Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002637.1 Hibiscus syriacus cultivar Beakdansim tig00005377_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: 3156206
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:424351 original size:5 final size:5
Alignment explanation
Indices: 424335--424438 Score: 97
Period size: 5 Copynumber: 19.8 Consensus size: 5
424325 TGAACCCTCT
*
424335 TTTTC ATTTTC TTTTC TCTTTC TTTTTC TTTT- TTTCC TTTT- TTTTC
1 TTTTC -TTTTC TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTTC TTTTC
*
424381 TTTTC TTTTC TTTTC GTTTTTC TTTTC TTTTA TTTTC ATTTTTCC TTTTC
1 TTTTC TTTTC TTTTC --TTTTC TTTTC TTTTC TTTTC --TTTT-C TTTTC
424431 -TTTC TTTT
1 TTTTC TTTT
424439 TCTTCAAGCA
Statistics
Matches: 84, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
4 11 0.13
5 45 0.54
6 17 0.20
7 10 0.12
8 1 0.01
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:424361 original size:17 final size:16
Alignment explanation
Indices: 424335--424442 Score: 102
Period size: 17 Copynumber: 6.8 Consensus size: 16
424325 TGAACCCTCT
*
424335 TTTTCATTTTCTTTTC
1 TTTTCTTTTTCTTTTC
424351 TCTTTCTTTTTC-TTT-
1 T-TTTCTTTTTCTTTTC
*
424366 TTTTCCTTTT-TTTTC
1 TTTTCTTTTTCTTTTC
424381 TTTTC-TTTTCTTTTC
1 TTTTCTTTTTCTTTTC
*
424396 GTTTT-TCTTTTCTTTTA
1 -TTTTCT-TTTTCTTTTC
424413 TTTTCATTTTTCCTTTTC
1 TTTTC-TTTTT-CTTTTC
424431 -TTTCTTTTTCTT
1 TTTTCTTTTTCTT
424443 CAAGCATAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
14 15 0.19
15 14 0.18
16 17 0.22
17 26 0.33
18 6 0.08
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTC
Found at i:424385 original size:40 final size:39
Alignment explanation
Indices: 424334--424442 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 39
424324 TTGAACCCTC
424334 TTTTTCATTTTCTTTTCTCTTTCTTTTTCTTTTTTTCCTTT
1 TTTTTCATTTTCTTTTCTCTTTCTTTTTC-TTTTTT-CTTT
424375 TTTTTC-TTTTCTTTTCT-TTTCGTTTTTC--TTTTCTTT
1 TTTTTCATTTTCTTTTCTCTTTC-TTTTTCTTTTTTCTTT
*
424411 TATTTTCATTTTTCCTTT-TCTTTCTTTTTCTT
1 T-TTTTCA-TTTTCTTTTCTCTTTCTTTTTCTT
424443 CAAGCATAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 15
0.79 0.01 0.20
Matches are distributed among these distances:
36 5 0.08
37 9 0.15
38 7 0.12
39 16 0.27
40 17 0.28
41 6 0.10
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (39 bp):
TTTTTCATTTTCTTTTCTCTTTCTTTTTCTTTTTTCTTT
Found at i:424391 original size:45 final size:44
Alignment explanation
Indices: 424335--424442 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 44
424325 TGAACCCTCT
* *
424335 TTTTCATTTTCTTTTCTCTTTCTTTTTCTTTT-TTTCCTTTTTTTTC
1 TTTTC-TTTTCTTTTCTCTTTC-TTTTCTTTTATTTCC-ATTTTTCC
* *
424381 TTTTCTTTTCTTTTCGTTTTTCTTTTCTTTTATTTTCATTTTTCC
1 TTTTCTTTTCTTTTC-TCTTTCTTTTCTTTTATTTCCATTTTTCC
424426 TTTTC-TTTCTTTT-TCTT
1 TTTTCTTTTCTTTTCTCTT
424443 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
42 3 0.05
44 8 0.15
45 30 0.55
46 14 0.25
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.78
Consensus pattern (44 bp):
TTTTCTTTTCTTTTCTCTTTCTTTTCTTTTATTTCCATTTTTCC
Found at i:434539 original size:14 final size:14
Alignment explanation
Indices: 434520--434548 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
434510 AGTCAGACCC
434520 TCGATCCTCAAGCA
1 TCGATCCTCAAGCA
434534 TCGATCCTCAAGCA
1 TCGATCCTCAAGCA
434548 T
1 T
434549 TACAGGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (14 bp):
TCGATCCTCAAGCA
Found at i:439574 original size:15 final size:15
Alignment explanation
Indices: 439549--439591 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
439539 TTACTTTGGA
439549 ATATT-AAATGGAAT
1 ATATTAAAATGGAAT
439563 ATATTAAAATGGAAT
1 ATATTAAAATGGAAT
439578 ATATTAAAATGGAA
1 ATATTAAAATGGAA
439592 AGTTGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (15 bp):
ATATTAAAATGGAAT
Found at i:439610 original size:13 final size:13
Alignment explanation
Indices: 439594--439619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
439584 AAATGGAAAG
439594 TTGAAATTATCAT
1 TTGAAATTATCAT
439607 TTGAAATTATCAT
1 TTGAAATTATCAT
439620 ATTTCAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
TTGAAATTATCAT
Found at i:442976 original size:3 final size:3
Alignment explanation
Indices: 442970--442997 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
442960 ATAATAATAA
442970 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
442998 TTCAAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:443448 original size:25 final size:25
Alignment explanation
Indices: 443397--443455 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
443387 CTTTATCAAT
*
443397 TCTTTATTTTATATTTATCTTCCTAG
1 TCTTTA-TTTATATTCATCTTCCTAG
*
443423 TCTTTATTTATATTCAT-TATCTTAG
1 TCTTTATTTATATTCATCT-TCCTAG
443448 TCTTTATT
1 TCTTTATT
443456 CTTGATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 23 0.77
26 6 0.20
ACGTcount: A:0.20, C:0.14, G:0.03, T:0.63
Consensus pattern (25 bp):
TCTTTATTTATATTCATCTTCCTAG
Found at i:449530 original size:25 final size:25
Alignment explanation
Indices: 449502--449549 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
449492 AAAAGATTGA
*
449502 AGATGAAAGGAGTGTGTTTTGTAAG
1 AGATGAAAGGAGTGTGTTATGTAAG
* *
449527 AGATTAAATGAGTGTGTTATGTA
1 AGATGAAAGGAGTGTGTTATGTA
449550 CGAGTTCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.35
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTATGTAAG
Found at i:460660 original size:30 final size:30
Alignment explanation
Indices: 460626--460714 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 30
460616 AGTATATAAA
* *
460626 TCACAACAACTTATAAGTCAAACAAACAAG
1 TCACAATAATTTATAAGTCAAACAAACAAG
* *
460656 TCACAATAATTTAGAAGTCAAACAAATAAG
1 TCACAATAATTTATAAGTCAAACAAACAAG
* * *
460686 TCACAATAGTTTATAAATCAAACTAACAA
1 TCACAATAATTTATAAGTCAAACAAACAA
460715 CAATTTTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.53, C:0.18, G:0.07, T:0.22
Consensus pattern (30 bp):
TCACAATAATTTATAAGTCAAACAAACAAG
Found at i:460677 original size:26 final size:26
Alignment explanation
Indices: 460648--460828 Score: 146
Period size: 23 Copynumber: 7.2 Consensus size: 26
460638 ATAAGTCAAA
* *
460648 CAAACAAGTCACAATAATTTAGAAGT
1 CAAACAAGTCACAACAATTTATAAGT
* * *
460674 CAAACAAATAAGTCACAATAGTTTATAAAT
1 CAAAC----AAGTCACAACAATTTATAAGT
* *
460704 CAAAC---TAACAACAATTTTTAAGT
1 CAAACAAGTCACAACAATTTATAAGT
460727 CAAAC---TCACAACAATTTATAAGT
1 CAAACAAGTCACAACAATTTATAAGT
*
460750 CAAACAAGTCACAACATTTTATAAGT
1 CAAACAAGTCACAACAATTTATAAGT
460776 C--A-AAGTCACAACAATTTATAAGT
1 CAAACAAGTCACAACAATTTATAAGT
* * * * *
460799 GAAACAAGACATAACAATTTTTAAAT
1 CAAACAAGTCACAACAATTTATAAGT
460825 CAAA
1 CAAA
460829 TACATGCATG
Statistics
Matches: 127, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
23 59 0.46
24 1 0.01
25 1 0.01
26 43 0.34
30 23 0.18
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (26 bp):
CAAACAAGTCACAACAATTTATAAGT
Found at i:460775 original size:49 final size:49
Alignment explanation
Indices: 460711--460828 Score: 175
Period size: 49 Copynumber: 2.4 Consensus size: 49
460701 AATCAAACTA
*
460711 ACAACAATTTTTAAGTCAAACTCACAACAATTTATAAGTCAAACAAGTC
1 ACAACAATTTTTAAGTCAAACTCACAACAATTTATAAGTCAAACAAGAC
* *
460760 ACAAC-ATTTTATAAGTCAAAGTCACAACAATTTATAAGTGAAACAAGAC
1 ACAACAATTTT-TAAGTCAAACTCACAACAATTTATAAGTCAAACAAGAC
* *
460809 ATAACAATTTTTAAATCAAA
1 ACAACAATTTTTAAGTCAAA
460829 TACATGCATG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
48 5 0.08
49 52 0.84
50 5 0.08
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (49 bp):
ACAACAATTTTTAAGTCAAACTCACAACAATTTATAAGTCAAACAAGAC
Found at i:462410 original size:25 final size:25
Alignment explanation
Indices: 462382--462436 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
462372 CATCCATATC
*
462382 TCATTGAACCCTAATTCTTATATTA
1 TCATTGAACCCTAATTCCTATATTA
462407 TCATTGAACCCTAATTCCTATATTA
1 TCATTGAACCCTAATTCCTATATTA
462432 TCATT
1 TCATT
462437 CTCCTAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.44
Consensus pattern (25 bp):
TCATTGAACCCTAATTCCTATATTA
Found at i:462520 original size:12 final size:12
Alignment explanation
Indices: 462503--462528 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
462493 CATCATATTA
462503 TTTTTCCTCAAC
1 TTTTTCCTCAAC
462515 TTTTTCCTCAAC
1 TTTTTCCTCAAC
462527 TT
1 TT
462529 CCTGCTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTTCCTCAAC
Found at i:465517 original size:4 final size:4
Alignment explanation
Indices: 465508--465534 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
465498 AAAACACACA
465508 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
465535 ATAGACACAC
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:467019 original size:22 final size:24
Alignment explanation
Indices: 466974--467022 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
466964 TCCAACAATA
466974 ATGCTTTATATACAAGTAGACAAGC
1 ATGCTTTATATAC-AGTAGACAAGC
466999 ATGCTTTATATAC-G-AGACAAGC
1 ATGCTTTATATACAGTAGACAAGC
467021 AT
1 AT
467023 TTCATACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
25 13 0.54
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (24 bp):
ATGCTTTATATACAGTAGACAAGC
Found at i:468826 original size:40 final size:41
Alignment explanation
Indices: 468741--468826 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 41
468731 AAAAACACCA
* * * * * *
468741 CTAAAGGTTATGTTATTTAGTGGCATCCTTTTTACAAACGCCG
1 CTAAAGGTTATGTAATTTA--GGCATCATTTTGAAAAAAGACG
468784 CTAAAGGTTATGTAATTTA-GCATCATTTTGAAAAAAGACG
1 CTAAAGGTTATGTAATTTAGGCATCATTTTGAAAAAAGACG
468824 CTA
1 CTA
468827 TTTATCTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
40 19 0.51
43 18 0.49
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (41 bp):
CTAAAGGTTATGTAATTTAGGCATCATTTTGAAAAAAGACG
Found at i:469107 original size:21 final size:21
Alignment explanation
Indices: 469081--469125 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
469071 ATTATCCAAT
469081 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
469102 AAACTTGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
469123 AAA
1 AAA
469126 TCAAAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.22, G:0.04, T:0.18
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:477662 original size:24 final size:22
Alignment explanation
Indices: 477635--477679 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
477625 TATCAAAATC
477635 ATGATCCA-GTAGTATATTGTAAAA
1 ATGAT-CATGTAGT-TATT-TAAAA
477659 ATGATCATGTAGTTATTTAAA
1 ATGATCATGTAGTTATTTAAA
477680 TCACATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 6 0.30
24 10 0.50
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATCATGTAGTTATTTAAAA
Found at i:479591 original size:41 final size:41
Alignment explanation
Indices: 479546--479647 Score: 150
Period size: 41 Copynumber: 2.5 Consensus size: 41
479536 CGTTTTTTTA
* *
479546 AAAAACACTACTAAAGTATGAGTATTTAACGACGTTTGTCT
1 AAAAACGCCACTAAAGTATGAGTATTTAACGACGTTTGTCT
* * *
479587 AAAAACGCCACTAAAGTATGAGTATTTAACGGCGTTTTTTT
1 AAAAACGCCACTAAAGTATGAGTATTTAACGACGTTTGTCT
*
479628 AAAAACGCCACTATAGTATG
1 AAAAACGCCACTAAAGTATG
479648 GTTCTGTAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTATGAGTATTTAACGACGTTTGTCT
Found at i:479670 original size:41 final size:42
Alignment explanation
Indices: 479580--479723 Score: 129
Period size: 41 Copynumber: 3.5 Consensus size: 42
479570 TTTAACGACG
* *
479580 TTTGTCTAAAAACGCCACTAAAGTATGAGTAT-T-TA-ACGGCG
1 TTTGTTTAAAAACGCCACTAAAGTATG-GT-TCTGTAGACGGCA
* *
479621 TTTTTTTAAAAACGCCACTATAGTATGGTTCTGTAGA-GGCA
1 TTTGTTTAAAAACGCCACTAAAGTATGGTTCTGTAGACGGCA
* * * *
479662 TTTGTTTAAAAATGCAACTAAAGTATGGGTCTGTAG-CGCCA
1 TTTGTTTAAAAACGCCACTAAAGTATGGTTCTGTAGACGGCA
* * *
479703 ATTG-TAAAAAAAGCCACTAAA
1 TTTGTTTAAAAACGCCACTAAA
479724 ATACAACTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 17 0.20
41 66 0.78
42 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (42 bp):
TTTGTTTAAAAACGCCACTAAAGTATGGTTCTGTAGACGGCA
Found at i:483805 original size:17 final size:18
Alignment explanation
Indices: 483783--483821 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
483773 TTTTTAAGGT
483783 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
* *
483800 ATATTTTGTTAGTATTTT
1 ATATTTTATTAGTATTTA
483818 ATAT
1 ATAT
483822 AATTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:486118 original size:13 final size:12
Alignment explanation
Indices: 486100--486156 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
486090 CATTTAATAC
486100 TTAATTTATTTTG
1 TTAATTT-TTTTG
*
486113 TTAATTTTGTTG
1 TTAATTTTTTTG
*
486125 --GA-TTTTTTG
1 TTAATTTTTTTG
486134 TTAATTTATTTTG
1 TTAATTT-TTTTG
486147 TTAATTTTTT
1 TTAATTTTTT
486157 ATTACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 6 0.17
10 1 0.03
11 1 0.03
12 9 0.25
13 19 0.53
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.70
Consensus pattern (12 bp):
TTAATTTTTTTG
Found at i:489243 original size:25 final size:25
Alignment explanation
Indices: 489213--489267 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
489203 TTGGAAATTT
489213 GTACTGAAGCAATGACATTCTTCTA
1 GTACTGAAGCAATGACATTCTTCTA
489238 GTACTGAAGCAATGACATTCTTCTA
1 GTACTGAAGCAATGACATTCTTCTA
489263 GTACT
1 GTACT
489268 TCCAACATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (25 bp):
GTACTGAAGCAATGACATTCTTCTA
Found at i:490359 original size:17 final size:18
Alignment explanation
Indices: 490322--490359 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
490312 GTCGAGGGCC
*
490322 TATAATTATAAATTCATA
1 TATAATTATAAAATCATA
*
490340 TATAATTA-AAAATGATA
1 TATAATTATAAAATCATA
490357 TAT
1 TAT
490360 TATTTATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
TATAATTATAAAATCATA
Found at i:491515 original size:21 final size:21
Alignment explanation
Indices: 491471--491516 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
491461 ACTATAATAG
*
491471 AATTATAATCAAAATCATTAA
1 AATTATAATCAAAATCATCAA
*
491492 AATTATAATCGAAATCA-CACA
1 AATTATAATCAAAATCATCA-A
491513 AATT
1 AATT
491517 TTTCTTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (21 bp):
AATTATAATCAAAATCATCAA
Found at i:494946 original size:6 final size:6
Alignment explanation
Indices: 494935--494959 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
494925 TAAGGTTCAC
494935 GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA G
494960 GCTTCGATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTTGA
Found at i:503947 original size:16 final size:16
Alignment explanation
Indices: 503926--503960 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
503916 CAACGATCAA
503926 CGGTCAACAGTCGGGT
1 CGGTCAACAGTCGGGT
503942 CGGTCAACAGTCGGGT
1 CGGTCAACAGTCGGGT
503958 CGG
1 CGG
503961 GTCGGGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.40, T:0.17
Consensus pattern (16 bp):
CGGTCAACAGTCGGGT
Found at i:504032 original size:10 final size:9
Alignment explanation
Indices: 503983--504039 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
503973 GGTCGTGTCG
*
503983 GGTCAGACC
1 GGTCAAACC
*
503992 GGTTCAGACC
1 GG-TCAAACC
*
504002 GGTCAAACT
1 GGTCAAACC
*
504011 GGTTCGAACC
1 GG-TCAAACC
504021 GGTCGAAACC
1 GGTC-AAACC
504031 GGTCAAACC
1 GGTCAAACC
504040 TGTTTTCAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 16 0.40
10 24 0.60
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:504039 original size:19 final size:19
Alignment explanation
Indices: 503983--504039 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
503973 GGTCGTGTCG
* *
503983 GGTCAGACCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
* *
504002 GGTCAAACTGGTTCGAACC
1 GGTCAAACCGGTTCAAACC
504021 GGTCGAAACCGG-TCAAACC
1 GGTC-AAACCGGTTCAAACC
504040 TGTTTTCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:505010 original size:22 final size:21
Alignment explanation
Indices: 504981--505027 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
504971 GGTGTAACCG
*
504981 GTTAAAAGTGGAACACA-AAAT
1 GTTAAAAGTAGAAC-CAGAAAT
505002 GTTACAAAGTAGAACCAGAAAT
1 GTTA-AAAGTAGAACCAGAAAT
505024 GTTA
1 GTTA
505028 TCAATCCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.21
Consensus pattern (21 bp):
GTTAAAAGTAGAACCAGAAAT
Found at i:505336 original size:77 final size:77
Alignment explanation
Indices: 505253--505426 Score: 233
Period size: 77 Copynumber: 2.3 Consensus size: 77
505243 CCCATGAATG
* * *
505253 TCATGATTCACTAAGAAATAGGTTGTGATCTATAATGTTAATATTTTTATTAATAAAATGGGTTG
1 TCATGATTCACTAAGAAATAGGTTGTGATATAGAATGTTAATATTTTTATTAATAAAATGGGCTG
*
505318 AGCCCAAAAATA
66 AGCCAAAAAATA
* *
505330 TCATGATT-AGCTAAGAAATAGGTTGTGATATGGAATTTTAATATTTTTATTAATAAAATGGGCT
1 TCATGATTCA-CTAAGAAATAGGTTGTGATATAGAATGTTAATATTTTTATTAATAAAATGGGCT
* * *
505394 GCGTCAAAAAATG
65 GAGCCAAAAAATA
* *
505407 CCATGATTCACTGAGAAATA
1 TCATGATTCACTAAGAAATA
505427 AGTTACAATC
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
76 1 0.01
77 82 0.98
78 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (77 bp):
TCATGATTCACTAAGAAATAGGTTGTGATATAGAATGTTAATATTTTTATTAATAAAATGGGCTG
AGCCAAAAAATA
Found at i:505448 original size:77 final size:77
Alignment explanation
Indices: 505290--505460 Score: 191
Period size: 77 Copynumber: 2.2 Consensus size: 77
505280 ATCTATAATG
* * * * *
505290 TTAATATTTTTATTAATAAAATGGGTTGAGCCCAAAAATATCATGATTAGCTAAGAAATAGGTTG
1 TTAATATTTTTATTAATAAAATGGGCTGAGCCAAAAAATACCATGATTAGCTAAGAAATAAGTTA
** * * *
505355 TGATATGGAATT
66 CAATACGAAATA
* * * *
505367 TTAATATTTTTATTAATAAAATGGGCTGCGTCAAAAAATGCCATGATTCA-CTGAGAAATAAGTT
1 TTAATATTTTTATTAATAAAATGGGCTGAGCCAAAAAATACCATGATT-AGCTAAGAAATAAGTT
*
505431 ACAATCCGAAATA
65 ACAATACGAAATA
505444 TTAATATTTTTATTAAT
1 TTAATATTTTTATTAAT
505461 TAACAAACAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
77 77 0.99
78 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (77 bp):
TTAATATTTTTATTAATAAAATGGGCTGAGCCAAAAAATACCATGATTAGCTAAGAAATAAGTTA
CAATACGAAATA
Found at i:505623 original size:69 final size:69
Alignment explanation
Indices: 505490--505636 Score: 172
Period size: 69 Copynumber: 2.1 Consensus size: 69
505480 ATATTTTAAC
** * * ***
505490 TTTTGAATTTAAAACTATGGATACTTTTGAAAAAATATCAATACTTTACGGCTTTTTCATTTTTC
1 TTTTGAATTCGAAATTATGAATACTTTTGAAAAAATATCAATACTTTAAACCTTTTTCATTTTTC
505555 ATATT
66 AT-TT
* *
505560 TTTT-AATTCGAAATTATGAATACTTTTGGAAAAGTATCAATACTTTATAACCTTTTTCA-TTTT
1 TTTTGAATTCGAAATTATGAATACTTTTGAAAAAATATCAATACTTTA-AACCTTTTTCATTTTT
*
505623 CCTTT
65 CATTT
505628 TTTTGAATT
1 TTTTGAATT
505637 TTATATTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
68 6 0.09
69 47 0.72
70 12 0.18
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (69 bp):
TTTTGAATTCGAAATTATGAATACTTTTGAAAAAATATCAATACTTTAAACCTTTTTCATTTTTC
ATTT
Found at i:507385 original size:79 final size:79
Alignment explanation
Indices: 507215--507408 Score: 270
Period size: 79 Copynumber: 2.5 Consensus size: 79
507205 ATTTTGATTT
507215 TTTTTTAGCGCAACCTATTTTATTAATAAAAATATT-AACATAACATATCACAACCTATTTTGAT
1 TTTTTTAGCGCAACCTATTTTATTAATAAAAATATTAAACATAACATATCACAACCTATTTTGAT
*
507279 TCAAAACCATGATA
66 TCAAAACCATGACA
* ** * *
507293 TTCTTGGGCGCAACCTATTTTATTAATAAAAATATTAAACATAACATATCGCAACCTGTTTCT-A
1 TTTTTTAGCGCAACCTATTTTATTAATAAAAATATTAAACATAACATATCACAACCTATTT-TGA
*
507357 TTTAAAACCATGACA
65 TTCAAAACCATGACA
*
507372 TTTTTTAGAGCAA-CTCATTTTATTAAT-AAAATATTAA
1 TTTTTTAGCGCAACCT-ATTTTATTAATAAAAATATTAA
507409 CATTCCATAT
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
78 45 0.44
79 56 0.55
80 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (79 bp):
TTTTTTAGCGCAACCTATTTTATTAATAAAAATATTAAACATAACATATCACAACCTATTTTGAT
TCAAAACCATGACA
Found at i:507594 original size:20 final size:21
Alignment explanation
Indices: 507557--507609 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
507547 TATACATATC
*
507557 ATTTTTTAAGTTGATTAA-AAT
1 ATTTTTAAAG-TGATTAATAAT
*
507578 ATTTTTAAAGTGCTTAATAAT
1 ATTTTTAAAGTGATTAATAAT
**
507599 ACATTTAAAGT
1 ATTTTTAAAGT
507610 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTTTTAAAGTGATTAATAAT
Found at i:512711 original size:90 final size:90
Alignment explanation
Indices: 512548--512725 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 90
512538 TAATCCTGAA
* * *
512548 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
512613 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
512638 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
512703 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
512726 GTGTGTTAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:513546 original size:20 final size:19
Alignment explanation
Indices: 513523--513588 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
513513 CAAAGTATTA
513523 AAACTTTAAGGAAAGTTTCG
1 AAACTTTAA-GAAAGTTTCG
* * *
513543 AAACTCTTGAGATAGTTTTG
1 AAACT-TTAAGAAAGTTTCG
** *
513563 AAACTACAAGAAAGTTTCA
1 AAACTTTAAGAAAGTTTCG
513582 AAACTTT
1 AAACTTT
513589 TTAGGCTATT
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
19 13 0.38
20 18 0.53
21 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (19 bp):
AAACTTTAAGAAAGTTTCG
Found at i:514145 original size:15 final size:15
Alignment explanation
Indices: 514103--514151 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
514093 AGATTAGAGC
*
514103 ATAATAAGCCAAGAT
1 ATAATAAGCCAAAAT
* * *
514118 AAATATAATCCAACAT
1 ATA-ATAAGCCAAAAT
514134 ATAATAAGCCAAAAT
1 ATAATAAGCCAAAAT
514149 ATA
1 ATA
514152 TCCATCATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.22
Consensus pattern (15 bp):
ATAATAAGCCAAAAT
Found at i:514314 original size:3 final size:3
Alignment explanation
Indices: 514306--514335 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
514296 TAGTCAATCC
*
514306 TCA TCA TCA TCA TCG TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
514336 CCTGGATGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:515435 original size:2 final size:2
Alignment explanation
Indices: 515428--515462 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
515418 CATTAAAAGA
515428 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 A
515463 AACTCAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:516028 original size:19 final size:19
Alignment explanation
Indices: 516006--516042 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
515996 CTTGAGGTGT
516006 TTCGATACTTTACGAAAAG
1 TTCGATACTTTACGAAAAG
* *
516025 TTCGATTCTTTATGAAAA
1 TTCGATACTTTACGAAAA
516043 TTTTCGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
TTCGATACTTTACGAAAAG
Found at i:519534 original size:17 final size:16
Alignment explanation
Indices: 519512--519551 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
519502 AAGTTTTAAT
519512 TTTTGGTAACCAAATTC
1 TTTTGGT-ACCAAATTC
*
519529 TTTTGGGTCCCAAATTC
1 TTTT-GGTACCAAATTC
519546 TTTTGG
1 TTTTGG
519552 GTCCATTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (16 bp):
TTTTGGTACCAAATTC
Found at i:519552 original size:17 final size:17
Alignment explanation
Indices: 519521--519555 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
519511 TTTTTGGTAA
519521 CCAAATTCTTTTGGGTC
1 CCAAATTCTTTTGGGTC
519538 CCAAATTCTTTTGGGTC
1 CCAAATTCTTTTGGGTC
519555 C
1 C
519556 ATTGACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (17 bp):
CCAAATTCTTTTGGGTC
Found at i:525420 original size:13 final size:14
Alignment explanation
Indices: 525402--525430 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
525392 ATTATATATT
525402 AATAATA-TTTTAA
1 AATAATATTTTTAA
525415 AATAATATTTTTAA
1 AATAATATTTTTAA
525429 AA
1 AA
525431 ATTCTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATATTTTTAA
Found at i:526442 original size:24 final size:26
Alignment explanation
Indices: 526415--526469 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
526405 AGATTTTAGG
*
526415 TTAAAGA-AAATAAATTTCTAAAA-T
1 TTAAAGATAAATAAATTTATAAAATT
**
526439 TTAAA-ATGGATAAATTTATAAAATT
1 TTAAAGATAAATAAATTTATAAAATT
526464 TTAAAG
1 TTAAAG
526470 GACGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 18 0.72
25 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (26 bp):
TTAAAGATAAATAAATTTATAAAATT
Found at i:530544 original size:19 final size:20
Alignment explanation
Indices: 530506--530544 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
530496 GGACAAAAAT
530506 AAATAATTAACAAAATATAA
1 AAATAATTAACAAAATATAA
* *
530526 AAATATTTAA-AATATATAA
1 AAATAATTAACAAAATATAA
530545 TAATTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATAATTAACAAAATATAA
Found at i:533063 original size:2 final size:2
Alignment explanation
Indices: 533056--533101 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
533046 TGTTAGTAAC
533056 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
533098 AT AT
1 AT AT
533102 TTCAATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:539046 original size:3 final size:3
Alignment explanation
Indices: 539038--539072 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
539028 CTTTAGTATT
539038 GAA GAA GAA GAA GAA GAA GAA GAA GAA GATA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA G
539073 GCCTTGGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:540214 original size:8 final size:8
Alignment explanation
Indices: 540195--540291 Score: 78
Period size: 9 Copynumber: 11.8 Consensus size: 8
540185 TTAAAGATAA
540195 AAAAAATG
1 AAAAAATG
540203 -AAAAATG
1 AAAAAATG
540210 AAAAAAATG
1 -AAAAAATG
540219 AAAAAAATG
1 -AAAAAATG
540228 AAAAAAATG
1 -AAAAAATG
540237 AAAAAAAAATG
1 ---AAAAAATG
540248 AAAAAATG
1 AAAAAATG
*
540256 -AAATA-G
1 AAAAAATG
540262 -AAAAATAG
1 AAAAAAT-G
540270 AAAAAATGG
1 AAAAAAT-G
540279 AAAAAAT-
1 AAAAAATG
540286 AAAAAA
1 AAAAAA
540292 AGAAGAAGAA
Statistics
Matches: 79, Mismatches: 3, Indels: 15
0.81 0.03 0.15
Matches are distributed among these distances:
6 5 0.06
7 17 0.22
8 9 0.11
9 39 0.49
11 9 0.11
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:540215 original size:9 final size:9
Alignment explanation
Indices: 540194--540258 Score: 91
Period size: 9 Copynumber: 7.3 Consensus size: 9
540184 CTTAAAGATA
540194 AAAAAAATG
1 AAAAAAATG
540203 --AAAAATG
1 AAAAAAATG
540210 AAAAAAATG
1 AAAAAAATG
540219 AAAAAAATG
1 AAAAAAATG
540228 AAAAAAATG
1 AAAAAAATG
540237 AAAAAAAAATG
1 --AAAAAAATG
540248 -AAAAAATG
1 AAAAAAATG
540256 AAA
1 AAA
540259 TAGAAAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.14
8 8 0.16
9 27 0.53
11 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:540216 original size:18 final size:18
Alignment explanation
Indices: 540193--540275 Score: 62
Period size: 20 Copynumber: 4.3 Consensus size: 18
540183 GCTTAAAGAT
540193 AAAAAAAATGAAAAATG-
1 AAAAAAAATGAAAAATGA
540210 -AAAAAAATGAAAAAAATGA
1 AAAAAAAATG--AAAAATGA
**
540229 AAAAAATGAAAAAAAAATGA
1 AAAAAA--AATGAAAAATGA
540249 AAAAATGAAATAGAAAAATAGA
1 AAAAA--AAAT-GAAAAAT-GA
540271 AAAAA
1 AAAAA
540276 TGGAAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
16 9 0.17
18 7 0.13
20 20 0.38
21 6 0.12
22 10 0.19
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAAAAATGAAAAATGA
Found at i:540292 original size:8 final size:8
Alignment explanation
Indices: 540194--540322 Score: 70
Period size: 9 Copynumber: 15.5 Consensus size: 8
540184 CTTAAAGATA
540194 AAAAAAAT
1 AAAAAAAT
*
540202 -GAAAAAT
1 AAAAAAAT
540209 GAAAAAAAT
1 -AAAAAAAT
540218 GAAAAAAAT
1 -AAAAAAAT
540227 GAAAAAAAT
1 -AAAAAAAT
540236 GAAAAAAA-
1 -AAAAAAAT
*
540244 AATGAAAA-
1 AA-AAAAAT
**
540252 AATGAAAT
1 AAAAAAAT
*
540260 AGAAAAAT
1 AAAAAAAT
540268 AGAAAAAAT
1 A-AAAAAAT
*
540277 GGAAAAAAT
1 -AAAAAAAT
*
540286 AAAAAAAG
1 AAAAAAAT
540294 AAGAAGAAA-
1 AA-AA-AAAT
540303 AAAAAACA-
1 AAAAAA-AT
540311 AAAAAAAT
1 AAAAAAAT
540319 AAAA
1 AAAA
540323 GGGGGTTCAA
Statistics
Matches: 99, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
7 14 0.14
8 33 0.33
9 49 0.49
10 3 0.03
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.09
Consensus pattern (8 bp):
AAAAAAAT
Found at i:541684 original size:55 final size:55
Alignment explanation
Indices: 541600--541879 Score: 447
Period size: 55 Copynumber: 5.1 Consensus size: 55
541590 TGAAGCAAAA
* *
541600 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATTGGGGGCAGATGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
541655 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
541710 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
541763 GAAGATTGTTCGAGTCTTGTACTCTCTGAATAAATAGGGGACAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
541818 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
541873 GGAGATT
1 GAAGATT
541880 ATTGTTCGAG
Statistics
Matches: 204, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
53 47 0.23
54 6 0.03
55 151 0.74
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:541808 original size:108 final size:110
Alignment explanation
Indices: 541600--541882 Score: 471
Period size: 108 Copynumber: 2.6 Consensus size: 110
541590 TGAAGCAAAA
* *
541600 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATTGGGGGCAGATGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
*
541665 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGAT
* *
541710 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* * *
541773 CGAGTCTTGTACTCTCTGAATAAATAGGGGACAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGAT
*
541818 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
541883 GTTCGAGTTC
Statistics
Matches: 160, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
108 97 0.61
109 6 0.04
110 57 0.36
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGAT
Found at i:541935 original size:52 final size:52
Alignment explanation
Indices: 541875--542155 Score: 418
Period size: 52 Copynumber: 5.4 Consensus size: 52
541865 CGATCGTTGG
541875 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
541927 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
541979 ATATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
542031 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * ** * **
542083 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAATAGAGGGCAAACCCGTAAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA-ATTGGGCAGACCCGTAGGA
**
542136 AGAAGATTGTTCGAGTTCTA
1 AGATTATTGTTCGAGTTCTA
542156 TACTCCCAGA
Statistics
Matches: 206, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
52 177 0.86
53 29 0.14
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:542406 original size:3 final size:3
Alignment explanation
Indices: 542400--542457 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
542390 AATAATAATA
*
542400 ATT ATT A-T ATT A-T ATG ATT ATT ATT ATT ATT ATTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
542444 ATT AAT ATTT ATT A
1 ATT ATT A-TT ATT A
542458 CAACTATTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 38 0.81
4 5 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:542436 original size:16 final size:16
Alignment explanation
Indices: 542417--542447 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
542407 TATTATATGA
542417 TTATTATTATTATTAT
1 TTATTATTATTATTAT
542433 TTATTATTATTATTA
1 TTATTATTATTATTA
542448 ATATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:542446 original size:19 final size:19
Alignment explanation
Indices: 542400--542457 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
542390 AATAATAATA
*
542400 ATTATTA-TATTATATGATT
1 ATTATTATTATTAT-TTATT
542419 ATTATTATTATTATTTATT
1 ATTATTATTATTATTTATT
*
542438 ATTATTATTAATATTTATT
1 ATTATTATTATTATTTATT
542457 A
1 A
542458 CAACTATTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 30 0.83
20 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTATTATTATTATTTATT
Found at i:546553 original size:3 final size:3
Alignment explanation
Indices: 546540--546578 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
546530 TGGTATTTTT
546540 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
546579 TAAGAGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:549096 original size:10 final size:9
Alignment explanation
Indices: 549066--549167 Score: 53
Period size: 10 Copynumber: 10.2 Consensus size: 9
549056 TTATCATAAA
549066 TTTAATAGTCT
1 TTTAATA-T-T
549077 TTTGAATATT
1 TTT-AATATT
549087 TTATAATATT
1 TT-TAATATT
*
549097 ATTAAT-TT
1 TTTAATATT
**
549105 TAAAAATATCT
1 T-TTAATAT-T
549116 TTTAATATT
1 TTTAATATT
549125 TTTAAATAAATT
1 TTT-AAT--ATT
549137 TTTAAATATT
1 TTT-AATATT
549147 TTTATATATT
1 TTTA-ATATT
**
549157 AATAATATT
1 TTTAATATT
549166 TT
1 TT
549168 AAAATAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
8 2 0.03
9 17 0.24
10 32 0.44
11 7 0.10
12 14 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTAATATT
Found at i:549128 original size:22 final size:22
Alignment explanation
Indices: 549102--549150 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
549092 ATATTATTAA
549102 TTTTAAA-AATATCTTTT-AATAT
1 TTTTAAATAA-AT-TTTTAAATAT
549124 TTTTAAATAAATTTTTAAATAT
1 TTTTAAATAAATTTTTAAATAT
549146 TTTTA
1 TTTTA
549151 TATATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATAAATTTTTAAATAT
Found at i:549167 original size:28 final size:26
Alignment explanation
Indices: 549081--549170 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
549071 TAGTCTTTTG
* *
549081 AATATTTTATAATATTATTAATTTTAAA
1 AATATTTTA-AATATTTTTAATATT-AA
*
549109 AATATCTTTTAATATTTTTAA-A-T-A
1 AATAT-TTTAAATATTTTTAATATTAA
549133 AAT-TTTTAAATATTTTTATATATTAA
1 AATATTTTAAATATTTTTA-ATATTAA
549159 TAATATTTTAAA
1 -AATATTTTAAA
549171 ATAATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
22 13 0.25
23 2 0.04
24 5 0.10
25 1 0.02
26 2 0.04
27 3 0.06
28 22 0.43
29 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTAAATATTTTTAATATTAA
Found at i:549182 original size:14 final size:13
Alignment explanation
Indices: 549118--549185 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 13
549108 AAATATCTTT
*
549118 TAATATTTTTAAA
1 TAATATTTTAAAA
*
549131 TAA-ATTTTTAAA
1 TAATATTTTAAAA
*
549143 T-ATTTTTATATATTAA
1 TAATATTT-TA-A--AA
549159 TAATATTTTAAAA
1 TAATATTTTAAAA
549172 TAATAATTTTAAAA
1 TAAT-ATTTTAAAA
549186 ATTCTAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 13 0.29
13 10 0.22
14 10 0.22
15 1 0.02
16 5 0.11
17 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTTTAAAA
Found at i:549196 original size:42 final size:41
Alignment explanation
Indices: 549118--549197 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
549108 AAATATCTTT
* * * * *
549118 TAATATTTTTAAATAAATTTTTAAATATTTTTATATATTAA
1 TAATATTTTAAAATAAAATTTTAAAAATTCTAATATATTAA
549159 TAATATTTTAAAATAATAATTTTAAAAATTCTAATATAT
1 TAATATTTTAAAATAA-AATTTTAAAAATTCTAATATAT
549198 CACGCGACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 15 0.45
42 18 0.55
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (41 bp):
TAATATTTTAAAATAAAATTTTAAAAATTCTAATATATTAA
Found at i:549747 original size:31 final size:32
Alignment explanation
Indices: 549675--549753 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
549665 TAAAGATTTA
** * **
549675 AGTACTAAAAGGAAACAAAAAGTTAACGATGG
1 AGTACTAAAATAAAACAAAAAGTAAACGACCG
*
549707 ATTACTAAAATAAAACAAAAAGTAAACG-CCG
1 AGTACTAAAATAAAACAAAAAGTAAACGACCG
549738 AGTACTAAAATTAAAA
1 AGTACTAAAA-TAAAA
549754 AATAAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (32 bp):
AGTACTAAAATAAAACAAAAAGTAAACGACCG
Found at i:552258 original size:14 final size:15
Alignment explanation
Indices: 552232--552261 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
552222 GTTTCATCTT
552232 TATTTTGAATGATGA
1 TATTTTGAATGATGA
552247 TATTTT-AATGATGA
1 TATTTTGAATGATGA
552261 T
1 T
552262 TTCGATGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATTTTGAATGATGA
Found at i:552502 original size:20 final size:20
Alignment explanation
Indices: 552479--552542 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 20
552469 TTATCTTTTT
552479 ATATTTTAAATAAATTTTAA
1 ATATTTTAAATAAATTTTAA
*
552499 ATATTTTTAAAT-AA-TTAATA
1 ATA-TTTTAAATAAATTTTA-A
552519 ATATTTTAAAATAATAATTTTAA
1 ATATTTT-AAAT-A-AATTTTAA
552542 A
1 A
552543 AATTCTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
19 7 0.20
20 13 0.37
21 8 0.23
23 4 0.11
24 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTTTAAATAAATTTTAA
Found at i:552508 original size:10 final size:10
Alignment explanation
Indices: 552481--552514 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
552471 ATCTTTTTAT
552481 ATTTTAAATAA
1 ATTTTAAAT-A
552492 ATTTTAAATA
1 ATTTTAAATA
*
552502 TTTTTAAATA
1 ATTTTAAATA
552512 ATT
1 ATT
552515 AATAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTTAAATA
Found at i:552533 original size:13 final size:14
Alignment explanation
Indices: 552515--552543 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
552505 TTAAATAATT
552515 AATAAT-ATTTTAA
1 AATAATAATTTTAA
552528 AATAATAATTTTAA
1 AATAATAATTTTAA
552542 AA
1 AA
552544 ATTCTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATAATTTTAA
Found at i:552535 original size:16 final size:15
Alignment explanation
Indices: 552498--552545 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
552488 ATAAATTTTA
*
552498 AATATTTTTAAATAATT
1 AATAATTTTAAA-AA-T
*
552515 AATAATATTTTAAAAT
1 AATAAT-TTTAAAAAT
552531 AATAATTTTAAAAAT
1 AATAATTTTAAAAAT
552546 TCTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 7 0.26
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATTTTAAAAAT
Found at i:552874 original size:43 final size:41
Alignment explanation
Indices: 552710--552950 Score: 268
Period size: 42 Copynumber: 5.7 Consensus size: 41
552700 CCGCTAATGT
* * *
552710 TAGCGGCGTTTGTGAAATAAAAACGTCGCAAAAGTCAAGATCTA
1 TAGCGGCGTTTTTG--ATACAAACGCCGCAAAAGTC-AGATCTA
* *
552754 TAGCAGCGTTTTTGAAACAAACGCCGCAAAAGTCAAGATCTA
1 TAGCGGCGTTTTTGATACAAACGCCGCAAAAGTC-AGATCTA
* * * * *
552796 TAACAGCGTTTTTGAAACAAACGCCGTAAATGGTCAGATCTA
1 TAGCGGCGTTTTTGATACAAACGCCGCAAA-AGTCAGATCTA
552838 TAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTCAGATCTA
1 TAGCGGCGTTTTTG-ATACAAACGCCGCAAAA-GTCAGATCTA
* * *
552881 TAGCGGCGATTTTGTATACAAACGCCGCGAAACGTCAGATCTG
1 TAGCGGCGTTTTTG-ATACAAACGCCGC-AAAAGTCAGATCTA
552924 TAGCGGCGTTTTTAGA-ACAAACGCCGC
1 TAGCGGCGTTTTT-GATACAAACGCCGC
552951 TAATTACCAT
Statistics
Matches: 175, Mismatches: 17, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
42 83 0.47
43 76 0.43
44 16 0.09
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (41 bp):
TAGCGGCGTTTTTGATACAAACGCCGCAAAAGTCAGATCTA
Found at i:552882 original size:85 final size:84
Alignment explanation
Indices: 552730--552950 Score: 261
Period size: 85 Copynumber: 2.6 Consensus size: 84
552720 TGTGAAATAA
* * *
552730 AAACGTCGC-AAAAGTCAAGATCTATAGCAGCGTTTTTGAAACAAACGCCGCAAAAGTCAAGATC
1 AAACGCCGCGAAACGTC-AGATCTATAGCGGCGTTTTTG-AACAAACGCCGCAAAAGTCAAGATC
*
552794 TATAACAGCGTTTTTG-AAAC
64 TATAACAGCGATTTTGTAAAC
* *
552814 AAACGCCG-TAAATGGTCAGATCTATAGCGGCGTTTTTGTATACAAACGCCGCAAAAGGTC-AGA
1 AAACGCCGCGAAA-CGTCAGATCTATAGCGGCGTTTTTG-A-ACAAACGCCGCAAAA-GTCAAGA
* * *
552877 TCTATAGCGGCGATTTTGTATAC
62 TCTATAACAGCGATTTTGTAAAC
*
552900 AAACGCCGCGAAACGTCAGATCTGTAGCGGCGTTTTTAGAACAAACGCCGC
1 AAACGCCGCGAAACGTCAGATCTATAGCGGCGTTTTT-GAACAAACGCCGC
552951 TAATTACCAT
Statistics
Matches: 119, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
84 31 0.26
85 47 0.39
86 37 0.31
87 4 0.03
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (84 bp):
AAACGCCGCGAAACGTCAGATCTATAGCGGCGTTTTTGAACAAACGCCGCAAAAGTCAAGATCTA
TAACAGCGATTTTGTAAAC
Found at i:552943 original size:128 final size:128
Alignment explanation
Indices: 552710--552949 Score: 317
Period size: 128 Copynumber: 1.9 Consensus size: 128
552700 CCGCTAATGT
* *
552710 TAGCGGCGTTTGTGAAATAAAAACGTCGCAAAAGTCAAGATCTATAGCAGCGTTTTTGAAACAAA
1 TAGCGGCGTTTGTGAAATAAAAACGCCGCAAAAGTCAAGATCTATAGCAGCGATTTTGAAACAAA
552775 CGCCGCAAAAGTCAAGATCTATAACAGCGTTTTTGAAACAAACGCCGTAAATGGTCAGATCTA
66 CGCCGCAAAAGTCAAGATCTATAACAGCGTTTTTGAAACAAACGCCGTAAATGGTCAGATCTA
* * * * *
552838 TAGCGGCGTTTTTG-TATACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCGATTTTGTATACA
1 TAGCGGCGTTTGTGAAATAAAAACGCCGCAAAA-GTCAAGATCTATAGCAGCGATTTTG-AAACA
* * * *
552901 AACGCCGCGAAACGTC-AGATCTGTAGCGGCGTTTTT-AGAACAAACGCCG
64 AACGCCGC-AAAAGTCAAGATCTATAACAGCGTTTTTGA-AACAAACGCCG
552950 CTAATTACCA
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
127 35 0.36
128 56 0.58
129 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (128 bp):
TAGCGGCGTTTGTGAAATAAAAACGCCGCAAAAGTCAAGATCTATAGCAGCGATTTTGAAACAAA
CGCCGCAAAAGTCAAGATCTATAACAGCGTTTTTGAAACAAACGCCGTAAATGGTCAGATCTA
Found at i:556984 original size:41 final size:41
Alignment explanation
Indices: 556832--557296 Score: 471
Period size: 41 Copynumber: 11.4 Consensus size: 41
556822 ACAATTTGCA
*
556832 GCGTTTGTA-AAAAATGCCACTAAAG-ACGAGTCTATA-CG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
* * * * *
556870 TCGTTTGTATAAAAACGCCACTAAAGTACAAGCCTATTGCG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
*
556911 GCGTTTGTA-AACACAAACGCCACTAAAGTACGAGTCTATAGAG
1 GCGTTTGTATAA-A-AAA-GCCACTAAAGTACGAGTCTATAGCG
*
556954 GCATTTGTATAAAAAAGCCACTAATA-TACGAGTCTATAGCG
1 GCGTTTGTATAAAAAAGCCACTAA-AGTACGAGTCTATAGCG
** * * * *
556995 GCGTTTGTGCAAAACA-CCACTAAAGTACAAGCCTATTGCG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
** *
557035 GCGTTTACA-AACACAAACGCCACTAAAATACGAGTCTATAGCG
1 GCGTTTGTATAA-A-AAA-GCCACTAAAGTACGAGTCTATAGCG
* * *
557078 GCGTTTGTATAAAAACGCCTCTAAAGTACAAGTCTATAGCG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
* * * *
557119 GCGTTTATAT-AAAACGCCACTAAAGTAGGCGTCTATAGCG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
* ** * * *
557159 GCGTTTGTATAAAACA-CTGCAAAAGTACTACTCTATAGCG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
* * **
557199 GCGTTTGTTTAAAAACGCCACTAAAGTACGAGTCTATAATG
1 GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
* *
557240 GCGTTTTGTATAAAAATGCCACTAAAGTACTAGTCTATAGCG
1 GCG-TTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
557282 GCGTTTGTATAAAAA
1 GCGTTTGTATAAAAA
557297 CGCTGCTAAC
Statistics
Matches: 346, Mismatches: 64, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
38 8 0.02
39 18 0.05
40 101 0.29
41 113 0.33
42 44 0.13
43 58 0.17
44 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
GCGTTTGTATAAAAAAGCCACTAAAGTACGAGTCTATAGCG
Found at i:557031 original size:124 final size:124
Alignment explanation
Indices: 556832--557290 Score: 506
Period size: 124 Copynumber: 3.7 Consensus size: 124
556822 ACAATTTGCA
* * * *
556832 GCGTTTGTA-AAAAATGCCACTAAAG-ACGAGTCTATA-CGTCGTTTGTATAAAAACGCCACTAA
1 GCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTGT-AAAACACCACTAA
* *
556894 AGTACAAGCCTATTGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGAG
65 AGTACAAGCCTATAGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCG
* * *
556954 GCATTTGTATAAAAAAGCCACTAATA-TACGAGTCTATAGCGGCGTTTGTGCAAAACACCACTAA
1 GCGTTTGTATAAAAACGCCACTAA-AGTACGAGTCTATAGCGGCGTTTGTGTAAAACACCACTAA
* ** *
557018 AGTACAAGCCTATTGCGGCGTTTACAAACACAAACGCCACTAAAATACGAGTCTATAGCG
65 AGTACAAGCCTATAGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCG
* * * * *
557078 GCGTTTGTATAAAAACGCCTCTAAAGTACAAGTCTATAGCGGCGTTTATATAAAACGCCACTAAA
1 GCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTGTAAAACACCACTAAA
*** * * * *
557143 GTAGGCGTCTATAGCGGCGTTTGTATAA-A-ACACTG-CA--AAAGTACTACTCTATAGCG
66 GTACAAGCCTATAGCGGCGTTTGTA-AACACAAAC-GCCACTAAAGTACGAGTCTATAGCG
* ** *
557199 GCGTTTGTTTAAAAACGCCACTAAAGTACGAGTCTATAATGGCGTTT-TGTATAAAAATGCCACT
1 GCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTGTA-AAACA--CCACT
* *
557263 AAAGTACTAGTCTATAGCGGCGTTTGTA
63 AAAGTACAAGCCTATAGCGGCGTTTGTA
557291 TAAAAACGCT
Statistics
Matches: 287, Mismatches: 40, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
120 3 0.01
121 61 0.21
122 8 0.03
123 49 0.17
124 155 0.54
125 11 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (124 bp):
GCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTGTAAAACACCACTAAA
GTACAAGCCTATAGCGGCGTTTGTAAACACAAACGCCACTAAAGTACGAGTCTATAGCG
Found at i:561178 original size:111 final size:111
Alignment explanation
Indices: 560987--561208 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
560977 TGTAAATCAT
* *
560987 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
561052 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
561098 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
561163 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
561209 TTTTCGTAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:563368 original size:35 final size:33
Alignment explanation
Indices: 563329--563413 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
563319 ATATTTCAGT
563329 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
563364 TAATTTGGTTATCATTTATCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
563399 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
563414 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:566801 original size:21 final size:21
Alignment explanation
Indices: 566775--566821 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
566765 CTCACGAAGC
566775 GGTTCTTCTGGTGGACATGAT
1 GGTTCTTCTGGTGGACATGAT
*
566796 GGTTCTTCTGGTGGAGATGAT
1 GGTTCTTCTGGTGGACATGAT
566817 GGTTC
1 GGTTC
566822 CTCTATGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.36, T:0.38
Consensus pattern (21 bp):
GGTTCTTCTGGTGGACATGAT
Found at i:569389 original size:37 final size:35
Alignment explanation
Indices: 569279--569717 Score: 280
Period size: 36 Copynumber: 11.9 Consensus size: 35
569269 GTCCGGGGTT
* * * *
569279 TATATAATATATAGTTGTTAGAAGATGGTTTTTGAAAA
1 TATATATTATATAGTT-TT-GAAAAT-ATTTTTAAAAA
* * * *
569317 CATATAATATAT-GCTTT-AAAATCGATTTTTGAAAA
1 TATATATTATATAGTTTTGAAAAT--ATTTTTAAAAA
**
569352 TATATATTATATAGTTTTGAAAACGGTTTTCTAAAAATA
1 TATATATTATATAGTTTTGAAAA-TATTTT-T-AAAA-A
*
569391 TATATATTATATAGTTTTG-AAAT-TTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
*
569425 TATTTATATTATATAGTTTTTGAAAATATTTTTGAATATA
1 TA--TATATTATATAG-TTTTGAAAATATTTTT-AA-AAA
* * *
569465 TATATAATATATAGTTTT-AAAACATTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
* * *
569500 TATATATAATCTATAGTTTTTTAAAATATTTTGAAAATA
1 TATATAT--TATATAG-TTTTGAAAATATTTTTAAAA-A
* * *
569539 TATATAATATATATTTTTGAAAATGTTTTTAAAAAA
1 TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* * *
569575 TGTATATAATATATAGTTTTG-AATTTTTTTTGAAAAA
1 --TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* *
569612 TATATATTATATAGTTTTAAAAAAATAATTTTTGAAAA
1 TATATATTATATAGTTTT--GAAAAT-ATTTTTAAAAA
* *
569650 TATATTATTATAT-GTTTTGAAAACAATTTTCAAAAA
1 TATA-TATTATATAGTTTTGAAAA-TATTTTTAAAAA
* * *
569686 TGTATATAATATAGTTTTAAAAATTATTTTTA
1 TATATATTATATAGTTTTGAAAA-TATTTTTA
569718 TTTTTATTAT
Statistics
Matches: 326, Mismatches: 46, Indels: 60
0.75 0.11 0.14
Matches are distributed among these distances:
34 13 0.04
35 54 0.17
36 80 0.25
37 44 0.13
38 70 0.21
39 59 0.18
40 5 0.02
41 1 0.00
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (35 bp):
TATATATTATATAGTTTTGAAAATATTTTTAAAAA
Found at i:569493 original size:75 final size:74
Alignment explanation
Indices: 569279--569707 Score: 325
Period size: 74 Copynumber: 5.8 Consensus size: 74
569269 GTCCGGGGTT
* * * *
569279 TATATAATATATAGTTGTTAGAAGATGGTTTTTG-AAA-ACATATAATATAT-GCTTTAAAATCG
1 TATATAATATATAGTT-TT-GAAAAT-ATTTTTGAAAATATATATAATATATAGTTTTAAAA-C-
569341 ATTTTTG-AAA-ATA
61 A-TTTTGAAAATATA
** * * * *
569354 TATAT--TATATAGTTTTGAAAACGGTTTTCTAAAAATATATATATTATATAGTTTTGAAA-TTT
1 TATATAATATATAGTTTTGAAAA-TATTTT-TGAAAATATATATAATATATAGTTTTAAAACATT
569416 TTGAAAATATA
64 TTGAAAATATA
* * *
569427 TTTATATTATATAGTTTTTGAAAATATTTTTGAATATATATATAATATATAGTTTTAAAACATTT
1 TATATAATATATAG-TTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTAAAACATTT
569492 TGAAAATATA
65 TGAAAATATA
* * * **
569502 TATATAATCTATAGTTTTTTAAAATA-TTTTGAAAATATATATAATATATATTTTTGAAAATGTT
1 TATATAATATATAG-TTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTT-AAAACATT
* * *
569566 TTTAAAAAATG
64 TTGAAAATATA
* * * *
569577 TATATAATATATAGTTTTG-AATTTTTTTTGAAAA-ATATATATTATATAGTTTTAAAAAAATAA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTT---AAAA-CA
569640 TTTTTGAAAATATA
62 -TTTTGAAAATATA
* * * *
569654 T-TAT--TATAT-GTTTTGAAAACAATTTTCAAAA-ATGTAT-ATAATATAGTTTTAAAA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAAT-ATATAGTTTTAAAA
569708 ATTATTTTTA
Statistics
Matches: 289, Mismatches: 46, Indels: 42
0.77 0.12 0.11
Matches are distributed among these distances:
71 18 0.06
72 6 0.02
73 46 0.16
74 107 0.37
75 89 0.31
76 12 0.04
77 11 0.04
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (74 bp):
TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTAAAACATTTT
GAAAATATA
Found at i:569736 original size:16 final size:16
Alignment explanation
Indices: 569708--569761 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
569698 AGTTTTAAAA
569708 ATTATT-TTTATTTTT
1 ATTATTATTTATTTTT
569723 ATTA-TATATTA-TTTT
1 ATTATTAT-TTATTTTT
*
569738 AATATTATTTATTTTT
1 ATTATTATTTATTTTT
569754 ATT-TTATT
1 ATTATTATT
569762 AATATTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 12 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTATTATTTATTTTT
Found at i:569759 original size:11 final size:11
Alignment explanation
Indices: 569708--569767 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
569698 AGTTTTAAAA
569708 ATTATTTTTATT
1 ATTA-TTTTATT
* *
569720 TTTATTATA-T
1 ATTATTTTATT
*
569730 ATTATTTTAAT
1 ATTATTTTATT
569741 ATTA-TTTATT
1 ATTATTTTATT
*
569751 TTTATTTTATT
1 ATTATTTTATT
*
569762 AATATT
1 ATTATT
569768 CTCTTTTCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 16 0.42
11 19 0.50
12 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:570961 original size:24 final size:22
Alignment explanation
Indices: 570905--570974 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
570895 GTCCTTTAAA
570905 TTTTTAGTTATTCATTTTTTCC
1 TTTTTAGTTATTCATTTTTTCC
* *
570927 TTTTTA-ATATTATCATTTTTT-T
1 TTTTTAGTTA-T-TCATTTTTTCC
570949 TATTTTAGTTATTCATTTTTT-C
1 T-TTTTAGTTATTCATTTTTTCC
570971 TTTT
1 TTTT
570975 AATTTTAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
21 5 0.12
22 18 0.45
23 15 0.38
24 2 0.05
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTTAGTTATTCATTTTTTCC
Found at i:570991 original size:43 final size:45
Alignment explanation
Indices: 570906--570996 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 45
570896 TCCTTTAAAT
*
570906 TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATTTTTTTTA
1 TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATGTTTTTTA
*
570951 TTTTAGTTATTCATTTTTT-C-TTTTAATTTTAGT-ATGTTTTTTA
1 TTTTAGTTATTCATTTTTTCCTTTTTAATATTA-TCATGTTTTTTA
570994 TTT
1 TTT
570997 GTTTTGTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 22 0.51
44 2 0.05
45 19 0.44
ACGTcount: A:0.19, C:0.07, G:0.04, T:0.70
Consensus pattern (45 bp):
TTTTAGTTATTCATTTTTTCCTTTTTAATATTATCATGTTTTTTA
Found at i:571084 original size:25 final size:25
Alignment explanation
Indices: 571056--571134 Score: 68
Period size: 32 Copynumber: 2.8 Consensus size: 25
571046 ACTTTTAAAA
571056 TTTAATTTTTTATTTTATTTTTTCC
1 TTTAATTTTTTATTTTATTTTTTCC
571081 TTTAATTTATTTAATATTTTTTTATTTTTTCC
1 TTTAA-TT-TTT--TA---TTTTATTTTTTCC
* *
571113 TTTGATTTATTTTTTTTATTTT
1 TTTAATTT-TTTATTTTATTTT
571135 CATTAATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
25 5 0.11
26 11 0.25
27 3 0.07
29 3 0.07
30 1 0.02
31 4 0.09
32 17 0.39
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.76
Consensus pattern (25 bp):
TTTAATTTTTTATTTTATTTTTTCC
Found at i:571123 original size:17 final size:16
Alignment explanation
Indices: 571064--571127 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
571054 AATTTAATTT
571064 TTTATTTTATTTTTTCC
1 TTTA-TTTATTTTTTCC
** *
571081 TTTAATTTATTTAAT-A
1 TTT-ATTTATTTTTTCC
*
571097 TTTTTTTATTTTTTCC
1 TTTATTTATTTTTTCC
571113 TTTGATTTATTTTTT
1 TTT-ATTTATTTTTT
571128 TTATTTTCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
15 8 0.22
16 6 0.17
17 21 0.58
18 1 0.03
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTATTTATTTTTTCC
Found at i:572330 original size:35 final size:34
Alignment explanation
Indices: 572252--572681 Score: 242
Period size: 37 Copynumber: 11.6 Consensus size: 34
572242 GTCCGGGGTT
**
572252 TATATAATATATAGTTGTTAGAAGATGGTTTTTGAAAA
1 TATATAATATATAGTT-TTA-AA-A-CATTTTTGAAAA
* *
572290 CATATAATATAT-GCTTTAAAATCGATTTTTGAAAA
1 TATATAATATATAGTTTTAAAA-C-ATTTTTGAAAA
* * *
572325 TATATATTATATAGTTTTGAAAACGGTTTTCTAAAAA
1 TATATAATATATAGTTTT-AAAAC-ATTTT-TGAAAA
*
572362 TATATATATTATATAGTTTTGAAA-ATTTTTGAAAA
1 TATATA-A-TATATAGTTTTAAAACATTTTTGAAAA
*
572397 TATATTTATATTATATAGTTTTTGAAAATATTTTTGAATATA
1 TATA--TA-A-TATATAG-TTTT-AAAACATTTTTGAA-A-A
572439 TATATAATATATAGTTTTAAAACA-TTTTGAAAA
1 TATATAATATATAGTTTTAAAACATTTTTGAAAA
*
572472 TATATATATAATCTATAGTTTTTTAAA-ATATTTTGAAAATA
1 TATATA-AT-A--TATAG-TTTTAAAACAT-TTTTG-AAA-A
* ** *
572513 TATATAATATATATTTTTGAAAATGTTTTTAAAAAA
1 TATATAATATATAGTTTT-AAAACATTTTT-GAAAA
* ***
572549 TGTATATAATATATAGTTTTGAATTTTTTTTGAAAAA
1 --TATATAATATATAGTTTTAAAACATTTTTG-AAAA
* *
572586 TATATATTATATAGTTTTAAAAAAATAATTTTTGAAAA
1 TATATAATATATAGTTTT---AAAA-CATTTTTGAAAA
* * *
572624 TATATTAT-TATATGTTTTGAAAACAATTTTCAAAA
1 TATATAATATATA-GTTTT-AAAACATTTTTGAAAA
*
572659 -ATGTATATAATATAGTTTTAAAA
1 TATATA-AT-ATATAGTTTTAAAA
572682 ATTATTTTTA
Statistics
Matches: 318, Mismatches: 38, Indels: 75
0.74 0.09 0.17
Matches are distributed among these distances:
33 7 0.02
34 8 0.03
35 71 0.22
36 36 0.11
37 73 0.23
38 67 0.21
39 27 0.08
40 16 0.05
41 8 0.03
42 5 0.02
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (34 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAAA
Found at i:572362 original size:37 final size:35
Alignment explanation
Indices: 572252--572691 Score: 289
Period size: 38 Copynumber: 11.9 Consensus size: 35
572242 GTCCGGGGTT
* * * *
572252 TATATAATATATAGTTGTTAGAAGATGGTTTTTGAAAA
1 TATATATTATATAGTT-TT-GAAAAT-ATTTTTAAAAA
* * * *
572290 CATATAATATAT-GCTTT-AAAATCGATTTTTGAAAA
1 TATATATTATATAGTTTTGAAAAT--ATTTTTAAAAA
**
572325 TATATATTATATAGTTTTGAAAACGGTTTTCTAAAAATA
1 TATATATTATATAGTTTTGAAAA-TATTTT-T-AAAA-A
*
572364 TATATATTATATAGTTTTGAAAAT-TTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
*
572399 TATTTATATTATATAGTTTTTGAAAATATTTTTGAATATA
1 TA--TATATTATATAG-TTTTGAAAATATTTTT-AA-AAA
* * *
572439 TATATAATATATAGTTTT-AAAACATTTTGAAAATA
1 TATATATTATATAGTTTTGAAAATATTTTTAAAA-A
* * *
572474 TATATATAATCTATAGTTTTTTAAAATATTTTGAAAATA
1 TATATAT--TATATAG-TTTTGAAAATATTTTTAAAA-A
* * *
572513 TATATAATATATATTTTTGAAAATGTTTTTAAAAAA
1 TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* * *
572549 TGTATATAATATATAGTTTTG-AATTTTTTTTGAAAAA
1 --TATATATTATATAGTTTTGAAAATATTTTT-AAAAA
* *
572586 TATATATTATATAGTTTTAAAAAAATAATTTTTGAAAA
1 TATATATTATATAGTTTT--GAAAAT-ATTTTTAAAAA
* *
572624 TATATTATTATAT-GTTTTGAAAACAATTTTCAAAAA
1 TATA-TATTATATAGTTTTGAAAA-TATTTTTAAAAA
* * *
572660 TGTATATAATATAGTTTTAAAAATTATTTTTA
1 TATATATTATATAGTTTTGAAAA-TATTTTTA
572692 TTTTTATTAT
Statistics
Matches: 328, Mismatches: 46, Indels: 58
0.76 0.11 0.13
Matches are distributed among these distances:
34 5 0.02
35 62 0.19
36 64 0.20
37 55 0.17
38 73 0.22
39 63 0.19
40 5 0.02
41 1 0.00
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (35 bp):
TATATATTATATAGTTTTGAAAATATTTTTAAAAA
Found at i:572467 original size:75 final size:74
Alignment explanation
Indices: 572252--572681 Score: 327
Period size: 75 Copynumber: 5.8 Consensus size: 74
572242 GTCCGGGGTT
* * * *
572252 TATATAATATATAGTTGTTAGAAGATGGTTTTTG-AAA-ACATATAATATAT-GCTTTAAAATCG
1 TATATAATATATAGTT-TT-GAAAAT-ATTTTTGAAAATATATATAATATATAGTTTTAAAA-C-
572314 ATTTTTG-AAA-ATA
61 A-TTTTGAAAATATA
** * * *
572327 TATAT--TATATAGTTTTGAAAACGGTTTTCTAAAAATATATATATTATATAGTTTTGAAAA-TT
1 TATATAATATATAGTTTTGAAAA-TATTTT-TGAAAATATATATAATATATAGTTTT-AAAACAT
572389 TTTGAAAATATA
63 TTTGAAAATATA
* * *
572401 TTTATATTATATAGTTTTTGAAAATATTTTTGAATATATATATAATATATAGTTTTAAAACATTT
1 TATATAATATATAG-TTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTAAAACATTT
572466 TGAAAATATA
65 TGAAAATATA
* * * **
572476 TATATAATCTATAGTTTTTTAAAATA-TTTTGAAAATATATATAATATATATTTTTGAAAATGTT
1 TATATAATATATAG-TTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTT-AAAACATT
* * *
572540 TTTAAAAAATG
64 TTGAAAATATA
* * * *
572551 TATATAATATATAGTTTTG-AATTTTTTTTGAAAA-ATATATATTATATAGTTTTAAAAAAATAA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTT---AAAA-CA
572614 TTTTTGAAAATATA
62 -TTTTGAAAATATA
* * * *
572628 T-TAT--TATAT-GTTTTGAAAACAATTTTCAAAA-ATGTAT-ATAATATAGTTTTAAAA
1 TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAAT-ATATAGTTTTAAAA
572682 ATTATTTTTA
Statistics
Matches: 291, Mismatches: 44, Indels: 44
0.77 0.12 0.12
Matches are distributed among these distances:
71 13 0.04
72 8 0.03
73 42 0.14
74 92 0.32
75 98 0.34
76 18 0.06
77 20 0.07
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (74 bp):
TATATAATATATAGTTTTGAAAATATTTTTGAAAATATATATAATATATAGTTTTAAAACATTTT
GAAAATATA
Found at i:572710 original size:16 final size:16
Alignment explanation
Indices: 572682--572735 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
572672 AGTTTTAAAA
572682 ATTATT-TTTATTTTT
1 ATTATTATTTATTTTT
572697 ATTA-TATATTA-TTTT
1 ATTATTAT-TTATTTTT
*
572712 AATATTATTTATTTTT
1 ATTATTATTTATTTTT
572728 ATT-TTATT
1 ATTATTATT
572736 AATATTCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 20 0.61
16 12 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTATTATTTATTTTT
Found at i:572733 original size:11 final size:11
Alignment explanation
Indices: 572682--572741 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
572672 AGTTTTAAAA
572682 ATTATTTTTATT
1 ATTA-TTTTATT
* *
572694 TTTATTATA-T
1 ATTATTTTATT
*
572704 ATTATTTTAAT
1 ATTATTTTATT
572715 ATTA-TTTATT
1 ATTATTTTATT
*
572725 TTTATTTTATT
1 ATTATTTTATT
*
572736 AATATT
1 ATTATT
572742 CTCTTTTCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
10 16 0.42
11 19 0.50
12 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:573491 original size:37 final size:36
Alignment explanation
Indices: 573381--573510 Score: 129
Period size: 35 Copynumber: 3.5 Consensus size: 36
573371 GTCCGGGGTT
* *
573381 TATATAATATATAGTTGTTAGAAGATGGTTTTTGAAAA
1 TATATAATATATAGTT-TT-GAAAACGGTTTTTGAAAA
* * *
573419 CATATAATATAT-GCTTT-AAAATCGATTTTTGAAAA
1 TATATAATATATAGTTTTGAAAA-CGGTTTTTGAAAA
* *
573454 TATATATTATATAGTTTTGAAAACGGTTTTCTAAAAA
1 TATATAATATATAGTTTTGAAAACGGTTTT-TGAAAA
573491 TATATATATTATATAGTTTT
1 TATATA-A-TATATAGTTTT
573511 CTCACGTCGT
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
34 3 0.04
35 21 0.28
36 12 0.16
37 17 0.23
38 11 0.15
39 11 0.15
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAACGGTTTTTGAAAA
Found at i:575869 original size:3 final size:3
Alignment explanation
Indices: 575858--575899 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
575848 GGTATTTTTT
575858 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
575900 TAAGAGTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:576416 original size:17 final size:17
Alignment explanation
Indices: 576394--576431 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
576384 GTTGAACAAG
576394 TTCTTCTCA-TTATGAAC
1 TTCTTCTCATTTA-GAAC
*
576411 TTCTTCTCCTTTAGAAC
1 TTCTTCTCATTTAGAAC
576428 TTCT
1 TTCT
576432 ATTCAAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTTAGAAC
Found at i:577031 original size:22 final size:21
Alignment explanation
Indices: 577003--577052 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
576993 GCTGGGTAGC
577003 ATCGATACTCTGTTCATAGAGT
1 ATCGATACT-TGTTCATAGAGT
* * *
577025 ATCGATA-TTGTTCCTTGGGT
1 ATCGATACTTGTTCATAGAGT
577045 ATCGATAC
1 ATCGATAC
577053 CCAATGGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (21 bp):
ATCGATACTTGTTCATAGAGT
Found at i:578224 original size:14 final size:15
Alignment explanation
Indices: 578198--578227 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
578188 GTTTCATCTT
578198 TATTTTGAATGATGA
1 TATTTTGAATGATGA
578213 TATTTT-AATGATGA
1 TATTTTGAATGATGA
578227 T
1 T
578228 TTCGACGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATTTTGAATGATGA
Found at i:578419 original size:10 final size:9
Alignment explanation
Indices: 578389--578490 Score: 53
Period size: 10 Copynumber: 10.2 Consensus size: 9
578379 TTATCATAAA
578389 TTTAATAGTCT
1 TTTAATA-T-T
578400 TTTGAATATT
1 TTT-AATATT
578410 TTATAATATT
1 TT-TAATATT
*
578420 ATTAAT-TT
1 TTTAATATT
**
578428 TAAAAATATCT
1 T-TTAATAT-T
578439 TTTAATATT
1 TTTAATATT
578448 TTTAAATAAATT
1 TTT-AAT--ATT
578460 TTTAAATATT
1 TTT-AATATT
578470 TTTATATATT
1 TTTA-ATATT
**
578480 AATAATATT
1 TTTAATATT
578489 TT
1 TT
578491 AAAATAATAA
Statistics
Matches: 72, Mismatches: 10, Indels: 20
0.71 0.10 0.20
Matches are distributed among these distances:
8 2 0.03
9 17 0.24
10 32 0.44
11 7 0.10
12 14 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTAATATT
Found at i:578451 original size:22 final size:22
Alignment explanation
Indices: 578425--578473 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
578415 ATATTATTAA
578425 TTTTAAA-AATATCTTTT-AATAT
1 TTTTAAATAA-AT-TTTTAAATAT
578447 TTTTAAATAAATTTTTAAATAT
1 TTTTAAATAAATTTTTAAATAT
578469 TTTTA
1 TTTTA
578474 TATATTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATAAATTTTTAAATAT
Found at i:578490 original size:28 final size:26
Alignment explanation
Indices: 578404--578493 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 26
578394 TAGTCTTTTG
* *
578404 AATATTTTATAATATTATTAATTTTAAA
1 AATATTTTA-AATATTTTTAATATT-AA
*
578432 AATATCTTTTAATATTTTTAA-A-T-A
1 AATAT-TTTAAATATTTTTAATATTAA
578456 AAT-TTTTAAATATTTTTATATATTAA
1 AATATTTTAAATATTTTTA-ATATTAA
578482 TAATATTTTAAA
1 -AATATTTTAAA
578494 ATAATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
22 13 0.25
23 2 0.04
24 5 0.10
25 1 0.02
26 2 0.04
27 3 0.06
28 22 0.43
29 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTAAATATTTTTAATATTAA
Found at i:578511 original size:16 final size:13
Alignment explanation
Indices: 578441--578508 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 13
578431 AAATATCTTT
*
578441 TAATATTTTTAAA
1 TAATATTTTAAAA
*
578454 TAA-ATTTTTAAA
1 TAATATTTTAAAA
*
578466 T-ATTTTTATATATTAA
1 TAATATTT-TA-A--AA
578482 TAATATTTTAAAA
1 TAATATTTTAAAA
578495 TAATAATTTTAAAA
1 TAAT-ATTTTAAAA
578509 AATCTAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 1 0.02
12 13 0.29
13 10 0.22
14 10 0.22
15 1 0.02
16 5 0.11
17 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTTTAAAA
Found at i:578516 original size:15 final size:14
Alignment explanation
Indices: 578480--578508 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
578470 TTTATATATT
578480 AATAAT-ATTTTAA
1 AATAATAATTTTAA
578493 AATAATAATTTTAA
1 AATAATAATTTTAA
578507 AA
1 AA
578509 AATCTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATAATTTTAA
Found at i:579072 original size:31 final size:32
Alignment explanation
Indices: 579000--579086 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 32
578990 TAAACATTTA
* * **
579000 AGTACTAAAATGAAACAAAAAGTTAACAATGG
1 AGTACTAAAATAAAACAAAAAGTAAACAACCG
* *
579032 ATTACTAAAATAAAACAAAAAGTAAAC-GCCG
1 AGTACTAAAATAAAACAAAAAGTAAACAACCG
*
579063 AGTACTAAAATTAAA-AAAAA-TAAA
1 AGTACTAAAATAAAACAAAAAGTAAA
579087 TGTTAGTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 14 0.30
32 24 0.51
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (32 bp):
AGTACTAAAATAAAACAAAAAGTAAACAACCG
Found at i:581574 original size:14 final size:15
Alignment explanation
Indices: 581548--581577 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
581538 GTTTCATCTT
581548 TATTTTGAATGATGA
1 TATTTTGAATGATGA
581563 TATTTT-AATGATGA
1 TATTTTGAATGATGA
581577 T
1 T
581578 TTCGATGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (15 bp):
TATTTTGAATGATGA
Found at i:581837 original size:20 final size:19
Alignment explanation
Indices: 581799--581849 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
581789 CTTTTTATAC
581799 TTTAAATAAATTTAAAATATT
1 TTTAAAT-AA-TTAAAATATT
581820 TTTAAATAATTAATAATATT
1 TTTAAATAATTAA-AATATT
*
581840 TTAAAATAAT
1 TTTAAATAAT
581850 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 17 0.61
21 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAAATAATTAAAATATT
Found at i:581849 original size:13 final size:14
Alignment explanation
Indices: 581831--581859 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
581821 TTAAATAATT
581831 AATAAT-ATTTTAA
1 AATAATAATTTTAA
581844 AATAATAATTTTAA
1 AATAATAATTTTAA
581858 AA
1 AA
581860 ATTCTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAATAATTTTAA
Found at i:581851 original size:16 final size:15
Alignment explanation
Indices: 581814--581861 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
581804 ATAAATTTAA
*
581814 AATATTTTTAAATAATT
1 AATAATTTTAAA-AA-T
*
581831 AATAATATTTTAAAAT
1 AATAAT-TTTAAAAAT
581847 AATAATTTTAAAAAT
1 AATAATTTTAAAAAT
581862 TCTAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.30
16 7 0.26
17 7 0.26
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATTTTAAAAAT
Found at i:581938 original size:20 final size:22
Alignment explanation
Indices: 581913--581952 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
581903 ATCAAAATAG
581913 AGTTTTA-A-CGGCGTTTTTTT
1 AGTTTTATAGCGGCGTTTTTTT
581933 AGTTTTATAGCGGCGTTTTT
1 AGTTTTATAGCGGCGTTTTT
581953 ATGCGCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.53
Consensus pattern (22 bp):
AGTTTTATAGCGGCGTTTTTTT
Found at i:583110 original size:35 final size:34
Alignment explanation
Indices: 583060--583462 Score: 217
Period size: 37 Copynumber: 10.9 Consensus size: 34
583050 TAGAAGATGG
* *
583060 TTTTTGAAAACATATAATATAT-GCTTTAAAATCGA
1 TTTTTGAAAATATATAATATATAGTTTTAAAA-C-A
* *
583095 TTTTTGAAAATATATATTATATAGTTTTGAAAACGG
1 TTTTTGAAAATATATAATATATAGTTTT-AAAAC-A
* *
583131 TTTTCTAAAAATATATATATTATATAGTTTTGAAA-A
1 TTTT-TGAAAATATATA-A-TATATAGTTTTAAAACA
*
583167 TTTTTGAAAATATATTTATAGTATATAGTTTTTGAAAATA
1 TTTTTGAAAATATA--TA-A-TATATAG-TTTT-AAAACA
583207 TTTTTGAAAATATATATAATATATAGTTTTAAAACA
1 TTTTTG-AAA-ATATATAATATATAGTTTTAAAACA
* *
583243 -TTTTGAAAAAATATATATAATCTATAGTTTTTTAAA-A
1 TTTTTG---AAA-ATATATAATATATAG-TTTTAAAACA
* **
583280 TATTTTGAAAATATATATAATATATATTTTTGAAAATG
1 T-TTTTG-AAA-ATATATAATATATAGTTTT-AAAACA
* ****
583318 TTTTTAAAAAATGTATATAATATATAGTTTTGAATTTT
1 TTTTT-GAAAA--TATATAATATATAGTTTT-AAAACA
* *
583356 TTTTTGAAAAATATATATTATATAGTTTTAAAAAAATAA
1 TTTTTG-AAAATATATAATATATAGTTTT---AAAA-CA
*
583395 TTTTTGAAAATATATTAT-TATATGTTTTGAAAACA
1 TTTTTGAAAATATATAATATATA-GTTTT-AAAACA
* *
583430 ATTTTCAAAA-ACGTAT-ATAATATAGTTTTAAAA
1 TTTTTGAAAATA--TATAAT-ATATAGTTTTAAAA
583463 ATGATTTTTA
Statistics
Matches: 301, Mismatches: 36, Indels: 62
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.00
35 49 0.16
36 53 0.18
37 86 0.29
38 69 0.23
39 26 0.09
40 9 0.03
41 3 0.01
42 5 0.02
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTTTGAAAATATATAATATATAGTTTTAAAACA
Found at i:583216 original size:112 final size:109
Alignment explanation
Indices: 583094--583463 Score: 342
Period size: 112 Copynumber: 3.3 Consensus size: 109
583084 TTTAAAATCG
*
583094 ATTTTTGAAAATATATATTATATAGTTTTGAAAACGGTTTTCTAAAAATATATATATTATATAGT
1 ATTTTTGAAAATATATATTATATAGTTTTGAAAAC-ATTTTCTAAAAATATATATATTATATAGT
* *
583159 TTTGAAAAT-TTTTGAAAATATATTTATAGTATATAGTTTTTGAAAAT
65 TTTAAAAATATTTTGAAAATATA--TATAATATATA-TTTTTGAAAAT
** * *
583206 ATTTTTGAAAATATATATAATATATAGTTTT-AAAACATTTTGAAAAAATATATATAATCTATAG
1 ATTTTTGAAAATATATAT--TATATAGTTTTGAAAACATTTTCTAAAAATATATATATTATATAG
*
583270 TTTTTTAAAATATTTTGAAAATATATATAATATATATTTTTGAAAAT
64 -TTTTAAAAATATTTTGAAAATATATATAATATATATTTTTGAAAAT
* * * *** * *
583317 GTTTTTAAAAAATGTATATAATATATAGTTTTG-AATTTTTTTTTGAAAA-ATATATATTATATA
1 ATTTTT-GAAAA--TATATATTATATAGTTTTGAAAACATTTTCTAAAAATATATATATTATATA
*
583380 GTTTTAAAAAAATAATTTTTGAAAATATAT-T-AT-TATATGTTTTGAAAAC
63 GTTTT--AAAAAT-A-TTTTGAAAATATATATAATATATAT-TTTTGAAAAT
* * * *
583429 AATTTTCAAAA-ACGTATATAATATAGTTTTAAAAA
1 ATTTTTGAAAATA--TATATTATATAGTTTTGAAAA
583464 TGATTTTTAT
Statistics
Matches: 215, Mismatches: 27, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
108 1 0.00
110 18 0.08
111 40 0.19
112 96 0.45
113 16 0.07
114 44 0.20
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (109 bp):
ATTTTTGAAAATATATATTATATAGTTTTGAAAACATTTTCTAAAAATATATATATTATATAGTT
TTAAAAATATTTTGAAAATATATATAATATATATTTTTGAAAAT
Found at i:583470 original size:36 final size:36
Alignment explanation
Indices: 583101--583470 Score: 164
Period size: 38 Copynumber: 9.9 Consensus size: 36
583091 TCGATTTTTG
* * ***
583101 AAAATATATATTATATAGTTTTGAAAACGGTTTTCTAA
1 AAAATGTATATAATATAGTTTTGAAAA-TAATTT-TAA
* *
583139 AAATATATATATTATATAGTTTTGAAAAT--TTTTGAA
1 AAA-ATGTATATAATATAGTTTTGAAAATAATTTT-AA
* **
583175 AATATATTTATAGT-ATATAGTTTTTGAAAAT-ATTTTTG
1 AA-A-ATGTATA-TAATATAG-TTTTGAAAATAATTTTAA
* *
583213 AAAATATATATAATATATAGTTTT-AAAA-CATTTTGAA
1 AAAATGTATAT-A-ATATAGTTTTGAAAATAATTTT-AA
* * *
583250 AAAATATATATAATCTATAGTTTTTTAAAAT-ATTTT-G
1 AAAATGTATATAA--TATAG-TTTTGAAAATAATTTTAA
* * **
583287 AAAATATATATAATATATATTTTTGAAAATGTTTTTAA
1 AAAATGTATAT-A-ATATAGTTTTGAAAATAATTTTAA
** ** *
583325 AAAATGTATATAATATATAGTTTTGAATTTTTTTTTGA
1 AAAATGTATAT-A-ATATAGTTTTGAAAATAATTTTAA
* * * **
583363 AAAATATATATTATATAGTTTTAAAAAAATAATTTTTG
1 AAAATGTATATAATATAGTTTT--GAAAATAATTTTAA
* * * *
583401 AAAATATAT-TATTATATGTTTTGAAAACAATTTTCA
1 AAAATGTATATAATATA-GTTTTGAAAATAATTTTAA
* * *
583437 AAAACGTATATAATATAGTTTTAAAAATGATTTT
1 AAAATGTATATAATATAGTTTTGAAAATAATTTT
583471 TATTTTTTAT
Statistics
Matches: 269, Mismatches: 39, Indels: 50
0.75 0.11 0.14
Matches are distributed among these distances:
35 3 0.01
36 73 0.27
37 65 0.24
38 90 0.33
39 38 0.14
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (36 bp):
AAAATGTATATAATATAGTTTTGAAAATAATTTTAA
Found at i:583471 original size:112 final size:110
Alignment explanation
Indices: 583060--583471 Score: 329
Period size: 114 Copynumber: 3.7 Consensus size: 110
583050 TAGAAGATGG
* * * *
583060 TTTTTGAAAACATA-TA-ATATATGCTTT-AAAATCGATTTTT-GAAAA-TATATATTATATAGT
1 TTTTTGAAAATATATTATATATATGTTTTGAAAAT--ATTTTTAAAAAAGTATATAATATATAGT
* * * * *
583120 TTTGAAAACGGTTTTCTAAAAATATATATATTATATAGTTTT-GAA-AA
64 TTT-AAAATGATTTTTTGAAAA-ATATATATTATATAGTTTTAAAATAA
*
583167 TTTTTGAAAATATATTTATAGTATATAGTTTTTGAAAATATTTTTGAAAATA-TATATAATATAT
1 TTTTTGAAAATATA-TTATA-TATAT-G-TTTTGAAAATATTTTT-AAAAAAGTATATAATATAT
* *
583231 AGTTTTAAAA-CA--TTTTGAAAAAATATATATAATCTATAGTTTTTTAAAAT-A
61 AGTTTTAAAATGATTTTTTG-AAAAATATATAT--TATATAG--TTTTAAAATAA
*
583282 -TTTTGAAAATATATATAATATATAT-TTTTGAAAATGTTTTTAAAAAATGTATATAATATATAG
1 TTTTTGAAAATATAT-T-ATATATATGTTTTGAAAATATTTTTAAAAAA-GTATATAATATATAG
* **
583345 TTTT-GAATTTTTTTTTGAAAAATATATATTATATAGTTTTAAAAAAATAA
63 TTTTAAAATGATTTTTTGAAAAATATATATTATATAGTTTT---AAAATAA
* * *
583395 TTTTTGAAAATATATTAT-TATATGTTTTGAAAACAATTTTCAAAAACGTATAT-A-ATATAGTT
1 TTTTTGAAAATATATTATATATATGTTTTGAAAA-TATTTTTAAAAAAGTATATAATATATAGTT
583457 TTAAAAATGATTTTT
65 TT-AAAATGATTTTT
583472 ATTTTTTATA
Statistics
Matches: 249, Mismatches: 24, Indels: 59
0.75 0.07 0.18
Matches are distributed among these distances:
107 13 0.05
109 6 0.02
110 27 0.11
111 38 0.15
112 61 0.24
113 31 0.12
114 67 0.27
115 6 0.02
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.46
Consensus pattern (110 bp):
TTTTTGAAAATATATTATATATATGTTTTGAAAATATTTTTAAAAAAGTATATAATATATAGTTT
TAAAATGATTTTTTGAAAAATATATATTATATAGTTTTAAAATAA
Found at i:583514 original size:11 final size:11
Alignment explanation
Indices: 583470--583520 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
583460 AAAATGATTT
583470 TTATT-TTTTA
1 TTATTATTTTA
583480 TATATTATTTTA
1 T-TATTATTTTA
*
583492 ATATTA-TTTA
1 TTATTATTTTA
*
583502 TTTTTATTTTA
1 TTATTATTTTA
*
583513 TTAATATT
1 TTATTATT
583521 CTCTTTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 9 0.27
11 19 0.58
12 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:584920 original size:17 final size:16
Alignment explanation
Indices: 584883--584919 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
584873 TAACTTTTTC
584883 TTTTTCTTATTTCATT
1 TTTTTCTTATTTCATT
* *
584899 TTTTTCTTCTTTTATT
1 TTTTTCTTATTTCATT
584915 TTTTT
1 TTTTT
584920 TATCATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTATTTCATT
Found at i:584928 original size:16 final size:16
Alignment explanation
Indices: 584883--584928 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
584873 TAACTTTTTC
584883 TTTTTCTT-ATTTCATT
1 TTTTTCTTCATTT-ATT
*
584899 TTTTTCTTCTTTTATT
1 TTTTTCTTCATTTATT
584915 TTTTT-TATCATTTA
1 TTTTTCT-TCATTTA
584929 CATCATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 22 0.85
17 3 0.12
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTCATTTATT
Found at i:586997 original size:150 final size:144
Alignment explanation
Indices: 586722--587003 Score: 393
Period size: 150 Copynumber: 1.9 Consensus size: 144
586712 AAATTCGATA
*
586722 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGTGGGCT
1 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGAGGGCT
*
586787 TCCATAAATGTAATCTGAGACTGGCCCGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
66 TCCATAAATGTAATCTGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
586852 GAATCCTTAAACTG
131 GAATCCTTAAACTG
* *
586866 CTTCAACAGAGAATTCTTGTAAAGAACATAAGGCGCGAAAGGATGGAAAAGGAAATCCAAGCAGA
1 CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAA--C-AG--G-
* * ** * * * **
586931 AGTGCTTCCATGAATGTAATCTGAGGTTGTCCAGTGGGTTTAAGAATGGATGGGGCAGTTGTAGC
60 AGGGCTTCCATAAATGTAATCTGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGC
586996 CTTGAAGA
125 CTTGAAGA
587004 CGCCTCAAAC
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
144 53 0.45
146 1 0.01
147 2 0.02
149 1 0.01
150 62 0.52
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (144 bp):
CTTCAACAGAGAATTCATGTAAAGAACATAAGGCGCAAAAGGATGGAAAAGGAAACAGGAGGGCT
TCCATAAATGTAATCTGAGACTGGCCAGTGGGTTTAAGAATAGATGGGGCAGATACAGCCTTGAA
GAATCCTTAAACTG
Found at i:588039 original size:99 final size:99
Alignment explanation
Indices: 587932--588137 Score: 342
Period size: 99 Copynumber: 2.1 Consensus size: 99
587922 ATTATAATAT
*
587932 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-AGCTTTATGG
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGA-CTTTATGG
* *
587996 ATAAGATTCAACTAGCATGATAAAGGTGCTTATAA
65 ATAAGATTCAACTAGCATGATAAAGATGATTATAA
* *
588031 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGTCTCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGACTTTATGGA
*
588096 TAAGATTCAACTAGCCTGATAAAGATGATTATAA
66 TAAGATTCAACTAGCATGATAAAGATGATTATAA
588130 TATATATA
1 TATATATA
588138 TATATATATA
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
99 99 0.99
100 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (99 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGATTAAACGCCCCGACTTTATGGA
TAAGATTCAACTAGCATGATAAAGATGATTATAA
Found at i:588136 original size:2 final size:2
Alignment explanation
Indices: 588125--588163 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
588115 TAAAGATGAT
588125 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
588164 AAGCTTGAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:592586 original size:3 final size:3
Alignment explanation
Indices: 592573--592611 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
592563 TGGTATTTTT
592573 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
592612 TAAGAGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.