Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 52 of 126
Found at i:10279323 original size:32 final size:32
Alignment explanation
Indices: 10279282--10279367 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
10279272 TTCGAATGAT
* *
10279282 ACATGAAAATCAATTTTTTTTTATTTCAAAGG
1 ACATAAAAATAAATTTTTTTTTATTTCAAAGG
* * *
10279314 ACATAAAAATTAAATATCTTTTTATTTCAAATG
1 ACATAAAAA-TAAATTTTTTTTTATTTCAAAGG
*
10279347 ACA-AGAAAATAAAATTTTTTT
1 ACATA-AAAATAAATTTTTTTT
10279368 AGAACTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 18 0.41
33 26 0.59
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
ACATAAAAATAAATTTTTTTTTATTTCAAAGG
Found at i:10279809 original size:16 final size:15
Alignment explanation
Indices: 10279788--10279831 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
10279778 AGTATTTTAG
10279788 TAATTTAATATATAGT
1 TAATTTAATATATA-T
*
10279804 TAATTTTATATTATAT
1 TAATTTAATA-TATAT
10279820 TAAATTTAATAT
1 T-AATTTAATAT
10279832 GTAATTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TAATTTAATATATAT
Found at i:10280489 original size:60 final size:62
Alignment explanation
Indices: 10280328--10280489 Score: 166
Period size: 63 Copynumber: 2.6 Consensus size: 62
10280318 CCCTCTATTT
* * ** * * *
10280328 ATTATAGTAATTTTGGCCAATTATGGTAGGAGAGAAATTTTTGTAATTATGGTATAAAGGGGT
1 ATTATAGTAATTTTGACCAATTATGGTAGGAGGGGTATTCTTGTAATTAT-GAATAAAGGGGC
* * * * * *
10280391 ATTATTGTAATTTTAATCAATTATGATATGAGGAGTATTCTTGTAATTAT-AAT-AAGGGGC
1 ATTATAGTAATTTTGACCAATTATGGTAGGAGGGGTATTCTTGTAATTATGAATAAAGGGGC
* *
10280451 ATTAAAGTAATTTTGACCAATTAGGGTAGGAGGGGTATT
1 ATTATAGTAATTTTGACCAATTATGGTAGGAGGGGTATT
10280490 TTTTATGATT
Statistics
Matches: 78, Mismatches: 21, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
60 37 0.47
61 2 0.03
63 39 0.50
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (62 bp):
ATTATAGTAATTTTGACCAATTATGGTAGGAGGGGTATTCTTGTAATTATGAATAAAGGGGC
Found at i:10285306 original size:333 final size:333
Alignment explanation
Indices: 10284687--10285306 Score: 854
Period size: 333 Copynumber: 1.9 Consensus size: 333
10284677 AGAGACCAAA
10284687 GCTCTGATACCAGTTTTCAAGATCAAACGCTTACCATTACACCAAAAGCTATAGCTGATAGTGAA
1 GCTCTGATACCAGTTTTCAAGATCAAACGCTTACCATTACACCAAAAGCTATAGCTGATAGTGAA
* * ** * * * *
10284752 TGTGCAACTCTATTTTCTTATTCTCTTTTGGTAGTGTAGAGCCCTATACTAAGCGACATATGGAC
66 GGCGCAACTCTATTTTCTTATTCTCTTTTGGTAACGCAAAGCCCTATACTAAGCAACAGATGGAC
** * *
10284817 ATAAGGGGCTTTACAAAGCCTTCATGGGATACTTCACCCATTGGATCTCGACAAGTTGGGTTGTC
131 ATAAGGGGCTACACAAAGCCTTCATAGGATACTTCACCCATTGGACCTCGACAAGTTGGGTTGTC
* * * *
10284882 ATACACCGAAATTCGATCCACCATGGGATACCCCACCTAGATGAATCGACATATCGAGTCCTTAA
196 ATACACCGAAATCCGATCCACAATGGGATACCCCACCTAGATGAATCGACATACCGAGTCCCTAA
* * *
10284947 GAGAGATCGTTAGACCTCAGAATCCAATAATCTCTCTTCCAGCAACACCTAGAGGACTCAAACCT
261 GAGAAACCGTTAGACCCCAGAATCCAATAATCTCTCTTCCAGCAACACCTAGAGGACTCAAACCT
10285012 GTAACCTC
326 GTAACCTC
* *
10285020 GCTCTGATACCAGTTTTCATGATCAAGCGCTTACCATTACACCAAAAGCTATAGCTGATAGTGAA
1 GCTCTGATACCAGTTTTCAAGATCAAACGCTTACCATTACACCAAAAGCTATAGCTGATAGTGAA
*
10285085 GGCGCAACTCTATTTTCTTATTCTCTTTTGGTAACGCAAAGCCCCT-TACTAA-CTAACAGGTGG
66 GGCGCAACTCTATTTTCTTATTCTCTTTTGGTAACGCAAAG-CCCTATACTAAGC-AACAGATGG
* * * ** *
10285148 ATATAAGGGGCTACGCAAAGCTTTCATAGGATACTTCACCCATTAGG-CCTCGGTAGGTTGGGTT
129 ACATAAGGGGCTACACAAAGCCTTCATAGGATACTTCACCCATT-GGACCTCGACAAGTTGGGTT
* * * *
10285212 GTCATACACC-AGAATCCGATCTATAATGGGATATCCCACCTAGATGAATTGACATACCGAGTCC
193 GTCATACACCGA-AATCCGATCCACAATGGGATACCCCACCTAGATGAATCGACATACCGAGTCC
* *
10285276 CTAA-AGCAAACCGTTGGACCCCATAATCCAA
257 CTAAGAG-AAACCGTTAGACCCCAGAATCCAA
10285307 CATAATAAAT
Statistics
Matches: 248, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
332 4 0.02
333 238 0.96
334 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (333 bp):
GCTCTGATACCAGTTTTCAAGATCAAACGCTTACCATTACACCAAAAGCTATAGCTGATAGTGAA
GGCGCAACTCTATTTTCTTATTCTCTTTTGGTAACGCAAAGCCCTATACTAAGCAACAGATGGAC
ATAAGGGGCTACACAAAGCCTTCATAGGATACTTCACCCATTGGACCTCGACAAGTTGGGTTGTC
ATACACCGAAATCCGATCCACAATGGGATACCCCACCTAGATGAATCGACATACCGAGTCCCTAA
GAGAAACCGTTAGACCCCAGAATCCAATAATCTCTCTTCCAGCAACACCTAGAGGACTCAAACCT
GTAACCTC
Found at i:10292200 original size:40 final size:40
Alignment explanation
Indices: 10292145--10292224 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
10292135 AGGTCCTCCA
10292145 TTCATTTGTGGTTGCTTTATGTGTTTCACAGAACTTATTT
1 TTCATTTGTGGTTGCTTTATGTGTTTCACAGAACTTATTT
* *
10292185 TTCATTTTTGGTTGCTTTATGTGTTTCACAGAATTTATTT
1 TTCATTTGTGGTTGCTTTATGTGTTTCACAGAACTTATTT
10292225 CTTTATGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.17, C:0.11, G:0.16, T:0.55
Consensus pattern (40 bp):
TTCATTTGTGGTTGCTTTATGTGTTTCACAGAACTTATTT
Found at i:10296856 original size:3 final size:3
Alignment explanation
Indices: 10296811--10296838 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10296801 TCCTTTATAT
10296811 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10296839 GTCATAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10298366 original size:20 final size:21
Alignment explanation
Indices: 10298341--10298381 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
10298331 GAAACAAAAT
* *
10298341 TGGCAGTACATAAAA-AGAAC
1 TGGCAGAAAATAAAATAGAAC
10298361 TGGCAGAAAATAAAATAGAAC
1 TGGCAGAAAATAAAATAGAAC
10298382 ATAAAGGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.15
Consensus pattern (21 bp):
TGGCAGAAAATAAAATAGAAC
Found at i:10304672 original size:20 final size:20
Alignment explanation
Indices: 10304635--10304673 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10304625 ATAATCAAGC
* *
10304635 AAAATTAAATCAAGTAAGTT
1 AAAATTAAACCAACTAAGTT
*
10304655 AAAATTTAACCAACTAAGT
1 AAAATTAAACCAACTAAGT
10304674 ACATGATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (20 bp):
AAAATTAAACCAACTAAGTT
Found at i:10311824 original size:22 final size:23
Alignment explanation
Indices: 10311789--10311832 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
10311779 GACATGATTT
*
10311789 TAAATTTTAGCAAAAACAATATA
1 TAAATTTTAACAAAAACAATATA
*
10311812 TAAA-TTTAACAAAAACTATAT
1 TAAATTTTAACAAAAACAATAT
10311833 TTCATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
TAAATTTTAACAAAAACAATATA
Found at i:10312778 original size:15 final size:16
Alignment explanation
Indices: 10312752--10312786 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
10312742 TATCTAGACA
10312752 TTTCATATCTTTTTAC
1 TTTCATATCTTTTTAC
*
10312768 TTTCATA-CTTTTTCC
1 TTTCATATCTTTTTAC
10312783 TTTC
1 TTTC
10312787 TAATTTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTCATATCTTTTTAC
Found at i:10318571 original size:21 final size:21
Alignment explanation
Indices: 10318545--10318585 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10318535 ACCATCAAAT
*
10318545 TAGATTTTCAAGTTAATTTAA
1 TAGATTCTCAAGTTAATTTAA
10318566 TAGATTCTCAAGTTAATTTA
1 TAGATTCTCAAGTTAATTTA
10318586 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (21 bp):
TAGATTCTCAAGTTAATTTAA
Found at i:10322960 original size:21 final size:21
Alignment explanation
Indices: 10322915--10322954 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10322905 TTACTACTAC
10322915 TAATAAAATTTCATAATTAAG
1 TAATAAAATTTCATAATTAAG
* *
10322936 TAATGAAATTTCGTAATTA
1 TAATAAAATTTCATAATTA
10322955 GTTAATTCAA
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:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
TAATAAAATTTCATAATTAAG
Found at i:10328323 original size:7 final size:6
Alignment explanation
Indices: 10328293--10328322 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
10328283 ATTTGGGAAG
10328293 TTTTTA TTTTTTA TTTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTT
10328323 TGTGAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:10334514 original size:12 final size:12
Alignment explanation
Indices: 10334497--10334529 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
10334487 ATGTATATAT
10334497 ATATATAGATAG
1 ATATATAGATAG
10334509 ATATATAGATAG
1 ATATATAGATAG
*
10334521 ATAGATAGA
1 ATATATAGA
10334530 GAGAGAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (12 bp):
ATATATAGATAG
Found at i:10339588 original size:26 final size:25
Alignment explanation
Indices: 10339549--10339673 Score: 96
Period size: 26 Copynumber: 4.9 Consensus size: 25
10339539 TCCAAACCCC
10339549 AAACC-AAACCCTAAACCTAAACCT
1 AAACCTAAACCCTAAACCTAAACCT
* * *
10339573 ATACCTTAAACCCTAAA-ATCAAACCA
1 AAACC-TAAACCCTAAACCT-AAACCT
*
10339599 AAATCCTAAACCCTAAACCCAAATCCT
1 AAA-CCTAAACCCTAAACCTAAA-CCT
* *
10339626 AAACCCTAAAACC-AAACTTAAACCCT
1 AAA-CCTAAACCCTAAACCTAAA-CCT
*
10339652 AAACCCAAA-CCTAAACCCTAAA
1 AAACCTAAACCCTAAA-CCTAAA
10339674 ACTAGCTTGA
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
24 6 0.08
25 9 0.11
26 49 0.62
27 15 0.19
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (25 bp):
AAACCTAAACCCTAAACCTAAACCT
Found at i:10339596 original size:13 final size:15
Alignment explanation
Indices: 10339579--10339674 Score: 52
Period size: 13 Copynumber: 6.8 Consensus size: 15
10339569 ACCTATACCT
10339579 TAAACCCTAAAAT-C
1 TAAACCCTAAAATCC
10339593 -AAA-CC-AAAATCC
1 TAAACCCTAAAATCC
10339605 TAAACCCTAAACCCAAATCC
1 TAAACCCT--A---AAATCC
10339625 TAAACCCTAAAA-CC
1 TAAACCCTAAAATCC
* *
10339639 -AAA--CTTAAACCC
1 TAAACCCTAAAATCC
10339651 TAAACCC--AAA-CC
1 TAAACCCTAAAATCC
10339663 TAAACCCTAAAA
1 TAAACCCTAAAA
10339675 CTAGCTTGAT
Statistics
Matches: 66, Mismatches: 1, Indels: 30
0.68 0.01 0.31
Matches are distributed among these distances:
11 10 0.15
12 14 0.21
13 15 0.23
14 7 0.11
15 4 0.06
17 1 0.02
18 1 0.02
20 14 0.21
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (15 bp):
TAAACCCTAAAATCC
Found at i:10339615 original size:7 final size:7
Alignment explanation
Indices: 10339542--10339673 Score: 97
Period size: 7 Copynumber: 20.4 Consensus size: 7
10339532 CCTTAAATCC
*
10339542 AAACCCC
1 AAACCCT
10339549 AAA-CC-
1 AAACCCT
10339554 AAACCCT
1 AAACCCT
10339561 AAA-CCT
1 AAACCCT
10339567 AAA-CCT
1 AAACCCT
* *
10339573 ATACCTT
1 AAACCCT
10339580 AAACCCT
1 AAACCCT
**
10339587 AAAATC-
1 AAACCCT
*
10339593 AAA-CCA
1 AAACCCT
*
10339599 AAATCCT
1 AAACCCT
10339606 AAACCCT
1 AAACCCT
10339613 AAACCC-
1 AAACCCT
*
10339619 AAATCCT
1 AAACCCT
10339626 AAACCCT
1 AAACCCT
*
10339633 AAAACC-
1 AAACCCT
*
10339639 AAA-CTT
1 AAACCCT
10339645 AAACCCT
1 AAACCCT
10339652 AAACCC-
1 AAACCCT
10339658 AAA-CCT
1 AAACCCT
10339664 AAACCCT
1 AAACCCT
10339671 AAA
1 AAA
10339674 ACTAGCTTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
5 7 0.07
6 38 0.38
7 56 0.55
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:10339622 original size:20 final size:19
Alignment explanation
Indices: 10339554--10339673 Score: 118
Period size: 19 Copynumber: 6.2 Consensus size: 19
10339544 ACCCCAAACC
10339554 AAACCCTAAACCTAAA-CCT
1 AAACCC-AAACCTAAACCCT
* * **
10339573 ATACCTTAAACCCTAAAATC-
1 AAACC-CAAA-CCTAAACCCT
*
10339593 AAACCAAAATCCTAAACCCT
1 AAACCCAAA-CCTAAACCCT
10339613 AAACCCAAATCCTAAACCCT
1 AAACCCAAA-CCTAAACCCT
* *
10339633 AAAACCAAACTTAAACCCT
1 AAACCCAAACCTAAACCCT
10339652 AAACCCAAACCTAAACCCT
1 AAACCCAAACCTAAACCCT
10339671 AAA
1 AAA
10339674 ACTAGCTTGA
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
19 46 0.55
20 37 0.44
21 1 0.01
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (19 bp):
AAACCCAAACCTAAACCCT
Found at i:10340108 original size:20 final size:22
Alignment explanation
Indices: 10340083--10340123 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
10340073 ATAAATAATT
10340083 TTATTT-TTTCAAAA-AAAAAA
1 TTATTTCTTTCAAAAGAAAAAA
10340103 TTATTTGCTTTCAAAAGAAAA
1 TTATTT-CTTTCAAAAGAAAA
10340124 TTAAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (22 bp):
TTATTTCTTTCAAAAGAAAAAA
Found at i:10341767 original size:37 final size:37
Alignment explanation
Indices: 10341527--10341792 Score: 223
Period size: 37 Copynumber: 7.1 Consensus size: 37
10341517 GAGTTGGAAA
* * * * * *
10341527 TAATAAGATTGTACATCCATTCCCTTTCATCCACATTT
1 TAAT-AGATAGTACATGCATTCCATCTCATGCACATCT
*
10341565 TAATAAGATAAAGT--ATGCATTCCATCTCATGCACATTT
1 TAAT-AGAT--AGTACATGCATTCCATCTCATGCACATCT
* * * *
10341603 TAATAAAATAATACATGCATTCCATCTCATCCATATCT
1 TAAT-AGATAGTACATGCATTCCATCTCATGCACATCT
* * ** *
10341641 TAATAGATAGTATATACATTCCATCTCATATATATCT
1 TAATAGATAGTACATGCATTCCATCTCATGCACATCT
* * *
10341678 TAATAGATAGTACATACATTCCATCACATGCACATAT
1 TAATAGATAGTACATGCATTCCATCTCATGCACATCT
* * * *
10341715 CAATGGATTGTACATGCATTCCAAT-TCATGCACATGT
1 TAATAGATAGTACATGCATTCC-ATCTCATGCACATCT
* * *
10341752 TAATAGATAGTACATGTACTCCATCTTATGCACATCT
1 TAATAGATAGTACATGCATTCCATCTCATGCACATCT
10341789 TAAT
1 TAAT
10341793 GCTAGTATCA
Statistics
Matches: 187, Mismatches: 35, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
36 4 0.02
37 117 0.63
38 64 0.34
40 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (37 bp):
TAATAGATAGTACATGCATTCCATCTCATGCACATCT
Found at i:10344331 original size:13 final size:13
Alignment explanation
Indices: 10344313--10344359 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
10344303 AAATTTAGGG
10344313 TTAGGGTTTTGGT
1 TTAGGGTTTTGGT
*
10344326 TTAGGGTTTGGGT
1 TTAGGGTTTTGGT
*
10344339 TTA--GATTTGGAT
1 TTAGGGTTTTGG-T
10344351 TTAGGGTTT
1 TTAGGGTTT
10344360 AGGATTTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 5 0.19
12 4 0.15
13 15 0.56
14 3 0.11
ACGTcount: A:0.13, C:0.00, G:0.36, T:0.51
Consensus pattern (13 bp):
TTAGGGTTTTGGT
Found at i:10344362 original size:7 final size:7
Alignment explanation
Indices: 10344306--10344380 Score: 54
Period size: 6 Copynumber: 11.4 Consensus size: 7
10344296 GGCTTTAAAA
10344306 TTTAGGG
1 TTTAGGG
10344313 -TTAGGG
1 TTTAGGG
*
10344319 TTT-TGG
1 TTTAGGG
10344325 TTTAGGG
1 TTTAGGG
10344332 TTT-GGG
1 TTTAGGG
*
10344338 TTTA-GA
1 TTTAGGG
*
10344344 TTT-GGA
1 TTTAGGG
10344350 TTTAGGG
1 TTTAGGG
*
10344357 TTTAGGA
1 TTTAGGG
10344364 TTT-GTGG
1 TTTAG-GG
*
10344371 TTCAGGG
1 TTTAGGG
10344378 TTT
1 TTT
10344381 TAAGAATTGG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
6 27 0.51
7 25 0.47
8 1 0.02
ACGTcount: A:0.13, C:0.01, G:0.37, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:10348455 original size:78 final size:78
Alignment explanation
Indices: 10348322--10348476 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 78
10348312 TAATCCTTTC
* * * * *
10348322 ACAAATATAAGAAATTTATCCTTTGCCATCTCTTTGAGCCTAATAAAATTATTTCAGAAGAAACC
1 ACAAATATAAGAAATTTATCCCTTGCCACCCCTTTAAGCCTAATAAAATTATTTCAAAAGAAACC
10348387 CTAACTAAGGATT
66 CTAACTAAGGATT
* * * * *
10348400 ACAAATATAAGAAATTTATCCCTTGCTACCCCTTTAAGGCTGATAAAATTTTTTCAAAATAAACC
1 ACAAATATAAGAAATTTATCCCTTGCCACCCCTTTAAGCCTAATAAAATTATTTCAAAAGAAACC
* *
10348465 TTGACTAAGGAT
66 CTAACTAAGGAT
10348477 CACCCTCCAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (78 bp):
ACAAATATAAGAAATTTATCCCTTGCCACCCCTTTAAGCCTAATAAAATTATTTCAAAAGAAACC
CTAACTAAGGATT
Found at i:10348687 original size:19 final size:18
Alignment explanation
Indices: 10348652--10348693 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
10348642 AAAAAGGGCT
*
10348652 AAAAATGAAAGAAAGAAG
1 AAAAATGAAAGAAAGAAC
10348670 AAAAATGAAA-AAGGAGAAC
1 AAAAATGAAAGAA--AGAAC
10348689 AAAAA
1 AAAAA
10348694 AAAAAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 10 0.48
19 9 0.43
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (18 bp):
AAAAATGAAAGAAAGAAC
Found at i:10350689 original size:419 final size:407
Alignment explanation
Indices: 10349992--10351039 Score: 1290
Period size: 419 Copynumber: 2.6 Consensus size: 407
10349982 AGAGTAAGCA
* *
10349992 AAGGAACAGTAAAATGGTAAGTTTAGATGATTTT-GAAAAATTGAAAATTTAATTGGATGGGCAA
1 AAGGAACAGTAAAATGGTAAGTTTAGATCATTTTGGAAAAATTGAAGATTTAATTGGATGGGCAA
* * * *
10350056 CAAGAGAACT-ACAAATTTAAGAAAGAATTTCCTTTTG-AAAAATGAGTATTTTTGTGTTTGCAT
66 CAAGAG-ATTAACAAAATTGAGAAAGAATTTCC-TTTGAAAAAAAGAGTATTTTTGTGTTTGCAT
* * * * ** * *
10350119 CCATGATT-AGGCACATACATTAGGTAGTTTTTGCATTTGCA--TG-GGGGGCATTAGCATTTTT
129 CCATGATTGGGGCACATACATCAGGGA-TTTTTGCATTTGTATTTGCATGGGCATTGGCATTGTT
*
10350180 GAAATGAAATTCTACAATGGCATTTACATCATTAAAAAACAATTGAACTTGCAAAATTTGTATTT
193 GAAATGAAATTCTACAATGGCATTTACATCATTAAAAAATAATTGAACTTGCAAAATTTGTATTT
* * **
10350245 ATATTTTTTCTGCATCTATATCATGTATGAACATTGGCATTTGCATTCATAAGAGG-AGCTTGCA
258 ATATTTTTTCGGCATCTAAATCATGTATGAACATTGGCATTTGCATTCATAAGAGGCA-CCCGCA
* * * **
10350309 TGATGAAAAAGAAATTTGCTAGTAAGAGATAATCTTTC-CAAAAGTAAAGGAAGGTTAAAACCAA
322 TCATGAAAAA-AAA-TTGCTAGTAAAAGATAATCTTTCTCAAAA-CAAAAAAAGG-T-AAA--AA
10350373 CAAAAAAAAAAAAAACAAAAGAAAGAGCAGGTG
380 C----AAAAAAAAAA-AAAAGAAAGAGCAGGTG
* *
10350406 AAGGAACAGTAAAATGGTAAGTTTAGATTATTTTGGAAAAAATTGAAGATTTAATTGGATAGGCA
1 AAGGAACAGTAAAATGGTAAGTTTAGATCATTTTGG-AAAAATTGAAGATTTAATTGGATGGGCA
* * *
10350471 ACAAGAGATTAACAAAATTGAGGAATAA-TTCCTTTGAAAAAAAGAGTGTTTTTGTGTTTGCATC
65 ACAAGAGATTAACAAAATTGAGAAAGAATTTCCTTTGAAAAAAAGAGTATTTTTGTGTTTGCATC
*
10350535 CATGATTGGGGCACATACATCAGGGGATTTTTGCATTTGTATTTGCATGGGCATTGGCATTGCTG
130 CATGATTGGGGCACATACATCA-GGGATTTTTGCATTTGTATTTGCATGGGCATTGGCATTGTTG
*
10350600 AAATGAAATTCTACAATGGCATTTACACCATTAAAAAATAATTGAACTTGCAAAATTTGTATTTA
194 AAATGAAATTCTACAATGGCATTTACATCATTAAAAAATAATTGAACTTGCAAAATTTGTATTTA
* *
10350665 TATTTTTTGGGC-TTTCAAATCATGTATGAACATTGGCATTTGCATTCATAAGAGGCACCCGCAT
259 TATTTTTTCGGCATCT-AAATCATGTATGAACATTGGCATTTGCATTCATAAGAGGCACCCGCAT
* * *
10350729 CATGAAAAAAAATTGCTAGTAAAAGATAATCTTTCTTAAAACAAAAAAAGGTAAAAACCAATAAA
323 CATGAAAAAAAATTGCTAGTAAAAGATAATCTTTCTCAAAACAAAAAAAGGTAAAAACAAAAAAA
*
10350794 AAAAAAAGAAAGAGTAGGTG
388 AAAAAAAGAAAGAGCAGGTG
* *
10350814 AAGGAACTGTAAAATAGTAAGTTTACG-TCATTTTGGGAAAAATTGAAGATTTAATTGGATGGGC
1 AAGGAACAGTAAAATGGTAAGTTTA-GATCATTTT-GGAAAAATTGAAGATTTAATTGGATGGGC
* * * * * * *
10350878 AATAGGAGATCAGCAAAATTGAGAAAGAATTTCTGTTTGAAAAAGAGAGTATTTTTATGTTTGCA
64 AACAAGAGATTAACAAAATTGAGAAAGAATTTC-CTTTGAAAAAAAGAGTATTTTTGTGTTTGCA
* *
10350943 TCCATGATTGGGGCACATACATCAGAGA-----G--TTTTTATTTGCATGGGCATTGGCATTGTT
128 TCCATGATTGGGGCACATACATCAGGGATTTTTGCATTTGTATTTGCATGGGCATTGGCATTGTT
* * * *
10351001 GAAATGATATTCTA-TATGGGATTTATATCATTAAAAAAT
193 GAAATGAAATTCTACAATGGCATTTACATCATTAAAAAAT
10351040 TGGATGTTTT
Statistics
Matches: 560, Mismatches: 58, Indels: 45
0.84 0.09 0.07
Matches are distributed among these distances:
401 21 0.04
402 40 0.07
404 1 0.00
408 94 0.17
409 17 0.03
410 51 0.09
413 3 0.01
414 37 0.07
415 42 0.08
416 72 0.13
417 32 0.06
418 11 0.02
419 138 0.25
420 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (407 bp):
AAGGAACAGTAAAATGGTAAGTTTAGATCATTTTGGAAAAATTGAAGATTTAATTGGATGGGCAA
CAAGAGATTAACAAAATTGAGAAAGAATTTCCTTTGAAAAAAAGAGTATTTTTGTGTTTGCATCC
ATGATTGGGGCACATACATCAGGGATTTTTGCATTTGTATTTGCATGGGCATTGGCATTGTTGAA
ATGAAATTCTACAATGGCATTTACATCATTAAAAAATAATTGAACTTGCAAAATTTGTATTTATA
TTTTTTCGGCATCTAAATCATGTATGAACATTGGCATTTGCATTCATAAGAGGCACCCGCATCAT
GAAAAAAAATTGCTAGTAAAAGATAATCTTTCTCAAAACAAAAAAAGGTAAAAACAAAAAAAAAA
AAAAGAAAGAGCAGGTG
Found at i:10351755 original size:19 final size:19
Alignment explanation
Indices: 10351733--10351770 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10351723 AAACTTTATT
10351733 CCACCTCCCAAACCCTAAA
1 CCACCTCCCAAACCCTAAA
* *
10351752 CCACTTCCTAAACCCTAAA
1 CCACCTCCCAAACCCTAAA
10351771 TTACCTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.16
Consensus pattern (19 bp):
CCACCTCCCAAACCCTAAA
Found at i:10351876 original size:14 final size:13
Alignment explanation
Indices: 10351854--10351890 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
10351844 ACAAATTGTT
10351854 ATGCATTCATACC
1 ATGCATTCATACC
*
10351867 TTGTCATTCATACC
1 ATG-CATTCATACC
10351881 ATGCATTCAT
1 ATGCATTCAT
10351891 TATATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGCATTCATACC
Found at i:10352781 original size:10 final size:9
Alignment explanation
Indices: 10352755--10352794 Score: 57
Period size: 8 Copynumber: 4.6 Consensus size: 9
10352745 GGATATTTTG
10352755 AAAAT-AAA
1 AAAATGAAA
10352763 AAAAT-AAA
1 AAAATGAAA
10352771 AAAATTGAAA
1 AAAA-TGAAA
10352781 AAAATGAAA
1 AAAATGAAA
10352790 AAAAT
1 AAAAT
10352795 ATTTTGATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 12 0.40
9 11 0.37
10 7 0.23
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (9 bp):
AAAATGAAA
Found at i:10353881 original size:36 final size:35
Alignment explanation
Indices: 10353816--10354039 Score: 166
Period size: 35 Copynumber: 6.3 Consensus size: 35
10353806 GAAAATAATA
* *
10353816 AGATAATACATACACCCCATCTCATGCATCTCAAT
1 AGATAGTACATGCACCCCATCTCATGCATCTCAAT
10353851 AGATAGTACATGCACCCCTATCTCATGCATCTCAAT
1 AGATAGTACATGCACCCC-ATCTCATGCATCTCAAT
* **
10353887 AGACAGTACATGCATTCCATCTCATGCATTCTC-AT
1 AGATAGTACATGCACCCCATCTCATGCA-TCTCAAT
* * ** *
10353922 AAATGGTACATATATCCCATCTCATGCATCAT-AAT
1 AGATAGTACATGCACCCCATCTCATGCATC-TCAAT
* * ** * * * *
10353957 AGATCGTATATGCATTCCATCTAATACAACTCTTAGT
1 AGATAGTACATGCACCCCATCTCATGC-A-TCTCAAT
* * *
10353994 GGATAGTACATGCGCTCTC-TCTCATGTACATCTCAAT
1 AGATAGTACATGCAC-CCCATCTCATG--CATCTCAAT
10354031 AGATAGTAC
1 AGATAGTAC
10354040 TTGTATTCCA
Statistics
Matches: 147, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
34 2 0.01
35 72 0.49
36 38 0.26
37 32 0.22
38 2 0.01
39 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.30
Consensus pattern (35 bp):
AGATAGTACATGCACCCCATCTCATGCATCTCAAT
Found at i:10353970 original size:70 final size:71
Alignment explanation
Indices: 10353832--10353978 Score: 185
Period size: 70 Copynumber: 2.1 Consensus size: 71
10353822 TACATACACC
* *
10353832 CCATCTCATGCATCTCAATAGATAGTACATGCACCCCTATCTCATGCATCTCAATAGACAGTACA
1 CCATCTCATGCATCTCAATAAATAGTACATACACCCCTATCTCATGCATCTCAATAGACAGTACA
10353897 TGCATT
66 TGCATT
* * *
10353903 CCATCTCATGCATTCTC-ATAAATGGTACATATATCCC-ATCTCATGCATCAT-AATAGATC-GT
1 CCATCTCATGCA-TCTCAATAAATAGTACATACACCCCTATCTCATGCATC-TCAATAGA-CAGT
*
10353964 ATATGCATT
63 ACATGCATT
10353973 CCATCT
1 CCATCT
10353979 AATACAACTC
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
70 34 0.51
71 29 0.43
72 4 0.06
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (71 bp):
CCATCTCATGCATCTCAATAAATAGTACATACACCCCTATCTCATGCATCTCAATAGACAGTACA
TGCATT
Found at i:10354056 original size:37 final size:37
Alignment explanation
Indices: 10354015--10354087 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
10354005 GCGCTCTCTC
* *
10354015 TCATGTACATCTCA-ATAGATAGTACTTGTATTCCATT
1 TCATGCACATCT-AGATAGATAGTACATGTATTCCATT
*
10354052 TCATGCACATCTAGATAGATTGTACATGTATTCCAT
1 TCATGCACATCTAGATAGATAGTACATGTATTCCAT
10354088 CTTGATAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 1 0.03
37 31 0.97
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.38
Consensus pattern (37 bp):
TCATGCACATCTAGATAGATAGTACATGTATTCCATT
Found at i:10355917 original size:10 final size:10
Alignment explanation
Indices: 10355902--10355939 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
10355892 AAATGCCTTG
10355902 AAAAAAGAGA
1 AAAAAAGAGA
*
10355912 AAAAAAAAGA
1 AAAAAAGAGA
10355922 AAAAAAGAGA
1 AAAAAAGAGA
10355932 AAAAAAGA
1 AAAAAAGA
10355940 AATTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:10355934 original size:18 final size:19
Alignment explanation
Indices: 10355901--10355941 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
10355891 AAAATGCCTT
10355901 GAAAAAAGAGAAAAAAAAA
1 GAAAAAAGAGAAAAAAAAA
*
10355920 GAAAAAA-AGAGAAAAAAA
1 GAAAAAAGAGAAAAAAAAA
10355938 GAAA
1 GAAA
10355942 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
GAAAAAAGAGAAAAAAAAA
Found at i:10357143 original size:21 final size:22
Alignment explanation
Indices: 10357102--10357143 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10357092 AGGAAGTAAG
*
10357102 AAAGAGAAAAGAAATAAGGAAA
1 AAAGAGAAAAGAAAGAAGGAAA
*
10357124 AAAGA-AAAAGAAAGAGGGAA
1 AAAGAGAAAAGAAAGAAGGAA
10357144 GAACAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.02
Consensus pattern (22 bp):
AAAGAGAAAAGAAAGAAGGAAA
Found at i:10362890 original size:23 final size:24
Alignment explanation
Indices: 10362864--10362915 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
10362854 TTATCACTTT
10362864 AAAACTTTTGAGAATC-CTTTTTG
1 AAAACTTTTGAGAATCTCTTTTTG
* *
10362887 AAAACTTTTGGGCATCTCTTTTTG
1 AAAACTTTTGAGAATCTCTTTTTG
10362911 AAAAC
1 AAAAC
10362916 CACTAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (24 bp):
AAAACTTTTGAGAATCTCTTTTTG
Found at i:10363090 original size:21 final size:21
Alignment explanation
Indices: 10363041--10363092 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
10363031 AGTACCATAA
* *
10363041 CAAAACATTCGAGTATCTTTT
1 CAAAACCTTCGAGTATATTTT
10363062 CCAAAACCTTCGAGTATATCTTT
1 -CAAAACCTTCGAGTATAT-TTT
10363085 -AAAACCTT
1 CAAAACCTT
10363093 TGGGTATCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 8 0.30
22 16 0.59
23 3 0.11
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (21 bp):
CAAAACCTTCGAGTATATTTT
Found at i:10364245 original size:15 final size:17
Alignment explanation
Indices: 10364212--10364250 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
10364202 AAATCTTCAA
*
10364212 ATTATCATATAAAATTT
1 ATTATCATATAAAAATT
10364229 A-TATCAT-TAAAAATT
1 ATTATCATATAAAAATT
10364244 ATTATCA
1 ATTATCA
10364251 CATAGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 11 0.55
17 1 0.05
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATCATATAAAAATT
Found at i:10366540 original size:3 final size:3
Alignment explanation
Indices: 10366532--10366559 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10366522 TGGCTGAAAG
10366532 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10366560 AAAAGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10369303 original size:30 final size:30
Alignment explanation
Indices: 10369262--10369347 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
10369252 TATATATATT
*
10369262 AAGAGTTTATTTAAGTGCAAAATAAAAGTTA
1 AAGA-TTTATTTAAGTGCAAATTAAAAGTTA
** *
10369293 AAGATTTATTTGAA-TATAAATTAAAGGTTA
1 AAGATTTATTT-AAGTGCAAATTAAAAGTTA
* * *
10369323 CAGGTTTATTTAGGTGCAAATTAAA
1 AAGATTTATTTAAGTGCAAATTAAA
10369348 GTTTAAAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 37 0.84
31 6 0.14
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.36
Consensus pattern (30 bp):
AAGATTTATTTAAGTGCAAATTAAAAGTTA
Found at i:10375005 original size:11 final size:11
Alignment explanation
Indices: 10374989--10375023 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
10374979 TTATGTACTA
10374989 ATATAAAATTT
1 ATATAAAATTT
10375000 ATATAAAATTTT
1 ATATAAAA-TTT
10375012 ATTATAAAATTT
1 A-TATAAAATTT
10375024 TAATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 7 0.32
13 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATAAAATTT
Found at i:10375019 original size:13 final size:12
Alignment explanation
Indices: 10374989--10375025 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
10374979 TTATGTACTA
10374989 ATATAAAA-TTT
1 ATATAAAATTTT
10375000 ATATAAAATTTT
1 ATATAAAATTTT
10375012 ATTATAAAATTTT
1 A-TATAAAATTTT
10375025 A
1 A
10375026 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATAAAATTTT
Found at i:10375089 original size:13 final size:14
Alignment explanation
Indices: 10375068--10375100 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
10375058 ACATAAAAAT
*
10375068 AAAAGAAAAG-TAA
1 AAAATAAAAGTTAA
10375081 AAAATAAAAGTTAA
1 AAAATAAAAGTTAA
10375095 AAAATA
1 AAAATA
10375101 GTAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (14 bp):
AAAATAAAAGTTAA
Found at i:10377563 original size:25 final size:25
Alignment explanation
Indices: 10377531--10377583 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
10377521 TTTAGTTGTA
10377531 TTTATAGTAAAAAATGCCACTAAAT
1 TTTATAGTAAAAAATGCCACTAAAT
* * *
10377556 TTTATAGTAGAAAGTGCCACTACAT
1 TTTATAGTAAAAAATGCCACTAAAT
10377581 TTT
1 TTT
10377584 GGCATTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (25 bp):
TTTATAGTAAAAAATGCCACTAAAT
Found at i:10379073 original size:184 final size:183
Alignment explanation
Indices: 10378813--10379196 Score: 464
Period size: 183 Copynumber: 2.1 Consensus size: 183
10378803 TTAACAATCC
* * * * * * * * *
10378813 TTTTTTGGGGATTATTCAAGGCGTTTCTAGCCAAAAATGCCTTGAGTAATCCTCTTCCATTTTTT
1 TTTTTTTGGGATTATTCAAAGCATTTATAGCAAAAAATACCTTAACTAATCATCTTCCATTTTTT
* * * *
10378878 GAGGGGATTATTCAAGGCATTTTTTTATCATAAAACACCTTGAATAATCATTTACAAAAAATTGA
66 GAGGGGATTATTCAAGGC-GTTTTTGACCAAAAAACACCTTGAATAATCATTTACAAAAAATTGA
* *
10378943 ATAGGATTATTCAAGGTCTTTTGGCAAAAAACGCCTTCAATAATCCCTCTAA-T
130 ATAGGATTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAACT
* *
10378996 TTTGTTTTGGGATTATTCAAAGCATTTATGGCAAAAAATACCTTAACTAATCATCTTTCATTTTT
1 TTT-TTTTGGGATTATTCAAAGCATTTATAGCAAAAAATACCTTAACTAATCATCTTCCATTTTT
*** * * * * * *
10379061 TTTTGTGATTATTTAAGGCGTTTTTGGCCAAAAAACACGTTGAATAATCCTTTATAAAAAATTGA
65 TGAGGGGATTATTCAAGGCGTTTTTGACCAAAAAACACCTTGAATAATCATTTACAAAAAATTGA
* * * * *
10379126 ATGGGGTTATTCAAGGTATTTTGGCCAAAAACACCTTCAATAATCCTTTTAACT
130 ATAGGATTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAACT
10379180 TTTTTTTGGGATTATTC
1 TTTTTTTGGGATTATTC
10379197 GAGATGTTTC
Statistics
Matches: 168, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
183 100 0.60
184 68 0.40
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (183 bp):
TTTTTTTGGGATTATTCAAAGCATTTATAGCAAAAAATACCTTAACTAATCATCTTCCATTTTTT
GAGGGGATTATTCAAGGCGTTTTTGACCAAAAAACACCTTGAATAATCATTTACAAAAAATTGAA
TAGGATTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAACT
Found at i:10379243 original size:183 final size:181
Alignment explanation
Indices: 10378699--10379565 Score: 542
Period size: 182 Copynumber: 4.8 Consensus size: 181
10378689 TCATTATTCA
* * * *
10378699 ATTTTTTTT-GGTATTATTCGAGGC-GTTTTGGCC-AAAAACACCTCGAATAATCCCTTAC-AAA
1 ATTTTTTTTAGG-ATTATTCAAGGCATTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAAAA
* * * * * * *
10378760 AACTGAATGGGGTTATTCAAGATATTTCTAGCTAAAAATACCTTTAACAAT-CCT-T--TTTTG-
65 AATTGAATGGGGTTATTCAAGGTATTT-TGGCAAAAAACACCTTCAATAATCCCTCTAATTTTGT
* * * * * * * *
10378820 ---GGGATTATTCAAGGCGTTTCT-AGCCAAAAATGCCTTGAGTAATC-CTCTTCC
129 TTTGGGATTATTCAAAG-ATTTATGA-CAAAAAATACCTTAACTAATCAC-CTGCC
* *** * *
10378871 A-TTTTTTGAGGGGATTATTCAAGGCATTTTTTTATCATAAAACACCTTGAATAATCATTTACAA
1 ATTTTTTTTA--GGATTATTCAAGGCA-TTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAA
* * * *
10378935 AAAATTGAATAGGATTATTCAAGGTCTTTTGGCAAAAAACGCCTTCAATAATCCCTCTAATTTTG
63 AAAATTGAATGGGGTTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAATTTTG
* * **
10379000 TTTTGGGATTATTCAAAGCATTTATGGCAAAAAATACCTTAACTAATCATCTTTC
128 TTTTGGGATTATTCAAAG-ATTTATGACAAAAAATACCTTAACTAATCACCTGCC
* * * * *
10379055 ATTTTTTTTTGTGATTATTTAAGGCGTTTTTGGCCAAAAAACACGTTGAATAATCCTTTATAAAA
1 ATTTTTTTTAG-GATTATTCAAGGCATTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAAAA
* * *
10379120 AATTGAATGGGGTTATTCAAGGTATTTTGGCCAAAAACACCTTCAATAATCCTTTTAACTTTT-T
65 AATTGAATGGGGTTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAA-TTTTGT
* * ** *
10379184 TTTGGGATTATTC-GAGATGTTTCTGATTAAAAATGCCTTGAA-TAATTC-CCTGCC
129 TTTGGGATTATTCAAAGA--TTTATGACAAAAAATACCTT-AACTAA-TCACCTGCC
* ** * *
10379238 ATTTTTTTTAGGATTATTCAAGGCATTTTTTGCCAAAAAATGCCTTAAATATTCCTTTACAAAAA
1 ATTTTTTTTAGGATTATTCAAGGCATTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAAAAA
* * * * ** * ** * **
10379303 ATTGAATGGGGTTATTTAAGGCATTTCTAGTAAAAAATGCCTTGAATAAT-TTTCTTACATT-TT
66 ATTGAATGGGGTTATTCAAGGTATTT-TGGCAAAAAACACCTTCAATAATCCCTCTAATTTTGTT
* * * * *
10379366 TTGGAGATTATTCAAGGTATTTTTTGTCAAAAACAT--CTTCAA-TAATCCCCTTCC
130 TTGG-GATTATTCAAAG-A-TTTATGACAAAAA-ATACCTT-AACTAATCACCTGCC
** * * ** * ** * * *
10379420 ATTTTTTTGGGGATTATTTAAGGCATTTTTAGTTAGAAAATGCATTGAATAATCCCTTGCAAAAA
1 ATTTTTTTTAGGATTATTCAAGGCATTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAAAAA
* * * * * * * *
10379485 ATTGAATGGGATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCTCCTCCAATTTAT-
66 ATTGAATGGGGTTATTCAAGGTATTT-TGGCAAAAAACACCTTCAATAATC-CCTCTAATTT-TG
10379549 TTTTGAGGATTATTCAA
128 TTTTG-GGATTATTCAA
10379566 TGCGTTTTTG
Statistics
Matches: 543, Mismatches: 118, Indels: 55
0.76 0.16 0.08
Matches are distributed among these distances:
171 6 0.01
172 1 0.00
173 11 0.02
174 2 0.00
175 5 0.01
176 38 0.07
177 28 0.05
178 1 0.00
180 5 0.01
181 11 0.02
182 189 0.35
183 156 0.29
184 67 0.12
185 22 0.04
186 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (181 bp):
ATTTTTTTTAGGATTATTCAAGGCATTTTTGGCCAAAAAACACCTTGAATAATCCTTTACAAAAA
ATTGAATGGGGTTATTCAAGGTATTTTGGCAAAAAACACCTTCAATAATCCCTCTAATTTTGTTT
TGGGATTATTCAAAGATTTATGACAAAAAATACCTTAACTAATCACCTGCC
Found at i:10379477 original size:60 final size:58
Alignment explanation
Indices: 10379309--10379477 Score: 164
Period size: 60 Copynumber: 2.9 Consensus size: 58
10379299 AAAAATTGAA
* **
10379309 TGGGG-TTATTTAAGGCATTTCTAG-TAAAAAATGCCTTGAATAATTTTCTTACATTTTT
1 TGGGGATTATTTAAGGCATTTTTAGTTAAAAAATG-CTTGAATAA-TCCCTTACATTTTT
* * * * * * *
10379367 TGGAGATTATTCAAGGTATTTTTTGTCAAAAACAT-CTTCAATAATCCCCTTCCATTTTTT
1 TGGGGATTATTTAAGGCATTTTTAGTTAAAAA-ATGCTTGAATAAT-CCCTTACA-TTTTT
*
10379427 TGGGGATTATTTAAGGCATTTTTAGTTAGAAAATGCATTGAATAATCCCTT
1 TGGGGATTATTTAAGGCATTTTTAGTTAAAAAATGC-TTGAATAATCCCTT
10379478 GCAAAAAATT
Statistics
Matches: 87, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
58 5 0.06
59 30 0.34
60 42 0.48
61 10 0.11
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (58 bp):
TGGGGATTATTTAAGGCATTTTTAGTTAAAAAATGCTTGAATAATCCCTTACATTTTT
Found at i:10379593 original size:125 final size:123
Alignment explanation
Indices: 10379371--10379596 Score: 285
Period size: 125 Copynumber: 1.8 Consensus size: 123
10379361 ATTTTTTGGA
* * * * *
10379371 GATTATTCAAGGTATTTTTTGTCAAAAACATCTTCAATAATCCCCTTCCATTTTTTTGGGGATTA
1 GATTATTCAAGGTATTTCTAGCCAAAAACATCTTCAACAATCCCCTTCCATTTTTTTGAGGATTA
* *
10379436 TTTAAGGCATTTTTAGTTAGAAAATGCATTGAATAATCCCTTGCAAAAAATTGAATGG
66 TTCAAGGCATTTTTAGTTAGAAAACGCATTGAATAATCCCTTGCAAAAAATTGAATGG
* * *
10379494 GATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCTCC-TCCAATTTATTTTTGAGGA
1 GATTATTCAAGGTATTTCTAGCCAAAAACATCTTCAACAATCCCCTTCC-A-TT-TTTTTGAGGA
* * *
10379558 TTATTCAATGCGTTTTTGGTTAGAAAACGTC-TTGAATAA
63 TTATTCAAGGCATTTTTAGTTAGAAAACG-CATTGAATAA
10379597 CCCCATTCAA
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
122 3 0.03
123 39 0.45
124 2 0.02
125 41 0.48
126 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (123 bp):
GATTATTCAAGGTATTTCTAGCCAAAAACATCTTCAACAATCCCCTTCCATTTTTTTGAGGATTA
TTCAAGGCATTTTTAGTTAGAAAACGCATTGAATAATCCCTTGCAAAAAATTGAATGG
Found at i:10379623 original size:125 final size:123
Alignment explanation
Indices: 10379369--10379692 Score: 282
Period size: 125 Copynumber: 2.6 Consensus size: 123
10379359 ACATTTTTTG
* * * * * * *
10379369 GAGATTATTCAAGGTATTTTTTGTCAAAAACATCTTCAATAATCCCCTTCC-A-TTTTTTTGGGG
1 GAGATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCCCC-TCCAATTTTTTTTGAGG
* * *
10379432 ATTATTTAAGGCATTTTTAGTTAGAAAATGCATTGAATAATCCCTTGCAAAAAATTGAAT
65 ATTA-TTAATGCATTTTTAGTTAGAAAACGCATTGAATAACCCCTTGCAAAAAATTGAAT
* *
10379492 GGGATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCTCCTCCAATTTATTTTTGAGG
1 GAGATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCCCCTCCAATTT-TTTTTGAGG
* * ****
10379557 ATTATTCAATGCGTTTTTGGTTAGAAAACGTC-TTGAATAACCCCATT-CAATTTTTTGTAA-
65 ATTATT-AATGCATTTTTAGTTAGAAAACG-CATTGAATAACCCC-TTGCAAAAAATTG-AAT
* * * ** ** *
10379617 GAGATTATTTAAGG-GATTTCTGGCAAAAAATGCCTTCAACAATCCCCTTTAATTTTTTTTTAAG
1 GAGATTATTCAAGGTG-TTTCTAGCCAAAAATATCTTCAACAATCCCCTCCAA-TTTTTTTTGAG
*
10379681 AATTATTAATGC
64 GATTATTAATGC
10379693 CTTGAATAAT
Statistics
Matches: 163, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
122 3 0.02
123 40 0.25
124 10 0.06
125 102 0.63
126 8 0.05
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (123 bp):
GAGATTATTCAAGGTGTTTCTAGCCAAAAATATCTTCAACAATCCCCTCCAATTTTTTTTGAGGA
TTATTAATGCATTTTTAGTTAGAAAACGCATTGAATAACCCCTTGCAAAAAATTGAAT
Found at i:10387857 original size:21 final size:21
Alignment explanation
Indices: 10387833--10387892 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
10387823 TAGGATTTGC
10387833 ATGTGAACATAATAATCTGTA
1 ATGTGAACATAATAATCTGTA
10387854 ATGTGAACATAATAATCTGTA
1 ATGTGAACATAATAATCTGTA
*
10387875 ATGTGAACATAATTATCT
1 ATGTGAACATAATAATCT
10387893 ATCCATTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTGAACATAATAATCTGTA
Found at i:10393374 original size:26 final size:25
Alignment explanation
Indices: 10393335--10393767 Score: 187
Period size: 26 Copynumber: 16.7 Consensus size: 25
10393325 GAGATTTTTG
* *
10393335 AGATAAGATTTTAAGCCTATGGCACT
1 AGATGAGA-TTTAAGCCCATGGCACT
* *
10393361 AGATGAGATCTTAAACCCATGGCATT
1 AGATGAGAT-TTAAGCCCATGGCACT
* * *
10393387 AGATAAGACCTTAAGCCCATGGCACC
1 AGATGAGA-TTTAAGCCCATGGCACT
* * *
10393413 AAATGAGATTTTAAGCTCATTGCACT
1 AGATGAGA-TTTAAGCCCATGGCACT
* *
10393439 AGTTGAGATTTTAAG-CCAGTGGCACC
1 AGATGAGA-TTTAAGCCCA-TGGCACT
* * * * *
10393465 ATATGACAATCTAAGCCCAGGGCACC
1 AGATGA-GATTTAAGCCCATGGCACT
* * *
10393491 AAATGATAGACTTAAACCCATGGCACT
1 AGATG--AGATTTAAGCCCATGGCACT
* *
10393518 AGATAAGAATTTAAACCCA-GGCA-T
1 AGATGAG-ATTTAAGCCCATGGCACT
* * * *
10393542 CGGATAAAAATTTAAGCTCATGGCA-T
1 -AGAT-GAGATTTAAGCCCATGGCACT
* * * *
10393568 CAGATAAGAACTTAAACCCATGGCTCT
1 -AGATGAG-ATTTAAGCCCATGGCACT
* ** *
10393595 AGCTGAGAATTTAATTCCATGGCACC
1 AGATGAG-ATTTAAGCCCATGGCACT
* *
10393621 AAATGAGATATTAAGCCCATGGCACC
1 AGATGAGAT-TTAAGCCCATGGCACT
* * * *
10393647 AAATGTGATATAAAGCCTATGGCAC-
1 AGATGAGAT-TTAAGCCCATGGCACT
* * * *
10393672 CGATTGAGATTTTAATCTCATAGCACT
1 AGA-TGAGA-TTTAAGCCCATGGCACT
10393699 -GAATGAGATTTGAA-CCCTATGGCACT
1 AG-ATGAGATTT-AAGCCC-ATGGCACT
* *
10393725 AGATGAAAATTTAAGCCTATGGCACT
1 AGATG-AGATTTAAGCCCATGGCACT
*
10393751 AGTTGAGATTTAAGCCC
1 AGATGAGATTTAAGCCC
10393768 CTAGTAGCAT
Statistics
Matches: 309, Mismatches: 75, Indels: 47
0.72 0.17 0.11
Matches are distributed among these distances:
24 1 0.00
25 41 0.13
26 235 0.76
27 31 0.10
28 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (25 bp):
AGATGAGATTTAAGCCCATGGCACT
Found at i:10394421 original size:20 final size:20
Alignment explanation
Indices: 10394396--10394440 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
10394386 AGCTAAAACC
10394396 AAAAGAAACTAA-AACTA-AAG
1 AAAAG-AACTAAGAA-TAGAAG
10394416 AAAAGAACTAAGAATAGAAG
1 AAAAGAACTAAGAATAGAAG
10394436 AAAAG
1 AAAAG
10394441 GAGAAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.69, C:0.07, G:0.16, T:0.09
Consensus pattern (20 bp):
AAAAGAACTAAGAATAGAAG
Found at i:10396528 original size:18 final size:18
Alignment explanation
Indices: 10396505--10396542 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
10396495 TAAAGCATTC
10396505 TTCCCCCAAATACTTAAA
1 TTCCCCCAAATACTTAAA
*
10396523 TTCCCCCTAATACTTAAA
1 TTCCCCCAAATACTTAAA
10396541 TT
1 TT
10396543 AAACAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (18 bp):
TTCCCCCAAATACTTAAA
Found at i:10401198 original size:69 final size:68
Alignment explanation
Indices: 10401072--10401205 Score: 178
Period size: 69 Copynumber: 2.0 Consensus size: 68
10401062 TGTATGGATA
* * * * * *
10401072 TTAAACTTAATGAAGTTGGCACCTATTGGATTGTGAATCTCAATCTAACTAGCACCAAGATGAGA
1 TTAAACCTAATGAAGTTGGCACCTATCGGATGGTAAAGCCCAATCTAACTAGCACCAAGATGAGA
10401137 ATT
66 ATT
* * *
10401140 TTAAACCTAGTGAAGTTGGCATCTACTCGGATGGTAAAGCCCAATCTAGCTAGCACCAAGATGAG
1 TTAAACCTAATGAAGTTGGCACCTA-TCGGATGGTAAAGCCCAATCTAACTAGCACCAAGATGAG
10401205 A
65 A
10401206 TTTGTAAGCT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
68 22 0.39
69 34 0.61
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (68 bp):
TTAAACCTAATGAAGTTGGCACCTATCGGATGGTAAAGCCCAATCTAACTAGCACCAAGATGAGA
ATT
Found at i:10407547 original size:48 final size:48
Alignment explanation
Indices: 10407474--10407567 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
10407464 CAATTGGGTG
* * * *
10407474 ACAACTCCTTTTTAAATCACTTCTTATATGATTCACCCAATTATTGTC
1 ACAACTCCTTATCAAACCACATCTTATATGATTCACCCAATTATTGTC
*
10407522 ACAACTCCTTATCAAACCACATCTTATGTGATTCACCCAATTATTG
1 ACAACTCCTTATCAAACCACATCTTATATGATTCACCCAATTATTG
10407568 CCTCCAACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (48 bp):
ACAACTCCTTATCAAACCACATCTTATATGATTCACCCAATTATTGTC
Found at i:10409004 original size:17 final size:17
Alignment explanation
Indices: 10408982--10409014 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10408972 TGTTCTAGGT
10408982 CATTTAGGAATCCTAAC
1 CATTTAGGAATCCTAAC
*
10408999 CATTTAGGAATTCTAA
1 CATTTAGGAATCCTAA
10409015 TTTGATTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (17 bp):
CATTTAGGAATCCTAAC
Found at i:10429299 original size:12 final size:12
Alignment explanation
Indices: 10429284--10429313 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10429274 AAATAAAATT
*
10429284 AAAAAGCCCATA
1 AAAAAGCCCACA
10429296 AAAAAGCCCACA
1 AAAAAGCCCACA
10429308 AAAAAG
1 AAAAAG
10429314 AGCTAACTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.23, G:0.10, T:0.03
Consensus pattern (12 bp):
AAAAAGCCCACA
Found at i:10429533 original size:13 final size:13
Alignment explanation
Indices: 10429515--10429552 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
10429505 TGGGAAAGGT
10429515 AGAAAAAAATAAA
1 AGAAAAAAATAAA
*
10429528 AGAAAAAAAT-GA
1 AGAAAAAAATAAA
*
10429540 ATAAAAAAATAAA
1 AGAAAAAAATAAA
10429553 TGAGTGAGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11
Consensus pattern (13 bp):
AGAAAAAAATAAA
Found at i:10429542 original size:17 final size:16
Alignment explanation
Indices: 10429522--10429555 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10429512 GGTAGAAAAA
10429522 AATAAAAGAAAAAAATG
1 AATAAAA-AAAAAAATG
*
10429539 AATAAAAAAATAAATG
1 AATAAAAAAAAAAATG
10429555 A
1 A
10429556 GTGAGCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AATAAAAAAAAAAATG
Found at i:10429796 original size:22 final size:21
Alignment explanation
Indices: 10429747--10429801 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
10429737 TGTGGAACAG
*
10429747 CAAAAAAAAAAAGCAAAAAAT
1 CAAAAAAAAAAAGCAAAAAAC
*
10429768 TAGAAAAAAAAGAAGCAAAAAAC
1 CA-AAAAAAAA-AAGCAAAAAAC
10429791 CAAAAAAAAAA
1 CAAAAAAAAAA
10429802 GAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 16 0.55
23 11 0.38
ACGTcount: A:0.80, C:0.09, G:0.07, T:0.04
Consensus pattern (21 bp):
CAAAAAAAAAAAGCAAAAAAC
Found at i:10429797 original size:23 final size:23
Alignment explanation
Indices: 10429748--10429804 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
10429738 GTGGAACAGC
**
10429748 AAAAAAAAA-AAGCAAAAAATTA
1 AAAAAAAAAGAAGCAAAAAACCA
*
10429770 GAAAAAAAAGAAGCAAAAAACCA
1 AAAAAAAAAGAAGCAAAAAACCA
10429793 AAAAAAAAAGAA
1 AAAAAAAAAGAA
10429805 AAATAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.81, C:0.07, G:0.09, T:0.04
Consensus pattern (23 bp):
AAAAAAAAAGAAGCAAAAAACCA
Found at i:10430535 original size:29 final size:28
Alignment explanation
Indices: 10430503--10430581 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 28
10430493 AAAAAAAAAT
* *
10430503 ATAATATAATAATATTAATAAGTTTTTTA-
1 ATAA-ATAATAATAATAATAAG-TTTTAAC
10430532 ATAAAATAGA-AATAATAATATAGTTTTAAC
1 AT-AAATA-ATAATAATAATA-AGTTTTAAC
*
10430562 ATAAATAATAATAGTAATAA
1 ATAAATAATAATAATAATAA
10430582 AAAAATCTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
28 2 0.05
29 33 0.79
30 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (28 bp):
ATAAATAATAATAATAATAAGTTTTAAC
Found at i:10432249 original size:13 final size:13
Alignment explanation
Indices: 10432231--10432327 Score: 65
Period size: 13 Copynumber: 7.4 Consensus size: 13
10432221 CTCATAAATT
10432231 CCTAAATTGAAAC
1 CCTAAATTGAAAC
10432244 CCTAAAAATCT-AAAC
1 CCT--AAAT-TGAAAC
* *
10432259 ACTAAA-TGAGAC
1 CCTAAATTGAAAC
* *
10432271 CCT-AACTAAAAC
1 CCTAAATTGAAAC
*
10432283 CCTAAAGTGAAAC
1 CCTAAATTGAAAC
* *
10432296 CCTAAAATTAAAAT
1 CCT-AAATTGAAAC
*
10432310 CCTAAAATGAAAC
1 CCTAAATTGAAAC
10432323 CCTAA
1 CCTAA
10432328 TCTAAAACTT
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
11 3 0.05
12 12 0.19
13 28 0.44
14 10 0.16
15 10 0.16
16 1 0.02
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.20
Consensus pattern (13 bp):
CCTAAATTGAAAC
Found at i:10432294 original size:52 final size:52
Alignment explanation
Indices: 10432231--10432335 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 52
10432221 CTCATAAATT
* *
10432231 CCTAAATTGAAACCCTAAAAATCT-AAACACT-AAATGAGACCCTAA-CTAAAAC
1 CCTAAAGTGAAACCCT-AAAAT-TAAAAC-CTAAAATGAAACCCTAATCTAAAAC
10432283 CCTAAAGTGAAACCCTAAAATTAAAATCCTAAAATGAAACCCTAATCTAAAAC
1 CCTAAAGTGAAACCCTAAAATTAAAA-CCTAAAATGAAACCCTAATCTAAAAC
10432336 TTTAAAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
50 1 0.02
51 10 0.21
52 29 0.62
53 7 0.15
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (52 bp):
CCTAAAGTGAAACCCTAAAATTAAAACCTAAAATGAAACCCTAATCTAAAAC
Found at i:10432313 original size:27 final size:26
Alignment explanation
Indices: 10432225--10432327 Score: 88
Period size: 27 Copynumber: 3.9 Consensus size: 26
10432215 AAGAGGCTCA
*
10432225 TAAATTCCTAAATTGAAACCCTAAAAAT
1 TAAAATCCTAAA-TGAAACCCT-AAAAT
* *
10432253 CT-AAA-CACTAAATGAGACCCT--AAC
1 -TAAAATC-CTAAATGAAACCCTAAAAT
*
10432277 TAAAACCCTAAAGTGAAACCCTAAAAT
1 TAAAATCCTAAA-TGAAACCCTAAAAT
10432304 TAAAATCCTAAAATGAAACCCTAA
1 TAAAATCCT-AAATGAAACCCTAA
10432328 TCTAAAACTT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
23 1 0.02
24 10 0.16
25 9 0.15
27 30 0.49
28 10 0.16
29 1 0.02
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.21
Consensus pattern (26 bp):
TAAAATCCTAAATGAAACCCTAAAAT
Found at i:10432335 original size:13 final size:13
Alignment explanation
Indices: 10432269--10432335 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
10432259 ACTAAATGAG
10432269 ACCCT-AACTAAA
1 ACCCTAAACTAAA
* *
10432281 ACCCTAAAGTGAA
1 ACCCTAAACTAAA
*
10432294 ACCCTAAAATTAAA
1 ACCCT-AAACTAAA
* * *
10432308 ATCCTAAAATGAA
1 ACCCTAAACTAAA
*
10432321 ACCCTAATCTAAA
1 ACCCTAAACTAAA
10432334 AC
1 AC
10432336 TTTAAAATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
12 5 0.12
13 27 0.64
14 10 0.24
ACGTcount: A:0.51, C:0.25, G:0.04, T:0.19
Consensus pattern (13 bp):
ACCCTAAACTAAA
Found at i:10432428 original size:20 final size:19
Alignment explanation
Indices: 10432358--10432410 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
10432348 GCCTTCAATG
10432358 AAACCCTAGGTAAAAATCA
1 AAACCCTAGGTAAAAATCA
10432377 AAACCCTAGGTAAAAATCA
1 AAACCCTAGGTAAAAATCA
10432396 AAACCCTAGGTAAAA
1 AAACCCTAGGTAAAA
10432411 CCCAAAAGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (19 bp):
AAACCCTAGGTAAAAATCA
Found at i:10433144 original size:155 final size:155
Alignment explanation
Indices: 10432959--10433271 Score: 527
Period size: 155 Copynumber: 2.0 Consensus size: 155
10432949 AAAAGTTCTT
*
10432959 AAAAATTAATTTTAAACAAATAAAATTAAAATACCATTCTATGAAATATAATTTTTTGTCCTCTA
1 AAAAATTAATTTTAAACAAATAAAATTAAAATACCATTCTATGAAATATAATTTTTTGTACTCTA
* * *
10433024 CTTAGATGGTAGAGAGTCATCATTGATTATCATTTACAAAGAATGTTGTTTTATTATTTTTGACC
66 CCTAGACGGTAGAGAGTCATCATTGATTATCATTTACAAAGAATGTTATTTTATTATTTTTGACC
10433089 GAATGTTACGATAAATCTTAGATGG
131 GAATGTTACGATAAATCTTAGATGG
* * *
10433114 AAAAATTAATTTTAAACAAATAAAATTAAAATAGCATTCTGTGAAATATAATTTTTTGTACTTTA
1 AAAAATTAATTTTAAACAAATAAAATTAAAATACCATTCTATGAAATATAATTTTTTGTACTCTA
* * *
10433179 CCTAGACGGTAGAGAGTCATCATTGATTATCATTTATAAATAATGTTATTTTATTATTTTTGACT
66 CCTAGACGGTAGAGAGTCATCATTGATTATCATTTACAAAGAATGTTATTTTATTATTTTTGACC
*
10433244 GAATGTTACTATAAATCTTAGATGG
131 GAATGTTACGATAAATCTTAGATGG
10433269 AAA
1 AAA
10433272 GACTATCTTT
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
155 147 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (155 bp):
AAAAATTAATTTTAAACAAATAAAATTAAAATACCATTCTATGAAATATAATTTTTTGTACTCTA
CCTAGACGGTAGAGAGTCATCATTGATTATCATTTACAAAGAATGTTATTTTATTATTTTTGACC
GAATGTTACGATAAATCTTAGATGG
Found at i:10451399 original size:13 final size:13
Alignment explanation
Indices: 10451381--10451419 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
10451371 TTTAAATTTT
10451381 AAATTATTTAAAA
1 AAATTATTTAAAA
*
10451394 AAATTATTTATAA
1 AAATTATTTAAAA
10451407 AAATTATTTAAAA
1 AAATTATTTAAAA
10451420 TTTTCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTATTTAAAA
Found at i:10453948 original size:34 final size:32
Alignment explanation
Indices: 10453910--10454010 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 32
10453900 TTTGAAATAG
* *
10453910 ATTTTTAGGAAAATAATGTAATTCTCGAAAAT
1 ATTTTTAGGAATACAATGTAATTCTCGAAAAT
*
10453942 GAATTTTTGGGAATACAATGTAATTCTCGAAAAT
1 --ATTTTTAGGAATACAATGTAATTCTCGAAAAT
* *
10453976 ATGTTTTCAAGAATACAATATAATTCTCGAAAAT
1 AT-TTTT-AGGAATACAATGTAATTCTCGAAAAT
10454010 A
1 A
10454011 AATATTCGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
32 2 0.03
33 4 0.07
34 53 0.90
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (32 bp):
ATTTTTAGGAATACAATGTAATTCTCGAAAAT
Found at i:10454023 original size:34 final size:34
Alignment explanation
Indices: 10453928--10454032 Score: 129
Period size: 34 Copynumber: 3.1 Consensus size: 34
10453918 GAAAATAATG
* * * *
10453928 TAATTCTCGAAAATGAATTTTTGGGAATACAATG
1 TAATTCTCGAAAATAAATTTTCGAGAATACAATA
** *
10453962 TAATTCTCGAAAATATGTTTTCAAGAATACAATA
1 TAATTCTCGAAAATAAATTTTCGAGAATACAATA
* *
10453996 TAATTCTCGAAAATAAATATTCGAGAATACAACA
1 TAATTCTCGAAAATAAATTTTCGAGAATACAATA
10454030 TAA
1 TAA
10454033 GAGTCAGAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (34 bp):
TAATTCTCGAAAATAAATTTTCGAGAATACAATA
Found at i:10454883 original size:27 final size:27
Alignment explanation
Indices: 10454822--10454886 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
10454812 AATTTCTCAT
* *
10454822 TAAATTTTATTTTAATCACAGCTATAG
1 TAAATTTTATTTTAATCACAGCTACAA
*
10454849 TAACTTTT-TTTTCAATCACAGCTACAA
1 TAAATTTTATTTT-AATCACAGCTACAA
10454876 TAAATTTTATT
1 TAAATTTTATT
10454887 ACTACTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 26 0.81
28 2 0.06
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (27 bp):
TAAATTTTATTTTAATCACAGCTACAA
Found at i:10457439 original size:17 final size:18
Alignment explanation
Indices: 10457411--10457455 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
10457401 AAACATTTTG
10457411 TATTAATGTTTATTG-TTTA
1 TATT-ATGTTTA-TGCTTTA
10457430 TATT-TGTTTATGCTTTA
1 TATTATGTTTATGCTTTA
10457447 TATTATGTT
1 TATTATGTT
10457456 ATGAACTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 4 0.17
19 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.64
Consensus pattern (18 bp):
TATTATGTTTATGCTTTA
Found at i:10457580 original size:6 final size:6
Alignment explanation
Indices: 10457563--10457594 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
10457553 TTCTGTTAAT
10457563 ATAAAC -TAAAC ATAAAC ATAAAC ATAAAC ATA
1 ATAAAC ATAAAC ATAAAC ATAAAC ATAAAC ATA
10457595 TAAAATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAC
Found at i:10457641 original size:19 final size:19
Alignment explanation
Indices: 10457594--10457644 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
10457584 ACATAAACAT
*
10457594 ATAAAATCAATATGTAAAA
1 ATAAAATCAGTATGTAAAA
*
10457613 ATAAAATCAGTATGTCAAA
1 ATAAAATCAGTATGTAAAA
*
10457632 ATCAAATCAGTAT
1 ATAAAATCAGTAT
10457645 CAGCATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (19 bp):
ATAAAATCAGTATGTAAAA
Found at i:10459574 original size:9 final size:9
Alignment explanation
Indices: 10459556--10459589 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
10459546 TCACTCCTGT
10459556 AACAATAAC
1 AACAATAAC
*
10459565 AACAACAAC
1 AACAATAAC
10459574 AACAATAAC
1 AACAATAAC
*
10459583 AAAAATA
1 AACAATA
10459590 TTAATACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.71, C:0.21, G:0.00, T:0.09
Consensus pattern (9 bp):
AACAATAAC
Found at i:10460185 original size:34 final size:34
Alignment explanation
Indices: 10460126--10460239 Score: 131
Period size: 34 Copynumber: 3.4 Consensus size: 34
10460116 ATTTCTGAAA
* * *
10460126 GGGTTTCCAAGAGGCCTAAAGTCTTCTAAAAAAT
1 GGGTGTCCAAAAGGCTTAAAGTCTTCTAAAAAAT
* *
10460160 GGGTGTCCAAAAGGCTTAAATTCTTCTAGAAAAT
1 GGGTGTCCAAAAGGCTTAAAGTCTTCTAAAAAAT
* * *
10460194 GGGTGTTCAAAAGGCTTTAAGTATTCT-AAAAAT
1 GGGTGTCCAAAAGGCTTAAAGTCTTCTAAAAAAT
*
10460227 AGGTGTCCGAAAA
1 GGGTGTCC-AAAA
10460240 TAATGCTGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
33 11 0.16
34 56 0.84
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (34 bp):
GGGTGTCCAAAAGGCTTAAAGTCTTCTAAAAAAT
Found at i:10463599 original size:20 final size:20
Alignment explanation
Indices: 10463562--10463613 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
10463552 ACAACAAATT
* **
10463562 TTTAAAATAATTGTTTAAAA
1 TTTAAAATTATTACTTAAAA
*
10463582 TTTAATATTATTACTTAAAA
1 TTTAAAATTATTACTTAAAA
10463602 TTTAAAATTATT
1 TTTAAAATTATT
10463614 TCATTTCAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAAAATTATTACTTAAAA
Found at i:10463664 original size:18 final size:19
Alignment explanation
Indices: 10463638--10463675 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
10463628 ATACAATTTT
* *
10463638 AAATCAAGTGTAAAACTTA
1 AAATCAAGTATAAAAATTA
10463657 AAAT-AAGTATAAAAATTA
1 AAATCAAGTATAAAAATTA
10463675 A
1 A
10463676 TTTGATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (19 bp):
AAATCAAGTATAAAAATTA
Found at i:10469582 original size:24 final size:24
Alignment explanation
Indices: 10469550--10469597 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
10469540 AAAAACATAG
10469550 CCATTTTAAGACTTGATATCATCA
1 CCATTTTAAGACTTGATATCATCA
10469574 CCATTTTAAGACTTGATATCATCA
1 CCATTTTAAGACTTGATATCATCA
10469598 TTGTCAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (24 bp):
CCATTTTAAGACTTGATATCATCA
Found at i:10479591 original size:17 final size:17
Alignment explanation
Indices: 10479548--10479605 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
10479538 GCAAACTTGC
10479548 AAAATAAAAGAA-AAAAA
1 AAAATAAAA-AACAAAAA
** * *
10479565 ATCATGAAAAA-AAAGA
1 AAAATAAAAAACAAAAA
10479581 AAAATAAAAAACAAAAA
1 AAAATAAAAAACAAAAA
10479598 AAAATAAA
1 AAAATAAA
10479606 GTGGTGACAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 14 0.44
17 18 0.56
ACGTcount: A:0.83, C:0.03, G:0.05, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAACAAAAA
Found at i:10480895 original size:15 final size:15
Alignment explanation
Indices: 10480877--10480921 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
10480867 TTTTTTGTTT
10480877 CTTTAATTTTTTGCA
1 CTTTAATTTTTTGCA
*
10480892 CTTTACTTTTTTGCA
1 CTTTAATTTTTTGCA
*
10480907 -TTTCATTTTCTTGCA
1 CTTTAATTTT-TTGCA
10480922 TTTTCTTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.60
Consensus pattern (15 bp):
CTTTAATTTTTTGCA
Found at i:10484052 original size:2 final size:2
Alignment explanation
Indices: 10484045--10484085 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10484035 GGATGCCTTC
*
10484045 AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10484086 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10487058 original size:25 final size:25
Alignment explanation
Indices: 10487006--10487058 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
10486996 TTATTGGCGA
* *
10487006 AAAATTTTGTCAATAATTTTTTTGT
1 AAAATTTTGCCAATAATTTTTTTAT
*
10487031 AAAATTTTGCCAA-ATTTTTATTTAT
1 AAAATTTTGCCAATAATTTT-TTTAT
10487056 AAA
1 AAA
10487059 TTATAGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
AAAATTTTGCCAATAATTTTTTTAT
Found at i:10489310 original size:16 final size:16
Alignment explanation
Indices: 10489291--10489321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10489281 TAAAACCACG
*
10489291 TGGAAATAAACTTTAT
1 TGGAAACAAACTTTAT
10489307 TGGAAACAAACTTTA
1 TGGAAACAAACTTTA
10489322 AGCCTTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (16 bp):
TGGAAACAAACTTTAT
Found at i:10490966 original size:142 final size:142
Alignment explanation
Indices: 10490664--10491159 Score: 423
Period size: 142 Copynumber: 3.4 Consensus size: 142
10490654 ATTTAAAAAG
* * * * * *
10490664 CACCAAAAATTATGAAATATTAT-AAATTTGAGATATGAAAAGTTTCATGAAAATCCAAGCTCAG
1 CACCAAAAATCATGAAATATTATGAAA-TTAAGATCTAAAAAATTTCATGAAAATCCAAGCT-TG
* * * * * ** ** *
10490728 GAATGTCAAATTATAAAAATATCACTAAATGAGTA-TTTTGCTAATTTCACACCTCT-TGGGTTA
64 GGAGGCCAAATTA-CAAAATA-CACTAAAAG-GTATTTTTG-TAATTTCACATATCTCAAGGCTA
* *
10490791 CTGTTATGATTTCAAATA
125 TTGCTATGATTTCAAATA
*
10490809 CACCAAAAATTATGAAATATTATGAAATTAAGATCTAAAAAATTTCATGAAAATCCAAGCTTGGG
1 CACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAATTTCATGAAAATCCAAGCTTGGG
*
10490874 AGGCCAAATTACAAAATACCCTTAAAAGGTATTTTTGTAATTTCACATATCTCAAGG-TATTGCT
66 AGGCCAAATTACAAAATACAC-TAAAAGGTATTTTTGTAATTTCACATATCTCAAGGCTATTGCT
*
10490938 ATGATTTCAAATT
130 ATGATTTCAAATA
* ** * * * *
10490951 CACCAAAAATCATGAAATATTATGAAATTGAGAT-TTGAAAAGTTCAATGAAAATTCGAGCTCGG
1 CACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAATTTC-ATGAAAATCCAAGCTTGG
* * *
10491015 GAAGGCCAAATTACGAAAATATTCA-T-AAAGGTATTTTGGTAATTTTAAATAT-TCATAAGGCC
65 G-AGGCCAAATTAC-AAAATA--CACTAAAAGGTATTTTTGTAATTTCACATATCTC--AAGG-C
* * * *
10491077 AAATTACTGTGATTTCAAATG
123 -TATTGCTATGATTTCAAATA
* * * * * *
10491098 CACCAAAAATCATGAAATATTATGAAATTAAAATCCAAAAAGTTTTATGAAATTCCTAGCTT
1 CACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAATTTCATGAAAATCCAAGCTT
10491160 AGATATGTCA
Statistics
Matches: 290, Mismatches: 46, Indels: 28
0.80 0.13 0.08
Matches are distributed among these distances:
141 8 0.03
142 85 0.29
143 53 0.18
144 22 0.08
145 53 0.18
146 4 0.01
147 60 0.21
148 5 0.02
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (142 bp):
CACCAAAAATCATGAAATATTATGAAATTAAGATCTAAAAAATTTCATGAAAATCCAAGCTTGGG
AGGCCAAATTACAAAATACACTAAAAGGTATTTTTGTAATTTCACATATCTCAAGGCTATTGCTA
TGATTTCAAATA
Found at i:10505059 original size:21 final size:24
Alignment explanation
Indices: 10505014--10505068 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
10505004 TTTTTTTTAT
*
10505014 TTTTTATATATTATTTTAATAAGA
1 TTTTTATATATTATTTAAATAAGA
10505038 TTTTTA-ATA-TATTTAAAT-AGA
1 TTTTTATATATTATTTAAATAAGA
*
10505059 TTTATATATA
1 TTTTTATATA
10505069 AAATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.29
22 11 0.39
23 3 0.11
24 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTTATATATTATTTAAATAAGA
Found at i:10506463 original size:17 final size:17
Alignment explanation
Indices: 10506427--10506475 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
10506417 TTAAAACTTA
* *
10506427 CTAAAAAAAGAAA-TTG
1 CTAAAAATAGAAAGTTT
10506443 CTAAAAATAGAAAGTTT
1 CTAAAAATAGAAAGTTT
10506460 CTAAAAAT-GAAAGTTT
1 CTAAAAATAGAAAGTTT
10506476 GGACCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 20 0.67
17 10 0.33
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (17 bp):
CTAAAAATAGAAAGTTT
Found at i:10506524 original size:22 final size:24
Alignment explanation
Indices: 10506481--10506531 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
10506471 AGTTTGGACC
*
10506481 AAAATTAACTAAAGCATGAAATA-
1 AAAATTAACTAAAGCATAAAATAG
**
10506504 AAAATTAACTGTAGC-TAAAATAG
1 AAAATTAACTAAAGCATAAAATAG
10506527 AAAAT
1 AAAAT
10506532 AAATAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAAATTAACTAAAGCATAAAATAG
Found at i:10507562 original size:143 final size:141
Alignment explanation
Indices: 10507303--10507673 Score: 426
Period size: 143 Copynumber: 2.6 Consensus size: 141
10507293 TTGAAATTTG
* * * *** *
10507303 TGATTTTAATCCACTAAAAACCTTGATTGCACCTTGGAGGTTGTAAAGTTACCAAAATACCATTT
1 TGATTTTAATGCATTAAAAACCTTGATTGTACCTAAAAGGTT-TAAA-TTACCAAAATACCCTTT
** * * * ***
10507368 AAGGGTATTTTTGTAATTTGATCTTTTCAAGTTTGGTATTTTGTGAAAAGCT-ACAAATCATGTT
64 AAGGGTATTTTCATAATTTGATCTTCTCAAGGTTGATATTTTCACAAAAGCTCA-AAATCATGTT
10507432 TTGATATTATTTTA
128 TTGATATTATTTTA
*
10507446 TGATTTTTAGTGCATTAAAAACCTTGATTGTACCATAAAAGGTTTAAATTACCAAAATACCCTTT
1 TGA-TTTTAATGCATTAAAAACCTTGATTGTACC-TAAAAGGTTTAAATTACCAAAATACCCTTT
10507511 AAGGGTATTTTCATAATTTGATCTTC-CTAAGGTTGAT-TTTTCACAACAAGCTCAAAATCATGT
64 AAGGGTATTTTCATAATTTGATCTTCTC-AAGGTTGATATTTTCACAA-AAGCTCAAAATCATGT
10507574 TTTGATATTATTTTA
127 TTTGATATTATTTTA
* * * * *
10507589 TGATTTTAATGCATTAAAAACCTTGATTGTACCTTGAAAGATGTGAAATTATCAAAATACCC-CT
1 TGATTTTAATGCATTAAAAACCTTGATTGTACC-TAAAAGGT-TTAAATTACCAAAATACCCTTT
* *
10507653 ATGAGTATTTTCATAATTTGA
64 AAGGGTATTTTCATAATTTGA
10507674 CCGTCCAAAG
Statistics
Matches: 197, Mismatches: 25, Indels: 13
0.84 0.11 0.06
Matches are distributed among these distances:
142 62 0.31
143 98 0.50
144 31 0.16
145 6 0.03
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (141 bp):
TGATTTTAATGCATTAAAAACCTTGATTGTACCTAAAAGGTTTAAATTACCAAAATACCCTTTAA
GGGTATTTTCATAATTTGATCTTCTCAAGGTTGATATTTTCACAAAAGCTCAAAATCATGTTTTG
ATATTATTTTA
Found at i:10507709 original size:143 final size:143
Alignment explanation
Indices: 10507413--10507702 Score: 388
Period size: 142 Copynumber: 2.0 Consensus size: 143
10507403 GTATTTTGTG
*
10507413 AAAAGCT-ACAAATCATGTTTTGATATTATTTTATGATTTTTAGTGCATTAAAAACCTTGATTGT
1 AAAAGCTCA-AAATCATGTTTTGATATTATTTTATGATTTTTAATGCATTAAAAACCTTGATTGT
* * * * * * *
10507477 ACCATAAAAGGTTTAAATTACCAAAATACCCTTTAAGGGTATTTTCATAATTTGATCTTCCTAAG
65 ACCATAAAAGATTGAAATTACCAAAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAG
* * *
10507542 GTTGATTTTTCACA
130 GTCGATTCTTCAAA
*
10507556 ACAAGCTCAAAATCATGTTTTGATATTATTTTATGA-TTTTAATGCATTAAAAACCTTGATTGTA
1 AAAAGCTCAAAATCATGTTTTGATATTATTTTATGATTTTTAATGCATTAAAAACCTTGATTGTA
* * * *
10507620 CCTTGAAAGATGTGAAATTATCAAAATACCC-CTATGAGTATTTTCATAATTTGACCGTCCAAAG
66 CCATAAAAGAT-TGAAATTACCAAAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAG
10507684 GTCGATTCTTCATAA
130 GTCGATTCTTCA-AA
10507699 AAAA
1 AAAA
10507703 TTTCAAATAA
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
142 72 0.57
143 54 0.43
144 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (143 bp):
AAAAGCTCAAAATCATGTTTTGATATTATTTTATGATTTTTAATGCATTAAAAACCTTGATTGTA
CCATAAAAGATTGAAATTACCAAAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAGG
TCGATTCTTCAAA
Found at i:10507725 original size:142 final size:142
Alignment explanation
Indices: 10507434--10507742 Score: 345
Period size: 142 Copynumber: 2.2 Consensus size: 142
10507424 ATCATGTTTT
* * *
10507434 GATATTATTTTATGATTTTTAGTGCATTAAAAACCTTGATTGTACCATAAAAGGTTTAAATTACC
1 GATATTATTTTATGA-TTTTAATGCATTAAAAACCTTGATTGTACCATAAAAGATTGAAATTACC
* * * * * * * * *
10507499 AAAATACCCTTTAAGGGTATTTTCATAATTTGATCTTCCTAAGGTTGATTTTTCACAACAAGCTC
65 AAAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAGGTCGATTCTTCAAAAAAAGCTC
* ***
10507564 AAAATCATGTTTT
130 AAAATAATGTCAA
* * *
10507577 GATATTATTTTATGATTTTAATGCATTAAAAACCTTGATTGTACCTTGAAAGATGTGAAATTATC
1 GATATTATTTTATGATTTTAATGCATTAAAAACCTTGATTGTACCATAAAAGAT-TGAAATTACC
* **
10507642 AAAATACCC-CTATGAGTATTTTCATAATTTGACCGTCCAAAGGTCGATTCTTCATAAAAAATTT
65 AAAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAGGTCGATTCTTCA-AAAAAAGCT
10507706 C-AAATAATGGTCAA
129 CAAAATAAT-GTCAA
*
10507720 G-TATTATTTTATAATTTTCAATG
1 GATATTATTTTATGATTTT-AATG
10507743 TAGTAAAATC
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
142 94 0.68
143 45 0.32
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (142 bp):
GATATTATTTTATGATTTTAATGCATTAAAAACCTTGATTGTACCATAAAAGATTGAAATTACCA
AAATACCCTCTAAGAGTATTTTCATAATTTGACCGTCCAAAGGTCGATTCTTCAAAAAAAGCTCA
AAATAATGTCAA
Found at i:10509194 original size:12 final size:12
Alignment explanation
Indices: 10509158--10509199 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
10509148 TAAAAATCCA
10509158 AAACAAAACCCTT
1 AAACAAAACCC-T
10509171 AAATCAAAACCCT
1 AAA-CAAAACCCT
*
10509184 AAACTAAACCCT
1 AAACAAAACCCT
10509196 AAAC
1 AAAC
10509200 CACCCAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 7 0.26
14 8 0.30
ACGTcount: A:0.55, C:0.31, G:0.00, T:0.14
Consensus pattern (12 bp):
AAACAAAACCCT
Found at i:10509229 original size:13 final size:13
Alignment explanation
Indices: 10509158--10509269 Score: 52
Period size: 13 Copynumber: 8.3 Consensus size: 13
10509148 TAAAAATCCA
10509158 AAACA-AAACCCTT
1 AAACACAAACCC-T
10509171 AAATCA-AAACCCT
1 AAA-CACAAACCCT
*
10509184 AAAC-TAAACCCT
1 AAACACAAACCCT
*
10509196 AAACCACCCAAAACCT
1 AAA-CA--CAAACCCT
10509212 CAAACACAAACCCT
1 -AAACACAAACCCT
* **
10509226 AAACCTCAAATGC-
1 AAA-CACAAACCCT
* *
10509239 AAACCCTAAACCTT
1 AAACAC-AAACCCT
*
10509253 AAACACAAACCTT
1 AAACACAAACCCT
10509266 AAAC
1 AAAC
10509270 CCCAAACACA
Statistics
Matches: 78, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
12 13 0.17
13 28 0.36
14 26 0.33
16 8 0.10
17 3 0.04
ACGTcount: A:0.51, C:0.35, G:0.01, T:0.13
Consensus pattern (13 bp):
AAACACAAACCCT
Found at i:10509229 original size:20 final size:20
Alignment explanation
Indices: 10509201--10509288 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
10509191 ACCCTAAACC
*
10509201 ACCCAAAACCTCAAACACAA
1 ACCCTAAACCTCAAACACAA
**
10509221 ACCCTAAACCTCAAATGCAA
1 ACCCTAAACCTCAAACACAA
*
10509241 ACCCTAAACCTTAAACACAA
1 ACCCTAAACCTCAAACACAA
* *
10509261 ACCTTAAACCCCAAACACAA
1 ACCCTAAACCTCAAACACAA
10509281 ACCCTAAA
1 ACCCTAAA
10509289 GCCTAAATCT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.50, C:0.38, G:0.01, T:0.11
Consensus pattern (20 bp):
ACCCTAAACCTCAAACACAA
Found at i:10509342 original size:19 final size:19
Alignment explanation
Indices: 10509290--10509357 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
10509280 AACCCTAAAG
*
10509290 CCTAAAT-CTAAAACCAAAC
1 CCTAAATCCT-AAACCAAAA
*
10509309 CCT-AA-CC-ATAACCAAAT
1 CCTAAATCCTA-AACCAAAA
10509326 CCTAAATCCTAAACCAAAA
1 CCTAAATCCTAAACCAAAA
*
10509345 CCTAAACCCTAAA
1 CCTAAATCCTAAA
10509358 TGAAACCCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 1 0.02
17 10 0.24
18 5 0.12
19 24 0.59
20 1 0.02
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (19 bp):
CCTAAATCCTAAACCAAAA
Found at i:10509371 original size:7 final size:7
Alignment explanation
Indices: 10509177--10509357 Score: 68
Period size: 7 Copynumber: 27.4 Consensus size: 7
10509167 CCTTAAATCA
10509177 AAACCCT
1 AAACCCT
10509184 AAA--CT
1 AAACCCT
10509189 AAACCCT
1 AAACCCT
*
10509196 AAACCACCC
1 AAA-C-CCT
*
10509205 AAAACCT
1 AAACCCT
*
10509212 CAAACAC-
1 -AAACCCT
10509219 AAACCCT
1 AAACCCT
10509226 AAA-CCT
1 AAACCCT
**
10509232 CAAATGC-
1 -AAACCCT
10509239 AAACCCT
1 AAACCCT
*
10509246 AAACCTT
1 AAACCCT
*
10509253 AAACAC-
1 AAACCCT
*
10509259 AAACCTT
1 AAACCCT
*
10509266 AAACCCC
1 AAACCCT
*
10509273 AAACAC-
1 AAACCCT
10509279 AAACCCT
1 AAACCCT
*
10509286 AAAGCCT
1 AAACCCT
*
10509293 AAA-TCT
1 AAACCCT
*
10509299 AAAACC-
1 AAACCCT
10509305 AAACCCT
1 AAACCCT
*
10509312 -AACCAT
1 AAACCCT
10509318 -AA-CC-
1 AAACCCT
*
10509322 AAATCCT
1 AAACCCT
*
10509329 AAATCCT
1 AAACCCT
10509336 AAA-CC-
1 AAACCCT
*
10509341 AAAACCT
1 AAACCCT
10509348 AAACCCT
1 AAACCCT
10509355 AAA
1 AAA
10509358 TGAAACCCTA
Statistics
Matches: 131, Mismatches: 25, Indels: 36
0.68 0.13 0.19
Matches are distributed among these distances:
5 11 0.08
6 44 0.34
7 65 0.50
8 6 0.05
9 5 0.04
ACGTcount: A:0.50, C:0.36, G:0.01, T:0.13
Consensus pattern (7 bp):
AAACCCT
Found at i:10509727 original size:16 final size:16
Alignment explanation
Indices: 10509706--10509763 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
10509696 CAAGATAAAT
*
10509706 CCTAAACCAAACCCAC
1 CCTAAACCAAACCAAC
*
10509722 CCTAAACCGAACCAAC
1 CCTAAACCAAACCAAC
* *
10509738 CCATAAAGCTAAACTAAC
1 CC-TAAA-CCAAACCAAC
*
10509756 TCTAAACC
1 CCTAAACC
10509764 CTAAATAATC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 17 0.52
17 8 0.24
18 8 0.24
ACGTcount: A:0.45, C:0.40, G:0.03, T:0.12
Consensus pattern (16 bp):
CCTAAACCAAACCAAC
Found at i:10511482 original size:10 final size:10
Alignment explanation
Indices: 10511455--10511495 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 10
10511445 TTTTTGTTTT
*
10511455 AAGAAAAAAA
1 AAGAAAATAA
10511465 AAGCAAAATAA
1 AAG-AAAATAA
10511476 AAGAAAAT-A
1 AAGAAAATAA
10511485 AA-AAAATAA
1 AAGAAAATAA
10511494 AA
1 AA
10511496 AAACAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 5 0.18
9 6 0.21
10 8 0.29
11 9 0.32
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (10 bp):
AAGAAAATAA
Found at i:10518108 original size:21 final size:21
Alignment explanation
Indices: 10518083--10518126 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
10518073 AATTTTTTTT
*
10518083 AATATTTCTTTTATTCTTGCC
1 AATATATCTTTTATTCTTGCC
10518104 AATATATCTTTTATTCTTGCC
1 AATATATCTTTTATTCTTGCC
10518125 AA
1 AA
10518127 AATGTCCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (21 bp):
AATATATCTTTTATTCTTGCC
Found at i:10518895 original size:20 final size:20
Alignment explanation
Indices: 10518870--10518907 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
10518860 ATTTTATGAC
10518870 AAACCCT-AACCACCAAACCT
1 AAACCCTAAACC-CCAAACCT
10518890 AAACCCTAAACCCCAAAC
1 AAACCCTAAACCCCAAAC
10518908 ATAGCGCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.45, G:0.00, T:0.08
Consensus pattern (20 bp):
AAACCCTAAACCCCAAACCT
Found at i:10518937 original size:19 final size:19
Alignment explanation
Indices: 10518915--10518985 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
10518905 AACATAGCGC
10518915 TAAACCATAGACCAAACCA
1 TAAACCATAGACCAAACCA
* *
10518934 TAAACCCTAGACCAAACCC
1 TAAACCATAGACCAAACCA
* *
10518953 TAAAGCATA-AGCCAAA-CT
1 TAAACCATAGA-CCAAACCA
*
10518971 TAAACCATAAACCAA
1 TAAACCATAGACCAA
10518986 CCCGCAAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.32
19 30 0.68
ACGTcount: A:0.51, C:0.31, G:0.06, T:0.13
Consensus pattern (19 bp):
TAAACCATAGACCAAACCA
Found at i:10519377 original size:17 final size:16
Alignment explanation
Indices: 10519345--10519392 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
10519335 AGCCAAGATA
*
10519345 AAACCAATCCTAAACC
1 AAACCAACCCTAAACC
10519361 AAACCAACCCATAAACC
1 AAACCAACCC-TAAACC
* *
10519378 CAACTAACCCTAAAC
1 AAACCAACCCTAAAC
10519393 TTTAAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (16 bp):
AAACCAACCCTAAACC
Found at i:10519853 original size:17 final size:17
Alignment explanation
Indices: 10519831--10519865 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
10519821 GTTTTTTTTT
10519831 ATAAAAAAAAGTTAAAA
1 ATAAAAAAAAGTTAAAA
* *
10519848 ATAAAAATAATTTAAAA
1 ATAAAAAAAAGTTAAAA
10519865 A
1 A
10519866 ACAACATAAT
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:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
ATAAAAAAAAGTTAAAA
Found at i:10522849 original size:20 final size:21
Alignment explanation
Indices: 10522816--10522855 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
10522806 AGGAATTAAG
*
10522816 ATTAAACACTAAC-TAGGACC
1 ATTAAACACAAACTTAGGACC
*
10522836 ATTAAACCCAAACTTAGGAC
1 ATTAAACACAAACTTAGGAC
10522856 AACATGCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (21 bp):
ATTAAACACAAACTTAGGACC
Found at i:10524531 original size:20 final size:19
Alignment explanation
Indices: 10524482--10524531 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
10524472 TAAAAGGGAC
10524482 AAAGAAGAAAATAACTAAAG
1 AAAGAA-AAAATAACTAAAG
10524502 AAA-ACTAAAAATAAACTAAAG
1 AAAGA--AAAAAT-AACTAAAG
10524523 AAAGAAAAA
1 AAAGAAAAA
10524532 TGGAAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 12 0.46
22 1 0.04
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAGAAAAAATAACTAAAG
Found at i:10525568 original size:12 final size:12
Alignment explanation
Indices: 10525547--10525600 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
10525537 ATAATTGAGG
10525547 GTTT-GGGTTTA
1 GTTTGGGGTTTA
10525558 GTTTGGGGTTTA
1 GTTTGGGGTTTA
*
10525570 GGTT-GGGTTTA
1 GTTTGGGGTTTA
10525581 GTGTTTGGGGTTTA
1 --GTTTGGGGTTTA
*
10525595 GGTTGG
1 GTTTGG
10525601 TTTTAGGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 11 0.31
12 15 0.42
13 3 0.08
14 7 0.19
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.48
Consensus pattern (12 bp):
GTTTGGGGTTTA
Found at i:10525592 original size:25 final size:24
Alignment explanation
Indices: 10525549--10525613 Score: 96
Period size: 25 Copynumber: 2.7 Consensus size: 24
10525539 AATTGAGGGT
10525549 TTGGGTTTA-GTTTGGGGTTTAGG
1 TTGGGTTTAGGTTTGGGGTTTAGG
10525572 TTGGGTTTAGTGTTTGGGGTTTAGG
1 TTGGGTTTAG-GTTTGGGGTTTAGG
*
10525597 TTGGTTTTAGGATTTGG
1 TTGGGTTTAGG-TTTGG
10525614 ATTTGGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
23 9 0.24
24 1 0.03
25 28 0.74
ACGTcount: A:0.09, C:0.00, G:0.42, T:0.49
Consensus pattern (24 bp):
TTGGGTTTAGGTTTGGGGTTTAGG
Found at i:10525607 original size:11 final size:11
Alignment explanation
Indices: 10525549--10525607 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
10525539 AATTGAGGGT
*
10525549 TTGGGTTTAGT
1 TTGGGTTTAGG
10525560 TTGGGGTTTAGG
1 TT-GGGTTTAGG
10525572 TTGGGTTTAGTG
1 TTGGGTTTAG-G
10525584 TTTGGGGTTTAGG
1 -TT-GGGTTTAGG
*
10525597 TTGGTTTTAGG
1 TTGGGTTTAGG
10525608 ATTTGGATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 18 0.43
12 13 0.31
13 3 0.07
14 8 0.19
ACGTcount: A:0.08, C:0.00, G:0.42, T:0.49
Consensus pattern (11 bp):
TTGGGTTTAGG
Found at i:10525663 original size:18 final size:18
Alignment explanation
Indices: 10525640--10525680 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
10525630 TGAAAGTTTG
10525640 GGTTCAGTTTAAGGATTT
1 GGTTCAGTTTAAGGATTT
**
10525658 GGTTCAGTTTTGGGATTT
1 GGTTCAGTTTAAGGATTT
10525676 GGTTC
1 GGTTC
10525681 GATTGGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.07, G:0.32, T:0.46
Consensus pattern (18 bp):
GGTTCAGTTTAAGGATTT
Found at i:10525901 original size:20 final size:18
Alignment explanation
Indices: 10525865--10525924 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
10525855 AGGATTGAAG
*
10525865 GTTTGGTTTTGGTGTTTAAGA
1 GTTTGG-TTTGGGGTTT--GA
10525886 GTTTGGTTTGGGGTTTGA
1 GTTTGGTTTGGGGTTTGA
10525904 GTTTAAGGTTTGAGGGTTTGA
1 GTTT--GGTTTG-GGGTTTGA
10525925 TTTAGGGTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 6 0.17
20 15 0.43
21 14 0.40
ACGTcount: A:0.13, C:0.00, G:0.38, T:0.48
Consensus pattern (18 bp):
GTTTGGTTTGGGGTTTGA
Found at i:10525928 original size:20 final size:20
Alignment explanation
Indices: 10525890--10525950 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
10525880 TTAAGAGTTT
10525890 GGTTTGGGGTTTGAGTTTAA
1 GGTTTGGGGTTTGAGTTTAA
*
10525910 GGTTTGAGGGTTTGA-TTTAG
1 GGTTTG-GGGTTTGAGTTTAA
* *
10525930 GGTCT-GAGTTTAGAGTTTAA
1 GGTTTGGGGTTT-GAGTTTAA
10525950 G
1 G
10525951 TGATACATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.15
19 2 0.06
20 19 0.56
21 8 0.24
ACGTcount: A:0.18, C:0.02, G:0.38, T:0.43
Consensus pattern (20 bp):
GGTTTGGGGTTTGAGTTTAA
Found at i:10527866 original size:10 final size:10
Alignment explanation
Indices: 10527847--10527898 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 10
10527837 CTCGAGTTCA
10527847 ACCAAATTTG
1 ACCAAATTTG
*
10527857 ACCAATTTTG
1 ACCAAATTTG
*
10527867 ACAAAATTTG
1 ACCAAATTTG
* * *
10527877 ATCAATTTTA
1 ACCAAATTTG
*
10527887 ACAAAATTTG
1 ACCAAATTTG
10527897 AC
1 AC
10527899 TAATTTTGAT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (10 bp):
ACCAAATTTG
Found at i:10527875 original size:20 final size:20
Alignment explanation
Indices: 10527850--10527907 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
10527840 GAGTTCAACC
10527850 AAATTTGACCAATTTTGACA
1 AAATTTGACCAATTTTGACA
* *
10527870 AAATTTGATCAATTTTAACA
1 AAATTTGACCAATTTTGACA
*
10527890 AAATTTGACTAATTTTGA
1 AAATTTGACCAATTTTGA
10527908 TCATGGGACA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATTTGACCAATTTTGACA
Found at i:10528747 original size:26 final size:26
Alignment explanation
Indices: 10528714--10528769 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
10528704 ATTTGAGTTT
10528714 AAAA-GCTTCTAAAAGAATTAAAAGA
1 AAAATGCTTCTAAAAGAATTAAAAGA
10528739 AAAATGCTTCTAAAAGAATTAAAAGA
1 AAAATGCTTCTAAAAGAATTAAAAGA
10528765 AAAAT
1 AAAAT
10528770 AATAAGGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.13
26 26 0.87
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.21
Consensus pattern (26 bp):
AAAATGCTTCTAAAAGAATTAAAAGA
Found at i:10531099 original size:2 final size:2
Alignment explanation
Indices: 10531092--10531118 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10531082 TGAAAGATAA
10531092 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
10531119 ATGGGCTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10531724 original size:16 final size:16
Alignment explanation
Indices: 10531705--10531739 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
10531695 CATGTTTGAG
*
10531705 TTTTTTATGTTTTATA
1 TTTTTTATATTTTATA
*
10531721 TTTTTTATATTTTTTA
1 TTTTTTATATTTTATA
10531737 TTT
1 TTT
10531740 ATTACTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTTATATTTTATA
Found at i:10531726 original size:9 final size:9
Alignment explanation
Indices: 10531705--10531737 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
10531695 CATGTTTGAG
10531705 TTTTT-TAT
1 TTTTTATAT
*
10531713 GTTTTATAT
1 TTTTTATAT
10531722 TTTTTATAT
1 TTTTTATAT
10531731 TTTTTAT
1 TTTTTAT
10531738 TTATTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTTTATAT
Found at i:10535246 original size:18 final size:19
Alignment explanation
Indices: 10535210--10535248 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
10535200 TTTTTTTCAC
*
10535210 TTTTTTCATTTAGGTTTTA
1 TTTTTTCATTTAGGCTTTA
*
10535229 TTTTTTTATTT-GGCTTTA
1 TTTTTTCATTTAGGCTTTA
10535247 TT
1 TT
10535249 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.13, C:0.05, G:0.10, T:0.72
Consensus pattern (19 bp):
TTTTTTCATTTAGGCTTTA
Found at i:10535264 original size:52 final size:54
Alignment explanation
Indices: 10535181--10535282 Score: 147
Period size: 52 Copynumber: 1.9 Consensus size: 54
10535171 CACTTTATTA
*
10535181 ATTTAGGCTTTACTATACTTTTTTTTCACTTTTTTCA-TTTAGGTTTTATTTTTTT
1 ATTTAGGCTTTACTATAC-TTTTTTTCACTTTTTT-AGTTTAGGCTTTATTTTTTT
*
10535236 ATTT-GGCTTTATTATA-TTTTTTTCACTTTTTTAGTTTAGGCTTTATT
1 ATTTAGGCTTTACTATACTTTTTTTCACTTTTTTAGTTTAGGCTTTATT
10535283 ATATTGTCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
51 1 0.02
52 28 0.64
54 11 0.25
55 4 0.09
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.65
Consensus pattern (54 bp):
ATTTAGGCTTTACTATACTTTTTTTCACTTTTTTAGTTTAGGCTTTATTTTTTT
Found at i:10535323 original size:22 final size:22
Alignment explanation
Indices: 10535262--10535324 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
10535252 TTTTTTTCAC
10535262 TTTTTTAGTTTAGGCTTTATTATA
1 TTTTTTA-TTT-GGCTTTATTATA
* * * * *
10535286 TTGTCTGTATGACTTTATTATA
1 TTTTTTATTTGGCTTTATTATA
10535308 TTTTTTATTTGGCTTTA
1 TTTTTTATTTGGCTTTA
10535325 AAGTTGAAAG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
22 23 0.79
23 2 0.07
24 4 0.14
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (22 bp):
TTTTTTATTTGGCTTTATTATA
Done.