Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397280.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_77.0, 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: 1703557
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 66023 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:418413 original size:395 final size:396
Alignment explanation
Indices: 417641--418434 Score: 1104
Period size: 395 Copynumber: 2.0 Consensus size: 396
417631 TGTGTGACCC
* *
417641 ATTACGTTCCCCACATGTTGGCAATAAATATAAAATTAATTCAATTAAGAACTTATATTTATATT
1 ATTACGTTCCCCACATGCTGGCAATAAATATAAAATTAACTCAATTAAGAACTTATATTTATATT
* * * *
417706 TATTGTTTATGAGTAGCATCTAGCAATACATCATAACCACCCAAATGTTAAGAGAATCAATATGG
66 TATTGTTCATGAGCAGCATCTAGCAATACATCATAACCACCCAAATGTCAAAAGAATCAATATGG
* * * * * * *
417771 TTTGACTAACCTTTTAGTGTACAGTATCTTAGTGTAATTCGATCCTTTCATTAGATATTTCAGAT
131 TTTGAATAACCTTTGAATGCACAGTATCTTAGTGTAATTCGATCCTTTCATTAAAAATCTCAGAT
* * * *
417836 AGATACAAAGCTTGGCTCATTGTCTACTTTCTAACTTATTCATATTACTCCTACAGTTTTCATAT
196 AAATACAAAGCTTGGCTCAGTGTCTACTTTCTAACTTATACATATTACTCCTACAGCTTTCATAT
* * * *
417901 TAACCTATCAAAATTGCCTTGGCCAAGGACTTTTATTCAATATAAGCCAGAAGTATGGTTTATGC
261 TAACCTATCAAAATTACCTTGGCCAAGGACTTTTAGTCAATATAAGCCAGAAGCATGCTTTATGC
* * * **
417966 CATACCCAAAAGCACCCTGTTTAGGCATATCATCGCCTCCATACCTATAGAGGTGAAATCAAAGC
326 CACACCCAAAAGCACCCTGTTTAGGCATATCATCGCCTCCAAACCCATAGAGGAAAAATCAAAGC
418031 GTGACA
391 GTGACA
*
418037 ATTACGTTCCTCACATGCTGGCAATAAATAT-AAATTAACTCAATTAAGAACTTATATTTATATT
1 ATTACGTTCCCCACATGCTGGCAATAAATATAAAATTAACTCAATTAAGAACTTATATTTATATT
* * *
418101 TATTGTTCATTAGCAGCATCTAGCAATACATCATGACCACCCAAATGTCAAAAGAGTCAATATGG
66 TATTGTTCATGAGCAGCATCTAGCAATACATCATAACCACCCAAATGTCAAAAGAATCAATATGG
** *
418166 TTTGAATAACCTTTGAATGCATTGTATCTTAGTGTAATTCGATCTTTTCATTAAAAATCTCAGAT
131 TTTGAATAACCTTTGAATGCACAGTATCTTAGTGTAATTCGATCCTTTCATTAAAAATCTCAGAT
* * * * * *
418231 AAATAGAAAGCTTGGCTCGGTGTCTACTTTCTAATTTATACATATTAGTCTTGCAGCTTTCATAT
196 AAATACAAAGCTTGGCTCAGTGTCTACTTTCTAACTTATACATATTACTCCTACAGCTTTCATAT
* * * * * *
418296 TCACCTATCAAGATTACCTTTGCCAAGTACTTTTAGTCAATATATGCTAGAAGCATGCTTTATGC
261 TAACCTATCAAAATTACCTTGGCCAAGGACTTTTAGTCAATATAAGCCAGAAGCATGCTTTATGC
* ** * ** * *
418361 CACATCGGAAAGCACCCTGTTTAGGCATCTGGTGGCCTCCAAACCCATAGAGGAAAAATTAAAGC
326 CACACCCAAAAGCACCCTGTTTAGGCATATCATCGCCTCCAAACCCATAGAGGAAAAATCAAAGC
418426 GTGACA
391 GTGACA
418432 ATT
1 ATT
418435 CACATACAAG
Statistics
Matches: 345, Mismatches: 53, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
395 316 0.92
396 29 0.08
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (396 bp):
ATTACGTTCCCCACATGCTGGCAATAAATATAAAATTAACTCAATTAAGAACTTATATTTATATT
TATTGTTCATGAGCAGCATCTAGCAATACATCATAACCACCCAAATGTCAAAAGAATCAATATGG
TTTGAATAACCTTTGAATGCACAGTATCTTAGTGTAATTCGATCCTTTCATTAAAAATCTCAGAT
AAATACAAAGCTTGGCTCAGTGTCTACTTTCTAACTTATACATATTACTCCTACAGCTTTCATAT
TAACCTATCAAAATTACCTTGGCCAAGGACTTTTAGTCAATATAAGCCAGAAGCATGCTTTATGC
CACACCCAAAAGCACCCTGTTTAGGCATATCATCGCCTCCAAACCCATAGAGGAAAAATCAAAGC
GTGACA
Found at i:429427 original size:20 final size:21
Alignment explanation
Indices: 429388--429432 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
429378 TCAAATTTTC
*
429388 TTTATCGAACATTCACTCATA
1 TTTATCGAACATTCAATCATA
* *
429409 TTTATCGAGC-TTCAATCATC
1 TTTATCGAACATTCAATCATA
429429 TTTA
1 TTTA
429433 AGCTTAGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (21 bp):
TTTATCGAACATTCAATCATA
Found at i:440075 original size:18 final size:18
Alignment explanation
Indices: 440052--440096 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
440042 CTCAGTGCAC
440052 TAAACCATCAT-AAACATA
1 TAAACC-TCATAAAACATA
440070 TAAACCTCATAAAACATA
1 TAAACCTCATAAAACATA
440088 TAAACCTCA
1 TAAACCTCA
440097 CAAACTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAACCTCATAAAACATA
Found at i:451085 original size:56 final size:56
Alignment explanation
Indices: 451002--451130 Score: 127
Period size: 56 Copynumber: 2.3 Consensus size: 56
450992 TGGAATTCAG
* * *
451002 TATT-TATATGGCCACCCCCTCAACCAATCA-AATTGCTTGCACACTTTTATCTTTT
1 TATTCTATTTGGCCACCCACTCAACCAATCACAATT-CATGCACACTTTTATCTTTT
* * * ** *
451057 TATTCTATTTGGCCACCCACTTAGCCAATTACAATTCATGCATTCTTTTATTTTTT
1 TATTCTATTTGGCCACCCACTCAACCAATCACAATTCATGCACACTTTTATCTTTT
* *
451113 TCATGCTATTTGGTCACC
1 T-ATTCTATTTGGCCACC
451131 TTGCCAACCT
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
55 4 0.07
56 38 0.63
57 18 0.30
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (56 bp):
TATTCTATTTGGCCACCCACTCAACCAATCACAATTCATGCACACTTTTATCTTTT
Found at i:480486 original size:16 final size:17
Alignment explanation
Indices: 480465--480497 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
480455 TAGTAAATAA
480465 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
480481 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
480498 CTAATTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:480504 original size:17 final size:18
Alignment explanation
Indices: 480471--480504 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
480461 ATAATTAATT
*
480471 AAAACTAAATTTAATTAG
1 AAAACTAAATCTAATTAG
480489 AAAACTAAA-CTAATTA
1 AAAACTAAATCTAATTA
480505 ATGAATACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACTAAATCTAATTAG
Found at i:507980 original size:28 final size:28
Alignment explanation
Indices: 507896--508109 Score: 207
Period size: 28 Copynumber: 7.5 Consensus size: 28
507886 GACAGCTTTT
* *
507896 ACATGCTTGTCTAAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* *
507924 ACACTTTTTGTCTTAATTTAGAAAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* *
507953 ACATGTTTATCTTAATTTAGACACGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
* * *
507981 ATATAG--TGTCTTAATATAGACAAGGAA
1 ACAT-GTTTGTCTTAATTTAGACAAGAAA
*
508008 ACATGTTTGTCTTAATGTAAGACAAGAAAA
1 ACATGTTTGTCTTAAT-TTAGACAAG-AAA
* * *
508038 ATATGACTTGTCTTAATTTAGATAAGAAA
1 ACATG-TTTGTCTTAATTTAGACAAGAAA
* * *
508067 ACATATTTGTCTAAATTTAGACAAGATA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
*
508095 ACATATTTTGTCTTA
1 ACAT-GTTTGTCTTA
508110 CCTAAAGACA
Statistics
Matches: 149, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.01
27 20 0.13
28 59 0.40
29 46 0.31
30 13 0.09
31 10 0.07
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:508014 original size:55 final size:58
Alignment explanation
Indices: 507932--508092 Score: 202
Period size: 55 Copynumber: 2.8 Consensus size: 58
507922 AAACACTTTT
* *
507932 TGTCTTAATTTAGAAAAGAAAACATGTTTATCTTAATTTAGACACG-AAAATAT-A-G
1 TGTCTTAATTTAGAAAAGAAAACATGTTTGTCTTAATTTAGACAAGAAAAATATGACG
* * * * *
507987 TGTCTTAATATAGACAAGGAAACATGTTTGTCTTAATGTAAGACAAGAAAAATATGACT
1 TGTCTTAATTTAGAAAAGAAAACATGTTTGTCTTAAT-TTAGACAAGAAAAATATGACG
* * *
508046 TGTCTTAATTTAGATAAGAAAACATATTTGTCTAAATTTAGACAAGA
1 TGTCTTAATTTAGAAAAGAAAACATGTTTGTCTTAATTTAGACAAGA
508093 TAACATATTT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
55 33 0.37
56 7 0.08
57 7 0.08
58 10 0.11
59 32 0.36
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (58 bp):
TGTCTTAATTTAGAAAAGAAAACATGTTTGTCTTAATTTAGACAAGAAAAATATGACG
Found at i:514932 original size:29 final size:29
Alignment explanation
Indices: 514895--515133 Score: 263
Period size: 29 Copynumber: 8.3 Consensus size: 29
514885 TTTTACTTGG
*
514895 TTGTCTTAATTTAGACAAAAAAACATGTT
1 TTGTCTTAATTTAGACAAGAAAACATGTT
* *
514924 TTGCCTTAATTTAGACAAGAAAAGATGTT
1 TTGTCTTAATTTAGACAAGAAAACATGTT
* *
514953 TTGTCTTAATTT-GTATAGGAAAACATG-T
1 TTGTCTTAATTTAG-ACAAGAAAACATGTT
* *
514981 TTGTCTTACA-TTAAACAAGAAAAGATGTT
1 TTGTCTTA-ATTTAGACAAGAAAACATGTT
* * *
515010 TTGTCCTAATTTAGGCAAGAAAACATGTC
1 TTGTCTTAATTTAGACAAGAAAACATGTT
* *
515039 TTGTCTTAATTTAGATAAGAAAGCATG-T
1 TTGTCTTAATTTAGACAAGAAAACATGTT
* * *
515067 TTGGCTTAATTTAAGACAAGAATACAT-AT
1 TTGTCTTAATTT-AGACAAGAAAACATGTT
* *
515096 TTGTCTCAATTTAGACAAGATAACATGTT
1 TTGTCTTAATTTAGACAAGAAAACATGTT
515125 TTGTCTTAA
1 TTGTCTTAA
515134 CTAAAGACAA
Statistics
Matches: 171, Mismatches: 31, Indels: 16
0.78 0.14 0.07
Matches are distributed among these distances:
28 46 0.27
29 125 0.73
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (29 bp):
TTGTCTTAATTTAGACAAGAAAACATGTT
Found at i:515020 original size:57 final size:56
Alignment explanation
Indices: 514895--515129 Score: 208
Period size: 57 Copynumber: 4.1 Consensus size: 56
514885 TTTTACTTGG
* * * *
514895 TTGTCTTAATTTAGACAAAAAAACATGTTTTGCCTTAATTTAGACAAGAAAAGATGTT
1 TTGTCCTAATTTAG-CAAGAAAACATG-TTTGTCTTAATTTAAACAAGAAAAGATGTT
* *
514953 TTGTCTTAATTT-GTATAGGAAAACATGTTTGTCTTACA-TTAAACAAGAAAAGATGTT
1 TTGTCCTAATTTAGCA-A-GAAAACATGTTTGTCTTA-ATTTAAACAAGAAAAGATGTT
* *
515010 TTGTCCTAATTTAGGCAAGAAAACATGTCTTGTCTTAATTTAGATAAG-AAAGCATG-T
1 TTGTCCTAATTTA-GCAAGAAAACATGT-TTGTCTTAATTTAAACAAGAAAAG-ATGTT
* * * * * * * *
515067 TTGGCTTAATTTAAGACAAGAATACATATTTGTCTCAATTTAGACAAGATAACATGTT
1 TTGTCCTAATTT-AG-CAAGAAAACATGTTTGTCTTAATTTAAACAAGAAAAGATGTT
515125 TTGTC
1 TTGTC
515130 TTAACTAAAG
Statistics
Matches: 148, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
56 1 0.01
57 86 0.58
58 59 0.40
59 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (56 bp):
TTGTCCTAATTTAGCAAGAAAACATGTTTGTCTTAATTTAAACAAGAAAAGATGTT
Found at i:515043 original size:86 final size:86
Alignment explanation
Indices: 514895--515133 Score: 290
Period size: 86 Copynumber: 2.8 Consensus size: 86
514885 TTTTACTTGG
* * *
514895 TTGTCTTAATTTAGACAAAAAAACATGTTTTG-CCTTAATTTAGACAAGAAAAGATGTTTTGTCT
1 TTGTCTTAATTTAAACAAGAAAACATGTTTTGTCC-TAATTTAGACAAGAAAACATGTTTTGTCT
*
514959 TAATTT-GTATAGGAAAACATGT
65 TAATTTAG-ATAAGAAAACATGT
* * *
514981 TTGTCTTACA-TTAAACAAGAAAAGATGTTTTGTCCTAATTTAGGCAAGAAAACATGTCTTGTCT
1 TTGTCTTA-ATTTAAACAAGAAAACATGTTTTGTCCTAATTTAGACAAGAAAACATGTTTTGTCT
*
515045 TAATTTAGATAAGAAAGCATGT
65 TAATTTAGATAAGAAAACATGT
* * * *
515067 TTGGCTTAATTTAAGACAAGAATACAT-ATTTGT-CTCAATTTAGACAAGATAACATGTTTTGTC
1 TTGTCTTAATTTAA-ACAAGAAAACATGTTTTGTCCT-AATTTAGACAAGAAAACATGTTTTGTC
515130 TTAA
64 TTAA
515134 CTAAAGACAA
Statistics
Matches: 132, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
85 3 0.02
86 115 0.87
87 14 0.11
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (86 bp):
TTGTCTTAATTTAAACAAGAAAACATGTTTTGTCCTAATTTAGACAAGAAAACATGTTTTGTCTT
AATTTAGATAAGAAAACATGT
Found at i:529758 original size:28 final size:28
Alignment explanation
Indices: 529726--529990 Score: 243
Period size: 28 Copynumber: 9.4 Consensus size: 28
529716 AACCTTTTAA
*
529726 ATGTTTGTCTTAATTTAGAGAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAC
* *
529754 ATGTTATGTGTTAATTTAGACTAGAAAAC
1 ATGTT-TGTCTTAATTTAGACAAGAAAAC
** * *
529783 ATGTTTGTCCGAATTTAGCCAAG--AAT
1 ATGTTTGTCTTAATTTAGACAAGAAAAC
*
529809 ATGTTTTGTCTTAATTTAGATAAGAAAAC
1 ATG-TTTGTCTTAATTTAGACAAGAAAAC
* * *
529838 AT-TATGCCTTAATTTAGAGAAGAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAC
* *
529865 ATAGTTT-CCTTAATTTAGATAAGAAAAC
1 AT-GTTTGTCTTAATTTAGACAAGAAAAC
* *
529893 ATGTATGTCTTAATTTAGACAATAAAAAC
1 ATGTTTGTCTTAATTTAGACAA-GAAAAC
* * *
529922 ATGTATGCCTTAATTTCATACAAGAAAA-
1 ATGTTTGTCTTAATTT-AGACAAGAAAAC
* *
529950 ATAGGCTTTTTCTTAATGTAGACAAGAAAAC
1 AT--G-TTTGTCTTAATTTAGACAAGAAAAC
529981 ATGTTTGTCT
1 ATGTTTGTCT
529991 CCCGATGGTA
Statistics
Matches: 192, Mismatches: 32, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.03
27 43 0.22
28 61 0.32
29 56 0.29
30 16 0.08
31 11 0.06
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAC
Found at i:529877 original size:55 final size:57
Alignment explanation
Indices: 529818--529937 Score: 174
Period size: 55 Copynumber: 2.1 Consensus size: 57
529808 TATGTTTTGT
* * *
529818 CTTAATTTAGATAAGAAAACAT-TATGCCTTAATTTAGAGAA-GAAAACATAGT-TTC
1 CTTAATTTAGATAAGAAAACATGTATGCCTTAATTTAGACAATAAAAACAT-GTATGC
*
529873 CTTAATTTAGATAAGAAAACATGTATGTCTTAATTTAGACAATAAAAACATGTATGC
1 CTTAATTTAGATAAGAAAACATGTATGCCTTAATTTAGACAATAAAAACATGTATGC
529930 CTTAATTT
1 CTTAATTT
529938 CATACAAGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
55 22 0.38
56 19 0.33
57 17 0.29
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (57 bp):
CTTAATTTAGATAAGAAAACATGTATGCCTTAATTTAGACAATAAAAACATGTATGC
Found at i:530294 original size:63 final size:63
Alignment explanation
Indices: 530195--530320 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 63
530185 ATAGCACTAG
* * * *
530195 AGTATTCTCAGACAGGTGGCATCAAAGCAATGCAAGCGAGAATCACAAGCAGGACTAATACCA
1 AGTATTCTCAGACACGTGACATCAAAGCAATACAAGCAAGAATCACAAGCAGGACTAATACCA
** *
530258 AGTATTCTCAGACACGTGACATCAAAGCACA-ACAAGCAAGAATCACGGGTAGGACTAATACCA
1 AGTATTCTCAGACACGTGACATCAAAGCA-ATACAAGCAAGAATCACAAGCAGGACTAATACCA
530321 CCATCCCTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 54 0.98
64 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (63 bp):
AGTATTCTCAGACACGTGACATCAAAGCAATACAAGCAAGAATCACAAGCAGGACTAATACCA
Found at i:532443 original size:11 final size:11
Alignment explanation
Indices: 532415--532455 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
532405 CCTTTCTCCA
*
532415 TTTCTCTCTTTG
1 TTTCTCT-TTTC
532427 TTTCTCTTTTC
1 TTTCTCTTTTC
532438 TTTCTCTTTTC
1 TTTCTCTTTTC
*
532449 TTCCTCT
1 TTTCTCT
532456 CAGGTGAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 20 0.74
12 7 0.26
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTCTCTTTTC
Found at i:538759 original size:65 final size:65
Alignment explanation
Indices: 538655--538785 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
538645 ATATAGGCAT
* * *
538655 GATGGCCTCATTGCAAATTTGTGTTCCATTAGAGGGATGATTTTCAAACGTTGATTTAACTAGAG
1 GATGGCCTCATTGCAAATTTGTGTTCCATTAGAGGGATGAATTCCAAACATTGATTTAACTAGAG
* ** * *
538720 GATGGCCTCATTGCAAATTTTTGTTCTGTTTA-AGGGATGAATTCCAAATATTGATTTAACTTGA
1 GATGGCCTCATTGCAAATTTGTGTTC-CATTAGAGGGATGAATTCCAAACATTGATTTAACTAGA
538784 G
65 G
538785 G
1 G
538786 TTGAATGGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 54 0.95
66 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (65 bp):
GATGGCCTCATTGCAAATTTGTGTTCCATTAGAGGGATGAATTCCAAACATTGATTTAACTAGAG
Found at i:547096 original size:29 final size:29
Alignment explanation
Indices: 546915--547205 Score: 239
Period size: 29 Copynumber: 10.0 Consensus size: 29
546905 TTAAGACAAC
* * *
546915 TCTTGTCTTTAATTAAGACAAAATATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
* * * *
546945 TGTTCTCTAAATTGAGAC-AAATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* ** *
546973 TCTTGTCTAGATTAAGACAAGGCATATTGT
1 TCTTGTCTAAATTAAGACAAAACATGTT-T
* ** * *
547003 TCTTATCTTAAATTAAG-GTAAACGTATATT
1 TCTTGTC-TAAATTAAGACAAAACATGT-TT
* * ** *
547033 CCTTATCTTAAATTTCGAC-AAACATATTT
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
* *
547062 TCTTGTCTAAATTAAGATAAAATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* *
547091 TTTTGTCTAAATTACGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
547120 TCTTGTCTAAATTAAGACAAAACATGTTA
1 TCTTGTCTAAATTAAGACAAAACATGTTT
*
547149 ACTTGTCTAAATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* *
547178 TTTTGTCTAAATTATA-ACAAAATATGTT
1 TCTTGTCTAAATTA-AGACAAAACATGTT
547206 GAAGCAACCA
Statistics
Matches: 210, Mismatches: 44, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
28 31 0.15
29 130 0.62
30 40 0.19
31 9 0.04
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:549183 original size:16 final size:16
Alignment explanation
Indices: 549162--549201 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
549152 CTTGTTCTTA
*
549162 TGATCCTTTATAATTT
1 TGATCCCTTATAATTT
549178 TGATCCCTTATAATTT
1 TGATCCCTTATAATTT
549194 TGATCCCT
1 TGATCCCT
549202 AGAACATAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (16 bp):
TGATCCCTTATAATTT
Found at i:575195 original size:3 final size:3
Alignment explanation
Indices: 575189--575231 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
575179 ATTCATGTAG
575189 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
575232 GAAGCCACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:575492 original size:23 final size:23
Alignment explanation
Indices: 575464--575511 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
575454 AATCCAAGGC
*
575464 TAAAAAAATTAATTTTCTA-AAAAT
1 TAAAAAAA-TAAATTT-TAGAAAAT
575488 TAAAAAAATAAATTTTAGAAAAT
1 TAAAAAAATAAATTTTAGAAAAT
575511 T
1 T
575512 TTTAAGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 2 0.09
23 12 0.55
24 8 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAAAATAAATTTTAGAAAAT
Found at i:575509 original size:24 final size:24
Alignment explanation
Indices: 575464--575509 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
575454 AATCCAAGGC
* **
575464 TAAAAAAATTAATTTTCTAAAAAT
1 TAAAAAAATAAATTTTAGAAAAAT
575488 TAAAAAAATAAATTTTAGAAAA
1 TAAAAAAATAAATTTTAGAAAA
575510 TTTTTAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAAAAATAAATTTTAGAAAAAT
Found at i:577239 original size:28 final size:28
Alignment explanation
Indices: 577185--577461 Score: 295
Period size: 28 Copynumber: 9.6 Consensus size: 28
577175 TCTTGCCTTT
* * *
577185 AATTAAGACAAAGCATGTTATGTTATCTA
1 AATTAAGACAAA-CATGTTTTCTTGTCTA
** * *
577214 AATTGGGACAAATATGTTTTCTTATCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* *
577242 GATTAAGACAAAACATATTTTTCTTGTCTTA
1 AATTAAGAC-AAACAT-GTTTTCTTGTC-TA
* **
577273 AATTAAGATAAACA-AATTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* **
577300 AATTAAGACAAAACATATTTTCTCATCTA
1 AATTAAGAC-AAACATGTTTTCTTGTCTA
* * *
577329 AATTAAGACAAGCTTGTTTTCTAGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
577357 AATTAAGACAAACATGTTTTCTTTGTCTA
1 AATTAAGACAAACATGTTTTC-TTGTCTA
577386 AATTAAGACAAAACATGTTTTCTTGTCTA
1 AATTAAGAC-AAACATGTTTTCTTGTCTA
* *
577415 AATTAAGAGAAACATATTTTCTTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
577443 AATTAAGACAAAACATGTT
1 AATTAAGAC-AAACATGTT
577462 AAAGCTGCCA
Statistics
Matches: 209, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.05
28 92 0.44
29 72 0.34
30 26 0.12
31 9 0.04
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:577310 original size:86 final size:87
Alignment explanation
Indices: 577210--577454 Score: 304
Period size: 86 Copynumber: 2.9 Consensus size: 87
577200 TGTTATGTTA
** * *
577210 TCTAAATTGGGAC-AAATATGTTTTCTTATCTAGATTAAGACAAAACATATTTTTCTTGTCTTAA
1 TCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAGAC-AAACATATTTTTCTTGTC-TAA
*
577274 ATTAAGATAAACA-AATTTC-TTG
64 ATTAAGACAAACATAATTTCTTTG
* * * *
577296 TCTAAATTAAGACAAAACATATTTTCTCATCTAAATTAAGACAAGC-T-TGTTTTCTAGTCTAAA
1 TCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAGACAAACATAT-TTTTCTTGTCTAAA
**
577359 TTAAGACAAACATGTTTTCTTTG
65 TTAAGACAAACATAATTTCTTTG
* *
577382 TCTAAATTAAGACAAAACATGTTTTCTTGTCTAAATTAAGAGAAACATA-TTTTCTTGTCTAAAT
1 TCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAGACAAACATATTTTTCTTGTCTAAAT
577446 TAAGACAAA
66 TAAGACAAA
577455 ACATGTTAAA
Statistics
Matches: 136, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
84 16 0.12
85 14 0.10
86 81 0.60
87 25 0.18
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (87 bp):
TCTAAATTAAGACAAAACATGTTTTCTTATCTAAATTAAGACAAACATATTTTTCTTGTCTAAAT
TAAGACAAACATAATTTCTTTG
Found at i:577358 original size:57 final size:56
Alignment explanation
Indices: 577185--577454 Score: 267
Period size: 57 Copynumber: 4.7 Consensus size: 56
577175 TCTTGCCTTT
* * * * * ** *
577185 AATTAAGACAAAGCATGTTATGTTATCTAAATTGGGACAAATATGTTTTCTTA-TCTA
1 AATTAAGACAAAACATATTTTCTTGTCTAAATTAAGACAAA-CTGTTTTC-TAGTCTA
* * *** *
577242 GATTAAGACAAAACATATTTTTCTTGTCTTAAATTAAGATAAACAAATTTCTTGTCTA
1 AATTAAGACAAAACATA-TTTTCTTGTC-TAAATTAAGACAAACTGTTTTCTAGTCTA
** *
577300 AATTAAGACAAAACATATTTTCTCATCTAAATTAAGACAAGCTTGTTTTCTAGTCTA
1 AATTAAGACAAAACATATTTTCTTGTCTAAATTAAGACAAAC-TGTTTTCTAGTCTA
* *
577357 AATTAAGAC-AAACATGTTTTCTTTGTCTAAATTAAGACAAAACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATATTTTC-TTGTCTAAATTAAGAC-AAAC-TGTTTTCTAGTCTA
*
577415 AATTAAGA-GAAACATATTTTCTTGTCTAAATTAAGACAAA
1 AATTAAGACAAAACATATTTTCTTGTCTAAATTAAGACAAA
577455 ACATGTTAAA
Statistics
Matches: 176, Mismatches: 30, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
56 27 0.15
57 72 0.41
58 66 0.38
59 11 0.06
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (56 bp):
AATTAAGACAAAACATATTTTCTTGTCTAAATTAAGACAAACTGTTTTCTAGTCTA
Found at i:579875 original size:24 final size:24
Alignment explanation
Indices: 579847--579894 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
579837 AGGAGAGTAT
* *
579847 GAAAGGGGGAAAGAA-AGAAAGGAA
1 GAAAGGAGG-AAGAAGAAAAAGGAA
579871 GAAAGGAGGAAGAAGAAAAAGGAA
1 GAAAGGAGGAAGAAGAAAAAGGAA
579895 AAGAAAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (24 bp):
GAAAGGAGGAAGAAGAAAAAGGAA
Found at i:580214 original size:22 final size:22
Alignment explanation
Indices: 580169--580214 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
580159 TTGTGGCAGC
580169 AATGGTGACTATGAATGTGAGGA
1 AATGGTGACTAT-AATGTGAGGA
*
580192 AATGGTGAACTAT-ATGTGTGGA
1 AATGGTG-ACTATAATGTGAGGA
580214 A
1 A
580215 CTCAAGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.28
Consensus pattern (22 bp):
AATGGTGACTATAATGTGAGGA
Found at i:582425 original size:67 final size:67
Alignment explanation
Indices: 582317--582449 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
582307 TTTTACAGTA
* *
582317 GCTTTTCATAGGCTCAGCCACAACCTTTAACAATAGTTTTTCACAAGATTAACCAAAACCCAAAA
1 GCTTTTCAAAGGCTCAGCCACAACCTTTAACAATAGTTTTTCACAAGATCAACCAAAACCCAAAA
582382 TG
66 TG
* * *
582384 GCTTTTCAAAGGCTCCA-CCACAACCTTTAACAATGGTTTTTCTCAAGATCAACCAAAATCCAAA
1 GCTTTTCAAAGGCT-CAGCCACAACCTTTAACAATAGTTTTTCACAAGATCAACCAAAACCCAAA
582448 AT
65 AT
582450 CTAACTTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 58 0.97
68 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (67 bp):
GCTTTTCAAAGGCTCAGCCACAACCTTTAACAATAGTTTTTCACAAGATCAACCAAAACCCAAAA
TG
Found at i:605478 original size:35 final size:35
Alignment explanation
Indices: 605451--605635 Score: 259
Period size: 35 Copynumber: 5.3 Consensus size: 35
605441 TTAATTGTTT
605451 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
605486 AATTTAATTAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
605521 AATTTGATCAATTAAGCCTAATAACTTGATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
605556 AAATTTAATCAATTAGGCCCAATAACATAATTAAAC
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* *
605592 AATTTAATGAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
605624 AATTTTAATCAA
1 AA-TTTAATCAA
605636 GTGTTTCAGA
Statistics
Matches: 133, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
32 15 0.11
33 9 0.07
35 79 0.59
36 30 0.23
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:605516 original size:18 final size:18
Alignment explanation
Indices: 605460--605517 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
605450 TAATTTAATC
605460 AATTAGGCCCAATAACTT
1 AATTAGGCCCAATAACTT
**
605478 AATTA--AACAATTTAA-TT
1 AATTAGGCCCAA--TAACTT
605495 AATTAGGCCCAATAACTT
1 AATTAGGCCCAATAACTT
605513 AATTA
1 AATTA
605518 AACAATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
16 3 0.10
17 10 0.32
18 15 0.48
19 3 0.10
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.33
Consensus pattern (18 bp):
AATTAGGCCCAATAACTT
Found at i:605574 original size:71 final size:70
Alignment explanation
Indices: 605451--605635 Score: 250
Period size: 71 Copynumber: 2.7 Consensus size: 70
605441 TTAATTGTTT
* * *
605451 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATTAATTAGGCCCAATAACTTAA
1 AATTTAATCAATTAAG-CCAATAACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACATAA
605515 TTAAAC
65 TTAAAC
* *
605521 AATTTGATCAATTAAGCCTAATAACTTGATTAAACAAATTTAATCAATTAGGCCCAATAACATAA
1 AATTTAATCAATTAAGCC-AATAACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACATAA
605586 TTAAAC
65 TTAAAC
* * * *
605592 AATTTAATGAATT-AGGC-ACAACTTAATTAAACAATTTTAATCAA
1 AATTTAATCAATTAAGCCAATAACTTAATTAAACAAATTTAATCAA
605636 GTGTTTCAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
68 24 0.24
69 2 0.02
70 32 0.31
71 44 0.43
ACGTcount: A:0.46, C:0.15, G:0.06, T:0.32
Consensus pattern (70 bp):
AATTTAATCAATTAAGCCAATAACTTAATTAAACAAATTTAATCAATTAGGCCCAATAACATAAT
TAAAC
Found at i:611730 original size:77 final size:77
Alignment explanation
Indices: 611602--611765 Score: 220
Period size: 77 Copynumber: 2.1 Consensus size: 77
611592 AATGCCATCT
** ** * * *
611602 ATTTTAATTTTGGGTGATTCATTAAGAATAGGTAATTGTTTCCCACTTTAAAAGCAATTCCTAAA
1 ATTTTAATTTTGGGTGATTCACAAAGAATAGAAAATTATTTCCCACCTTAAAAGAAATTCCTAAA
611667 ATTAACGATAGA
66 ATTAACGATAGA
*
611679 ATTTTAATTTTGGGTGATTCACAAAGAATAGAAAATTATTTCCTACCTTAAAAGAAATTCCTAAA
1 ATTTTAATTTTGGGTGATTCACAAAGAATAGAAAATTATTTCCCACCTTAAAAGAAATTCCTAAA
** *
611744 ATTAGGGATAGT
66 ATTAACGATAGA
*
611756 ACTTTAATTT
1 ATTTTAATTT
611766 GTGAAATTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (77 bp):
ATTTTAATTTTGGGTGATTCACAAAGAATAGAAAATTATTTCCCACCTTAAAAGAAATTCCTAAA
ATTAACGATAGA
Found at i:612085 original size:7 final size:7
Alignment explanation
Indices: 612066--612105 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
612056 TGACTTTTCA
612066 TTTAGGTG
1 TTTAGG-G
612074 TTTAGGG
1 TTTAGGG
612081 TTTAGGG
1 TTTAGGG
*
612088 TTTAAGG
1 TTTAGGG
*
612095 TTTGGGG
1 TTTAGGG
612102 TTTA
1 TTTA
612106 CTTTAAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:622346 original size:19 final size:19
Alignment explanation
Indices: 622299--622353 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
622289 GAGAACAGTG
*
622299 ATAAATAAAAAGAATATTTT
1 ATAAAT-AAAATAATATTTT
* *
622319 -GAAACAAAATAATATTTT
1 ATAAATAAAATAATATTTT
*
622337 ATAAATAAAATATTATT
1 ATAAATAAAATAATATT
622354 AAAATATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (19 bp):
ATAAATAAAATAATATTTT
Found at i:622350 original size:16 final size:17
Alignment explanation
Indices: 622329--622371 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
622319 GAAACAAAAT
622329 AATATTTTATAAATA-A
1 AATATTTTATAAATATA
*
622345 AATATTATTA-AAATATT
1 AATATT-TTATAAATATA
622362 AATATTTTAT
1 AATATTTTAT
622372 TTATTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTTATAAATATA
Found at i:630292 original size:33 final size:33
Alignment explanation
Indices: 630250--630322 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
630240 TTATATTATC
* * *
630250 ATAAGATATTAATATATTACG-TCATCATTAATT
1 ATAACATATTAACATATTACGTTC-TCATCAATT
*
630283 ATAACATATTAGCATATTACGTTCTCATCAATT
1 ATAACATATTAACATATTACGTTCTCATCAATT
*
630316 ATGACAT
1 ATAACAT
630323 GTCGATTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (33 bp):
ATAACATATTAACATATTACGTTCTCATCAATT
Found at i:630407 original size:30 final size:30
Alignment explanation
Indices: 630373--630509 Score: 115
Period size: 30 Copynumber: 4.7 Consensus size: 30
630363 CAACTATTAG
* *
630373 ATATAATAGTTTATTTGATTTAAAATAAAA
1 ATATAAAAGTTTATTTAATTTAAAATAAAA
*
630403 ATATAAAAATTTATTTAATTTAAAATAAAA
1 ATATAAAAGTTTATTTAATTTAAAATAAAA
* * * **
630433 ATATAAGAGTTCGATTGAACGT--AATAAAA
1 ATATAAAAGTT-TATTTAATTTAAAATAAAA
* *
630462 AT-TAAAAATTTATTTAACTT--AATAAAA
1 ATATAAAAGTTTATTTAATTTAAAATAAAA
*
630489 AT-TAAAAATTTATTTACATTT
1 ATATAAAAGTTTATTTA-ATTT
630510 TTTTAAATAT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
27 30 0.33
28 9 0.10
29 9 0.10
30 36 0.40
31 6 0.07
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (30 bp):
ATATAAAAGTTTATTTAATTTAAAATAAAA
Found at i:630489 original size:27 final size:28
Alignment explanation
Indices: 630396--630504 Score: 123
Period size: 27 Copynumber: 3.9 Consensus size: 28
630386 TTTGATTTAA
*
630396 AATAAAAATATAAAAATTTATTTAATTT
1 AATAAAAATATAAAAATTTATTTAACTT
* * * * *
630424 AAAATAAAAATATAAGAGTTCGATTGAACGT
1 --AATAAAAATATAAAAATT-TATTTAACTT
630455 AATAAAAAT-TAAAAATTTATTTAACTT
1 AATAAAAATATAAAAATTTATTTAACTT
630482 AATAAAAAT-TAAAAATTTATTTA
1 AATAAAAATATAAAAATTTATTTA
630505 CATTTTTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
27 30 0.45
28 6 0.09
29 9 0.13
30 16 0.24
31 6 0.09
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.37
Consensus pattern (28 bp):
AATAAAAATATAAAAATTTATTTAACTT
Found at i:637560 original size:14 final size:14
Alignment explanation
Indices: 637541--637570 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
637531 CTTAGAATAA
*
637541 AATAAAATTTTATT
1 AATAAAATATTATT
637555 AATAAAATATTATT
1 AATAAAATATTATT
637569 AA
1 AA
637571 AATATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAAATATTATT
Found at i:637571 original size:11 final size:11
Alignment explanation
Indices: 637551--637580 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
637541 AATAAAATTT
637551 TATTAATAAAA
1 TATTAATAAAA
*
637562 TATTATTAAAA
1 TATTAATAAAA
637573 TATTAATA
1 TATTAATA
637581 TTTTAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:638702 original size:15 final size:15
Alignment explanation
Indices: 638672--638718 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
638662 GAATTGGCTT
638672 GGAAGCAAAGAGAGAAA
1 GGAAG-AAA-AGAGAAA
638689 GGAAGAAAAGAGAAA
1 GGAAGAAAAGAGAAA
* *
638704 GAAAGAAAGGAGAAA
1 GGAAGAAAAGAGAAA
638719 AAAGAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 20 0.71
16 3 0.11
17 5 0.18
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (15 bp):
GGAAGAAAAGAGAAA
Found at i:638704 original size:23 final size:22
Alignment explanation
Indices: 638678--638725 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
638668 GCTTGGAAGC
* *
638678 AAAGAGAGAAAGGAAGAAAAGAG
1 AAAGAAAGAAAGG-AGAAAAAAG
638701 AAAGAAAGAAAGGAGAAAAAAG
1 AAAGAAAGAAAGGAGAAAAAAG
638723 AAA
1 AAA
638726 AAGATATGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAGGAGAAAAAAG
Found at i:638722 original size:14 final size:15
Alignment explanation
Indices: 638682--638726 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
638672 GGAAGCAAAG
*
638682 AGAGAAAGGAAGAAA
1 AGAGAAAGAAAGAAA
638697 AGAGAAAGAAAGAAA
1 AGAGAAAGAAAGAAA
*
638712 GGAGAAA-AAAGAAA
1 AGAGAAAGAAAGAAA
638726 A
1 A
638727 AGATATGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AGAGAAAGAAAGAAA
Found at i:639568 original size:2 final size:2
Alignment explanation
Indices: 639526--639556 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
639516 TGTCTTGACC
*
639526 AT AT AT AC 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 A
639557 CAAGCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:642184 original size:20 final size:20
Alignment explanation
Indices: 642159--642233 Score: 150
Period size: 20 Copynumber: 3.8 Consensus size: 20
642149 AACCTGTAAG
642159 AATGTATCGATACATTTATA
1 AATGTATCGATACATTTATA
642179 AATGTATCGATACATTTATA
1 AATGTATCGATACATTTATA
642199 AATGTATCGATACATTTATA
1 AATGTATCGATACATTTATA
642219 AATGTATCGATACAT
1 AATGTATCGATACAT
642234 GCTTGTAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTATA
Found at i:642778 original size:11 final size:10
Alignment explanation
Indices: 642751--642783 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
642741 AACTAAGAGG
642751 GTATATATAT
1 GTATATATAT
*
642761 CTATATA-AT
1 GTATATATAT
642770 GTATATATAT
1 GTATATATAT
642780 GTAT
1 GTAT
642784 CAATGTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (10 bp):
GTATATATAT
Found at i:643538 original size:73 final size:73
Alignment explanation
Indices: 643461--643632 Score: 211
Period size: 73 Copynumber: 2.4 Consensus size: 73
643451 ATTCTCTGTC
* * *
643461 GGTTGCTTTGGCACTGAGCATGATTTGCTT-TCCATCAACTACTTTAGCATCACGCGTGTTTTGT
1 GGTTGCTTTGGCACTGAGCATGATTTG-TTCTCCACCAAATACTTTAGCATCACGCGTGGTTTGT
643525 TTCTCCATT
65 TTCTCCATT
* * ** * * * **
643534 GGTTGCTTTAGCATTGAGGGTGATTTGTTCTTCACCAAATGCTTTGGCATCGTGCGTGGTTTGTT
1 GGTTGCTTTGGCACTGAGCATGATTTGTTCTCCACCAAATACTTTAGCATCACGCGTGGTTTGTT
643599 TCTCCATT
66 TCTCCATT
*
643607 GGTTGCTTTGGCACTGTGCATGATTT
1 GGTTGCTTTGGCACTGAGCATGATTT
643633 ATTTCTCTAT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
72 2 0.02
73 79 0.98
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.42
Consensus pattern (73 bp):
GGTTGCTTTGGCACTGAGCATGATTTGTTCTCCACCAAATACTTTAGCATCACGCGTGGTTTGTT
TCTCCATT
Found at i:643561 original size:37 final size:37
Alignment explanation
Indices: 643502--643615 Score: 97
Period size: 37 Copynumber: 3.1 Consensus size: 37
643492 CCATCAACTA
*
643502 CTTTAGCATC-ACGCGTGTTTTGTTTCTCCATTGGTTG
1 CTTTAGCATCGA-GCGTGATTTGTTTCTCCATTGGTTG
* * * *****
643539 CTTTAGCATTGAGGGTGATTTG-TTCTTCACCAAATG
1 CTTTAGCATCGAGCGTGATTTGTTTCTCCATTGGTTG
* * *
643575 CTTTGGCATCGTGCGTGGTTTGTTTCTCCATTGGTTG
1 CTTTAGCATCGAGCGTGATTTGTTTCTCCATTGGTTG
643612 CTTT
1 CTTT
643616 GGCACTGTGC
Statistics
Matches: 55, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
36 25 0.45
37 29 0.53
38 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (37 bp):
CTTTAGCATCGAGCGTGATTTGTTTCTCCATTGGTTG
Found at i:643616 original size:37 final size:37
Alignment explanation
Indices: 643514--643619 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 37
643504 TTAGCATCAC
* * *
643514 GCGTGTTTTGTTTCTCCATTGGTTGCTTTAGCATTGA
1 GCGTGATTTGTTTCTCCATTGGTTGCTTTGGCATCGA
* * ***** *
643551 GGGTGATTTG-TTCTTCACCAAATGCTTTGGCATCGT
1 GCGTGATTTGTTTCTCCATTGGTTGCTTTGGCATCGA
*
643587 GCGTGGTTTGTTTCTCCATTGGTTGCTTTGGCA
1 GCGTGATTTGTTTCTCCATTGGTTGCTTTGGCA
643620 CTGTGCATGA
Statistics
Matches: 49, Mismatches: 19, Indels: 2
0.70 0.27 0.03
Matches are distributed among these distances:
36 25 0.51
37 24 0.49
ACGTcount: A:0.11, C:0.18, G:0.26, T:0.44
Consensus pattern (37 bp):
GCGTGATTTGTTTCTCCATTGGTTGCTTTGGCATCGA
Found at i:643649 original size:37 final size:37
Alignment explanation
Indices: 643573--643651 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
643563 CTTCACCAAA
* * * **
643573 TGCTTTGGCATCGTGCGTGGTTTGTTTCTCCATTGGT
1 TGCTTTGGCATCGTGCATGATTTATTTCTCCATCAGT
*
643610 TGCTTTGGCA-CTGTGCATGATTTATTTCTCTATCAGT
1 TGCTTTGGCATC-GTGCATGATTTATTTCTCCATCAGT
643647 TGCTT
1 TGCTT
643652 CGACACTGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (37 bp):
TGCTTTGGCATCGTGCATGATTTATTTCTCCATCAGT
Found at i:646441 original size:18 final size:18
Alignment explanation
Indices: 646418--646452 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
646408 TTGAACCTAG
646418 TTTGAAATGCT-GGAAATT
1 TTTGAAA-GCTAGGAAATT
646436 TTTGAAAGCTAGGAAAT
1 TTTGAAAGCTAGGAAAT
646453 AATTATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (18 bp):
TTTGAAAGCTAGGAAATT
Found at i:649239 original size:29 final size:29
Alignment explanation
Indices: 649173--649240 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
649163 TTTCCTGTCT
*
649173 TAAATTAAGA-CAAACATATTTTCTTATC
1 TAAATTAAGACCAAACACATTTTCTTATC
* * *
649201 TAAGTAAAGACCAAACACGTTTTCTTATC
1 TAAATTAAGACCAAACACATTTTCTTATC
649230 TAAATTAAGAC
1 TAAATTAAGAC
649241 AAATATGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTAAGACCAAACACATTTTCTTATC
Found at i:649651 original size:19 final size:18
Alignment explanation
Indices: 649614--649656 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
649604 AGACAAGTGA
649614 AATATTTTAAAATAAAAT
1 AATATTTTAAAATAAAAT
649632 AATATTTTATTAAA-AAAAT
1 AATATTTTA--AAATAAAAT
649651 AATATT
1 AATATT
649657 AAAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTTTAAAATAAAAT
Found at i:652036 original size:18 final size:18
Alignment explanation
Indices: 652010--652046 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
652000 GTAGTGGGCA
652010 AAAAGAATATTTTTAAAT
1 AAAAGAATATTTTTAAAT
* *
652028 AAAATAATATTTTTTAAT
1 AAAAGAATATTTTTAAAT
652046 A
1 A
652047 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAAAGAATATTTTTAAAT
Found at i:657203 original size:14 final size:14
Alignment explanation
Indices: 657184--657219 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
657174 ATCACATATG
657184 AAATATTTATTTTA
1 AAATATTTATTTTA
657198 AAATATTTATTTTA
1 AAATATTTATTTTA
657212 AAATATTT
1 AAATATTT
657220 CTTTCACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AAATATTTATTTTA
Found at i:657734 original size:8 final size:8
Alignment explanation
Indices: 657673--657735 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
657663 AGATTTGCTT
657673 AGGAAGCAA
1 AGGAAG-AA
657682 AGGAAGAA
1 AGGAAGAA
*
657690 AGAAAGAA
1 AGGAAGAA
657698 AGG-AGAA
1 AGGAAGAA
*
657705 AAGAAGCAA
1 AGGAAG-AA
*
657714 AGAAAGAA
1 AGGAAGAA
*
657722 GGGAAGAA
1 AGGAAGAA
657730 AGGAAG
1 AGGAAG
657736 GTTCGGCCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
7 6 0.14
8 26 0.59
9 12 0.27
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (8 bp):
AGGAAGAA
Found at i:661028 original size:12 final size:12
Alignment explanation
Indices: 660992--661028 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
660982 TTTGGGGAAA
660992 ATGTATCGATAC
1 ATGTATCGATAC
661004 AT-TAT-GA-AC
1 ATGTATCGATAC
661013 ATGTATCGATAC
1 ATGTATCGATAC
661025 ATGT
1 ATGT
661029 TCATCAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:662180 original size:21 final size:21
Alignment explanation
Indices: 662137--662184 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
662127 CTCTTAAAGT
*
662137 AAATTAAAATAAAATGACCTA
1 AAATTAAAATAAAATAACCTA
* * *
662158 AAATTTAATTAAAATAA-CTT
1 AAATTAAAATAAAATAACCTA
662178 AAATTAA
1 AAATTAA
662185 TCACTTAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATTAAAATAAAATAACCTA
Found at i:667746 original size:62 final size:63
Alignment explanation
Indices: 667667--667794 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 63
667657 TCGAAAAAAA
* * * * *
667667 AAACAGTCGGTGCAAAAGTAGCTGACAAAAGATAATGGGTC-AACAGTATCTGTCCCACCGAC
1 AAACAGTCGGTCCAAAAGCAGCTGACAAAAGATAATGAGTCAAAAAGTATCTGTCCCAACGAC
* * * *
667729 AAACAGTTGGTCCAAAAGCAGCTGACAAAAGATGATGAGTCAAAAAGTATTTGTCTCAACGAC
1 AAACAGTCGGTCCAAAAGCAGCTGACAAAAGATAATGAGTCAAAAAGTATCTGTCCCAACGAC
667792 AAA
1 AAA
667795 ATCAAATGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
62 36 0.64
63 20 0.36
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.19
Consensus pattern (63 bp):
AAACAGTCGGTCCAAAAGCAGCTGACAAAAGATAATGAGTCAAAAAGTATCTGTCCCAACGAC
Found at i:668638 original size:37 final size:37
Alignment explanation
Indices: 668551--668638 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
668541 TTCGGCATCG
*
668551 TGTGTGATTTGACCCTCAGCTAGTTACTTTGGCACTA
1 TGTGTGATTTGACTCTCAGCTAGTTACTTTGGCACTA
* * * * * * *
668588 TGTATGATTTGACTCTCCGTTGGTTGCTTTTGCATTA
1 TGTGTGATTTGACTCTCAGCTAGTTACTTTGGCACTA
668625 TGTGTGATTTGACT
1 TGTGTGATTTGACT
668639 TCGTCGACTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.44
Consensus pattern (37 bp):
TGTGTGATTTGACTCTCAGCTAGTTACTTTGGCACTA
Found at i:681478 original size:21 final size:22
Alignment explanation
Indices: 681453--681496 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
681443 AAGTGATTAA
681453 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
681474 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
681496 T
1 T
681497 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:689387 original size:20 final size:21
Alignment explanation
Indices: 689340--689407 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 21
689330 TTTAGCTTAA
* *
689340 TTTATGTTTA-AATCTTTA-T
1 TTTATGTTAATAATGTTTAGT
*
689359 TTTAAGTTAATAATG-TTAGT
1 TTTATGTTAATAATGTTTAGT
* * *
689379 TTTATGTTACTTATGTTTATT
1 TTTATGTTAATAATGTTTAGT
689400 TTTATGTT
1 TTTATGTT
689408 TTTGTAGGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 11 0.28
20 16 0.41
21 12 0.31
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTATGTTAATAATGTTTAGT
Found at i:695552 original size:17 final size:18
Alignment explanation
Indices: 695520--695553 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
695510 GGAACCTGGC
*
695520 TTGAAATGCTAGAAAATT
1 TTGAAATGCTAAAAAATT
695538 TTGAAA-GCTAAAAAAT
1 TTGAAATGCTAAAAAAT
695554 ATTTATATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (18 bp):
TTGAAATGCTAAAAAATT
Found at i:705094 original size:24 final size:24
Alignment explanation
Indices: 705058--705111 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
705048 ACTTGTACCC
*
705058 TTTTAACTCTCCATGTACTTAAGA
1 TTTTTACTCTCCATGTACTTAAGA
* *
705082 TTTTTACTTTCCATTTACTTAAGA
1 TTTTTACTCTCCATGTACTTAAGA
*
705106 TATTTA
1 TTTTTA
705112 ATGTAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (24 bp):
TTTTTACTCTCCATGTACTTAAGA
Found at i:707857 original size:21 final size:21
Alignment explanation
Indices: 707828--707874 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
707818 AAATGAGTTT
*
707828 TTGAAGAACAAGTATCAATAC
1 TTGAAGAACAAATATCAATAC
* **
707849 TTGATGAACAAATATTGATAC
1 TTGAAGAACAAATATCAATAC
707870 TTGAA
1 TTGAA
707875 ACCCAAAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (21 bp):
TTGAAGAACAAATATCAATAC
Found at i:710595 original size:67 final size:68
Alignment explanation
Indices: 710459--710615 Score: 196
Period size: 67 Copynumber: 2.4 Consensus size: 68
710449 TGGTATGATA
* * * *
710459 AATGCCATAAGATTGTGTATATGACAAAAATTCCATATGCCATATGAGATGATTAAGTATTCATG
1 AATGCCATAAGATTGTGTATATGACAAAAATTCCATATACCATACGAGATGATTAAGTATACATA
710524 ATG
66 ATG
*** *
710527 AATGCCATAAGATTGTGTATATGATGTAAA-TCGATATACCATACGAGATGATTAAGTATACATA
1 AATGCCATAAGATTGTGTATATGACAAAAATTCCATATACCATACGAGATGATTAAGTATACATA
710591 ATG
66 ATG
*
710594 AACTG---TAAGATTGTTTATATGA
1 AA-TGCCATAAGATTGTGTATATGA
710616 GGCATGATGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 16 0.20
67 34 0.43
68 29 0.37
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (68 bp):
AATGCCATAAGATTGTGTATATGACAAAAATTCCATATACCATACGAGATGATTAAGTATACATA
ATG
Found at i:712129 original size:14 final size:12
Alignment explanation
Indices: 712108--712146 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
712098 ATAGCTTTTC
712108 TTCTTTCTTCTCT
1 TTCTTTCTTCT-T
712121 TTCCTTTC-TCTT
1 TT-CTTTCTTCTT
712133 TTCTTTCTTCTT
1 TTCTTTCTTCTT
712145 TT
1 TT
712147 TGCTTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.21
12 9 0.38
13 5 0.21
14 5 0.21
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
TTCTTTCTTCTT
Found at i:712152 original size:14 final size:13
Alignment explanation
Indices: 712108--712153 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
712098 ATAGCTTTTC
712108 TTCTTTCTTCTCTT
1 TTCTTTCTTCT-TT
*
712122 TCCTTTC-TC-TT
1 TTCTTTCTTCTTT
712133 TTCTTTCTTCTTT
1 TTCTTTCTTCTTT
712146 TTGCTTTC
1 TT-CTTTC
712154 AAAACTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.30
12 2 0.07
13 6 0.22
14 11 0.41
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (13 bp):
TTCTTTCTTCTTT
Found at i:712280 original size:14 final size:14
Alignment explanation
Indices: 712243--712282 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
712233 ATCTCATTGG
*
712243 ACCAATTTGTCATCC
1 ACCAATTT-TCATAC
712258 ACTCAATTTTCATAC
1 AC-CAATTTTCATAC
712273 ACCAATTTTC
1 ACCAATTTTC
712283 TCCCTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 9 0.39
16 6 0.26
ACGTcount: A:0.30, C:0.30, G:0.03, T:0.38
Consensus pattern (14 bp):
ACCAATTTTCATAC
Found at i:728037 original size:4 final size:4
Alignment explanation
Indices: 728030--728063 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
728020 CCCTTCCTTC
728030 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
728064 CCCCTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:732127 original size:36 final size:34
Alignment explanation
Indices: 732100--732196 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 34
732090 TTTCATGAGC
*
732100 TCAAGAGATAACCTTTACACTTGCTTTTTCAAGA
1 TCAAGAGATAACCTTTACACTAGCTTTTTCAAGA
* * * * *
732134 TCAAGCGATAACCCTAACACTAGCTTATTAACCAGA
1 TCAAGAGATAACCTTTACACTAGCTT-TT-TCAAGA
*
732170 TCAAGAGATAA-CTTTCACACTAACTTT
1 TCAAGAGATAACCTTT-ACACTAGCTTT
732197 CAAGGTTAAG
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
34 22 0.44
35 5 0.10
36 23 0.46
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (34 bp):
TCAAGAGATAACCTTTACACTAGCTTTTTCAAGA
Found at i:732144 original size:34 final size:36
Alignment explanation
Indices: 732100--732191 Score: 100
Period size: 34 Copynumber: 2.6 Consensus size: 36
732090 TTTCATGAGC
* *
732100 TCAAGAGATAACCTTTACACTTGCTT-TT-TCAAGA
1 TCAAGAGATAACCTTTACACTAGCTTATTAACAAGA
* * * *
732134 TCAAGCGATAACCCTAACACTAGCTTATTAACCAGA
1 TCAAGAGATAACCTTTACACTAGCTTATTAACAAGA
732170 TCAAGAGATAA-CTTTCACACTA
1 TCAAGAGATAACCTTT-ACACTA
732192 ACTTTCAAGG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
34 22 0.48
35 4 0.09
36 20 0.43
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (36 bp):
TCAAGAGATAACCTTTACACTAGCTTATTAACAAGA
Found at i:735189 original size:15 final size:14
Alignment explanation
Indices: 735169--735234 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 14
735159 TAGGCCAAAC
*
735169 CTTCTTTGTCTTTTT
1 CTTCTTTCTC-TTTT
735184 CTTCTTTCTCTTTT
1 CTTCTTTCTCTTTT
735198 CTTTCTTTCTCTTTT
1 C-TTCTTTCTCTTTT
735213 CTTCCTTTCTCTCTTT
1 CTT-CTTTCTCT-TTT
735229 GCTTCT
1 -CTTCT
735235 AAGCTGATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 7 0.15
15 31 0.67
16 5 0.11
17 3 0.07
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (14 bp):
CTTCTTTCTCTTTT
Found at i:757410 original size:5 final size:5
Alignment explanation
Indices: 757400--757440 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
757390 CTTAAAGAAG
*
757400 ATGAA ATGAA ATGTAA ATTGAA ATGAA ATGAA AGGAA ATGA
1 ATGAA ATGAA ATG-AA A-TGAA ATGAA ATGAA ATGAA ATGA
757441 TGCCATTTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 24 0.75
6 6 0.19
7 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (5 bp):
ATGAA
Found at i:759051 original size:27 final size:25
Alignment explanation
Indices: 759007--759063 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
758997 ATGTGGCTGG
759007 GGCCATAGTCTGTGATATACGTGGCAA
1 GGCCATAGTCTGTGATAT--GTGGCAA
* *
759034 GGCCATAGGT-TGTTATATGTGGCTA
1 GGCCATA-GTCTGTGATATGTGGCAA
759059 GGCCA
1 GGCCA
759064 CAAGTGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.41
27 14 0.52
28 2 0.07
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (25 bp):
GGCCATAGTCTGTGATATGTGGCAA
Found at i:771971 original size:77 final size:77
Alignment explanation
Indices: 771844--772006 Score: 213
Period size: 77 Copynumber: 2.1 Consensus size: 77
771834 TGAATTTCTC
* * * * *
771844 AAATTAAAATACTATCCTTAATTTTATAAATTTCTTTCAAAGTAGGAAACAATTTCCTATTCTTT
1 AAATTAAAATACTATCCGTAATATTAGAAATTACTTTCAAAGTAAGAAACAATTTCCTATT-TTT
771909 T-GGAATCACCCA
65 TAGGAATCACCCA
* * *
771921 AAATTAAAAT-CTTATCCGTAATATTAGGAATTACTTTTAAAGTAAGAAACAATTTCTTATTTTT
1 AAATTAAAATAC-TATCCGTAATATTAGAAATTACTTTCAAAGTAAGAAACAATTTCCTATTTTT
*
771985 TATGAATCACCCA
65 TAGGAATCACCCA
771998 AAATTAAAA
1 AAATTAAAA
772007 AAGATGGCAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 5 0.07
77 70 0.93
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (77 bp):
AAATTAAAATACTATCCGTAATATTAGAAATTACTTTCAAAGTAAGAAACAATTTCCTATTTTTT
AGGAATCACCCA
Found at i:774406 original size:40 final size:40
Alignment explanation
Indices: 774362--774446 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
774352 TTTAACCTTG
*
774362 AAAAGGTAGCGATGTTGTAAAGTTATGCTTACTGCTCTTA
1 AAAAGCTAGCGATGTTGTAAAGTTATGCTTACTGCTCTTA
* * * * * * *
774402 AAAAGCTAGTGATGTTGTGAGGTTGTGCTTGCTTCTCTTG
1 AAAAGCTAGCGATGTTGTAAAGTTATGCTTACTGCTCTTA
774442 AAAAG
1 AAAAG
774447 TAGTGTGAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (40 bp):
AAAAGCTAGCGATGTTGTAAAGTTATGCTTACTGCTCTTA
Found at i:775197 original size:36 final size:35
Alignment explanation
Indices: 775157--775332 Score: 126
Period size: 36 Copynumber: 4.9 Consensus size: 35
775147 GGATTCATGA
* *
775157 TTTTTAATGGGATCAAGTGATAACCCTTT-CATCGGC
1 TTTTTTATGGGATCAAGTGATAA-CCTTTACA-CTGC
** ** *
775193 TTTTTTACAGGATCAAGCAATAACCTTTACACCTAC
1 TTTTTTATGGGATCAAGTGATAACCTTTACA-CTGC
*
775229 TTTTTTATGGGATCAAGTGATAACTTTTACACTTGC
1 TTTTTTATGGGATCAAGTGATAACCTTTACAC-TGC
* * *
775265 -TTTTCATGAGATCAAGTGATAACCCTT-CAACTAG-
1 TTTTTTATGGGATCAAGTGATAACCTTTAC-ACT-GC
* * * *
775299 TTTTTTAATGAGATTAAGTGACAACCTTCACACT
1 TTTTTT-ATGGGATCAAGTGATAACCTTTACACT
775333 AACTTTTCAA
Statistics
Matches: 110, Mismatches: 23, Indels: 14
0.75 0.16 0.10
Matches are distributed among these distances:
34 2 0.02
35 36 0.33
36 71 0.65
37 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (35 bp):
TTTTTTATGGGATCAAGTGATAACCTTTACACTGC
Found at i:800944 original size:160 final size:161
Alignment explanation
Indices: 800761--801056 Score: 468
Period size: 160 Copynumber: 1.8 Consensus size: 161
800751 TGGGTAACAG
* * *
800761 ATTAGTTCTCCAATGTAAAGAAGCAAGAATACCTACCTTGGAATGATTAATTATATCCTTCAATA
1 ATTAGATCTCCAAGGTAAAGAAGCAAGAATACCTACCTTGGAACGATTAATTATATCCTTCAATA
* *
800826 TCTTATTTAAT-CACGATCCATGTGTAGATCACCATCGGCACACAAAGGACCGTCATGAAGCACA
66 TCTTATTTAATGCACGACCCATGTGTAGATCACCATCGGCACACAAAGGACCATCATGAAGCACA
800890 AAATTTATAAATCTAAGTTCACGGATAGCAA
131 AAATTTATAAATCTAAGTTCACGGATAGCAA
* *
800921 ATTAGATCTCCAAGGTCAAGAAGCAAGAATACCTACCTTGTAACGATTAATTATATCCTTCAATA
1 ATTAGATCTCCAAGGTAAAGAAGCAAGAATACCTACCTTGGAACGATTAATTATATCCTTCAATA
* * * ***
800986 TCTTATTTAATGCATGACCCATGTGTAGATCACCATTGGCATATGGAGGACCATCATGAAGCACA
66 TCTTATTTAATGCACGACCCATGTGTAGATCACCATCGGCACACAAAGGACCATCATGAAGCACA
801051 AAATTT
131 AAATTT
801057 CCCTGTAAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
160 71 0.58
161 51 0.42
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (161 bp):
ATTAGATCTCCAAGGTAAAGAAGCAAGAATACCTACCTTGGAACGATTAATTATATCCTTCAATA
TCTTATTTAATGCACGACCCATGTGTAGATCACCATCGGCACACAAAGGACCATCATGAAGCACA
AAATTTATAAATCTAAGTTCACGGATAGCAA
Found at i:803285 original size:23 final size:24
Alignment explanation
Indices: 803230--803290 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
803220 CATTTTCCTT
*
803230 TTTTTTCTTTTTGCACTAATTTTTC
1 TTTTTT-TTTTTGCACTAATTTTTA
803255 TTTGTTTTTTTT-C-CTAATTTTTA
1 TTT-TTTTTTTTGCACTAATTTTTA
* *
803278 ATTTTTTTATTGC
1 TTTTTTTTTTTGC
803291 TAACTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 7 0.23
23 12 0.39
24 1 0.03
25 8 0.26
26 3 0.10
ACGTcount: A:0.13, C:0.11, G:0.05, T:0.70
Consensus pattern (24 bp):
TTTTTTTTTTTGCACTAATTTTTA
Found at i:808259 original size:22 final size:22
Alignment explanation
Indices: 808237--808302 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
808227 TTCTTCCTCT
808237 TTTCTTCCTTT-CTCTCCTTTC
1 TTTCTTCCTTTCCTCTCCTTTC
*
808258 TTTCTTCTTTTCCTCTCCTTTC
1 TTTCTTCCTTTCCTCTCCTTTC
*
808280 TTTCTTCCTTTCCTCTTCTTTC
1 TTTCTTCCTTTCCTCTCCTTTC
808302 T
1 T
808303 CTTTTTCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 10 0.24
22 31 0.76
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTCTTCCTTTCCTCTCCTTTC
Found at i:808266 original size:44 final size:41
Alignment explanation
Indices: 808218--808310 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 41
808208 AACCTTTCCT
*
808218 TTCTTTTTCTTCTTCCTCT-TTTCTTCCTTTCTCTCCTTTCTTTC
1 TTCTTTTTCCTC-TCCTCTCTTTCTTCCTTTC-CT-C-TTCTTTC
*
808262 TTC-TTTTCCTCTCCTTTCTTTCTTCCTTTCCTCTTCTTTC
1 TTCTTTTTCCTCTCCTCTCTTTCTTCCTTTCCTCTTCTTTC
808302 -TCTTTTTCC
1 TTCTTTTTCC
808311 CTTGGTAGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
39 2 0.04
40 13 0.29
41 1 0.02
42 7 0.16
43 19 0.42
44 3 0.07
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (41 bp):
TTCTTTTTCCTCTCCTCTCTTTCTTCCTTTCCTCTTCTTTC
Found at i:808271 original size:17 final size:17
Alignment explanation
Indices: 808212--808300 Score: 60
Period size: 17 Copynumber: 5.1 Consensus size: 17
808202 TAAGCCAACC
808212 TTTCCTTTCTTT-TTCT
1 TTTCCTTTCTTTCTTCT
*
808228 TCTTCCTCT-TTTCTTCCTT
1 T-TTCCTTTCTTTCTT-C-T
808247 TCTCTCCTTTCTTTCTTCT
1 T-T-TCCTTTCTTTCTTCT
*
808266 TTTCCTCTCCTTTCTT-T
1 TTTCCT-TTCTTTCTTCT
* *
808283 CTTCCTTTC-CTCTTCT
1 TTTCCTTTCTTTCTTCT
808299 TT
1 TT
808301 CTCTTTTTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
15 4 0.07
16 8 0.14
17 18 0.31
18 10 0.17
19 6 0.10
20 6 0.10
21 6 0.10
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCCTTTCTTTCTTCT
Found at i:819920 original size:14 final size:14
Alignment explanation
Indices: 819898--819936 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
819888 CTTAAATGAA
819898 ATATATATACATAT
1 ATATATATACATAT
*
819912 ATATTTATACATAT
1 ATATATATACATAT
* *
819926 GTATGTATACA
1 ATATATATACA
819937 ACTGCCTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:821697 original size:15 final size:15
Alignment explanation
Indices: 821673--821709 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
821663 ACTAACATTT
821673 ATTTTCGGAACAATGA
1 ATTTT-GGAACAATGA
*
821689 ATTTTGGAATAATGA
1 ATTTTGGAACAATGA
821704 ATTTTG
1 ATTTTG
821710 AAATTTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (15 bp):
ATTTTGGAACAATGA
Found at i:821719 original size:15 final size:15
Alignment explanation
Indices: 821684--821713 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
821674 TTTTCGGAAC
*
821684 AATGAATTTTGGAAT
1 AATGAATTTTGAAAT
821699 AATGAATTTTGAAAT
1 AATGAATTTTGAAAT
821714 TTTGAAAATG
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:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (15 bp):
AATGAATTTTGAAAT
Found at i:832900 original size:8 final size:8
Alignment explanation
Indices: 832887--832913 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
832877 TAGGTTTTGA
832887 TTTAAAGG
1 TTTAAAGG
832895 TTTAAAGG
1 TTTAAAGG
832903 TTTAAAGG
1 TTTAAAGG
832911 TTT
1 TTT
832914 GCATTCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (8 bp):
TTTAAAGG
Found at i:835139 original size:20 final size:20
Alignment explanation
Indices: 835101--835139 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
835091 AGCCTTTGTC
*
835101 TTTCAAGAATTGATATCTTT
1 TTTCAAGAATTAATATCTTT
835121 TTTCATAGAATTAAT-TCTT
1 TTTCA-AGAATTAATATCTT
835140 CCTCTAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTCAAGAATTAATATCTTT
Found at i:837420 original size:36 final size:36
Alignment explanation
Indices: 837373--837469 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
837363 TATTAACTTA
837373 CCTTTTCAACAAAATCAGGCATAACCTTTACAACATG
1 CCTTTT-AACAAAATCAGGCATAACCTTTACAACATG
* **
837410 CCTTTTAACAAAATCAAGTGTAACCTTTACAACATG
1 CCTTTTAACAAAATCAGGCATAACCTTTACAACATG
** * *
837446 CCTTTTCGCAAGATTAGGCATAAC
1 CCTTTTAACAAAATCAGGCATAAC
837470 ATCACCAAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 44 0.88
37 6 0.12
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (36 bp):
CCTTTTAACAAAATCAGGCATAACCTTTACAACATG
Found at i:839489 original size:26 final size:22
Alignment explanation
Indices: 839469--839513 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
839459 GCTTGAGTTG
839469 TTTATTTCAATCTTGTTCTTGA
1 TTTATTTCAATCTTGTTCTTGA
*
839491 TTTGTTTCAATCTTGTTCTTGA
1 TTTATTTCAATCTTGTTCTTGA
839513 T
1 T
839514 GCGTCTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.60
Consensus pattern (22 bp):
TTTATTTCAATCTTGTTCTTGA
Found at i:841699 original size:62 final size:61
Alignment explanation
Indices: 841514--841701 Score: 205
Period size: 62 Copynumber: 3.0 Consensus size: 61
841504 CCAAGCAAAT
** * * * *
841514 TTCTACTAACTTACAGCATAATCATCAATAATTTCAACATACTTATCATTAAGGAAACAAAA
1 TTCTACTAACCCACA-CATAATCATCAAGAATTTCTACATACTTATCATTAAGCAAACAACA
* * **** * *
841576 TTATACTAACCCAAACCATAATCATCAAGAATTTCTACATACTTATTGGCAATCAAGCAACA
1 TTCTACTAACCCACA-CATAATCATCAAGAATTTCTACATACTTATCATTAAGCAAACAACA
**
841638 TTCTACTAACCCACACAATAATCATCAAGAATTTCTACATACCCATCATTAAGCAAACAACA
1 TTCTACTAACCCACAC-ATAATCATCAAGAATTTCTACATACTTATCATTAAGCAAACAACA
841700 TT
1 TT
841702 AACCCATTTA
Statistics
Matches: 100, Mismatches: 25, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
61 1 0.01
62 99 0.99
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.28
Consensus pattern (61 bp):
TTCTACTAACCCACACATAATCATCAAGAATTTCTACATACTTATCATTAAGCAAACAACA
Found at i:841857 original size:16 final size:16
Alignment explanation
Indices: 841818--841858 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
841808 CTATGTTGAA
*
841818 AACATGAAGGATGTAG
1 AACATGATGGATGTAG
*
841834 AACATGATGGATGTGG
1 AACATGATGGATGTAG
841850 AACATGATG
1 AACATGATG
841859 CAAACTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.22
Consensus pattern (16 bp):
AACATGATGGATGTAG
Found at i:845815 original size:57 final size:57
Alignment explanation
Indices: 845716--845883 Score: 205
Period size: 57 Copynumber: 2.9 Consensus size: 57
845706 TTAAGACAAC
* * * * * **
845716 TCTTGTCTTTAATTAGGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTC-TAAATTAAGACTAAAATATTTT-TCTTGTCTAAATTAAGACAAACATAATT
*
845775 TCTTGTCTAGATTAAGA-TAAAATATTTTTCTTGTCTTAAATTAAGACAAACATAATT
1 TCTTGTCTAAATTAAGACTAAAATATTTTTCTTGTC-TAAATTAAGACAAACATAATT
*
845832 TCTTGTCTAAATTAAGACTAAACAT-GTTTTCTTGTCTAAATTAAGACAAACA
1 TCTTGTCTAAATTAAGACTAAA-ATATTTTTCTTGTCTAAATTAAGACAAACA
845884 GATTAAAGAT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
56 7 0.07
57 59 0.61
58 21 0.22
59 9 0.09
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (57 bp):
TCTTGTCTAAATTAAGACTAAAATATTTTTCTTGTCTAAATTAAGACAAACATAATT
Found at i:845878 original size:29 final size:28
Alignment explanation
Indices: 845747--845883 Score: 177
Period size: 29 Copynumber: 4.8 Consensus size: 28
845737 AAATATTTTA
* *
845747 TCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTCTAAATTAAGACAAACATGTTT
* * *
845775 TCTTGTCTAGATTAAGATAAA-ATATTTT
1 TCTTGTCTAAATTAAGACAAACAT-GTTT
**
845803 TCTTGTCTTAAATTAAGACAAACATAATT
1 TCTTGTC-TAAATTAAGACAAACATGTTT
845832 TCTTGTCTAAATTAAGACTAAACATGTTT
1 TCTTGTCTAAATTAAGAC-AAACATGTTT
845861 TCTTGTCTAAATTAAGACAAACA
1 TCTTGTCTAAATTAAGACAAACA
845884 GATTAAAGAT
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
27 2 0.02
28 44 0.46
29 47 0.49
30 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATGTTT
Found at i:850480 original size:10 final size:10
Alignment explanation
Indices: 850461--850492 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
850451 TATCCTAGAA
850461 AAAT-ATAAT
1 AAATAATAAT
850470 AAATAATAAT
1 AAATAATAAT
850480 AAATAATAA-
1 AAATAATAAT
850489 AAAT
1 AAAT
850493 TACAACTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAATAAT
Found at i:850729 original size:18 final size:19
Alignment explanation
Indices: 850698--850737 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
850688 ATCCAAGAAT
*
850698 AAAATAAATTAATTTTCCA
1 AAAATAAATAAATTTTCCA
*
850717 AAAAT-AATAAATTTTGCA
1 AAAATAAATAAATTTTCCA
850735 AAA
1 AAA
850738 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATAAATAAATTTTCCA
Found at i:859406 original size:36 final size:35
Alignment explanation
Indices: 859308--859468 Score: 171
Period size: 36 Copynumber: 4.5 Consensus size: 35
859298 AATTGTTTAG
* * *
859308 TTTAATCAATTAAGCCCAATAACTTAATTAAATGA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAATAA
* * * *
859343 TTTAATTAATT-GAGCCCAATAATTTAATTAAGTAA
1 TTTAATCAATTAG-GCCCAATGACTTAATTAAATAA
*** *
859378 TTTTAATCAATTAGGTGTAATGACTTAATTAAACAAA
1 -TTTAATCAATTAGGCCCAATGACTTAATTAAA-TAA
*
859415 TTTAATCAACTAGGCCCAATGACTTAATTAAATAA
1 TTTAATCAATTAGGCCCAATGACTTAATTAAATAA
*
859450 TTTAATTAATTAGGCCCAA
1 TTTAATCAATTAGGCCCAA
859469 NNNNNNNNNN
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
35 48 0.47
36 51 0.50
37 3 0.03
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (35 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAATAA
Found at i:867189 original size:35 final size:35
Alignment explanation
Indices: 867150--867292 Score: 126
Period size: 35 Copynumber: 4.1 Consensus size: 35
867140 AATTAATGCA
867150 GCCCAATAACTTAATTAAACAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAACAATTTAATCAATTAG
* *
867185 GCCCAATAACTTGATTAAACAAATGTAATCAATTAG
1 GCCCAATAACTTAATTAAAC-AATTTAATCAATTAG
** * **** *
867221 GCTAAATAAATTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAACAATTTAATCAATTAG
* * * * *
867256 ACACAATGAA-TTAATTAAATAATATAATGAATTAG
1 GCCCAAT-AACTTAATTAAACAATTTAATCAATTAG
867291 GC
1 GC
867293 ACAACTTCTT
Statistics
Matches: 85, Mismatches: 21, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
35 57 0.67
36 28 0.33
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAACAATTTAATCAATTAG
Found at i:867221 original size:36 final size:35
Alignment explanation
Indices: 867150--867236 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 35
867140 AATTAATGCA
*
867150 GCCCAATAACTTAATTAAACAATTTAATCAATTAG
1 GCCCAATAACTTAATTAAACAATGTAATCAATTAG
*
867185 GCCCAATAACTTGATTAAACAAATGTAATCAATTAG
1 GCCCAATAACTTAATTAAAC-AATGTAATCAATTAG
** *
867221 GCTAAATAAATTAATT
1 GCCCAATAACTTAATT
867237 GTTTAATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
35 19 0.42
36 26 0.58
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAACAATGTAATCAATTAG
Found at i:873018 original size:20 final size:20
Alignment explanation
Indices: 872989--873042 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
872979 AAATTAGTGA
872989 TGAC-TCAAAATAAGACTTT
1 TGACTTCAAAATAAGACTTT
873008 TGACTTCAAAATAAGACTTT
1 TGACTTCAAAATAAGACTTT
*
873028 TGACTTGAAAATAAG
1 TGACTTCAAAATAAG
873043 CTCAAATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (20 bp):
TGACTTCAAAATAAGACTTT
Found at i:884744 original size:21 final size:21
Alignment explanation
Indices: 884716--884795 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
884706 TGTATTCTAT
884716 TTCA-AATGTATCGATACATA
1 TTCATAATGTATCGATACATA
*
884736 TTCATAATGTATCGATATATA
1 TTCATAATGTATCGATACATA
** * * *
884757 -TGGTCATGTATCCATACATG
1 TTCATAATGTATCGATACATA
*
884777 TTCATAATGTATTGATACA
1 TTCATAATGTATCGATACA
884796 ATTTTTGCAA
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 18 0.39
21 28 0.61
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (21 bp):
TTCATAATGTATCGATACATA
Found at i:889493 original size:29 final size:29
Alignment explanation
Indices: 889452--889508 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
889442 AAACATTTAT
* *
889452 AATATCTATAGTAACTAAACAAGATATAC
1 AATATCCAAAGTAACTAAACAAGATATAC
* *
889481 AATATCCAAAGTAGCTAAGCAAGATATA
1 AATATCCAAAGTAACTAAACAAGATATA
889509 TTGAATATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (29 bp):
AATATCCAAAGTAACTAAACAAGATATAC
Found at i:895080 original size:37 final size:37
Alignment explanation
Indices: 895030--895104 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
895020 GGCCTATATT
895030 TCTACTCATGCTACAAAGTGGGTGAACACTATGTTAC
1 TCTACTCATGCTACAAAGTGGGTGAACACTATGTTAC
895067 TCTACTCATGCTACAAAGTGGGTGAACACTATGTTAC
1 TCTACTCATGCTACAAAGTGGGTGAACACTATGTTAC
895104 T
1 T
895105 TAATGAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (37 bp):
TCTACTCATGCTACAAAGTGGGTGAACACTATGTTAC
Found at i:896117 original size:35 final size:35
Alignment explanation
Indices: 896091--896380 Score: 237
Period size: 35 Copynumber: 8.3 Consensus size: 35
896081 TAATGGATTG
* *
896091 ATTTAATTAATTAGGCCCAATAACTTAATTAAACA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
* ** *
896126 ATTTAATCAATTAGGCCTAATAACTTGGTTAAACAA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAAC-A
* ***
896162 ATTTAATCAATTAGACCCAATAACTTAATTG-TTTA
1 ATTTAATCAATTAGGCCCAATAACTTAA-TGAAACA
** * *
896197 ATTTAATCAATGGGGCCCAGTAACTTAATTAAACA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
* ** * *
896232 ATTTTATCAATTAGGAACAATAACTTGATTAAACAA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAAC-A
* *
896268 ATTTAATCAATTGGGCCCAATAACTTAATTAAACA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
* ** * * *
896303 ATTTAATTAATTAAACCCAATGACTTAATTAAATA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
* * * *
896338 ATTTTATGAATTAGG--C-ACAACTTAATTAAACA
1 ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
896370 ATTTTAATCAA
1 A-TTTAATCAA
896381 GTGCTTGAGA
Statistics
Matches: 203, Mismatches: 47, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
32 14 0.07
33 8 0.04
34 1 0.00
35 124 0.61
36 55 0.27
37 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (35 bp):
ATTTAATCAATTAGGCCCAATAACTTAATGAAACA
Found at i:896174 original size:71 final size:70
Alignment explanation
Indices: 896091--896380 Score: 309
Period size: 71 Copynumber: 4.1 Consensus size: 70
896081 TAATGGATTG
* * * **
896091 ATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGCCTAATAACTTGGTT
1 ATTTAATCAATTAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAATT
896156 AAACAA
66 AAAC-A
**** ** *
896162 ATTTAATCAATTAGACCCAATAACTTAATTGTTTAATTTAATCAATGGGGCCCAGTAACTTAATT
1 ATTTAATCAATTAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAATT
896227 AAACA
66 AAACA
* * * *
896232 ATTTTATCAATTAGGA-ACAATAACTTGATTAAACAAATTTAATCAATTGGGCCCAATAACTTAA
1 ATTTAATCAATTA-GACCCAATAACTTAATTAAAC-AATTTAATCAATTAGGCCCAATAACTTAA
896296 TTAAACA
64 TTAAACA
* * * * * * *
896303 ATTTAATTAATTAAACCCAATGACTTAATTAAATAATTTTATGAATTAGG--C-ACAACTTAATT
1 ATTTAATCAATTAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAATT
896365 AAACA
66 AAACA
896370 ATTTTAATCAA
1 A-TTTAATCAA
896381 GTGCTTGAGA
Statistics
Matches: 182, Mismatches: 33, Indels: 11
0.81 0.15 0.05
Matches are distributed among these distances:
67 16 0.09
68 9 0.05
70 39 0.21
71 118 0.65
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (70 bp):
ATTTAATCAATTAGACCCAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAATT
AAACA
Found at i:896188 original size:106 final size:105
Alignment explanation
Indices: 896070--896380 Score: 374
Period size: 106 Copynumber: 3.0 Consensus size: 105
896060 CCTTAAGAAG
* * *
896070 CCCAATTAACTTAATGGATTGATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTAATCA
1 CCCAA-TAACTTAATTGATTAATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTTATCA
*
896135 ATTAGGCCTAATAACTTGGTTAAACAAATTTAATCAATTAGA
65 ATTAGGCC-AATAACTTGATTAAACAAATTTAATCAATTAGA
* * ** *
896177 CCCAATAACTTAATTGTTTAATTTAATCAATGGGGCCCAGTAACTTAATTAAACAATTTTATCAA
1 CCCAATAACTTAATTGATTAATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTTATCAA
* * *
896242 TTAGGAACAATAACTTGATTAAACAAATTTAATCAATTGGG
66 TTAGG-CCAATAACTTGATTAAACAAATTTAATCAATTAGA
* ** ** * * *
896283 CCCAATAACTTAATTAAACAATTTAATTAATTAAACCCAATGACTTAATTAAATAATTTTATGAA
1 CCCAATAACTTAATTGATTAATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTTATCAA
* * *
896348 TTAGG-C-ACAACTTAATTAAACAATTTTAATCAA
66 TTAGGCCAATAACTTGATTAAACAAATTTAATCAA
896381 GTGCTTGAGA
Statistics
Matches: 175, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
103 24 0.14
104 1 0.01
106 144 0.82
107 6 0.03
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.34
Consensus pattern (105 bp):
CCCAATAACTTAATTGATTAATTTAATTAATTAGGCCCAATAACTTAATTAAACAATTTTATCAA
TTAGGCCAATAACTTGATTAAACAAATTTAATCAATTAGA
Found at i:897821 original size:67 final size:67
Alignment explanation
Indices: 897688--897826 Score: 154
Period size: 67 Copynumber: 2.1 Consensus size: 67
897678 CCCATAGATA
* * * * *
897688 GCATCACTCGAAGTATTCACCATGGGTGGCATCATAATCATCATCTGAGGCAATATCCCAATGGA
1 GCATCACTCGAAGTATTCACCATAGGTGGCATCACAATCATCATCTGAAGCAATACCCCAACGGA
897753 TG
66 TG
* * * * * * *
897755 GCATCACTTGGAGTATTCTCCATAGGTGGCATCACAGTCATCAT-TCGAAGTAATCCCCCGACGG
1 GCATCACTCGAAGTATTCACCATAGGTGGCATCACAATCATCATCT-GAAGCAATACCCCAACGG
897819 ATG
65 ATG
897822 GCATC
1 GCATC
897827 CTACACAACA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 1 0.02
67 58 0.98
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (67 bp):
GCATCACTCGAAGTATTCACCATAGGTGGCATCACAATCATCATCTGAAGCAATACCCCAACGGA
TG
Found at i:904725 original size:29 final size:30
Alignment explanation
Indices: 904681--904737 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
904671 GGCCAATGCT
904681 ATTATGTACCCCTAAATTTTT-CTTCACGA
1 ATTATGTACCCCTAAATTTTTGCTTCACGA
* *
904710 ATTATTTACCCTTAAATTTTTGCTTCAC
1 ATTATGTACCCCTAAATTTTTGCTTCAC
904738 AAGATAGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.46
Consensus pattern (30 bp):
ATTATGTACCCCTAAATTTTTGCTTCACGA
Found at i:905995 original size:68 final size:69
Alignment explanation
Indices: 905866--906001 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 69
905856 TTCAATGAAG
*
905866 GATAATGCTTGATGAAAATTAAAAATGCTAAATGATGCTTGATGATGTATGAAAATGATGCTTAA
1 GATAATGCTTGATGAAAATT-AAAATGCTAAATGATGCTTGATAATGTATGAAAATGATGCTTAA
905931 TGATT
65 TGATT
* * * * *
905936 GATAATGCTTGATGAAAATT-GAATGCTTAATGATGCTTGGTAATG-ATTAAGAATGATGCTTGA
1 GATAATGCTTGATGAAAATTAAAATGCTAAATGATGCTTGATAATGTATGAA-AATGATGCTTAA
905999 TGA
65 TGA
906002 CTAATGATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
67 4 0.07
68 35 0.59
70 20 0.34
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (69 bp):
GATAATGCTTGATGAAAATTAAAATGCTAAATGATGCTTGATAATGTATGAAAATGATGCTTAAT
GATT
Found at i:910801 original size:19 final size:18
Alignment explanation
Indices: 910765--910804 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
910755 CAAGTGGAGA
*
910765 ATTTTTTATTAAAATAAT
1 ATTTTTTAATAAAATAAT
*
910783 ATTTTATTAATAAACTAAT
1 ATTTT-TTAATAAAATAAT
910802 ATT
1 ATT
910805 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTTAATAAAATAAT
Found at i:914083 original size:28 final size:27
Alignment explanation
Indices: 914050--914190 Score: 111
Period size: 28 Copynumber: 4.9 Consensus size: 27
914040 TAATTAAGAT
914050 AAAAATATTTTATCTTGTCTAAATTGAG
1 AAAAATATTTT-TCTTGTCTAAATTGAG
* * *
914078 AAAAATACGTTTTCTTGTCTAGATTAAGACA
1 AAAAATA-TTTTTCTTGTCTAAATT--GA-G
* *
914109 AAAAATATTTTTCTTATCTTAAATTAAG
1 AAAAATATTTTTCTTGTC-TAAATTGAG
* *
914137 AAAAACATATTTTCTTGTCTAAATTAAG
1 AAAAATAT-TTTTCTTGTCTAAATTGAG
* * *
914165 ACCACACATGTTTTCTTGTCTAAATT
1 A-AAAATAT-TTTTCTTGTCTAAATT
914191 AAGACAAACA
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
28 36 0.39
29 34 0.37
30 11 0.12
31 12 0.13
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (27 bp):
AAAAATATTTTTCTTGTCTAAATTGAG
Found at i:914132 original size:59 final size:59
Alignment explanation
Indices: 914041--914200 Score: 166
Period size: 59 Copynumber: 2.8 Consensus size: 59
914031 AATTGTCTTT
* * * * *
914041 AATTAAGA-TAAAAATATTTTATCTTGTCTAAATTGAGAAAAATACGTTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTATCTAAATTAAGAAAAACACATTTTCTTGTCTA
* *
914099 GATTAAGACAAAAAATATTTT-TCTTATCTTAAATTAAGAAAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATATTTTATCTTATC-TAAATTAAGAAAAACACATTTTCTTGTCTA
* * * * * *
914158 AATTAAGACCACACAT-GTTT-TCTTGTCTAAATTAAGACAAACA
1 AATTAAGACAAAAAATATTTTATCTTATCTAAATTAAGAAAAACA
914201 TGTTAAAGTT
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
57 15 0.17
58 22 0.26
59 49 0.57
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (59 bp):
AATTAAGACAAAAAATATTTTATCTTATCTAAATTAAGAAAAACACATTTTCTTGTCTA
Found at i:914173 original size:29 final size:29
Alignment explanation
Indices: 914041--914198 Score: 160
Period size: 29 Copynumber: 5.4 Consensus size: 29
914031 AATTGTCTTT
*
914041 AATTAAGATAAAA-ATATTTTATCTTGTCTA
1 AATTAAGACAAAACATA-TTT-TCTTGTCTA
* * **
914071 AATTGAGA-AAAATACGTTTTCTTGTCTA
1 AATTAAGACAAAACATATTTTCTTGTCTA
* * *
914099 GATTAAGACAAAAAATATTTTTCTTATCTTA
1 AATTAAGACAAAACATA-TTTTCTTGTC-TA
914130 AATTAAGA-AAAACATATTTTCTTGTCTA
1 AATTAAGACAAAACATATTTTCTTGTCTA
* * *
914158 AATTAAGACCACACATGTTTTCTTGTCTA
1 AATTAAGACAAAACATATTTTCTTGTCTA
914187 AATTAAGACAAA
1 AATTAAGACAAA
914199 CATGTTAAAG
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 25 0.24
29 48 0.45
30 24 0.23
31 9 0.08
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (29 bp):
AATTAAGACAAAACATATTTTCTTGTCTA
Found at i:920509 original size:16 final size:17
Alignment explanation
Indices: 920485--920517 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
920475 AATTTTTAAG
*
920485 AATATATTTTTTAAAAA
1 AATATATTTATTAAAAA
920502 AATA-ATTTATTAAAAA
1 AATATATTTATTAAAAA
920518 GGTTTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATTTATTAAAAA
Found at i:920862 original size:34 final size:33
Alignment explanation
Indices: 920798--920868 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
920788 TAACAAAATT
* * *
920798 TTAATATAAGAAAAACTCTTTTTCTTAAAAAAG
1 TTAATACAAGAAAAACTCTTTTTCTAAAAAAAA
*
920831 TTAATACAAGAAAAATTCCTTTTTAC-AAAAAAAA
1 TTAATACAAGAAAAACT-CTTTTT-CTAAAAAAAA
920865 TTAA
1 TTAA
920869 AAATCGTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 15 0.47
34 16 0.50
35 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (33 bp):
TTAATACAAGAAAAACTCTTTTTCTAAAAAAAA
Found at i:921977 original size:12 final size:13
Alignment explanation
Indices: 921958--922005 Score: 66
Period size: 12 Copynumber: 3.9 Consensus size: 13
921948 CAGAATAGTT
921958 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
921971 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
*
921982 TCTTGCTGCC-CT
1 TCTTGCTGCCTCC
921994 TCTTGCTGCCTC
1 TCTTGCTGCCTC
922006 AAAAATCTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:922696 original size:21 final size:22
Alignment explanation
Indices: 922660--922702 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
922650 CTCTTAAAGT
922660 ATTTAAAATAAAATAACCTAAA
1 ATTTAAAATAAAATAACCTAAA
* *
922682 ATTTAAACT-AAATAACTTAAA
1 ATTTAAAATAAAATAACCTAAA
922703 TTAATCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
ATTTAAAATAAAATAACCTAAA
Found at i:926464 original size:12 final size:12
Alignment explanation
Indices: 926445--926492 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
926435 CAGAATAGTT
926445 TCTTGCTGCCTC
1 TCTTGCTGCCTC
926457 -CTTTGCTGCCTC
1 TC-TTGCTGCCTC
926469 TCTTGCTGCCTC
1 TCTTGCTGCCTC
926481 TCTTGCTGCCTC
1 TCTTGCTGCCTC
926493 AAAAATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:928328 original size:30 final size:29
Alignment explanation
Indices: 928289--928414 Score: 132
Period size: 28 Copynumber: 4.3 Consensus size: 29
928279 TATTATTTTT
*
928289 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAAAATATTTT-TCTTATCTA
*
928319 AATTGAGAC--AAATATGTTTTCTTATCTA
1 AATTAAGACAAAAATAT-TTTTCTTATCTA
* * *
928347 GATTAAGATAAAAAATATTTTTCTTCTCTTA
1 AATTAAGA-CAAAAATATTTTTCTTATC-TA
* *
928378 AATTAAGACAAACATA-TCTTCTTATCTA
1 AATTAAGACAAAAATATTTTTCTTATCTA
928406 AATTAAGAC
1 AATTAAGAC
928415 CAAACATGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
28 31 0.39
29 11 0.14
30 23 0.29
31 15 0.19
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (29 bp):
AATTAAGACAAAAATATTTTTCTTATCTA
Found at i:928381 original size:59 final size:58
Alignment explanation
Indices: 928289--928413 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 58
928279 TATTATTTTT
* * * * * *
928289 AATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTATCTA
1 AATTAAGAAAAAAATATTTTATCTTCTCTAAATTAAGACAAACATATCTTCTTATCTA
*
928347 GATTAAGATAAAAAATATTTT-TCTTCTCTTAAATTAAGACAAACATATCTTCTTATCTA
1 AATTAAGA-AAAAAATATTTTATCTTCTC-TAAATTAAGACAAACATATCTTCTTATCTA
928406 AATTAAGA
1 AATTAAGA
928414 CCAAACATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 13 0.23
59 44 0.77
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (58 bp):
AATTAAGAAAAAAATATTTTATCTTCTCTAAATTAAGACAAACATATCTTCTTATCTA
Found at i:928418 original size:29 final size:28
Alignment explanation
Indices: 928289--928427 Score: 125
Period size: 30 Copynumber: 4.8 Consensus size: 28
928279 TATTATTTTT
* *
928289 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACATA-TTT-TCTTATCTA
* * *
928319 AATTGAGACAAATATGTTTTCTTATCTA
1 AATTAAGACAAACATATTTTCTTATCTA
* * * *
928347 GATTAAGATAAAAAATATTTTTCTTCTCTTA
1 AATTAAGA-CAAACATA-TTTTCTTATC-TA
*
928378 AATTAAGACAAACATATCTTCTTATCTA
1 AATTAAGACAAACATATTTTCTTATCTA
*
928406 AATTAAGACCAAACATGTTTTC
1 AATTAAGA-CAAACATATTTTC
928428 CTGTTTAAAC
Statistics
Matches: 88, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
28 24 0.27
29 27 0.31
30 28 0.32
31 9 0.10
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTATCTA
Done.