Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009149.1 Hibiscus syriacus cultivar Beakdansim tig00112673_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: 1143513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 3 of 6
Found at i:401928 original size:14 final size:14
Alignment explanation
Indices: 401876--401959 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
401866 TCATTTCGCT
*
401876 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
401890 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
401907 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
401923 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
401940 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
401956 TTGC
1 TTGC
401960 AATTTTCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 16 0.29
16 14 0.25
17 13 0.24
19 12 0.22
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:402000 original size:20 final size:20
Alignment explanation
Indices: 401965--402047 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
401955 GTTGCAATTT
*
401965 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCGTTGCGATAG
401984 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
* ** *
402004 ACA-TTAAGATGATTGCGA-ACG
1 TCATTTCCG-CG-TTGCGATA-G
*
402025 TCATTTCCGTGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
402045 TCA
1 TCA
402048 AATGAATGCC
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.18
20 26 0.52
21 12 0.24
22 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:404552 original size:24 final size:24
Alignment explanation
Indices: 404518--404571 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
404508 CTGAAAAATC
404518 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
404542 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
404566 ATCAAA
1 ATCAAA
404572 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:404585 original size:24 final size:24
Alignment explanation
Indices: 404518--404585 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
404508 CTGAAAAATC
* * *
404518 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
404542 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
404566 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
404586 TAGTATTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:405467 original size:21 final size:21
Alignment explanation
Indices: 405442--405577 Score: 161
Period size: 21 Copynumber: 6.6 Consensus size: 21
405432 TGCGATTTAC
405442 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
405463 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
* *
405484 AAAATCGCAATGCGAA-TACG
1 TAAATCGCAATGCGAATTAGG
* * *
405504 T-AATCGCATTGCGATTTACG
1 TAAATCGCAATGCGAATTAGG
*
405524 T-AATCGCATTGCGAATTAGG
1 TAAATCGCAATGCGAATTAGG
* * *
405544 AAAATCGCAACGCGAATTTGG
1 TAAATCGCAATGCGAATTAGG
*
405565 GAAATCGCAATGC
1 TAAATCGCAATGC
405578 AATAGTCAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
19 12 0.12
20 25 0.25
21 63 0.63
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (21 bp):
TAAATCGCAATGCGAATTAGG
Found at i:405522 original size:81 final size:80
Alignment explanation
Indices: 405431--405581 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 80
405421 CAGAATCTCG
* *
405431 TTGCGATTTAC-TAAATCGCAATGCGAATTAGGTAAATCGCAATGCGAATTAGGAAAATCGCAAT
1 TTGCGATTTACGT-AATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTAGGAAAATCGCAAT
405495 GCGAATACGTAATCGCA
65 GC-AATACGTAATCGCA
* * *
405512 TTGCGATTTACGTAATCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAATCGCAATG
1 TTGCGATTTACGTAATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTAGGAAAATCGCAATG
405577 CAATA
66 CAATA
405582 GTCAGAATCG
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 4 0.06
81 59 0.92
82 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (80 bp):
TTGCGATTTACGTAATCGCAATGCGAATTAGGAAAATCGCAACGCGAATTAGGAAAATCGCAATG
CAATACGTAATCGCA
Found at i:405538 original size:60 final size:61
Alignment explanation
Indices: 405444--405560 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 61
405434 CGATTTACTA
* *
405444 AATCGCAATGCGAATTAGGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGT
1 AATCGCAATGCGAATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGT
* * *
405505 AATCGCATTGCGATTTACGT-AATCGCATTGCGAATTAGGAAAATCGCAACGCGAAT
1 AATCGCAATGCGAATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACGCGAAT
405561 TTGGGAAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 34 0.67
61 17 0.33
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (61 bp):
AATCGCAATGCGAATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAACGCGAATACGT
Found at i:405920 original size:15 final size:14
Alignment explanation
Indices: 405897--405930 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
405887 TGTATCAAAA
*
405897 TATTTTTATTACTTT
1 TATTATTATTA-TTT
405912 TATTATTATTATTT
1 TATTATTATTATTT
405926 TATTA
1 TATTA
405931 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:407747 original size:22 final size:22
Alignment explanation
Indices: 407707--407751 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
407697 GTCCCTAACA
*
407707 TTATCGATCCATTAGATTTTAG
1 TTATCGATCCATTACATTTTAG
* *
407729 TTATCGATCCGTTCCATTTTAG
1 TTATCGATCCATTACATTTTAG
407751 T
1 T
407752 CCCTTAGCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (22 bp):
TTATCGATCCATTACATTTTAG
Found at i:408985 original size:16 final size:16
Alignment explanation
Indices: 408961--409000 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
408951 GCCATCCAAA
* *
408961 AATGTATGTCCAATTG
1 AATGAATGTCCAAATG
*
408977 AATGAATGTTCAAATG
1 AATGAATGTCCAAATG
408993 AATGAATG
1 AATGAATG
409001 ACTAGAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (16 bp):
AATGAATGTCCAAATG
Found at i:420501 original size:23 final size:23
Alignment explanation
Indices: 420474--420521 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
420464 ACGGTCATTG
* *
420474 TTTTTCTATAT-ATTT-TTTAAT
1 TTTTTTTATATAATTTAATTAAT
420495 TTTTTTTATATAATTTAATTAAT
1 TTTTTTTATATAATTTAATTAAT
420518 TTTT
1 TTTT
420522 ATATTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 4 0.17
23 9 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTTTATATAATTTAATTAAT
Found at i:420504 original size:19 final size:20
Alignment explanation
Indices: 420482--420529 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
420472 TGTTTTTCTA
*
420482 TATATTTTTTAATT-TTTTT
1 TATATTTTTTAATTAATTTT
**
420501 TATATAATTTAATTAATTTT
1 TATATTTTTTAATTAATTTT
420521 TATATTTTT
1 TATATTTTT
420530 CATTGATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATATTTTTTAATTAATTTT
Found at i:420972 original size:23 final size:25
Alignment explanation
Indices: 420932--420986 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
420922 TAATAATGTG
*
420932 ACATATATTATATCATTA-ATTAA-
1 ACATATATTAAATCATTATATTAAT
420955 ACATATATTAAAAT-ATTATATTAAT
1 ACATATATT-AAATCATTATATTAAT
420980 A-ATATAT
1 ACATATAT
420987 ATTGACTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 13 0.46
24 14 0.50
25 1 0.04
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
ACATATATTAAATCATTATATTAAT
Found at i:420976 original size:13 final size:13
Alignment explanation
Indices: 420957--420989 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
420947 TTAATTAAAC
420957 ATATATTAA-AAT
1 ATATATTAATAAT
420969 ATTATATTAATAAT
1 A-TATATTAATAAT
420983 ATATATT
1 ATATATT
420990 GACTATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 14 0.74
14 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATTAATAAT
Found at i:425277 original size:23 final size:23
Alignment explanation
Indices: 425251--425294 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
425241 TAAAATTCTC
*
425251 TCTTCTATTTT-CTTTCATTTTTT
1 TCTTATATTTTACTTT-ATTTTTT
*
425274 TCTTATTTTTTACTTTATTTT
1 TCTTATATTTTACTTTATTTT
425295 AAGTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (23 bp):
TCTTATATTTTACTTTATTTTTT
Found at i:432966 original size:23 final size:21
Alignment explanation
Indices: 432913--432991 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 21
432903 TCGAAATGGA
* *
432913 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
* *
432933 GTGCATCGATGCACTAG-TGGTAG
1 GTGCATGGATGCACT-GCAGG--G
432956 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
432977 GTGCATGGATGCACT
1 GTGCATGGATGCACT
432992 TTGACACCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 1 0.02
23 17 0.35
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:433677 original size:25 final size:24
Alignment explanation
Indices: 433626--433695 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 24
433616 ATAATTTTAG
*
433626 ATTTTTAAAATTACATTATAAAAA
1 ATTTTTAAAAATACATTATAAAAA
** *
433650 ATTTATTAAAAATACATTATTGATA
1 ATTT-TTAAAAATACATTATAAAAA
*
433675 A-TTTTAAAAATATATTA-AAAA
1 ATTTTTAAAAATACATTATAAAA
433696 TTTTATAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 1 0.03
23 13 0.35
24 6 0.16
25 17 0.46
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (24 bp):
ATTTTTAAAAATACATTATAAAAA
Found at i:433850 original size:21 final size:21
Alignment explanation
Indices: 433824--433863 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
433814 ATAACACCCC
433824 AAACCCCAAACCTTAAACCAT
1 AAACCCCAAACCTTAAACCAT
*
433845 AAACCCTAAACCTTAAACC
1 AAACCCCAAACCTTAAACC
433864 CTAAGTCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACCCCAAACCTTAAACCAT
Found at i:433875 original size:21 final size:21
Alignment explanation
Indices: 433831--433928 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
433821 CCCAAACCCC
* *
433831 AAACCTTAAACCATAAACCCT
1 AAACCTTAAACCCTAAGCCCT
* *
433852 AAACCTTAAACCCTAAGTCTT
1 AAACCTTAAACCCTAAGCCCT
* *
433873 AAACCCTAAGCCCTAAGCCCT
1 AAACCTTAAACCCTAAGCCCT
* *
433894 AAGCCATAAACCCTAAGCCCT
1 AAACCTTAAACCCTAAGCCCT
433915 AAA-CTCTAAACCCT
1 AAACCT-TAAACCCT
433929 TAATTTGATT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 1 0.02
21 62 0.98
ACGTcount: A:0.40, C:0.36, G:0.05, T:0.19
Consensus pattern (21 bp):
AAACCTTAAACCCTAAGCCCT
Found at i:433888 original size:7 final size:7
Alignment explanation
Indices: 433848--433916 Score: 66
Period size: 7 Copynumber: 9.9 Consensus size: 7
433838 AAACCATAAA
*
433848 CCCTAAA
1 CCCTAAG
* *
433855 CCTTAAA
1 CCCTAAG
433862 CCCTAAG
1 CCCTAAG
* * *
433869 TCTTAAA
1 CCCTAAG
433876 CCCTAAG
1 CCCTAAG
433883 CCCTAAG
1 CCCTAAG
433890 CCCTAAG
1 CCCTAAG
* *
433897 CCATAAA
1 CCCTAAG
433904 CCCTAAG
1 CCCTAAG
433911 CCCTAA
1 CCCTAA
433917 ACTCTAAACC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.36, C:0.38, G:0.07, T:0.19
Consensus pattern (7 bp):
CCCTAAG
Found at i:433928 original size:14 final size:14
Alignment explanation
Indices: 433819--433928 Score: 94
Period size: 14 Copynumber: 7.9 Consensus size: 14
433809 GTTAGATAAC
* *
433819 ACCCCAAACCCCAA
1 ACCCTAAACCCTAA
* *
433833 ACCTTAAACCATAA
1 ACCCTAAACCCTAA
*
433847 ACCCTAAACCTTAA
1 ACCCTAAACCCTAA
** *
433861 ACCCTAAGTCTTAA
1 ACCCTAAACCCTAA
*
433875 ACCCTAAGCCCTAA
1 ACCCTAAACCCTAA
* * *
433889 GCCCTAAGCCATAA
1 ACCCTAAACCCTAA
*
433903 ACCCTAAGCCCTAA
1 ACCCTAAACCCTAA
*
433917 ACTCTAAACCCT
1 ACCCTAAACCCT
433929 TAATTTGATT
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 80 1.00
ACGTcount: A:0.39, C:0.39, G:0.05, T:0.17
Consensus pattern (14 bp):
ACCCTAAACCCTAA
Found at i:435426 original size:23 final size:23
Alignment explanation
Indices: 435387--435474 Score: 135
Period size: 23 Copynumber: 3.9 Consensus size: 23
435377 TAACCCATAT
435387 TCGAGCTTCAAA--CGAGCTTGAA
1 TCGAGC-TCAAAGTCGAGCTTGAA
*
435409 TTGAGCTCAAAGTCGAGCTTGAA
1 TCGAGCTCAAAGTCGAGCTTGAA
435432 TCGAGCTCAAAGTCGAGCTTGAA
1 TCGAGCTCAAAGTCGAGCTTGAA
*
435455 TCGAGCTCAAAATCGAGCTT
1 TCGAGCTCAAAGTCGAGCTT
435475 CAATTGGTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.08
22 5 0.08
23 51 0.84
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.24
Consensus pattern (23 bp):
TCGAGCTCAAAGTCGAGCTTGAA
Found at i:435449 original size:12 final size:11
Alignment explanation
Indices: 435387--435473 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
435377 TAACCCATAT
435387 TCGAGCTTCAAA
1 TCGAGC-TCAAA
**
435399 -CGAGCTTGAA
1 TCGAGCTCAAA
*
435409 TTGAGCTCAAA
1 TCGAGCTCAAA
**
435420 GTCGAGCTTGAA
1 -TCGAGCTCAAA
435432 TCGAGCTCAAA
1 TCGAGCTCAAA
**
435443 GTCGAGCTTGAA
1 -TCGAGCTCAAA
435455 TCGAGCTCAAAA
1 TCGAGCTC-AAA
435467 TCGAGCT
1 TCGAGCT
435474 TCAATTGGTC
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
10 3 0.05
11 28 0.49
12 26 0.46
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (11 bp):
TCGAGCTCAAA
Found at i:438274 original size:22 final size:22
Alignment explanation
Indices: 438234--438275 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
438224 AATTTTCAGA
* *
438234 TATTTTCTTTTATTAAATTTCT
1 TATTTTATTTCATTAAATTTCT
*
438256 TATTTTATTTCATTTAATTT
1 TATTTTATTTCATTAAATTT
438276 TTAGTATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATTTCATTAAATTTCT
Found at i:441780 original size:11 final size:11
Alignment explanation
Indices: 441760--441802 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
441750 GCAAATCATT
441760 CACC-AAATCC
1 CACCAAAATCC
441770 CACCAAAATCC
1 CACCAAAATCC
*
441781 CATCAAAATCC
1 CACCAAAATCC
* *
441792 AACCTAAATCC
1 CACCAAAATCC
441803 ATTAATCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 4 0.14
11 24 0.86
ACGTcount: A:0.44, C:0.42, G:0.00, T:0.14
Consensus pattern (11 bp):
CACCAAAATCC
Found at i:442780 original size:29 final size:29
Alignment explanation
Indices: 442746--442817 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
442736 TATTTCTGAT
*
442746 TTTTTGACACTTTACTTTATGTTATTTTA
1 TTTTTGACACTTAACTTTATGTTATTTTA
* * *
442775 TTTTTGTCACTTAAGTTTTTGTTATTTTA
1 TTTTTGACACTTAACTTTATGTTATTTTA
* *
442804 TTTTAGTCACTTAA
1 TTTTTGACACTTAA
442818 GTTTCTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.61
Consensus pattern (29 bp):
TTTTTGACACTTAACTTTATGTTATTTTA
Found at i:442793 original size:15 final size:15
Alignment explanation
Indices: 442775--442821 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
442765 TGTTATTTTA
442775 TTTTTGTCACTTAAG
1 TTTTTGTCACTTAAG
* * *
442790 TTTTTGTTATTTTA-
1 TTTTTGTCACTTAAG
*
442804 TTTTAGTCACTTAAG
1 TTTTTGTCACTTAAG
442819 TTT
1 TTT
442822 CTATTTTTGC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.62
Consensus pattern (15 bp):
TTTTTGTCACTTAAG
Found at i:442818 original size:29 final size:29
Alignment explanation
Indices: 442765--442821 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
442755 CTTTACTTTA
*
442765 TGTTATTTTATTTTTGTCACTTAAGTTTT
1 TGTTATTTTATTTTAGTCACTTAAGTTTT
442794 TGTTATTTTATTTTAGTCACTTAAGTTT
1 TGTTATTTTATTTTAGTCACTTAAGTTT
442822 CTATTTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.07, G:0.11, T:0.63
Consensus pattern (29 bp):
TGTTATTTTATTTTAGTCACTTAAGTTTT
Found at i:442903 original size:29 final size:29
Alignment explanation
Indices: 442813--442908 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
442803 ATTTTAGTCA
* * *
442813 CTTAAGTTTCTATTTTTGCAATTTTTATC
1 CTTAAGTCTCTATTTTTGCTATTTTGATC
* * *
442842 CTTCAAATGTCTATTTTTGCTATTTAG-TCC
1 CTT-AAGTCTCTATTTTTGCTATTTTGAT-C
*
442872 CTTAAGTCTCTGTTTTTGCTATTTTGATC
1 CTTAAGTCTCTATTTTTGCTATTTTGATC
442901 CTTTAAGT
1 C-TTAAGT
442909 TTATGTAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
29 25 0.46
30 29 0.54
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (29 bp):
CTTAAGTCTCTATTTTTGCTATTTTGATC
Found at i:442966 original size:29 final size:29
Alignment explanation
Indices: 442855--443014 Score: 122
Period size: 30 Copynumber: 5.4 Consensus size: 29
442845 CAAATGTCTA
* * *
442855 TTTTTGCTATTTAGTCCCTTAAGTCTCTG
1 TTTTTGCTATTTAGTCCTTTAAGTTTATG
*
442884 TTTTTGCTATTTTGATCCTTTAAGTTTATG
1 TTTTTGCTATTTAG-TCCTTTAAGTTTATG
** * * **
442914 TAATTACTGTTTTAGGACTTTAAGTTTATG
1 TTTTTGCT-ATTTAGTCCTTTAAGTTTATG
* *
442944 TTTTTTCTATTTAGTTCTTTAAGTTTATG
1 TTTTTGCTATTTAGTCCTTTAAGTTTATG
* * * * *
442973 ATGTTGCCATTTTAATCCTTTAAATTTATG
1 TTTTTGCTA-TTTAGTCCTTTAAGTTTATG
* *
443003 TTTGTGTTATTT
1 TTTTTGCTATTT
443015 TGGTTCTTGT
Statistics
Matches: 99, Mismatches: 29, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
29 39 0.39
30 56 0.57
31 4 0.04
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (29 bp):
TTTTTGCTATTTAGTCCTTTAAGTTTATG
Found at i:444599 original size:17 final size:17
Alignment explanation
Indices: 444574--444620 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
444564 CTAATAAAAG
*
444574 CATGCTCGGGTAGATGT
1 CATGATCGGGTAGATGT
444591 CATGATCGGGTAGATGT
1 CATGATCGGGTAGATGT
*
444608 CATGATTGGGTAG
1 CATGATCGGGTAG
444621 GTGTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (17 bp):
CATGATCGGGTAGATGT
Found at i:444816 original size:63 final size:63
Alignment explanation
Indices: 444712--444835 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
444702 CGTTCCTTGT
* * * ** * *
444712 TGCATTGCTTTTCAGATGATCATCAATTTTGCATCTACATTTGTATCTTCACATTCTGCATGA
1 TGCATTGCATTTCAGAGGATCATCAATTTTGCATATACATTTACATATTCACAATCTGCATGA
* * *
444775 TGCATTGCATTTCAGAGGATTATCACTTTTGCATATGCATTTACATATTCACAATCTGCAT
1 TGCATTGCATTTCAGAGGATCATCAATTTTGCATATACATTTACATATTCACAATCTGCAT
444836 TATCATCATA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (63 bp):
TGCATTGCATTTCAGAGGATCATCAATTTTGCATATACATTTACATATTCACAATCTGCATGA
Found at i:447010 original size:21 final size:21
Alignment explanation
Indices: 446984--447031 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
446974 AAAAGCAAAG
*
446984 GAAAAAAAGCAAAGGAAAAAAA
1 GAAAAAAAACAAAGG-AAAAAA
447006 GAAAAAAAACAAAGGAAAAAA
1 GAAAAAAAACAAAGGAAAAAA
447027 GAAAA
1 GAAAA
447032 TAAGGAGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (21 bp):
GAAAAAAAACAAAGGAAAAAA
Found at i:447026 original size:14 final size:14
Alignment explanation
Indices: 446970--447006 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
446960 GAAGAGAAAA
446970 GAAAAAAAGCAAAG
1 GAAAAAAAGCAAAG
446984 GAAAAAAAGCAAAG
1 GAAAAAAAGCAAAG
446998 GAAAAAAAG
1 GAAAAAAAG
447007 AAAAAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAAAAAGCAAAG
Found at i:448147 original size:33 final size:32
Alignment explanation
Indices: 448075--448162 Score: 104
Period size: 33 Copynumber: 2.7 Consensus size: 32
448065 GGAACAATGA
* * *
448075 GGGCATCATTGAAGATTCAACATTAAATATTG
1 GGGCATCTTTGGAGATTTAACATTAAATATTG
* * *
448107 GGCCATCTTTGGAGATTTAACATTCGATTATTG
1 GGGCATCTTTGGAGATTTAACATT-AAATATTG
*
448140 GGGCATCTTTGGGGATTTAACAT
1 GGGCATCTTTGGAGATTTAACAT
448163 CTTGATGCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 20 0.43
33 27 0.57
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTTAACATTAAATATTG
Found at i:448313 original size:37 final size:38
Alignment explanation
Indices: 448244--448316 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
448234 TTTGATATTG
*
448244 TTTCTCTCGAAACAAAATGTTGTCTCGCTTGAGACAAT
1 TTTCTCTCGAAACAAAATGTTGTCTCACTTGAGACAAT
* *
448282 TTTCTCTC-AAATC-AAATTTTGTCTCATTTGAGACA
1 TTTCTCTCGAAA-CAAAATGTTGTCTCACTTGAGACA
448317 TAAAACAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 22 0.71
38 9 0.29
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (38 bp):
TTTCTCTCGAAACAAAATGTTGTCTCACTTGAGACAAT
Found at i:448532 original size:46 final size:44
Alignment explanation
Indices: 448441--448552 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 44
448431 CGACCAGATC
* **
448441 TCCTCATCACGTAGGAGCCGTG-TCACCCTTAGATAACCAGTCG
1 TCCTCATCACGTAGGAACCGTGTTCACCCTTAGATAACCACCCG
* *
448484 TCCTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCTCCCG
1 TCCTCATCACGTAGGAACCGTG-T-TCACCCTTAGATAACCACCCG
* *
448530 TCCTCATCGCGTAGGAACTGTGT
1 TCCTCATCACGTAGGAACCGTGT
448553 CATCTCCCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 21 0.36
45 1 0.02
46 37 0.63
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (44 bp):
TCCTCATCACGTAGGAACCGTGTTCACCCTTAGATAACCACCCG
Found at i:448660 original size:128 final size:128
Alignment explanation
Indices: 448431--448772 Score: 488
Period size: 128 Copynumber: 2.7 Consensus size: 128
448421 TCCCTAAAGA
* * * *
448431 CGACCAGATCTCCTCATCACGTAGGAGCCGTGTC-ACCCTTAGATAACCAGTCGTCCTCATCACG
1 CGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCC--AGATAACCAGCCGTCCTCATCACG
** * *
448495 TAGGAACCGTGTTATCACCCTTAGATGACCTCCCGTCCTCATCGCGTAGGAACTGTGTCATCTCC
64 TAGGAACCGTGTTATCACCCTTAGATGACCTCCCGTCCTCATCAAGTAGGAACCGTGTCATCGCC
* *
448560 CGACCAGATCTCCTCATTATGTAGGAGCTATGTCAACCCAGATAACCAGCCGTCCTCATCATGTA
1 CGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCCTCATCACGTA
** ** *
448625 GGAACCGTGTTATCACCCTTAGATGGTCTGTCGTCCTCATCAAGTAGGAACCGTGTCATCGCT
66 GGAACCGTGTTATCACCCTTAGATGACCTCCCGTCCTCATCAAGTAGGAACCGTGTCATCGCC
* * *
448688 CGACCAGATCTCCTCATTATGTAGGAGTTGTGTCAACCCAGATAAACAACCGTCCTCATCACGTA
1 CGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCCTCATCACGTA
*
448753 GGAACCGAGTTATCACCCTT
66 GGAACCGTGTTATCACCCTT
448773 CTTAAAGATG
Statistics
Matches: 191, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
128 157 0.82
129 30 0.16
130 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (128 bp):
CGACCAGATCTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACCAGCCGTCCTCATCACGTA
GGAACCGTGTTATCACCCTTAGATGACCTCCCGTCCTCATCAAGTAGGAACCGTGTCATCGCC
Found at i:449070 original size:19 final size:19
Alignment explanation
Indices: 449046--449082 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
449036 GACAAAAATA
449046 TATTA-TTTATTATTATTAG
1 TATTATTTTA-TATTATTAG
449065 TATTATTTTATATTATTA
1 TATTATTTTATATTATTA
449083 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTATTTTATATTATTAG
Found at i:449634 original size:3 final size:3
Alignment explanation
Indices: 449626--449703 Score: 131
Period size: 3 Copynumber: 26.3 Consensus size: 3
449616 GACAAAAATA
449626 TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
449673 TAT TAT TAT TAT TAT TAT TAG TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
449704 CTTTTACAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:450594 original size:29 final size:29
Alignment explanation
Indices: 450562--450626 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
450552 TTGATTTTGA
* *
450562 CACTTTACTTTTTCTTATTTTATTTTAGT
1 CACTTAACTTTTTCTTATTTTAATTTAGT
* *
450591 CACTTAAGTTTTTGTTATTTTAATTTAGT
1 CACTTAACTTTTTCTTATTTTAATTTAGT
450620 CACTTAA
1 CACTTAA
450627 GTTTATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (29 bp):
CACTTAACTTTTTCTTATTTTAATTTAGT
Found at i:450627 original size:29 final size:29
Alignment explanation
Indices: 450570--450635 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
450560 GACACTTTAC
* *
450570 TTTTTCTTATTTTATTTTAGTCACTTAAG
1 TTTTTGTTATTTTAATTTAGTCACTTAAG
450599 TTTTTGTTATTTTAATTTAGTCACTTAAG
1 TTTTTGTTATTTTAATTTAGTCACTTAAG
*
450628 TTTATGTT
1 TTTTTGTT
450636 TTTGCTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.08, G:0.09, T:0.62
Consensus pattern (29 bp):
TTTTTGTTATTTTAATTTAGTCACTTAAG
Found at i:450645 original size:29 final size:30
Alignment explanation
Indices: 450585--450777 Score: 102
Period size: 29 Copynumber: 6.6 Consensus size: 30
450575 CTTATTTTAT
*
450585 TTTAGTCAC-TTAAGTTTTTGTTATTT--TAA
1 TTTAGTCACTTTAAGTTTATGTT-TTTGCT-A
450614 TTTAGTCAC-TTAAGTTTATGTTTTTGCTA
1 TTTAGTCACTTTAAGTTTATGTTTTTGCTA
**
450643 TTTTTTC-CTTTAAATGTTTA--TTTTTGCTA
1 TTTAGTCACTTT-AA-GTTTATGTTTTTGCTA
* * * * *
450672 TTTAGTC-CCTTAAGTCTCTTTTTTTTCTA
1 TTTAGTCACTTTAAGTTTATGTTTTTGCTA
* * * ** *
450701 TTTTGATC-CTTTACGTTTCTGTAATTACTA
1 TTTAG-TCACTTTAAGTTTATGTTTTTGCTA
* *
450731 TTTTAG-GACTTTAAGTTTATGTTTTTTCTA
1 -TTTAGTCACTTTAAGTTTATGTTTTTGCTA
*
450761 TTTAGT-TCTTTAAGTTT
1 TTTAGTCACTTTAAGTTT
450778 CCGTTGTTGC
Statistics
Matches: 128, Mismatches: 25, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
27 3 0.02
28 6 0.05
29 73 0.57
30 37 0.29
31 9 0.07
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.59
Consensus pattern (30 bp):
TTTAGTCACTTTAAGTTTATGTTTTTGCTA
Found at i:451039 original size:29 final size:29
Alignment explanation
Indices: 451007--451071 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
450997 TTGATTTTGA
* *
451007 CACTTTACTTTTTCTTATTTTATTTTAGT
1 CACTTAACTTTTTCTTATTTTATTTTAGC
* *
451036 CACTTAAGTTTTTGTTATTTTATTTTAGC
1 CACTTAACTTTTTCTTATTTTATTTTAGC
451065 CACTTAA
1 CACTTAA
451072 GTTTATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.14, G:0.06, T:0.58
Consensus pattern (29 bp):
CACTTAACTTTTTCTTATTTTATTTTAGC
Found at i:451072 original size:29 final size:29
Alignment explanation
Indices: 451015--451080 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
451005 GACACTTTAC
* *
451015 TTTTTCTTATTTTATTTTAGTCACTTAAG
1 TTTTTGTTATTTTATTTTAGCCACTTAAG
451044 TTTTTGTTATTTTATTTTAGCCACTTAAG
1 TTTTTGTTATTTTATTTTAGCCACTTAAG
*
451073 TTTATGTT
1 TTTTTGTT
451081 TTTGCTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (29 bp):
TTTTTGTTATTTTATTTTAGCCACTTAAG
Found at i:451100 original size:29 final size:29
Alignment explanation
Indices: 451068--451222 Score: 107
Period size: 30 Copynumber: 5.3 Consensus size: 29
451058 TTTTAGCCAC
*
451068 TTAAGTTTATGTTTTTGCTATTTTTTCCT
1 TTAAGTTTATGTTTTTGCTATTTTGTCCT
* *
451097 TTAAATGTTTA--TTTTTGCTATTTAGTCCC
1 TT-AA-GTTTATGTTTTTGCTATTTTGTCCT
* * * *
451126 TTAAGTCTCTTTTTTTTCTATTTTGATCCT
1 TTAAGTTTATGTTTTTGCTATTTTG-TCCT
* * ** * **
451156 TTACGTTTCTGTAATTACTATTTTAGGACT
1 TTAAGTTTATGTTTTTGCTATTTT-GTCCT
* * *
451186 TTAAGTTTATGTTTTTTCTATTTAGTTCT
1 TTAAGTTTATGTTTTTGCTATTTTGTCCT
451215 TTAAGTTT
1 TTAAGTTT
451223 CCGTTGTTGC
Statistics
Matches: 96, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
27 3 0.03
28 2 0.02
29 42 0.44
30 43 0.45
31 6 0.06
ACGTcount: A:0.18, C:0.12, G:0.10, T:0.60
Consensus pattern (29 bp):
TTAAGTTTATGTTTTTGCTATTTTGTCCT
Found at i:456778 original size:19 final size:19
Alignment explanation
Indices: 456735--456778 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
456725 CTTATCAATT
* *
456735 TTATTGATTTATATTATAG
1 TTATTTATTTATATTACAG
* *
456754 TCATTTATTTATATTCCAG
1 TTATTTATTTATATTACAG
456773 TTATTT
1 TTATTT
456779 TAATTTTGAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (19 bp):
TTATTTATTTATATTACAG
Found at i:460466 original size:37 final size:37
Alignment explanation
Indices: 460416--460489 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
460406 CTGTGCCACC
*
460416 CCTTGTCGCATTGTCTCAGACTGGCACCCTTAGAGCT
1 CCTTGTCGCATTGTCTCAGACTGGCACCCCTAGAGCT
460453 CCTTGTCGCATTGTCTCAGACTGGCACCCCTAGAGCT
1 CCTTGTCGCATTGTCTCAGACTGGCACCCCTAGAGCT
460490 AAGGAAAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (37 bp):
CCTTGTCGCATTGTCTCAGACTGGCACCCCTAGAGCT
Found at i:467169 original size:5 final size:5
Alignment explanation
Indices: 467159--467187 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
467149 ATTTATCAAA
467159 AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATA
467188 GTAGTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:468726 original size:24 final size:24
Alignment explanation
Indices: 468675--468726 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
468665 ACAAACAATG
** *
468675 TTATTTATTATTAACGTTATAATA
1 TTATTTATTATTAAAATTAAAATA
468699 TTATTTATTATTATAAATTAAAAT-
1 TTATTTATTATTA-AAATTAAAATA
468723 TTAT
1 TTAT
468727 GTGTCAAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
TTATTTATTATTAAAATTAAAATA
Found at i:480699 original size:60 final size:60
Alignment explanation
Indices: 480587--480699 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
480577 TAGAGGGTGA
* * *
480587 TGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAATATTGTTCTTCGACTATAGGATGT
1 TGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAATAATATTCCTCGACTATAGGATGT
* * *
480647 TGCTTTGTTGAGTCCATCGACTATTAAAAGTTACAA-AATATTCACTCTACTAT
1 TGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAATAATATTC-CTCGACTAT
480700 TTAGTATGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 5 0.11
60 41 0.89
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (60 bp):
TGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAATAATATTCCTCGACTATAGGATGT
Found at i:481059 original size:25 final size:26
Alignment explanation
Indices: 481031--481083 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
481021 ATCAATGTTA
481031 ATTGAA-TTTTAAT-TTAATTAATATT
1 ATTGAATTTTTAATATT-ATTAATATT
*
481056 ATTGAATTTTTAATATTTTTAATATT
1 ATTGAATTTTTAATATTATTAATATT
481082 AT
1 AT
481084 AAATTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 17 0.68
27 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
ATTGAATTTTTAATATTATTAATATT
Found at i:487129 original size:14 final size:15
Alignment explanation
Indices: 487100--487132 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
487090 AGTGAGAAAA
*
487100 AGAAAAACATACGAG
1 AGAAAAAAATACGAG
487115 AGAAAAAAATA-GAG
1 AGAAAAAAATACGAG
487129 AGAA
1 AGAA
487133 TTGAGAGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.67, C:0.06, G:0.21, T:0.06
Consensus pattern (15 bp):
AGAAAAAAATACGAG
Found at i:494410 original size:21 final size:21
Alignment explanation
Indices: 494386--494448 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
494376 TTAAAATTTT
494386 CAAGCTCGACTCAAAAACTAA
1 CAAGCTCGACTCAAAAACTAA
* **
494407 CAAGCT----T--AAAATTTT
1 CAAGCTCGACTCAAAAACTAA
494422 CAAGCTCGACTCAAAAACTAA
1 CAAGCTCGACTCAAAAACTAA
494443 CAAGCT
1 CAAGCT
494449 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 11 0.37
17 1 0.03
19 1 0.03
21 17 0.57
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (21 bp):
CAAGCTCGACTCAAAAACTAA
Found at i:494420 original size:36 final size:36
Alignment explanation
Indices: 494364--494474 Score: 181
Period size: 36 Copynumber: 3.1 Consensus size: 36
494354 GTTCAACACG
*
494364 AAAACTAACGAG-TTAAAATTTTCAAGCTCGACTCA
1 AAAACTAACAAGCTTAAAATTTTCAAGCTCGACTCA
494399 AAAACTAACAAGCTTAAAATTTTCAAGCTCGACTCA
1 AAAACTAACAAGCTTAAAATTTTCAAGCTCGACTCA
*
494435 AAAACTAACAAGCTTAAAATTTTCAAAC-CTGACTCA
1 AAAACTAACAAGCTTAAAATTTTCAAGCTC-GACTCA
494471 AAAA
1 AAAA
494475 TGAAACAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
35 12 0.17
36 60 0.83
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.24
Consensus pattern (36 bp):
AAAACTAACAAGCTTAAAATTTTCAAGCTCGACTCA
Found at i:495979 original size:21 final size:21
Alignment explanation
Indices: 495955--496005 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
495945 AATTGGACGT
* * *
495955 ATTTGTAAATGTTTAATTATG
1 ATTTTTAAATGCTTAAATATG
495976 ATTTTTAAA-GCTTAAATATG
1 ATTTTTAAATGCTTAAATATG
495996 ATTTTTAAAT
1 ATTTTTAAAT
496006 AACTGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
ATTTTTAAATGCTTAAATATG
Found at i:497806 original size:2 final size:2
Alignment explanation
Indices: 497799--497827 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
497789 TTACTCAATT
497799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
497828 TATTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:498166 original size:2 final size:2
Alignment explanation
Indices: 498161--498186 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
498151 CACTATTTTA
498161 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
498187 TCCTAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:512477 original size:28 final size:29
Alignment explanation
Indices: 512446--512511 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
512436 AATTTTATGT
512446 ATTTTAATTTCAAT-CTTTAAATTCCAGC
1 ATTTTAATTTCAATCCTTTAAATTCCAGC
* *
512474 A-TTTATATTTCATTCCTTTAGATTCCAGC
1 ATTTTA-ATTTCAATCCTTTAAATTCCAGC
512503 -TTTTAATTT
1 ATTTTAATTT
512512 TCTGTATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
28 12 0.36
29 17 0.52
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTTAATTTCAATCCTTTAAATTCCAGC
Found at i:513607 original size:3 final size:3
Alignment explanation
Indices: 513588--513682 Score: 64
Period size: 3 Copynumber: 31.7 Consensus size: 3
513578 ATACTTATCC
* * * * * *
513588 AAT ATT AAT AAT TAT AAT AAT GAT AAT GAT AAT AAT AAT AAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
513636 GAT GAT GAT GAT GAT GAT AAT GAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
513683 GAGAAAATCG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:513912 original size:21 final size:21
Alignment explanation
Indices: 513888--513942 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
513878 CGATTTTCCC
*
513888 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
* **
513909 AATT-GCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGGA
*
513929 AAATCGCAATGCGA
1 AATTCGCAATGCGA
513943 TACTTACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGGA
Found at i:513956 original size:20 final size:20
Alignment explanation
Indices: 513931--514065 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
513921 AATTGGGAAA
513931 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
513951 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
* *
513971 ATCGCAATGCGATA-ATACAAA
1 ATCGCAATGCGATACTTAC--T
* * *
513992 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTTACT
* * * *
514012 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTTACT
* * *
514032 TTCGCAACGCGATA-ATACAT
1 ATCGCAATGCGATACTTAC-T
514052 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
514066 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.68
21 23 0.24
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:513993 original size:61 final size:61
Alignment explanation
Indices: 513928--514065 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
513918 GCGAATTGGG
* * * *
513928 AAAATCGCAATGCGATACTTACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * *
513989 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
514050 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
514066 TTTCAAAGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:514261 original size:22 final size:22
Alignment explanation
Indices: 514233--514276 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
514223 CACTCTCTCA
514233 CCCATCTCCGAAGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
**
514255 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGAAGAAATCCGTC
514277 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.43, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGAAGAAATCCGTC
Found at i:514591 original size:20 final size:20
Alignment explanation
Indices: 514537--514595 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
514527 GCGATTCTCT
**
514537 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
514557 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
514577 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
514596 AGTAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:514786 original size:25 final size:24
Alignment explanation
Indices: 514732--514786 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
514722 TGTTTATTAT
* *
514732 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
514756 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
514782 TGTTT
1 TGTTT
514787 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:515935 original size:18 final size:18
Alignment explanation
Indices: 515914--515958 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
515904 TCCACTTCGG
*
515914 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
515932 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
515950 GAGCCATCA
1 GAGCCATCA
515959 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:516494 original size:19 final size:20
Alignment explanation
Indices: 516440--516495 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
516430 TAGTTTACTT
* *
516440 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
516460 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
516480 TCGTAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
516496 AAATTGCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:516518 original size:14 final size:14
Alignment explanation
Indices: 516495--516552 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
516485 ATGCGAAATG
*
516495 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
516509 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
516525 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
516541 AAAATCGCAACG
1 AAAATCGCAACG
516553 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:516542 original size:32 final size:33
Alignment explanation
Indices: 516479--516569 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
516469 GGAAATGGCT
* *
516479 ATCGTAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
516512 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
516544 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
516570 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:516563 original size:19 final size:19
Alignment explanation
Indices: 516509--516574 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
516499 TTGCAACGAC
516509 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
516528 -AAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
*
516541 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
516560 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
516575 TTTGTATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
14 10 0.26
16 4 0.11
18 10 0.26
19 14 0.37
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:516605 original size:14 final size:14
Alignment explanation
Indices: 516586--516643 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
516576 TTGTATTTCG
516586 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
516600 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
516616 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
516632 CATTGCGATTTT
1 CGTTGCGATTTT
516644 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:516624 original size:32 final size:32
Alignment explanation
Indices: 516570--516659 Score: 135
Period size: 33 Copynumber: 2.8 Consensus size: 32
516560 AAAATCGCAA
* * *
516570 TGCGATTTGTATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTT-CATTTCGCATTGCGATTTTGTCAT
516603 TGCGATTTCATTTCGCATTGCGATTTTGTCAT
1 TGCGATTTCATTTCGCATTGCGATTTTGTCAT
516635 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGA-TTTCATTTCGCATTGCGAT
516660 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
32 26 0.49
33 27 0.51
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (32 bp):
TGCGATTTCATTTCGCATTGCGATTTTGTCAT
Found at i:516650 original size:33 final size:33
Alignment explanation
Indices: 516570--516659 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
516560 AAAATCGCAA
* *
516570 TGCGATTTGT-ATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTT-TCATTTCGCATTGCGATTTTGTCAT
516603 TGCGA-TTTCATTTCGCATTGCGATTTTGTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTGTCAT
516635 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
516660 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.02
32 28 0.53
33 24 0.45
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTTTGTCAT
Found at i:516656 original size:19 final size:18
Alignment explanation
Indices: 516564--516659 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 18
516554 GAAATGAAAA
* *
516564 TCGCAATGCGATTTGTATT
1 TCGCATTGCGATTT-CATT
* *
516583 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
516599 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
516615 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
516631 T--CATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
516648 TCGCATTGCGAT
1 TCGCATTGCGAT
516660 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
14 17 0.27
15 3 0.05
16 10 0.16
17 2 0.03
18 10 0.16
19 20 0.32
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:516699 original size:20 final size:20
Alignment explanation
Indices: 516644--516687 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
516634 TTGCGATTTT
*
516644 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
* *
516663 CATTTCCGCGTTACGATAGT
1 CATTTCCGCGTTGCGATAGC
516683 CATTT
1 CATTT
516688 TTGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:518587 original size:14 final size:14
Alignment explanation
Indices: 518568--518603 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
518558 ATTGTTTAAT
518568 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
518582 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
518596 TGATTTGT
1 TGATTTGT
518604 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:518711 original size:20 final size:20
Alignment explanation
Indices: 518686--518724 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
518676 ATGTTGAAGG
518686 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
518706 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
518725 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:518754 original size:19 final size:19
Alignment explanation
Indices: 518730--518794 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
518720 GCAACGAGAG
518730 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
518749 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
518768 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
518782 AATCGCAATGCGA
1 AATCGCAATGCGA
518795 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:518845 original size:19 final size:20
Alignment explanation
Indices: 518820--518909 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
518810 GCGATTTTTT
*
518820 CGTTGCGATAGGCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
518839 TGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
** *
518859 CGTTGCGATCTCCATTTTTG
1 CGTTGCGATAGCCATTTTCG
*
518879 CGTTGCGATAGCCATTGTCG
1 CGTTGCGATAGCCATTTTCG
518899 CGTTGCGATAG
1 CGTTGCGATAG
518910 TCAAATGAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 48 0.80
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:519147 original size:20 final size:20
Alignment explanation
Indices: 519122--519172 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
519112 AAATGATTGC
519122 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
519142 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
519162 CTTTCGCAACG
1 CTTTCGCAACG
519173 AGATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:520161 original size:12 final size:12
Alignment explanation
Indices: 520144--520168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
520134 ATATAATCCT
520144 GAAGAAGAAAAA
1 GAAGAAGAAAAA
520156 GAAGAAGAAAAA
1 GAAGAAGAAAAA
520168 G
1 G
520169 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:522482 original size:19 final size:19
Alignment explanation
Indices: 522460--522590 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
522450 GGAAATTACT
522460 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
522479 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
522493 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
522512 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
522526 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
522545 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
522559 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
522578 ATCGCAACGCGAA
1 ATCGCAATGCGAA
522591 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:522502 original size:33 final size:33
Alignment explanation
Indices: 522460--522586 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
522450 GGAAATTACT
522460 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
522493 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
522525 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
522559 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
522587 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:522567 original size:66 final size:66
Alignment explanation
Indices: 522461--522593 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
522451 GAAATTACTA
*
522461 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
522526 T
66 T
*
522527 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
522592 T
66 T
522593 T
1 T
522594 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:522618 original size:14 final size:14
Alignment explanation
Indices: 522601--522657 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
522591 TTTAATTTCG
522601 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
522615 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
522634 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
522648 CGTTGCGATT
1 CGTTGCGATT
522658 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:522637 original size:33 final size:33
Alignment explanation
Indices: 522586--522675 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
522576 AAATCGCAAC
* *
522586 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
522619 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
522652 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
522676 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:522639 original size:19 final size:19
Alignment explanation
Indices: 522615--522675 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
522605 GCGATTCTCT
522615 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
522634 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
522648 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
522667 CATTGCGAT
1 CGTTGCGAT
522676 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:522801 original size:14 final size:14
Alignment explanation
Indices: 522782--522818 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
522772 CATCAATTAA
*
522782 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
522796 ACAAATCACCTTTT
1 ACAAATCAACTTTT
522810 ACAAATCAA
1 ACAAATCAA
522819 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:524027 original size:91 final size:90
Alignment explanation
Indices: 523850--524036 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 90
523840 AAAAATACTA
*
523850 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
523915 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
523943 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
524007 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
524034 ACT
1 ACT
524037 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.23
95 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:524239 original size:63 final size:63
Alignment explanation
Indices: 524180--524321 Score: 160
Period size: 63 Copynumber: 2.3 Consensus size: 63
524170 CTTAGAGCGG
* * *
524180 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** *
524243 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
524306 CGATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
524322 GGCATTGACC
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
62 1 0.01
63 69 0.99
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:524322 original size:63 final size:63
Alignment explanation
Indices: 524203--524333 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
524193 TAAAGTAGAC
524203 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
524266 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
524329 ACCTC
1 ACCTC
524334 ATCACGTAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:525837 original size:19 final size:19
Alignment explanation
Indices: 525786--525902 Score: 171
Period size: 19 Copynumber: 6.1 Consensus size: 19
525776 TCTTTTGGTT
*
525786 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
525805 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
525825 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
525844 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
525863 GAAATGAAAATCGCAACGT
1 GAAATGAAAATCGCAACGC
*
525882 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
525901 GA
1 GA
525903 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 71 0.81
20 17 0.19
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:525920 original size:19 final size:18
Alignment explanation
Indices: 525898--525964 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 18
525888 AAAATCGCAA
*
525898 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
525917 TGCGTTTTTTATTTCGCGT
1 TGCG-ATTTTATTTCGCGT
*
525936 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
525956 TGCGATTTT
1 TGCGATTTT
525965 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 15 0.38
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.49
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:526504 original size:20 final size:20
Alignment explanation
Indices: 526479--526531 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
526469 ACGCTATGTA
*
526479 AATCGCGTTGTGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
526499 AATCGCGTTGCGAAAGTCA-
1 AATCGCGTTGCGAAAGTCAG
*
526518 ATATCTCGTTGCGA
1 A-ATCGCGTTGCGA
526532 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:526565 original size:20 final size:20
Alignment explanation
Indices: 526540--526593 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
526530 GATTTTGTAT
526540 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
526560 TATCGCATTACGATAGTCAG
1 TATCGCATTGCGATAGTAAG
526580 TATCGCATTGCGAT
1 TATCGCATTGCGAT
526594 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:529441 original size:21 final size:21
Alignment explanation
Indices: 529402--529441 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
529392 AAAAAAATCT
*
529402 AACCCGATCGGGTCTGGTCGA
1 AACCCGATCGGGTCAGGTCGA
529423 AACCCG-TCGGGTTCAGGTC
1 AACCCGATCGGG-TCAGGTC
529442 CTATGCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (21 bp):
AACCCGATCGGGTCAGGTCGA
Found at i:534696 original size:19 final size:22
Alignment explanation
Indices: 534672--534722 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 22
534662 ATGCCAAAAT
534672 GGTATCGGTA-CCTT-AAGG-A
1 GGTATCGGTACCCTTGAAGGAA
*
534691 GGTATCGATACCCTTGAAGGAA
1 GGTATCGGTACCCTTGAAGGAA
*
534713 AGTATCGGTA
1 GGTATCGGTA
534723 TTGGAGAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 4 0.15
22 9 0.35
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (22 bp):
GGTATCGGTACCCTTGAAGGAA
Found at i:535308 original size:23 final size:23
Alignment explanation
Indices: 535281--535414 Score: 186
Period size: 23 Copynumber: 5.9 Consensus size: 23
535271 TCGAGAAAAA
535281 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
535304 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
535327 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
*
535350 TATGTGGCACTTCGGTGCAATCC
1 TATGTGGCACTTCGGTGCAAACC
* * *
535373 TTTGTGGTC-CTTTGG-G-ACAA-T
1 TATGTGG-CACTTCGGTGCA-AACC
535394 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTTCGGTGCAAA
535415 TTACGAGCTG
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.01
21 12 0.12
22 5 0.05
23 80 0.81
24 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:536556 original size:26 final size:26
Alignment explanation
Indices: 536511--536584 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
536501 GACGTGGTAA
* * *
536511 TTTCTAGAAGGTCCAATCAGTGGTGG
1 TTTCTAGAAGGTCTAATCAGCGGCGG
* *
536537 TTTCTATAAGGTCTAGTCAGCGGCGG
1 TTTCTAGAAGGTCTAATCAGCGGCGG
* *
536563 TTTCTAGAAGATCTACTCAGCG
1 TTTCTAGAAGGTCTAATCAGCG
536585 CGTATTCTGG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (26 bp):
TTTCTAGAAGGTCTAATCAGCGGCGG
Found at i:541632 original size:7 final size:7
Alignment explanation
Indices: 541620--541646 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
541610 AGGTAAACTC
541620 AATTTTA
1 AATTTTA
541627 AATTTTA
1 AATTTTA
541634 AATTTTA
1 AATTTTA
541641 AATTTT
1 AATTTT
541647 TTCCATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:542810 original size:19 final size:20
Alignment explanation
Indices: 542783--542821 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
542773 ATCAAAATAG
*
542783 GGTACCGATATCCT-TATAT
1 GGTACCGATACCCTGTATAT
*
542802 GGTATCGATACCCTGTATAT
1 GGTACCGATACCCTGTATAT
542822 AGTGGTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
GGTACCGATACCCTGTATAT
Found at i:543479 original size:20 final size:20
Alignment explanation
Indices: 543454--543508 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
543444 TTTACACTTA
*
543454 GGGAACCGATTCCCCTTATG
1 GGGAACCGATTCCCCTTAAG
*
543474 GGGAACCGATTTCCCTTAAG
1 GGGAACCGATTCCCCTTAAG
*
543494 GGGTACCGATTCCCC
1 GGGAACCGATTCCCC
543509 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.25, T:0.24
Consensus pattern (20 bp):
GGGAACCGATTCCCCTTAAG
Found at i:549234 original size:20 final size:21
Alignment explanation
Indices: 549211--549290 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
549201 TTTGTGCAGA
*
549211 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
549231 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
*
549254 GGGAACCGATTACCCCCA-CAG
1 GGGAACCGA-TACCCCCATGAG
*
549275 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
549291 CTGGGGTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 21 0.43
21 12 0.24
22 1 0.02
23 9 0.18
24 6 0.12
ACGTcount: A:0.26, C:0.34, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:549291 original size:21 final size:21
Alignment explanation
Indices: 549252--549290 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
549242 CCCCCTTTGA
549252 AGGGGAACCGATTACCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
549273 AGGGGAATCGA-TACCCCC
1 AGGGGAACCGATTACCCCC
549291 CTGGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.36, G:0.26, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:550937 original size:12 final size:12
Alignment explanation
Indices: 550922--550950 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
550912 AGATGAGCCT
550922 GAGCAGCCCGAG
1 GAGCAGCCCGAG
550934 GAGCAGCCCGAG
1 GAGCAGCCCGAG
550946 GAGCA
1 GAGCA
550951 AGCACAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.31, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGCAGCCCGAG
Found at i:551585 original size:16 final size:16
Alignment explanation
Indices: 551540--551586 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
551530 AACAAAAAGG
551540 GGGAGAAGTGTTAAAT
1 GGGAGAAGTGTTAAAT
** *
551556 GTTA-AATGTTTTAAAT
1 GGGAGAA-GTGTTAAAT
551572 GGGAGAAGTGTTAAA
1 GGGAGAAGTGTTAAA
551587 GTAAGGGGGA
Statistics
Matches: 23, Mismatches: 6, Indels: 4
0.70 0.18 0.12
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.38, C:0.00, G:0.30, T:0.32
Consensus pattern (16 bp):
GGGAGAAGTGTTAAAT
Found at i:556478 original size:22 final size:21
Alignment explanation
Indices: 556438--556478 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
556428 TATGCGTTTA
*
556438 TTTTTCAAAATCAAAATAGTT
1 TTTTTCAAAATAAAAATAGTT
*
556459 TTTTTCTAAATAAAAGATAG
1 TTTTTCAAAATAAAA-ATAG
556479 ACTTTGGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTTCAAAATAAAAATAGTT
Found at i:557697 original size:21 final size:21
Alignment explanation
Indices: 557673--557722 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
557663 GTCGAGGGTT
*
557673 TTATGTGGTCCTCCGGGACAA
1 TTATGTGGTCATCCGGGACAA
*
557694 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATCCGGGACAA
*
557715 ATATGTGG
1 TTATGTGG
557723 CACTTCGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (21 bp):
TTATGTGGTCATCCGGGACAA
Found at i:557729 original size:21 final size:21
Alignment explanation
Indices: 557686--557796 Score: 70
Period size: 23 Copynumber: 5.1 Consensus size: 21
557676 TGTGGTCCTC
*
557686 CGGGACAATTATGTGGTCA-TT
1 CGGGACAAATATGTGG-CACTT
557707 CGGGACAAATATGTGGCACTT
1 CGGGACAAATATGTGGCACTT
*
557728 CGGTGA-AAACCTATGTGACACTT
1 CGG-GACAAA--TATGTGGCACTT
*
557751 CGGTG-CAATCCTATGTGGTC-CTT
1 CGG-GACAA--ATATGTGG-CACTT
* *
557774 CGGGAC-ATTATGTGACACTT
1 CGGGACAAATATGTGGCACTT
557794 CGG
1 CGG
557797 TGAAAATTAC
Statistics
Matches: 74, Mismatches: 6, Indels: 21
0.73 0.06 0.21
Matches are distributed among these distances:
19 1 0.01
20 14 0.19
21 23 0.31
22 4 0.05
23 31 0.42
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
CGGGACAAATATGTGGCACTT
Found at i:557743 original size:23 final size:23
Alignment explanation
Indices: 557716--557802 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
557706 TCGGGACAAA
*
557716 TATGTGGCACTTCGGTGAAAACC
1 TATGTGACACTTCGGTGAAAACC
* *
557739 TATGTGACACTTCGGTGCAATCC
1 TATGTGACACTTCGGTGAAAACC
* * *
557762 TATGTGGTC-CTTCGG-G-ACA-T
1 TATGT-GACACTTCGGTGAAAACC
557782 TATGTGACACTTCGGTGAAAA
1 TATGTGACACTTCGGTGAAAA
557803 TTACGAGCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.04
20 11 0.22
21 2 0.04
22 3 0.06
23 31 0.61
24 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
TATGTGACACTTCGGTGAAAACC
Found at i:558211 original size:17 final size:17
Alignment explanation
Indices: 558185--558217 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
558175 TGAAATTGCT
*
558185 CTTATCTATTTTGTAAA
1 CTTATATATTTTGTAAA
558202 CTTATATATTTTGTAA
1 CTTATATATTTTGTAA
558218 CTCTGTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (17 bp):
CTTATATATTTTGTAAA
Found at i:559751 original size:135 final size:137
Alignment explanation
Indices: 559595--559869 Score: 407
Period size: 135 Copynumber: 2.0 Consensus size: 137
559585 AGAAAAATAA
* *
559595 TTTAGTTAATTCGGTTCGGTTAATAATTTT-AAATAAATTTTGGTTCGATTAACCGAACCGAATT
1 TTTAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGATTCGATTAACCGAACCGAATT
*
559659 AACCAAATTTTTACTTCGATTAATT-TGGTTAATAA-TTT-AAAAATC-AGTTAATTCAGTTCGG
66 AACCAAA-TTTTACTTCGATTAATTCT-GTTAATAATTTTAAAAAATCGA-TTAATTCAGTTCGA
559720 TTAATAATTT
128 TTAATAATTT
*
559730 TTTAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGATTCGATTAACCGAACTGAATT
1 TTTAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGATTCGATTAACCGAACCGAATT
** *
559795 AACTGAATTTTACTTCGATTAATTCTGTTAATAATTTTTTAAAAAATCGATTATTTCAGTTCGAT
66 AACCAAATTTTACTTCGATTAATTCTGTTAATAA--TTTTAAAAAATCGATTAATTCAGTTCGAT
559860 TAATAATTT
129 TAATAATTT
559869 T
1 T
559870 CAAATATATT
Statistics
Matches: 126, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
135 54 0.43
136 38 0.30
138 3 0.02
139 30 0.24
140 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (137 bp):
TTTAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGATTCGATTAACCGAACCGAATT
AACCAAATTTTACTTCGATTAATTCTGTTAATAATTTTAAAAAATCGATTAATTCAGTTCGATTA
ATAATTT
Found at i:559769 original size:29 final size:29
Alignment explanation
Indices: 559708--559769 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
559698 AAAATCAGTT
** *
559708 AATTCAGTTCGGTTAATAATTTTTTAATT
1 AATTCAGTTCGGTTAATAATTTTCAAATA
*
559737 AATTCGGTTCGGTTAATAATTTTCAAATA
1 AATTCAGTTCGGTTAATAATTTTCAAATA
559766 AATT
1 AATT
559770 TTGATTCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (29 bp):
AATTCAGTTCGGTTAATAATTTTCAAATA
Found at i:559908 original size:136 final size:133
Alignment explanation
Indices: 559600--559918 Score: 324
Period size: 136 Copynumber: 2.3 Consensus size: 133
559590 AATAATTTAG
* * * *
559600 TTAATTCGGTTCGGTTAATAATTTTAAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCAA
1 TTAATTCGGTTCGATTAATAATATCAAAT--ATTTTGATTCGATTAACCGAACCGAATTAACCAA
*
559665 ATTTTTACTTCGATTAATTTGGTTAATAATTTAAAAATCAGTTAATTCAGTTCGGTTAATAATTT
64 ATTTTTACTTCGATTAATTTGGTTAATAATTTAAAAATCAGTTAATTCAGTTCGATTAATAATTT
**
559730 TTTAA
129 TCAAA
* * * **
559735 TTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGATTCGATTAACCGAACTGAATTAACTG
1 TTAATTCGGTTCGATTAATAA-TATCAAAT--ATTTTGATTCGATTAACCGAACCGAATTAACCA
*
559800 AA-TTTTACTTCGATTAATTCT-GTTAATAATTTTTTAAAAAATC-GATTATTTCAGTTCGATTA
63 AATTTTTACTTCGATTAATT-TGGTTAATAA---TTT-AAAAATCAG-TTAATTCAGTTCGATTA
559862 ATAATTTTCAAA
122 ATAATTTTCAAA
* * ** *
559874 TATATTTTGGTTCGATTAACTAA-ATCGGAT-TTTTGCTTCGATTAA
1 T-TAATTCGGTTCGATTAA-TAATATCAAATATTTTGATTCGATTAA
559919 TTCGGTTAAT
Statistics
Matches: 159, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
135 46 0.29
136 55 0.35
138 4 0.03
139 37 0.23
140 14 0.09
141 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.44
Consensus pattern (133 bp):
TTAATTCGGTTCGATTAATAATATCAAATATTTTGATTCGATTAACCGAACCGAATTAACCAAAT
TTTTACTTCGATTAATTTGGTTAATAATTTAAAAATCAGTTAATTCAGTTCGATTAATAATTTTC
AAA
Found at i:559979 original size:29 final size:29
Alignment explanation
Indices: 559947--560010 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
559937 AAAAAATTGG
559947 TTAATTCAGTTTGGTTAATAATTTTCAAA
1 TTAATTCAGTTTGGTTAATAATTTTCAAA
*
559976 TTAATTCGGTTTGGTTAATAATTTTCAAA
1 TTAATTCAGTTTGGTTAATAATTTTCAAA
*
560005 TAAATT
1 TTAATT
560011 TTGGTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.48
Consensus pattern (29 bp):
TTAATTCAGTTTGGTTAATAATTTTCAAA
Found at i:560096 original size:125 final size:129
Alignment explanation
Indices: 559844--560153 Score: 475
Period size: 125 Copynumber: 2.4 Consensus size: 129
559834 TAAAAAATCG
* * * *
559844 ATTATTTCAGTTCGATTAATAATTTTCAAATATATTTTGGTTCGATTAACTAAATCGGATTTTTG
1 ATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAATC-G-TTTTTG
* ** *
559909 CTTCGATTAATTCGGTTAATAATTTAAAAAAAAATTGGTTAATTCAGTTTGGTTAATAATTTTCA
64 CTTCGATTAATTCGATTAATAATTTAAAAAAAAATCAGTTAATTCAGTTCGGTTAATAATTTTCA
559974 A
129 A
* * *
559975 ATTAATTCGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAA-C-TTTTT-CT
1 ATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAATCGTTTTTGCT
560037 TCGATTAATTCGATTAATAATTT-AAAAAAAATCAGTTAATTCAGTTCGGTTAATAATTTTCAA
66 TCGATTAATTCGATTAATAATTTAAAAAAAAATCAGTTAATTCAGTTCGGTTAATAATTTTCAA
560100 ATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAA
1 ATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAA
560154 CCGATTTAAC
Statistics
Matches: 165, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
125 88 0.53
126 24 0.15
127 5 0.03
130 1 0.01
131 47 0.28
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (129 bp):
ATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAATCGTTTTTGCT
TCGATTAATTCGATTAATAATTTAAAAAAAAATCAGTTAATTCAGTTCGGTTAATAATTTTCAA
Found at i:560144 original size:30 final size:29
Alignment explanation
Indices: 560074--560148 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
560064 AAAATCAGTT
* * *
560074 AATTCAGTTCGGTTAATAATTTTCAAATT
1 AATTCGGTTCGATTAATAATTTTCAAATA
560103 AATTCGGTTCGATTAATAATTTTCAAATA
1 AATTCGGTTCGATTAATAATTTTCAAATA
*
560132 AATTTTGGTTCGATTAA
1 AA-TTCGGTTCGATTAA
560149 CCAAACCGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (29 bp):
AATTCGGTTCGATTAATAATTTTCAAATA
Found at i:560345 original size:68 final size:69
Alignment explanation
Indices: 560253--560404 Score: 238
Period size: 69 Copynumber: 2.2 Consensus size: 69
560243 TTTTGGTTTG
*
560253 ATTAACTGAA-CAGAATTAACCGA-TTTTTTTCTTTAACCATTAATCGAA-CAAAAAGTTATTTA
1 ATTAACCGAACCA-AATTAACCGATTTTTTTTCTTTAACCATTAATCGAATC-AAAAGTTATTTA
560315 AAAATT
64 AAAATT
* *
560321 ATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAAGCATTAATCGAATCAAAATTTATTTAAA
1 ATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACCATTAATCGAATCAAAAGTTATTTAAA
560386 AATT
66 AATT
560390 ATTAACCGAACCAAA
1 ATTAACCGAACCAAA
560405 CAAATTTAGG
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
68 19 0.24
69 58 0.74
70 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.36
Consensus pattern (69 bp):
ATTAACCGAACCAAATTAACCGATTTTTTTTCTTTAACCATTAATCGAATCAAAAGTTATTTAAA
AATT
Found at i:560534 original size:16 final size:16
Alignment explanation
Indices: 560510--560552 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
560500 AATAGTTTAC
* *
560510 AATTAATTTAAATAAT
1 AATTTATTTAAAAAAT
560526 AATTTATTTAAAAAAT
1 AATTTATTTAAAAAAT
*
560542 AATTTGTTTAA
1 AATTTATTTAA
560553 TTGTTTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
AATTTATTTAAAAAAT
Done.