Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 108 of 133
Found at i:20977566 original size:45 final size:44
Alignment explanation
Indices: 20977517--20977651 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 44
20977507 ATGAATGAGA
**
20977517 GGTTGATTTTTACTAGAGATACAAAAGAACATGCAGTGGATCATG
1 GGTTGATTTTTACTAGAGATA-AAAAGAACATATAGTGGATCATG
* * * *
20977562 GGTTGATTTTGAGTGGAGAGATTTAAAGGAACATATAGTGGATCATG
1 GGTTGATTTTTACT--AGAGA-TAAAAAGAACATATAGTGGATCATG
** *
20977609 AATTGATTTTTACTAGAGATATAAAGAAACATATAGTGGATCA
1 GGTTGATTTTTACTAGAGATAAAAAG-AACATATAGTGGATCA
20977652 GAGAACGATT
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
44 4 0.05
45 33 0.45
47 35 0.48
48 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.31
Consensus pattern (44 bp):
GGTTGATTTTTACTAGAGATAAAAAGAACATATAGTGGATCATG
Found at i:20977602 original size:47 final size:45
Alignment explanation
Indices: 20977519--20977651 Score: 142
Period size: 45 Copynumber: 2.9 Consensus size: 45
20977509 GAATGAGAGG
* * ** **
20977519 TTGATTTTTACTAGAGATACAAA-AGAACATGCAGTGGATCATGGG
1 TTGATTTTGACTAGAGATATAAAGA-AACATATAGTGGATCATGAA
* * *
20977564 TTGATTTTGAGTGGAGAGATTTAAAGGAACATATAGTGGATCATGAA
1 TTGATTTTGACT--AGAGATATAAAGAAACATATAGTGGATCATGAA
*
20977611 TTGATTTTTACTAGAGATATAAAGAAACATATAGTGGATCA
1 TTGATTTTGACTAGAGATATAAAGAAACATATAGTGGATCA
20977652 GAGAACGATT
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 37 0.51
47 35 0.49
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (45 bp):
TTGATTTTGACTAGAGATATAAAGAAACATATAGTGGATCATGAA
Found at i:20977898 original size:20 final size:21
Alignment explanation
Indices: 20977873--20977924 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
20977863 ACTAAAGCTC
*
20977873 TAGAGGATGATGGG-AAGATA
1 TAGAGGATGACGGGAAAGATA
20977893 TAGAGGATGACGGGAAAGATA
1 TAGAGGATGACGGGAAAGATA
20977914 TA-AGGGATGAC
1 TAGA-GGATGAC
20977925 ACTATAAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.40, C:0.04, G:0.38, T:0.17
Consensus pattern (21 bp):
TAGAGGATGACGGGAAAGATA
Found at i:20982840 original size:21 final size:21
Alignment explanation
Indices: 20982816--20982868 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
20982806 GCAATATCAG
20982816 CAATTTAATAGATTAAATAAT
1 CAATTTAATAGATTAAATAAT
* *
20982837 CAATTATCATAGATTAAATGAT
1 CAATT-TAATAGATTAAATAAT
20982859 -AATTTCAATA
1 CAATTT-AATA
20982869 ATAAAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 12 0.44
22 14 0.52
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (21 bp):
CAATTTAATAGATTAAATAAT
Found at i:20983648 original size:22 final size:22
Alignment explanation
Indices: 20983599--20983640 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
20983589 AATGGTCAGA
20983599 GAACTGTAAATAATGATTCAAT
1 GAACTGTAAATAATGATTCAAT
20983621 GAACTG-AAACTAATGATTCA
1 GAACTGTAAA-TAATGATTCA
20983641 TCTAACTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (22 bp):
GAACTGTAAATAATGATTCAAT
Found at i:20983811 original size:98 final size:98
Alignment explanation
Indices: 20983621--20983904 Score: 455
Period size: 98 Copynumber: 2.9 Consensus size: 98
20983611 ATGATTCAAT
* * * * * * * *
20983621 GAACTG-AAACTAATGATTCATCTAACTGTTCTTTTGAAAGTTGCCATCACATTTAA-ATCCTTT
1 GAACTGTAAA-TAATAATTCAACGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTT
20983684 ATACTAAGTTTCTTTGATATTATCAATGGTCAGA
65 ATACTAAGTTTCTTTGATATTATCAATGGTCAGA
20983718 GAACTGTAAATAATAATTCAACGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTTA
1 GAACTGTAAATAATAATTCAACGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTTA
20983783 TACTAAGTTTCTTTGATATTATCAATGGTCAGA
66 TACTAAGTTTCTTTGATATTATCAATGGTCAGA
*
20983816 GAACTGTAAATAATAATTCAATGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTTA
1 GAACTGTAAATAATAATTCAACGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTTA
*
20983881 TACTGAGTTTCTTTGATATTATCA
66 TACTAAGTTTCTTTGATATTATCA
20983905 TCCCTTCTAC
Statistics
Matches: 175, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
97 45 0.26
98 130 0.74
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (98 bp):
GAACTGTAAATAATAATTCAACGAACTGTTCCTTTCAAAGTTTCTATCACATTTAATTTCCTTTA
TACTAAGTTTCTTTGATATTATCAATGGTCAGA
Found at i:20984707 original size:3 final size:3
Alignment explanation
Indices: 20984699--20984729 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
20984689 CTGTTAAAAT
20984699 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
20984730 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20985416 original size:130 final size:130
Alignment explanation
Indices: 20985159--20985416 Score: 303
Period size: 130 Copynumber: 2.0 Consensus size: 130
20985149 ATGAAATTAG
* * * * * *
20985159 TAATTTAATACATAATTAATTTTATATTATATTAAAATTTAATATATGTAATTTAATAATAGTAT
1 TAATTTAATAAATAATTAATTATATATTATATTAAAATTTAATATATGTAAATTAAAAAAAATAT
* * * * **
20985224 TATAGCAATTTTCAAATAAAATTTCACACGTCAAATTTTTATGAATGATGATAAAGGTATTTTAA
66 TATAGCAATTTTAAAATAAAATTTCACACGTCAAATTCTTATGAATAATCATAAAGACATTTTAA
20985289 TAATTTAATAAATAATTAATTCATATTATTATATTAAAATTT-A-ATATGTAAATTAAAAAAAAT
1 TAATTTAATAAATAATTAATT-ATA-TATTATATTAAAATTTAATATATGTAAATTAAAAAAAAT
*
20985352 ATTATAGCAATTTTAAAATAAAATATT-AC-CTGT-AACTTCTTATGAAGTAATCATAGAA-ACA
64 ATTATAGCAATTTTAAAATAAAAT-TTCACAC-GTCAAATTCTTATGAA-TAATCATA-AAGACA
20985413 TTTT
125 TTTT
20985417 TGTAATAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
129 12 0.11
130 74 0.68
131 7 0.06
132 16 0.15
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (130 bp):
TAATTTAATAAATAATTAATTATATATTATATTAAAATTTAATATATGTAAATTAAAAAAAATAT
TATAGCAATTTTAAAATAAAATTTCACACGTCAAATTCTTATGAATAATCATAAAGACATTTTAA
Found at i:20985693 original size:24 final size:24
Alignment explanation
Indices: 20985665--20985712 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
20985655 ACGGTCGTGA
**
20985665 GAGTCACTAAGTGTTACACGGTGG
1 GAGTCACTAAGTACTACACGGTGG
20985689 GAGTCACTAAGTACTACACGGTGG
1 GAGTCACTAAGTACTACACGGTGG
20985713 TCTGGTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (24 bp):
GAGTCACTAAGTACTACACGGTGG
Found at i:20990569 original size:10 final size:10
Alignment explanation
Indices: 20990554--20990583 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
20990544 ATCAAACTTT
20990554 TATATTTTAA
1 TATATTTTAA
20990564 TATATTTTAA
1 TATATTTTAA
20990574 T-TATTTTAA
1 TATATTTTAA
20990583 T
1 T
20990584 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:20990580 original size:9 final size:9
Alignment explanation
Indices: 20990556--20990585 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
20990546 CAAACTTTTA
20990556 TATTTTAAT
1 TATTTTAAT
20990565 ATATTTTAAT
1 -TATTTTAAT
20990575 TATTTTAAT
1 TATTTTAAT
20990584 TA
1 TA
20990586 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:20991148 original size:80 final size:80
Alignment explanation
Indices: 20991005--20991158 Score: 229
Period size: 80 Copynumber: 1.9 Consensus size: 80
20990995 ATTGTTGGAG
* * * * * *
20991005 GTAGCATAGTTCATTTTTCTTAGTTATTTTTATTAGCCCTTTAAAAAATTGAAATTGTTTTTTTT
1 GTAGCATAGTTCATTTATCTGAGTTATTTTGATTAGCCCTCTAAAAAATTGAAAATGTGTTTTTT
20991070 TTTTTGTTATATATA
66 TTTTTGTTATATATA
*
20991085 GTAGCATAGTTCATTTATCTGAGTTATTTTGATTTGTCCCTCTAAAAAATTGAAAATG-GTTTTT
1 GTAGCATAGTTCATTTATCTGAGTTATTTTGATTAG-CCCTCTAAAAAATTGAAAATGTGTTTTT
20991149 TTTTTTGTTA
65 TTTTTTGTTA
20991159 AATACGGACC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 47 0.71
81 19 0.29
ACGTcount: A:0.26, C:0.08, G:0.12, T:0.53
Consensus pattern (80 bp):
GTAGCATAGTTCATTTATCTGAGTTATTTTGATTAGCCCTCTAAAAAATTGAAAATGTGTTTTTT
TTTTTGTTATATATA
Found at i:20993078 original size:21 final size:21
Alignment explanation
Indices: 20993052--20993093 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
20993042 CAAAAGTCAC
20993052 ATTGTTTGAATTGATAGTTTT
1 ATTGTTTGAATTGATAGTTTT
20993073 ATTGTTTGAATTGATAGTTTT
1 ATTGTTTGAATTGATAGTTTT
20993094 TTTATATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (21 bp):
ATTGTTTGAATTGATAGTTTT
Found at i:20998300 original size:21 final size:20
Alignment explanation
Indices: 20998251--20998300 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
20998241 TATTTATTAA
*
20998251 AATTTTATTATTTTAAATAT
1 AATTTAATTATTTTAAATAT
* *
20998271 ATTTGTAATTATTTTAATATTT
1 AATT-TAATTATTTTAA-ATAT
20998293 AATTTAAT
1 AATTTAAT
20998301 AAAGATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTTAATTATTTTAAATAT
Found at i:20999040 original size:78 final size:78
Alignment explanation
Indices: 20998947--20999093 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 78
20998937 AATTTTTGGA
* * * * *
20998947 GGTAGCACAGTTCATTTATCTAAATTATTTTTATTCGTCCTTTTAAAACATTGAAAGTGATTTTT
1 GGTAGCACAGTTCATTTATCTAAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTTT
20999012 TTTTGTTATATAT
66 TTTTGTTATATAT
* * * *
20999025 GGTAGCATAGTTCATTTATCTGAGTTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGGTTTTT
1 GGTAGCACAGTTCATTTATCTAAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTTT
20999090 TTTT
66 TTTT
20999094 TTTGTTGTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.49
Consensus pattern (78 bp):
GGTAGCACAGTTCATTTATCTAAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTTT
TTTTGTTATATAT
Found at i:21001961 original size:43 final size:44
Alignment explanation
Indices: 21001907--21001999 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 44
21001897 ATGAGCAATT
* *
21001907 AAAAA-AGGGGTTAGGAATTTTTGTTGATCAGGGGATGAA-AAA
1 AAAAAGAGGGGTTAGGAATTTTTGTCGATCAGGGGATCAAGAAA
21001949 AAAAAGAGGGGTTAGGAATTTTTGTCGATCAGGGGATCAAGAAA
1 AAAAAGAGGGGTTAGGAATTTTTGTCGATCAGGGGATCAAGAAA
21001993 AAAAAGA
1 AAAAAGA
21002000 TGATTTGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 5 0.11
43 32 0.68
44 10 0.21
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.23
Consensus pattern (44 bp):
AAAAAGAGGGGTTAGGAATTTTTGTCGATCAGGGGATCAAGAAA
Found at i:21002456 original size:17 final size:17
Alignment explanation
Indices: 21002434--21002469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21002424 CCACCGATAA
*
21002434 TTGTTGATGAAAATTTT
1 TTGTTGATAAAAATTTT
*
21002451 TTGTTGGTAAAAATTTT
1 TTGTTGATAAAAATTTT
21002468 TT
1 TT
21002470 TTTGTTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.56
Consensus pattern (17 bp):
TTGTTGATAAAAATTTT
Found at i:21008060 original size:12 final size:12
Alignment explanation
Indices: 21008043--21008067 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21008033 TTAAAAACAA
21008043 TAAAAATATTAT
1 TAAAAATATTAT
21008055 TAAAAATATTAT
1 TAAAAATATTAT
21008067 T
1 T
21008068 TTGCTCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:21012012 original size:10 final size:10
Alignment explanation
Indices: 21011997--21012026 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21011987 ATTGAGCTTT
21011997 TATATTTTAA
1 TATATTTTAA
21012007 TATATTTTAA
1 TATATTTTAA
21012017 T-TATTTTAA
1 TATATTTTAA
21012026 T
1 T
21012027 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:21012023 original size:9 final size:9
Alignment explanation
Indices: 21011999--21012028 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
21011989 TGAGCTTTTA
21011999 TATTTTAAT
1 TATTTTAAT
21012008 ATATTTTAAT
1 -TATTTTAAT
21012018 TATTTTAAT
1 TATTTTAAT
21012027 TA
1 TA
21012029 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:21014806 original size:10 final size:10
Alignment explanation
Indices: 21014793--21014822 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21014783 ATCAAGCTTT
21014793 TATATTTTAA
1 TATATTTTAA
21014803 TATATTTTAA
1 TATATTTTAA
21014813 T-TATTTTAA
1 TATATTTTAA
21014822 T
1 T
21014823 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:21014819 original size:9 final size:9
Alignment explanation
Indices: 21014795--21014824 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
21014785 CAAGCTTTTA
21014795 TATTTTAAT
1 TATTTTAAT
21014804 ATATTTTAAT
1 -TATTTTAAT
21014814 TATTTTAAT
1 TATTTTAAT
21014823 TA
1 TA
21014825 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:21015366 original size:78 final size:78
Alignment explanation
Indices: 21015237--21015382 Score: 231
Period size: 78 Copynumber: 1.9 Consensus size: 78
21015227 AATTTTTGGA
* *
21015237 GGTAGCATAGTTCATTTATTTGAATTTTTTTGATTTGTCCCTTTACAAAATTGAAAATGATTTTT
1 GGTAGCATAGTTCATTTATTTGAATTATTTTGATTTGTCCCTTTAAAAAATTGAAAATGATTTTT
21015302 TTTTGTTATATAT
66 TTTTGTTATATAT
* * *
21015315 GGTAGCATAGTTCATTTATTTGAGTTATTTTGATTAT-TCCCTTTAAAAAATTTAAAATGGTTTT
1 GGTAGCATAGTTCATTTATTTGAATTATTTTGATT-TGTCCCTTTAAAAAATTGAAAATGATTTT
21015379 TTTT
65 TTTT
21015383 CTTTCTTGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 61 0.98
79 1 0.02
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (78 bp):
GGTAGCATAGTTCATTTATTTGAATTATTTTGATTTGTCCCTTTAAAAAATTGAAAATGATTTTT
TTTTGTTATATAT
Found at i:21016131 original size:22 final size:22
Alignment explanation
Indices: 21016088--21016133 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
21016078 TTGCTAATAC
** * *
21016088 TTCATTTTTTGGTAGTTTTTTT
1 TTCATTTTTTAATAATTGTTTT
21016110 TTCATTTTTTAATAATTGTTTT
1 TTCATTTTTTAATAATTGTTTT
21016132 TT
1 TT
21016134 TGGGTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.72
Consensus pattern (22 bp):
TTCATTTTTTAATAATTGTTTT
Found at i:21022401 original size:21 final size:21
Alignment explanation
Indices: 21022358--21022401 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21022348 TTAATTTTTT
*
21022358 ATTATTTTAAATATATTTATA
1 ATTATTTTAAATATAATTATA
*
21022379 ATTATTTTAATATTTAATT-TA
1 ATTATTTTAA-ATATAATTATA
21022400 AT
1 AT
21022402 AAAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTTTAAATATAATTATA
Found at i:21023535 original size:12 final size:12
Alignment explanation
Indices: 21023518--21023542 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21023508 TTAAAAACAA
21023518 TAAAAATATTAT
1 TAAAAATATTAT
21023530 TAAAAATATTAT
1 TAAAAATATTAT
21023542 T
1 T
21023543 TTGCTCATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:21024688 original size:26 final size:25
Alignment explanation
Indices: 21024612--21024688 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
21024602 TAGGAAGACA
* *
21024612 TTTTGTAAATATAATAAGAGAATAT
1 TTTTATAATTATAATAAGAGAATAT
* * * * *
21024637 TTTAATAATTTTGATAATAAACATAT
1 TTTTATAATTATAATAAGAGA-ATAT
21024663 TTTTATAATTATAATAAGAGAGATAT
1 TTTTATAATTATAATAAGAGA-ATAT
21024689 ATAATAATTT
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (25 bp):
TTTTATAATTATAATAAGAGAATAT
Found at i:21028034 original size:78 final size:78
Alignment explanation
Indices: 21027940--21028087 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 78
21027930 GAATTTTTCG
* *
21027940 TGGTAGCATAGTTCATTTATCTGAATTATTTTGATTCGTCCCTTTAAAAAATTGAAAGTGATTTT
1 TGGTAGCATAGTTCATTTATCTGAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTT
21028005 TTTTTGTTATATA
66 TTTTTGTTATATA
* * *
21028018 TGGTAGCATAGTTCATTTATCTGAGTTATTTTGATTATTCCCTTTAAAAAATTGAAAATGGTTTT
1 TGGTAGCATAGTTCATTTATCTGAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTT
21028083 TTTTT
66 TTTTT
21028088 TTTTGTTGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.49
Consensus pattern (78 bp):
TGGTAGCATAGTTCATTTATCTGAATTATTTTGATTAGTCCCTTTAAAAAATTGAAAATGATTTT
TTTTTGTTATATA
Found at i:21031033 original size:54 final size:53
Alignment explanation
Indices: 21030975--21031084 Score: 134
Period size: 54 Copynumber: 2.1 Consensus size: 53
21030965 TTTTAAATGT
* * *
21030975 TTTTAGCAACGGATTATCAATGAAATTT-TCATCGATAATTCAAA-TTTTTATAAC
1 TTTTAACAACGGATTACCAATAAAATTTGT--T-GATAATTCAAATTTTTTATAAC
* *
21031029 TTTTAACAATGGATTACCAATAAAATTTGTTGATAATTCAAATTTTTTATGAC
1 TTTTAACAACGGATTACCAATAAAATTTGTTGATAATTCAAATTTTTTATAAC
21031082 TTT
1 TTT
21031085 CATCAACGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
52 11 0.22
53 13 0.27
54 24 0.49
55 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (53 bp):
TTTTAACAACGGATTACCAATAAAATTTGTTGATAATTCAAATTTTTTATAAC
Found at i:21035128 original size:21 final size:21
Alignment explanation
Indices: 21035085--21035128 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
21035075 TTAATTTTTT
*
21035085 ATTATTTTAAATATATTTATA
1 ATTATTTTAAATATAATTATA
*
21035106 ATTATTTTAATATTTAATT-TA
1 ATTATTTTAA-ATATAATTATA
21035127 AT
1 AT
21035129 AAAGATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATTTTAAATATAATTATA
Found at i:21037426 original size:26 final size:25
Alignment explanation
Indices: 21037350--21037426 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
21037340 TAGGAAGACA
* *
21037350 TTTTGTAAATATAATAAGAGAATAT
1 TTTTATAATTATAATAAGAGAATAT
* * * * *
21037375 TTTAATAATTTTGATAATAAACATAT
1 TTTTATAATTATAATAAGAGA-ATAT
21037401 TTTTATAATTATAATAAGAGAGATAT
1 TTTTATAATTATAATAAGAGA-ATAT
21037427 ATAATAATTT
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
25 14 0.37
26 24 0.63
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (25 bp):
TTTTATAATTATAATAAGAGAATAT
Found at i:21044583 original size:19 final size:19
Alignment explanation
Indices: 21044559--21044595 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21044549 GCCACTTCAA
21044559 TTTTTTGTTGTTTTTTATG
1 TTTTTTGTTGTTTTTTATG
* *
21044578 TTTTTTTTTTTTTTTTAT
1 TTTTTTGTTGTTTTTTAT
21044596 TAATTTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTGTTTTTTATG
Found at i:21045578 original size:43 final size:42
Alignment explanation
Indices: 21045472--21045598 Score: 141
Period size: 43 Copynumber: 3.0 Consensus size: 42
21045462 ATGCTTAATG
** *
21045472 ACTTTAAAATTTAGGAAAAATTCCTTTAAACA-AAGACTCGACA
1 ACTTTAAAATTTAGGAAAAGCT-CTTTAAACAGAAG-CTTGACA
* *
21045515 ACTTTAAAAACTAAGG-AAAGCTCTTCTAAACAGAAGCTTGACA
1 ACTTT-AAAATTTAGGAAAAGCTCTT-TAAACAGAAGCTTGACA
*
21045558 ACTTTAAAATTTTGGAAAAGCTCTTTTAAACAGAAGCTTGA
1 ACTTTAAAATTTAGGAAAAGCTC-TTTAAACAGAAGCTTGA
21045599 TGAGTTTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
42 10 0.14
43 48 0.68
44 13 0.18
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (42 bp):
ACTTTAAAATTTAGGAAAAGCTCTTTAAACAGAAGCTTGACA
Found at i:21046366 original size:35 final size:35
Alignment explanation
Indices: 21046327--21046394 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
21046317 GCTAAAAATC
*
21046327 TGGGTGCCAACTAACCTAGGCTTAGATCTTATCAA
1 TGGGTGCCAACTAACCTAGGCTTAAATCTTATCAA
* *
21046362 TGGGTGCTAACTAACTTAGGCTTAAATCTTATC
1 TGGGTGCCAACTAACCTAGGCTTAAATCTTATC
21046395 GGTGTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (35 bp):
TGGGTGCCAACTAACCTAGGCTTAAATCTTATCAA
Found at i:21046526 original size:23 final size:21
Alignment explanation
Indices: 21046472--21046531 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
21046462 CTTAGGTGCT
21046472 AGCTAATTTAGGCTTAAAATG
1 AGCTAATTTAGGCTTAAAATG
*
21046493 AGCT-ATATTAGGCTTAAAGTG
1 AGCTAAT-TTAGGCTTAAAATG
*
21046514 CCTGCTAATTTAGGCTTA
1 --AGCTAATTTAGGCTTA
21046532 GATCTTATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 17 0.52
23 12 0.36
24 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (21 bp):
AGCTAATTTAGGCTTAAAATG
Found at i:21046613 original size:32 final size:30
Alignment explanation
Indices: 21046527--21046627 Score: 121
Period size: 31 Copynumber: 3.2 Consensus size: 30
21046517 GCTAATTTAG
** *
21046527 GCTTAGATCTTATCAGTGCTAGCTAAACTAG
1 GCTTA-ATCTTATTGGTGCTAGCTAAACTAA
*
21046558 GCATAAATCTTATTGGTGCTAGCTAAACTAA
1 GC-TTAATCTTATTGGTGCTAGCTAAACTAA
*
21046589 GCTTAATCTTCTTTGGGTGCTAGCTAAACTAA
1 GCTTAATCTT-ATT-GGTGCTAGCTAAACTAA
21046621 GCTTAAT
1 GCTTAAT
21046628 TCTCACTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
30 7 0.11
31 28 0.46
32 26 0.43
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (30 bp):
GCTTAATCTTATTGGTGCTAGCTAAACTAA
Found at i:21047535 original size:45 final size:45
Alignment explanation
Indices: 21047482--21047588 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
21047472 GGAAATATCT
* *
21047482 TCAGATATCACCATTGAGAAAAGATGCAAATTTAGAAATAGG-TAC
1 TCAGATATCACCATTGAGAAAAGATGCAAACTCA-AAATAGGATAC
** * * *
21047527 TCAGATATCACCATCAAGAAAATATGCAAACTCAAACTTGGATAC
1 TCAGATATCACCATTGAGAAAAGATGCAAACTCAAAATAGGATAC
*
21047572 TCAAATATCACCATTGA
1 TCAGATATCACCATTGA
21047589 ATAGATTTCG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 5 0.10
45 46 0.90
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (45 bp):
TCAGATATCACCATTGAGAAAAGATGCAAACTCAAAATAGGATAC
Found at i:21049052 original size:15 final size:15
Alignment explanation
Indices: 21049027--21049060 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
21049017 TTTTTTTTTC
21049027 TTTTATTCTCTC-TT
1 TTTTATTCTCTCATT
21049041 TTTTATTTCTCTCATT
1 TTTTA-TTCTCTCATT
21049057 TTTT
1 TTTT
21049061 TTAGTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 7 0.39
16 6 0.33
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTCTCTCATT
Found at i:21049468 original size:7 final size:6
Alignment explanation
Indices: 21049408--21049495 Score: 65
Period size: 6 Copynumber: 14.2 Consensus size: 6
21049398 CAATCAAATA
* * *
21049408 TTTCTT TTTC-T TTTCTTT TGTTCCT CTTCATCT TTTCTT TTT-TT TTCTCCT
1 TTTCTT TTTCTT TTTC-TT T-TTCTT TTTC-T-T TTTCTT TTTCTT TT-TCTT
*
21049459 TTCCTT TTTCTT TTT-TT TTTCTT CTTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT TTTCTT T
21049496 CATTTTTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
5 14 0.22
6 31 0.48
7 13 0.20
8 7 0.11
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:21049468 original size:14 final size:12
Alignment explanation
Indices: 21049408--21049493 Score: 56
Period size: 11 Copynumber: 6.9 Consensus size: 12
21049398 CAATCAAATA
21049408 TTTCTTTTTCT-
1 TTTCTTTTTCTC
21049419 TTTCTTTTGT-TCC
1 TTTCTTTT-TCT-C
21049432 TCTTCATCTTTTCT-
1 T-TTC-T-TTTTCTC
21049446 TTT-TTTTTCTCC
1 TTTCTTTTTCT-C
21049458 TTTCCTTTTTCT-
1 TTT-CTTTTTCTC
*
21049470 TTTTTTTTTCTTC
1 TTTCTTTTTC-TC
21049483 TTTCTTTTTCT
1 TTTCTTTTTCT
21049494 TTCATTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
10 6 0.10
11 16 0.27
12 9 0.15
13 12 0.20
14 11 0.18
15 2 0.03
16 4 0.07
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTCTTTTTCTC
Found at i:21049473 original size:25 final size:25
Alignment explanation
Indices: 21049411--21049505 Score: 97
Period size: 25 Copynumber: 3.7 Consensus size: 25
21049401 TCAAATATTT
*
21049411 CTTTTTCTTTTCTTTTGT-TCCTCTTC
1 CTTTTTCTTTT-TTTTTTCTCCT-TTC
*
21049437 ATCTTTTC-TTTTTTTTTCTCCTTTC
1 CT-TTTTCTTTTTTTTTTCTCCTTTC
*
21049462 CTTTTTCTTTTTTTTTTCTTCTTT-
1 CTTTTTCTTTTTTTTTTCTCCTTTC
21049486 CTTTTTCTTTCATTTTTTTC
1 CTTTTTCTTT--TTTTTTTC
21049506 ATTGATTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
24 15 0.25
25 24 0.40
26 16 0.27
27 5 0.08
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.75
Consensus pattern (25 bp):
CTTTTTCTTTTTTTTTTCTCCTTTC
Found at i:21049479 original size:35 final size:34
Alignment explanation
Indices: 21049440--21049580 Score: 89
Period size: 35 Copynumber: 4.1 Consensus size: 34
21049430 CCTCTTCATC
*
21049440 TTTTCTTTTTTTTTCTCCTTTCCTTTTTCTT-TT-TT
1 TTTTCTTTTTTTTT-T-CTTTCATTTTT-TTATTATT
21049475 TTTTCTTCTTTCTTTTTCTTTCATTTTTTTCATTGATT
1 TTTTCTT-TTT-TTTTTCTTTCATTTTTTT-ATT-ATT
* *
21049513 TTTTCTTTTTTTCTT-TTT--TTTTTTTATT-TC
1 TTTTCTTTTTTTTTTCTTTCATTTTTTTATTATT
* *** * *
21049543 CTTTCCCCTTTTATTCTTTCATTTTTCT-TTATT
1 TTTTCTTTTTTTTTTCTTTCATTTTTTTATTATT
21049576 TTTTC
1 TTTTC
21049581 ATTGAGTGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
30 11 0.13
31 3 0.04
32 5 0.06
33 18 0.21
34 2 0.02
35 20 0.24
36 10 0.12
37 7 0.08
38 9 0.11
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.77
Consensus pattern (34 bp):
TTTTCTTTTTTTTTTCTTTCATTTTTTTATTATT
Found at i:21049507 original size:9 final size:8
Alignment explanation
Indices: 21049438--21049537 Score: 53
Period size: 8 Copynumber: 11.9 Consensus size: 8
21049428 TTCCTCTTCA
*
21049438 TCTTTTCT
1 TCTTTTTT
21049446 T-TTTTTT
1 TCTTTTTT
**
21049453 TCTCCTTT
1 TCTTTTTT
*
21049461 CCTTTTTCT
1 TCTTTTT-T
*
21049470 TTTTTTTT
1 TCTTTTTT
21049478 TCTTCTTTCT
1 TCTT-TTT-T
*
21049488 T-TTTCTT
1 TCTTTTTT
21049495 TCATTTTTT
1 TC-TTTTTT
21049504 TCATTGATTTTT
1 TC--T--TTTTT
21049516 TCTTTTTT
1 TCTTTTTT
21049524 TCTTTTTT
1 TCTTTTTT
21049532 T-TTTTT
1 TCTTTTT
21049538 ATTTCCTTTC
Statistics
Matches: 71, Mismatches: 12, Indels: 19
0.70 0.12 0.19
Matches are distributed among these distances:
7 13 0.18
8 29 0.41
9 18 0.25
10 4 0.06
12 7 0.10
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:21049537 original size:13 final size:13
Alignment explanation
Indices: 21049463--21049537 Score: 62
Period size: 13 Copynumber: 5.4 Consensus size: 13
21049453 TCTCCTTTCC
21049463 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
21049476 TTTCTTCTTTCTTTT
1 TTT-TTCTTT-TTTT
*
21049491 TCTTTCATTTTTTT
1 TTTTTC-TTTTTTT
* *
21049505 CATTGATT-TTTTCTT
1 --TT-TTTCTTTTTTT
21049520 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
21049533 TTTTT
1 TTTTT
21049538 ATTTCCTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
12 2 0.04
13 16 0.33
14 13 0.27
15 15 0.31
16 1 0.02
17 2 0.04
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:21049542 original size:25 final size:25
Alignment explanation
Indices: 21049412--21049542 Score: 86
Period size: 24 Copynumber: 4.9 Consensus size: 25
21049402 CAAATATTTC
* * *
21049412 TTTTTCTTTTCTTTTGTTCCTCTTCAT
1 TTTTTCTTTT-TTTTTTTTCT-TTCTT
* * * *
21049439 CTTTTCTTTTTTTTTCTCCTTTC-C
1 TTTTTCTTTTTTTTTTTTCTTTCTT
21049463 TTTTTCTTTTTTTTTTCTTCTTTCTTT
1 TTTTTCTTTTTTTTTT-TTCTTTC-TT
21049490 TTCTTTCATTTTTTTCATTGATTT-TTTCTT
1 TT-TTTC-TTTTTTT--TT--TTTCTTTCTT
*
21049520 TTTTTCTTTTTTTTTTTTATTTC
1 TTTTTCTTTTTTTTTTTTCTTTC
21049543 CTTTCCCCTT
Statistics
Matches: 86, Mismatches: 8, Indels: 22
0.74 0.07 0.19
Matches are distributed among these distances:
24 17 0.20
25 13 0.15
26 10 0.12
27 11 0.13
28 11 0.13
29 11 0.13
30 4 0.05
31 6 0.07
32 2 0.02
33 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTTCTTTTTTTTTTTTCTTTCTT
Found at i:21051747 original size:19 final size:18
Alignment explanation
Indices: 21051719--21051761 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
21051709 TTCTAAGAAA
*
21051719 TAAAAATTAAATTGGGCC
1 TAAAACTTAAATTGGGCC
*
21051737 TTAAAACTTAATTTGGGCC
1 -TAAAACTTAAATTGGGCC
21051756 TAAAAC
1 TAAAAC
21051762 AAGGTTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (18 bp):
TAAAACTTAAATTGGGCC
Found at i:21057878 original size:5 final size:5
Alignment explanation
Indices: 21057868--21057955 Score: 54
Period size: 6 Copynumber: 16.0 Consensus size: 5
21057858 AAAAAATTAG
**
21057868 TAAAA TAAAA TAAATAA TAAAA CTGAAAA TAAAA TAAAA -AACT TAATATA
1 TAAAA TAAAA T-AA-AA TAAAA -T-AAAA TAAAA TAAAA TAAAA TAA-A-A
21057918 TAAAA T-AAA TAAAAA TAAAA TGAAAA TGAAAA TGAAAA
1 TAAAA TAAAA T-AAAA TAAAA T-AAAA T-AAAA T-AAAA
21057956 AGGAAAAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
4 6 0.09
5 26 0.38
6 27 0.39
7 10 0.14
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:21057886 original size:12 final size:12
Alignment explanation
Indices: 21057845--21057929 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 12
21057835 TTGTTTTCCA
21057845 AAAATAAATAAT
1 AAAATAAATAAT
*
21057857 AAAA-AAATTAGT
1 AAAATAAA-TAAT
21057869 AAAATAAAATAA-
1 AAAAT-AAATAAT
* *
21057881 ATAATAAA-ACT
1 AAAATAAATAAT
21057892 GAAAATAAAATAA-
1 -AAAAT-AAATAAT
*
21057905 AAAACTTAATATAT
1 AAAA-TAAATA-AT
21057919 AAAATAAATAA
1 AAAATAAATAA
21057930 AAATAAAATG
Statistics
Matches: 55, Mismatches: 8, Indels: 20
0.66 0.10 0.24
Matches are distributed among these distances:
10 1 0.02
11 6 0.11
12 28 0.51
13 12 0.22
14 8 0.15
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (12 bp):
AAAATAAATAAT
Found at i:21057888 original size:17 final size:17
Alignment explanation
Indices: 21057854--21057944 Score: 61
Period size: 17 Copynumber: 5.5 Consensus size: 17
21057844 AAAAATAAAT
*
21057854 AATAAAA-AAATTAGTAA
1 AATAAAATAAA-TAATAA
21057871 AATAAAATAAATAATAA
1 AATAAAATAAATAATAA
21057888 AACTGAAAAT-AA-AAT-A
1 AA-T-AAAATAAATAATAA
* *
21057904 AA-AAACTTAATATATAA
1 AATAAAATAAATA-ATAA
21057921 AAT-AAATAAA-AATAA
1 AATAAAATAAATAATAA
21057936 AATGAAAAT
1 AAT-AAAAT
21057945 GAAAATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.07
14 2 0.03
15 8 0.13
16 6 0.10
17 29 0.48
18 6 0.10
19 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (17 bp):
AATAAAATAAATAATAA
Found at i:21057898 original size:19 final size:19
Alignment explanation
Indices: 21057874--21057926 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
21057864 TTAGTAAAAT
21057874 AAAAT-AAATAATAAAACTG
1 AAAATAAAATAA-AAAACTG
*
21057893 AAAATAAAATAAAAAACTT
1 AAAATAAAATAAAAAACTG
21057912 AATATATAAAATAAA
1 AA-A-ATAAAATAAA
21057927 TAAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 7 0.23
21 10 0.33
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAATAAAATAAAAAACTG
Found at i:21057949 original size:12 final size:11
Alignment explanation
Indices: 21057869--21057955 Score: 61
Period size: 12 Copynumber: 7.4 Consensus size: 11
21057859 AAAAATTAGT
*
21057869 AAAATAAAATA
1 AAAATAAAATG
21057880 AATAATAAAACTG
1 AA-AATAAAA-TG
*
21057893 AAAATAAAATAA
1 AAAATAAAAT-G
21057905 AAAACTTAATATAT-
1 AAAA--TAA-A-ATG
*
21057919 AAAAT-AAATA
1 AAAATAAAATG
21057929 AAAATAAAATG
1 AAAATAAAATG
21057940 AAAATGAAAATG
1 AAAAT-AAAATG
21057952 AAAA
1 AAAA
21057956 AGGAAAAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 19
0.74 0.04 0.22
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 13 0.21
12 29 0.46
13 3 0.05
14 7 0.11
15 1 0.02
16 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (11 bp):
AAAATAAAATG
Found at i:21063376 original size:20 final size:21
Alignment explanation
Indices: 21063346--21063389 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
21063336 ACATAAAATT
21063346 AATACAGTAAAAATAT-ATTAA
1 AATACAGTAAAAA-ATCATTAA
21063367 AATA-AGTAAAAAATCATTAA
1 AATACAGTAAAAAATCATTAA
21063387 AAT
1 AAT
21063390 TGATATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 16 0.73
21 4 0.18
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
AATACAGTAAAAAATCATTAA
Found at i:21072575 original size:17 final size:17
Alignment explanation
Indices: 21072553--21072587 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21072543 CAACAACTCA
21072553 AAATATCATAATACCAT
1 AAATATCATAATACCAT
21072570 AAATATCATAATACCAT
1 AAATATCATAATACCAT
21072587 A
1 A
21072588 TTTTGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATCATAATACCAT
Found at i:21076649 original size:8 final size:8
Alignment explanation
Indices: 21076636--21076670 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
21076626 CATATAGATG
21076636 TGTATGTT
1 TGTATGTT
21076644 TGTATGTT
1 TGTATGTT
*
21076652 TGTATATT
1 TGTATGTT
21076660 TGTATGTT
1 TGTATGTT
21076668 TGT
1 TGT
21076671 GAGTGGACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.14, C:0.00, G:0.23, T:0.63
Consensus pattern (8 bp):
TGTATGTT
Found at i:21084564 original size:52 final size:52
Alignment explanation
Indices: 21084497--21084653 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
21084487 TATAACTATA
* *
21084497 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * *
21084549 CAAACTTGCCTATTAAGAATCCTTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * **
21084601 CAAACTTACCTATTAAGAAT-CCTCTTTCTCTTAGAATTATTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTC-TCCTCTTAGAATTCTTCTCCTGCAAGT
21084653 C
1 C
21084654 TTCTTGTCCA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
51 2 0.02
52 89 0.98
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:21091617 original size:34 final size:34
Alignment explanation
Indices: 21091578--21091649 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
21091568 TGGTCAACAT
* *
21091578 TTTTCAAGAG-TTCTTAGAAATGAATTTTTAAAAA
1 TTTTCAAGAGTTTCTTA-AAATGAATCTCTAAAAA
* *
21091612 TTTTCAAGAGTTTTTTAAAATGCATCTCTAAAAA
1 TTTTCAAGAGTTTCTTAAAATGAATCTCTAAAAA
21091646 TTTT
1 TTTT
21091650 TAAAAGATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 28 0.85
35 5 0.15
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (34 bp):
TTTTCAAGAGTTTCTTAAAATGAATCTCTAAAAA
Found at i:21095644 original size:6 final size:6
Alignment explanation
Indices: 21095635--21095718 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
21095625 AAAGCCCAAA
* * * * *
21095635 AATTTT AATTTT GATTTT AGTTTT AATTTT AGTTCT AA-TTT GATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
* * ** *
21095682 AGTTTT AATTTT GATTTT GGTTTTT AATTTT AGTTTT
1 AATTTT AATTTT AATTTT -AATTTT AATTTT AATTTT
21095719 TATTATTTTT
Statistics
Matches: 59, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
5 3 0.05
6 51 0.86
7 5 0.08
ACGTcount: A:0.23, C:0.01, G:0.11, T:0.65
Consensus pattern (6 bp):
AATTTT
Found at i:21095660 original size:18 final size:19
Alignment explanation
Indices: 21095635--21095718 Score: 77
Period size: 18 Copynumber: 4.6 Consensus size: 19
21095625 AAAGCCCAAA
21095635 AATTTTAATTTT-GATTTT
1 AATTTTAATTTTAGATTTT
* *
21095653 AGTTTTAATTTTAG-TTCT
1 AATTTTAATTTTAGATTTT
*
21095671 AA-TTTGATTTTAG-TTTT
1 AATTTTAATTTTAGATTTT
* * *
21095688 AATTTTGATTTTGGTTTTT
1 AATTTTAATTTTAGATTTT
*
21095707 AATTTTAGTTTT
1 AATTTTAATTTT
21095719 TATTATTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
17 15 0.27
18 25 0.45
19 15 0.27
ACGTcount: A:0.23, C:0.01, G:0.11, T:0.65
Consensus pattern (19 bp):
AATTTTAATTTTAGATTTT
Found at i:21095682 original size:17 final size:18
Alignment explanation
Indices: 21095655--21095699 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
21095645 TTGATTTTAG
*
21095655 TTTTAATTTTAGTTCTAA
1 TTTTGATTTTAGTTCTAA
*
21095673 -TTTGATTTTAGTTTTAA
1 TTTTGATTTTAGTTCTAA
21095690 TTTTGATTTT
1 TTTTGATTTT
21095700 GGTTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.22, C:0.02, G:0.09, T:0.67
Consensus pattern (18 bp):
TTTTGATTTTAGTTCTAA
Found at i:21095776 original size:13 final size:12
Alignment explanation
Indices: 21095758--21095792 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
21095748 GTCAAAAAGT
21095758 AAATAAAATAAAA
1 AAATAAAA-AAAA
21095771 AAATAAAAAAAA
1 AAATAAAAAAAA
21095783 AAACTAAAAA
1 AAA-TAAAAA
21095793 CATGGTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (12 bp):
AAATAAAAAAAA
Found at i:21100746 original size:20 final size:20
Alignment explanation
Indices: 21100718--21100765 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
21100708 TGAAAAGTAC
21100718 AAAATAAAAAAT-AAAAAAATG
1 AAAA-AAAAAATGAAAAAAA-G
* *
21100739 AAAAAAAAATTGAAAATAAG
1 AAAAAAAAAATGAAAAAAAG
21100759 AAAAAAA
1 AAAAAAA
21100766 GAGAAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAATGAAAAAAAG
Found at i:21102155 original size:46 final size:46
Alignment explanation
Indices: 21102102--21102413 Score: 258
Period size: 47 Copynumber: 7.0 Consensus size: 46
21102092 TAAGCATAAT
* *
21102102 CACTAAAGTTTTTCGAATGAGAATTTTTGAAATTTTGGATGTAAAA
1 CACTAAAGTTTTTTGAATGAGAATTTTTGAAATTTTGGATGTGAAA
* * *
21102148 C-CATAAAGTTTTTTTAATGAGAACCTTTTGAAATTTTGGATATGAAA
1 CAC-TAAAGTTTTTTGAATGAGAA-TTTTTGAAATTTTGGATGTGAAA
* *
21102195 CACTAAAGTTTTTTTAAT-ATGAATCTTTGAAA--TT---T-TG-AA
1 CACTAAAGTTTTTTGAATGA-GAATTTTTGAAATTTTGGATGTGAAA
* * ** ** *
21102234 TA-T-GA-TTTTTTGAATGAGAACCTTTGAAATTTAAGATATGAAA
1 CACTAAAGTTTTTTGAATGAGAATTTTTGAAATTTTGGATGTGAAA
* ** *
21102277 TCACTCAAGTTTTTCAAATGAGAATTTTTGAAATTTTGGATATGAAA
1 -CACTAAAGTTTTTTGAATGAGAATTTTTGAAATTTTGGATGTGAAA
* *
21102324 C-CATAAAATTTTTTGAATGAGAA-CTTTGAAATTTTGGATGTGAAA
1 CAC-TAAAGTTTTTTGAATGAGAATTTTTGAAATTTTGGATGTGAAA
* * *
21102369 CACTAAATTTTTTTTAATGTGAATTTTT-AAATTTTTGGATGTGAA
1 CACTAAAGTTTTTTGAATGAGAATTTTTGAAA-TTTTGGATGTGAA
21102414 TCCCTAAGTT
Statistics
Matches: 216, Mismatches: 30, Indels: 40
0.76 0.10 0.14
Matches are distributed among these distances:
36 20 0.09
37 2 0.01
38 2 0.01
39 3 0.01
40 2 0.01
41 2 0.01
42 2 0.01
43 2 0.01
44 3 0.01
45 44 0.20
46 62 0.29
47 71 0.33
48 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (46 bp):
CACTAAAGTTTTTTGAATGAGAATTTTTGAAATTTTGGATGTGAAA
Found at i:21102235 original size:22 final size:22
Alignment explanation
Indices: 21102205--21102247 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
21102195 CACTAAAGTT
*
21102205 TTTTTAATATGAATCTTTGAAA
1 TTTTGAATATGAATCTTTGAAA
* *
21102227 TTTTGAATATGATTTTTTGAA
1 TTTTGAATATGAATCTTTGAA
21102248 TGAGAACCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (22 bp):
TTTTGAATATGAATCTTTGAAA
Found at i:21102243 original size:83 final size:82
Alignment explanation
Indices: 21102156--21102403 Score: 250
Period size: 83 Copynumber: 2.9 Consensus size: 82
21102146 AACCATAAAG
21102156 TTTTTTTAATGAGAACCTTTTGAAATTTTGGATATGAAACACTAAAGTTTTTTTAATATGAATCT
1 TTTTTTTAATGAGAACC-TTTGAAATTTTGGATATGAAACACTAAAGTTTTTTTAATATGAAT-T
21102221 TTGAAATTTTGAATATG-A
64 TTGAAATTTTGAATATGAA
* ** * **
21102239 TTTTTTGAATGAGAACCTTTGAAATTTAAGATATGAAATCACTCAAGTTTTTCAAATGA-GAATT
1 TTTTTTTAATGAGAACCTTTGAAATTTTGGATATGAAA-CACTAAAGTTTTTTTAAT-ATGAA-T
*
21102303 TTTGAAATTTTGGATATGAAACCA
63 TTTGAAATTTTGAATATG--A--A
* * *
21102327 TAAAATTTTTTGAATGAGAA-CTTTGAAATTTTGGATGTGAAACACTAAATTTTTTTTAATGTGA
1 T----TTTTTT-AATGAGAACCTTTGAAATTTTGGATATGAAACACTAAAGTTTTTTTAATATGA
*
21102391 ATTTTTAAATTTT
61 ATTTTGAAATTTT
21102404 TGGATGTGAA
Statistics
Matches: 134, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
82 19 0.14
83 51 0.38
84 2 0.01
88 2 0.01
90 11 0.08
91 17 0.13
92 24 0.18
93 8 0.06
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (82 bp):
TTTTTTTAATGAGAACCTTTGAAATTTTGGATATGAAACACTAAAGTTTTTTTAATATGAATTTT
GAAATTTTGAATATGAA
Found at i:21102360 original size:45 final size:46
Alignment explanation
Indices: 21102238--21102413 Score: 169
Period size: 45 Copynumber: 3.8 Consensus size: 46
21102228 TTTGAATATG
** *
21102238 ATTTTTTGAATGAGAACCTTTGAAATTTAAGATATGAAATCACTCAA
1 ATTTTTTGAATGAGAACCTTTGAAATTTTGGATATGAAA-CACTAAA
* ** **
21102285 GTTTTTCAAATGAGAATTTTTGAAATTTTGGATATGAAAC-CATAAA
1 ATTTTTTGAATGAGAACCTTTGAAATTTTGGATATGAAACAC-TAAA
*
21102331 ATTTTTTGAATGAGAA-CTTTGAAATTTTGGATGTGAAACACTAAA
1 ATTTTTTGAATGAGAACCTTTGAAATTTTGGATATGAAACACTAAA
* * * * * *
21102376 TTTTTTTTAATGTGAA-TTTTTAAATTTTTGGATGTGAA
1 ATTTTTTGAATGAGAACCTTTGAAA-TTTTGGATATGAA
21102414 TCCCTAAGTT
Statistics
Matches: 108, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
45 45 0.42
46 31 0.29
47 32 0.30
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (46 bp):
ATTTTTTGAATGAGAACCTTTGAAATTTTGGATATGAAACACTAAA
Found at i:21102751 original size:17 final size:17
Alignment explanation
Indices: 21102731--21102765 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21102721 TACCAATTTG
*
21102731 AATTCTTGTGAACCTAA
1 AATTCTTGCGAACCTAA
*
21102748 AATTCTTGCGAATCTAA
1 AATTCTTGCGAACCTAA
21102765 A
1 A
21102766 TACTTCTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (17 bp):
AATTCTTGCGAACCTAA
Found at i:21103257 original size:15 final size:15
Alignment explanation
Indices: 21103237--21103268 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
21103227 AATGTCTAGA
21103237 TAATAAAGCTAATGG
1 TAATAAAGCTAATGG
21103252 TAATAAAGCTAATGG
1 TAATAAAGCTAATGG
21103267 TA
1 TA
21103269 GTCTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
TAATAAAGCTAATGG
Found at i:21116190 original size:27 final size:28
Alignment explanation
Indices: 21116160--21116218 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
21116150 TGGGTTAAGC
21116160 TCATAAGGTTAACTATATGTAGCTT-GG
1 TCATAAGGTTAACTATATGTAGCTTGGG
21116187 TCATAAGGTTAACTATATGTAGCTTGGG
1 TCATAAGGTTAACTATATGTAGCTTGGG
21116215 TCAT
1 TCAT
21116219 TTCTAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (28 bp):
TCATAAGGTTAACTATATGTAGCTTGGG
Found at i:21117512 original size:23 final size:23
Alignment explanation
Indices: 21117443--21117513 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
21117433 AACAATAATA
* * *
21117443 ATAATAATAATAACAAAAGAAAAT
1 ATAAAAATAA-AATAAAATAAAAT
*
21117467 CTAAAAATAAAAT-AAATAAAAAT
1 ATAAAAATAAAATAAAAT-AAAAT
21117490 ATAAACAA-AAAATAAAATAAAAT
1 ATAAA-AATAAAATAAAATAAAAT
21117513 A
1 A
21117514 ACCTGCGATC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 3 0.08
23 22 0.56
24 14 0.36
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (23 bp):
ATAAAAATAAAATAAAATAAAAT
Found at i:21118327 original size:34 final size:34
Alignment explanation
Indices: 21118289--21118366 Score: 79
Period size: 34 Copynumber: 2.3 Consensus size: 34
21118279 ACACGAATAA
*
21118289 AAGAATGAAAGACAAAAAAAATTAA-GAGTAAAA-T
1 AAGAATGAAA-A-AAAAAAAATTAAGGAATAAAATT
* *
21118323 AAGAAATTAAAAAAATAAAATTAAGGAATAAAATT
1 AAG-AATGAAAAAAAAAAAATTAAGGAATAAAATT
*
21118358 AAAAATGAA
1 AAGAATGAA
21118367 TAATAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
33 11 0.31
34 16 0.44
35 9 0.25
ACGTcount: A:0.69, C:0.01, G:0.12, T:0.18
Consensus pattern (34 bp):
AAGAATGAAAAAAAAAAAATTAAGGAATAAAATT
Found at i:21118790 original size:3 final size:3
Alignment explanation
Indices: 21118782--21118815 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21118772 TGCAAAATAT
21118782 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21118816 CTAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:21123259 original size:23 final size:24
Alignment explanation
Indices: 21123218--21123266 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
21123208 CAGTTCAAAG
21123218 AAATTCCAATATTGTTTTTCTTGA
1 AAATTCCAATATTGTTTTTCTTGA
21123242 AAATTCCAATATTGTTTTTCTTGA
1 AAATTCCAATATTGTTTTTCTTGA
21123266 A
1 A
21123267 CAGGGTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (24 bp):
AAATTCCAATATTGTTTTTCTTGA
Found at i:21125838 original size:19 final size:19
Alignment explanation
Indices: 21125814--21125852 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21125804 GATCCCATCA
*
21125814 ATTATCTTCACTCATAGCT
1 ATTATCATCACTCATAGCT
21125833 ATTATCATCACTCATAGCT
1 ATTATCATCACTCATAGCT
21125852 A
1 A
21125853 CAAATGCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTATCATCACTCATAGCT
Found at i:21127373 original size:24 final size:23
Alignment explanation
Indices: 21127346--21127400 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
21127336 TAAAGATTAA
* *
21127346 TAATTTTTATAATATAAAATAATT
1 TAATTTTTATAAAATAAAA-AAAT
*
21127370 TAATTTTTTTAAAATAAAAAAAT
1 TAATTTTTATAAAATAAAAAAAT
21127393 T-ATTTTTA
1 TAATTTTTA
21127401 AGTCATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 6 0.22
23 4 0.15
24 17 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATTTTTATAAAATAAAAAAAT
Found at i:21130136 original size:25 final size:26
Alignment explanation
Indices: 21130102--21130158 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
21130092 CGCCTTCAAT
21130102 GTTTT-TGTTAGGGATGATTGAA-GA
1 GTTTTCTGTTAGGGATGATTGAAGGA
*
21130126 GTTTTCTGTTAGGGATGATTGAAGGC
1 GTTTTCTGTTAGGGATGATTGAAGGA
21130152 GTTTTCT
1 GTTTTCT
21130159 TACTAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.17
25 17 0.57
26 8 0.27
ACGTcount: A:0.19, C:0.05, G:0.32, T:0.44
Consensus pattern (26 bp):
GTTTTCTGTTAGGGATGATTGAAGGA
Found at i:21133688 original size:42 final size:42
Alignment explanation
Indices: 21133558--21133689 Score: 110
Period size: 42 Copynumber: 3.1 Consensus size: 42
21133548 CAAAATAATA
* * *
21133558 TCAGACAACAAGGTTGAGTAAACCATTCAGCATATATATGAT
1 TCAGACAACAAGGTTAAGCAAACCATTTAGCATATATATGAT
** ** * **
21133600 TCAGACTCCTAATATCATA-CAAACCCATTTAGCA-A-A-ACAAT
1 TCAGACAAC-AAGGTTA-AGCAAA-CCATTTAGCATATATATGAT
21133641 ATCAGACAACAAGGTTAAGCAAACCATTTAGCATATATATGAT
1 -TCAGACAACAAGGTTAAGCAAACCATTTAGCATATATATGAT
21133684 TCAGAC
1 TCAGAC
21133690 CCCCAATATC
Statistics
Matches: 65, Mismatches: 17, Indels: 16
0.66 0.17 0.16
Matches are distributed among these distances:
40 11 0.17
41 12 0.18
42 22 0.34
43 10 0.15
44 10 0.15
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (42 bp):
TCAGACAACAAGGTTAAGCAAACCATTTAGCATATATATGAT
Found at i:21133724 original size:84 final size:84
Alignment explanation
Indices: 21133513--21133705 Score: 314
Period size: 84 Copynumber: 2.3 Consensus size: 84
21133503 TTTAGCATAC
* * * * *
21133513 GATTCAGTCCCTCAATATCATACAAACCCATTTAGCAAAATAATATCAGACAACAAGGTTGAGTA
1 GATTCAGACCCCCAATATCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGGTTAAGCA
21133578 AACCATTCAGCATATATAT
66 AACCATTCAGCATATATAT
* *
21133597 GATTCAGACTCCTAATATCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGGTTAAGCA
1 GATTCAGACCCCCAATATCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGGTTAAGCA
*
21133662 AACCATTTAGCATATATAT
66 AACCATTCAGCATATATAT
21133681 GATTCAGACCCCCAATATCATACAA
1 GATTCAGACCCCCAATATCATACAA
21133706 TACCATTCGG
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 99 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (84 bp):
GATTCAGACCCCCAATATCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGGTTAAGCA
AACCATTCAGCATATATAT
Found at i:21133737 original size:84 final size:84
Alignment explanation
Indices: 21133513--21133748 Score: 296
Period size: 84 Copynumber: 2.8 Consensus size: 84
21133503 TTTAGCATAC
* * * * * *
21133513 GATTCAGTCCCTCAATATCATACAAACCCATTTAGCAAAATAATATCAGACAACAAGGTTGAGTA
1 GATTCAGACCCCCAATATCATACAAACCCATTCAGCAAAACAATATCAGACAACAAGGTTAAGCA
21133578 AACCATTCAGCATATATAT
66 AACCATTCAGCATATATAT
* * *
21133597 GATTCAGACTCCTAATATCATACAAACCCATTTAGCAAAACAATATCAGACAACAAGGTTAAGCA
1 GATTCAGACCCCCAATATCATACAAACCCATTCAGCAAAACAATATCAGACAACAAGGTTAAGCA
*
21133662 AACCATTTAGCATATATAT
66 AACCATTCAGCATATATAT
* ** * * *
21133681 GATTCAGACCCCCAATATCATACAATA-CCATTCGGCATTACAATGTCATACTACAAGGTTTAA-
1 GATTCAGACCCCCAATATCATACAA-ACCCATTCAGCAAAACAATATCAGACAACAAGG-TTAAG
21133744 CAAAC
64 CAAAC
21133749 TACAATATTT
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
84 128 0.96
85 5 0.04
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (84 bp):
GATTCAGACCCCCAATATCATACAAACCCATTCAGCAAAACAATATCAGACAACAAGGTTAAGCA
AACCATTCAGCATATATAT
Found at i:21134976 original size:221 final size:221
Alignment explanation
Indices: 21134543--21134940 Score: 562
Period size: 221 Copynumber: 1.8 Consensus size: 221
21134533 TTTATGTGAC
* ** * * * *
21134543 GGTATATTGAAGGCATTTTACCTTAGAAGACGCCTTTAATAATTTCTAAAATTTTTTGAGGGAAA
1 GGTATATTAAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCCAAAATTTTTAGAGAGAAA
* * * *
21134608 ATATTGAAGGTGTCTGTTATTAACAAATACCTTCGGTAATGGATTACTAAATTTAAAGGTATATT
66 ATATTGAAGGTGTCTATTATTAACAAACACCTTCCGTAATAGATTACTAAATTTAAAGGTATATT
* * * * *
21134673 GAAAGTACTTTTTCAAATAAACGCCTTCTATAACAATTGTGCTATATCGAATGCATTTTATAATG
131 GAAAGCACATATTCAAATAAACACCTTCTATAACAATCGTGCTATATCGAATGCATTTTATAATG
*
21134738 AAAGACGCCTTTAATAATCCCATCAT
196 AAAGACGCCGTTAATAATCCCATCAT
* *
21134764 GGTATATTAAAGGTATTTTATAGTAGAAGACGCCTTTAATAATGTCCAAAATTTTTAGAGAGAAA
1 GGTATATTAAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCCAAAATTTTTAGAGAGAAA
* * *
21134829 ATATTGAAGGTGTCTATTATTAACAAACGCCTTCCGTAATAGATTACTAAGTTTAAGGGTATATT
66 ATATTGAAGGTGTCTATTATTAACAAACACCTTCCGTAATAGATTACTAAATTTAAAGGTATATT
* * * *
21134894 GAAAGCGCATATTCGAATAAACACCTTCTATAACCATCGTGGTATAT
131 GAAAGCACATATTCAAATAAACACCTTCTATAACAATCGTGCTATAT
21134941 TGAAGGTGTT
Statistics
Matches: 152, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
221 152 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (221 bp):
GGTATATTAAAGGCATTTTACAGTAGAAGACGCCTTTAATAATGTCCAAAATTTTTAGAGAGAAA
ATATTGAAGGTGTCTATTATTAACAAACACCTTCCGTAATAGATTACTAAATTTAAAGGTATATT
GAAAGCACATATTCAAATAAACACCTTCTATAACAATCGTGCTATATCGAATGCATTTTATAATG
AAAGACGCCGTTAATAATCCCATCAT
Found at i:21146107 original size:21 final size:21
Alignment explanation
Indices: 21146083--21146125 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21146073 CTAGATTTCA
*
21146083 CGTCCAAATATCCTTTAACAT
1 CGTCCAAATATCCTTCAACAT
*
21146104 CGTCTAAATATCCTTCAACAT
1 CGTCCAAATATCCTTCAACAT
21146125 C
1 C
21146126 ATGGCTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.33
Consensus pattern (21 bp):
CGTCCAAATATCCTTCAACAT
Found at i:21148195 original size:3 final size:3
Alignment explanation
Indices: 21148187--21148216 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21148177 TTTACAAATT
21148187 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21148217 TATTCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21149903 original size:12 final size:12
Alignment explanation
Indices: 21149888--21149938 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
21149878 TTCATTTTTA
21149888 TTATTTATTA-TT
1 TTATTT-TTAGTT
21149900 TTATTTTTTAGTT
1 TTA-TTTTTAGTT
21149913 GTTA-TTTTAGTT
1 -TTATTTTTAGTT
*
21149925 TTAGTTTTAGTT
1 TTATTTTTAGTT
21149937 TT
1 TT
21149939 TTTATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.09
12 24 0.69
13 5 0.14
14 3 0.09
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (12 bp):
TTATTTTTAGTT
Found at i:21149926 original size:6 final size:6
Alignment explanation
Indices: 21149905--21149938 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
21149895 TTATTTTATT
21149905 TTTTAG TTGTTA- TTTTAG TTTTAG TTTTAG TTTT
1 TTTTAG TT-TTAG TTTTAG TTTTAG TTTTAG TTTT
21149939 TTTATTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.12
6 20 0.77
7 3 0.12
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (6 bp):
TTTTAG
Found at i:21149928 original size:18 final size:19
Alignment explanation
Indices: 21149895--21149930 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21149885 TTATTATTTA
*
21149895 TTATTTTATTTTTTAGTTG
1 TTATTTTATGTTTTAGTTG
21149914 TTATTTTA-GTTTTAGTT
1 TTATTTTATGTTTTAGTT
21149931 TTAGTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.17, C:0.00, G:0.11, T:0.72
Consensus pattern (19 bp):
TTATTTTATGTTTTAGTTG
Found at i:21150982 original size:17 final size:17
Alignment explanation
Indices: 21150929--21150986 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
21150919 GATTTTGATT
*
21150929 TTATTTGTTTTATTTTC
1 TTATTTATTTTATTTTC
**
21150946 TT-TTT-TTACATTTT-
1 TTATTTATTTTATTTTC
21150960 TATATTTATTTTATTTTC
1 T-TATTTATTTTATTTTC
21150978 TTATTTATT
1 TTATTTATT
21150987 ATTTTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 8 0.24
16 6 0.18
17 17 0.52
18 1 0.03
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTATTTTATTTTC
Found at i:21150991 original size:32 final size:31
Alignment explanation
Indices: 21150930--21150993 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
21150920 ATTTTGATTT
*
21150930 TATTTGTTTTATTTTCTTTTTTTACATTTTTA
1 TATTTATTTTATTTTCTTTTTTTA-ATTTTTA
21150962 TATTTATTTTATTTTCTTATTTATT-ATTTTTA
1 TATTTATTTTATTTTCTT-TTT-TTAATTTTTA
21150994 ATTATGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 24 0.83
33 3 0.10
34 2 0.07
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (31 bp):
TATTTATTTTATTTTCTTTTTTTAATTTTTA
Found at i:21151104 original size:25 final size:26
Alignment explanation
Indices: 21151055--21151104 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
21151045 TATAGTCTAT
* *
21151055 TTTGCATGATTTTTTTTATGGTATTCA
1 TTTGCATGA-TTTTATTATGATATTCA
21151082 TTTGCATGA-TTTATTATGATATT
1 TTTGCATGATTTTATTATGATATT
21151105 TGTTACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
27 9 0.43
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (26 bp):
TTTGCATGATTTTATTATGATATTCA
Found at i:21151238 original size:25 final size:27
Alignment explanation
Indices: 21151201--21151250 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
21151191 TTACATAATA
21151201 TTTTGTATGGATTTTATTTGCATGAAG
1 TTTTGTATGGATTTTATTTGCATGAAG
*
21151228 TTTT-TAT-GATTTTTTTTGCATGA
1 TTTTGTATGGATTTTATTTGCATGA
21151251 TAATTTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.68
26 3 0.14
27 4 0.18
ACGTcount: A:0.20, C:0.04, G:0.18, T:0.58
Consensus pattern (27 bp):
TTTTGTATGGATTTTATTTGCATGAAG
Found at i:21151992 original size:38 final size:39
Alignment explanation
Indices: 21151949--21152097 Score: 122
Period size: 39 Copynumber: 3.7 Consensus size: 39
21151939 TTTTCATGTG
*
21151949 TACTAACCCATTTG-TTTATTTTGTAGCTTATAATATTT
1 TACTAACCTATTTGTTTTATTTTGTAGCTTATAATATTT
** * ** *
21151987 TACTAATTTATTTGTTTTATTTTGTAGATTTTGATTTTTGTATGTG
1 TACTAACCTATTTGTTTTATTTTGTAG--CTT-A---TAATAT-TT
* *
21152033 TACTAACCTATTTG-TTTATTTTGTAGCTTATGATGTTT
1 TACTAACCTATTTGTTTTATTTTGTAGCTTATAATATTT
**
21152071 TACTAATTTATTTGTTTTATTTTGTAG
1 TACTAACCTATTTGTTTTATTTTGTAG
21152098 ATTTTGATTT
Statistics
Matches: 86, Mismatches: 16, Indels: 17
0.72 0.13 0.14
Matches are distributed among these distances:
38 24 0.28
39 27 0.31
41 2 0.02
42 2 0.02
43 2 0.02
45 16 0.19
46 13 0.15
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.58
Consensus pattern (39 bp):
TACTAACCTATTTGTTTTATTTTGTAGCTTATAATATTT
Found at i:21152046 original size:84 final size:83
Alignment explanation
Indices: 21151930--21152121 Score: 330
Period size: 84 Copynumber: 2.3 Consensus size: 83
21151920 TTATATAATT
21151930 ATTTATGATTTTTCATGTGTACTAACCCATTTGTTTATTTTGTAGCTTATAATATTTTACTAATT
1 ATTT-TGATTTTTCATGTGTACTAACCCATTTGTTTATTTTGTAGCTTATAATATTTTACTAATT
21151995 TATTTGTTTTATTTTGTAG
65 TATTTGTTTTATTTTGTAG
* * * *
21152014 ATTTTGATTTTTGTATGTGTACTAACCTATTTGTTTATTTTGTAGCTTATGATGTTTTACTAATT
1 ATTTTGATTTTT-CATGTGTACTAACCCATTTGTTTATTTTGTAGCTTATAATATTTTACTAATT
21152079 TATTTGTTTTATTTTGTAG
65 TATTTGTTTTATTTTGTAG
21152098 ATTTTGATTTTTCATGTGTACTAA
1 ATTTTGATTTTTCATGTGTACTAA
21152122 TTTATTTAAT
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
83 19 0.19
84 83 0.81
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.58
Consensus pattern (83 bp):
ATTTTGATTTTTCATGTGTACTAACCCATTTGTTTATTTTGTAGCTTATAATATTTTACTAATTT
ATTTGTTTTATTTTGTAG
Found at i:21153302 original size:12 final size:12
Alignment explanation
Indices: 21153285--21153309 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21153275 TCATCCTTAT
21153285 TGCATTCATTCA
1 TGCATTCATTCA
21153297 TGCATTCATTCA
1 TGCATTCATTCA
21153309 T
1 T
21153310 TCTCATACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TGCATTCATTCA
Found at i:21157115 original size:41 final size:41
Alignment explanation
Indices: 21157061--21157290 Score: 153
Period size: 41 Copynumber: 5.5 Consensus size: 41
21157051 GTTGATTTTC
*
21157061 TTTAAAGTTTCATAGCCTTTGGTAAAAAGAGCTTTTTCATT
1 TTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTTTTTCATT
* * * *
21157102 TTTCAAGTTTCATAGCCTCTAGCAAGAAGAG-TTCTTTCATTTTTTT
1 TTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTT-TTTCA-----TT
* * * *
21157148 TTTAAAGTTTCATAGTCTTTAGTGAAATGAGCTCTTTCATT
1 TTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTTTTTCATT
* * * *
21157189 TTTAAAGTTTCATAACCTCTAGTGAGAGAAG-G-TCTTTCATTT
1 TTTAAAGTTTCATAGCCTTTAGT-A-AAAAGAGCTTTTTCA-TT
* * * * * * * *
21157231 TTTAAAGTTT-AAAACCTCTGGTGAGAGGAGTTTTTTCATT
1 TTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTTTTTCATT
*
21157271 TTTAAAGTTTCATAACCTTT
1 TTTAAAGTTTCATAGCCTTT
21157291 GGTGAGAGGA
Statistics
Matches: 150, Mismatches: 26, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
39 4 0.03
40 15 0.10
41 83 0.55
42 13 0.09
43 3 0.02
46 31 0.21
47 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (41 bp):
TTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTTTTTCATT
Found at i:21157186 original size:87 final size:87
Alignment explanation
Indices: 21157056--21157324 Score: 243
Period size: 87 Copynumber: 3.2 Consensus size: 87
21157046 AAAATGTTGA
* * * *
21157056 TTTTCTTTAAAGTTTCATAGCCTTTGGTAAAAAGAGCTTTTTCATTTTTCAAGTTTCATAGCCTC
1 TTTTCTTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTCTTTCATTTTTAAAGTTTCATAACCTC
21157121 TAG-CA-AGAAGAGTTCTTTCATT
66 TAGTCAGAGAAG-G-TCTTTCATT
* * * *
21157143 TTTTTTTTAAAGTTTCATAGTCTTTAGTGAAATGAGCTCTTTCATTTTTAAAGTTTCATAACCTC
1 TTTTCTTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTCTTTCATTTTTAAAGTTTCATAACCTC
*
21157208 TAGTGAGAGAAGGTCTTTCA--
66 TAGTCAGAGAAGGTCTTTCATT
* * * * * * * * * *
21157228 -TTT-TTTAAAGTTT-AAAACCTCTGGTGAGAGGAGTTTTTTCATTTTTAAAGTTTCATAACCTT
1 TTTTCTTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTCTTTCATTTTTAAAGTTTCATAACCTC
* * *
21157290 TGGTGAGAGGAA-ATCTTTCA-T
66 TAGTCAGA-GAAGGTCTTTCATT
21157311 TTTTC-TTAAAGTTT
1 TTTTCTTTAAAGTTT
21157325 AAAGCCTCTA
Statistics
Matches: 155, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
82 53 0.34
83 13 0.08
84 15 0.10
87 67 0.43
88 2 0.01
89 5 0.03
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (87 bp):
TTTTCTTTAAAGTTTCATAGCCTTTAGTAAAAAGAGCTCTTTCATTTTTAAAGTTTCATAACCTC
TAGTCAGAGAAGGTCTTTCATT
Found at i:21157288 original size:82 final size:84
Alignment explanation
Indices: 21157093--21157343 Score: 247
Period size: 82 Copynumber: 3.0 Consensus size: 84
21157083 TAAAAAGAGC
* * ** * ** *
21157093 TTTTTCATTTTTCAAGTTTCATAGCCTCTAGCAAGAAGAGTTCTTTCATTTTTTTTTTAAAGTTT
1 TTTTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAAATCTTTCA--TTTTTCTTAAAGTTT
* ** * * * *
21157158 CATAGTCTTTAGTGAAATGAGC
64 -AAAACCTCTAGTGAGAGGAGT
* *
21157180 TCTTTCATTTTTAAAGTTTCATAACCTCTAGTGAGA-GAAGGTCTTTCA-TTTT-TTAAAGTTTA
1 TTTTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAA-ATCTTTCATTTTTCTTAAAGTTTA
*
21157242 AAACCTCTGGTGAGAGGAGT
65 AAACCTCTAGTGAGAGGAGT
* *
21157262 TTTTTCATTTTTAAAGTTTCATAACCTTTGGTGAGAGGAAATCTTTCATTTTTCTTAAAGTTTAA
1 TTTTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAAATCTTTCATTTTTCTTAAAGTTTAA
* *
21157327 AGCCTCTATTGAGAGGA
66 AACCTCTAGTGAGAGGA
21157344 AACATTTTAA
Statistics
Matches: 138, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
82 53 0.38
83 16 0.12
84 29 0.21
86 2 0.01
87 38 0.28
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (84 bp):
TTTTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAAATCTTTCATTTTTCTTAAAGTTTAA
AACCTCTAGTGAGAGGAGT
Found at i:21157294 original size:41 final size:41
Alignment explanation
Indices: 21157095--21157314 Score: 190
Period size: 41 Copynumber: 5.2 Consensus size: 41
21157085 AAAAGAGCTT
* * ** * *
21157095 TTTCATTTTTCAAGTTTCATAGCCTCTAGCAAGAAGAGTTC
1 TTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
** * * * *
21157136 TTTCATTTTTTTTTTAAAGTTTCATAGTCTTTAGTGAAATGAGCTC
1 TTTCA-----TTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
* *
21157182 TTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGAAGGTC
1 TTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
* * * *
21157223 TTTCATTTTTTAAAGTTT-AAAACCTCTGGTGAGAGGAGTTT
1 TTTCA-TTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
* * *
21157264 TTTCATTTTTAAAGTTTCATAACCTTTGGTGAGAGGAAATC
1 TTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
21157305 TTTCATTTTT
1 TTTCATTTTT
21157315 CTTAAAGTTT
Statistics
Matches: 147, Mismatches: 25, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
40 12 0.08
41 90 0.61
42 12 0.08
46 33 0.22
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.45
Consensus pattern (41 bp):
TTTCATTTTTAAAGTTTCATAACCTCTAGTGAGAGGAGATC
Found at i:21158680 original size:6 final size:6
Alignment explanation
Indices: 21158671--21158714 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
21158661 TTCTTTTTCT
*
21158671 TTTTTA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT-A TTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTT
21158715 CGTTTATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.73
Consensus pattern (6 bp):
TTTTGA
Found at i:21158742 original size:22 final size:22
Alignment explanation
Indices: 21158717--21158770 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
21158707 TTTTATTTCG
*
21158717 TTTATTTTCTATTTTTTC-CTTT
1 TTTATTTT-TATGTTTTCTCTTT
* *
21158739 TTTATGGTTTATGTTTTCTTTTT
1 TTTAT-TTTTATGTTTTCTCTTT
21158762 TTTATTTTT
1 TTTATTTTT
21158771 GATTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.09, C:0.07, G:0.06, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATGTTTTCTCTTT
Found at i:21158949 original size:50 final size:49
Alignment explanation
Indices: 21158872--21158979 Score: 155
Period size: 50 Copynumber: 2.2 Consensus size: 49
21158862 TTATAGTTTA
*
21158872 TTTTGCAT-TTTTTTTTATGGTTTCATTTGCATAATTTATCATGATATT
1 TTTTGCATGATTTTTTTATGGTTTCATTTGCATAATTTATCATGATATT
* * *
21158920 TTTTGCATGATTTTTTTATGGTATTCATTTGCTTGATTTATTATGATATT
1 TTTTGCATGATTTTTTTATGGT-TTCATTTGCATAATTTATCATGATATT
*
21158970 TTTTGTATGA
1 TTTTGCATGA
21158980 ATAATTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
48 8 0.15
49 12 0.23
50 33 0.62
ACGTcount: A:0.20, C:0.06, G:0.13, T:0.60
Consensus pattern (49 bp):
TTTTGCATGATTTTTTTATGGTTTCATTTGCATAATTTATCATGATATT
Found at i:21158963 original size:25 final size:25
Alignment explanation
Indices: 21158893--21158969 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
21158883 TTTTTATGGT
* *
21158893 TTCATTTGCATAATTTATCATGATA
1 TTCATTTGCATGATTTATTATGATA
* * *
21158918 TT-TTTTGCATGATTTTTTTATGGTA
1 TTCATTTGCATGA-TTTATTATGATA
*
21158943 TTCATTTGCTTGATTTATTATGATA
1 TTCATTTGCATGATTTATTATGATA
21158968 TT
1 TT
21158970 TTTTGTATGA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 8 0.20
25 25 0.61
26 8 0.20
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.57
Consensus pattern (25 bp):
TTCATTTGCATGATTTATTATGATA
Found at i:21159082 original size:43 final size:43
Alignment explanation
Indices: 21158997--21159082 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
21158987 TAATATATAT
*
21158997 TTACATAATATTTTGCAATAATTTAATTTATTTACATGATTTA
1 TTACATAATATTTTGCAATAATTTAATTTATTGACATGATTTA
* *
21159040 TTACATAATATTTTGC-ATGGAATTT-ATTTATTGGCATTATTTA
1 TTACATAATATTTTGCAAT--AATTTAATTTATTGACATGATTTA
21159083 CTATGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.05
43 31 0.82
44 5 0.13
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.51
Consensus pattern (43 bp):
TTACATAATATTTTGCAATAATTTAATTTATTGACATGATTTA
Found at i:21159111 original size:14 final size:15
Alignment explanation
Indices: 21159085--21159121 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
21159075 ATTATTTACT
21159085 ATGATTTATTTTTGC
1 ATGATTTATTTTTGC
21159100 ATGATTTA-TTTTGC
1 ATGATTTATTTTTGC
*
21159114 ATGTTTTA
1 ATGATTTA
21159122 ATTATGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.22, C:0.05, G:0.14, T:0.59
Consensus pattern (15 bp):
ATGATTTATTTTTGC
Found at i:21160649 original size:12 final size:12
Alignment explanation
Indices: 21160629--21160663 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21160619 CATTTGTTTA
*
21160629 TTTAGTTATTTG
1 TTTATTTATTTG
*
21160641 TTTATTTATCTG
1 TTTATTTATTTG
21160653 TTTATTTATTT
1 TTTATTTATTT
21160664 TGGGTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:21160732 original size:23 final size:23
Alignment explanation
Indices: 21160683--21160735 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
21160673 TTTTTTATTC
*
21160683 ATTTATCTTTAATTTTTCGTTTA
1 ATTTATCTTTAATTTTTCGTCTA
* *
21160706 ATTTATCTTTGATTTTAT-GTCTG
1 ATTTATCTTTAATTTT-TCGTCTA
21160729 ATTTATC
1 ATTTATC
21160736 ATTAGCTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTATCTTTAATTTTTCGTCTA
Found at i:21161674 original size:21 final size:22
Alignment explanation
Indices: 21161650--21161693 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
21161640 CAAGTCGAGC
* *
21161650 TATTTTGGTATTTTATTT-TTT
1 TATTTAGGTATTATATTTATTT
*
21161671 TATTTAGTTATTATATTTATTT
1 TATTTAGGTATTATATTTATTT
21161693 T
1 T
21161694 GTAAGTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (22 bp):
TATTTAGGTATTATATTTATTT
Found at i:21163525 original size:16 final size:15
Alignment explanation
Indices: 21163490--21163532 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
21163480 TGCATCATTT
21163490 TCATTGTCATATGCA
1 TCATTGTCATATGCA
* *
21163505 ACATTGTGCATCTGCA
1 TCATTGT-CATATGCA
*
21163521 TCATTTTCATAT
1 TCATTGTCATAT
21163533 TAGATGTCAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (15 bp):
TCATTGTCATATGCA
Found at i:21165966 original size:25 final size:26
Alignment explanation
Indices: 21165933--21165986 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 26
21165923 AAAATGTCTC
21165933 AAAGATAAAA-AGCAAAAAAA-AAAAGA
1 AAAGATAAAACA--AAAAAAAGAAAAGA
21165959 AAAG-TAAAACAAAAAAAAGAAAAGA
1 AAAGATAAAACAAAAAAAAGAAAAGA
21165984 AAA
1 AAA
21165987 TTTAAATGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (26 bp):
AAAGATAAAACAAAAAAAAGAAAAGA
Found at i:21165974 original size:20 final size:19
Alignment explanation
Indices: 21165940--21165986 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
21165930 CTCAAAGATA
*
21165940 AAAAGCAAA-AAAAAAAAG
1 AAAAGAAAACAAAAAAAAG
21165958 AAAAGTAAAACAAAAAAAAG
1 AAAAG-AAAACAAAAAAAAG
21165978 AAAAGAAAA
1 AAAAGAAAA
21165987 TTTAAATGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 14 0.54
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (19 bp):
AAAAGAAAACAAAAAAAAG
Found at i:21166395 original size:7 final size:8
Alignment explanation
Indices: 21166384--21166437 Score: 92
Period size: 8 Copynumber: 6.8 Consensus size: 8
21166374 AAAAATGACA
21166384 AAAAAATG
1 AAAAAATG
21166392 -AAAAATG
1 AAAAAATG
21166399 AAAAAATG
1 AAAAAATG
21166407 AAAAAATG
1 AAAAAATG
21166415 AAAAAATG
1 AAAAAATG
21166423 AGAAAAATG
1 A-AAAAATG
21166432 AAAAAA
1 AAAAAA
21166438 GAGAGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.16
8 29 0.66
9 8 0.18
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:21166443 original size:18 final size:17
Alignment explanation
Indices: 21166360--21166447 Score: 94
Period size: 16 Copynumber: 5.2 Consensus size: 17
21166350 AATAAATAAT
21166360 AAATGAAAAACAA-A-AA
1 AAATGAAAAA-AAGAGAA
21166376 AAATGACAAAAAA-ATGAA
1 AAATGA-AAAAAAGA-GAA
*
21166394 AAATGAAAAAATGA-AA
1 AAATGAAAAAAAGAGAA
*
21166410 AAATGAAAAAATGAGAA
1 AAATGAAAAAAAGAGAA
21166427 AAATGAAAAAAGAGAGAA
1 AAATGAAAAAA-AGAGAA
21166445 AAA
1 AAA
21166448 AAAGACTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
16 25 0.39
17 22 0.34
18 17 0.27
ACGTcount: A:0.75, C:0.02, G:0.14, T:0.09
Consensus pattern (17 bp):
AAATGAAAAAAAGAGAA
Found at i:21167376 original size:25 final size:25
Alignment explanation
Indices: 21167348--21167400 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
21167338 TTATGACTTA
21167348 AGAGTATGGCATCTACATTATTGTG
1 AGAGTATGGCATCTACATTATTGTG
21167373 AGAGTATGGCATCTACATTATTGTG
1 AGAGTATGGCATCTACATTATTGTG
21167398 AGA
1 AGA
21167401 ATCCAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (25 bp):
AGAGTATGGCATCTACATTATTGTG
Found at i:21167577 original size:21 final size:21
Alignment explanation
Indices: 21167553--21167660 Score: 85
Period size: 22 Copynumber: 5.0 Consensus size: 21
21167543 AATAAGAGTC
*
21167553 TTTTAGTTTTCAAGTGAGAATT
1 TTTTAGTTTTCAAATGAGAA-T
*
21167575 TTTTGAGTTTTCAAACGAGAAT
1 TTTT-AGTTTTCAAATGAGAAT
* * *
21167597 ATTT-GAATTTCAAATGAGAAAC
1 TTTTAG-TTTTCAAATGAG-AAT
*
21167619 TTTAAGTTTTCAAATGAGAAT
1 TTTTAGTTTTCAAATGAGAAT
* *
21167640 CTTTGAG-TTTCAAATAAGAAT
1 -TTTTAGTTTTCAAATGAGAAT
21167661 CTTTGACATG
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.01
21 25 0.36
22 28 0.41
23 15 0.22
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (21 bp):
TTTTAGTTTTCAAATGAGAAT
Found at i:21167638 original size:43 final size:43
Alignment explanation
Indices: 21167580--21167664 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
21167570 GAATTTTTTG
*
21167580 AGTTTTCAAACGAGAATATTTGAATTTCAAATGAGAAACTTTA
1 AGTTTTCAAACGAGAATATTTGAATTTCAAATAAGAAACTTTA
* * * *
21167623 AGTTTTCAAATGAGAATCTTTGAGTTTCAAATAAGAATCTTT
1 AGTTTTCAAACGAGAATATTTGAATTTCAAATAAGAAACTTT
21167665 GACATGTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (43 bp):
AGTTTTCAAACGAGAATATTTGAATTTCAAATAAGAAACTTTA
Found at i:21167661 original size:21 final size:22
Alignment explanation
Indices: 21167540--21167666 Score: 132
Period size: 21 Copynumber: 5.8 Consensus size: 22
21167530 TTGTGAATCC
* * *
21167540 TCAAATAAGAGTCTTTTAGTTT
1 TCAAATGAGAATCTTTGAGTTT
* *
21167562 TCAAGTGAGAATTTTTTGAGTTT
1 TCAAATGAGAA-TCTTTGAGTTT
* * *
21167585 TCAAACGAGAATATTTGA-ATT
1 TCAAATGAGAATCTTTGAGTTT
* *
21167606 TCAAATGAGAAACTTTAAGTTT
1 TCAAATGAGAATCTTTGAGTTT
21167628 TCAAATGAGAATCTTTGAG-TT
1 TCAAATGAGAATCTTTGAGTTT
*
21167649 TCAAATAAGAATCTTTGA
1 TCAAATGAGAATCTTTGA
21167667 CATGTGAAAC
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
21 35 0.41
22 33 0.38
23 18 0.21
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TCAAATGAGAATCTTTGAGTTT
Found at i:21167750 original size:42 final size:41
Alignment explanation
Indices: 21167691--21167794 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 41
21167681 AAATTTGTTG
* * *
21167691 GATGTGAATAT-TCAAA-TTCGAATGAGAAGCTTTGAACTCTCA
1 GATGTGAATCTCT-AAATTTCGAATAAGAACCTTTGAACT-T-A
**
21167733 GATGTGAATCTCTAAATTTTTTAATAAGAACCTTTGAACTTA
1 GATGTGAATCTCTAAA-TTTCGAATAAGAACCTTTGAACTTA
*
21167775 GATGTGAAACTCTAAGATTT
1 GATGTGAATCTCTAA-ATTT
21167795 ATCAAATGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
42 31 0.60
43 3 0.06
44 18 0.35
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (41 bp):
GATGTGAATCTCTAAATTTCGAATAAGAACCTTTGAACTTA
Found at i:21168262 original size:19 final size:18
Alignment explanation
Indices: 21168236--21168280 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
21168226 AATTTTGGTG
21168236 AATTCTTGCAAAGCTAAA
1 AATTCTTGCAAAGCTAAA
** *
21168254 AAGTTCTTGTGAATCTAAA
1 AA-TTCTTGCAAAGCTAAA
21168273 AATTCTTG
1 AATTCTTG
21168281 TGAATCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (18 bp):
AATTCTTGCAAAGCTAAA
Found at i:21168292 original size:20 final size:19
Alignment explanation
Indices: 21168249--21168287 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
21168239 TCTTGCAAAG
21168249 CTAAAAAGTTCTTGTGAAT
1 CTAAAAAGTTCTTGTGAAT
21168268 CTAAAAA-TTCTTGTGAAT
1 CTAAAAAGTTCTTGTGAAT
21168286 CT
1 CT
21168288 TTAAATTGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (19 bp):
CTAAAAAGTTCTTGTGAAT
Found at i:21168436 original size:43 final size:43
Alignment explanation
Indices: 21168383--21168838 Score: 445
Period size: 43 Copynumber: 10.5 Consensus size: 43
21168373 ATCGAAGAGT
* * *
21168383 TTTACTTTTCAAAGTTATTTAGCCTCTGATTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
** * * * **
21168426 TTTATTTTTCAAAGTCATTGAGTCTTTTATTAGAATAGCTTTA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
* *
21168469 TTTATTTTTCCAAAGTTGTTGAACCTCTAATTAGAGGAGCTTTA
1 TTTATTTTT-CAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
* * * *
21168513 TTTATTTTCCAAAGTTGTTAAGTCTTTGATTAGAGGAGCTTTA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
* * ** * *
21168556 TTTATTTTTCAAATTTGTTGAGCCTTTGATTAGAAAAGCCTTG
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
* * *
21168599 TTTA-TTTTCAAAGTTGTTGTGCCTCTGATTAAAGGAGCTTTG
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
** * * * *
21168641 TTTATTTTTCAAAAGTCATTGTGTCTCTAATTAGAAGAGCTTT-
1 TTTATTTTTC-AAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
* * *
21168684 TTTATTTTTCAAAGTTATTGAGCCTCTGTTTAGAGAAGCTTTA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
*
21168727 TTTATTTTTTCAAAGTTGTTTAAGCCTCTG-TTCAGAGGAGCTTTA
1 TTTA-TTTTTCAAAGTTG-TTGAGCCTCTGATT-AGAGGAGCTTTA
* * * **
21168772 TTAAATTTTCAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCCATA
1 TTTATTTTTCAAAGTTGTTGAGCCTCTGA-TTAGAGGAGCTTTA
21168815 TTTATTTTTCCAAAAGTTG-TGAGC
1 TTTATTTTT-C-AAAGTTGTTGAGC
21168839 TTTTCCTTAT
Statistics
Matches: 340, Mismatches: 62, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
42 60 0.18
43 157 0.46
44 93 0.27
45 30 0.09
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (43 bp):
TTTATTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTA
Found at i:21168568 original size:130 final size:127
Alignment explanation
Indices: 21168383--21168824 Score: 453
Period size: 130 Copynumber: 3.4 Consensus size: 127
21168373 ATCGAAGAGT
* * *
21168383 TTTACTTTTCAAAGTTATTTAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAG
1 TTTACTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTTATTGAG
*
21168448 TCTTTTATTAGAATAGCTTTATTTATTTTTCCAAAGTTGTTGAACCTCTAATTAGAGGAGCTTTA
66 CCTTTTATTAGAA-AGCTTTATTTATTTTT-CAAAGTTGTTGAACCTCT-ATTAGAGGAGCTTTA
** * * * * *
21168513 TTTA-TTTTCCAAAGTTGTTAAGTCTTTGATTAGAGGAGCTTTATTTATTTTTCAAATTTGTTGA
1 TTTACTTTT-CAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTTATTGA
* * * ** * *
21168577 GCCTTTGATTAGAAAAGCCTTGTTTA-TTTTCAAAGTTGTTGTGCCTCTGATTAAAGGAGCTTTG
65 GCCTTTTATTAG-AAAGCTTTATTTATTTTTCAAAGTTGTTGAACCTCT-ATTAGAGGAGCTTTA
* * * * *
21168641 TTTATTTTTCAAAAGTCATTGTGTCTCTAATTAGAAGAGCTTT-TTTATTTTTCAAAGTTATTGA
1 TTTACTTTTC-AAAGTCATTGAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTTATTGA
* * *
21168705 GCCTCTGT-TTAGAGAAGCTTTATTTATTTTTTCAAAGTTGTTTAAGCCTCTGTTCAGAGGAGCT
65 GCCT-TTTATTAGA-AAGCTTTATTTA-TTTTTCAAAGTTGTTGAA-CCTCTATT-AGAGGAGCT
21168769 TTA
125 TTA
* * * **
21168772 TTAAATTTTCAAAGTCGTTGAGCCTCT-ATTTAGAGGAGCCATATTTATTTTTC
1 TTTACTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGGAGCTTTATTTATTTTTC
21168825 CAAAAGTTGT
Statistics
Matches: 257, Mismatches: 43, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
127 1 0.00
128 71 0.28
129 39 0.15
130 111 0.43
131 35 0.14
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (127 bp):
TTTACTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTTATTGAG
CCTTTTATTAGAAAGCTTTATTTATTTTTCAAAGTTGTTGAACCTCTATTAGAGGAGCTTTA
Found at i:21168724 original size:86 final size:87
Alignment explanation
Indices: 21168383--21168838 Score: 399
Period size: 87 Copynumber: 5.3 Consensus size: 87
21168373 ATCGAAGAGT
* * * * * *
21168383 TTTACTTTTC-AAAGTTATTTAGCCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGA
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
* * *
21168447 GTCTTTTATTAGA-ATAGCTTTA
66 GCCTCTGATTAGAGA-AGCTTTA
* * * * * *
21168469 TTTATTTTTCCAAAGTTGTTGAACCTCTAATTAGAGGAGCTTTATTTATTTTCCAAAGTTGTTAA
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
* * *
21168534 GTCTTTGATTAGAGGAGCTTTA
66 GCCTCTGATTAGAGAAGCTTTA
* * * * * * * *
21168556 TTTATTTTTC-AAATTTGTTGAGCCTTTGATTAGAAAAGCCTTGTTTA-TTTTCAAAGTTGTTGT
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
* * *
21168619 GCCTCTGATTAAAGGAGCTTTG
66 GCCTCTGATTAGAGAAGCTTTA
** * *
21168641 TTTATTTTTCAAAAGTCATTGTGTCTCTAATTAGAAGAGCTTT-TTTATTTTTCAAAGTTATTGA
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
*
21168705 GCCTCTGTTTAGAGAAGCTTTA
66 GCCTCTGATTAGAGAAGCTTTA
* * * * * **
21168727 TTTATTTTTTC-AAAGTTGTTTAAGCCTCT-GTTCAGAGGAGCTTTATTAAATTTTCAAAGTCGT
1 TTTA-TTTTTCAAAAGTTG-TTGAGCCTCTAATT-AGAAGAGCTTTATTTATTTTTCAAAGTTAT
* **
21168790 TGAGCCTCT-ATTTAGAGGAGCCATA
63 TGAGCCTCTGA-TTAGAGAAGCTTTA
21168815 TTTATTTTTCCAAAAGTTG-TGAGC
1 TTTATTTTT-CAAAAGTTGTTGAGC
21168839 TTTTCCTTAT
Statistics
Matches: 302, Mismatches: 57, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
85 45 0.15
86 104 0.34
87 107 0.35
88 39 0.13
89 7 0.02
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (87 bp):
TTTATTTTTCAAAAGTTGTTGAGCCTCTAATTAGAAGAGCTTTATTTATTTTTCAAAGTTATTGA
GCCTCTGATTAGAGAAGCTTTA
Found at i:21169098 original size:4 final size:4
Alignment explanation
Indices: 21169070--21169121 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
21169060 TGTTAAGCCC
* * * * *
21169070 ATTT GTTT ATTT AGTT ATTT GTTT ATTT ATAT GTTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
21169118 ATTT
1 ATTT
21169122 TTGGGTTTTA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (4 bp):
ATTT
Done.