Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 4 of 47
Found at i:454414 original size:68 final size:68
Alignment explanation
Indices: 454287--454437 Score: 176
Period size: 68 Copynumber: 2.2 Consensus size: 68
454277 TCTCGAGTTG
* ** * *
454287 ATGGAAATGACTTGGCATCACTAAATGTGATGCCATGGTGGTGATCAGACTTATGAAGTCCTAAT
1 ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
*
454352 TTA
66 ATA
* * * * * *
454355 ATGGAAATGACTTGGCATCAGTGAATGTGATATCATGGTGGCAATTAGACATGTAAAGTCTTAAT
1 ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
*
454420 ATG
66 ATA
*
454423 ATGGAAGTGACTTGG
1 ATGGAAATGACTTGG
454438 TGTCACTGAG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (68 bp):
ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
ATA
Found at i:461296 original size:21 final size:21
Alignment explanation
Indices: 461272--461322 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
461262 AATCAATCAA
*
461272 ATAAAGAGCAGGAGAAATTTG
1 ATAAAAAGCAGGAGAAATTTG
461293 ATAAAAAAGCAGGAGAAATTTG
1 AT-AAAAAGCAGGAGAAATTTG
461315 ATAAAAAG
1 ATAAAAAG
461323 ATGAGAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.18
Consensus pattern (21 bp):
ATAAAAAGCAGGAGAAATTTG
Found at i:461304 original size:22 final size:22
Alignment explanation
Indices: 461278--461321 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
461268 TCAAATAAAG
461278 AGCAGGAGAAATTTGATAAAAA
1 AGCAGGAGAAATTTGATAAAAA
461300 AGCAGGAGAAATTTGATAAAAA
1 AGCAGGAGAAATTTGATAAAAA
461322 GATGAGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (22 bp):
AGCAGGAGAAATTTGATAAAAA
Found at i:461661 original size:12 final size:12
Alignment explanation
Indices: 461646--461701 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
461636 GAATTTAAAA
461646 ATATATTTTAAT
1 ATATATTTTAAT
*
461658 ATATATATTTAAAAA
1 ATATAT-TTT--AAT
461673 ATATATTTTAAT
1 ATATATTTTAAT
**
461685 ATATATTAAAAT
1 ATATATTTTAAT
461697 ATATA
1 ATATA
461702 AATATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 23 0.62
13 3 0.08
14 3 0.08
15 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTTTAAT
Found at i:461665 original size:14 final size:14
Alignment explanation
Indices: 461646--461690 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
461636 GAATTTAAAA
461646 ATATATTTTAATAT
1 ATATATTTTAATAT
* *
461660 ATATA-TTTAAAAA
1 ATATATTTTAATAT
461673 ATATATTTTAATAT
1 ATATATTTTAATAT
461687 ATAT
1 ATAT
461691 TAAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTTTAATAT
Found at i:461672 original size:27 final size:26
Alignment explanation
Indices: 461638--461690 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
461628 TTTTACTTGA
461638 ATTTAAAAATATATTTTAATATATAT
1 ATTTAAAAATATATTTTAATATATAT
461664 ATTTAAAAAATATATTTTAATATATAT
1 ATTT-AAAAATATATTTTAATATATAT
461691 TAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAAAATATATTTTAATATATAT
Found at i:464031 original size:2 final size:2
Alignment explanation
Indices: 464024--464071 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
464014 TCATATGCAC
* **
464024 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT CAT GG AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
464066 AT AT AT
1 AT AT AT
464072 GTACATTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (2 bp):
AT
Found at i:467069 original size:20 final size:19
Alignment explanation
Indices: 467028--467071 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
467018 TCTACATTAT
*
467028 TTAAAAATTTAACTTTATA
1 TTAAAAATTTAACTTTAAA
* *
467047 TTAAAAATTTTATTATTAAA
1 TTAAAAATTTAACT-TTAAA
467067 TTAAA
1 TTAAA
467072 TATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAAATTTAACTTTAAA
Found at i:467096 original size:17 final size:16
Alignment explanation
Indices: 467059--467110 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
467049 AAAAATTTTA
* *
467059 TTATTAAATTAAATAT
1 TTATTATATTAAACAT
* *
467075 ATATTTTTATTAAACAT
1 TTA-TTATATTAAACAT
*
467092 TTATTATATTTAACAT
1 TTATTATATTAAACAT
467108 TTA
1 TTA
467111 AGCCATAAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATATTAAACAT
Found at i:467639 original size:16 final size:16
Alignment explanation
Indices: 467596--467653 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
467586 AAATTTACAT
*
467596 ATAATTTTTGTTCAAA
1 ATAATTTTTATTCAAA
* * *
467612 ACAACTTATATTCAAA
1 ATAATTTTTATTCAAA
* *
467628 ATAATTTTTATTTATA
1 ATAATTTTTATTCAAA
467644 ATAATTTTTA
1 ATAATTTTTA
467654 CAAAAAAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (16 bp):
ATAATTTTTATTCAAA
Found at i:476739 original size:2 final size:2
Alignment explanation
Indices: 476732--476771 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
476722 TGCTGGCTGC
476732 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
476772 GTAGTATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:477070 original size:2 final size:2
Alignment explanation
Indices: 477050--477094 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
477040 CCTCTCCCTT
* * *
477050 TC TC TC TG TC TA TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
477092 TC T
1 TC T
477095 TTCATCCGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:479791 original size:17 final size:17
Alignment explanation
Indices: 479769--479806 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
479759 AAAAAATCAT
*
479769 AAAAAAATAC-ATTTTA
1 AAAAAAATACTATTCTA
479785 AAAAAAATACTATTCTA
1 AAAAAAATACTATTCTA
479802 AAAAA
1 AAAAA
479807 GCTATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAAATACTATTCTA
Found at i:479835 original size:3 final size:3
Alignment explanation
Indices: 479827--479852 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
479817 AAATTAAAAA
479827 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
479853 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:480273 original size:20 final size:20
Alignment explanation
Indices: 480250--480288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
480240 TTAGTTTAAT
480250 TATAAAAATATTAATATTTG
1 TATAAAAATATTAATATTTG
* *
480270 TATAAAATTTTTAATATTT
1 TATAAAAATATTAATATTT
480289 TTTAAATAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATAAAAATATTAATATTTG
Found at i:480955 original size:25 final size:26
Alignment explanation
Indices: 480922--480984 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
480912 ATATAATTTT
480922 ATATATAATATTTAAATTTTA-ATT-A
1 ATATATAATATTT-AATTTTATATTCA
* *
480947 TTATATAATATGTAATTTTATATTCA
1 ATATATAATATTTAATTTTATATTCA
480973 ATATATAA-ATTT
1 ATATATAATATTT
480985 TTATAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.22
25 17 0.53
26 8 0.25
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATATAATATTTAATTTTATATTCA
Found at i:480998 original size:18 final size:19
Alignment explanation
Indices: 480972--481017 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
480962 TTTTATATTC
*
480972 AATATATAAA-TTTTTATA
1 AATAAATAAATTTTTTATA
480990 AATAAATAAATTTTTTATA
1 AATAAATAAATTTTTTATA
481009 ATATAAATA
1 A-ATAAATA
481018 TTTATCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.36
19 9 0.36
20 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAAATAAATTTTTTATA
Found at i:481020 original size:18 final size:18
Alignment explanation
Indices: 480972--481017 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
480962 TTTTATATTC
* *
480972 AATATATAAATTTTTATA
1 AATAAATAATTTTTTATA
480990 AATAAATAAATTTTTTATA
1 AATAAAT-AATTTTTTATA
481009 ATATAAATA
1 A-ATAAATA
481018 TTTATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAATAATTTTTTATA
Found at i:482325 original size:16 final size:18
Alignment explanation
Indices: 482300--482344 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 18
482290 CATGGGACAT
*
482300 AATAATTAAAAATAA-TA
1 AATAAATAAAAATAAGTA
482317 AA-AAAT-AAAATAAGTA
1 AATAAATAAAAATAAGTA
*
482333 AATAATTAAAAA
1 AATAAATAAAAA
482345 CTTGAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 5 0.22
18 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAATAAAAATAAGTA
Found at i:484735 original size:13 final size:13
Alignment explanation
Indices: 484717--484757 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
484707 TACAAAACTT
484717 ATGTATCGATACA
1 ATGTATCGATACA
*
484730 ATGTATCGATATA
1 ATGTATCGATACA
* *
484743 TTATATCGATACA
1 ATGTATCGATACA
484756 AT
1 AT
484758 TTGTATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:485450 original size:22 final size:21
Alignment explanation
Indices: 485403--485456 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
485393 TGGTTTAATG
*
485403 ATCAT-ATATAAAATATATAT
1 ATCATAATATAAAATATAAAT
*
485423 -TAATAATATATAAATATAAAT
1 ATCATAATATA-AAATATAAAT
*
485444 ATCATAAGATAAA
1 ATCATAATATAAA
485457 TAAGTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.11
20 5 0.19
21 11 0.41
22 8 0.30
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (21 bp):
ATCATAATATAAAATATAAAT
Found at i:485864 original size:43 final size:44
Alignment explanation
Indices: 485780--485874 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 44
485770 TATTCGATGA
* * * *
485780 AAATAAAATAAAATAAGAATAAGTATTATAAAATTTGATTGGAT
1 AAATTAAATAAAAGAAAAATAAGTATTATAAAATTTAATTGGAT
** *
485824 AAATTAAATAAAAGAAAAATAA-TATTATATTATTTAATTGGTT
1 AAATTAAATAAAAGAAAAATAAGTATTATAAAATTTAATTGGAT
*
485867 ATATTAAA
1 AAATTAAA
485875 AATAGATAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 24 0.56
44 19 0.44
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (44 bp):
AAATTAAATAAAAGAAAAATAAGTATTATAAAATTTAATTGGAT
Found at i:486123 original size:14 final size:14
Alignment explanation
Indices: 486100--486131 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
486090 TGATAATTAA
486100 ATAT-TTTAATATT
1 ATATATTTAATATT
486113 ATATATTTAATATT
1 ATATATTTAATATT
486127 ATATA
1 ATATA
486132 AAAATATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTTAATATT
Found at i:486182 original size:37 final size:35
Alignment explanation
Indices: 486098--486182 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
486088 TATGATAATT
* *
486098 AAATAT-TTTAATATTATATATTTAATATTATATAA
1 AAATATATTTAA-ATTATATATTTAAAATTAAATAA
*
486133 AAATATACTTAAATTATAT-TTTAAAATATAAATATA
1 AAATATATTTAAATTATATATTTAAAAT-TAAATA-A
486169 AAATATTATTTAAA
1 AAATA-TATTTAAA
486183 ACCCTTCAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
34 7 0.17
35 18 0.43
36 10 0.24
37 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
AAATATATTTAAATTATATATTTAAAATTAAATAA
Found at i:488322 original size:21 final size:22
Alignment explanation
Indices: 488298--488346 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
488288 GTAAATCTGT
*
488298 ATTTTGTACAG-AAAATTTTGA
1 ATTTTGTACAGCAAAATTTTAA
* * *
488319 ATTTTTTTCAGCTAAATTTTAA
1 ATTTTGTACAGCAAAATTTTAA
488341 ATTTTG
1 ATTTTG
488347 AGAAGAAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (22 bp):
ATTTTGTACAGCAAAATTTTAA
Found at i:489544 original size:2 final size:2
Alignment explanation
Indices: 489539--489572 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
489529 ATATATATAT
489539 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
489573 GGAGGTCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:490163 original size:2 final size:2
Alignment explanation
Indices: 490156--490187 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
490146 TGGAACTAGA
*
490156 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
490188 TTTCGAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493079 original size:19 final size:19
Alignment explanation
Indices: 493052--493089 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
493042 TATATAGTAA
493052 TTTTATTAAAAAATTATTT
1 TTTTATTAAAAAATTATTT
* *
493071 TTTTCTTAAATAATTATTT
1 TTTTATTAAAAAATTATTT
493090 ACTTTTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATTAAAAAATTATTT
Found at i:496351 original size:2 final size:2
Alignment explanation
Indices: 496344--496370 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
496334 GAAAGCTATT
496344 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 T
496371 GTTTGTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:497864 original size:39 final size:39
Alignment explanation
Indices: 497821--497895 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
497811 TGAACAATCA
* *
497821 TAGGAAGATTCAAGCTCGTTATTAGAAGTATCCATGGCT
1 TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATGGCT
*
497860 TAGGAAGATTCAAGCTCATTATCAGATGTATCCATG
1 TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATG
497896 ATCTAAGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (39 bp):
TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATGGCT
Found at i:504057 original size:2 final size:2
Alignment explanation
Indices: 504050--504079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
504040 CTAAGAGGAG
504050 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
504080 GCAGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:505563 original size:15 final size:16
Alignment explanation
Indices: 505534--505571 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
505524 TAATTTATAA
* *
505534 ATTTAATATTTTTTAT
1 ATTTAATATTATTTAC
505550 ATTTAA-ATTATTTAC
1 ATTTAATATTATTTAC
505565 ATTTAAT
1 ATTTAAT
505572 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTAATATTATTTAC
Found at i:505597 original size:21 final size:20
Alignment explanation
Indices: 505531--505597 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
505521 ATTTAATTTA
*
505531 TAAATTTAATATTTTTTATATT
1 TAAA-TTAAT-TTTTTTAAATT
* *
505553 TAAATT-ATTTACATTTAATTT
1 TAAATTAATTT--TTTTAAATT
505574 TAAATTAATTTTTTTAAATAT
1 TAAATTAATTTTTTTAAAT-T
505595 TAA
1 TAA
505598 TTATAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 18 0.50
22 8 0.22
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAATTAATTTTTTTAAATT
Found at i:506236 original size:18 final size:18
Alignment explanation
Indices: 506213--506255 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
506203 TTTTTAAGTT
*
506213 TTTTTAATTATTTTATAG
1 TTTTTAATTATTTTAAAG
* * *
506231 TTTTTAGTTTTTTTAAAT
1 TTTTTAATTATTTTAAAG
506249 TTTTTAA
1 TTTTTAA
506256 GTATGTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTAATTATTTTAAAG
Found at i:506404 original size:19 final size:19
Alignment explanation
Indices: 506380--506423 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
506370 GATCTGATAA
*
506380 TTTTTTAATTTTATTTTAT
1 TTTTTTAATTTTATATTAT
506399 TTTTTTAATTTTATATTAT
1 TTTTTTAATTTTATATTAT
506418 TTTTTT
1 TTTTTT
506424 GTTAAGTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTAATTTTATATTAT
Found at i:506985 original size:18 final size:18
Alignment explanation
Indices: 506964--507006 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
506954 AGATACTTAA
*
506964 TAAAAAATAATGCAAAAC
1 TAAAAAATAAAGCAAAAC
* *
506982 TAAAAAAAAAAGTAAAAC
1 TAAAAAATAAAGCAAAAC
507000 -AAAAAAT
1 TAAAAAAT
507007 TTATAAGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (18 bp):
TAAAAAATAAAGCAAAAC
Found at i:507080 original size:15 final size:16
Alignment explanation
Indices: 507048--507085 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
507038 AAATAATATT
**
507048 AAAAAATAACTTCTCA
1 AAAAAATAAAATCTCA
507064 AAAAAATAAAATC-CA
1 AAAAAATAAAATCTCA
507079 AAAAAAT
1 AAAAAAT
507086 TAATAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAATAAAATCTCA
Found at i:507658 original size:24 final size:24
Alignment explanation
Indices: 507624--507709 Score: 93
Period size: 24 Copynumber: 3.5 Consensus size: 24
507614 ATTCAATTTG
*
507624 AAAATTTTAAAATAAAAAATTATA
1 AAAATTATAAAATAAAAAATTATA
*
507648 AAAATTGT-AAATATAAAAATTATA
1 AAAATTATAAAATA-AAAAATTATA
* *
507672 AAAATTATAAAAATATAAAAAATCTA
1 AAAATTAT-AAAATA-AAAAATTATA
*
507698 TAAATTATAAAA
1 AAAATTATAAAA
507710 ATTCAAAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.09
24 24 0.44
25 4 0.07
26 21 0.39
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (24 bp):
AAAATTATAAAATAAAAAATTATA
Found at i:507662 original size:15 final size:15
Alignment explanation
Indices: 507644--507673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
507634 AATAAAAAAT
*
507644 TATAAAAATTGTAAA
1 TATAAAAATTATAAA
507659 TATAAAAATTATAAA
1 TATAAAAATTATAAA
507674 AATTATAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
TATAAAAATTATAAA
Found at i:507683 original size:17 final size:17
Alignment explanation
Indices: 507624--507777 Score: 111
Period size: 17 Copynumber: 8.8 Consensus size: 17
507614 ATTCAATTTG
*
507624 AAAATTTTAAAA-TA-A
1 AAAATTATAAAATTATA
*
507639 AAAATTATAAAAATTGTA
1 AAAATTAT-AAAATTATA
*
507657 AATA-TA-AAAATTATA
1 AAAATTATAAAATTATA
*
507672 AAAATTATAAAAATATAA
1 AAAATTATAAAATTAT-A
507690 AAAATCTAT-AAATTATA
1 AAAAT-TATAAAATTATA
*
507707 AAAATTCAAAGTAAATTTATAAA
1 AAAATT---A-TAAAATTAT--A
*
507730 AAAATCTATAAAATTAAA
1 AAAAT-TATAAAATTATA
*
507748 AAAATTTTAAAATTATA
1 AAAATTATAAAATTATA
*
507765 GAAATTATAAAAT
1 AAAATTATAAAAT
507778 AAAATTCAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 28
0.72 0.09 0.18
Matches are distributed among these distances:
15 18 0.16
16 7 0.06
17 37 0.34
18 22 0.20
19 4 0.04
20 8 0.07
21 7 0.06
23 6 0.05
24 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAATTATA
Found at i:507685 original size:26 final size:26
Alignment explanation
Indices: 507624--507711 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
507614 ATTCAATTTG
*
507624 AAAATT-TTAAAATA-AAAAATTATA
1 AAAATTATAAAAATATAAAAATTATA
*
507648 AAAATTGT--AAATATAAAAATTATA
1 AAAATTATAAAAATATAAAAATTATA
* *
507672 AAAATTATAAAAATATAAAAAATCTA
1 AAAATTATAAAAATATAAAAATTATA
*
507698 TAAATTATAAAAAT
1 AAAATTATAAAAAT
507712 TCAAAGTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.09
24 23 0.41
25 1 0.02
26 27 0.48
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
AAAATTATAAAAATATAAAAATTATA
Found at i:507703 original size:59 final size:55
Alignment explanation
Indices: 507639--507798 Score: 162
Period size: 59 Copynumber: 2.8 Consensus size: 55
507629 TTTAAAATAA
507639 AAAATTATAAAAATTGTAAATATAAAAATTATAAAAATTATAAAAATATAAAAAATCTAT
1 AAAATTATAAAAATT-TAAA-AT-AAAATTATAAAAATTATAAAAATA-AAAAAAT-TAT
* * * * *
507699 -AAATTATAAAAATTCAAAGTAAATTTATAAAAAAATCTATAAAATTAAAAAAATTTT
1 AAAATTATAAAAATTTAAAATAAAATTAT--AAAAAT-TATAAAAATAAAAAAATTAT
*
507756 AAAATTATAGAAATTATAAAATAAAATTCA-AAAAATTATAAAA
1 AAAATTATAAAAATT-TAAAATAAAATT-ATAAAAATTATAAAA
507799 TTTTTATTTC
Statistics
Matches: 85, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
56 14 0.16
57 9 0.11
58 29 0.34
59 32 0.38
60 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (55 bp):
AAAATTATAAAAATTTAAAATAAAATTATAAAAATTATAAAAATAAAAAAATTAT
Found at i:507798 original size:9 final size:9
Alignment explanation
Indices: 507638--507776 Score: 103
Period size: 9 Copynumber: 15.4 Consensus size: 9
507628 TTTTAAAATA
507638 AAAAATTAT
1 AAAAATTAT
*
507647 AAAAATTGT
1 AAAAATTAT
507656 --AAA-TAT
1 AAAAATTAT
507662 AAAAATTAT
1 AAAAATTAT
507671 AAAAATTAT
1 AAAAATTAT
507680 AAAAA-TAT
1 AAAAATTAT
* *
507688 AAAAAATCT
1 AAAAATTAT
*
507697 ATAAATTAT
1 AAAAATTAT
507706 AAAAATTCA-
1 AAAAATT-AT
507715 AAGTAAATTTAT
1 AA--AAA-TTAT
507727 AAAAAAATCTAT
1 --AAAAAT-TAT
*
507739 -AAAATTAA
1 AAAAATTAT
507747 AAAAATT-T
1 AAAAATTAT
*
507755 TAAAATTAT
1 AAAAATTAT
*
507764 AGAAATTAT
1 AAAAATTAT
507773 AAAA
1 AAAA
507777 TAAAATTCAA
Statistics
Matches: 103, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 19 0.18
9 63 0.61
10 1 0.01
11 5 0.05
12 8 0.08
14 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:507828 original size:10 final size:9
Alignment explanation
Indices: 507813--508013 Score: 83
Period size: 9 Copynumber: 23.1 Consensus size: 9
507803 TATTTCTTAA
507813 TTTTATACAT
1 TTTTATA-AT
507823 TTTTATAAT
1 TTTTATAAT
507832 TTTT-TAAT
1 TTTTATAAT
* *
507840 TTTCA-AAC
1 TTTTATAAT
507848 TTTT-TAA-
1 TTTTATAAT
*
507855 -TTTATATT
1 TTTTATAAT
507863 TTTTAATAAT
1 TTTT-ATAAT
507873 TTTT-TGAA-
1 TTTTAT-AAT
*
507881 TTTCA-AA-
1 TTTTATAAT
507888 TTTTAT--T
1 TTTTATAAT
* *
507895 TTTGA-ATT
1 TTTTATAAT
507903 TTTTATAAT
1 TTTTATAAT
507912 TTTTA-AA-
1 TTTTATAAT
507919 TTTTATATAT
1 TTTTATA-AT
*
507929 TTTTATGAT
1 TTTTATAAT
*
507938 TTTCTA-AAC
1 TTT-TATAAT
507947 TTTTATTAAT
1 TTTTA-TAAT
* *
507957 ATTTCAAAAT
1 -TTTTATAAT
*
507967 TTGTTAAAAT
1 TT-TTATAAT
* *
507977 TTTTTTACT
1 TTTTATAAT
507986 TTTTATAATT
1 TTTTATAA-T
*
507996 TTTTAAAAT
1 TTTTATAAT
508005 TTTT-TAAT
1 TTTTATAAT
508013 T
1 T
508014 AAAAAAATAT
Statistics
Matches: 145, Mismatches: 24, Indels: 46
0.67 0.11 0.21
Matches are distributed among these distances:
6 3 0.02
7 17 0.12
8 32 0.22
9 45 0.31
10 44 0.30
11 4 0.03
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:507851 original size:26 final size:26
Alignment explanation
Indices: 507804--507853 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
507794 TAAAATTTTT
*
507804 ATTTCTTAATTTTATACATTTTTATA
1 ATTTCTTAATTTTAAACATTTTTATA
*
507830 ATTTTTTAATTTTCAAAC-TTTTTA
1 ATTTCTTAATTTT-AAACATTTTTA
507854 ATTTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTCTTAATTTTAAACATTTTTATA
Found at i:507931 original size:40 final size:38
Alignment explanation
Indices: 507796--507931 Score: 91
Period size: 40 Copynumber: 3.4 Consensus size: 38
507786 AAAAATTATA
* *
507796 AAATTTTTAT-TTCTTAATTTTATACATTTTTATAATTTTT
1 AAATTTTAATATT-TTAA-TTTATA-TTTTTTATAATTTTT
*
507836 TAATTTTCAA-ACTTTTTAATTTATATTTTTTAATAATTTTTT
1 AAATTTT-AATA--TTTTAATTTATATTTTTT-ATAA-TTTTT
* * *
507878 GAATTTCAA-ATTTT-ATTTTTGAATTTTTTATAATTTTT
1 AAATTTTAATATTTTAATTTAT--ATTTTTTATAATTTTT
507916 AAATTTTATATATTTT
1 AAATTTTA-ATATTTT
507932 TATGATTTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
38 16 0.21
39 9 0.12
40 23 0.29
41 14 0.18
42 14 0.18
43 2 0.03
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (38 bp):
AAATTTTAATATTTTAATTTATATTTTTTATAATTTTT
Found at i:507933 original size:41 final size:39
Alignment explanation
Indices: 507822--507939 Score: 107
Period size: 40 Copynumber: 2.9 Consensus size: 39
507812 ATTTTATACA
*
507822 TTTTTATAATTTTTTAATTTTCAAACTTTTTA-ATTTATAT
1 TTTTTATAATTTTTAAATTTT-AAA-TTTTTATATTTATAT
* * *
507862 TTTTTAATAATTTTTTGAATTTCAAA-TTTTATTTTTGA-AT
1 TTTTT-ATAA-TTTTTAAATTTTAAATTTTTATATTT-ATAT
507902 TTTTTATAATTTTTAAATTTTATATATTTTTATGATTT
1 TTTTTATAATTTTTAAATTTTA-A-ATTTTTAT-ATTT
507940 TCTAAACTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
38 11 0.17
39 10 0.16
40 16 0.25
41 14 0.22
42 13 0.20
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (39 bp):
TTTTTATAATTTTTAAATTTTAAATTTTTATATTTATAT
Found at i:507940 original size:18 final size:16
Alignment explanation
Indices: 507823--507933 Score: 63
Period size: 16 Copynumber: 6.9 Consensus size: 16
507813 TTTTATACAT
*
507823 TTTTATAATTTTTTAA
1 TTTTATAATTTTTAAA
507839 TTTTCA-AACTTTTT-AA
1 TTTT-ATAA-TTTTTAAA
*
507855 -TTTATATTTTTTAATAA
1 TTTTATAATTTTT-A-AA
* *
507872 TTTTTTGAA-TTTCAAA
1 TTTTAT-AATTTTTAAA
* *
507888 TTTTAT--TTTTGAATT
1 TTTTATAATTTTTAA-A
507903 TTTTATAATTTTTAAA
1 TTTTATAATTTTTAAA
507919 TTTTATATATTTTTA
1 TTTTATA-ATTTTTA
507934 TGATTTTCTA
Statistics
Matches: 73, Mismatches: 9, Indels: 25
0.68 0.08 0.23
Matches are distributed among these distances:
14 11 0.15
15 10 0.14
16 22 0.30
17 22 0.30
18 7 0.10
19 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTTATAATTTTTAAA
Found at i:508736 original size:19 final size:20
Alignment explanation
Indices: 508714--508764 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
508704 ATATTTAATA
* *
508714 AAAATATATTTAAT-TTTTT
1 AAAATATTTTTAATATATTT
*
508733 AAAA-ATTTTTTATATATTT
1 AAAATATTTTTAATATATTT
508752 AAAATATTTTTAA
1 AAAATATTTTTAA
508765 AAAATCATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.27
19 12 0.46
20 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATATTTTTAATATATTT
Found at i:510736 original size:17 final size:17
Alignment explanation
Indices: 510716--510813 Score: 52
Period size: 18 Copynumber: 5.1 Consensus size: 17
510706 GTATTAATAA
510716 TTTATATTATTTAAATTT
1 TTTATATTATTTAAA-TT
*
510734 TTATATATTTTATATTTATATTTT
1 TT-TATA---T-TATTTA-AAT-T
510758 TTTATATTATTTAAAATT
1 TTTATATTATTT-AAATT
* *
510776 TTATATAATATTTTAATT
1 TT-TATATTATTTAAATT
* *
510794 TTTTTATATATTTATATT
1 TTTATAT-TATTTAAATT
510812 TT
1 TT
510814 ATAATTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
17 3 0.05
18 21 0.34
19 20 0.32
20 2 0.03
22 1 0.02
23 11 0.18
24 4 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTTAAATT
Found at i:510742 original size:19 final size:19
Alignment explanation
Indices: 510718--510813 Score: 86
Period size: 19 Copynumber: 4.9 Consensus size: 19
510708 ATTAATAATT
510718 TATATTATTTAAATTTTTA
1 TATATTATTTAAATTTTTA
* *
510737 TATATTTTATATTTATATTTTTT
1 TATA---T-TATTTAAATTTTTA
*
510760 TATATTATTTAAAATTTTA
1 TATATTATTTAAATTTTTA
* * *
510779 TATAATATTTTAATTTTTT
1 TATATTATTTAAATTTTTA
*
510798 TATA-TATTTATATTTT
1 TATATTATTTAAATTTT
510814 ATAATTTAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
18 10 0.16
19 34 0.55
20 1 0.02
22 1 0.02
23 16 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATTATTTAAATTTTTA
Found at i:510763 original size:42 final size:39
Alignment explanation
Indices: 510716--510820 Score: 128
Period size: 42 Copynumber: 2.7 Consensus size: 39
510706 GTATTAATAA
510716 TTTATATTATTTAAATTTTTATATATTTTATATTTATATTTT
1 TTTATATTATTTAAA-TTTTATATATTTTAT-TTTA-ATTTT
*
510758 TTTATATTATTTAAAATTTTATATA--ATATTTTAATTTT
1 TTTATATTATTT-AAATTTTATATATTTTATTTTAATTTT
*
510796 TTTATA-TATTTATATTTTATA-ATTT
1 TTTATATTATTTAAATTTTATATATTT
510821 AAAATTATCA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
35 1 0.02
36 9 0.16
37 5 0.09
38 11 0.19
39 4 0.07
40 3 0.05
42 21 0.37
43 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (39 bp):
TTTATATTATTTAAATTTTATATATTTTATTTTAATTTT
Found at i:511084 original size:22 final size:21
Alignment explanation
Indices: 511029--511084 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
511019 TAAATTAATC
* *
511029 TTTAATCAATTTTTTTAAATT
1 TTTAATTAATTATTTTAAATT
* *
511050 TTAAATTTTATTATTTTAAATAT
1 TTTAA-TTAATTATTTTAAAT-T
511073 TTTAATTAATTA
1 TTTAATTAATTA
511085 AATTTTACAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATTAATTATTTTAAATT
Found at i:511160 original size:15 final size:14
Alignment explanation
Indices: 511142--511193 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
511132 AAAAATATTT
511142 ATAAAATAATGAAAA
1 ATAAAATAAT-AAAA
511157 ATAAAA-AATAAAAA
1 ATAAAATAAT-AAAA
* *
511171 ATTAATTAATAAAA
1 ATAAAATAATAAAA
511185 ATTAAAATA
1 A-TAAAATA
511194 TGATATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 16 0.53
15 14 0.47
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
ATAAAATAATAAAA
Found at i:511167 original size:22 final size:23
Alignment explanation
Indices: 511142--511193 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
511132 AAAAATATTT
511142 ATAAAATAATGAA-AAATAAAAA
1 ATAAAATAATGAATAAATAAAAA
* *
511164 ATAAAA-AATTAATTAATAAAAA
1 ATAAAATAATGAATAAATAAAAA
*
511186 TTAAAATA
1 ATAAAATA
511194 TGATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 19 0.76
23 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
ATAAAATAATGAATAAATAAAAA
Found at i:511685 original size:23 final size:23
Alignment explanation
Indices: 511659--511741 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 23
511649 TTTAATTTAA
511659 AATTTTATATTATTATATAAATT
1 AATTTTATATTATTATATAAATT
* *
511682 AATTTAAAATT-TTA-A-AAATT
1 AATTTTATATTATTATATAAATT
* *
511702 -A-TTTA-ATTAATATTTATAATT
1 AATTTTATATTATTATATA-AATT
*
511723 AAATTTTATATTATAATAT
1 -AATTTTATATTATTATAT
511742 TTTTATTTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
17 3 0.07
18 5 0.11
19 1 0.02
20 6 0.14
21 5 0.11
22 3 0.07
23 10 0.23
24 4 0.09
25 7 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTTATATTATTATATAAATT
Found at i:511686 original size:30 final size:31
Alignment explanation
Indices: 511634--511695 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
511624 TAAATTAAAA
* *
511634 ATATTTTTATTTAAATTTAATTTAAAATTTT
1 ATATTATTATATAAATTTAATTTAAAATTTT
511665 ATATTATTATATAAA-TTAATTTAAAATTTT
1 ATATTATTATATAAATTTAATTTAAAATTTT
511695 A
1 A
511696 AAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.55
31 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
ATATTATTATATAAATTTAATTTAAAATTTT
Found at i:511717 original size:30 final size:29
Alignment explanation
Indices: 511640--511712 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
511630 AAAAATATTT
**
511640 TTATTTAAATTTAATTTAAAATTTTATATTA
1 TTATTT-AA-TTAATTTAAAATTTTATAAAA
*
511671 TTATATAAATTAATTTAAAATTTTA-AAAA
1 TTAT-TTAATTAATTTAAAATTTTATAAAA
511700 TTATTTAATTAAT
1 TTATTTAATTAAT
511713 ATTTATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 8 0.22
29 6 0.16
30 16 0.43
31 6 0.16
32 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATTTAATTAATTTAAAATTTTATAAAA
Found at i:511727 original size:65 final size:63
Alignment explanation
Indices: 511605--511741 Score: 156
Period size: 65 Copynumber: 2.1 Consensus size: 63
511595 TGGTTGAGGT
* * *
511605 TTATAAGT-TAAATTAATTATAAATTAAAAATATTTTTATTTAAATTTAATTTAAAATTTTATA
1 TTATAA-TATAAATTAATTATAAATTAAAAATATATTTAATTAAATTTAAATTAAAATTTTATA
*
511668 TTATTATATAAATTAATT-TAAAATTTTAAAAAT-TATTTAATTAATATTTATAATT-AAATTTT
1 TTATAATATAAATTAATTAT-AAA--TTAAAAATATATTTAATTAA-ATTTA-AATTAAAATTTT
511730 ATA
61 ATA
511733 TTATAATAT
1 TTATAATAT
511742 TTTTATTTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
62 2 0.03
63 18 0.29
64 9 0.14
65 31 0.49
66 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (63 bp):
TTATAATATAAATTAATTATAAATTAAAAATATATTTAATTAAATTTAAATTAAAATTTTATA
Found at i:511751 original size:15 final size:17
Alignment explanation
Indices: 511712--511752 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
511702 ATTTAATTAA
511712 TATTTATAATTAAATTT
1 TATTTATAATTAAATTT
*
511729 TATATTATAA-T-ATTTT
1 TAT-TTATAATTAAATTT
511745 TATTTATA
1 TATTTATA
511753 TAAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 4 0.18
18 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTATAATTAAATTT
Found at i:512953 original size:14 final size:13
Alignment explanation
Indices: 512934--512966 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
512924 ACAAAATAAA
512934 TTGTTAGAATATTT
1 TTGTTA-AATATTT
512948 TTGTT-AATATTT
1 TTGTTAAATATTT
512960 TTGTTAA
1 TTGTTAA
512967 GTGTGTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 12 0.67
13 1 0.06
14 5 0.28
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (13 bp):
TTGTTAAATATTT
Found at i:512958 original size:12 final size:12
Alignment explanation
Indices: 512941--512966 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
512931 AAATTGTTAG
512941 AATATTTTTGTT
1 AATATTTTTGTT
512953 AATATTTTTGTT
1 AATATTTTTGTT
512965 AA
1 AA
512967 GTGTGTTAAG
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
AATATTTTTGTT
Found at i:513041 original size:22 final size:22
Alignment explanation
Indices: 513016--513077 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
513006 TTAAGTGAGC
* *
513016 AATATATTACGTGTTTTAGATA
1 AATATATTAAGTGTGTTAGATA
* *
513038 AATATATTAAGTATGTTAGGTA
1 AATATATTAAGTGTGTTAGATA
*
513060 AATATATTAGGTGTGTTA
1 AATATATTAAGTGTGTTA
513078 ATAGACCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.44
Consensus pattern (22 bp):
AATATATTAAGTGTGTTAGATA
Found at i:517691 original size:22 final size:22
Alignment explanation
Indices: 517666--517731 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 22
517656 TAGTTAAGTA
* *
517666 TGTTAAGTAAACATATTAGGTG
1 TGTTAAATAAATATATTAGGTG
*
517688 TGTTAAATGAGTAATATATTAAGTG
1 TGTTAAAT-A--AATATATTAGGTG
517713 TGTTAAATAAATATATTAG
1 TGTTAAATAAATATATTAG
517732 ATAAACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 16 0.43
23 1 0.03
24 1 0.03
25 19 0.51
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTTAAATAAATATATTAGGTG
Found at i:517952 original size:41 final size:42
Alignment explanation
Indices: 517895--517977 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
517885 AAGGCTCATC
517895 CAACATAGTCTTATCCTATC-TTTTCAGCATTCTTTTCACAT
1 CAACATAGTCTTATCCTATCTTTTTCAGCATTCTTTTCACAT
517936 CAACATAGTCTTATCCTATCTTTTTCAGCATTCTTTTCACAT
1 CAACATAGTCTTATCCTATCTTTTTCAGCATTCTTTTCACAT
517978 GATCCAGGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 20 0.49
42 21 0.51
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.45
Consensus pattern (42 bp):
CAACATAGTCTTATCCTATCTTTTTCAGCATTCTTTTCACAT
Found at i:519709 original size:20 final size:20
Alignment explanation
Indices: 519682--519719 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
519672 GAGAATTAAT
*
519682 ATAAAAGTTAAA-AAATTTA
1 ATAAAAGTAAAATAAATTTA
519701 ATAATAAGTAAAATAAATT
1 ATAA-AAGTAAAATAAATT
519720 GAAGGGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 7 0.44
21 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
ATAAAAGTAAAATAAATTTA
Found at i:526692 original size:100 final size:101
Alignment explanation
Indices: 526583--526783 Score: 323
Period size: 102 Copynumber: 2.0 Consensus size: 101
526573 AATGAAGTTG
* **
526583 ATTTTATATTAATTTTACTA-TTTTTATTAAAATTATTTTATATATAATGAGTTATGAATTTTTA
1 ATTTTATATTAATTTTACTATTTTTTATTAAAATTATTTTATATATAATAAAATATGAATTTTTA
526647 ACCTCTAAACTATATTAAAACTTAATCTATTAAATT
66 ACCTCTAAACTATATTAAAACTTAATCTATTAAATT
*
526683 ATTTTATATTAATTTTACTATTTTTTTATTAAAATTATTTTTTATATAATAAAATATGAATTTTT
1 ATTTTATATTAATTTTACTA-TTTTTTATTAAAATTATTTTATATATAATAAAATATGAATTTTT
* * *
526748 GACCTCTAAACTATATTAAAATTTTATCTATTAAAT
65 AACCTCTAAACTATATTAAAACTTAATCTATTAAAT
526784 CAAATACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 20 0.22
102 72 0.78
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.52
Consensus pattern (101 bp):
ATTTTATATTAATTTTACTATTTTTTATTAAAATTATTTTATATATAATAAAATATGAATTTTTA
ACCTCTAAACTATATTAAAACTTAATCTATTAAATT
Found at i:526919 original size:21 final size:19
Alignment explanation
Indices: 526895--526945 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
526885 ATAAAAATAT
526895 ATAACAAATAAAATAATTAAA
1 ATAA-AAATAAAATAA-TAAA
*
526916 ATAAAATATAAAATTATAAA
1 ATAAAA-ATAAAATAATAAA
526936 ATAAAAATAA
1 ATAAAAATAA
526946 TTAACATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 12 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAAAATAAAATAATAAA
Found at i:526924 original size:28 final size:28
Alignment explanation
Indices: 526879--526939 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 28
526869 ATATTGTTAG
*
526879 ATAATTATAAAAATATATAACAA-ATAAA
1 ATAATTATAAAAAAATATAA-AATATAAA
526907 ATAATTA-AAATAAAATATAAAATTATAAA
1 ATAATTATAAA-AAAATATAAAA-TATAAA
526936 ATAA
1 ATAA
526940 AAATAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.17
28 15 0.52
29 9 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (28 bp):
ATAATTATAAAAAAATATAAAATATAAA
Found at i:526936 original size:15 final size:15
Alignment explanation
Indices: 526916--526974 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
526906 AATAATTAAA
526916 ATAAAATATAAAATT
1 ATAAAATATAAAATT
*
526931 ATAAAATA-AAAATA
1 ATAAAATATAAAATT
*
526945 ATTAACATATTAAAATTT
1 A-TAAAATA-TAAAA-TT
*
526963 ATATAAT-TAAAA
1 ATAAAATATAAAA
526975 AATATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.17
15 19 0.54
17 8 0.23
18 2 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATATAAAATT
Found at i:526971 original size:40 final size:35
Alignment explanation
Indices: 526900--526978 Score: 88
Period size: 40 Copynumber: 2.1 Consensus size: 35
526890 AATATATAAC
*
526900 AAAT-AAAATAATTAAAATAAAATATAAAATTATA
1 AAATAAAAATAATTAAAATAAAATATAAAATTAAA
*
526934 AAATAAAAATAATTAACATATTAAAATTTATATAATTAAA
1 AAATAAAAATAATTAA-A-A-TAAAA--TATAAAATTAAA
526974 AAATA
1 AAATA
526979 TTTTAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 4 0.11
35 11 0.30
36 1 0.03
37 1 0.03
38 5 0.14
40 15 0.41
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (35 bp):
AAATAAAAATAATTAAAATAAAATATAAAATTAAA
Found at i:526991 original size:22 final size:21
Alignment explanation
Indices: 526963--527010 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
526953 ATTAAAATTT
*
526963 ATATAATTAAAAAATATTTTAA
1 ATATAATTAAAAAATA-ATTAA
* *
526985 ATATAATTATAATATAATTAA
1 ATATAATTAAAAAATAATTAA
527006 ATATA
1 ATATA
527011 TATACCAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATAATTAAAAAATAATTAA
Found at i:527000 original size:11 final size:10
Alignment explanation
Indices: 526981--527010 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
526971 AAAAAATATT
526981 TTAAATATAA
1 TTAAATATAA
526991 TTATAATATAA
1 TTA-AATATAA
527002 TTAAATATA
1 TTAAATATA
527011 TATACCAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAAATATAA
Found at i:529034 original size:20 final size:21
Alignment explanation
Indices: 528989--529039 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
528979 AAATTAATAT
*
528989 TAAATAAATTTTATCTCATAA
1 TAAATAAATTTAATCTCATAA
529010 TAAATAAATTTAAT-TCA-AA
1 TAAATAAATTTAATCTCATAA
*
529029 TCAAATTAATT
1 T-AAATAAATT
529040 AAAATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 11 0.41
21 13 0.48
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATAAATTTAATCTCATAA
Found at i:530346 original size:21 final size:22
Alignment explanation
Indices: 530308--530352 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
530298 ATAATTTTTA
530308 ATAAATAAAATTAATTATATAT
1 ATAAATAAAATTAATTATATAT
* *
530330 ATAAAT-ATATTATTTATATAT
1 ATAAATAAAATTAATTATATAT
530351 AT
1 AT
530353 TCATATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAATAAAATTAATTATATAT
Found at i:530795 original size:21 final size:20
Alignment explanation
Indices: 530744--530803 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
530734 AATAATGATA
530744 ATAGTAAAATTAAATATTAT
1 ATAGTAAAATTAAATATTAT
* *
530764 ACT-GTTGAAATTAGATATTAT
1 A-TAG-TAAAATTAAATATTAT
530785 ATAGATAAAATTAAA-ATTA
1 ATAG-TAAAATTAAATATTA
530804 GTAATAAGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (20 bp):
ATAGTAAAATTAAATATTAT
Found at i:530948 original size:19 final size:20
Alignment explanation
Indices: 530903--530950 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
530893 TAAATAAGAT
530903 ATATTATAATAATAGTTAAAA
1 ATATT-TAATAATAGTTAAAA
**
530924 AT-TTTAAT-ATAGTTTTAA
1 ATATTTAATAATAGTTAAAA
530942 ATATTTAAT
1 ATATTTAAT
530951 TAATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 2 0.08
21 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
ATATTTAATAATAGTTAAAA
Found at i:530961 original size:20 final size:20
Alignment explanation
Indices: 530938--530979 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
530928 TAATATAGTT
*
530938 TTAAATATT-TAATTAATTTA
1 TTAAATATTAT-ATAAATTTA
*
530958 TTAATTATTATATAAATTTA
1 TTAAATATTATATAAATTTA
530978 TT
1 TT
530980 TATTACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAAATATTATATAAATTTA
Found at i:530980 original size:24 final size:23
Alignment explanation
Indices: 530942--530997 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
530932 ATAGTTTTAA
*
530942 ATATTTAATTAATTTATTA-ATT
1 ATATTAAATTAATTTATTACATT
*
530964 ATTATATAAATTTATTTATTACATT
1 A-TAT-TAAATTAATTTATTACATT
530989 ATATTAAAT
1 ATATTAAAT
530998 AAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 1 0.03
23 8 0.28
24 16 0.55
25 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTAAATTAATTTATTACATT
Found at i:530995 original size:34 final size:33
Alignment explanation
Indices: 530943--531031 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 33
530933 TAGTTTTAAA
* **
530943 TATTTAATTAATT-TATTAATTATTATATAAATT
1 TATTT-ATTAATTATATTAAATAAAATATAAATT
530976 TATTTATTACATTATATTAAATAAAATATAAATT
1 TATTTATTA-ATTATATTAAATAAAATATAAATT
*
531010 TATTTGTTATATTATATTAAAT
1 TATTTATTA-ATTATATTAAAT
531032 TACATACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
32 4 0.08
33 8 0.16
34 37 0.76
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (33 bp):
TATTTATTAATTATATTAAATAAAATATAAATT
Found at i:531076 original size:24 final size:25
Alignment explanation
Indices: 531045--531094 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
531035 ATACAAATAT
531045 ATATTTTTAAAATAAAAATA-TGAA
1 ATATTTTTAAAATAAAAATATTGAA
531069 ATATTTTTAAAATAAAAATATTGAA
1 ATATTTTTAAAATAAAAATATTGAA
531094 A
1 A
531095 AAATTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
ATATTTTTAAAATAAAAATATTGAA
Found at i:531097 original size:17 final size:17
Alignment explanation
Indices: 531077--531113 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
531067 AAATATTTTT
531077 AAAA-TAAAAATATTGAA
1 AAAATTAAAAATATT-AA
531094 AAAATTAAAAATATTAA
1 AAAATTAAAAATATTAA
531111 AAA
1 AAA
531114 TATATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATTAAAAATATTAA
Found at i:531104 original size:24 final size:24
Alignment explanation
Indices: 531053--531106 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
531043 ATATATTTTT
** *
531053 AAAATAAAAATATGAAATATTTTT
1 AAAATAAAAATATGAAATAAATTA
531077 AAAATAAAAATATTGAAA-AAATTA
1 AAAATAAAAATA-TGAAATAAATTA
531101 AAAATA
1 AAAATA
531107 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAAATAAAAATATGAAATAAATTA
Found at i:531114 original size:9 final size:9
Alignment explanation
Indices: 531081--531116 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
531071 ATTTTTAAAA
531081 TAAAAATAT
1 TAAAAATAT
531090 TGAAAAA-AT
1 T-AAAAATAT
531099 TAAAAATAT
1 TAAAAATAT
531108 TAAAAATAT
1 TAAAAATAT
531117 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 5 0.20
9 15 0.60
10 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (9 bp):
TAAAAATAT
Found at i:531422 original size:45 final size:45
Alignment explanation
Indices: 531373--531462 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
531363 ATAATAAATA
*
531373 ATTAAAAATTATATTTATGTTAAA-TAATAATGAACATA-TATTTAT
1 ATTAAAAATTATATTTAT-ATAAATTAATAATGAA-ATATTATTTAT
*
531418 ATTAAAAATTATATTTATATAAATTAATAATTAAATATTATTTAT
1 ATTAAAAATTATATTTATATAAATTAATAATGAAATATTATTTAT
531463 TAAACATTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 7 0.17
45 34 0.83
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (45 bp):
ATTAAAAATTATATTTATATAAATTAATAATGAAATATTATTTAT
Found at i:531449 original size:22 final size:22
Alignment explanation
Indices: 531372--531461 Score: 74
Period size: 22 Copynumber: 4.0 Consensus size: 22
531362 TATAATAAAT
531372 AATTAAAAATTATATTTATGTTA
1 AATTAAAAATTATATTTAT-TTA
* * * *
531395 AA-TAATAATGAACATATATTTA
1 AATTAAAAAT-TATATTTATTTA
* *
531417 TATTAAAAATTATATTTATATA
1 AATTAAAAATTATATTTATTTA
* *
531439 AATTAATAATTAAATATTATTTA
1 AATTAAAAATTATAT-TTATTTA
531462 TTAAACATTT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
22 30 0.60
23 20 0.40
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (22 bp):
AATTAAAAATTATATTTATTTA
Found at i:531574 original size:28 final size:27
Alignment explanation
Indices: 531521--531574 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
531511 AAGGCATAAA
* *
531521 AAATTATATTTACAATAAATATTAATT
1 AAATTATATTTACAATAAAAAATAATT
* *
531548 AAATTATTATTTATATTAAAAAATAAT
1 AAATTA-TATTTACAATAAAAAATAAT
531575 ATAATTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATTATATTTACAATAAAAAATAATT
Found at i:532530 original size:17 final size:19
Alignment explanation
Indices: 532508--532546 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
532498 ATTTTTTAAA
*
532508 TTTTTTACTTA-AAA-TAT
1 TTTTTTAATTATAAATTAT
532525 TTTTTTAATTATAAATTAT
1 TTTTTTAATTATAAATTAT
532544 TTT
1 TTT
532547 AATTATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTAATTATAAATTAT
Found at i:532546 original size:16 final size:15
Alignment explanation
Indices: 532504--532552 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
532494 ATTTATTTTT
*
532504 TAAATTTTTTACTTA
1 TAAATTTTTTAATTA
*
532519 AAATATTTTTTTAATTA
1 TAA-A-TTTTTTAATTA
532536 TAAATTATTTTAATTA
1 TAAATT-TTTTAATTA
532552 T
1 T
532553 TATCAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 4 0.14
16 12 0.43
17 12 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTTTTTAATTA
Found at i:533053 original size:14 final size:15
Alignment explanation
Indices: 533036--533101 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 15
533026 TAATTAATTA
533036 ATTTAAA-TAAAAAT
1 ATTTAAATTAAAAAT
*
533050 ATTTAAA-T-AAATT
1 ATTTAAATTAAAAAT
*
533063 CATTCAAAGTTAATAAAT
1 -ATTTAAA-TTAA-AAAT
*
533081 AATTAAATTAAAAAT
1 ATTTAAATTAAAAAT
533096 ATTTAA
1 ATTTAA
533102 CATGCACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.10
14 14 0.34
15 9 0.22
16 5 0.12
17 6 0.15
18 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTTAAATTAAAAAT
Found at i:533191 original size:25 final size:24
Alignment explanation
Indices: 533145--533192 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
533135 ATTGAAAATA
533145 ATTTTAAATTAACTAAATTTTTATT
1 ATTTTAAATTAAC-AAATTTTTATT
533170 ATTTTATAATTAA-AAATATTTTA
1 ATTTTA-AATTAACAAAT-TTTTA
533193 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 11 0.52
26 6 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATTTTAAATTAACAAATTTTTATT
Found at i:533200 original size:15 final size:17
Alignment explanation
Indices: 533169--533216 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
533159 AAATTTTTAT
533169 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
*
533186 TATTTTA-AATAAAAAAA
1 TATTTTATAAT-TAAAAA
*
533203 TATTTAATAATTAA
1 TATTTTATAATTAA
533217 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:539810 original size:24 final size:25
Alignment explanation
Indices: 539779--539826 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
539769 AAATTTTATA
**
539779 TTTTTTATAT-ATTTAATAATTAAT
1 TTTTTTATATCAAATAATAATTAAT
539803 TTTTTTATATCAAATAATAATTAA
1 TTTTTTATATCAAATAATAATTAA
539827 ATATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTTTATATCAAATAATAATTAAT
Found at i:539818 original size:22 final size:22
Alignment explanation
Indices: 539778--539824 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
539768 AAAATTTTAT
**
539778 ATTTTTTATATATTTAATAATTA
1 ATTTTTTATATATCAAATAA-TA
539801 ATTTTTT-TATATCAAATAATA
1 ATTTTTTATATATCAAATAATA
539822 ATT
1 ATT
539825 AAATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 10 0.45
23 7 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTTTATATATCAAATAATA
Found at i:540434 original size:17 final size:16
Alignment explanation
Indices: 540407--540439 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
540397 TTTTTATTTG
540407 ATTTTTTATTGTTTTT
1 ATTTTTTATTGTTTTT
540423 ATTTTATTATTGTTTTT
1 ATTTT-TTATTGTTTTT
540440 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
ATTTTTTATTGTTTTT
Found at i:540442 original size:21 final size:21
Alignment explanation
Indices: 540396--540454 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
540386 TTTTCTTGTC
*
540396 TTTTTTATTTGATT-TTTTAT
1 TTTTTTATTTTATTATTTTAT
540416 TGTTTTTATTTTATTATTGTT-T
1 T-TTTTTATTTTATTATT-TTAT
* *
540438 TTTTTAATTTTTTTATT
1 TTTTTTATTTTATTATT
540455 AATAAATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 26 0.79
22 4 0.12
23 2 0.06
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTTATTATTTTAT
Found at i:541974 original size:2 final size:2
Alignment explanation
Indices: 541967--541995 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
541957 ACTACTACTT
541967 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
541996 GTATGTATGT
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:542812 original size:6 final size:6
Alignment explanation
Indices: 542786--542820 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
542776 TCACATTCAT
542786 ATATAA TATATAA AT-TAA ATATAA ATATAA ATATA
1 ATATAA -ATATAA ATATAA ATATAA ATATAA ATATA
542821 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAA
Found at i:544319 original size:2 final size:2
Alignment explanation
Indices: 544314--544346 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
544304 TTTTCTTTTA
*
544314 AT AT AT AT AT AT AT AT AT AT AT GT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
544347 GTTGAAGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:546235 original size:11 final size:10
Alignment explanation
Indices: 546181--546242 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 10
546171 TAAGAAAAAA
546181 TTTAAAATA-
1 TTTAAAATAT
546190 TTTAAAATAT
1 TTTAAAATAT
546200 TAGTCTAAAACTATTT
1 T--T-TAAAA-TA--T
546216 TTTAAAATAT
1 TTTAAAATAT
546226 TTTAATAATAT
1 TTTAA-AATAT
546237 TTTAAA
1 TTTAAA
546243 TTAAAAGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
9 9 0.20
10 8 0.18
11 10 0.22
12 3 0.07
13 10 0.22
14 3 0.07
16 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:546870 original size:15 final size:15
Alignment explanation
Indices: 546852--546898 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
546842 CTTTACAATA
*
546852 TTAATATTTAATAAT
1 TTAATATTTAAAAAT
546867 TTAATATTTAAAAATT
1 TTAATATTTAAAAA-T
*
546883 TTAGACATTTAAAAAT
1 TTA-ATATTTAAAAAT
546899 GAAGATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.46
16 5 0.18
17 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTAATATTTAAAAAT
Found at i:547601 original size:76 final size:74
Alignment explanation
Indices: 547448--547606 Score: 180
Period size: 74 Copynumber: 2.1 Consensus size: 74
547438 GTAATTTCTC
* * * * *
547448 AAATACAAATAAAATTTAATTAAATTTTAAAAATTCATATTGAAATTAATATATTAATTATCAAT
1 AAATAAAAAGAAAATTTAATTAAATTTAAAAAATTCATATTAAAATAAATATATTAATTATCAAT
547513 TTTTAATAA
66 TTTTAATAA
*
547522 AAATAAAAAGAAAATTTAATTAAATTTGAAAAAATT-GTATTTAAAAATCAAAT-TATTAATTAT
1 AAATAAAAAGAAAATTTAATTAAATTT-AAAAAATTCATA-TT-AAAAT-AAATATATTAATTAT
* *
547585 TAATTTTTTAA-GA
62 CAA-TTTTTAATAA
547598 AAATAAAAA
1 AAATAAAAA
547607 ATTTAAATTA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
74 27 0.38
75 9 0.12
76 26 0.36
77 10 0.14
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (74 bp):
AAATAAAAAGAAAATTTAATTAAATTTAAAAAATTCATATTAAAATAAATATATTAATTATCAAT
TTTTAATAA
Found at i:547619 original size:13 final size:14
Alignment explanation
Indices: 547597--547634 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
547587 ATTTTTTAAG
*
547597 AAAATAAAAAATT-
1 AAAATTAAAAATTA
*
547610 TAAATTAAAAATTA
1 AAAATTAAAAATTA
547624 AAAATTAAAAA
1 AAAATTAAAAA
547635 GTAAGGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:547626 original size:6 final size:7
Alignment explanation
Indices: 547597--547634 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
547587 ATTTTTTAAG
*
547597 AAAATAA
1 AAAATTA
547604 AAAATT-
1 AAAATTA
*
547610 TAAATTA
1 AAAATTA
547617 AAAATTA
1 AAAATTA
547624 AAAATTA
1 AAAATTA
547631 AAAA
1 AAAA
547635 GTAAGGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:547791 original size:47 final size:47
Alignment explanation
Indices: 547700--547791 Score: 139
Period size: 47 Copynumber: 2.0 Consensus size: 47
547690 TTTAAATTTT
* * *
547700 TAGGGCATTATTTATCTTTATTTGTAAAAGTTTAAATTTGTTTTTGG
1 TAGGGCATAATTTATCTTTATTTGTAAAAGTTTAAATGTATTTTTGG
* *
547747 TAGGGTATAATTTATTTTTATTTGTAAAAGTTTAAATGTATTTTT
1 TAGGGCATAATTTATCTTTATTTGTAAAAGTTTAAATGTATTTTT
547792 AAGATATGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.54
Consensus pattern (47 bp):
TAGGGCATAATTTATCTTTATTTGTAAAAGTTTAAATGTATTTTTGG
Found at i:548003 original size:72 final size:73
Alignment explanation
Indices: 547751--548002 Score: 269
Period size: 74 Copynumber: 3.5 Consensus size: 73
547741 TTTTGGTAGG
* ** * *
547751 GTATAATTTATTTTTATTTGTAAAAGTTTAAATGTATTTTTAAGATATGCTTATAAGAGTTTAAA
1 GTATAATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTTTGGTATGATTATAAGAGTTTAAA
*
547816 TTTTTGATA
66 TTTTT-AGA
* * * * * *
547825 GTATAATTTAGTTTTATTTGTAAAAATTTCAATGTGTTTCTTTGGTATAATTATACA-AGTTTAT
1 GTATAATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTTTGGTATGATTATA-AGAGTTTAA
547889 ATTTTTATG-
65 ATTTTTA-GA
* * *
547898 GTATAATTTATTTTTATTTATAAAAATTTAAAT-TAATTTTTTTGGT-TGATTACATGAGTTTAA
1 GTATAATTTATTTTTATTTGTAAAAATTTAAATGT-ATTTTTTTGGTATGATTATAAGAGTTTAA
547961 ATTTTTAGA
65 ATTTTTAGA
* * * *
547970 GTGTTATTTATTTTTACTTGTAAAAGTTTAAAT
1 GTATAATTTATTTTTATTTGTAAAAATTTAAAT
548003 TTTTATTTAA
Statistics
Matches: 147, Mismatches: 26, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
71 1 0.01
72 48 0.33
73 40 0.27
74 57 0.39
75 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (73 bp):
GTATAATTTATTTTTATTTGTAAAAATTTAAATGTATTTTTTTGGTATGATTATAAGAGTTTAAA
TTTTTAGA
Found at i:548765 original size:63 final size:63
Alignment explanation
Indices: 548642--548773 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 63
548632 AGTTGAAATT
* * *
548642 TTAATATGTAAAAACCATGAATTAGAGCTTTCGCTAATAAAAAAAAAATCTTAAAATGAATAG
1 TTAATATGTAAAAACCATGAATTAGAGCTTCCACCAATAAAAAAAAAATCTTAAAATGAATAG
* * **
548705 TTAATCATGTAAAAACCATGAATTAGAGCTTCCACCAA-CAAATAAAAATCTTGGAATGAATAG
1 TTAAT-ATGTAAAAACCATGAATTAGAGCTTCCACCAATAAAAAAAAAATCTTAAAATGAATAG
548768 TTAATA
1 TTAATA
548774 AGAGACTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 1 0.02
63 31 0.51
64 29 0.48
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.28
Consensus pattern (63 bp):
TTAATATGTAAAAACCATGAATTAGAGCTTCCACCAATAAAAAAAAAATCTTAAAATGAATAG
Found at i:549855 original size:74 final size:72
Alignment explanation
Indices: 549727--549936 Score: 227
Period size: 74 Copynumber: 2.9 Consensus size: 72
549717 CTGATCATTG
* *
549727 TACCT-AAAAATTTAAACTTATATAATCAAATCAAAAAATAAATTCTAAACTTTTATAAATAAAA
1 TACCTAAAAAATTTAAACTTATATAATC-AATCAAAAAAAAAATTCTAAACTTTTACAAATAAAA
*
549791 ATAAATTT
65 ATAAATTA
* *
549799 TACCATAAAAAATTTAAACTTATATAATC-ATGCAAAAAAAACACATT-TAAATTTTTACAAATC
1 TACC-TAAAAAATTTAAACTTATATAATCAAT-CAAAAAAAA-A-ATTCTAAACTTTTACAAATA
549862 AAAATAAATTA
62 AAAATAAATTA
* * * * *
549873 TACCTTAAAAATTTAAAC-CACATAAATAAAT--AAAAATAAATT-TAAACTTTTACAAATAAAA
1 TACCTAAAAAATTTAAACTTATAT-AATCAATCAAAAAAAAAATTCTAAACTTTTACAAATAAAA
549934 ATA
65 ATA
549937 TTTAATACCT
Statistics
Matches: 119, Mismatches: 12, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
69 23 0.19
70 1 0.01
71 6 0.05
72 9 0.08
73 25 0.21
74 52 0.44
75 3 0.03
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (72 bp):
TACCTAAAAAATTTAAACTTATATAATCAATCAAAAAAAAAATTCTAAACTTTTACAAATAAAAA
TAAATTA
Found at i:549945 original size:69 final size:71
Alignment explanation
Indices: 549759--549947 Score: 199
Period size: 69 Copynumber: 2.6 Consensus size: 71
549749 TAATCAAATC
* * * *
549759 AAAAAATAAATTCTAAACTTTTATAAATAAAAATAAATTT-TACCATAAAAAATTTAAACTTATA
1 AAAAAATAAATT-TAAACTTTTACAAATAAAAAT-AATTTATACC-TTAAAAATTTAAACTCACA
549823 TAATCATGCAA
63 TAA-CAT-CAA
* * * * *
549834 AAAAAACACATTTAAATTTTTACAAATCAAAATAAATTATACCTTAAAAATTTAAAC-CACATAA
1 AAAAAATAAATTTAAACTTTTACAAATAAAAATAATTTATACCTTAAAAATTTAAACTCACATAA
549898 -AT-AA
66 CATCAA
549902 ATAAAAATAAATTTAAACTTTTACAAATAAAAAT-ATTTAATACCTT
1 A-AAAAATAAATTTAAACTTTTACAAATAAAAATAATTT-ATACCTT
549948 TAGTCAAATT
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
68 6 0.06
69 35 0.36
70 2 0.02
72 5 0.05
73 17 0.18
74 22 0.23
75 10 0.10
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.33
Consensus pattern (71 bp):
AAAAAATAAATTTAAACTTTTACAAATAAAAATAATTTATACCTTAAAAATTTAAACTCACATAA
CATCAA
Found at i:550429 original size:75 final size:76
Alignment explanation
Indices: 550350--550517 Score: 225
Period size: 75 Copynumber: 2.2 Consensus size: 76
550340 AAGCGATATT
550350 TTAAAATTTTTAATTTTATTAAAAAT-AATAATTAATAT-TTTATTTTAAATACAAATTTTTTAA
1 TTAAAATTTTTAATTTTATTAAAAATAAATAATTAATATATTTA-TTTAAATACAAATTTTTTAA
*
550413 AATTTAGTTAAA
65 AATTTAATTAAA
* * * **
550425 TTAAAATTTTT-ATTTTATTAAAATTAAATAATTAATATATTTATTTCAATATAAATTTTTTTTA
1 TTAAAATTTTTAATTTTATTAAAAATAAATAATTAATATATTTATTTAAATACAAATTTTTTAAA
550489 ATTTAATTAAA
66 ATTTAATTAAA
**
550500 TTTTAATTTTTAAATTTT
1 TTAAAATTTTT-AATTTT
550518 TATGATAATT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
74 13 0.16
75 59 0.73
76 4 0.05
77 5 0.06
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (76 bp):
TTAAAATTTTTAATTTTATTAAAAATAAATAATTAATATATTTATTTAAATACAAATTTTTTAAA
ATTTAATTAAA
Found at i:550505 original size:16 final size:14
Alignment explanation
Indices: 550484--550517 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
550474 TATAAATTTT
550484 TTTTAATTTAATTAAA
1 TTTTAATTT--TTAAA
550500 TTTTAATTTTTAAA
1 TTTTAATTTTTAAA
550514 TTTT
1 TTTT
550518 TATGATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTAATTTTTAAA
Found at i:550813 original size:15 final size:14
Alignment explanation
Indices: 550789--550845 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 14
550779 TTTTTGGGCA
*
550789 AGAAAGAAAAAAAGG
1 AGAAA-AAAAAAAAG
*
550804 AGAAAAAAAAGAAAA
1 AGAAAAAAAA-AAAG
550819 AGAAAAGAAAGAAAAAG
1 AG-AAA-AAA-AAAAAG
550836 AGAAAAAAAA
1 AGAAAAAAAA
550846 TTTTATATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 7 0.20
15 12 0.34
16 6 0.17
17 8 0.23
18 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAAAAAG
Found at i:550816 original size:9 final size:9
Alignment explanation
Indices: 550791--550844 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 9
550781 TTTGGGCAAG
550791 AAAGAAAAA
1 AAAGAAAAA
550800 AAGGAGAAAAA
1 AA--AGAAAAA
550811 AAAGAAAAAGA
1 AAAG-AAAA-A
550822 AAAGAAAGAA
1 AAAGAAA-AA
550832 AAAGAGAAAA
1 AAAGA-AAAA
550842 AAA
1 AAA
550845 ATTTTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.10
10 18 0.46
11 17 0.44
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:550845 original size:11 final size:11
Alignment explanation
Indices: 550793--550845 Score: 65
Period size: 11 Copynumber: 4.9 Consensus size: 11
550783 TGGGCAAGAA
*
550793 AGAAAAAAAGG
1 AGAAAAAAAAG
550804 AGAAAAAAAAG
1 AGAAAAAAAAG
550815 A-AAAAGAAAAG
1 AGAAAA-AAAAG
*
550826 A-AAGAAAAAG
1 AGAAAAAAAAG
550836 AGAAAAAAAA
1 AGAAAAAAAA
550846 TTTTATATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.27
11 27 0.73
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:551479 original size:23 final size:23
Alignment explanation
Indices: 551446--551489 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
551436 TCATATTCAT
*
551446 ATTATTTTTTATGCTGTGTTTTA
1 ATTATTCTTTATGCTGTGTTTTA
*
551469 ATTATTCTTTATGTTGTGTTT
1 ATTATTCTTTATGCTGTGTTT
551490 ATATCGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.66
Consensus pattern (23 bp):
ATTATTCTTTATGCTGTGTTTTA
Found at i:551882 original size:11 final size:10
Alignment explanation
Indices: 551847--551907 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
551837 TATTTCCTGT
551847 AAAAAAA-AG
1 AAAAAAAGAG
*
551856 AAATAAAGA-
1 AAAAAAAGAG
* *
551865 AATAAAGGAG
1 AAAAAAAGAG
551875 AAAAAAAGA-
1 AAAAAAAGAG
551884 AAAAAGAA-AG
1 AAAAA-AAGAG
551894 AAAAAAAGA-
1 AAAAAAAGAG
551903 AAAAA
1 AAAAA
551908 TTTATGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 25 0.61
10 16 0.39
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:551882 original size:19 final size:19
Alignment explanation
Indices: 551847--551907 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
551837 TATTTCCTGT
*
551847 AAAAA-AAAGAAATAAAGA
1 AAAAAGAAAGAAAAAAAGA
*
551865 AATAAAG-GAGAAAAAAAGA
1 AA-AAAGAAAGAAAAAAAGA
551884 AAAAAGAAAGAAAAAAAGA
1 AAAAAGAAAGAAAAAAAGA
551903 AAAAA
1 AAAAA
551908 TTTATGTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.16
19 31 0.84
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAAGA
Found at i:551884 original size:8 final size:8
Alignment explanation
Indices: 551848--551907 Score: 57
Period size: 8 Copynumber: 6.8 Consensus size: 8
551838 ATTTCCTGTA
551848 AAAAAAAG
1 AAAAAAAG
*
551856 AAATAAAG
1 AAAAAAAG
551864 AAATAAAGGAG
1 AAA-AAA--AG
551875 AAAAAAAG
1 AAAAAAAG
551883 AAAAAAGAAAG
1 --AAAA-AAAG
551894 AAAAAAAG
1 AAAAAAAG
551902 AAAAAA
1 AAAAAA
551908 TTTATGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
8 22 0.50
9 6 0.14
10 7 0.16
11 9 0.20
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:551903 original size:27 final size:27
Alignment explanation
Indices: 551848--551907 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
551838 ATTTCCTGTA
* **
551848 AAAAAAAGAAATAAAGAAATAAAGGAG
1 AAAAAAAGAAATAAAGAAAAAAAAAAG
551875 AAAAAAAGAAA-AAAGAAAGAAAAAAAG
1 AAAAAAAGAAATAAAGAAA-AAAAAAAG
551902 AAAAAA
1 AAAAAA
551908 TTTATGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (27 bp):
AAAAAAAGAAATAAAGAAAAAAAAAAG
Found at i:552159 original size:27 final size:26
Alignment explanation
Indices: 552129--552179 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
552119 ATTTTAATTT
552129 TAAA-TTTATTTAATAAATAATTTTAAA
1 TAAATTTTA-TTAAT-AATAATTTTAAA
*
552156 TAAATTTTATTAATTATAATTTTA
1 TAAATTTTATTAATAATAATTTTA
552180 TTTAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 9 0.41
28 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TAAATTTTATTAATAATAATTTTAAA
Done.