Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 109 of 129
Found at i:19655590 original size:13 final size:14
Alignment explanation
Indices: 19655567--19655697 Score: 54
Period size: 13 Copynumber: 8.7 Consensus size: 14
19655557 TAAAAATTAG
19655567 AAAAATAAAATAAT
1 AAAAATAAAATAAT
19655581 AAAAAT-AAATAAT
1 AAAAATAAAATAAT
* *
19655594 AATTGAATAATCAATATT
1 AA--AAATAA--AATAAT
*
19655612 AGATATATACAAATGAAT
1 A-A-AAATA-AAAT-AAT
*
19655630 AAAGATAAAAT-AT
1 AAAAATAAAATAAT
* *
19655643 AAAATTAAATTAA-
1 AAAAATAAAATAAT
19655656 AAAAATAAACA-AAT
1 AAAAATAAA-ATAAT
*
19655670 AAATATAAATAGATATAT
1 AAAAAT-AA-A-ATA-AT
19655688 AAAAATAAAA
1 AAAAATAAAA
19655698 ATAAAATGGG
Statistics
Matches: 88, Mismatches: 14, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
13 29 0.33
14 12 0.14
15 10 0.11
16 8 0.09
17 7 0.08
18 20 0.23
19 2 0.02
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:19656042 original size:39 final size:38
Alignment explanation
Indices: 19655975--19656107 Score: 149
Period size: 39 Copynumber: 3.4 Consensus size: 38
19655965 AAAAGCACTC
*
19655975 GACTTTAAAAATAAAAGGCTCTTTCATAATAGAGGCATAT
1 GACTTTAAAAAT-AAAGGCTC-ATCATAATAGAGGCATAT
* *
19656015 GACTTTCAAAATAAAGGCTCATCCATAATAGAGGCACAT
1 GACTTTAAAAATAAAGGCTCAT-CATAATAGAGGCATAT
* * * * * *
19656054 AACTTTAAAAATAAAAGTTCATCTTCAATAAAGGCATAC
1 GACTTTAAAAATAAAGGCTCATCAT-AATAGAGGCATAT
19656093 GACTTTAAAAATAAA
1 GACTTTAAAAATAAA
19656108 TGTAACACAT
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
38 3 0.04
39 65 0.82
40 11 0.14
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (38 bp):
GACTTTAAAAATAAAGGCTCATCATAATAGAGGCATAT
Found at i:19663773 original size:25 final size:27
Alignment explanation
Indices: 19663745--19663807 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 27
19663735 TTAATTATCC
19663745 AATGATGAAATTTATA-AAAATTTC-A
1 AATGATGAAATTTATATAAAATTTCTA
*
19663770 AATGAT-AAATTTTTATAAAATTTCTA
1 AATGATGAAATTTATATAAAATTTCTA
*
19663796 AGTGA-GAAATTT
1 AATGATGAAATTT
19663808 TGTCTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 8 0.24
25 14 0.42
26 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.40
Consensus pattern (27 bp):
AATGATGAAATTTATATAAAATTTCTA
Found at i:19663992 original size:11 final size:11
Alignment explanation
Indices: 19663976--19664014 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
19663966 TTCAAATAGC
19663976 AAATTTTCAAG
1 AAATTTTCAAG
*
19663987 AAATTTTAAATG
1 AAATTTTCAA-G
19663999 ATAATTTTCAAG
1 A-AATTTTCAAG
19664011 AAAT
1 AAAT
19664015 CTCTAGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 12 0.50
12 4 0.17
13 8 0.33
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (11 bp):
AAATTTTCAAG
Found at i:19664009 original size:24 final size:25
Alignment explanation
Indices: 19663955--19664014 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
19663945 AATCATAAGA
19663955 TTCATAGAAATTTCAAATAGCAAATT
1 TTCA-AGAAATTTCAAATAGCAAATT
*
19663981 TTCAAGAAATTTTAAAT-G-ATAATT
1 TTCAAGAAATTTCAAATAGCA-AATT
19664005 TTCAAGAAAT
1 TTCAAGAAAT
19664015 CTCTAGGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 1 0.03
24 15 0.47
25 12 0.38
26 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (25 bp):
TTCAAGAAATTTCAAATAGCAAATT
Found at i:19664415 original size:104 final size:104
Alignment explanation
Indices: 19664295--19664506 Score: 293
Period size: 104 Copynumber: 2.0 Consensus size: 104
19664285 ATAAATAAAG
* * *
19664295 AAAAAACATTTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATCCAA-CAACAAAGGAGAGAA
1 AAAAAAAAATTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATCCAATCAA-AAAAGAGAGAA
* *
19664359 TTTCTAAATAGGCCCAAATGGTG-AAAATTTAGAAATTTCA
65 TTTCTAAATAGGCCCAAATCGTGAAAAATTTAGAAA-CTCA
* * * *
19664399 AAAAAAAAATTCTAAATTGACCCAAATGGTGGAAAATTTAGAAATCTAATGAAAAAAGAGAGAAT
1 AAAAAAAAATTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATCCAATCAAAAAAGAGAGAAT
* *
19664464 TTCTAAATAGGCTCAAGTCGTGAAAAATTTAGAAACTCA
66 TTCTAAATAGGCCCAAATCGTGAAAAATTTAGAAACTCA
19664503 AAAA
1 AAAA
19664507 GAGAAAATAT
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
104 81 0.85
105 14 0.15
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (104 bp):
AAAAAAAAATTCTAAATTAACCCAAATGGTGAAAAATTTAGAAATCCAATCAAAAAAGAGAGAAT
TTCTAAATAGGCCCAAATCGTGAAAAATTTAGAAACTCA
Found at i:19664454 original size:49 final size:48
Alignment explanation
Indices: 19664295--19664445 Score: 144
Period size: 48 Copynumber: 3.0 Consensus size: 48
19664285 ATAAATAAAG
* *
19664295 AAAAAACATTTCTAAATTA-ACCCAAATGGTGAAAAATTTAGAAATC-CAA
1 AAAAAAAAATTCTAAA-TAGACCCAAATGGTG-AAAATTTAGAAATCTC-A
* *
19664344 CAACAAAGGAGAGAATTTCTAAATAGGCCCAAATGGTGAAAATTTAGAAATTTCA
1 -AA-AAA--A-A-AA-TTCTAAATAGACCCAAATGGTGAAAATTTAGAAATCTCA
*
19664399 AAAAAAAAATTCTAAATTGACCCAAATGGTGGAAAATTTAGAAATCT
1 AAAAAAAAATTCTAAATAGACCCAAATGGT-GAAAATTTAGAAATCT
19664446 AATGAAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
48 19 0.22
49 17 0.20
50 3 0.04
51 4 0.05
53 4 0.05
54 2 0.02
55 17 0.20
56 19 0.22
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.25
Consensus pattern (48 bp):
AAAAAAAAATTCTAAATAGACCCAAATGGTGAAAATTTAGAAATCTCA
Found at i:19665513 original size:18 final size:18
Alignment explanation
Indices: 19665471--19665507 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
19665461 AAAAAAGGAA
*
19665471 AAAAATAAATGAGATAAAT
1 AAAAA-AAATGAGAAAAAT
19665490 AAAAAAAATGAGAAAAAT
1 AAAAAAAATGAGAAAAAT
19665508 GGAAAACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
AAAAAAAATGAGAAAAAT
Found at i:19665537 original size:31 final size:28
Alignment explanation
Indices: 19665490--19665568 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 28
19665480 TGAGATAAAT
19665490 AAAAAAAATGAGAAAAATGGAAAACGAAAAA
1 AAAAAAAATGAGAAAAAT-G-AAA-GAAAAA
19665521 AAAAAAAAT-AGAAAAAATGAAAGAAAAA
1 AAAAAAAATGAG-AAAAATGAAAGAAAAA
*
19665549 AAGGATAAAAAAGAGAAAAA
1 AA--A-AAAAATGAGAAAAA
19665569 AATGAAGACT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
28 8 0.19
29 3 0.07
30 4 0.10
31 25 0.60
32 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.06
Consensus pattern (28 bp):
AAAAAAAATGAGAAAAATGAAAGAAAAA
Found at i:19666375 original size:79 final size:80
Alignment explanation
Indices: 19666239--19666489 Score: 294
Period size: 79 Copynumber: 3.2 Consensus size: 80
19666229 TGCAATCGAA
* * * *
19666239 TGATGAAAATAATGTA-AATCAATAGACAAAATTTATTTTGGAATGGCTAGTGCTGAGAAGCCTG
1 TGATGAACATAATGTAGAATCAGTGGACAAAATTTATTTTGAAATGGCTAGTGCTGAGAAGCCTG
19666303 TCAATGGTGATCAAG
66 TCAATGGTGATCAAG
*
19666318 TGATGAACATAATG-AGAATCAGTGGACAAAATTTATTTTGAAATGGCTAGTGTTGAGAAGCCTG
1 TGATGAACATAATGTAGAATCAGTGGACAAAATTTATTTTGAAATGGCTAGTGCTGAGAAGCCTG
* *
19666382 TCAATGGTGATTAAA
66 TCAATGGTGATCAAG
* * * * * * * *
19666397 TGATGAACATAATGTAG-ATTAGAGGGCAGAATTCATTTT-AGAATGGTTACTGCTAAGAAGCCT
1 TGATGAACATAATGTAGAATCAGTGGACAAAATTTATTTTGA-AATGGCTAGTGCTGAGAAGCCT
* *
19666460 ATGAATGGTGATCAAG
65 GTCAATGGTGATCAAG
* *
19666476 TGATAAATATAATG
1 TGATGAACATAATG
19666490 GGGATTAATT
Statistics
Matches: 147, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 2 0.01
79 143 0.97
80 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (80 bp):
TGATGAACATAATGTAGAATCAGTGGACAAAATTTATTTTGAAATGGCTAGTGCTGAGAAGCCTG
TCAATGGTGATCAAG
Found at i:19666496 original size:79 final size:78
Alignment explanation
Indices: 19666263--19666540 Score: 272
Period size: 79 Copynumber: 3.5 Consensus size: 78
19666253 TAAATCAATA
19666263 GACAAAATTTATTTTGGAATGGCTAGTGCTGAGAAGCCTGTCAATGGTGATCAAGTGATGAACAT
1 GACAAAATTTATTTT-GAATGGCTAGTGCTGAGAAGCCTGTCAATGGTGATCAAGTGATGAACAT
* * *
19666328 AATGAGAATCAGTG
65 AATGAGGATTAGAG
* * *
19666342 GACAAAATTTATTTTGAAATGGCTAGTGTTGAGAAGCCTGTCAATGGTGATTAAATGATGAACAT
1 GACAAAATTTATTTTG-AATGGCTAGTGCTGAGAAGCCTGTCAATGGTGATCAAGTGATGAACAT
19666407 AATGTA-GATTAGAG
65 AATG-AGGATTAGAG
* * * * * * * * * *
19666421 GGCAGAATTCATTTTAGAATGGTTACTGCTAAGAAGCCTATGAATGGTGATCAAGTGATAAATAT
1 GACAAAATTTATTTT-GAATGGCTAGTGCTGAGAAGCCTGTCAATGGTGATCAAGTGATGAACAT
* *
19666486 AATGGGGATTA-ATT
65 AATGAGGATTAGA-G
* * * * * *
19666500 GATAGAATTTATTATGAGATTGCCAATGCTGAGAAGCCTGT
1 GACAAAATTTATTTTGA-ATGGCTAGTGCTGAGAAGCCTGT
19666541 GATTAAATGA
Statistics
Matches: 162, Mismatches: 31, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
78 4 0.02
79 156 0.96
80 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (78 bp):
GACAAAATTTATTTTGAATGGCTAGTGCTGAGAAGCCTGTCAATGGTGATCAAGTGATGAACATA
ATGAGGATTAGAG
Found at i:19667090 original size:59 final size:57
Alignment explanation
Indices: 19666969--19667149 Score: 202
Period size: 58 Copynumber: 3.1 Consensus size: 57
19666959 TGAATCTTTT
* ** *
19666969 AATGAGAATTTTTAAGTTTTCAAATGAGAATCTTTGAGATGTGAAACCAAAATTTGTTG
1 AATGAGAATTTTGAA-TTTT-AAATGAGAATCTTTGAGGCGTGAAACCAAAATTTGTCG
*
19667028 AATGAGAATATTTGAATTTTAAATGAGAATCTTTGAGGCGTGAAACTCAAAATGTGTCG
1 AATGAGAAT-TTTGAATTTTAAATGAGAATCTTTGAGGCGTGAAAC-CAAAATTTGTCG
* * * * *
19667087 AATGTGAATTTTCGAA-CTCAAATGAGAATCTTTGAGGGGTGAAACCCTAAAATTTGTCA
1 AATGAGAATTTT-GAATTTTAAATGAGAATCTTTGAGGCGTGAAA-CC-AAAATTTGTCG
19667146 AATG
1 AATG
19667150 TGAGCTTGTG
Statistics
Matches: 106, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
58 53 0.50
59 48 0.45
60 5 0.05
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (57 bp):
AATGAGAATTTTGAATTTTAAATGAGAATCTTTGAGGCGTGAAACCAAAATTTGTCG
Found at i:19667515 original size:42 final size:42
Alignment explanation
Indices: 19667451--19667599 Score: 178
Period size: 42 Copynumber: 3.6 Consensus size: 42
19667441 ATGATTGTCA
* *
19667451 AGGAGTAATTTTATTTTT-TAAAGTTACGGTGCCTCTGTTTAG
1 AGGAGCAA-TTTATTTTTCTAAAGTTGCGGTGCCTCTGTTTAG
*
19667493 AGGAGCAATTTATTTTTCTAAAGTTGCAGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCTAAAGTTGCGGTGCCTCTGTTTAG
* * * * *
19667535 AGGAACATTTTACTTTTC-AAAGTTGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTATTTTTCTAAAGTTGCGGTGCCTCTGTTTAG
*
19667576 AGAAGC-ATTTATTTTTCTCAAAGT
1 AGGAGCAATTTATTTTTCT-AAAGT
19667600 GATTGAGCCT
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
40 9 0.10
41 33 0.36
42 49 0.54
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (42 bp):
AGGAGCAATTTATTTTTCTAAAGTTGCGGTGCCTCTGTTTAG
Found at i:19667610 original size:42 final size:42
Alignment explanation
Indices: 19667479--19667619 Score: 125
Period size: 41 Copynumber: 3.4 Consensus size: 42
19667469 TAAAGTTACG
* *
19667479 GTGCCTCTGTTTAGAGGAGCAATTTATTTTTCT-AAAGTTGCA-
1 GTGCCTCTGTTTAAAGAAGC-ATTTATTTTTCTCAAAGTTG-AT
* *
19667521 GTGCCTCTGTTTAGAGGAA-CATTT-TACTTT-TCAAAGTTG-T
1 GTGCCTCTGTTTA-AAGAAGCATTTAT-TTTTCTCAAAGTTGAT
19667561 GGTGCCTCTGTTTAAAGAAGCATTTATTTTTCTCAAAG-TGATT
1 -GTGCCTCTGTTTAAAGAAGCATTTATTTTTCTCAAAGTTGA-T
* *
19667604 GAGCCTCTTTTTAAAG
1 GTGCCTCTGTTTAAAG
19667620 GAGCTTTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 20
0.74 0.07 0.18
Matches are distributed among these distances:
40 6 0.07
41 37 0.46
42 35 0.43
43 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (42 bp):
GTGCCTCTGTTTAAAGAAGCATTTATTTTTCTCAAAGTTGAT
Found at i:19667610 original size:83 final size:83
Alignment explanation
Indices: 19667458--19667621 Score: 199
Period size: 83 Copynumber: 2.0 Consensus size: 83
19667448 TCAAGGAGTA
* * * * *
19667458 ATTTTATTTTTTAAAGTTACGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCTAAAGTTGCAGT
1 ATTTTACTTTTCAAAGTTACGGTGCCTCTGTTTAAAGAAGCAATTTATTTTTCTAAAGTTGCAGA
*
19667523 GCCTCTGTTTAGAGGAAC
66 GCCTCTGTTTAAAGGAAC
**
19667541 ATTTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAAAGAAGC-ATTTATTTTTCTCAAAG-TG-AT
1 ATTTTACTTTTCAAAGTTACGGTGCCTCTGTTTAAAGAAGCAATTTATTTTTCT-AAAGTTGCA-
*
19667603 TGAGCCTCTTTTTAAAGGA
64 -GAGCCTCTGTTTAAAGGA
19667622 GCTTTGTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
81 1 0.01
82 14 0.20
83 54 0.78
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (83 bp):
ATTTTACTTTTCAAAGTTACGGTGCCTCTGTTTAAAGAAGCAATTTATTTTTCTAAAGTTGCAGA
GCCTCTGTTTAAAGGAAC
Found at i:19667654 original size:13 final size:14
Alignment explanation
Indices: 19667636--19667665 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
19667626 TGTTTACTTT
19667636 AAAAAAAAAACA-A
1 AAAAAAAAAACAGA
19667649 AAAAAAAAAACAGA
1 AAAAAAAAAACAGA
19667663 AAA
1 AAA
19667666 TGGGTGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAGA
Found at i:19673713 original size:24 final size:25
Alignment explanation
Indices: 19673673--19673723 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
19673663 AGATTTCTTA
* *
19673673 AAAAATTTATCATTTGA-AATTTTT
1 AAAAATTCATCATTTGATAATTATT
19673697 AAAAATCTCATCA-TTGATAATTATT
1 AAAAAT-TCATCATTTGATAATTATT
19673722 AA
1 AA
19673724 TTCAATCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (25 bp):
AAAAATTCATCATTTGATAATTATT
Found at i:19675220 original size:18 final size:18
Alignment explanation
Indices: 19675197--19675235 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19675187 AAAAATAAAC
*
19675197 AAATAAACAAATAAATAT
1 AAATAAACAAATAAAAAT
* *
19675215 AAATAAATATATAAAAAT
1 AAATAAACAAATAAAAAT
19675233 AAA
1 AAA
19675236 ATGAGTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATAAACAAATAAAAAT
Found at i:19675285 original size:14 final size:14
Alignment explanation
Indices: 19675258--19675292 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
19675248 GCTTGGATTA
*
19675258 ATTTAGACCTAATTG
1 ATTT-GACCCAATTG
19675273 ATTTGACCCAATTG
1 ATTTGACCCAATTG
19675287 ATTTGA
1 ATTTGA
19675293 GTCGGTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (14 bp):
ATTTGACCCAATTG
Found at i:19680124 original size:15 final size:15
Alignment explanation
Indices: 19680104--19680153 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
19680094 ATGACTCTTC
19680104 ATTAATATACTTTTT
1 ATTAATATACTTTTT
* * **
19680119 ATTAATAAAATCCTT
1 ATTAATATACTTTTT
*
19680134 ATTAATATACTTTCT
1 ATTAATATACTTTTT
19680149 ATTAA
1 ATTAA
19680154 ATTAAATATT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATATACTTTTT
Found at i:19690438 original size:15 final size:15
Alignment explanation
Indices: 19690418--19690447 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19690408 ATATAATAAA
19690418 ATTCATTAATATTTT
1 ATTCATTAATATTTT
*
19690433 ATTCATTTATATTTT
1 ATTCATTAATATTTT
19690448 TAATTATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTCATTAATATTTT
Found at i:19691107 original size:32 final size:33
Alignment explanation
Indices: 19691042--19691108 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
19691032 AATGTTTGAC
19691042 TCCTTATATTCTATTGAATATAAAAAAAAAATGG
1 TCCTTATATTCTATTGAATAT-AAAAAAAAATGG
*
19691076 TCCTTATATTCTATTGAATAT-TAAAAAAATGG
1 TCCTTATATTCTATTGAATATAAAAAAAAATGG
19691108 T
1 T
19691109 TAAGTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 11 0.34
34 21 0.66
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (33 bp):
TCCTTATATTCTATTGAATATAAAAAAAAATGG
Found at i:19692065 original size:17 final size:17
Alignment explanation
Indices: 19692028--19692079 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
19692018 ATCTAAATTG
*
19692028 AAAAATTAAAAAAAATA
1 AAAAATTAAAAAAAAGA
*
19692045 AAAAATTGAAAAAAAGCA
1 AAAAATTAAAAAAAAG-A
*
19692063 AAAAA--AAAGAAAAGA
1 AAAAATTAAAAAAAAGA
19692078 AA
1 AA
19692080 GAAACATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 14 0.47
18 6 0.20
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.10
Consensus pattern (17 bp):
AAAAATTAAAAAAAAGA
Found at i:19692266 original size:12 final size:12
Alignment explanation
Indices: 19692236--19692288 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
19692226 ACTTTTATTA
*
19692236 ATATAA-TACAT
1 ATATAATTAAAT
19692247 ATATAATTAAAT
1 ATATAATTAAAT
*
19692259 AAATAATTTAAA-
1 ATATAA-TTAAAT
*
19692271 ATATAATTTAAT
1 ATATAATTAAAT
19692283 ATATAA
1 ATATAA
19692289 CCAAAAGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 10 0.29
12 20 0.57
13 5 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATAATTAAAT
Found at i:19694081 original size:23 final size:23
Alignment explanation
Indices: 19694044--19694091 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19694034 GCAGATTTTC
**
19694044 TTTTATTTTTCTTTTA-TCTTATT
1 TTTTATTTTGATTTTATTC-TATT
19694067 TTTTATTTTGATTTTATTCTATT
1 TTTTATTTTGATTTTATTCTATT
19694090 TT
1 TT
19694092 ACTTTTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (23 bp):
TTTTATTTTGATTTTATTCTATT
Found at i:19694121 original size:24 final size:22
Alignment explanation
Indices: 19694044--19694122 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 22
19694034 GCAGATTTTC
19694044 TTTTATTTTTCT-TTTA-TCTTA
1 TTTTATTTTTCTATTTATTC-TA
19694065 TTTT-TTATTT-TGATTTTATTCTA
1 TTTTATT-TTTCT-A-TTTATTCTA
19694088 TTTTACTTTTTCTATTCTATTCTCA
1 TTTTA-TTTTTCTATT-TATTCT-A
19694113 TTTTATTTTT
1 TTTTATTTTT
19694123 ACTTATTGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
20 3 0.06
21 7 0.15
23 12 0.25
24 17 0.35
25 9 0.19
ACGTcount: A:0.15, C:0.10, G:0.01, T:0.73
Consensus pattern (22 bp):
TTTTATTTTTCTATTTATTCTA
Found at i:19695862 original size:3 final size:3
Alignment explanation
Indices: 19695854--19695880 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19695844 ATGCATAATT
19695854 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
19695881 AATTCACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19703624 original size:16 final size:18
Alignment explanation
Indices: 19703603--19703635 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19703593 TTATATCCCA
19703603 AAACAA-AA-AAAAAAAG
1 AAACAATAACAAAAAAAG
19703619 AAACAATAACAAAAAAA
1 AAACAATAACAAAAAAA
19703636 AAAAAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (18 bp):
AAACAATAACAAAAAAAG
Found at i:19704840 original size:3 final size:3
Alignment explanation
Indices: 19704832--19704870 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
19704822 GAATAGTTTA
*
19704832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19704871 GATGATGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19705915 original size:21 final size:21
Alignment explanation
Indices: 19705877--19705916 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19705867 AAAAAAATAA
*
19705877 AATAAAATAATCTAAAATTTT
1 AATAAAATAATATAAAATTTT
19705898 AATAAAA-AATATATAAATT
1 AATAAAATAATATA-AAATT
19705917 AAAAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAATAATATAAAATTTT
Found at i:19707083 original size:15 final size:15
Alignment explanation
Indices: 19707063--19707100 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
19707053 CTTTGGCTCA
*
19707063 TAAATTTTGGATTTT
1 TAAATTTTGGATTGT
19707078 TAAATTTTGGATTGT
1 TAAATTTTGGATTGT
*
19707093 TAGATTTT
1 TAAATTTT
19707101 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (15 bp):
TAAATTTTGGATTGT
Found at i:19717649 original size:10 final size:10
Alignment explanation
Indices: 19717613--19717657 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
19717603 CTGCTTCTCC
19717613 TTTTTTCTTT
1 TTTTTTCTTT
*
19717623 ATTTCTTC-TT
1 -TTTTTTCTTT
*
19717633 CTTTTTCTTT
1 TTTTTTCTTT
19717643 TTTTTTCTTT
1 TTTTTTCTTT
19717653 TTTTT
1 TTTTT
19717658 CTCCCTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 5 0.17
10 18 0.62
11 6 0.21
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:19717650 original size:19 final size:20
Alignment explanation
Indices: 19717614--19717659 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
19717604 TGCTTCTCCT
19717614 TTTTTCTTTATTTCTTCTTC
1 TTTTTCTTTATTTCTTCTTC
* *
19717634 TTTTTCTTT-TTTTTTCTTT
1 TTTTTCTTTATTTCTTCTTC
19717653 TTTTTCT
1 TTTTTCT
19717660 CCCTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTTCTTTATTTCTTCTTC
Found at i:19719164 original size:10 final size:10
Alignment explanation
Indices: 19719149--19719184 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
19719139 TAAAAAATCA
19719149 AATAAATTCG
1 AATAAATTCG
19719159 AATAAATTCG
1 AATAAATTCG
* *
19719169 AATTAATTCA
1 AATAAATTCG
19719179 AATAAA
1 AATAAA
19719185 ATTAAGTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.31
Consensus pattern (10 bp):
AATAAATTCG
Found at i:19719323 original size:9 final size:8
Alignment explanation
Indices: 19719304--19719354 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
19719294 TACTTAAAAG
19719304 TTTTTT-T
1 TTTTTTGT
*
19719311 TTTTTGGT
1 TTTTTTGT
19719319 TTTTTTGT
1 TTTTTTGT
*
19719327 TTTTGTGT
1 TTTTTTGT
*
19719335 TTTTGTGT
1 TTTTTTGT
*
19719343 TTTTGTGT
1 TTTTTTGT
19719351 TTTT
1 TTTT
19719355 GATTTTGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
7 5 0.12
8 35 0.88
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (8 bp):
TTTTTTGT
Found at i:19719329 original size:16 final size:14
Alignment explanation
Indices: 19719303--19719366 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
19719293 TTACTTAAAA
19719303 GTTTTTTT-TTTTT
1 GTTTTTTTGTTTTT
19719316 GGTTTTTTTGTTTTT
1 -GTTTTTTTGTTTTT
19719331 GTGTTTTTGTGTTTTT
1 GT-TTTTT-TGTTTTT
* *
19719347 GTGTTTTTGATTTTG
1 GTTTTTTTG-TTTTT
19719362 GTTTT
1 GTTTT
19719367 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.28
15 22 0.51
16 9 0.21
ACGTcount: A:0.02, C:0.00, G:0.20, T:0.78
Consensus pattern (14 bp):
GTTTTTTTGTTTTT
Found at i:19719335 original size:8 final size:8
Alignment explanation
Indices: 19719311--19719355 Score: 74
Period size: 8 Copynumber: 5.8 Consensus size: 8
19719301 AAGTTTTTTT
19719311 TTTTTG-G
1 TTTTTGTG
*
19719318 TTTTTTTG
1 TTTTTGTG
19719326 TTTTTGTG
1 TTTTTGTG
19719334 TTTTTGTG
1 TTTTTGTG
19719342 TTTTTGTG
1 TTTTTGTG
19719350 TTTTTG
1 TTTTTG
19719356 ATTTTGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
7 5 0.14
8 30 0.86
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (8 bp):
TTTTTGTG
Found at i:19719466 original size:24 final size:23
Alignment explanation
Indices: 19719435--19719479 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
19719425 AAAACAAATT
*
19719435 TTAAAACTCTTT-TAAATAAAAAC
1 TTAAAACT-TTTGAAAATAAAAAC
19719458 TTAACAACTTTTGAAAATAAAA
1 TTAA-AACTTTTGAAAATAAAA
19719480 TAAAAAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAACTTTTGAAAATAAAAAC
Found at i:19719911 original size:23 final size:23
Alignment explanation
Indices: 19719885--19719962 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 23
19719875 ATTTGAAAAT
*
19719885 TTAAAATATTTTGCCTGAGAGTC
1 TTAAAATATTATGCCTGAGAGTC
19719908 TTAAAA-ATTATGCCCAT-AGA-TC
1 TTAAAATATTATG-CC-TGAGAGTC
* * *
19719930 TT-AAAGATTATGCCCGAAAGTC
1 TTAAAATATTATGCCTGAGAGTC
19719952 TTATAAATATT
1 TTA-AAATATT
19719963 TGAATGCACA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
21 7 0.16
22 19 0.43
23 11 0.25
24 7 0.16
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (23 bp):
TTAAAATATTATGCCTGAGAGTC
Found at i:19719953 original size:22 final size:21
Alignment explanation
Indices: 19719904--19719959 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
19719894 TTTGCCTGAG
*
19719904 AGTCTTAAAAATTATGCCCAT
1 AGTCTTAAAAATTATGCCCAA
*
19719925 AGATCTTAAAGATTATGCCCGAA
1 AG-TCTTAAAAATTATGCCC-AA
*
19719948 AGTCTTATAAAT
1 AGTCTTAAAAAT
19719960 ATTTGAATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.07
22 24 0.83
23 3 0.10
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (21 bp):
AGTCTTAAAAATTATGCCCAA
Found at i:19720050 original size:118 final size:116
Alignment explanation
Indices: 19719748--19720059 Score: 324
Period size: 118 Copynumber: 2.7 Consensus size: 116
19719738 TTTTCATAGT
*
19719748 AGAGGCATTGAAACTTTGAAAATTTAAAATGCTTTACCCAGAGGTCTTGAAAATTA---AAAAGG
1 AGAGGCATTGAAACTTTGAAAATTTAAAATGCTTT-GCCAGAGGTCTTGAAAATTATGCAAAAGG
* * * * * ** * *
19719810 TCTTAAGGATTATGTCTGAAAGTTTTACAAATCTTTAAATGCTTATTGTATT
65 TCTTAAAGATTATGCCCGAAAGTCTTACAAATATTTAAATGCACATCGTATC
* * ** * * * *
19719862 AGAGGTATTGAAAATTTGAAAATTTAAAATATTTTGCCTGAGAGTCTTAAAAATTATGCCCATAG
1 AGAGGCATTGAAACTTTGAAAATTTAAAATGCTTTGCCAGAG-GTCTTGAAAATTATG-CAAAAG
* * *
19719927 ATCTTAAAGATTATGCCCGAAAGTCTTATAAATATTTGAATGCACATCGTATC
64 GTCTTAAAGATTATGCCCGAAAGTCTTACAAATATTTAAATGCACATCGTATC
* * * *
19719980 CGAGGCATTGAAACTTTGAAAATTTAAAATGCTTTGCTCAAAGGTCTTGAAAATTATGCTTAGAG
1 AGAGGCATTGAAACTTTGAAAATTTAAAATGCTTTGC-CAGAGGTCTTGAAAATTATGC-AAAAG
*
19720045 GTCTTAGAGATTATG
64 GTCTTAAAGATTATG
19720060 TCTAGAGGTT
Statistics
Matches: 158, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
113 5 0.03
114 43 0.27
117 1 0.01
118 106 0.67
119 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (116 bp):
AGAGGCATTGAAACTTTGAAAATTTAAAATGCTTTGCCAGAGGTCTTGAAAATTATGCAAAAGGT
CTTAAAGATTATGCCCGAAAGTCTTACAAATATTTAAATGCACATCGTATC
Found at i:19720089 original size:22 final size:21
Alignment explanation
Indices: 19720032--19720090 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
19720022 GGTCTTGAAA
19720032 ATTATGCTTAGAGGTCTTAGAG
1 ATTATGC-TAGAGGTCTTAGAG
*
19720054 ATTATGTCTAGAGGTTTTAGAG
1 ATTATG-CTAGAGGTCTTAGAG
19720076 ATTATGCTAGGAGGT
1 ATTATGCTA-GAGGT
19720091 ATTACAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 3 0.09
22 30 0.88
23 1 0.03
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (21 bp):
ATTATGCTAGAGGTCTTAGAG
Found at i:19720378 original size:21 final size:21
Alignment explanation
Indices: 19720352--19720391 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19720342 ATTTTTTGTC
* *
19720352 CTTAATTTTAGGGATACAATA
1 CTTAATTCTAGAGATACAATA
19720373 CTTAATTCTAGAGATACAA
1 CTTAATTCTAGAGATACAA
19720392 ATATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
CTTAATTCTAGAGATACAATA
Found at i:19724704 original size:22 final size:22
Alignment explanation
Indices: 19724679--19724722 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
19724669 ATTTTTTATC
*
19724679 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
19724701 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
19724723 TAAATTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:19725616 original size:32 final size:32
Alignment explanation
Indices: 19725543--19725622 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
19725533 GAATACAAGT
* * *
19725543 AATGCAAATGTGAATATCCCTTTCATGATGTA
1 AATGCAAATGTGAATGTCCCTTTCATGAAGCA
**
19725575 AATGCAAATGTGAATGTCTTTTTCATGAAGCA
1 AATGCAAATGTGAATGTCCCTTTCATGAAGCA
* * *
19725607 TATGTAAATGCGAATG
1 AATGCAAATGTGAATG
19725623 CAACTGATGC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (32 bp):
AATGCAAATGTGAATGTCCCTTTCATGAAGCA
Found at i:19733111 original size:20 final size:20
Alignment explanation
Indices: 19733088--19733125 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19733078 TGTAAAAAAA
19733088 CATTTTTATTTAT-TTTTTAG
1 CATTTTT-TTTATATTTTTAG
19733108 CATTTTTTTTATATTTTT
1 CATTTTTTTTATATTTTT
19733126 GAAAAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (20 bp):
CATTTTTTTTATATTTTTAG
Found at i:19734101 original size:3 final size:3
Alignment explanation
Indices: 19734093--19734141 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
19734083 TTCAATTTAA
19734093 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19734141 A
1 A
19734142 GTTTAGCATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19740883 original size:29 final size:29
Alignment explanation
Indices: 19740849--19740920 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
19740839 TCCAATTTTG
*
19740849 ATTTAATTAATAAAAATTAAATATGAA-A
1 ATTTAATTAATAAAAATAAAATATGAACA
* * *
19740877 ATTTTAATTAATTATAATAAAATATTAACA
1 A-TTTAATTAATAAAAATAAAATATGAACA
*
19740907 ATTTAATTAGTAAA
1 ATTTAATTAATAAA
19740921 TGATATTTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
28 1 0.03
29 32 0.91
30 2 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (29 bp):
ATTTAATTAATAAAAATAAAATATGAACA
Found at i:19747390 original size:23 final size:23
Alignment explanation
Indices: 19747364--19747407 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19747354 TTTGTAGTTC
* *
19747364 CAAACCCTTTTTTTTATATGGTT
1 CAAACACTTTTATTTATATGGTT
*
19747387 CAAACAGTTTTATTTATATGG
1 CAAACACTTTTATTTATATGG
19747408 GATCTAAGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (23 bp):
CAAACACTTTTATTTATATGGTT
Found at i:19753811 original size:30 final size:30
Alignment explanation
Indices: 19753777--19753868 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
19753767 AATTTATGTA
* *
19753777 AAAGATTAATTTAGATACAAATTAAAAGTT
1 AAAGATTTATTTAGATACAAATTAAAAATT
*
19753807 AAAGATTTATTTCA-ATATAAATTAAAAATT
1 AAAGATTTATTT-AGATACAAATTAAAAATT
*
19753837 AAAAATTTATTT-GAATACAAATTAAAAATT
1 AAAGATTTATTTAG-ATACAAATTAAAAATT
19753867 AA
1 AA
19753869 TAGCTTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
30 53 0.98
31 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAGATTTATTTAGATACAAATTAAAAATT
Found at i:19753877 original size:30 final size:29
Alignment explanation
Indices: 19753791--19753878 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
19753781 ATTAATTTAG
*
19753791 ATACAAATTAAAAGTTAAAGATTTATTTCA
1 ATACAAATTAAAAATTAAAG-TTTATTTCA
* * *
19753821 ATATAAATTAAAAATTAAAAATTTATTTGA
1 ATACAAATTAAAAATT-AAAGTTTATTTCA
*
19753851 ATACAAATTAAAAATTAATAGCTTATTT
1 ATACAAATTAAAAATTAA-AGTTTATTT
19753879 AGTTATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 2 0.04
30 44 0.90
31 3 0.06
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (29 bp):
ATACAAATTAAAAATTAAAGTTTATTTCA
Found at i:19753877 original size:60 final size:59
Alignment explanation
Indices: 19753775--19753916 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 59
19753765 TGAATTTATG
* * * *
19753775 TAAAAGATTAATTTAGATACAAATTAAAAGTTAAAGATTTATTTCAA-TATAAATTAAAAAT-
1 TAAAA-ATTTATTTAAATACAAATTAAAAATTAAAGACTTATTT-AATTAT-AA-TAAAAATA
* *
19753836 TAAAAATTTATTTGAATACAAATTAAAAATTAATAG-CTTATTTAGTTATAATAAAAATA
1 TAAAAATTTATTTAAATACAAATTAAAAATTAA-AGACTTATTTAATTATAATAAAAATA
*
19753895 TGAAAATTTATTTAAATA-AAAT
1 TAAAAATTTATTTAAATACAAAT
19753917 GATAAAGTTC
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
58 11 0.16
59 19 0.27
60 33 0.47
61 7 0.10
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.38
Consensus pattern (59 bp):
TAAAAATTTATTTAAATACAAATTAAAAATTAAAGACTTATTTAATTATAATAAAAATA
Found at i:19754200 original size:23 final size:25
Alignment explanation
Indices: 19754148--19754214 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 25
19754138 TATTAGATGC
* *
19754148 ATTTAATCAATTATTATATTATTGA
1 ATTTAATCAATTAATAAATTATTGA
19754173 A--TAATCAATTAATAAATTA-T-A
1 ATTTAATCAATTAATAAATTATTGA
* *
19754194 ATTTAATTAAGTAATTAAATT
1 ATTTAATCAATTAA-TAAATT
19754215 CACACACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 25 0.71
24 6 0.17
25 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (25 bp):
ATTTAATCAATTAATAAATTATTGA
Found at i:19755833 original size:28 final size:28
Alignment explanation
Indices: 19755792--19755846 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
19755782 CAATTATAGT
* *
19755792 AAAATATTTCATATAATTTTTGAATTAA
1 AAAATATTTAATATAATATTTGAATTAA
* *
19755820 AAAATTTTTAATATGATATTTGAATTA
1 AAAATATTTAATATAATATTTGAATTA
19755847 CGTATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
AAAATATTTAATATAATATTTGAATTAA
Found at i:19756802 original size:30 final size:29
Alignment explanation
Indices: 19756733--19756803 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
19756723 TATATTATGA
* * *
19756733 TTCAATATTGTTGAATTTTATCAATGTAC
1 TTCAATTTTATTGAAATTTATCAATGTAC
*
19756762 TTCTAA-TTTATTGAAATTTATCATTGTAC
1 TTC-AATTTTATTGAAATTTATCAATGTAC
19756791 TTTCAATTTTATT
1 -TTCAATTTTATT
19756804 AAGTTTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.54
Consensus pattern (29 bp):
TTCAATTTTATTGAAATTTATCAATGTAC
Found at i:19760929 original size:17 final size:17
Alignment explanation
Indices: 19760907--19760939 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19760897 TTCTAAGGTT
19760907 TTTTTTATATTTATTTA
1 TTTTTTATATTTATTTA
19760924 TTTTTTATATTTATTT
1 TTTTTTATATTTATTT
19760940 TAAAATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTATATTTATTTA
Found at i:19760993 original size:5 final size:5
Alignment explanation
Indices: 19760985--19761012 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
19760975 TAATTTTATT
19760985 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
19761013 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:19761224 original size:135 final size:132
Alignment explanation
Indices: 19761026--19761373 Score: 447
Period size: 135 Copynumber: 2.6 Consensus size: 132
19761016 TTTTTAATGA
19761026 TTTTCTT-AAAATAAAATTTCCAAAAAAAATATTTTTGAGG-AAAAATTGAAAGTATCAATTTTT
1 TTTTCTTGAAAATAAAATTT-CAAAAAAAATATTTTT-AGGAAAAAATTGAAAGTATCAATTTTT
* * * * *
19761089 CTTAAAAATATAATTTCTAAAATACAAATT-TC-TAAAAGTATTTTGGGGGAAAGTTGAAAGTAT
64 CTTAAAAATAAAATTTCTAAAATAAAAATTATCAGAAAAGTATTTTGAGGAAAAGTTGAAAGTAT
19761152 TAAT
129 TAAT
* *
19761156 TTTAT-TTGAAAATAAAATGGTTTTAAAAAATATATATTTTTAGGAAAAAATTGAAAGTATCAAA
1 TTT-TCTTGAAAATAAAA---TTTCAAAAAA-A-ATATTTTTAGGAAAAAATTGAAAGTATCAAT
19761220 TTTTCTTAAAAATAAAATTTCTAAAATAAAAATTATCAAGAAAAGTATTTTGAGGAAAAGTTGAA
60 TTTTCTTAAAAATAAAATTTCTAAAATAAAAATTATC-AGAAAAGTATTTTGAGGAAAAGTTGAA
19761285 AGTATTAAT
124 AGTATTAAT
* * * *
19761294 TTTTCTTGAAATTAAAATTTCAGAAAAAAATAATTTGA-GAAAAAGTTGAAAGTATCAATTTTTC
1 TTTTCTTGAAAATAAAATTTCA-AAAAAAATATTTTTAGGAAAAAATTGAAAGTATCAATTTTTC
* *
19761358 TTGAAATTAAAATTTC
65 TTAAAAATAAAATTTC
19761374 AGAAAAAAAA
Statistics
Matches: 190, Mismatches: 15, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
130 5 0.03
131 10 0.05
133 44 0.23
134 14 0.07
135 63 0.33
136 7 0.04
137 1 0.01
138 46 0.24
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (132 bp):
TTTTCTTGAAAATAAAATTTCAAAAAAAATATTTTTAGGAAAAAATTGAAAGTATCAATTTTTCT
TAAAAATAAAATTTCTAAAATAAAAATTATCAGAAAAGTATTTTGAGGAAAAGTTGAAAGTATTA
AT
Found at i:19761310 original size:60 final size:58
Alignment explanation
Indices: 19761243--19761420 Score: 257
Period size: 59 Copynumber: 3.0 Consensus size: 58
19761233 AAAATTTCTA
* * * * *
19761243 AAATAAAAATTATCAAGAAAAGTATTTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTG
1 AAATTAAAATT-TCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
*
19761302 AAATTAAAATTTCAGAAAAAAATAATTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAATTAAAATTTCA-AAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
*
19761361 AAATTAAAATTTCAGAAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAATTAAAATTTC--AAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
19761421 TACAAAAGCA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
58 3 0.03
59 62 0.57
60 42 0.39
61 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.35
Consensus pattern (58 bp):
AAATTAAAATTTCAAAAAAAATATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:19761331 original size:59 final size:60
Alignment explanation
Indices: 19761268--19761420 Score: 263
Period size: 59 Copynumber: 2.6 Consensus size: 60
19761258 AGAAAAGTAT
* *
19761268 TTTGAGGAAAAGTTGAAAGTATTAATTTTTCTTGAAATTAAAATTTCAG-AAAAAAATAA
1 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAAAATAA
*
19761327 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAAAATAT
1 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAAAATAA
*
19761387 TTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
19761421 TACAAAAGCA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 47 0.53
60 42 0.47
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAGAAAAAAAATAA
Found at i:19761339 original size:74 final size:75
Alignment explanation
Indices: 19761190--19761328 Score: 183
Period size: 74 Copynumber: 1.9 Consensus size: 75
19761180 AAAAAATATA
* *
19761190 TATTTTTAGGAAAAAATTGAAAGTATCAAATTTTCTTAAAAATAAAATTTCTAAAATAAAAATTA
1 TATTTTGAGGAAAAAATTGAAAGTATCAAATTTTCTTAAAAATAAAATTTCTAAAAAAAAAATTA
19761255 TCAAGAAAAG
66 TCAAGAAAAG
* * * * *
19761265 TATTTTGAGG-AAAAGTTGAAAGTATTAATTTTTCTTGAAATTAAAATTTC-AGAAAAAAATAAT
1 TATTTTGAGGAAAAAATTGAAAGTATCAAATTTTCTTAAAAATAAAATTTCTA-AAAAAAA-AAT
19761328 T
64 T
19761329 TGAGAAAAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
73 1 0.02
74 41 0.75
75 13 0.24
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (75 bp):
TATTTTGAGGAAAAAATTGAAAGTATCAAATTTTCTTAAAAATAAAATTTCTAAAAAAAAAATTA
TCAAGAAAAG
Found at i:19761869 original size:16 final size:16
Alignment explanation
Indices: 19761850--19761883 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19761840 GAAAGAATAG
* *
19761850 ATTCTTTAGGTGGTCA
1 ATTCCTTAGGTGATCA
19761866 ATTCCTTAGGTGATCA
1 ATTCCTTAGGTGATCA
19761882 AT
1 AT
19761884 CGCACCTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (16 bp):
ATTCCTTAGGTGATCA
Found at i:19762292 original size:18 final size:19
Alignment explanation
Indices: 19762260--19762297 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
19762250 ATAATTTTTA
19762260 ATTAAAATAATAAAAATTT
1 ATTAAAATAATAAAAATTT
19762279 ATTAAAAT-ATAAAAATTT
1 ATTAAAATAATAAAAATTT
19762297 A
1 A
19762298 ATTAGATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTAAAATAATAAAAATTT
Found at i:19762301 original size:19 final size:20
Alignment explanation
Indices: 19762243--19762301 Score: 79
Period size: 19 Copynumber: 3.1 Consensus size: 20
19762233 TATATATAAA
**
19762243 TAAAATAAT-AATTTTTAAT
1 TAAAATAATAAAAATTTAAT
19762262 TAAAATAATAAAAATTT-AT
1 TAAAATAATAAAAATTTAAT
19762281 TAAAAT-ATAAAAATTTAAT
1 TAAAATAATAAAAATTTAAT
19762300 TA
1 TA
19762302 GATTTATGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.28
19 21 0.58
20 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATAATAAAAATTTAAT
Found at i:19763702 original size:22 final size:23
Alignment explanation
Indices: 19763659--19763702 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
19763649 TAATGATTAA
19763659 AATATTTTTATAATCAAAGAAATT
1 AATATTTTTATAA-CAAAGAAATT
19763683 AATATTTTTATAA-AAAGAAA
1 AATATTTTTATAACAAAGAAA
19763703 CATAGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (23 bp):
AATATTTTTATAACAAAGAAATT
Found at i:19764003 original size:25 final size:26
Alignment explanation
Indices: 19763963--19764047 Score: 97
Period size: 28 Copynumber: 3.3 Consensus size: 26
19763953 ATTTTTTATT
19763963 TAAAAT-AAAAA-TTTATTTAAAT-A
1 TAAAATAAAAAATTTTATTTAAATAA
*
19763986 T-AAGTGAAAAAATTTTATTTGAATATAA
1 TAAAAT-AAAAAATTTTATTT-AA-ATAA
*
19764014 TAAAATAAAAAATTTTATTTAAAAAA
1 TAAAATAAAAAATTTTATTTAAATAA
19764040 TAAAATAA
1 TAAAATAA
19764048 TTTAAAGATT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
22 3 0.06
23 1 0.02
24 5 0.10
25 7 0.13
26 13 0.25
27 4 0.08
28 16 0.31
29 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
TAAAATAAAAAATTTTATTTAAATAA
Found at i:19766191 original size:156 final size:153
Alignment explanation
Indices: 19765860--19766162 Score: 338
Period size: 156 Copynumber: 1.9 Consensus size: 153
19765850 TTTCAATACG
* * * * *
19765860 AAATTAAATAATTTATACTAATTTATAGACATATGATCATAAATATAAGAAAATTACCTTAAAAC
1 AAATTAAATGATATATATTAATTTACAGACATATAATCATAAATATAAGAAAATTACCTTAAAAC
* * * *
19765925 TTAGTTTTTAGGGTTTATAGAAACTCCTATTTGTAATAGTACAACAAATATATATAAGGTAAGTC
66 ATAGTTTTTAGGGTTTATAGAAACTCCTATTTGTAAAAGTACAACAAACACATATAAGGTAAGTC
** ** * **
19765990 AATAATTTATTTGGTCTTTCAATACG
131 AAT-ATGAAAATGG--TTACAATAAA
*
19766016 AAATTAAATGATTTATATTAATTTACAGACATATAATCATAAATATAAGAAAATTACCTTAAAAC
1 AAATTAAATGATATATATTAATTTACAGACATATAATCATAAATATAAGAAAATTACCTTAAAAC
* * *
19766081 ATAGTTTTTATGGTTTATGGAAACTCTTATTTGTAAAAGTACAATACATACACACACATATAAGG
66 ATAGTTTTTAGGGTTTATAGAAACTCCTATTTGTAAAAGTAC-A-AC--A-A-ACACATATAAGG
19766146 TAAGTCAAT-TGAAAATG
125 TAAGTCAATATGAAAATG
19766163 TAGAAAAAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
156 98 0.78
157 1 0.01
158 2 0.02
160 5 0.04
161 1 0.01
162 19 0.15
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (153 bp):
AAATTAAATGATATATATTAATTTACAGACATATAATCATAAATATAAGAAAATTACCTTAAAAC
ATAGTTTTTAGGGTTTATAGAAACTCCTATTTGTAAAAGTACAACAAACACATATAAGGTAAGTC
AATATGAAAATGGTTACAATAAA
Found at i:19770341 original size:3 final size:3
Alignment explanation
Indices: 19770326--19770386 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
19770316 TTCTATTACA
*
19770326 ATT ATT AAT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19770373 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
19770387 CACCAACTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 54 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19770703 original size:13 final size:13
Alignment explanation
Indices: 19770685--19770710 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19770675 AACTGAATAG
19770685 AATTTGGAATTTA
1 AATTTGGAATTTA
19770698 AATTTGGAATTTA
1 AATTTGGAATTTA
19770711 TTTTTTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
AATTTGGAATTTA
Found at i:19771582 original size:20 final size:21
Alignment explanation
Indices: 19771557--19771596 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19771547 TTATCGATAT
*
19771557 ATAAATTTTAT-ATATTATTA
1 ATAAATTATATGATATTATTA
19771577 ATAAATTATATGATATTATT
1 ATAAATTATATGATATTATT
19771597 TCATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATAAATTATATGATATTATTA
Found at i:19771693 original size:30 final size:30
Alignment explanation
Indices: 19771659--19771722 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
19771649 TTTTTTTAAA
* *
19771659 AATTTACTTATGAATAAAATGATATCATTT
1 AATTTACTTATGAATAAAATAACATCATTT
* * *
19771689 AATTTATTTATTAATAAAATAACATTATTT
1 AATTTACTTATGAATAAAATAACATCATTT
19771719 AATT
1 AATT
19771723 CATTAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (30 bp):
AATTTACTTATGAATAAAATAACATCATTT
Found at i:19780669 original size:37 final size:38
Alignment explanation
Indices: 19780628--19780732 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 38
19780618 GCAATGAAAT
* *
19780628 TGGGTTCTTCTATATAAA-ACTAAACAACTTTAAAAAA
1 TGGGTTCCTCTATACAAAGACTAAACAACTTTAAAAAA
* *
19780665 TGGGTTCCTCTATGCAAAGACTAAATAACTTTAAATAAGAAA
1 TGGGTTCCTCTATACAAAGACTAAACAACTTT--A-AA-AAA
* *
19780707 TAGGTTCCTCTATACAAAGGCTAAAC
1 TGGGTTCCTCTATACAAAGACTAAAC
19780733 CATTTTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 15 0.27
38 12 0.22
40 1 0.02
41 2 0.04
42 25 0.45
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (38 bp):
TGGGTTCCTCTATACAAAGACTAAACAACTTTAAAAAA
Found at i:19780725 original size:42 final size:42
Alignment explanation
Indices: 19780623--19780879 Score: 179
Period size: 44 Copynumber: 6.1 Consensus size: 42
19780613 ATTAAGCAAT
* * *
19780623 GAAATTGGGTTCTTCTATATAAA-ACTAAACAACTTT--A-AA
1 GAAA-TGGGTTCCTCTATACAAAGGCTAAACAACTTTAAATAA
* * *
19780662 -AAATGGGTTCCTCTATGCAAAGACTAAATAACTTTAAATAA
1 GAAATGGGTTCCTCTATACAAAGGCTAAACAACTTTAAATAA
* ** *
19780703 GAAATAGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATAT
1 GAAATGGGTTCCTCTATACAAAGGCTAAA-CA-ACTTTAAATAA
* * * ** *
19780747 GAAATGGGCTCCTCTATACATAGGCCAAACCATTTTTTAAATAT
1 GAAATGGGTTCCTCTATACAAAGGCTAAA-CA-ACTTTAAATAA
* *
19780791 GAAATGAGTTCCTCTATACAGAGGCTAAACAACTTTAAAATAA
1 GAAATGGGTTCCTCTATACAAAGGCTAAACAACTTT-AAATAA
* **
19780834 TAAATTGACTT-CTCTAT-CTAGAA-GCTAAACAACTTTAAAATAA
1 GAAA-TGGGTTCCTCTATAC-A-AAGGCTAAACAACTTT-AAATAA
19780877 GAA
1 GAA
19780880 TCCTCTAATC
Statistics
Matches: 181, Mismatches: 26, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
37 15 0.08
38 15 0.08
40 1 0.01
41 2 0.01
42 29 0.16
43 40 0.22
44 79 0.44
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.31
Consensus pattern (42 bp):
GAAATGGGTTCCTCTATACAAAGGCTAAACAACTTTAAATAA
Found at i:19780760 original size:44 final size:44
Alignment explanation
Indices: 19780662--19780820 Score: 196
Period size: 44 Copynumber: 3.7 Consensus size: 44
19780652 CAACTTTAAA
* * * ** *
19780662 AAATGGGTTCCTCTATGCAAAGACTAAA-TA-ACTTTAAATAAG
1 AAATGGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATATG
*
19780704 AAATAGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATATG
1 AAATGGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATATG
* * *
19780748 AAATGGGCTCCTCTATACATAGGCCAAACCATTTTTTAAATATG
1 AAATGGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATATG
* *
19780792 AAATGAGTTCCTCTATACAGAGGCTAAAC
1 AAATGGGTTCCTCTATACAAAGGCTAAAC
19780821 AACTTTAAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 25 0.25
43 1 0.01
44 74 0.74
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (44 bp):
AAATGGGTTCCTCTATACAAAGGCTAAACCATTTTTTAAATATG
Found at i:19791793 original size:30 final size:30
Alignment explanation
Indices: 19791746--19791802 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
19791736 TTTTGTTAGG
** *
19791746 TGAAAATAAATGTTTAAAATATCAATTGAA
1 TGAAAATAAATAATTAAAAGATCAATTGAA
*
19791776 TGAAAATAAATAATTAAAGGATCAATT
1 TGAAAATAAATAATTAAAAGATCAATT
19791803 AATTATACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.11, T:0.32
Consensus pattern (30 bp):
TGAAAATAAATAATTAAAAGATCAATTGAA
Found at i:19793915 original size:23 final size:23
Alignment explanation
Indices: 19793888--19793948 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
19793878 CAATTAATAA
*
19793888 TAAAATAATATCTTTTACA-TTTT
1 TAAAATAATATATTTTA-ATTTTT
* *
19793911 TAAAACATTATATTTTAATTTTT
1 TAAAATAATATATTTTAATTTTT
19793934 TAAAATTAA-ATATTT
1 TAAAA-TAATATATTT
19793949 CCAATCTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAAATAATATATTTTAATTTTT
Found at i:19794056 original size:20 final size:21
Alignment explanation
Indices: 19794021--19794062 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
19794011 ATTTGTAAAA
19794021 AAATCAAAATTTTAATTTTTT
1 AAATCAAAATTTTAATTTTTT
19794042 AAATCAAAA-TTTAATTTTTT
1 AAATCAAAATTTTAATTTTTT
19794062 A
1 A
19794063 GAACCCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATCAAAATTTTAATTTTTT
Found at i:19794075 original size:22 final size:20
Alignment explanation
Indices: 19794025--19794067 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
19794015 GTAAAAAAAT
*
19794025 CAAAATTTTAATTTTTTAAAT
1 CAAAA-TTTAATTTTTTAAAC
19794046 CAAAATTTAATTTTTTAGAAC
1 CAAAATTTAATTTTTTA-AAC
19794067 C
1 C
19794068 CAATATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (20 bp):
CAAAATTTAATTTTTTAAAC
Found at i:19794533 original size:21 final size:20
Alignment explanation
Indices: 19794507--19794587 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 20
19794497 CAAAAATTTC
*
19794507 TAAAAAATCTAAATATTGATT
1 TAAAAAAT-AAAATATTGATT
*
19794528 TAAAAAATAAAATTTTGATTT
1 TAAAAAATAAAATATTGA-TT
**
19794549 TAGAGTAAT-AAATATATGATTT
1 TA-AAAAATAAAATAT-TGA-TT
19794571 TAAAAAATTAAAATATT
1 TAAAAAA-TAAAATATT
19794588 TAAAAATATC
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 8 0.17
21 20 0.42
22 14 0.29
23 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (20 bp):
TAAAAAATAAAATATTGATT
Found at i:19794683 original size:20 final size:21
Alignment explanation
Indices: 19794634--19794683 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
19794624 AAATTGTAGA
* *
19794634 AAATTCCAAATATTATTTTTT
1 AAATTCAAAATACTATTTTTT
*
19794655 AAA-TAAAAATACT-TTTTTT
1 AAATTCAAAATACTATTTTTT
19794674 AAATTCAAAA
1 AAATTCAAAA
19794684 AATAGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTCAAAATACTATTTTTT
Found at i:19795980 original size:13 final size:14
Alignment explanation
Indices: 19795962--19795990 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19795952 TTGGCTCAAA
19795962 TAAAATA-TATAAT
1 TAAAATATTATAAT
19795975 TAAAATATTATAAT
1 TAAAATATTATAAT
19795989 TA
1 TA
19795991 TATAATTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:19798551 original size:23 final size:22
Alignment explanation
Indices: 19798525--19798620 Score: 68
Period size: 25 Copynumber: 4.0 Consensus size: 22
19798515 AATATACTTG
19798525 TTTGCATGATTAATATATTTATT
1 TTTG-ATGATTAATATATTTATT
*
19798548 TTTGTAATTTATTAATATATTTATT
1 TTTG--A-TGATTAATATATTTATT
* *
19798573 TGT-ATGATTATATTTAATTTGATT
1 TTTGATGATTA-ATAT-ATTT-ATT
* *
19798597 GCTTGATTATTAATATATTTATT
1 -TTTGATGATTAATATATTTATT
19798620 T
1 T
19798621 GCATGAATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
21 5 0.09
22 4 0.07
23 11 0.20
24 8 0.14
25 22 0.39
26 6 0.11
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.59
Consensus pattern (22 bp):
TTTGATGATTAATATATTTATT
Found at i:19798686 original size:31 final size:31
Alignment explanation
Indices: 19798640--19798700 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
19798630 ACATATTTTA
*
19798640 CATGGTTTATATATTATTATTTACATGATTG
1 CATGATTTATATATTATTATTTACATGATTG
* *
19798671 CATGATTTATGTATTATTATTTGCATGATT
1 CATGATTTATATATTATTATTTACATGATT
19798701 ATATATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (31 bp):
CATGATTTATATATTATTATTTACATGATTG
Found at i:19798716 original size:20 final size:22
Alignment explanation
Indices: 19798667--19798722 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
19798657 TATTTACATG
*
19798667 ATTGCATGATTTATGTATTATTA
1 ATTGCATGA-TTATATATTATTA
*
19798690 TTTGCATGATTATATA-T-TTA
1 ATTGCATGATTATATATTATTA
*
19798710 ATTGCATGTTTAT
1 ATTGCATGATTAT
19798723 TTGCATGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 6 0.21
23 8 0.28
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (22 bp):
ATTGCATGATTATATATTATTA
Found at i:19798727 original size:55 final size:55
Alignment explanation
Indices: 19798668--19798919 Score: 323
Period size: 55 Copynumber: 4.6 Consensus size: 55
19798658 ATTTACATGA
*
19798668 TTGCATGATTTATGTATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
* *
19798723 TTGCATGATTT-TATATTATTATTTGCATGAGTATATATTTAAGTTGTATGTTTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAA-TTGCATGTTTAT
** * *
19798778 TTGCATGATTTATATATTCCTATTTGTATGATTATATATTTAATTGCATATTTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
* * * * * *
19798833 TTGCATGGTTTATGTAATATTATTTGCATGATTTTATATTTAATTACATGTTTAA
1 TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
* * *
19798888 TTGTAT-AATTATATA-T-TTAATTGCATGATTAT
1 TTGCATGATTTATATATTATTATTTGCATGATTAT
19798920 TAATTTATTT
Statistics
Matches: 170, Mismatches: 25, Indels: 7
0.84 0.12 0.03
Matches are distributed among these distances:
52 14 0.08
53 1 0.01
54 35 0.21
55 93 0.55
56 27 0.16
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (55 bp):
TTGCATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATGTTTAT
Found at i:19798745 original size:22 final size:22
Alignment explanation
Indices: 19798719--19798761 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
19798709 AATTGCATGT
* *
19798719 TTATTTGCATGATTTTATATTA
1 TTATTTGCATGAGTATATATTA
19798741 TTATTTGCATGAGTATATATT
1 TTATTTGCATGAGTATATATT
19798762 TAAGTTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (22 bp):
TTATTTGCATGAGTATATATTA
Found at i:19798815 original size:22 final size:23
Alignment explanation
Indices: 19798775--19798832 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 23
19798765 GTTGTATGTT
19798775 TATTTGCATGATTTATATATTCC
1 TATTTGCATGATTTATATATTCC
*
19798798 TATTTGTATGA-TTATATATT--
1 TATTTGCATGATTTATATATTCC
*
19798818 TAATTGCAT-ATTTAT
1 TATTTGCATGATTTAT
19798833 TTGCATGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 11 0.35
22 9 0.29
23 10 0.32
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (23 bp):
TATTTGCATGATTTATATATTCC
Found at i:19798926 original size:20 final size:20
Alignment explanation
Indices: 19798873--19798919 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19798863 ATTTTATATT
* * *
19798873 TAATTACATGTTTAATTGTA
1 TAATTATATATTTAATTGCA
19798893 TAATTATATATTTAATTGCA
1 TAATTATATATTTAATTGCA
*
19798913 TGATTAT
1 TAATTAT
19798920 TAATTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (20 bp):
TAATTATATATTTAATTGCA
Found at i:19798943 original size:52 final size:55
Alignment explanation
Indices: 19798691--19798969 Score: 137
Period size: 55 Copynumber: 5.1 Consensus size: 55
19798681 GTATTATTAT
* * * * * * *
19798691 TTGCATGATTATATATTTAATTGCATGTTTATTTGCATGAT-TTTATAT-TATTAT
1 TTGCATGATTTTATATTTAATTACATGTGTAATTGTATGATATTAATATAT-TTAA
* * ** * * * *
19798745 TTGCATGAGTATATATTTAAGTTGTATGTTTATTTGCATGAT-TT-ATATATTCCTAT
1 TTGCATGATTTTATATTTAA-TTACATGTGTAATTGTATGATATTAATATATT--TAA
* * * * * * * * * *
19798801 TTGTATGATTATATATTTAATTGCATATTTATTTGCATGGT-TT-ATGTAATATTAT
1 TTGCATGATTTTATATTTAATTACATGTGTAATTGTATGATATTAATAT-AT-TTAA
*
19798856 TTGCATGATTTTATATTTAATTACATGTTTAATTGTAT-A-ATT-ATATATTTAA
1 TTGCATGATTTTATATTTAATTACATGTGTAATTGTATGATATTAATATATTTAA
* ** * *
19798908 TTGCATGATTATTA-ATTTATTTATTTGTGTGATTGTATGATTATTAATATATTTAT
1 TTGCATGATT-TTATATTTAATTACATGTGTAATTGTATGA-TATTAATATATTTAA
19798964 TTGCAT
1 TTGCAT
19798970 AGTTATTTAT
Statistics
Matches: 190, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
52 32 0.17
53 6 0.03
54 29 0.15
55 84 0.44
56 38 0.20
57 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (55 bp):
TTGCATGATTTTATATTTAATTACATGTGTAATTGTATGATATTAATATATTTAA
Found at i:19799031 original size:24 final size:23
Alignment explanation
Indices: 19798999--19799059 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
19798989 TATTATTGCA
*
19798999 TAATTTTATATTTATTACATGAT
1 TAATATTATATTTATTACATGAT
* *
19799022 ATGATATTATATATTATTGCATGAT
1 -TAATATTATAT-TTATTACATGAT
19799047 TAATATTATATTT
1 TAATATTATATTT
19799060 GAATGATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.06
24 19 0.59
25 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (23 bp):
TAATATTATATTTATTACATGAT
Found at i:19799056 original size:22 final size:22
Alignment explanation
Indices: 19798978--19799058 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 22
19798968 ATAGTTATTT
* *
19798978 ATTATTATTATTATTATTGCATA
1 ATTAATATTA-TATTATTGCATG
* *
19799001 ATT-TTA-TAT-TTATTACATG
1 ATTAATATTATATTATTGCATG
*
19799020 ATATGATATTATATATTATTGCATG
1 AT-TAATA-T-TATATTATTGCATG
19799045 ATTAATATTATATT
1 ATTAATATTATATT
19799059 TGAATGATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.21
20 2 0.04
21 4 0.09
22 9 0.19
23 4 0.09
24 7 0.15
25 11 0.23
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (22 bp):
ATTAATATTATATTATTGCATG
Found at i:19799159 original size:18 final size:19
Alignment explanation
Indices: 19799131--19799168 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
19799121 CTTACATAAT
*
19799131 TATTAATATATTTGTATGA
1 TATTAATATATTTATATGA
19799150 TATT-ATATATTTATATGA
1 TATTAATATATTTATATGA
19799168 T
1 T
19799169 TGTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (19 bp):
TATTAATATATTTATATGA
Found at i:19803603 original size:41 final size:40
Alignment explanation
Indices: 19803542--19803626 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 40
19803532 TCTCTAAATT
**
19803542 AATAACAAATCAATCTAGAATATTATTAAAATATTACTAG
1 AATAACAAATCAATCTAGAATATTACCAAAATATTACTAG
* * * *
19803582 AATAACATCATCAATTTAGAATATTGCCATAATATTACTAG
1 AATAACA-AATCAATCTAGAATATTACCAAAATATTACTAG
19803623 AATA
1 AATA
19803627 TCATTGACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 7 0.18
41 31 0.82
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (40 bp):
AATAACAAATCAATCTAGAATATTACCAAAATATTACTAG
Found at i:19810286 original size:6 final size:7
Alignment explanation
Indices: 19810268--19810292 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19810258 TTAAAGTCAT
19810268 ATTTTTA
1 ATTTTTA
19810275 ATTTTTA
1 ATTTTTA
19810282 ATTTTTA
1 ATTTTTA
19810289 ATTT
1 ATTT
19810293 AAAAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTTA
Found at i:19823695 original size:23 final size:22
Alignment explanation
Indices: 19823669--19823730 Score: 54
Period size: 23 Copynumber: 2.7 Consensus size: 22
19823659 ATACTATCGG
19823669 TATATAATTTTATAAATTGTTAT
1 TATATAATTTTATAAATT-TTAT
* * *
19823692 TATATCATATTATATTATTTTAT
1 TATATAATTTTATA-AATTTTAT
*
19823715 TAATAAAATTTT-TAAA
1 T-ATATAATTTTATAAA
19823731 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
22 1 0.03
23 19 0.63
24 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TATATAATTTTATAAATTTTAT
Found at i:19826888 original size:31 final size:31
Alignment explanation
Indices: 19826848--19826910 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
19826838 GTGATCATAC
* *
19826848 AAATGAAATCCATACAAAATATTATGTAAAT
1 AAATGAAATCCATACAAAATATCATGCAAAT
* **
19826879 AAATTAAATCCATATGAAATATCATGCAAAT
1 AAATGAAATCCATACAAAATATCATGCAAAT
19826910 A
1 A
19826911 TATATTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (31 bp):
AAATGAAATCCATACAAAATATCATGCAAAT
Found at i:19826988 original size:26 final size:26
Alignment explanation
Indices: 19826931--19826988 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
19826921 TCATTCAAGC
*
19826931 AAAAATATCATAATAAAATCTTACAA
1 AAAAATATCATAATAAAATCATACAA
** *
19826957 CTAAATATCATAA-ACAAATCATGCAA
1 AAAAATATCATAATA-AAATCATACAA
19826983 AAAAAT
1 AAAAAT
19826989 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (26 bp):
AAAAATATCATAATAAAATCATACAA
Found at i:19827100 original size:20 final size:21
Alignment explanation
Indices: 19827077--19827129 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
19827067 TAAAAATAAT
*
19827077 AAATAATAAAAT-AAACAAAA
1 AAATAAGAAAATAAAACAAAA
*
19827097 AAATTAGAAAATAGAAACAAAAA
1 AAATAAGAAAATA-AAAC-AAAA
19827120 AAATAA-AAAA
1 AAATAAGAAAA
19827130 CCTACAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
22 8 0.30
23 9 0.33
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (21 bp):
AAATAAGAAAATAAAACAAAA
Found at i:19827129 original size:22 final size:20
Alignment explanation
Indices: 19827077--19827129 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
19827067 TAAAAATAAT
19827077 AAATAATAAAATAAACAAAAA
1 AAATAA-AAAATAAACAAAAA
* *
19827098 AATTAGAAAATAGAAACAAAAA
1 AAATA-AAAA-ATAAACAAAAA
19827120 AAATAAAAAA
1 AAATAAAAAA
19827130 CCTACAATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.04
21 11 0.41
22 15 0.56
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (20 bp):
AAATAAAAAATAAACAAAAA
Found at i:19829649 original size:8 final size:8
Alignment explanation
Indices: 19829636--19829682 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
19829626 ATAAAAAGAA
19829636 ATTTTTTT
1 ATTTTTTT
19829644 ATTTTTCTT
1 ATTTTT-TT
19829653 -TTTTATTGT
1 ATTTT-TT-T
19829662 -TTTTTTT
1 ATTTTTTT
19829669 ATTTTTTT
1 ATTTTTTT
19829677 ATTTTT
1 ATTTTT
19829683 CAAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 1 0.03
8 26 0.74
9 8 0.23
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:19829656 original size:13 final size:12
Alignment explanation
Indices: 19829637--19829681 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
19829627 TAAAAAGAAA
19829637 TTTTTTTATTTT
1 TTTTTTTATTTT
*
19829649 TCTTTTTTATTGT
1 T-TTTTTTATTTT
19829662 TTTTTTTATTTT
1 TTTTTTTATTTT
19829674 TTTATTTT
1 TTT-TTTT
19829682 TCAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 14 0.48
13 15 0.52
ACGTcount: A:0.09, C:0.02, G:0.02, T:0.87
Consensus pattern (12 bp):
TTTTTTTATTTT
Found at i:19829738 original size:18 final size:17
Alignment explanation
Indices: 19829717--19829771 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
19829707 TTAATAAATG
*
19829717 ATAAATCACTCAATAAAA
1 ATAAATAACT-AATAAAA
19829735 ATAAATAACTAATAAAA
1 ATAAATAACTAATAAAA
* *
19829752 ATCAGTAA--AATAAAA
1 ATAAATAACTAATAAAA
19829767 ATAAA
1 ATAAA
19829772 ATCAAAGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 10 0.31
17 13 0.41
18 9 0.28
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (17 bp):
ATAAATAACTAATAAAA
Found at i:19829780 original size:22 final size:21
Alignment explanation
Indices: 19829748--19829818 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 21
19829738 AATAACTAAT
19829748 AAAAATC--AGTAAAATAAAA
1 AAAAATCAAAGTAAAATAAAA
19829767 ATAAAATCAAAGTATAAAATAAATA
1 A-AAAATCAAAG--TAAAATAAA-A
* *
19829792 AAAAATGAAATTAAAATAGAAA
1 AAAAATCAAAGTAAAATA-AAA
19829814 AAAAA
1 AAAAA
19829819 ACCTGCGATT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.14
22 15 0.35
23 2 0.05
24 17 0.40
25 2 0.05
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAAATCAAAGTAAAATAAAA
Found at i:19829788 original size:24 final size:21
Alignment explanation
Indices: 19829757--19829818 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 21
19829747 TAAAAATCAG
19829757 TAAAATAAAAATAAAATCAAAGT
1 TAAAATAAAAA-AAAATCAAA-T
*
19829780 ATAAAATAAATAAAAAATGAAAT
1 -TAAAATAAA-AAAAAATCAAAT
19829803 TAAAATAGAAAAAAAA
1 TAAAATA-AAAAAAAA
19829819 ACCTGCGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 13 0.37
23 3 0.09
24 17 0.49
25 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (21 bp):
TAAAATAAAAAAAAATCAAAT
Found at i:19829814 original size:29 final size:28
Alignment explanation
Indices: 19829759--19829814 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
19829749 AAAATCAGTA
* *
19829759 AAATAAAAATAAAATCAAAGTATAAAAT
1 AAATAAAAATAAAATCAAAATAGAAAAT
* *
19829787 AAATAAAAAATGAAATTAAAATAGAAAA
1 AAAT-AAAAATAAAATCAAAATAGAAAA
19829815 AAAAACCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (28 bp):
AAATAAAAATAAAATCAAAATAGAAAAT
Found at i:19830461 original size:15 final size:15
Alignment explanation
Indices: 19830452--19830500 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
19830442 GAATAAGATA
19830452 AAATAA-AATAAAAT
1 AAATAATAATAAAAT
19830466 AAATAATAATAATAAAT
1 AAATAATAAT-A-AAAT
19830483 ATAATAATAATAATAAT
1 A-AATAATAATAA-AAT
19830500 A
1 A
19830501 TATTATACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.20
15 3 0.10
16 2 0.07
17 10 0.33
18 9 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATAATAAAAT
Found at i:19830520 original size:3 final size:3
Alignment explanation
Indices: 19830449--19830500 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
19830439 GGGGAATAAG
19830449 ATA A-A ATA A-A ATA A-A ATAA ATA ATA ATA ATA A-A TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA
19830492 ATA ATA ATA
1 ATA ATA ATA
19830501 TATTATACCA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 7 0.16
3 32 0.74
4 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:19830658 original size:18 final size:19
Alignment explanation
Indices: 19830471--19830653 Score: 96
Period size: 20 Copynumber: 9.5 Consensus size: 19
19830461 AAAATAAATA
* *
19830471 ATAATAATAAATATAATAAT
1 ATAATAATATATATACT-AT
*
19830491 AATAATAATATATTATACCAT
1 -ATAATAATATA-TATACTAT
*
19830512 ATAATAATATATCACACTAAT
1 ATAATAATATAT-ATACT-AT
*
19830533 ACAATAATACTATA-A-TAT
1 ATAATAATA-TATATACTAT
** *
19830551 GAT-ATGCTATACTATATTAT
1 -ATAATAATATA-TATACTAT
*
19830571 ATACT-ATA-ATAATACTA-
1 ATAATAATATAT-ATACTAT
*
19830588 ATAATAATA-CTATA-T-T
1 ATAATAATATATATACTAT
*
19830604 ATAATAATATATTTTACTAT
1 ATAATAATATA-TATACTAT
19830624 ATAATAATATATTATACTAT
1 ATAATAATATA-TATACTAT
19830644 AGTAATAATA
1 A-TAATAATA
19830654 AATACAATAA
Statistics
Matches: 128, Mismatches: 17, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
16 10 0.08
17 10 0.08
18 21 0.16
19 9 0.07
20 40 0.31
21 31 0.24
22 7 0.05
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATAATATATATACTAT
Found at i:19837545 original size:17 final size:17
Alignment explanation
Indices: 19837525--19837562 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19837515 ATTTATGTTA
*
19837525 AAATTATATTATTAA-TT
1 AAATTAAATT-TTAATTT
19837542 AAATTAAATTTTAATTT
1 AAATTAAATTTTAATTT
19837559 AAAT
1 AAAT
19837563 ATGTTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTAAATTTTAATTT
Found at i:19839189 original size:33 final size:33
Alignment explanation
Indices: 19839147--19839241 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 33
19839137 TTGCATTAGC
19839147 TGAAACTAATGGGATTATGATGTACCGCATAAT
1 TGAAACTAATGGGATTATGATGTACCGCATAAT
* * * * *
19839180 TGAAACTAATTGGACTACGATGTGCCGCATAGT
1 TGAAACTAATGGGATTATGATGTACCGCATAAT
* *
19839213 TGGAACTAATTGGG-TTATGATGAACCGCA
1 TGAAACTAA-TGGGATTATGATGTACCGCA
19839242 CTATGTTTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 47 0.94
34 3 0.06
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (33 bp):
TGAAACTAATGGGATTATGATGTACCGCATAAT
Found at i:19843024 original size:16 final size:15
Alignment explanation
Indices: 19842996--19843061 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 15
19842986 TAATTTTTTA
19842996 TTTATAT-AT-ATAT
1 TTTATATAATAATAT
19843009 ATTTATATAATAATATT
1 -TTTATATAATAATA-T
* * *
19843026 TTTAAATATTTATAT
1 TTTATATAATAATAT
*
19843041 TTTA-AAAATAATAT
1 TTTATATAATAATAT
19843055 TTTATAT
1 TTTATAT
19843062 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
14 18 0.44
15 8 0.20
16 14 0.34
17 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATATAATAATAT
Found at i:19843042 original size:30 final size:30
Alignment explanation
Indices: 19842999--19843057 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
19842989 TTTTTTATTT
*
19842999 ATATATATATATTTATATAATAATATTTTTAA
1 ATATATATAT-TTTA-AAAATAATATTTTTAA
*
19843031 ATATTTATATTTTAAAAATAATATTTT
1 ATATATATATTTTAAAAATAATATTTT
19843058 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 12 0.48
31 4 0.16
32 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATATATATTTTAAAAATAATATTTTTAA
Found at i:19843056 original size:14 final size:15
Alignment explanation
Indices: 19843005--19843058 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
19842995 ATTTATATAT
*
19843005 ATATATTTATATAATA
1 ATAT-TTTAAATAATA
* *
19843021 ATATTTTTAAATATTT
1 ATA-TTTTAAATAATA
19843037 ATATTTTAAA-AATA
1 ATATTTTAAATAATA
19843051 ATATTTTA
1 ATATTTTA
19843059 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.31
15 7 0.22
16 14 0.44
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATATTTTAAATAATA
Found at i:19843072 original size:19 final size:20
Alignment explanation
Indices: 19843029--19843078 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
19843019 TAATATTTTT
19843029 AAATA-TTTATATTTTAAAA
1 AAATATTTTATATTTTAAAA
19843048 ATAATATTTTATA-TTTAAAA
1 A-AATATTTTATATTTTAAAA
19843068 AAATATTTTAT
1 AAATATTTTAT
19843079 TAATTTCGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.38
20 12 0.41
21 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTTATATTTTAAAA
Found at i:19843084 original size:21 final size:20
Alignment explanation
Indices: 19843029--19843084 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
19843019 TAATATTTTT
*
19843029 AAATA-TTTATATTTTAAAA
1 AAATATTTTATAATTTAAAA
19843048 ATAATATTTTAT-ATTTAAAA
1 A-AATATTTTATAATTTAAAA
19843068 AAATATTTTATTAATTT
1 AAATATTTTA-TAATTT
19843085 CGGATCGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.31
20 13 0.41
21 9 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAATATTTTATAATTTAAAA
Found at i:19843598 original size:13 final size:13
Alignment explanation
Indices: 19843582--19843608 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19843572 TTTGAAATGG
19843582 TCATTTAATTAAA
1 TCATTTAATTAAA
19843595 TCATTTAATTAAA
1 TCATTTAATTAAA
19843608 T
1 T
19843609 AAGAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TCATTTAATTAAA
Found at i:19847131 original size:11 final size:12
Alignment explanation
Indices: 19847115--19847154 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
19847105 CTTAATTGAC
19847115 TAATTAAT-AAT
1 TAATTAATCAAT
19847126 TAATTAATCAAT
1 TAATTAATCAAT
19847138 T--TTAATCCAAT
1 TAATTAAT-CAAT
19847149 TAATTA
1 TAATTA
19847155 TTAATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 5 0.20
11 13 0.52
12 4 0.16
13 3 0.12
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTAATCAAT
Found at i:19847558 original size:24 final size:25
Alignment explanation
Indices: 19847507--19847568 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
19847497 AAATTTTAAA
* * * *
19847507 ATTAATTTTTTATGAAATATTATTT
1 ATTAATTATATATAAAATATTATAT
19847532 ATTAATTATATATAAAAT-TTATAT
1 ATTAATTATATATAAAATATTATAT
* *
19847556 ATTTATAATATAT
1 ATTAATTATATAT
19847569 CAATAAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTAATTATATATAAAATATTATAT
Found at i:19847659 original size:20 final size:18
Alignment explanation
Indices: 19847625--19847675 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
19847615 GGAGAACATT
*
19847625 AATCAGTTTAAATTGATCA
1 AATCAATTTAAATTGAT-A
19847644 AATCAATTTAAAATTGATA
1 AATCAATTT-AAATTGATA
*
19847663 ATTCAA-TTAAATT
1 AATCAATTTAAATT
19847676 AGTTTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
19 14 0.48
20 8 0.28
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (18 bp):
AATCAATTTAAATTGATA
Found at i:19850883 original size:3 final size:3
Alignment explanation
Indices: 19850875--19850901 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
19850865 TTTAATATAA
19850875 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
19850902 TTTAATTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.