAGGAAGCC-TTGTGGCATAATAC
*
19384349 AAAAGGAAGCCTTTGTGGCATAATAT
1 AAAAGGAAGCC-TTGTGGCATAATAC
*
19384375 AAAAGAAAGCCTCTGTGGCA
1 AAAAGGAAGCCT-TGTGGCA
19384395 AAACTCGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
25 1 0.02
26 41 0.98
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (25 bp):
AAAAGGAAGCCTTGTGGCATAATAC
Found at i:19387030 original size:3 final size:3
Alignment explanation
Indices: 19387022--19387088 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
19387012 AAAGTACAGA
*
19387022 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19387070 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
19387089 GGTGATAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19392316 original size:43 final size:43
Alignment explanation
Indices: 19392247--19392388 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 43
19392237 TTTTTCACAT
* *
19392247 AAACGCCGCTATAGATCAT-TACCTTTAGCAGCGCTTTTATATC
1 AAACACCGCTAAAGATCATGT-CCTTTAGCAGCGCTTTTATATC
* * * * *
19392290 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAAC
1 AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTATATC
* * * * *
19392333 AAACACCACTAAAGAACATGACCTTTAGCAGCACTTTTTTCAT-
1 AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTAT-ATC
19392376 AAACACCGCTAAA
1 AAACACCGCTAAA
19392389 AGTACTGTTC
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
43 79 0.98
44 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
AAACACCGCTAAAGATCATGTCCTTTAGCAGCGCTTTTATATC
Found at i:19392402 original size:43 final size:43
Alignment explanation
Indices: 19392269--19392402 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 43
19392259 AGATCATTAC
* *
19392269 CTTTAGCAGCGCTTTTATATCAAACGCCGCTAAAGGT-CATGTT
1 CTTTAGCAGCGCTTTTATAT-AAACACCGCTAAAAGTACATGTT
* * * * **
19392312 CTTTAGCGGCGCTTTTATAACAAACACCACT-AAAGAACATGAC
1 CTTTAGCAGCGCTTTTAT-ATAAACACCGCTAAAAGTACATGTT
* *
19392355 CTTTAGCAGCACTTTTTTCATAAACACCGCTAAAAGTAC-TGTT
1 CTTTAGCAGCGCTTTTAT-ATAAACACCGCTAAAAGTACATGTT
19392398 CTTTA
1 CTTTA
19392403 ACGGCGTTTT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 3 0.04
43 61 0.86
44 7 0.10
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (43 bp):
CTTTAGCAGCGCTTTTATATAAACACCGCTAAAAGTACATGTT
Found at i:19397230 original size:9 final size:9
Alignment explanation
Indices: 19397216--19397706 Score: 180
Period size: 9 Copynumber: 53.9 Consensus size: 9
19397206 TAAGTATAAT
19397216 TAAGTTATG
1 TAAGTTATG
19397225 TAAGTTATG
1 TAAGTTATG
19397234 TAAGTTATG
1 TAAGTTATG
*
19397243 -ATA-TTATA
1 TA-AGTTATG
*
19397251 TATATTTATG
1 TA-AGTTATG
19397261 TAAGTTA--
1 TAAGTTATG
19397268 TAAG-TATG
1 TAAGTTATG
19397276 ATTAAGTTATG
1 --TAAGTTATG
*
19397287 TAAGCTATG
1 TAAGTTATG
* * *
19397296 ATATGATATA
1 -TAAGTTATG
*
19397306 T-ATTTATG
1 TAAGTTATG
19397314 T-A-TTATG
1 TAAGTTATG
19397321 TAAGTTATG
1 TAAGTTATG
19397330 TAAGTTATG
1 TAAGTTATG
*
19397339 TGAGTT-TCG
1 TAAGTTAT-G
19397348 TAAGTTATG
1 TAAGTTATG
* * *
19397357 ATATGATATA
1 -TAAGTTATG
*
19397367 TATG-TA--
1 TAAGTTATG
19397373 TAAGTTAT-
1 TAAGTTATG
19397381 TAAGTTATG
1 TAAGTTATG
19397390 TAAGTTATG
1 TAAGTTATG
* *
19397399 TGAGTTATCA
1 TAAGTTAT-G
* *
19397409 TATGATATATA
1 TAAG-T-TATG
* *
19397420 TAAGTAATT
1 TAAGTTATG
19397429 TAAGAATTTTATG
1 TAAG----TTATG
*
19397442 TATG-TATG
1 TAAGTTATG
*
19397450 TGAGTTATG
1 TAAGTTATG
19397459 TAAGTTATG
1 TAAGTTATG
19397468 TAAGTTATG
1 TAAGTTATG
* *
19397477 TATTTGTTTTG
1 TA--AGTTATG
19397488 TAAGTTATGG
1 TAAGTTAT-G
* *
19397498 TATGATATATA
1 TAAG-T-TATG
19397509 TAAGTTAT-
1 TAAGTTATG
19397517 TAAGTTATG
1 TAAGTTATG
*
19397526 TGAGTTATG
1 TAAGTTATG
* *
19397535 AAATGATATATA
1 TAA-G-T-TATG
19397547 TAAGTTAT-
1 TAAGTTATG
19397555 TAAGTTATG
1 TAAGTTATG
*
19397564 TATG-TATG
1 TAAGTTATG
*
19397572 TGAGTTATG
1 TAAGTTATG
19397581 TAAGTTATG
1 TAAGTTATG
* * *
19397590 ATATGATATA
1 -TAAGTTATG
*
19397600 T-ATTTATG
1 TAAGTTATG
* *
19397608 -CA-TTTTG
1 TAAGTTATG
19397615 TAAGTTATG
1 TAAGTTATG
19397624 TAAGTTATGTG
1 TAAGTTA--TG
** *
19397635 TTCGTTTTG
1 TAAGTTATG
19397644 TAAGTTATGG
1 TAAGTTAT-G
* *
19397654 TATGATATATA
1 TAAG-T-TATG
*
19397665 TAAGTTA-A
1 TAAGTTATG
19397673 TAAGTTATG
1 TAAGTTATG
*
19397682 TATG-TATG
1 TAAGTTATG
* *
19397690 TGAGTTATT
1 TAAGTTATG
19397699 TAAGTTAT
1 TAAGTTAT
19397707 TATCTGATAT
Statistics
Matches: 364, Mismatches: 71, Indels: 94
0.69 0.13 0.18
Matches are distributed among these distances:
6 5 0.01
7 16 0.04
8 69 0.19
9 178 0.49
10 44 0.12
11 32 0.09
12 14 0.04
13 6 0.02
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:19397325 original size:53 final size:52
Alignment explanation
Indices: 19397216--19397420 Score: 200
Period size: 53 Copynumber: 3.8 Consensus size: 52
19397206 TAAGTATAAT
* *
19397216 TAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTTA
1 TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
19397268 TAAG-TATGATTAAGTTATGTAAGCTATGATATGATATATATTTATGT-A-TTA
1 TAAGTTATG--TAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
* * * *
19397319 TGTAAGTTATGTAAGTTATGTGAGTTTCGTAAGTTATGATATGATATATATGTATAAGTTA
1 --TAAGTTATGTAAGTTATGTAAG---C-TATGATATGATAT-ATATTTATG--TAAGTTA
* * *
19397380 TTAAGTTATGTAAGTTATGTGAGTTATCATATGATATATAT
1 -TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATAT
19397421 AAGTAATTTA
Statistics
Matches: 128, Mismatches: 11, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
51 7 0.05
52 17 0.13
53 39 0.30
54 4 0.03
55 5 0.04
56 21 0.16
57 8 0.06
59 1 0.01
60 23 0.18
61 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (52 bp):
TAAGTTATGTAAGTTATGTAAGCTATGATATGATATATATTTATGTAAGTTA
Found at i:19397360 original size:61 final size:60
Alignment explanation
Indices: 19397286--19397404 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 60
19397276 ATTAAGTTAT
* *
19397286 GTAAGCTATGATATGATATATATTTATGTA-TTATGTAAGTTATGTAAGTTATGTGAGTTTC
1 GTAAGCTATGATATGATATATATGTAT-AAGTTAT-TAAGTTATGTAAGTTATGTGAGTTTC
*
19397347 GTAAGTTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTT
1 GTAAGCTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTT
19397405 ATCATATGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
60 25 0.46
61 29 0.54
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (60 bp):
GTAAGCTATGATATGATATATATGTATAAGTTATTAAGTTATGTAAGTTATGTGAGTTTC
Found at i:19397405 original size:51 final size:52
Alignment explanation
Indices: 19397214--19397420 Score: 215
Period size: 51 Copynumber: 3.8 Consensus size: 52
19397204 GATAAGTATA
* *
19397214 ATTAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTT
1 ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTA-GTAAGTT
*
19397267 A-TAAG-TATGATTAAGTTATGTAAGCTATGATATGATATATATTTATGTATTATGTAAGTT
1 ATTAAGTTATG--TAAGTTATGTAAGTTATGATATG--ATATA--TATG---TA-GTAAGTT
*
19397327 ATGTAAGTTATGTGAGTT-TCGTAAGTTATGATATGATATATATGTA-TAAGTT
1 AT-TAAGTTATGTAAGTTAT-GTAAGTTATGATATGATATATATGTAGTAAGTT
* *
19397379 ATTAAGTTATGTAAGTTATGTGAGTTATCATATGATATATAT
1 ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATAT
19397421 AAGTAATTTA
Statistics
Matches: 132, Mismatches: 8, Indels: 30
0.78 0.05 0.18
Matches are distributed among these distances:
51 39 0.30
52 13 0.10
53 22 0.17
54 2 0.02
55 5 0.04
57 7 0.05
59 5 0.04
60 12 0.09
61 19 0.14
62 4 0.03
63 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTAGTAAGTT
Found at i:19397421 original size:114 final size:112
Alignment explanation
Indices: 19397216--19397420 Score: 290
Period size: 114 Copynumber: 1.8 Consensus size: 112
19397206 TAAGTATAAT
* *
19397216 TAAGTTATGTAAGTTATGTAAGTTATGATATTATATATATTTATGTAAGTTATAAGTATGATTAA
1 TAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTA-GTAAGTTATAAGTATGA-TAA
*
19397281 GTTATGTAAGCTATGATATGATATATATTTATGTATTATGTAAGTTATG
64 GTTATGTAAGCTATCATATGATATATATTTATGTATTATGTAAGTTATG
*
19397330 TAAGTTATGTGAGTT-TCGTAAGTTATGATATGATATATATGTA-TAAGTTATTAAGTTATG-TA
1 TAAGTTATGTAAGTTAT-GTAAGTTATGATATGATATATATGTAGTAAGTTA-TAAG-TATGATA
* *
19397392 AGTTATGTGAGTTATCATATGATATATAT
63 AGTTATGTAAGCTATCATATGATATATAT
19397421 AAGTAATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
112 35 0.43
113 5 0.06
114 42 0.51
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (112 bp):
TAAGTTATGTAAGTTATGTAAGTTATGATATGATATATATGTAGTAAGTTATAAGTATGATAAGT
TATGTAAGCTATCATATGATATATATTTATGTATTATGTAAGTTATG
Found at i:19397492 original size:29 final size:29
Alignment explanation
Indices: 19397304--19397594 Score: 125
Period size: 30 Copynumber: 10.2 Consensus size: 29
19397294 TGATATGATA
19397304 TATAT-TTATGT-A-TTATGTAAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
*
19397330 TA-A-GTTATGTGAGTT-TCGTAAGTTATG
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
*
19397357 ATATGATATATATGTATAAGTTAT-TAAGTTATG
1 -TAT-ATGT-TATG--TAAGTTATGTAAGTTATG
* * * * *
19397390 TA-A-GTTATGTGAGTTATCATATGATATA
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
* * * *
19397418 TATAAGTAATTTAAGAATT-T-TATG-TATG
1 TATATGTTATGTAAG--TTATGTAAGTTATG
*
19397446 TATGTGAGTTATGTAAGTTATGTAAGTTATG
1 TATAT--GTTATGTAAGTTATGTAAGTTATG
* * * * *
19397477 TATTTGTTTTGTAAGTTATGGTATGATATA
1 TATATGTTATGTAAGTTAT-GTAAGTTATG
* *
19397507 TATAAGTTAT-TAAGTTATGTGAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
* *
19397535 -AAATGATATATATAAGTTAT-TAAGTTATG
1 TATATG-T-TATGTAAGTTATGTAAGTTATG
*
19397564 --TATG-TATGTGAGTTATGTAAGTTATG
1 TATATGTTATGTAAGTTATGTAAGTTATG
19397590 -ATATG
1 TATATG
19397595 ATATATATTT
Statistics
Matches: 202, Mismatches: 34, Indels: 57
0.69 0.12 0.19
Matches are distributed among these distances:
25 17 0.08
26 20 0.10
27 19 0.09
28 32 0.16
29 39 0.19
30 42 0.21
31 10 0.05
32 8 0.04
33 9 0.04
34 5 0.02
35 1 0.00
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (29 bp):
TATATGTTATGTAAGTTATGTAAGTTATG
Found at i:19397512 original size:21 final size:20
Alignment explanation
Indices: 19397488--19397554 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
19397478 ATTTGTTTTG
19397488 TAAGTTATGGTATGATATATA
1 TAAGTTAT-GTATGATATATA
* *
19397509 TAAGTTAT-TAAG-T-TATG
1 TAAGTTATGTATGATATATA
* *
19397526 TGAGTTATGAAATGATATATA
1 TAAGTTATG-TATGATATATA
19397547 TAAGTTAT
1 TAAGTTAT
19397555 TAAGTTATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
17 10 0.29
18 1 0.03
19 5 0.14
20 1 0.03
21 18 0.51
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (20 bp):
TAAGTTATGTATGATATATA
Found at i:19397532 original size:38 final size:38
Alignment explanation
Indices: 19397490--19397564 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
19397480 TTGTTTTGTA
**
19397490 AGTTATGGTATGATATATATAAGTTATTAAGTTATGTG
1 AGTTATGAAATGATATATATAAGTTATTAAGTTATGTG
19397528 AGTTATGAAATGATATATATAAGTTATTAAGTTATGT
1 AGTTATGAAATGATATATATAAGTTATTAAGTTATGT
19397565 ATGTATGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (38 bp):
AGTTATGAAATGATATATATAAGTTATTAAGTTATGTG
Found at i:19397720 original size:2 final size:2
Alignment explanation
Indices: 19397713--19397763 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
19397703 TTATTATCTG
19397713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19397755 AT AT AT AT A
1 AT AT AT AT A
19397764 AAAGTTATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19397825 original size:9 final size:9
Alignment explanation
Indices: 19397811--19397878 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
19397801 TCTTTAAAGG
*
19397811 TATGTAAAT
1 TATGTAAGT
19397820 TATGTAAGT
1 TATGTAAGT
*
19397829 TATGATATGGT
1 TATG-TA-AGT
19397840 TAT-TAAGT
1 TATGTAAGT
19397848 TATGTAAGT
1 TATGTAAGT
*
19397857 TATGTGAGT
1 TATGTAAGT
*
19397866 TAATGTAAAT
1 T-ATGTAAGT
19397876 TAT
1 TAT
19397879 ATGAGTTACG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
8 5 0.10
9 30 0.61
10 9 0.18
11 5 0.10
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:19397878 original size:28 final size:28
Alignment explanation
Indices: 19397811--19397878 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
19397801 TCTTTAAAGG
19397811 TATGTAAATTATGTAAGTTATGATATGGT
1 TATGTAAATTATGTAAGTTATGATA-GGT
*
19397840 TAT-TAAGTTATGTAAGTTATG-T-GAGT
1 TATGTAAATTATGTAAGTTATGATAG-GT
19397866 TAATGTAAATTAT
1 T-ATGTAAATTAT
19397879 ATGAGTTACG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 3 0.09
27 3 0.09
28 24 0.71
29 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (28 bp):
TATGTAAATTATGTAAGTTATGATAGGT
Found at i:19397893 original size:18 final size:18
Alignment explanation
Indices: 19397845--19397898 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
19397835 ATGGTTATTA
* *
19397845 AGTTATGTAAGTTATGTG
1 AGTTATGTAAATTATATG
19397863 AGTTAATGTAAATTATATG
1 AGTT-ATGTAAATTATATG
*
19397882 AGTTACGTAAATTATAT
1 AGTTATGTAAATTATAT
19397899 ATTCATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (18 bp):
AGTTATGTAAATTATATG
Found at i:19398149 original size:76 final size:74
Alignment explanation
Indices: 19398059--19398198 Score: 235
Period size: 76 Copynumber: 1.9 Consensus size: 74
19398049 TGAAATATAG
19398059 TTAATTTATCTATATTTATCAAAATAAGTAAAATATAAAAAAAAATAAGACTTTGAGTTGGCATT
1 TTAATTTATCTATATTTATCAAAATAAGTAAAAT-T-AAAAAAAATAAGACTTTGAGTTGGCATT
19398124 ACAAGATACAA
64 ACAAGATACAA
* * *
19398135 TTAATTTGTCTATATTTATCAAAATAAGTTAAATTAAAAAAAATAAGCCTTTGAGTTGGCATTA
1 TTAATTTATCTATATTTATCAAAATAAGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTA
19398199 GAGGTGCTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 28 0.46
75 1 0.02
76 32 0.52
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (74 bp):
TTAATTTATCTATATTTATCAAAATAAGTAAAATTAAAAAAAATAAGACTTTGAGTTGGCATTAC
AAGATACAA
Found at i:19398375 original size:17 final size:18
Alignment explanation
Indices: 19398353--19398404 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 18
19398343 AAAAGGTATT
*
19398353 TTAAAAATATTT-TAAAA
1 TTAAAAATATTTAAAAAA
19398370 TTAAAAAGTATTTAAAAAA
1 TTAAAAA-TATTTAAAAAA
19398389 TT-AAAA-ATTTAAAAAA
1 TTAAAAATATTTAAAAAA
19398405 AGTATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 10 0.31
17 7 0.22
18 9 0.28
19 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAAAAATATTTAAAAAA
Found at i:19398390 original size:19 final size:17
Alignment explanation
Indices: 19398353--19398396 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
19398343 AAAAGGTATT
*
19398353 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
19398370 TTAAAAAGTATTTAAAAAA
1 TTAAAAA-TATTT-AAAAA
19398389 TTAAAAAT
1 TTAAAAAT
19398397 TTAAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:19398433 original size:17 final size:17
Alignment explanation
Indices: 19398353--19398416 Score: 50
Period size: 18 Copynumber: 4.0 Consensus size: 17
19398343 AAAAGGTATT
*
19398353 TTAAAAATATTTTAAAA
1 TTAAAAGTATTTTAAAA
*
19398370 TTAAAAAGTATTTAAAAAA
1 TT-AAAAGTATTT-TAAAA
19398389 TTAAAA--A-TTT-AAA
1 TTAAAAGTATTTTAAAA
19398402 --AAAAGTATTTTAAAA
1 TTAAAAGTATTTTAAAA
19398417 GTATTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
11 4 0.11
13 4 0.11
14 3 0.08
15 5 0.13
16 1 0.03
17 2 0.05
18 13 0.34
19 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAAAAGTATTTTAAAA
Found at i:19398943 original size:66 final size:65
Alignment explanation
Indices: 19398846--19398996 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 65
19398836 TATAAAATCG
* ** * * * *
19398846 ATAATTTATTAAATTACATAAAAAATTGATAATTTATTGACATAAAATCAAATAAACTAATCAAA
1 ATAATTTATTCAATTA-ATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
19398911 C
65 C
* *
19398912 ATAATTTATTCAATTTAATCGATAATCGATAATTTATTCACATTAAACCGAATAAACTAATCAAA
1 ATAATTTATTCAA-TTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAA
19398977 C
65 C
19398978 ATAATTTATTCAATTAATC
1 ATAATTTATTCAATTAATC
19398997 AAATATATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
65 6 0.08
66 66 0.88
67 3 0.04
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (65 bp):
ATAATTTATTCAATTAATCGATAATCGATAATTTATTCACATAAAACCAAATAAACTAATCAAAC
Found at i:19400981 original size:30 final size:30
Alignment explanation
Indices: 19400947--19401006 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
19400937 TAAATTTGTT
19400947 TCTATATTTGAAAGGTTTAATTATTTCTTA
1 TCTATATTTGAAAGGTTTAATTATTTCTTA
19400977 TCTATATTTGAAAGGTTTAATTATTTCTTA
1 TCTATATTTGAAAGGTTTAATTATTTCTTA
19401007 AATTCCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
TCTATATTTGAAAGGTTTAATTATTTCTTA
Found at i:19401477 original size:8 final size:7
Alignment explanation
Indices: 19401390--19401601 Score: 83
Period size: 7 Copynumber: 29.7 Consensus size: 7
19401380 ACTAATTAAT
19401390 CTAAACC
1 CTAAACC
19401397 CTAAACCC
1 CTAAA-CC
*
19401405 CTAACCC
1 CTAAACC
*
19401412 CT-ATCC
1 CTAAACC
*
19401418 CTTAAATC
1 C-TAAACC
* * *
19401426 TTGAATC
1 CTAAACC
19401433 CTAAACTC
1 CTAAAC-C
19401441 CTAAACC
1 CTAAACC
19401448 CTAAACC
1 CTAAACC
*
19401455 TTAAA-C
1 CTAAACC
19401461 C-ACAACC
1 CTA-AACC
19401468 CTTAAACC
1 C-TAAACC
*
19401476 CTAAACT
1 CTAAACC
* *
19401483 ATAATCC
1 CTAAACC
19401490 CTAAACC
1 CTAAACC
*
19401497 CATAATCC
1 C-TAAACC
*
19401505 ATAAACC
1 CTAAACC
*
19401512 TTAAA--
1 CTAAACC
*
19401517 ATAGTAACTC
1 CTA--AAC-C
19401527 CTAAACC
1 CTAAACC
*
19401534 TTAAACC
1 CTAAACC
*
19401541 ATAAACC
1 CTAAACC
* *
19401548 ATAATCC
1 CTAAACC
19401555 CTAAACC
1 CTAAACC
*
19401562 TTAAACC
1 CTAAACC
* *
19401569 TTAAAAC
1 CTAAACC
19401576 CTAAACC
1 CTAAACC
* *
19401583 ATATACC
1 CTAAACC
*
19401590 ATAAACC
1 CTAAACC
*
19401597 ATAAA
1 CTAAA
19401602 TTCTAAACTA
Statistics
Matches: 156, Mismatches: 35, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
5 3 0.02
6 7 0.04
7 115 0.74
8 28 0.18
9 1 0.01
10 2 0.01
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:19401503 original size:15 final size:15
Alignment explanation
Indices: 19401464--19401511 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
19401454 CTTAAACCAC
* *
19401464 AACCCTTAAACCCTA
1 AACCCATAATCCCTA
*
19401479 AA-CTATAATCCCTA
1 AACCCATAATCCCTA
*
19401493 AACCCATAATCCATA
1 AACCCATAATCCCTA
19401508 AACC
1 AACC
19401512 TTAAAATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCCTA
Found at i:19401561 original size:21 final size:21
Alignment explanation
Indices: 19401442--19401601 Score: 119
Period size: 21 Copynumber: 7.5 Consensus size: 21
19401432 CCTAAACTCC
*
19401442 TAAACCCTAAACCTTAAACCA
1 TAAACCCTAAACCATAAACCA
* * *
19401463 -CAACCCTTAAACCCTAAACTA
1 TAAACCC-TAAACCATAAACCA
* *
19401484 TAATCCCTAAACCCATAATCCA
1 TAAACCCTAAA-CCATAAACCA
* *
19401506 TAAACCTTAAA--ATAGTAACTCC
1 TAAACCCTAAACCATA--AAC-CA
*
19401528 TAAACCTTAAACCATAAACCA
1 TAAACCCTAAACCATAAACCA
* * *
19401549 TAATCCCTAAACCTTAAACCT
1 TAAACCCTAAACCATAAACCA
* *
19401570 TAAAACCTAAACCATATACCA
1 TAAACCCTAAACCATAAACCA
*
19401591 TAAACCATAAA
1 TAAACCCTAAA
19401602 TTCTAAACTA
Statistics
Matches: 107, Mismatches: 24, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.03
20 5 0.05
21 61 0.57
22 35 0.33
24 3 0.03
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.22
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACCA
Found at i:19402098 original size:107 final size:109
Alignment explanation
Indices: 19401902--19402203 Score: 421
Period size: 114 Copynumber: 2.7 Consensus size: 109
19401892 ACAGATGTTT
* *
19401902 TTAATTTTTTTGCGGCGTTTTTCAAA-AGCGCCGCTAATGCTCGACATATAGCGACATTTTTCAA
1 TTAA-TTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTC-A
* *
19401966 AAAAGCGCCGCTAATGCCACTAAAGCTCAACAT-A-GGCGTTGTGC
64 ACAAGCGCCGCTAATGCCACTAAAGCTCAACATAAGGGCATTGTGC
* * *
19402010 TTAATTTTTTGTGGCGTGTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAC
1 TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
*
19402075 AAGCGCCGCTAATTCCACTAAAGCTCAACATAAAACGAGGGCATTGTGC
66 AAGCGCCGCTAATGCCACTAAAGCTCAACAT---A--AGGGCATTGTGC
* * *
19402124 TTAAATTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCAACCTATAGTGGCATTTTTCAAC
1 TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
19402189 AAGCGCCGCTAATGC
66 AAGCGCCGCTAATGC
19402204 ACGACATATT
Statistics
Matches: 171, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
107 51 0.30
108 37 0.22
113 1 0.01
114 82 0.48
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (109 bp):
TTAATTTTTTGCGGCGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGGCATTTTTCAAC
AAGCGCCGCTAATGCCACTAAAGCTCAACATAAGGGCATTGTGC
Found at i:19402224 original size:40 final size:40
Alignment explanation
Indices: 19402132--19402241 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 40
19402122 GCTTAAATTT
* *
19402132 TTGCGGCGTTTTTCAA-AGAGCGCCGCTAATGCTCAACCTA
1 TTGCGGCGTTTTTCAACA-AGCGCCGCTAATGCACAACATA
* * * *
19402172 TAGTGGCATTTTTCAACAAGCGCCGCTAATGCACGACATA
1 TTGCGGCGTTTTTCAACAAGCGCCGCTAATGCACAACATA
* * * *
19402212 TTGCGACGTTTTTCGACTATCGCCGCTAAT
1 TTGCGGCGTTTTTCAACAAGCGCCGCTAAT
19402242 TCCCAATATA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (40 bp):
TTGCGGCGTTTTTCAACAAGCGCCGCTAATGCACAACATA
Found at i:19402373 original size:52 final size:52
Alignment explanation
Indices: 19402303--19402408 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
19402293 AAAATCTATT
19402303 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
1 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
19402355 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
1 TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
19402407 TT
1 TT
19402409 AAACTTAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (52 bp):
TTGTTGTAGTGATGGTATATATATAAGTCATTAAAATCCTAATTAATCTTAA
Found at i:19402407 original size:10 final size:10
Alignment explanation
Indices: 19402389--19402422 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
19402379 AAGTCATTAA
*
19402389 AATCCTAATT
1 AATCTTAATT
19402399 AATCTTAATT
1 AATCTTAATT
*
19402409 AAACTTAATT
1 AATCTTAATT
19402419 AATC
1 AATC
19402423 ATTTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (10 bp):
AATCTTAATT
Found at i:19413405 original size:19 final size:19
Alignment explanation
Indices: 19413373--19413410 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19413363 TATATACATT
19413373 TTTAGTTTTCAAA-TAAAA
1 TTTAGTTTTCAAATTAAAA
*
19413391 TTTAGTTTTTTAAATTAAAA
1 TTTAG-TTTTCAAATTAAAA
19413411 AATTAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTAGTTTTCAAATTAAAA
Found at i:19418875 original size:43 final size:43
Alignment explanation
Indices: 19418814--19418901 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
19418804 CAGTAACAAA
19418814 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
19418857 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
1 CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
19418900 CA
1 CA
19418902 GCGAGTGAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
CAAAGGCGCGAGTGATATATTGATATCCATTTGGTATGCAGTT
Found at i:19423997 original size:14 final size:15
Alignment explanation
Indices: 19423974--19424014 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
19423964 TCAACCTTTA
19423974 TTTTAATTTTAT-AT
1 TTTTAATTTTATCAT
*
19423988 TTTTAGTTTTATCA-
1 TTTTAATTTTATCAT
19424002 TTTTAATGTTTAT
1 TTTTAAT-TTTAT
19424015 GAAGATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTAATTTTATCAT
Found at i:19424186 original size:35 final size:35
Alignment explanation
Indices: 19424104--19424192 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 35
19424094 CCTTAAATAT
*
19424104 ATCTATCCCAACCTTTTT-GAGGTTGCCTTAGACT
1 ATCTATCCCAACCTTTTTAGAGGTTGCCTTAGACG
* * *
19424138 AGTATATCTCAACCTTTTTAG-GGTTGTCTTAGACGG
1 A-TCTATCCCAACCTTTTTAGAGGTTGCCTTAGAC-G
19424174 ATCTATCCCAACCTTTTTA
1 ATCTATCCCAACCTTTTTA
19424193 AAGTCGTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
34 1 0.02
35 43 0.93
36 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (35 bp):
ATCTATCCCAACCTTTTTAGAGGTTGCCTTAGACG
Found at i:19424202 original size:35 final size:34
Alignment explanation
Indices: 19424104--19424202 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 34
19424094 CCTTAAATAT
* * *
19424104 ATCTATCCCAACCTTTTTGAGGTTGCCTTAGACT
1 ATCTATCCCAACCTTTTTAAGGTTGTCTTAGACG
* * *
19424138 AGTATATCTCAACCTTTTTAGGGTTGTCTTAGACGG
1 A-TCTATCCCAACCTTTTTAAGGTTGTCTTAGAC-G
* *
19424174 ATCTATCCCAACCTTTTTAAAGTCGTCTT
1 ATCTATCCCAACCTTTTTAAGGTTGTCTT
19424203 TGACTTGGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
34 1 0.02
35 50 0.96
36 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.39
Consensus pattern (34 bp):
ATCTATCCCAACCTTTTTAAGGTTGTCTTAGACG
Found at i:19426248 original size:6 final size:6
Alignment explanation
Indices: 19426237--19426277 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
19426227 TAATAAAGCA
19426237 AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG AATGG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG AATGG
19426278 TTAAGGACTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.49, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:19426656 original size:23 final size:25
Alignment explanation
Indices: 19426620--19426667 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
19426610 CACACATCTC
19426620 CATTTTGTTTTTAAT-TTTT-TTTT
1 CATTTTGTTTTTAATCTTTTATTTT
19426643 CATTTT-TTTATTAATCTTTTATTTT
1 CATTTTGTTT-TTAATCTTTTATTTT
19426668 TTTAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.14
23 11 0.50
24 4 0.18
25 4 0.18
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (25 bp):
CATTTTGTTTTTAATCTTTTATTTT
Found at i:19428670 original size:9 final size:9
Alignment explanation
Indices: 19428647--19428684 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
19428637 TAAATCTAGC
19428647 GATATA-TA
1 GATATATTA
*
19428655 TATATATTA
1 GATATATTA
19428664 GATATATTA
1 GATATATTA
19428673 GATATATTA
1 GATATATTA
19428682 GAT
1 GAT
19428685 TAGCACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 5 0.19
9 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (9 bp):
GATATATTA
Found at i:19428844 original size:28 final size:27
Alignment explanation
Indices: 19428804--19428858 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
19428794 ATAATTTTAT
*
19428804 ATTTTTATAATTTTTAAAGATTAAATTA
1 ATTTTTATAATTTTTAAAG-TCAAATTA
*
19428832 ATTTTTATCATTTTTAAAGTCAAATTA
1 ATTTTTATAATTTTTAAAGTCAAATTA
19428859 CAATTTTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTTTATAATTTTTAAAGTCAAATTA
Found at i:19428865 original size:28 final size:28
Alignment explanation
Indices: 19428806--19428871 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
19428796 AATTTTATAT
* * *
19428806 TTTTATAATTTTTAAAGATTAAATTAAT
1 TTTTATCATTTTTAAAGATCAAATTAAA
19428834 TTTTATCATTTTTAAAG-TCAAATTACAA
1 TTTTATCATTTTTAAAGATCAAATTA-AA
*
19428862 TTTTAGCATT
1 TTTTATCATT
19428872 AATAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 7 0.21
28 26 0.79
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTTATCATTTTTAAAGATCAAATTAAA
Found at i:19433307 original size:5 final size:5
Alignment explanation
Indices: 19433297--19433323 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19433287 TAAATTTTAT
19433297 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
19433324 CAATGAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:19434614 original size:34 final size:34
Alignment explanation
Indices: 19434576--19434653 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
19434566 CTACGGTGCC
*
19434576 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCTT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
* * *
19434610 TTGGTGTGGTGTAGTTATCGCTTTATTGAGCCAT
1 TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
*
19434644 TTGATGTGGT
1 TTGGTGTGGT
19434654 CTATTGAGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.15, C:0.12, G:0.28, T:0.45
Consensus pattern (34 bp):
TTGGTGTGGTGTAATTATCGCTCTATTAAGCCAT
Done.