Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008442.1 Hibiscus syriacus cultivar Beakdansim tig00111244_pilon, 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: 816021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:346725 original size:110 final size:112
Alignment explanation
Indices: 346441--346797 Score: 565
Period size: 112 Copynumber: 3.2 Consensus size: 112
346431 ATAACAATAT
* * * *
346441 AACCGGTTTATAAATGACAAAACAGGTAAAACGCTACTGGATATATTGAAAGTGTCGATACTTTA
1 AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTA
**
346506 TAAAAATGTATATATCCATAACAATATAACAGGTAAAAAAATGACAA
66 TAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
* * *
346553 AACCGGTCTATAAATGACAAAATAGGTAAAGCGCTACCGTATATATTGAAAGTGTTGATACTTTA
1 AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTA
346618 TAAAAATGTATCGATCCATAACAA-ATAACAGGTAAAAAAATGACAA
66 TAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
*
346664 AACCGGTCTATAAATGAC-AAACAGGTAAAGCGCTACCAAATATATTGAAAGTGTCGATACTTTA
1 AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTA
* * *
346728 TAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGATAA
66 TAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
**
346775 AACCGGTCTCGAAATGACAAAAC
1 AACCGGTCTATAAATGACAAAAC
346798 CGGTCTATAA
Statistics
Matches: 226, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
110 66 0.29
111 75 0.33
112 85 0.38
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (112 bp):
AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAAGTGTCGATACTTTA
TAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAA
Found at i:346796 original size:20 final size:20
Alignment explanation
Indices: 346768--346817 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
346758 AGGTAAAAAT
* *
346768 ATGATAAAACCGGTCTCGAA
1 ATGACAAAACCGGTCTAGAA
*
346788 ATGACAAAACCGGTCTATAA
1 ATGACAAAACCGGTCTAGAA
346808 ATGACAAAAC
1 ATGACAAAAC
346818 AGGTAAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGACAAAACCGGTCTAGAA
Found at i:346896 original size:132 final size:131
Alignment explanation
Indices: 346655--346933 Score: 497
Period size: 132 Copynumber: 2.1 Consensus size: 131
346645 ACAGGTAAAA
346655 AAATGACAAAACCGGTCTATAAATGACAAACAGGTAAAGCGCTACCAAATATATTGAAAGTGTCG
1 AAATGACAAAACCGGTCTATAAATGACAAACAGGTAAAGCGCTACCAAATATATTGAAAGTGTCG
346720 ATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGATAAAACCGGTCTC
66 ATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGATAAAACCGGTCTC
346785 G
131 G
* *
346786 AAATGACAAAACCGGTCTATAAATGACAAAACAGGTAAAGTGCTACCAGATATATTGAAAGTGTC
1 AAATGACAAAACCGGTCTATAAATGAC-AAACAGGTAAAGCGCTACCAAATATATTGAAAGTGTC
* *
346851 GATACTTTATAAAAATGTATTGATCTATAACAATATAACAA-GTAAAAATATGATAAAACCGGTC
65 GATACTTTATAAAAATGTATCGATCCATAACAATATAA-AAGGTAAAAATATGATAAAACCGGTC
346915 TCG
129 TCG
346918 AAATGACAAAACCGGT
1 AAATGACAAAACCGGT
346934 AAAACGCTAC
Statistics
Matches: 142, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
131 27 0.19
132 113 0.80
133 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (131 bp):
AAATGACAAAACCGGTCTATAAATGACAAACAGGTAAAGCGCTACCAAATATATTGAAAGTGTCG
ATACTTTATAAAAATGTATCGATCCATAACAATATAAAAGGTAAAAATATGATAAAACCGGTCTC
G
Found at i:347150 original size:182 final size:182
Alignment explanation
Indices: 346843--347823 Score: 1703
Period size: 182 Copynumber: 5.4 Consensus size: 182
346833 AGATATATTG
* * *
346843 AAAGTGTCGATACTTTATAAAAATGTATTGATCTATAACAATATAACAAGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
* * *
346908 ACCGGTCTCGAAATGACAAAACCGGTAAA-ACGCTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGA-GCTACCAGATATGTTGATAGTGTCGATACTTTA
* *
346972 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAAAAATTATAGCGCTAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
*
347025 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAT
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
** *
347090 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACTGGATATGTTAATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
347155 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
*
347207 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
*
347272 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
347337 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
347389 AAATTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
* *
347454 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTATCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
* *
347519 TATAAGTATCGACACTTTTTGAATTTAAAAGAGAAGAAGTTATAACGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* * *
347571 AAATTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
*
347636 ATCGGTCTCGAAATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
*
347701 TATAAGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
*
347753 AAAGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
*
347818 ACCGGT
66 ATCGGT
347824 AAAGAGCTAC
Statistics
Matches: 762, Mismatches: 36, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
182 761 1.00
183 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.29
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAAA
ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:347294 original size:364 final size:363
Alignment explanation
Indices: 346843--348006 Score: 1866
Period size: 364 Copynumber: 3.3 Consensus size: 363
346833 AGATATATTG
* * * *
346843 AAAGTGTCGATACTTTATAAAAATGTATTGATCTATAACAATATAACAAGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
* * * *
346908 ACCGGTCTCGAAATGACAAAACCGGTAAA-ACGCTACCGGATATGTTGAAAGTGTCGATACTTTA
66 ATCGATCTCGAAATGACAAAACCGGTAAAGA-GCTACCAGATATGTTGATAGTGTCGATACTTTA
* *
346972 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAAAAATTATAGCGCTAATAAAGTGTCGATA
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATA
347037 CTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAATATCGGTCTCGAA
195 CTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAATA-CGGTCTCGAA
* * *
347102 ATGACAAAACCGGTAAAGAGCTACTGGATATGTTAATAGTGTCGATACTTTATTATAAGTATCGA
259 ATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTATCGATACTTTATTATAAGTATCGA
347167 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
324 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
347207 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
347272 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
*
347337 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAATTGTCGATAC
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATAC
* *
347402 TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCGGTCTCGAAA
196 TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAATA-CGGTCTCGAAA
*
347467 TGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTATCGATACTTTATTATAAGTATCGAC
260 TGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTATCGATACTTTATTATAAGTATCGAC
* *
347532 ACTTTTTGAATTTAAAAGAGAAGAAGTTATAACGCTAAT
325 ACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
347571 AAATTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
* *
347636 ATCGGTCTCGAAATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
*
347701 TATAAGTATTGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATAC
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATAC
*
347766 TTTATAAAAATGTATTGATCCATAACAATATAACATGT----A-A--A-AATA-----T-G--AT
196 TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAATACGGTCTCGAAAT
* * *
347815 ---AAAACCGGTAAAGAGCTACCGGGTATGTTGATAGTACCGATACTTTATTACAAGTATCGACA
261 GACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTATCGATACTTTATTATAAGTATCGACA
*
347877 CTTTTGGAATTTAAAAGA-ATAGAAGTTATAGCGCCAAT
326 CTTTTGGAATTTAAAAGAGA-AGAAGTTATAGCGCTAAT
*
347915 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
*
347980 ATCGATCTCGAAATGACAAAACTGGTA
66 ATCGATCTCGAAATGACAAAACCGGTA
348007 GTAAAAAGTG
Statistics
Matches: 756, Mismatches: 42, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
343 1 0.00
344 177 0.23
347 2 0.00
349 1 0.00
350 1 0.00
356 3 0.00
357 1 0.00
359 1 0.00
360 1 0.00
364 567 0.75
365 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (363 bp):
AAAGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACATGTAAAAATATGATAAA
ATCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATAC
TTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGATAATACGGTCTCGAAAT
GACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTATCGATACTTTATTATAAGTATCGACA
CTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:347918 original size:162 final size:162
Alignment explanation
Indices: 347648--347980 Score: 560
Period size: 162 Copynumber: 2.1 Consensus size: 162
347638 CGGTCTCGAA
** * *
347648 ATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTATAAGTATTGA
1 ATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTACCGATACTTTATTACAAGTATCGA
* *
347713 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTTTATAAAAATG
66 CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATA
*
347778 TATTGATCCATAACAATATAACATGTAAAAAT
131 TATCGATCCATAACAATATAACATGTAAAAAT
* *
347810 ATGATAAAACCGGTAAAGAGCTACCGGGTATGTTGATAGTACCGATACTTTATTACAAGTATCGA
1 ATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTACCGATACTTTATTACAAGTATCGA
347875 CACTTTTGGAATTTAAAAGA-ATAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAAT
66 CACTTTTGGAATTTAAAAGAGA-AGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAAT
347939 ATATCGATCCATAACAATATAACATGTAAAAAT
130 ATATCGATCCATAACAATATAACATGTAAAAAT
*
347972 ATGACAAAA
1 ATGATAAAA
347981 TCGATCTCGA
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
161 1 0.01
162 159 0.99
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (162 bp):
ATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTACCGATACTTTATTACAAGTATCGA
CACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATA
TATCGATCCATAACAATATAACATGTAAAAAT
Found at i:348416 original size:23 final size:23
Alignment explanation
Indices: 348390--348437 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
348380 AAATATGTCA
* *
348390 ATATAAGCGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
348413 ATATAAACGCTACCTAATATATT
1 ATATAAACGCTACCTAATATATT
348436 AT
1 AT
348438 TGTATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:350591 original size:32 final size:32
Alignment explanation
Indices: 350530--350598 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
350520 GGATTAGAAT
350530 TTAAT-AAAATTAATAAAATAAATTTGAGTTA
1 TTAATAAAAATTAATAAAATAAATTTGAGTTA
*
350561 TTAATAAAATATTAAT-AAATTAATTTGAGTTA
1 TTAATAAAA-ATTAATAAAATAAATTTGAGTTA
350593 TTAATA
1 TTAATA
350599 GATGCCATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
31 5 0.14
32 24 0.69
33 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (32 bp):
TTAATAAAAATTAATAAAATAAATTTGAGTTA
Found at i:350694 original size:29 final size:29
Alignment explanation
Indices: 350628--350714 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
350618 ATTGATAAAA
* *
350628 TAAATTTGAATTATTAAAATAAGAGTAAT-TT
1 TAAATTTTAATAATTAAAATAA-A--AATATT
* *
350659 TATATTTTAATAATTAAATTAAAAATATT
1 TAAATTTTAATAATTAAAATAAAAATATT
* * *
350688 TAAATTTTAGTGATTAAAATAAGAATA
1 TAAATTTTAATAATTAAAATAAAAATA
350715 AGAAGATAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.07
29 24 0.52
30 1 0.02
31 18 0.39
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.43
Consensus pattern (29 bp):
TAAATTTTAATAATTAAAATAAAAATATT
Found at i:352446 original size:22 final size:22
Alignment explanation
Indices: 352418--352461 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
352408 AAATATAAAT
352418 AAATAAATTTGAGTTATTAATA
1 AAATAAATTTGAGTTATTAATA
352440 AAATAAATTTGAGTTATTAATA
1 AAATAAATTTGAGTTATTAATA
352462 GATGTCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATAAATTTGAGTTATTAATA
Found at i:355599 original size:66 final size:67
Alignment explanation
Indices: 355494--355620 Score: 231
Period size: 66 Copynumber: 1.9 Consensus size: 67
355484 TTAAACAGTG
355494 AAATGAAATTAAAGGATTAATTATATGTAGGTAGGGC-AAAAGCCCTCTCAT-GCAATTTACTAG
1 AAATGAAATTAAAGGATTAATTATATGTAGGTAGGGCAAAAAGCCCTCTCATAGCAATTTACTAG
355557 CT
66 CT
355559 AAATGAAATTAAAAGGATTAATTATATGTAGGTAGGGCAAAAAGCCCTCTCATAGCAATTTA
1 AAATGAAATT-AAAGGATTAATTATATGTAGGTAGGGCAAAAAGCCCTCTCATAGCAATTTA
355621 ATACTAGCTA
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
65 10 0.17
66 27 0.46
67 14 0.24
68 8 0.14
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (67 bp):
AAATGAAATTAAAGGATTAATTATATGTAGGTAGGGCAAAAAGCCCTCTCATAGCAATTTACTAG
CT
Found at i:356167 original size:15 final size:15
Alignment explanation
Indices: 356147--356182 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
356137 AAAAACAATA
356147 GGATGGTGTGGTCAC
1 GGATGGTGTGGTCAC
*
356162 GGATGGTGTGGTCAG
1 GGATGGTGTGGTCAC
356177 GGATGG
1 GGATGG
356183 ACTGGAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.08, G:0.53, T:0.25
Consensus pattern (15 bp):
GGATGGTGTGGTCAC
Found at i:356283 original size:15 final size:15
Alignment explanation
Indices: 356263--356298 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
356253 AAAAACAATA
356263 GGATGGTGTGGTCAC
1 GGATGGTGTGGTCAC
*
356278 GGATGGTGTGGTCAG
1 GGATGGTGTGGTCAC
356293 GGATGG
1 GGATGG
356299 ACTGGAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.08, G:0.53, T:0.25
Consensus pattern (15 bp):
GGATGGTGTGGTCAC
Found at i:356371 original size:116 final size:116
Alignment explanation
Indices: 356118--356356 Score: 444
Period size: 116 Copynumber: 2.1 Consensus size: 116
356108 TTTATTTTTT
*
356118 TTCATTTGAGTGTTAAATTAAAAACAATAGGATGGTGTGGTCACGGATGGTGTGGTCAGGGATGG
1 TTCATATGAGTGTTAAATTAAAAACAATAGGATGGTGTGGTCACGGATGGTGTGGTCAGGGATGG
356183 ACTGGAGGAAGAGAGGGTTGGGCTAGTCGTCCTCTTAAAAATTTAAAAATA
66 ACTGGAGGAAGAGAGGGTTGGGCTAGTCGTCCTCTTAAAAATTTAAAAATA
*
356234 TTCATTTGAGTGTTAAATTAAAAACAATAGGATGGTGTGGTCACGGATGGTGTGGTCAGGGATGG
1 TTCATATGAGTGTTAAATTAAAAACAATAGGATGGTGTGGTCACGGATGGTGTGGTCAGGGATGG
356299 ACTGGAGGAAGAGGAGGGTTGGGCTAGTCGTCCTCTTAAAAATTTAAAAATA
66 ACTGGAGGAAGA-GAGGGTTGGGCTAGTCGTCCTCTTAAAAATTTAAAAATA
356351 TT-ATAT
1 TTCATAT
356357 ATTTTAAATT
Statistics
Matches: 121, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
116 80 0.66
117 41 0.34
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (116 bp):
TTCATATGAGTGTTAAATTAAAAACAATAGGATGGTGTGGTCACGGATGGTGTGGTCAGGGATGG
ACTGGAGGAAGAGAGGGTTGGGCTAGTCGTCCTCTTAAAAATTTAAAAATA
Found at i:357525 original size:53 final size:53
Alignment explanation
Indices: 357438--357540 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 53
357428 GTGGGCACAT
* * *
357438 GCCCACCCTAAAATCCAAATTTTCTTCGTATAATTATCTATTTTATTGATGGC
1 GCCCACCCTAAAATCCAAATTTTCTTCATATAATTACCTATTTTACTGATGGC
357491 GCCCACCCTAAAA-CCTAAATTTTCTTCA-ATTAATTACCTATTTTACTGAT
1 GCCCACCCTAAAATCC-AAATTTTCTTCATA-TAATTACCTATTTTACTGAT
357541 TGTGTCCATC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
52 3 0.07
53 42 0.93
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (53 bp):
GCCCACCCTAAAATCCAAATTTTCTTCATATAATTACCTATTTTACTGATGGC
Found at i:358446 original size:130 final size:130
Alignment explanation
Indices: 358210--358445 Score: 314
Period size: 130 Copynumber: 1.8 Consensus size: 130
358200 GAGAAAAACA
* * * *
358210 ATAATATCTAATTATTTATAATCGTGAATAAATGACCTCTCATGCTTTAAAAAGTCATTTATTAC
1 ATAATATCTAATTATTTACAACCGAGAATAAATGACCTCTCATGCCTTAAAAAGTCATTTATTAC
* *
358275 TCCAATCAAAATGAAAAAATATCACTATTTCGTCTTAAAAATCAATATTGGTTCTAGAGAAAATG
66 TCCAACCAAAATGAAAAAATATCACTATTTCGTCCTAAAAATCAATATTGGTTCTAGAGAAAATG
* *
358340 ATAATATGTAATTATTTCCAACCGAGAATAAATGACCTCTCATGCCTTAAAGCAA-TCATTTATT
1 ATAATATCTAATTATTTACAACCGAGAATAAATGACCTCTCATGCCTTAAA--AAGTCATTTATT
* * * * *
358404 ATTCTAACCGAAAT-AAAAAGATATTACTATTTTGTCCTAAAA
64 ACTCCAACCAAAATGAAAAA-ATATCACTATTTCGTCCTAAAA
358446 TTTTAAATTA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
130 50 0.56
131 38 0.42
132 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (130 bp):
ATAATATCTAATTATTTACAACCGAGAATAAATGACCTCTCATGCCTTAAAAAGTCATTTATTAC
TCCAACCAAAATGAAAAAATATCACTATTTCGTCCTAAAAATCAATATTGGTTCTAGAGAAAATG
Found at i:359396 original size:104 final size:106
Alignment explanation
Indices: 359286--359516 Score: 265
Period size: 106 Copynumber: 2.2 Consensus size: 106
359276 TCACTACATA
* * * *
359286 TGACCAAAATAAAAAAACACGCCTAAA-TCAGGGGGACTAAACAA-CAA-ATATCCCAAAA-AAT
1 TGACCAACATACAAAAACACG-CTAAACT-AGAGGGACTAAACAATCAACAT-CCCCAAAACAAT
*
359347 AACATGCATGAAAAT-GGTAAATAACAACATCAGTCCCTACAGG
63 AACATGCATAAAAATGGGTAAATAACAACATCAGTCCCTACAGG
* * *
359390 TGACCAACATGCAAAAACACGCTAAACTATAGGGACTAAACAATCAACATCCCCAAAACTATAAC
1 TGACCAACATACAAAAACACGCTAAACTAGAGGGACTAAACAATCAACATCCCCAAAACAATAAC
* ** * *
359455 ATGCATAAAAATGGGTAAATAGCAAGTTCGGTCCTTACAGG
66 ATGCATAAAAATGGGTAAATAACAACATCAGTCCCTACAGG
* *
359496 TAACTAACATACAAAAACACG
1 TGACCAACATACAAAAACACG
359517 GTTAAGTTAG
Statistics
Matches: 106, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
103 18 0.17
104 29 0.27
105 18 0.17
106 41 0.39
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (106 bp):
TGACCAACATACAAAAACACGCTAAACTAGAGGGACTAAACAATCAACATCCCCAAAACAATAAC
ATGCATAAAAATGGGTAAATAACAACATCAGTCCCTACAGG
Found at i:360318 original size:6 final size:6
Alignment explanation
Indices: 360307--360362 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
360297 TTGGGTCTGC
* * *
360307 AAAAAT AAAAAT AAAAAT -AATAT AAATAT AAAAAAT AAAAAT AAAATT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
*
360355 AATAAT AA
1 AAAAAT AA
360363 TTAATATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
5 4 0.09
6 34 0.79
7 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:360358 original size:24 final size:24
Alignment explanation
Indices: 360313--360358 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
360303 CTGCAAAAAT
*
360313 AAAAATAAAAATAATATAAATATA
1 AAAAATAAAAATAAAATAAATATA
*
360337 AAAAATAAAAATAAAATTAATA
1 AAAAATAAAAATAAAATAAATA
360359 ATAATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAAATAAAAATAAAATAAATATA
Found at i:360359 original size:15 final size:15
Alignment explanation
Indices: 360310--360373 Score: 60
Period size: 16 Copynumber: 4.2 Consensus size: 15
360300 GGTCTGCAAA
*
360310 AATAAAAATAAAAAT
1 AATAAAAATAAAATT
360325 AATATAAATATAAAA--
1 AATA-AAA-ATAAAATT
360340 AATAAAAATAAAATT
1 AATAAAAATAAAATT
* *
360355 AATAATAATTAATATT
1 AATAA-AAATAAAATT
360371 AAT
1 AAT
360374 GTAAACAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 6 0.14
14 3 0.07
15 13 0.31
16 14 0.33
17 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAAATAAAATT
Found at i:360712 original size:86 final size:87
Alignment explanation
Indices: 360594--360791 Score: 254
Period size: 86 Copynumber: 2.3 Consensus size: 87
360584 TCCGCTGCTT
* * * ** * *
360594 CTTCAGGGTAGATCAAATATGGAAACGTTGATTCATTCCACTTTTCTTCAGGGAAGATTGAATCG
1 CTTCAGGGAAAATCAAATCTGGAAACGTTGATTCATTCCACAGTTCTTCAAGGAAAATTGAATCG
*
360659 AGGAAAACTTGTTCCACTTCTA
66 AGGAAAACTTGCTCCACTTCTA
* *
360681 C-TCATGGAAAATCAAATCTGGAGACGTTGATTCATTCCACAGTTCTTCAAGGAAAATTGAATCG
1 CTTCAGGGAAAATCAAATCTGGAAACGTTGATTCATTCCACAGTTCTTCAAGGAAAATTGAATCG
* * *
360745 AGGTAGACTTGCTCCACTTCTT
66 AGGAAAACTTGCTCCACTTCTA
* *
360767 CTTCAGGGAATATCAAATCTAGAAA
1 CTTCAGGGAAAATCAAATCTGGAAA
360792 AAGAAAGGGG
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
86 73 0.78
87 20 0.22
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (87 bp):
CTTCAGGGAAAATCAAATCTGGAAACGTTGATTCATTCCACAGTTCTTCAAGGAAAATTGAATCG
AGGAAAACTTGCTCCACTTCTA
Found at i:360937 original size:138 final size:138
Alignment explanation
Indices: 360696--360990 Score: 391
Period size: 138 Copynumber: 2.1 Consensus size: 138
360686 GGAAAATCAA
* * * *
360696 ATCTGGAGACGTTGATTCATTCCACAGTTCTTCAAGGAAAATTGAATCGAGGTAGACTTGCTCCA
1 ATCTGGAAACGTTGATTCATTCAACAGTTCTTCAAGGAAAATTGAATCAAGGCAGACTTGCTCCA
*
360761 CTTCTTCTTCAGGGAATATCAAATCTAGAAAAAGAAAGGGGAACTGCT-CAGCTGCTTTTTT-AG
66 CTTCTTCTTCAGGGAAGATCAAATCTAGAAAAAGAAAGGGGAACTGCTCCA-CTG-TTTTTTCAG
*
360824 GGTAAATCAG
129 GGTAAATAAG
* * ** * * *
360834 AT-TCGTAAACTTTGATTCATTCAATTGTTCTTTAGGGAAAATTGAATCAAGGCAGACTTGTTCC
1 ATCT-GGAAACGTTGATTCATTCAACAGTTCTTCAAGGAAAATTGAATCAAGGCAGACTTGCTCC
* *
360898 ACTGT-TTCTTCAGGGAAGATCAAATCTTGAAAAAGAAAGGGGATCTGCTCCACTGTTTTTTCAG
65 ACT-TCTTCTTCAGGGAAGATCAAATCTAGAAAAAGAAAGGGGAACTGCTCCACTGTTTTTTCAG
360962 GGTAAATAAG
129 GGTAAATAAG
360972 ATCTGGAAACGTTGATTCA
1 ATCTGGAAACGTTGATTCA
360991 ATCCATTAGA
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
137 7 0.05
138 124 0.92
139 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (138 bp):
ATCTGGAAACGTTGATTCATTCAACAGTTCTTCAAGGAAAATTGAATCAAGGCAGACTTGCTCCA
CTTCTTCTTCAGGGAAGATCAAATCTAGAAAAAGAAAGGGGAACTGCTCCACTGTTTTTTCAGGG
TAAATAAG
Found at i:362177 original size:45 final size:43
Alignment explanation
Indices: 362107--362192 Score: 111
Period size: 45 Copynumber: 2.0 Consensus size: 43
362097 TTTGAATGAT
* *
362107 TTTCAAGCCACCCTTTGAGGGTTTTCAACTTGAAACCTCCTTTGG
1 TTTCAAGACACCCTTTGAGGATTTTCAACTTG-AACC-CCTTTGG
*
362152 TTTCAAGACACCCTTT-ACGGATTTTCATCTTGAACCCCTTT
1 TTTCAAGACACCCTTTGA-GGATTTTCAACTTGAACCCCTTT
362193 TTTGTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 5 0.14
44 5 0.14
45 27 0.73
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (43 bp):
TTTCAAGACACCCTTTGAGGATTTTCAACTTGAACCCCTTTGG
Found at i:362217 original size:24 final size:24
Alignment explanation
Indices: 362190--362316 Score: 96
Period size: 27 Copynumber: 5.0 Consensus size: 24
362180 CTTGAACCCC
* *
362190 TTTTTTGTTTTTTTGTTTTTTGTTTT
1 TTTTTTGTTTTTTT-CTTTTT-TATT
362216 TTTCTTTGTTTTTTTCTTTGTTT-TT
1 TTT-TTTGTTTTTTTCTTT-TTTATT
* *
362241 TTCTTTGTTTTTTTCTTTTTCATT
1 TTTTTTGTTTTTTTCTTTTTTATT
*
362265 TTTTTCAT-TTTTTTTATTTTTTCATT
1 TTTTT--TGTTTTTTTCTTTTTT-ATT
* *
362291 TTTTTTCTTTCTTTTTCATTTTTATT
1 TTTTTT-GTT-TTTTTCTTTTTTATT
362317 CTTTCTTCAG
Statistics
Matches: 84, Mismatches: 8, Indels: 18
0.76 0.07 0.16
Matches are distributed among these distances:
23 2 0.02
24 22 0.26
25 16 0.19
26 21 0.25
27 23 0.27
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.83
Consensus pattern (24 bp):
TTTTTTGTTTTTTTCTTTTTTATT
Found at i:362223 original size:12 final size:12
Alignment explanation
Indices: 362190--362258 Score: 106
Period size: 12 Copynumber: 5.8 Consensus size: 12
362180 CTTGAACCCC
*
362190 TTTTTTGTTT-T
1 TTTTTTCTTTGT
362201 TTTGTTT-TTTGT
1 TTT-TTTCTTTGT
362213 TTTTTTCTTTGT
1 TTTTTTCTTTGT
362225 TTTTTTCTTTGT
1 TTTTTTCTTTGT
362237 TTTTTTCTTTGT
1 TTTTTTCTTTGT
362249 TTTTTTCTTT
1 TTTTTTCTTT
362259 TTCATTTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.16
12 46 0.84
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:362293 original size:9 final size:9
Alignment explanation
Indices: 362256--362313 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
362246 TGTTTTTTTC
362256 TTTTTCATT
1 TTTTTCATT
362265 TTTTTCATT
1 TTTTTCATT
*
362274 TTTTTTA-T
1 TTTTTCATT
362282 TTTTTCATTT
1 TTTTTCA-TT
*
362292 TTTTTCTTT
1 TTTTTCATT
362301 CTTTTTCATT
1 -TTTTTCATT
362311 TTT
1 TTT
362314 ATTCTTTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
8 7 0.17
9 20 0.48
10 15 0.36
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCATT
Found at i:362313 original size:1 final size:1
Alignment explanation
Indices: 362190--362306 Score: 63
Period size: 1 Copynumber: 117.0 Consensus size: 1
362180 CTTGAACCCC
* * * * * * * * *
362190 TTTTTTGTTTTTTTGTTTTTTGTTTTTTTCTTTGTTTTTTTCTTTGTTTTTTTCTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** * ** * *
362255 CTTTTTCATTTTTTTCATTTTTTTTATTTTTTCATTTTTTTTCTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
362307 CATTTTTATT
Statistics
Matches: 81, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (1 bp):
T
Found at i:362318 original size:20 final size:19
Alignment explanation
Indices: 362236--362323 Score: 87
Period size: 18 Copynumber: 4.7 Consensus size: 19
362226 TTTTTCTTTG
*
362236 TTTTTTTCTTTGTTTTT--
1 TTTTTTTCTTTCTTTTTCA
*
362253 TTCTTTTTCATT-TTTTTCA
1 TT-TTTTTCTTTCTTTTTCA
*
362272 TTTTTTT-TAT-TTTTTCA
1 TTTTTTTCTTTCTTTTTCA
362289 TTTTTTTTCTTTCTTTTTCA
1 -TTTTTTTCTTTCTTTTTCA
362309 TTTTTATTCTTTCTT
1 TTTTT-TTCTTTCTT
362324 CAGGTGAAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
17 15 0.25
18 20 0.33
19 9 0.15
20 16 0.27
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.81
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTTTCA
Found at i:362325 original size:17 final size:17
Alignment explanation
Indices: 362256--362325 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 17
362246 TGTTTTTTTC
362256 TTTTTCATT-TTT-TTCA
1 TTTTT-ATTCTTTCTTCA
* * *
362272 TTTTTTTTATTTTTTCA
1 TTTTTATTCTTTCTTCA
*
362289 TTTTTTTTCTTTCTTTTTCA
1 TTTTTATTCTTTC---TTCA
362309 TTTTTATTCTTTCTTCA
1 TTTTTATTCTTTCTTCA
362326 GGTGAAGTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
15 2 0.04
16 8 0.18
17 19 0.42
20 16 0.36
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTATTCTTTCTTCA
Found at i:369462 original size:21 final size:21
Alignment explanation
Indices: 369424--369463 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
369414 ATTCTGCCAT
* * *
369424 ATATTTTTTTTATTAATATTG
1 ATATTTTATTAATGAATATTG
369445 ATATTTTATTAATGAATAT
1 ATATTTTATTAATGAATAT
369464 GAAAAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATATTTTATTAATGAATATTG
Found at i:373651 original size:131 final size:130
Alignment explanation
Indices: 373275--373668 Score: 590
Period size: 130 Copynumber: 3.0 Consensus size: 130
373265 AGATTTTAAT
* * *
373275 AGAGAAAACGATAATATCTAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAATGCAG
1 AGAGAAAACGATAATATCTAATTATTTCCAATC-AGAATAAATGACCTCTCATGCCTTAAAGCAA
*
373340 TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTTAAATTCAATATTGATTC
65 TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTC
373405 G
130 G
*
373406 AGAGAAAACGATAATATCTAATTATTTCCAATCGGAATAAATGACCTCTCATGCCTTAAAGCAAT
1 AGAGAAAACGATAATATCTAATTATTTCCAATCAGAATAAATGACCTCTCATGCCTTAAAGCAAT
* *
373471 AATTTATTACTCCAATCGAAATGAAGATATATCACTATTTCATCTTAAAATTCAATATTGATTCG
66 CATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTCG
* * * **
373536 AGAGAAAACGATAATATCTAATTATTTTCAACCTAGAATAAATTATTTCTCATGCCTTAAAGCAA
1 AGAGAAAACGATAATATCTAATTATTTCCAATC-AGAATAAATGACCTCTCATGCCTTAAAGCAA
* * * * * * * *
373601 TCATTTATTACTCTAACCAAAATAAAAAGATATTACTATTTCATCATAAAATTCAATATTAATTC
65 TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTC
373666 G
130 G
373667 AG
1 AG
373669 TGTTACTTAT
Statistics
Matches: 239, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
130 121 0.51
131 118 0.49
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.34
Consensus pattern (130 bp):
AGAGAAAACGATAATATCTAATTATTTCCAATCAGAATAAATGACCTCTCATGCCTTAAAGCAAT
CATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTCG
Found at i:379745 original size:153 final size:153
Alignment explanation
Indices: 379588--379874 Score: 368
Period size: 153 Copynumber: 1.9 Consensus size: 153
379578 AATAAGAATA
* * *
379588 AAATAATTTGATTA-AAA-CAACTATATATATATATATATTTATAAATAATG-TATTTATTTA-T
1 AAATAATTTAAATACAAATCAACTA-A-ATATATATATA-TTAT-AAGAATGATATTTATTTATT
* * * * *
379649 TTAAAAATATCGGAATAGGACCTCTAGTTAATTTAGGACATACATTTCTTTGATA-TTAAAAAAT
62 TTAAAAATACCAGAATAGAACATCTAGTTAATTTAAGACATACATTTC-TTGATATTTAAAAAAT
379713 AAATAAATATTAATAATAATATGATAAT
126 AAATAAATATTAATAATAATATGATAAT
* * * *
379741 AAATAATTTAAATACAAATGAAGTAAATATATATATATTATAAGCATGATATTTATTTATTTTTA
1 AAATAATTTAAATACAAATCAACTAAATATATATATATTATAAGAATGATATTTATTTATTTTAA
* *
379806 AAATACCAGAATAGAACATCTAGTTATTTTAAGACATCCATTTCTTGATATTTAAAAAATAAATA
66 AAATACCAGAATAGAACATCTAGTTAATTTAAGACATACATTTCTTGATATTTAAAAAATAAATA
379871 AATA
131 AATA
379875 ATATTATTAA
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
151 5 0.04
152 20 0.17
153 82 0.71
154 4 0.03
155 4 0.03
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (153 bp):
AAATAATTTAAATACAAATCAACTAAATATATATATATTATAAGAATGATATTTATTTATTTTAA
AAATACCAGAATAGAACATCTAGTTAATTTAAGACATACATTTCTTGATATTTAAAAAATAAATA
AATATTAATAATAATATGATAAT
Found at i:379890 original size:26 final size:26
Alignment explanation
Indices: 379861--379925 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
379851 TGATATTTAA
*
379861 AAAATAAATAAATAATAT-TATTAAT
1 AAAATAAATAAATAATATATAATAAT
* *
379886 CAAAATATATATAT-ATATATAATAAT
1 -AAAATAAATAAATAATATATAATAAT
379912 AAAAT-AAT-AATAAT
1 AAAATAAATAAATAAT
379926 TAAAGTACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.06
24 4 0.12
25 9 0.28
26 17 0.53
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
AAAATAAATAAATAATATATAATAAT
Found at i:382309 original size:3 final size:3
Alignment explanation
Indices: 382301--382342 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
382291 TAAAATTACT
* * *
382301 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
382343 AAAAATGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:382570 original size:39 final size:39
Alignment explanation
Indices: 382526--383012 Score: 566
Period size: 39 Copynumber: 12.5 Consensus size: 39
382516 GGTTGAATAT
* * * * **
382526 GTTCTTCAGACTATGAACTTCC-TCTTCTTCTTTAGATAA
1 GTTCTTCAGATTATGAAC-TCCTTTTTCCTCTTCAGACGA
* * * *
382565 GTTCTTTAAACTATGAACTCATTTTTCCTCTTCAGACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* ** * *
382604 GTTCTTCATATTATGAACTCCTTTTTTTTTCTTTAGGCGA
1 GTTCTTCAGATTATGAACTCC-TTTTTCCTCTTCAGACGA
*
382644 GTTCTTCATATTATGAACTCCTTTTTCCTCTTCAGACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* * *
382683 TTTCTTCATATTATGAACTCCTTCTTCCTCTTCAGACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* * *
382722 GTTCTTCAAATTATGAACTCTTTTTTTTCTCTTCAGACGA
1 GTTCTTCAGATTATGAACTC-CTTTTTCCTCTTCAGACGA
*
382762 GTTCTTCAGATTATGAACTACTTTTTCCTCTTCAGACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* * ** *
382801 TTTCTTCAGATTATAAACTCCTTTTTTTTCTTCAGATGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* * * * **
382840 ATTCTTCATATTATGAACTCCTTCTTCCTCTTTAGATTA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
* * * *
382879 GTTCTTCAGATTATGCACTCATTTTTCCTCTTTAGATGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
*
382918 GTTCTTCAAATTATGAACTCCTTTTT--TCTTCAGACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
*
382955 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCATACGA
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
382994 GTTCTTCAGATTATGAACT
1 GTTCTTCAGATTATGAACT
383013 TCTTCTGAAA
Statistics
Matches: 385, Mismatches: 58, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
37 34 0.09
38 2 0.01
39 280 0.73
40 69 0.18
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (39 bp):
GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGA
Found at i:382709 original size:20 final size:20
Alignment explanation
Indices: 382645--382709 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
382635 TTTAGGCGAG
382645 TTCTTCATATTATGAACTCC
1 TTCTTCATATTATGAACTCC
* * * ***
382665 TTTTTCCTCTTCA-G-ACGAT
1 TTCTTCATATT-ATGAACTCC
382684 TTCTTCATATTATGAACTCC
1 TTCTTCATATTATGAACTCC
382704 TTCTTC
1 TTCTTC
382710 CTCTTCAGAC
Statistics
Matches: 30, Mismatches: 12, Indels: 6
0.62 0.25 0.12
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 17 0.57
21 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.06, T:0.48
Consensus pattern (20 bp):
TTCTTCATATTATGAACTCC
Found at i:382735 original size:118 final size:117
Alignment explanation
Indices: 382526--383012 Score: 584
Period size: 118 Copynumber: 4.2 Consensus size: 117
382516 GGTTGAATAT
* * * * ** * * * *
382526 GTTCTTCAGACTATGAACTTCC-TCTTCTTCTTTAGATAAGTTCTTTAAACTATGAACTCATTTT
1 GTTCTTCAGATTATGAAC-TCCTTTTTCCTCTTCAGACGATTTCTTCAAATTATGAACTCCTTTT
** * *
382590 TCCTCTTCAGACGAGTTCTTCATATTATGAACTCCTTTTTTTTTCTTTAGGCGA
65 TCCTCTTCAGACGAGTTCTTCATATTATGAACTCC-TTTTTCCTCTTCAGACGA
* * *
382644 GTTCTTCATATTATGAACTCCTTTTTCCTCTTCAGACGATTTCTTCATATTATGAACTCCTTCTT
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGATTTCTTCAAATTATGAACTCCTTTTT
* * *
382709 CCTCTTCAGACGAGTTCTTCAAATTATGAACTCTTTTTTTTCTCTTCAGACGA
66 CCTCTTCAGACGAGTTCTTCATATTATGAACTC-CTTTTTCCTCTTCAGACGA
* * *
382762 GTTCTTCAGATTATGAACTACTTTTTCCTCTTCAGACGATTTCTTCAGATTATAAACTCCTTTTT
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGATTTCTTCAAATTATGAACTCCTTTTT
** * * * * **
382827 TTTCTTCAGATGAATTCTTCATATTATGAACTCCTTCTTCCTCTTTAGATTA
66 CCTCTTCAGACGAGTTCTTCATATTATGAACTCCTTTTTCCTCTTCAGACGA
* * * * *
382879 GTTCTTCAGATTATGCACTCATTTTTCCTCTTTAGATGAGTTCTTCAAATTATGAACTCCTTTTT
1 GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGATTTCTTCAAATTATGAACTCCTTTTT
* *
382944 --TCTTCAGACGAGTTCTTCAGATTATGAACTCCTTTTTCCTCTTCATACGA
66 CCTCTTCAGACGAGTTCTTCATATTATGAACTCCTTTTTCCTCTTCAGACGA
382994 GTTCTTCAGATTATGAACT
1 GTTCTTCAGATTATGAACT
383013 TCTTCTGAAA
Statistics
Matches: 316, Mismatches: 51, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
115 60 0.19
117 73 0.23
118 183 0.58
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.45
Consensus pattern (117 bp):
GTTCTTCAGATTATGAACTCCTTTTTCCTCTTCAGACGATTTCTTCAAATTATGAACTCCTTTTT
CCTCTTCAGACGAGTTCTTCATATTATGAACTCCTTTTTCCTCTTCAGACGA
Found at i:382814 original size:157 final size:154
Alignment explanation
Indices: 382527--383018 Score: 635
Period size: 157 Copynumber: 3.2 Consensus size: 154
382517 GTTGAATATG
* * * *
382527 TTCTTCAGACTATGAACTTCC-TCTTCTTCTTTAGATAAGTTCTTTAAACTATGAACTCATTTTT
1 TTCTTCAGATTATGAAC-TCCTTCTTCCTCTTTAGATAAGTTCTTCAAATTATGAACTCATTTTT
* * * *
382591 CCTCTTCAGACGAGTTCTTCATATTATGAACTCCTTTTTTTTTCTTTAGGCGAGTTCTTCATATT
65 CCTCTTCAGACGAGTTCTTCAAATTATGAACTCC---TTTTTTCTTCAGACGAGTTCTTCAGATT
*
382656 ATGAACTCCTTTTTCCTCTTCAGACGAT
127 ATGAACTCCTTTTTCCTCTTCAGACGAA
* * ** *
382684 TTCTTCATATTATGAACTCCTTCTTCCTCTTCAGACGAGTTCTTCAAATTATGAACTCTTTTTTT
1 TTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGATAAGTTCTTCAAATTATGAACTC-ATTTTT
* * * *
382749 TCTCTTCAGACGAGTTCTTCAGATTATGAACTACTTTTTCCTCTTCAGACGATTTCTTCAGATTA
65 CCTCTTCAGACGAGTTCTTCAAATTATGAACTCCTTTTT--TCTTCAGACGAGTTCTTCAGATTA
* ** *
382814 TAAACTCCTTTTTTTTCTTCAGATGAA
128 TGAACTCCTTTTTCCTCTTCAGACGAA
* * * *
382841 TTCTTCATATTATGAACTCCTTCTTCCTCTTTAGATTAGTTCTTCAGATTATGCACTCATTTTTC
1 TTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGATAAGTTCTTCAAATTATGAACTCATTTTTC
* *
382906 CTCTTTAGATGAGTTCTTCAAATTATGAACTCCTTTTTTCTTCAGACGAGTTCTTCAGATTATGA
66 CTCTTCAGACGAGTTCTTCAAATTATGAACTCCTTTTTTCTTCAGACGAGTTCTTCAGATTATGA
* *
382971 ACTCCTTTTTCCTCTTCATACGAG
131 ACTCCTTTTTCCTCTTCAGACGAA
*
382995 TTCTTCAGATTATGAACTTCTTCT
1 TTCTTCAGATTATGAACTCCTTCT
383019 GAAAATGTTT
Statistics
Matches: 290, Mismatches: 41, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
154 66 0.23
155 5 0.02
156 42 0.14
157 141 0.49
158 36 0.12
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (154 bp):
TTCTTCAGATTATGAACTCCTTCTTCCTCTTTAGATAAGTTCTTCAAATTATGAACTCATTTTTC
CTCTTCAGACGAGTTCTTCAAATTATGAACTCCTTTTTTCTTCAGACGAGTTCTTCAGATTATGA
ACTCCTTTTTCCTCTTCAGACGAA
Found at i:383221 original size:45 final size:45
Alignment explanation
Indices: 383067--383317 Score: 315
Period size: 45 Copynumber: 5.5 Consensus size: 45
383057 TTGCTATTTC
* *
383067 AAAACATCCGGCACTG-ATGGTCTTATGGATGACCCGAATGCTTTTTTG
1 AAAACATCCTGCACTGTA-GGTCTTATGGATGACCCGAA-G--GTTTTG
* * *
383115 AAATCATCCTACACTGTAGGTCTTATGGATAACCCGAAGGCTTTTTG
1 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG--TTTTG
383162 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
1 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
383207 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
1 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
* * * * * * *
383252 AGAACATCCTACAATGAAGGTCTTATAGATAACTCGAAGGTTTTG
1 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
* *
383297 AAAACATCATGCACTGAAGGT
1 AAAACATCCTGCACTGTAGGT
383318 TTTACAGATG
Statistics
Matches: 181, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
45 105 0.58
47 43 0.24
48 32 0.18
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (45 bp):
AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTG
Found at i:387483 original size:72 final size:72
Alignment explanation
Indices: 387370--387504 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
387360 TATAACAGAC
* *
387370 TAGCTGAATATTATCCATAAAGCCGGGGTGATTAACTAATTGCTTTATGGGGACAACTCAAGCAT
1 TAGCTGAATATTATCCATAAAGCCGGGGTGATTAACCAATTGCTTTAGGGGGACAACTCAAGCAT
387435 AACAAGT
66 AACAAGT
*
387442 TAGCTGAATATTATCCATAAAGCCGGGGAT-ATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAGCCGGGG-TGATTAACCAATTGCTTTAGGGGGACAACTCAAGC
387505 TTTATTGTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 58 0.98
73 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGCCGGGGTGATTAACCAATTGCTTTAGGGGGACAACTCAAGCAT
AACAAGT
Found at i:389918 original size:12 final size:12
Alignment explanation
Indices: 389901--389937 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
389891 CTATACGAAG
389901 ATGCAAATGTAA
1 ATGCAAATGTAA
389913 ATGCAAATGTAA
1 ATGCAAATGTAA
389925 ATGCAAATGTAA
1 ATGCAAATGTAA
389937 A
1 A
389938 AATGTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGCAAATGTAA
Found at i:389985 original size:8 final size:8
Alignment explanation
Indices: 389958--389988 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
389948 TAAAACGGAA
389958 ATGCAAAG
1 ATGCAAAG
*
389966 ATGAAAAG
1 ATGCAAAG
389974 ATGCAAAG
1 ATGCAAAG
389982 ATGCAAA
1 ATGCAAA
389989 TGCATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.10, G:0.23, T:0.13
Consensus pattern (8 bp):
ATGCAAAG
Found at i:390114 original size:42 final size:43
Alignment explanation
Indices: 390068--390152 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
390058 CGGTACATCA
*
390068 AATAAAACTTTACATATA-GGGATAGA-TTTCACTCCTAACTTC
1 AATAAAACTTTACATATAGGGGATA-ACCTTCACTCCTAACTTC
390110 AATAAAACTTTACATATAGGGGATAACCTTCACTCCTAACTTC
1 AATAAAACTTTACATATAGGGGATAACCTTCACTCCTAACTTC
390153 TCTAAAGCCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 19 0.47
43 21 0.52
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (43 bp):
AATAAAACTTTACATATAGGGGATAACCTTCACTCCTAACTTC
Found at i:392407 original size:2 final size:2
Alignment explanation
Indices: 392400--392439 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
392390 ATTTAATCAA
392400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
392440 AAATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:393425 original size:202 final size:198
Alignment explanation
Indices: 393071--393474 Score: 722
Period size: 202 Copynumber: 2.0 Consensus size: 198
393061 TATACCTTCA
393071 ATATTTCGAATCTTCCAGCGGAGCGTGGAGGCGCGTGGGAGCTCCGGTCACGTGTAGTCTTCGGT
1 ATATTTCGAATCTTCCAGCGGAGCGTGGAGGCGCGTGGGAGCTCCGGTCACGTGTAGTCTTCGGT
393136 AGCTTCTACCTTTATTTTTTGATACTTGTTGATGTCGTTTTCTTTGCTTGCTAGGTTTTTACTCC
66 AGCTTCTACCTTTATTTTTTGATACTTGTTGATGTCGTTTTCTTTGCTTGCTAGGTTTTTACTCC
393201 GTTGTTGTTGGTGCTTGTTCCTCGGTGTTCCTC-TGTTCTTCTTTTGCAGG-TTGATGATGGCTT
131 GTTGTTGTTGGTGCTTGTTCCTCGGTGTTCCTCATGTTCTTCTTTTGCAGGTTTGATGATGGCTT
393264 TTT
196 TTT
393267 ATATTTCGAATCTTCCAGCGGAGCGTGGAGGCGCGTGGGAGCTCCGGTCACCGTGTAGTCTTCGG
1 ATATTTCGAATCTTCCAGCGGAGCGTGGAGGCGCGTGGGAGCTCCGGTCA-CGTGTAGTCTTCGG
*
393332 TAAGCTTCTCTCCCTTTATTTTTTGATACTTGTTTGATGTCGTTTTTCTTTGCTTGCTAGGTTTT
65 T-AGC-T-TCTACCTTTATTTTTTGATACTTG-TTGATGTCG-TTTTCTTTGCTTGCTAGGTTTT
393397 TACTCCGTTGTTGTTGGTGCTTGTTCCTCGGTGTTCCTCTATGTTCTTCTTTTGCAGGTTTGATG
125 TACTCCGTTGTTGTTGGTGCTTGTTCCTCGGTGTTCCTC-ATGTTCTTCTTTTGCAGGTTTGATG
393462 ATGGCTTTTT
189 ATGGCTTTTT
393472 ATA
1 ATA
393475 GCCTCGTCGG
Statistics
Matches: 198, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
196 50 0.25
197 15 0.08
198 3 0.02
199 1 0.01
200 23 0.12
201 9 0.05
202 61 0.31
204 17 0.09
205 19 0.10
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.44
Consensus pattern (198 bp):
ATATTTCGAATCTTCCAGCGGAGCGTGGAGGCGCGTGGGAGCTCCGGTCACGTGTAGTCTTCGGT
AGCTTCTACCTTTATTTTTTGATACTTGTTGATGTCGTTTTCTTTGCTTGCTAGGTTTTTACTCC
GTTGTTGTTGGTGCTTGTTCCTCGGTGTTCCTCATGTTCTTCTTTTGCAGGTTTGATGATGGCTT
TTT
Found at i:393767 original size:17 final size:17
Alignment explanation
Indices: 393745--393788 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
393735 TAAGGTTAGT
393745 CTTGGGTCGGGTCTTCA
1 CTTGGGTCGGGTCTTCA
**
393762 CTTGGGTCAAGTCTTCA
1 CTTGGGTCGGGTCTTCA
*
393779 CTTGGTTCGG
1 CTTGGGTCGG
393789 TTCGGGTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.32, T:0.36
Consensus pattern (17 bp):
CTTGGGTCGGGTCTTCA
Found at i:395178 original size:2 final size:2
Alignment explanation
Indices: 395171--395204 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
395161 ATATAACCCC
395171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
395205 CGTAATACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:395301 original size:19 final size:18
Alignment explanation
Indices: 395261--395310 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
395251 GAACTTAAAT
395261 ATTTAAAATTTTTGTTTC
1 ATTTAAAATTTTTGTTTC
*
395279 ATTTAATAATTTCTT-TTTG
1 ATTTAA-AATTT-TTGTTTC
*
395298 ATTTTAAATTTTT
1 ATTTAAAATTTTT
395311 TCCTTAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 13 0.46
20 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTTAAAATTTTTGTTTC
Found at i:396566 original size:118 final size:118
Alignment explanation
Indices: 396412--396743 Score: 416
Period size: 119 Copynumber: 2.8 Consensus size: 118
396402 CAGTGTTATC
* * * * * * *
396412 ATCATAATCAGAATATGTAAGCACACATAGTGTTATCATATTAGAATCGTAATGTGCAGACAAAG
1 ATCAGAATCGGAATATATAAGCACACATAATGTTATCATATCAGAATCATAATGTGCACACAAAG
* *
396477 TGCAATCAGATCAGAATATATATACTAGTGCACCCACA-AGTACACCATAGTAT
66 TGCAATCAGATCAGAAAATATATACTAGTGCACCCACAGA-TACACCACAGTAT
* * *
396530 ATCAGAATCGGAATATATAAGCACACACAATATTATCATATCATAATCATAATGTGCACACAAAG
1 ATCAGAATCGGAATATATAAGCACACATAATGTTATCATATCAGAATCATAATGTGCACACAAAG
* * * *
396595 AGCAATTAGATCA-ATAAATTATATACCAGTGCACCCACCGATACACCACAGTAT
66 TGCAATCAGATCAGA-AAA-TATATACTAGTGCACCCACAGATACACCACAGTAT
* * * * * *
396649 ATCAGAATCGTAACATATATGCAAACATAATGCTATCATATCAGAATCATAATATGCACACAAAG
1 ATCAGAATCGGAATATATAAGCACACATAATGTTATCATATCAGAATCATAATGTGCACACAAAG
*
396714 TGCAATCACATCAGAAAATATATACTAGTG
66 TGCAATCAGATCAGAAAATATATACTAGTG
396744 TACCTTTAGG
Statistics
Matches: 181, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
117 1 0.01
118 79 0.44
119 99 0.55
120 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (118 bp):
ATCAGAATCGGAATATATAAGCACACATAATGTTATCATATCAGAATCATAATGTGCACACAAAG
TGCAATCAGATCAGAAAATATATACTAGTGCACCCACAGATACACCACAGTAT
Found at i:403338 original size:15 final size:16
Alignment explanation
Indices: 403314--403346 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
403304 TCAAAATTTC
403314 ATCAAAATCAA-AATA
1 ATCAAAATCAACAATA
*
403329 ATCAACATCAACAATA
1 ATCAAAATCAACAATA
403345 AT
1 AT
403347 ATACTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (16 bp):
ATCAAAATCAACAATA
Found at i:403758 original size:118 final size:118
Alignment explanation
Indices: 403533--403862 Score: 473
Period size: 118 Copynumber: 2.8 Consensus size: 118
403523 CAGTGCTATC
* * *
403533 ATCATAATCAGAA-ATATAAGCACACACAGTGCTATCATATTAGAATCGTAATGTGCACACAAAG
1 ATCAGAATCAAAACATATAAGCACACACAGTGCTATCATATCAGAATCGTAATGTGCACACAAAG
* * * *
403597 TGCAATCAGATCATAATATATATACTAGTACACCCACCTGTACACCACAGTAT
66 TGCAATCAAATCAGAATATATATACTAGTGCACCCACCGGTACACCACAGTAT
* ** * *
403650 ATTAGAATCAAAATGTATAAGCACACACAGTGCTATCATATCATAATTGTAATGTGCACACAAAG
1 ATCAGAATCAAAACATATAAGCACACACAGTGCTATCATATCAGAATCGTAATGTGCACACAAAG
403715 TGCAATCAAATCAGAATATATATACTAGTGCACCCACCGGTACACCACAGTAT
66 TGCAATCAAATCAGAATATATATACTAGTGCACCCACCGGTACACCACAGTAT
* ** ** * *
403768 ATCATAATCCTAACATATAAATACACACAGTGCTATCCTATCAGAATCGTAATGCGCACACAAAG
1 ATCAGAATCAAAACATATAAGCACACACAGTGCTATCATATCAGAATCGTAATGTGCACACAAAG
*
403833 TGCAATCACATCAGAATATATATACTAGTG
66 TGCAATCAAATCAGAATATATATACTAGTG
403863 TACCTTCAGG
Statistics
Matches: 188, Mismatches: 24, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
117 10 0.05
118 178 0.95
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (118 bp):
ATCAGAATCAAAACATATAAGCACACACAGTGCTATCATATCAGAATCGTAATGTGCACACAAAG
TGCAATCAAATCAGAATATATATACTAGTGCACCCACCGGTACACCACAGTAT
Found at i:406849 original size:29 final size:31
Alignment explanation
Indices: 406801--406858 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
406791 TTTTGATCCC
*
406801 TAAACTTTTACAAAATTTATACTTTAGTCTT
1 TAAACTTTTACAAAACTTATACTTTAGTCTT
*
406832 TAAAC-TTT-CAAAACTTATATTTTAGTC
1 TAAACTTTTACAAAACTTATACTTTAGTC
406859 ACTAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 3 0.12
31 5 0.20
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (31 bp):
TAAACTTTTACAAAACTTATACTTTAGTCTT
Found at i:408091 original size:22 final size:22
Alignment explanation
Indices: 408063--408107 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
408053 AGAGAGAAAA
*
408063 GGTTGAACCTTGCCAACTTCAT
1 GGTTGAACCTTACCAACTTCAT
408085 GGTTGAACCTTACCAACTTCAT
1 GGTTGAACCTTACCAACTTCAT
408107 G
1 G
408108 AGTAATTTTG
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:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (22 bp):
GGTTGAACCTTACCAACTTCAT
Found at i:412148 original size:18 final size:18
Alignment explanation
Indices: 412125--412164 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
412115 ATTGGCATTC
412125 AAATATGTATATATAAAA
1 AAATATGTATATATAAAA
412143 AAATATGTATATATAAAA
1 AAATATGTATATATAAAA
412161 AAAT
1 AAAT
412165 TAATTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AAATATGTATATATAAAA
Found at i:413200 original size:6 final size:6
Alignment explanation
Indices: 413189--413214 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
413179 AAGGTATATC
413189 TCTTTT TCTTTT TCTTTT TCTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTTT TC
413215 AAAGGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:415889 original size:13 final size:12
Alignment explanation
Indices: 415860--415930 Score: 65
Period size: 13 Copynumber: 5.7 Consensus size: 12
415850 TATTCAAGAC
*
415860 AAAAAGAAAAAA
1 AAAAAGAAGAAA
415872 GAAAATGAGAAGAAA
1 -AAAA--AGAAGAAA
415887 AAAAAGAAAGAAA
1 AAAAAG-AAGAAA
415900 AAAAAG-AG-AA
1 AAAAAGAAGAAA
415910 AAAAAGAAGAACA
1 AAAAAGAAGAA-A
*
415923 AATAAGAA
1 AAAAAGAA
415931 ATAGAACATG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
10 8 0.16
11 4 0.08
12 3 0.06
13 24 0.48
14 4 0.08
15 7 0.14
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAGAAGAAA
Found at i:415895 original size:27 final size:26
Alignment explanation
Indices: 415860--415920 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
415850 TATTCAAGAC
*
415860 AAAAAGAAA-AAAGAAAATGAGAAGAAA
1 AAAAAGAAAGAAA-AAAAAGAGAA-AAA
415887 AAAAAGAAAGAAAAAAAAGAGAAAAA
1 AAAAAGAAAGAAAAAAAAGAGAAAAA
*
415913 AAGAAGAA
1 AAAAAGAA
415921 CAAATAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 10 0.32
27 18 0.58
28 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (26 bp):
AAAAAGAAAGAAAAAAAAGAGAAAAA
Found at i:415929 original size:23 final size:22
Alignment explanation
Indices: 415881--415931 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
415871 AGAAAATGAG
415881 AAGAAAAAAAAGAAAGAAAAAA
1 AAGAAAAAAAAGAAAGAAAAAA
*
415903 AAGAGAAAAAAAG-AAGAACAAAT
1 AAGA-AAAAAAAGAAAGAA-AAAA
415926 AAGAAA
1 AAGAAA
415932 TAGAACATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (22 bp):
AAGAAAAAAAAGAAAGAAAAAA
Found at i:417550 original size:45 final size:45
Alignment explanation
Indices: 417421--418083 Score: 775
Period size: 45 Copynumber: 15.0 Consensus size: 45
417411 GAAACCTCAA
** * * * *
417421 CTTGACTTTCTCATGAAAAAGAGTGAATCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
417466 ATTGACTTTCTCGCGATA-A--TGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGA-AGAGGAGTCAACCTTTTAGTGATGTCATT
417509 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
** * *
417554 CTTGACTTTCTCGCGAAGAGGAGTTGACCTTTTAATGATGTTATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
417599 CTTGGCTTTCTCGTGAAGAGGAGTCAACCTTTTAGT-A----A--
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * *
417637 C--G--TTTCTCGTGAAGAGGAGTCAACCTTTTAGTGACGTGATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
417678 CTTGACTTTCTCGCGAAGATGAGTCAACTTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * *
417723 CTTGACTTTCTCGTGAAGAGGAGTAAACCTTTTAGTGAAGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* ** * *
417768 ATTGACTTTCTCATGAAGAGGAGTTAACCTTTTAGTGATTTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
417813 ATTGACTTTCTCGC-AATGAGGAATCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAA-GAGGAGTCAACCTTTTAGTGATGTCATT
* * *
417858 CTTGAGTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTTATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* *
417903 CTTGAC-TTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
** **
417947 CTTGACTTTCTCGCGAAGAGGAGTCAATATTTTAGTGATGTGGTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
* * * *
417992 TTTGACTTTCTCGCAAAGAGGA-TCCAACCTTTAAATGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGT-CAACCTTTTAGTGATGTCATT
** *
418037 CTTGACTTTCTCATGAAGAGGAGCCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
418082 CT
1 CT
418084 CAACTTAACT
Statistics
Matches: 533, Mismatches: 65, Indels: 40
0.84 0.10 0.06
Matches are distributed among these distances:
34 30 0.06
35 1 0.00
36 1 0.00
38 1 0.00
39 1 0.00
40 1 0.00
41 1 0.00
42 1 0.00
43 38 0.07
44 46 0.09
45 409 0.77
46 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (45 bp):
CTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTCATT
Found at i:417648 original size:34 final size:34
Alignment explanation
Indices: 417605--417673 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
417595 TATTCTTGGC
417605 TTTCTCGTGAAGAGGAGTCAACCTTTTAGTAACG
1 TTTCTCGTGAAGAGGAGTCAACCTTTTAGTAACG
*
417639 TTTCTCGTGAAGAGGAGTCAACCTTTTAGTGACG
1 TTTCTCGTGAAGAGGAGTCAACCTTTTAGTAACG
417673 T
1 T
417674 GATTCTTGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (34 bp):
TTTCTCGTGAAGAGGAGTCAACCTTTTAGTAACG
Found at i:417779 original size:169 final size:173
Alignment explanation
Indices: 417486--418083 Score: 715
Period size: 179 Copynumber: 3.4 Consensus size: 173
417476 TCGCGATAAT
417486 GTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
1 GTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
* * *
417551 ATTCTTGACTTTCTCGCGAAGAGGAGTTGACCTTTTAATGATGTTATTCTTGGCTTTCTCGTGAA
66 ATTCTTGACTTTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAA
*
417616 GAGGAGTCAACCTTTTAGT-A-A-CG-TTTCTCGTGAA-GAGGA
131 GAGGAGTCAACCTTTTAGTCATATCGATTTCTCG-CAATGAGGA
* * * *
417655 GTCAACCTTTTAGTGACGTGATTCTTGACTTTCTCGCGAAGATGAGTCAACTTTTTAGTGATGTC
1 GTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
* * * * * *
417720 ATTCTTGACTTTCTCGTGAAGAGGAGTAAACCTTTTAGTGAAGTCATTATTGACTTTCTCATGAA
66 ATTCTTGACTTTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAA
* *
417785 GAGGAGTTAACCTTTTAGTGATTTCATTATTGACTTTCTCGCAATGAGGA
131 GAGGAGTCAACCTTTTA--G---TCA-TATCGA-TTTCTCGCAATGAGGA
* * * *
417835 ATCAACCTTTTAGTGATGTCATTCTTGAGTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTT
1 GTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
*
417900 ATTCTTGAC-TTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATTCTTGACTTTCTCGCGAA
66 ATTCTTGACTTTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAA
** * * * *
417964 GAGGAGTCAATATTTTAGTGATGTGGTTTTTGACTTTCTCGCAAAGAGGA
131 GAGGAGTCAACCTTTTAGTCA------TATCGA-TTTCTCGCAATGAGGA
* * ** *
418014 -TCCAACCTTTAAATGATGTCATTCTTGACTTTCTCATGAAGAGGAGCCAACCTTTTAGTGATGT
1 GT-CAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGT
418078 CATTCT
65 CATTCT
418084 CAACTTAACT
Statistics
Matches: 368, Mismatches: 43, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
169 133 0.36
171 1 0.00
174 3 0.01
175 1 0.00
177 2 0.01
178 2 0.01
179 148 0.40
180 78 0.21
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (173 bp):
GTCAACCTTTTAGTGATGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAACCTTTTAGTGATGTC
ATTCTTGACTTTCTCGCGAAGAGGAGTTAACCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAA
GAGGAGTCAACCTTTTAGTCATATCGATTTCTCGCAATGAGGA
Found at i:419342 original size:106 final size:106
Alignment explanation
Indices: 419152--419353 Score: 298
Period size: 106 Copynumber: 1.9 Consensus size: 106
419142 CTGAAGTGCA
* ***
419152 GTGAAGTGAATCAAAGTTTACATATCTGATCTACCCTGAAGAGCAGTTGAGCATATCCCTATTTC
1 GTGAAGTGAATCAAAGTTTACAAATCTGATCTACCCTGAAGAGCAAAGGAGCATATCCCTATTTC
* *
419217 CATATTTGATATTCTTTGAAGAGAAGTGAAGACAATCTTCC
66 CAGATTTGATATTCCTTGAAGAGAAGTGAAGACAATCTTCC
* *
419258 GTGAAGTGAATCAAAGTTTTCAAATCTGATCTACCTTGAAGAGCAAAGGAGCATATCCCCT-TTT
1 GTGAAGTGAATCAAAGTTTACAAATCTGATCTACCCTGAAGAGCAAAGGAGCATAT-CCCTATTT
* *
419322 CCAGATTTGATCTTCCTTGAAGAGGAGTGAAG
65 CCAGATTTGATATTCCTTGAAGAGAAGTGAAG
419354 TAAATCAACC
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 81 0.95
107 4 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (106 bp):
GTGAAGTGAATCAAAGTTTACAAATCTGATCTACCCTGAAGAGCAAAGGAGCATATCCCTATTTC
CAGATTTGATATTCCTTGAAGAGAAGTGAAGACAATCTTCC
Found at i:423516 original size:20 final size:20
Alignment explanation
Indices: 423491--423532 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
423481 TTGATAAAAA
*
423491 TTTTT-ATAAAAATATTAATT
1 TTTTTAATAAAAA-ATAAATT
423511 TTTTTAATAAAAAATAAATT
1 TTTTTAATAAAAAATAAATT
423531 TT
1 TT
423533 GACGTGTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTAATAAAAAATAAATT
Found at i:423803 original size:19 final size:19
Alignment explanation
Indices: 423770--423819 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
423760 TGCATTATGC
* *
423770 CATAGGTTTATATTAATTT
1 CATAGGATTAAATTAATTT
*
423789 CGTAGGATTAAATTAATTT
1 CATAGGATTAAATTAATTT
423808 CATAGGATTAAA
1 CATAGGATTAAA
423820 GTTATTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (19 bp):
CATAGGATTAAATTAATTT
Found at i:424203 original size:4 final size:4
Alignment explanation
Indices: 424194--424220 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
424184 GGGAGATTGT
424194 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
424221 TATGTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:424336 original size:26 final size:26
Alignment explanation
Indices: 424300--424353 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
424290 ATTTTTGCTT
424300 TGATAAATATTTCTTTCGTTTAGTTA
1 TGATAAATATTTCTTTCGTTTAGTTA
424326 TGATAAATATTTCTTTCGTTTAGTTA
1 TGATAAATATTTCTTTCGTTTAGTTA
424352 TG
1 TG
424354 CATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.13, T:0.54
Consensus pattern (26 bp):
TGATAAATATTTCTTTCGTTTAGTTA
Found at i:426447 original size:21 final size:22
Alignment explanation
Indices: 426414--426456 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
426404 AGTATTTTAT
*
426414 GATACATTGGATTT-TGAGATA
1 GATACATTAGATTTGTGAGATA
*
426435 GATATATTAGATTTGTGAGATA
1 GATACATTAGATTTGTGAGATA
426457 TAGAGAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (22 bp):
GATACATTAGATTTGTGAGATA
Found at i:427042 original size:23 final size:22
Alignment explanation
Indices: 427016--427061 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
427006 AAAAATACCA
427016 AAATAAAAATG-AGTAAAATAATG
1 AAATAAAAATGCA-TAAAA-AATG
*
427039 AAATAAATATGCATAAAAAATG
1 AAATAAAAATGCATAAAAAATG
427061 A
1 A
427062 CAAAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 15 0.71
24 1 0.05
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (22 bp):
AAATAAAAATGCATAAAAAATG
Found at i:427316 original size:18 final size:18
Alignment explanation
Indices: 427265--427310 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
427255 ACAATATAAT
*
427265 AATAAAACATAATATATTA
1 AATAAAA-ATAATAAATTA
427284 AATAAAAATAATAAATTA
1 AATAAAAATAATAAATTA
427302 AACTAAAAA
1 AA-TAAAAA
427311 ATTAAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAAAATAATAAATTA
Found at i:428958 original size:36 final size:34
Alignment explanation
Indices: 428854--428966 Score: 160
Period size: 34 Copynumber: 3.4 Consensus size: 34
428844 ACAAAAAAAA
* *
428854 TTTCAAGGGAAACAATCTCAAAGG---TTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTG
*
428885 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTG
428919 TTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTGTG
1 TTTCAAGAGAAACAATTTCAAAGG-TT-TTTTTGTG
428955 TTTCAAGAGAAA
1 TTTCAAGAGAAA
428967 ATGTCTCAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 21 0.29
34 30 0.41
35 2 0.03
36 20 0.27
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.38
Consensus pattern (34 bp):
TTTCAAGAGAAACAATTTCAAAGGTTTTTTTGTG
Found at i:429060 original size:67 final size:67
Alignment explanation
Indices: 428952--429128 Score: 309
Period size: 67 Copynumber: 2.6 Consensus size: 67
428942 GTTTCTTTTT
*
428952 GTGTTTCAAGAGAAAATGTCTCAAGGGTGACAAAATTTTGTTTTAAGAAAAACATATTCAAAGAT
1 GTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACATATTCAAAGAT
429017 TG
66 TG
*
429019 GTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACATATTCAAAGAT
1 GTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACATATTCAAAGAT
429084 TG
66 TG
* * *
429086 GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 GTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTTGTTT
429129 CAAGGGAAAC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 105 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (67 bp):
GTGTTTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACATATTCAAAGAT
TG
Found at i:429174 original size:36 final size:36
Alignment explanation
Indices: 429087--429364 Score: 306
Period size: 36 Copynumber: 7.8 Consensus size: 36
429077 CAAAGATTGG
429087 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
429124 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
429160 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
429196 TATTTCCAA-AGAAAATAGAT-TC-A-A-AG----ATTT
1 TGTTT-CAAGAGAAACT-G-TCTCAAGAGAGACAAAATT
* *
429226 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
429262 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
429298 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
429335 AGTTCCAA-AGAAAACTGTCTCAAGGGAGAC
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGAC
429365 GAATTTTTTT
Statistics
Matches: 204, Mismatches: 23, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.00
29 6 0.03
30 11 0.05
31 1 0.00
32 2 0.01
34 2 0.01
35 1 0.00
36 114 0.56
37 65 0.32
38 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:429307 original size:21 final size:21
Alignment explanation
Indices: 429245--429307 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
429235 GGAAACCGTC
429245 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
429266 TCAAG-G-G---AAA-CTATC
1 TCAAGAGAGACAAAATTTGTT
429281 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
429302 TCAAGA
1 TCAAGA
429308 AAAACTGTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 1 0.03
19 1 0.03
20 4 0.13
21 13 0.43
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:429313 original size:138 final size:140
Alignment explanation
Indices: 429020--429349 Score: 488
Period size: 138 Copynumber: 2.4 Consensus size: 140
429010 CAAAGATTGG
* * *** *
429020 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAA-TT-TTGTTTTAAGAAAAACATATTCAAAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATT-TCCAAAG-AAAACAGATTCAAAGA
* *
429083 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAG
64 TTGGTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAG
429148 AGAGACAAAATA
129 AGAGACAAAATA
*
429160 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAATAGATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAACAGATTCAAAGATT
* *
429225 -TTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAG
66 GGTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAG
*
429288 AGACAAAATT
131 AGACAAAATA
* *
429298 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAAC
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAAC
429350 TGTCTCAAGG
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
138 85 0.49
139 32 0.18
140 48 0.28
141 6 0.03
142 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (140 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTTCCAAAGAAAACAGATTCAAAGATT
GGTGTTTCAAGAGAAACCGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAG
AGACAAAATA
Found at i:429479 original size:36 final size:36
Alignment explanation
Indices: 429429--429499 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
429419 TCAAGGTTTA
*
429429 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
* *
429465 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
429500 CTTCTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
Found at i:430256 original size:13 final size:15
Alignment explanation
Indices: 430228--430262 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
430218 TTTGTTTTCC
430228 TTGCTCCAACAAATT
1 TTGCTCCAACAAATT
430243 TTGC-CCAA-AAATT
1 TTGCTCCAACAAATT
430256 TTGCTCC
1 TTGCTCC
430263 TCTTGCCCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (15 bp):
TTGCTCCAACAAATT
Found at i:431032 original size:95 final size:95
Alignment explanation
Indices: 430864--431045 Score: 274
Period size: 95 Copynumber: 1.9 Consensus size: 95
430854 ATATGTAAAT
* * * * *
430864 ACCTTTATCAAGTTAGCTGAATCTTATCCATTAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGCCTTAGAGGG
* * *
430929 ATAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAACTTTATTGTATAGTATAATC
* *
430959 ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCTGGAGCATTTAACCAATTGCTTTAGAGGG
1 ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGCCTTAGAGGG
431024 ACAACTCAAACTTTATTGTATA
66 ACAACTCAAACTTTATTGTATA
431046 TAAATAATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (95 bp):
ACCTTTATCAAGCTAGCTGAATATTATCCATAAAGCCGGAGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAACTTTATTGTATAGTATAATC
Found at i:434825 original size:12 final size:14
Alignment explanation
Indices: 434798--434847 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
434788 TATCATGCAC
434798 ATAA-AAAAATACA
1 ATAATAAAAATACA
434811 AT-ATAAAAATA-A
1 ATAATAAAAATACA
*
434823 ATAATAAAAAGACCA
1 ATAATAAAAATA-CA
434838 A-AATAAAAAT
1 ATAATAAAAAT
434848 GAGTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 4 0.13
13 17 0.55
14 8 0.26
15 2 0.06
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.18
Consensus pattern (14 bp):
ATAATAAAAATACA
Found at i:435089 original size:10 final size:10
Alignment explanation
Indices: 434990--435105 Score: 52
Period size: 10 Copynumber: 11.7 Consensus size: 10
434980 AAAACAAATA
434990 AATATATATAT
1 AATATATA-AT
*
435001 AATA-ATCA-
1 AATATATAAT
*
435009 AATATAGAAT
1 AATATATAAT
435019 AA-A-ATAGAT
1 AATATATA-AT
*
435028 AA-ATAGAAGT
1 AATATATAA-T
435038 AA-ATA-AAT
1 AATATATAAT
435046 AAATATATATAT
1 -AATATATA-AT
*
435058 ATATATACACAT
1 A-ATATATA-AT
435070 AATA-ATAAT
1 AATATATAAT
*
435079 ACTATATAAT
1 AATATATAAT
435089 AATATA-ACAT
1 AATATATA-AT
435099 AATATAT
1 AATATAT
435106 TAAATAAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 26
0.69 0.08 0.22
Matches are distributed among these distances:
8 7 0.09
9 20 0.24
10 35 0.43
11 9 0.11
12 11 0.13
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.33
Consensus pattern (10 bp):
AATATATAAT
Found at i:435100 original size:13 final size:14
Alignment explanation
Indices: 435060--435102 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
435050 ATATATATAT
435060 ATATACACATAATA
1 ATATACACATAATA
*
435074 ATAATACTATATAATA
1 AT-ATAC-ACATAATA
435090 ATATA-ACATAATA
1 ATATACACATAATA
435103 TATTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 7 0.28
14 2 0.08
15 7 0.28
16 9 0.36
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATACACATAATA
Found at i:436871 original size:66 final size:64
Alignment explanation
Indices: 436762--437128 Score: 281
Period size: 66 Copynumber: 5.6 Consensus size: 64
436752 GGAAACGATC
* * * *
436762 TCAAAGATATGTGTTTTCATGAGAAACGGCCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAA
1 TCAAAGATTTGTG-TTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTGTTTTAAGGGAAA-AA
436827 AT
63 AT
* * *
436829 TCAAAGATTTGTGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAA-TTGTTTCAAGGGAAACAAT
1 TCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAA-GGAGACAAAATTTGTTTTAAGGGAAAAAAT
* * ***** * *
436893 CTCAAAGGTTTTGTGTTTCAAGAGAAACAT-TTTCAA--AG-GTTTTTTTGTTTCAAGAGAAAAC
1 -TCAAA-GATTTGTGTTTCAAGAGAAAC-TGTCTCAAGGAGACAAAATTTGTTTTAAGGGAAAA-
436954 AATT
62 AA-T
* *
436958 TCAAAGTTTCTTTTTGTGTTTCAAGAGAAACTGTCTCAAGG-TACAAAATTTGTTTTAA--GAAA
1 TCAAAG-----ATTTGTGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTTGTTTTAAGGGAAA
437020 ACATAT
61 A-A-AT
* *
437026 TCAAAGA-TTG-GTTTCAAGAGAAATTGTCTCAAGGAGACAAAATTTTGTTTTAA--AAAAACAT
1 TCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGAGACAAAA-TTTGTTTTAAGGGAAAA-A-
437087 AT
63 AT
*
437089 TCAAAGATTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAG-GAGA
437129 TTTGTTACAG
Statistics
Matches: 250, Mismatches: 29, Indels: 43
0.78 0.09 0.13
Matches are distributed among these distances:
61 23 0.09
62 9 0.04
63 43 0.17
64 12 0.05
65 42 0.17
66 58 0.23
67 14 0.06
68 39 0.16
69 1 0.00
70 9 0.04
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (64 bp):
TCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGAGACAAAATTTGTTTTAAGGGAAAAAAT
Found at i:436947 original size:32 final size:32
Alignment explanation
Indices: 436874--436988 Score: 142
Period size: 31 Copynumber: 3.5 Consensus size: 32
436864 GGAGACAAAA
* *
436874 TTGTTTCAAGGGAAACAATCTCAAAGG-TTTT
1 TTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
* *
436905 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTT
1 TTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
*
436937 TTGTTTCAAGAGAAAACAATTTCAAAGTTTCTTTT
1 TTGTTTCAAGAG-AAACAATTTCAAAG-GT-TTTT
436972 TGTGTTTCAAGAGAAAC
1 T-TGTTTCAAGAGAAAC
436989 TGTCTCAAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
31 23 0.32
32 15 0.21
33 13 0.18
34 1 0.01
35 9 0.12
36 11 0.15
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TTGTTTCAAGAGAAACAATTTCAAAGGTTTTT
Found at i:437143 original size:63 final size:59
Alignment explanation
Indices: 436971--437174 Score: 223
Period size: 63 Copynumber: 3.3 Consensus size: 59
436961 AAGTTTCTTT
*
436971 TTGTGTTTCAAGAGAAACTGTCTCAAGGTACAAAATTTGTTTTAAGAAAACATATTCAAAGA
1 TTGTGTTTCAAGAGAAACTGTCTCAAGG-A-GAAATTTGTTTTAA-AAAACATATTCAAAGA
*
437033 TTG-GTTTCAAGAGAAATTGTCTCAAGGAGACAAAATTTTGTTTTAAAAAAACATATTCAAAGA
1 TTGTGTTTCAAGAGAAACTGTCTCAAGGAG---AAA-TTTGTTTT-AAAAAACATATTCAAAGA
* ** *
437096 TTGGTGTTTCAAGAGAAACTGTCTCAA-GAGAGATTTGTTACAGTAAAACATATTCAAAGA
1 TT-GTGTTTCAAGAGAAACTGTCTCAAGGAGAAATTTGTTTTA-AAAAACATATTCAAAGA
* * *
437156 TTTTGTTTTAAGGGAAACT
1 TTGTGTTTCAAGAGAAACT
437175 ATTTTCAAGG
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
59 15 0.12
60 25 0.20
61 25 0.20
62 6 0.05
63 26 0.21
64 6 0.05
65 21 0.17
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (59 bp):
TTGTGTTTCAAGAGAAACTGTCTCAAGGAGAAATTTGTTTTAAAAAACATATTCAAAGA
Found at i:437236 original size:36 final size:36
Alignment explanation
Indices: 437189--437259 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
437179 TCAAGGTTTA
* * *
437189 TGTTTCAAGGGAAACTGTCTCAAGGGAGATAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGCGAAATAAAATT
437225 TGTTTCAAGGGAAACTATCTCAAGCGAAATAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGCGAAATAAAAT
437260 ATTCTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAAATAAAATT
Found at i:437370 original size:36 final size:36
Alignment explanation
Indices: 437327--437426 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 36
437317 CTTAAGCGAG
**
437327 ACAAATCTTGTTTTAAGAAAAACAATCTTGAGGGAA
1 ACAAATCTTGTTTTAAGAAAAACAATCTAAAGGGAA
* * * * * * *
437363 ATAAATCTTCTTTTGAGTAAAACAGTCTAAAGTGAG
1 ACAAATCTTGTTTTAAGAAAAACAATCTAAAGGGAA
*
437399 ACAAAGTC-TGTTTTAAGAATAACAATCT
1 ACAAA-TCTTGTTTTAAGAAAAACAATCT
437427 CAAGTGAGAT
Statistics
Matches: 48, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
36 46 0.96
37 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (36 bp):
ACAAATCTTGTTTTAAGAAAAACAATCTAAAGGGAA
Found at i:437413 original size:72 final size:76
Alignment explanation
Indices: 437267--437426 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 76
437257 AATATTCTTT
* *
437267 AAAAACAATCTTGAGTGAAAATGAAATGCCTTCTTTCGCGTGAAAAAGCTCTTAAGCGAGACAAA
1 AAAAACAATCTTGAGTGAAAATGAAAT-CCTTCTTTCGAGTGAAAAAGCTCTAAAGCGAGACAAA
437332 TCTTGTTTTAAG
65 TCTTGTTTTAAG
* * *
437344 AAAAACAATCTTGAG-GGAAAT-AAAT-CTTCTTTTGAGT-AAAACAG-TCTAAAGTGAGACAAA
1 AAAAACAATCTTGAGTGAAAATGAAATCCTTCTTTCGAGTGAAAA-AGCTCTAAAGCGAGACAAA
437404 GTC-TGTTTTAAG
65 -TCTTGTTTTAAG
*
437416 AATAACAATCT
1 AAAAACAATCT
437427 CAAGTGAGAT
Statistics
Matches: 75, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
72 37 0.49
73 14 0.19
75 4 0.05
76 5 0.07
77 15 0.20
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAAATGAAATCCTTCTTTCGAGTGAAAAAGCTCTAAAGCGAGACAAAT
CTTGTTTTAAG
Found at i:442806 original size:19 final size:18
Alignment explanation
Indices: 442770--442821 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
442760 AAAAAAAAAG
*
442770 AAATAAAAAGATAGATAAAT
1 AAATAAAATGA-A-ATAAAT
*
442790 AAATTAAAGTGAAATAAAT
1 AAA-TAAAATGAAATAAAT
442809 AAATAAAATGAAA
1 AAATAAAATGAAA
442822 GATATAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.32
19 9 0.32
20 4 0.14
21 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAATGAAATAAAT
Found at i:442828 original size:18 final size:19
Alignment explanation
Indices: 442786--442828 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
442776 AAAGATAGAT
* *
442786 AAATAAATTAAAGTGAAAT
1 AAATAAATTAAAATGAAAG
442805 AAATAAA-TAAAATGAAAG
1 AAATAAATTAAAATGAAAG
*
442823 ATATAA
1 AAATAA
442829 CAAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (19 bp):
AAATAAATTAAAATGAAAG
Found at i:442919 original size:2 final size:2
Alignment explanation
Indices: 442912--442948 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
442902 ATAGAAGTAA
442912 AT AT AT AT 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 A
442949 ATAATAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:444039 original size:14 final size:14
Alignment explanation
Indices: 444020--444050 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
444010 CTGTAGAGAT
444020 AATTTGGTGTAACA
1 AATTTGGTGTAACA
444034 AATTTGGTGTAACA
1 AATTTGGTGTAACA
444048 AAT
1 AAT
444051 ATAACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (14 bp):
AATTTGGTGTAACA
Found at i:444354 original size:4 final size:4
Alignment explanation
Indices: 444345--444430 Score: 97
Period size: 4 Copynumber: 21.2 Consensus size: 4
444335 AGTGGACCCT
*
444345 CTCC CTCC CTCC CTCC CTCTC C-CT CTCC CTCC CTCC CTCC CTCC CTCC
1 CTCC CTCC CTCC CTCC CTC-C CTCC CTCC CTCC CTCC CTCC CTCC CTCC
*
444393 CTCC CTCTC C-CC CTCCC CTCC ACTCC C-CC CCCC CTCC C
1 CTCC CTC-C CTCC CT-CC CTCC -CTCC CTCC CTCC CTCC C
444431 CCCCCTCTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
3 6 0.08
4 54 0.75
5 12 0.17
ACGTcount: A:0.01, C:0.76, G:0.00, T:0.23
Consensus pattern (4 bp):
CTCC
Found at i:447562 original size:2 final size:2
Alignment explanation
Indices: 447555--447634 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
447545 TCTAACCATA
447555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447635 TTGTTTGTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:453052 original size:34 final size:34
Alignment explanation
Indices: 452993--453059 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
452983 TTCTTGAGAG
*
452993 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTGATC-AGAGAGAAGTTGTTA
453027 TTGTTTTCTCCTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-GATCAGAGAGAAGTTGT
453060 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTGATCAGAGAGAAGTTGTTA
Found at i:454654 original size:23 final size:23
Alignment explanation
Indices: 454628--454820 Score: 386
Period size: 23 Copynumber: 8.4 Consensus size: 23
454618 GGATTTACAA
454628 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454651 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454674 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454697 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454720 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454743 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454766 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454789 GAACCAATTCAAGCGAATGGCTT
1 GAACCAATTCAAGCGAATGGCTT
454812 GAACCAATT
1 GAACCAATT
454821 GCAACCATTT
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 170 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (23 bp):
GAACCAATTCAAGCGAATGGCTT
Found at i:454860 original size:54 final size:55
Alignment explanation
Indices: 454789--454909 Score: 165
Period size: 54 Copynumber: 2.2 Consensus size: 55
454779 CGAATGGCTT
* * ** *
454789 GAACCAA-TTCAAGCGAATGGCTTGAACCAATTGCAACCATTTATTTATTTGCAA
1 GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
* *
454843 GAACCAACTCCAA-CGAATGACTTGGACCAGTTGCAACCATTTATGGATTCGCAA
1 GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
454897 GAACCAACTCCAA
1 GAACCAACTCCAA
454910 TGATTGATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 55 0.93
55 4 0.07
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.24
Consensus pattern (55 bp):
GAACCAACTCCAAGCGAATGACTTGAACCAATTGCAACCATTTATGGATTCGCAA
Found at i:455302 original size:138 final size:130
Alignment explanation
Indices: 455120--455394 Score: 415
Period size: 138 Copynumber: 2.1 Consensus size: 130
455110 CTTCAACGAC
455120 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
1 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
** *
455185 AAAAGAAAGAAAAAGAAAAAAAGAATGTAAATTCCATGAAATCTGGGCATCCCATGCTGGTGCCC
66 ---A-AAAG--AAAG-AAAAAA-AATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCC
455250 ATGTCTGG
123 ATGTCTGG
* *
455258 TCACTGTAATCACCATTTTTTATCTCAAAATTATTTATTATTATATTATTATTACCAAAAAGCAT
1 TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
* *
455323 AAAAGAAAGAAAACAAATGTAAATTCCATGAAATCAAGGCATTCCATGCTGGAGCCCATGTCTGG
66 AAAAGAAAGAAAAAAAATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCCATGTCTGG
455388 TCACTGT
1 TCACTGT
455395 TGTTGCACCC
Statistics
Matches: 130, Mismatches: 7, Indels: 8
0.90 0.05 0.06
Matches are distributed among these distances:
130 53 0.41
131 5 0.04
132 4 0.03
134 4 0.03
135 1 0.01
138 63 0.48
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.31
Consensus pattern (130 bp):
TCACTGTAATCACCATTTTTTATCCCAAAATTAATTATTATTATATTATTATTACCAAAAAGCAT
AAAAGAAAGAAAAAAAATGTAAATTCCATGAAATCAAGGCATCCCATGCTGGAGCCCATGTCTGG
Found at i:456670 original size:22 final size:23
Alignment explanation
Indices: 456626--456671 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
456616 TTAATTACAA
**
456626 TTTAGTCCTTGATTTTATTTTAT
1 TTTAGTCCTTGATTTTAAATTAT
456649 TTTAGTCCTT-ATTTTAAATTAT
1 TTTAGTCCTTGATTTTAAATTAT
456671 T
1 T
456672 CCCTAACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.63
Consensus pattern (23 bp):
TTTAGTCCTTGATTTTAAATTAT
Found at i:459334 original size:17 final size:18
Alignment explanation
Indices: 459299--459334 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
459289 CAACTTAAAA
*
459299 AAGATGAACAATTCAAAG
1 AAGATGAACAATCCAAAG
459317 AAGATGAACAA-CCAAAG
1 AAGATGAACAATCCAAAG
459334 A
1 A
459335 TGAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.11
Consensus pattern (18 bp):
AAGATGAACAATCCAAAG
Found at i:473582 original size:20 final size:20
Alignment explanation
Indices: 473553--473591 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
473543 ATTCTACCAC
*
473553 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
473573 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
473592 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:488548 original size:29 final size:30
Alignment explanation
Indices: 488495--488551 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
488485 TTATATAAAT
488495 AATAATACATATAATTAATATAATATTTCA
1 AATAATACATATAATTAATATAATATTTCA
*
488525 AATAATATAT-TAGATT-ATATAATATTT
1 AATAATACATATA-ATTAATATAATATTT
488552 TGAGACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (30 bp):
AATAATACATATAATTAATATAATATTTCA
Found at i:488713 original size:30 final size:30
Alignment explanation
Indices: 488655--488713 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
488645 TAAATTATAA
*
488655 ATTTACTCATTAAATTTTATTTTTTTTCTT
1 ATTTACTCATTAAATTTTATTATTTTTCTT
**
488685 ATTTCACTCATTGCATTTT-TTATTTTTCT
1 ATTT-ACTCATTAAATTTTATTATTTTTCT
488714 AACATCGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.64
Consensus pattern (30 bp):
ATTTACTCATTAAATTTTATTATTTTTCTT
Found at i:491252 original size:18 final size:19
Alignment explanation
Indices: 491216--491252 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
491206 TACGGAATGT
491216 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
491236 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
491253 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:491439 original size:36 final size:36
Alignment explanation
Indices: 491399--491467 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
491389 TACAAATTGT
491399 AAAATATTTATAT-ATTTTCTCTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TCTAAAAAATTAAATTC
* *
491435 AAAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTCTAAAAAATTAAA
491468 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 25 0.83
37 5 0.17
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTCTAAAAAATTAAATTC
Found at i:494203 original size:18 final size:18
Alignment explanation
Indices: 494182--494227 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
494172 AAATTAACCT
494182 CAGAAGGGAAGAGAGCTC
1 CAGAAGGGAAGAGAGCTC
494200 CAGAAGGGAAGAGAGCTC
1 CAGAAGGGAAGAGAGCTC
494218 CAGAAGGGAA
1 CAGAAGGGAA
494228 AACAGCGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.15, G:0.39, T:0.04
Consensus pattern (18 bp):
CAGAAGGGAAGAGAGCTC
Found at i:496930 original size:26 final size:26
Alignment explanation
Indices: 496895--496948 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
496885 AAATTAAATG
496895 TATATTTAAATTACTGAAAAAATCTC
1 TATATTTAAATTACTGAAAAAATCTC
496921 TATATTTAAATTACTGAAAAAATCTC
1 TATATTTAAATTACTGAAAAAATCTC
496947 TA
1 TA
496949 CCTCCCTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (26 bp):
TATATTTAAATTACTGAAAAAATCTC
Found at i:497053 original size:9 final size:9
Alignment explanation
Indices: 497039--497091 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
497029 CTATAAAAAA
497039 TTAAAATAT
1 TTAAAATAT
497048 TTAAAATAT
1 TTAAAATAT
*
497057 ATTTAAATAT
1 -TTAAAATAT
497067 TTAAAAATTAT
1 TT-AAAA-TAT
497078 TTAAAATAT
1 TTAAAATAT
*
497087 GTAAA
1 TTAAA
497092 TGTTAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
9 18 0.47
10 15 0.39
11 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
TTAAAATAT
Found at i:497060 original size:11 final size:11
Alignment explanation
Indices: 497044--497086 Score: 56
Period size: 10 Copynumber: 4.2 Consensus size: 11
497034 AAAAATTAAA
497044 ATATTTAAAAT
1 ATATTTAAAAT
497055 ATATTT-AAAT
1 ATATTTAAAAT
*
497065 AT-TTAAAAAT
1 ATATTTAAAAT
497075 -TATTTAAAAT
1 ATATTTAAAAT
497085 AT
1 AT
497087 GTAAATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.11
10 17 0.63
11 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTTAAAAT
Found at i:497066 original size:19 final size:19
Alignment explanation
Indices: 497042--497082 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
497032 TAAAAAATTA
497042 AAATATTT-AAAATATATTT
1 AAATATTTAAAAAT-TATTT
497061 AAATATTTAAAAATTATTT
1 AAATATTTAAAAATTATTT
497080 AAA
1 AAA
497083 ATATGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATTTAAAAATTATTT
Found at i:497084 original size:20 final size:21
Alignment explanation
Indices: 497039--497091 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
497029 CTATAAAAAA
497039 TTAAAATATTT-AAAATATAT
1 TTAAAATATTTAAAAATATAT
497059 TT-AAATATTTAAAAAT-TAT
1 TTAAAATATTTAAAAATATAT
*
497078 TTAAAATATGTAAA
1 TTAAAATATTTAAA
497092 TGTTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAATATTTAAAAATATAT
Found at i:497117 original size:9 final size:9
Alignment explanation
Indices: 497103--497127 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
497093 GTTAAAATTT
497103 AAAATTATA
1 AAAATTATA
497112 AAAATTATA
1 AAAATTATA
497121 AAAATTA
1 AAAATTA
497128 GACATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:499049 original size:31 final size:31
Alignment explanation
Indices: 499009--499091 Score: 132
Period size: 30 Copynumber: 2.7 Consensus size: 31
498999 TTATCGGTTA
* *
499009 AGTCTTTTAACTTTCTATTTTTTTCTATTTT
1 AGTCCTTTAAGTTTCTATTTTTTTCTATTTT
499040 AGTCCTTTAAGTTTCTA-TTTTTTCTATTTT
1 AGTCCTTTAAGTTTCTATTTTTTTCTATTTT
*
499070 AGTCCTCTAAGTTTCTATTTTT
1 AGTCCTTTAAGTTTCTATTTTT
499092 GTAATTTCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 29 0.60
31 19 0.40
ACGTcount: A:0.17, C:0.14, G:0.06, T:0.63
Consensus pattern (31 bp):
AGTCCTTTAAGTTTCTATTTTTTTCTATTTT
Found at i:501492 original size:23 final size:23
Alignment explanation
Indices: 501458--501510 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
501448 TTCCAAAGGA
*
501458 CCACATAGGTTTGCA-CCGAAGTG
1 CCACATAAGTTTGCATCC-AAGTG
*
501481 CCACATAAGTTTTCATCCAAGTG
1 CCACATAAGTTTGCATCCAAGTG
501504 CCACATA
1 CCACATA
501511 TTTGTCCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (23 bp):
CCACATAAGTTTGCATCCAAGTG
Found at i:501539 original size:21 final size:21
Alignment explanation
Indices: 501504--501553 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
501494 CATCCAAGTG
* *
501504 CCACATATTTGTCCCAAAAGA
1 CCACATAATTATCCCAAAAGA
* *
501525 CCACATAATTATCCCGAAGGA
1 CCACATAATTATCCCAAAAGA
*
501546 CCATATAA
1 CCACATAA
501554 ACCCTCGACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCAAAAGA
Found at i:502172 original size:53 final size:54
Alignment explanation
Indices: 502109--502232 Score: 171
Period size: 53 Copynumber: 2.3 Consensus size: 54
502099 GATACTTCCC
*
502109 TTCAAGGGTATCGATACCTCCTCATGGTACCGATACCGAA-ATAACATTCGATG-
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACC-AATATAACATTCGATGT
* * * **
502162 TTCAAGGGTATCGATACCTTCTCAAGGTATCGATACCAATCTGGCATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
502216 TTCAAGGGTATCGATAC
1 TTCAAGGGTATCGATAC
502233 TACCCTTACA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.03
53 44 0.70
54 17 0.27
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATAACATTCGATGT
Found at i:502289 original size:3 final size:3
Alignment explanation
Indices: 502283--502373 Score: 130
Period size: 3 Copynumber: 30.7 Consensus size: 3
502273 TTTTTATCCA
* ** *
502283 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
502331 TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
502374 AATATATATA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:515585 original size:16 final size:16
Alignment explanation
Indices: 515559--515603 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
515549 TTTGAATACA
*
515559 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
515576 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
515591 ATTCAATTTATTT
1 ATTCAATTTATTT
515604 TCGAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:516592 original size:50 final size:50
Alignment explanation
Indices: 516441--516584 Score: 270
Period size: 50 Copynumber: 2.9 Consensus size: 50
516431 TGAATTTGCT
*
516441 AATAGCATCTTCTGGAAGTGTTCTTTGATTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
516491 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
*
516541 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
516585 TGGCAGAACC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 92 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
Found at i:516727 original size:82 final size:83
Alignment explanation
Indices: 516541--516869 Score: 504
Period size: 83 Copynumber: 4.0 Consensus size: 83
516531 GGTTAGACAG
* *
516541 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAAT
*
516606 TTGGAAGATGAATTTACC
66 TTGGAAGATGAATTTGCC
*
516624 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGAA-CAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAAT
*
516688 TTAGAAGATGAATTTGCC
66 TTGGAAGATGAATTTGCC
* * * *
516706 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCT-GATTATCTAGAACCAAGCATTGAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC-AGAACCAATCATTGAA
516770 TTTGGAAGATGAATTTGCC
65 TTTGGAAGATGAATTTGCC
* * *
516789 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGATAGAA-CAATCATTAAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAGAACCAATCATTGAA
516852 TTTGGAAGATGAATTTGC
65 TTTGGAAGATGAATTTGC
516870 TCATAGTAAA
Statistics
Matches: 225, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
81 5 0.02
82 97 0.43
83 122 0.54
84 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (83 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAAT
TTGGAAGATGAATTTGCC
Found at i:516741 original size:133 final size:132
Alignment explanation
Indices: 516359--516741 Score: 304
Period size: 133 Copynumber: 2.9 Consensus size: 132
516349 AAAGAGACTC
* * *
516359 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATATGGTTGGACAGAATCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-CAATCATTGAATT
* * ** *
516424 TAGAAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGATTTATCT-GATCTGGTTAGA
65 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA-TTATTTGGAGATGATTAGA
*
516488 CAGA
129 CACA
* * *
516492 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-TAGCATCT---TC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAATCAT-TGAATT
* ** *** * * **** *
516553 TGGAAG-TGTTCTTTG-GGTTATCTGATCTGGTTTGGCAGAACCAATCATTGA--ATTTGGAAGA
65 TAGAAGATG-AATTTGCCAATAGC--ATCT--TCT-G--GAAGTGTTCTTTGATTATTTGG-AGA
*
516614 TGAATT-TAC-CA
121 TG-ATTAGACACA
*
516625 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG-CAGAACAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAGACAGAACAATCATTGAATT
516689 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTG
65 TAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGA-TTATTTG
516742 ATCTGATTAT
Statistics
Matches: 186, Mismatches: 42, Indels: 44
0.68 0.15 0.16
Matches are distributed among these distances:
128 5 0.03
129 10 0.05
130 13 0.07
131 4 0.02
132 7 0.04
133 104 0.56
134 13 0.07
135 15 0.08
136 10 0.05
137 5 0.03
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (132 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAATCATTGAATTT
AGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGATTATTTGGAGATGATTAGACA
CA
Found at i:516760 original size:165 final size:164
Alignment explanation
Indices: 516541--516869 Score: 518
Period size: 165 Copynumber: 2.0 Consensus size: 164
516531 GGTTAGACAG
* * *
516541 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAAT
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT-GCAGAACCAAGCATTGAAT
516606 TTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAG
65 TTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGG-TTAG
*
516671 -CAGAACAATCATTGAATTTAGAAGATGAATTTGCC
129 ACAGAACAATCATTAAATTTAGAAGATGAATTTGCC
*
516706 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTAT-CTAGAACCAAGCATTGAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATT-TGC-AGAACCAAGCATTGAA
* * *
516770 TTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
64 TTTGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTAG
* *
516835 ATAGAACAATCATTAAATTTGGAAGATGAATTTGC
129 ACAGAACAATCATTAAATTTAGAAGATGAATTTGC
516870 TCATAGTAAA
Statistics
Matches: 151, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
164 4 0.03
165 146 0.97
166 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (164 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGCAGAACCAAGCATTGAATT
TGGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTAGAC
AGAACAATCATTAAATTTAGAAGATGAATTTGCC
Done.