Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold307
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: 622582
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 5
Found at i:442680 original size:18 final size:18
Alignment explanation
Indices: 442639--442691 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
442629 ATATATATAC
442639 AAATAT-ATAAATATAA-A
1 AAATATAATAAA-ATAACA
* * *
442656 TAATATATTACAATAACA
1 AAATATAATAAAATAACA
442674 AAATATAATAAAATAACA
1 AAATATAATAAAATAACA
442692 TTCATATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATATAATAAAATAACA
Found at i:442722 original size:24 final size:24
Alignment explanation
Indices: 442675--442722 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
442665 ACAATAACAA
*
442675 AATATAATAAAATAACATTCATAT
1 AATATAATAAAATAAAATTCATAT
*
442699 AATATATTATAAATAAAATT-ATAT
1 AATATAATA-AAATAAAATTCATAT
442723 TACAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATAATAAAATAAAATTCATAT
Found at i:442723 original size:17 final size:17
Alignment explanation
Indices: 442701--442745 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
442691 ATTCATATAA
442701 TATATTATAAATAAAAT
1 TATATTATAAATAAAAT
*
442718 TATATTACAAATAAAAT
1 TATATTATAAATAAAAT
*
442735 GATATT-TAAAT
1 TATATTATAAAT
442746 GATTTATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TATATTATAAATAAAAT
Found at i:443847 original size:3 final size:3
Alignment explanation
Indices: 443839--443870 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
443829 AGTTTAATCC
443839 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
443871 CATATACCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:449787 original size:82 final size:83
Alignment explanation
Indices: 449695--449855 Score: 247
Period size: 82 Copynumber: 1.9 Consensus size: 83
449685 ATTCATCTAT
* *
449695 TTTAAAATTAATAAAATTTT-TCTATTTAAATATGTGA-TTTTATTAATTTATTTAAACTTAAAA
1 TTTAAAATTAATAAACTTTTCT-TATTTAAATATGTAATTTTTATTAATTTATTTAAA-TTAAAA
449758 TTAA-TAAATATTAATTGAA
64 TTAATTAAATATTAATTGAA
*
449777 TTTAAAATTAATAAACTTTTCTTATTTAAATATGTAATTTTTTATTAATTTATTTAAATTTAAAT
1 TTTAAAATTAATAAACTTTTCTTATTTAAATATGTAA-TTTTTATTAATTTATTTAAATTAAAAT
449842 TAATTAAATATTAA
65 TAATTAAATATTAA
449856 AAAATAATAA
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
82 33 0.46
83 10 0.14
84 29 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (83 bp):
TTTAAAATTAATAAACTTTTCTTATTTAAATATGTAATTTTTATTAATTTATTTAAATTAAAATT
AATTAAATATTAATTGAA
Found at i:449854 original size:84 final size:82
Alignment explanation
Indices: 449695--449855 Score: 245
Period size: 84 Copynumber: 1.9 Consensus size: 82
449685 ATTCATCTAT
*
449695 TTTAAAATTAATAAAATTTTTCTATTTAAATATGTGATTTTATTAATTTATTTAAACTTAAAATT
1 TTTAAAATTAATAAAATTTTTCTATTTAAATATGTAATTTTATTAATTTATTTAAACTTAAAATT
449760 AATAAATATTAATTGAA
66 AATAAATATTAATTGAA
* *
449777 TTTAAAATTAAT-AAACTTTTCTTATTTAAATATGTAATTTTTTATTAATTTATTTAAA-TTTAA
1 TTTAAAATTAATAAAATTTTTC-TATTTAAATATGTAA--TTTTATTAATTTATTTAAACTTAAA
449840 ATTAATTAAATATTAA
63 ATTAA-TAAATATTAA
449856 AAAATAATAA
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
81 8 0.11
82 26 0.36
83 9 0.12
84 29 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (82 bp):
TTTAAAATTAATAAAATTTTTCTATTTAAATATGTAATTTTATTAATTTATTTAAACTTAAAATT
AATAAATATTAATTGAA
Found at i:449855 original size:16 final size:16
Alignment explanation
Indices: 449819--449856 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
449809 TGTAATTTTT
* *
449819 TATTAATTTATTTAAA
1 TATTAAATTAATTAAA
449835 T-TTAAATTAATTAAA
1 TATTAAATTAATTAAA
449850 TATTAAA
1 TATTAAA
449857 AAATAATAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTAAATTAATTAAA
Found at i:452319 original size:22 final size:22
Alignment explanation
Indices: 452294--452354 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
452284 AATATAATAG
* *
452294 TAGTAAAAAATTAATTACATAA
1 TAGTAAATAATTAATAACATAA
* * * *
452316 TAGTATATGATCAATAACATGA
1 TAGTAAATAATTAATAACATAA
452338 TAGTAAATAATTAATAA
1 TAGTAAATAATTAATAA
452355 TACGTACAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (22 bp):
TAGTAAATAATTAATAACATAA
Found at i:452888 original size:16 final size:16
Alignment explanation
Indices: 452860--452893 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
452850 GTTGCAATAA
452860 TTTATAATATTTATAT
1 TTTATAATATTTATAT
452876 TTTA-AATACTTTATAT
1 TTTATAATA-TTTATAT
452892 TT
1 TT
452894 GGATACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTATAATATTTATAT
Found at i:454321 original size:53 final size:54
Alignment explanation
Indices: 454253--454395 Score: 182
Period size: 53 Copynumber: 2.7 Consensus size: 54
454243 AATCAAATCT
* * *
454253 TAACTCAAAATCCCTAATCTCTCCCCGTTTTAATTTCTTAAATA-TTATAAACAC
1 TAACTCAAAATCCCTAATCTCTCCCCATTCTAATTTCTCAAA-AGTTATAAACAC
* * *
454307 TAACTC-AAATCCCTAAACTCTCTCCATTCTAATTTCTCAAAAGTTATAAACCC
1 TAACTCAAAATCCCTAATCTCTCCCCATTCTAATTTCTCAAAAGTTATAAACAC
* * *
454360 AAACTCAAAAACCCTAATCCCTCCCCATTCTAATTT
1 TAACTCAAAATCCCTAATCTCTCCCCATTCTAATTT
454396 TTCCACAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.01
53 44 0.58
54 31 0.41
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (54 bp):
TAACTCAAAATCCCTAATCTCTCCCCATTCTAATTTCTCAAAAGTTATAAACAC
Found at i:454613 original size:13 final size:15
Alignment explanation
Indices: 454585--454616 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
454575 GTATTAGGGA
454585 TTTGAGATTAAGGAT
1 TTTGAGATTAAGGAT
454600 TTTGAG-TT-AGGAT
1 TTTGAGATTAAGGAT
454613 TTTG
1 TTTG
454617 TTTCGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (15 bp):
TTTGAGATTAAGGAT
Found at i:460493 original size:18 final size:18
Alignment explanation
Indices: 460472--460514 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 18
460462 AATAATTTTT
*
460472 TAAAATAAAATATAGATA
1 TAAAATAAAATATAAATA
460490 T-AAA-AAAATATAAATA
1 TAAAATAAAATATAAATA
460506 TAAAATAAA
1 TAAAATAAA
460515 TACACGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 12 0.55
17 6 0.27
18 4 0.18
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAATAAAATATAAATA
Found at i:461414 original size:2 final size:2
Alignment explanation
Indices: 461407--461446 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
461397 TGTATCCAAG
461407 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
461447 GCGTTTGGCC
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:462851 original size:33 final size:33
Alignment explanation
Indices: 462808--462871 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
462798 TTATGATTGT
* *
462808 ATATGGTTATTCTTATATAATAAATTAAAAAAC
1 ATATGGTTATTATCATATAATAAATTAAAAAAC
* * *
462841 ATATGTTTATTATCATATGATTAATTAAAAA
1 ATATGGTTATTATCATATAATAAATTAAAAA
462872 TAAATAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (33 bp):
ATATGGTTATTATCATATAATAAATTAAAAAAC
Found at i:462899 original size:19 final size:18
Alignment explanation
Indices: 462860--462900 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
462850 TTATCATATG
*
462860 ATTAATTAAAAATAAATA
1 ATTAATTAAAAATAAAAA
*
462878 ATTAGTTAAAAATATAAAA
1 ATTAATTAAAAATA-AAAA
462897 ATTA
1 ATTA
462901 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTAATTAAAAATAAAAA
Found at i:462909 original size:20 final size:20
Alignment explanation
Indices: 462865--462910 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
462855 ATATGATTAA
462865 TTAAAA-ATAAATAATTAGT
1 TTAAAATATAAATAATTAGT
* *
462884 TAAAAATATAAA-AATTATTT
1 TTAAAATATAAATAATTA-GT
462904 TTAAAAT
1 TTAAAAT
462911 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTAAAATATAAATAATTAGT
Found at i:463018 original size:34 final size:34
Alignment explanation
Indices: 462951--463018 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
462941 ATTTTTAAAC
*
462951 AAATATAATTTCAATATATATTATTACTTAACAT
1 AAATATAATTTCAATATATATTATTACTAAACAT
*
462985 AAATATAATTTTAAT-TATTATTATATA-TAAACAT
1 AAATATAATTTCAATATA-TATTAT-TACTAAACAT
463019 TTTAATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.07
34 26 0.87
35 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATAATTTCAATATATATTATTACTAAACAT
Found at i:464900 original size:18 final size:19
Alignment explanation
Indices: 464877--464913 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
464867 TAAATTATTA
*
464877 TATTTATT-AGATAAATAT
1 TATTTATTGAGAAAAATAT
464895 TATTTATTGAGAAAAATAT
1 TATTTATTGAGAAAAATAT
464914 AGAGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TATTTATTGAGAAAAATAT
Found at i:470328 original size:16 final size:16
Alignment explanation
Indices: 470289--470333 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
470279 GTAAATTTTT
470289 TAAAAAAT-TATATAA
1 TAAAAAATATATATAA
*
470304 AAATTAAAATATATATAA
1 TAA--AAAATATATATAA
470322 TAAAAAATATAT
1 TAAAAAATATAT
470334 TTATAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 5 0.20
18 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAAATATATATAA
Found at i:471513 original size:148 final size:149
Alignment explanation
Indices: 471322--471619 Score: 400
Period size: 148 Copynumber: 2.0 Consensus size: 149
471312 TTAATATGAC
* *
471322 CTTATATTTAAAAAAAATTAAGAAATCAATTATAATAATAACATGTAACATAATTAAAAATTATT
1 CTTATATTTAAAAAAAATTAAGAAATCAATTATAATAACAACATATAACATAATTAAAAATTATT
** * * * *
471387 TAAATAACATCACATAATGTAACGTGAAAAAATAATAAAAATTTGACACAACACGAAAAATATCA
66 TAAATAACATCACATAACATAACATGAAAAAATAACAAAAATTTGACACAACACAAAAAATAACA
*
471452 TGACTTCGACATAAATACA
131 TAACTTCGACATAAATACA
** * *
471471 CTTATATTTTTAAAAAATTAAG-AATCAATTATAATAACAACATATGACATAATTAAATATTATT
1 CTTATATTTAAAAAAAATTAAGAAATCAATTATAATAACAACATATAACATAATTAAAAATTATT
* * * * *
471535 TGAATAGCGTCACATAACATAATATGAAAAAATAACAAAAATTTGACATAACACAAAAAATAACA
66 TAAATAACATCACATAACATAACATGAAAAAATAACAAAAATTTGACACAACACAAAAAATAACA
* * *
471600 TAATTTTGATATAAATACA
131 TAACTTCGACATAAATACA
471619 C
1 C
471620 AAATATATCA
Statistics
Matches: 128, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
148 108 0.84
149 20 0.16
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.30
Consensus pattern (149 bp):
CTTATATTTAAAAAAAATTAAGAAATCAATTATAATAACAACATATAACATAATTAAAAATTATT
TAAATAACATCACATAACATAACATGAAAAAATAACAAAAATTTGACACAACACAAAAAATAACA
TAACTTCGACATAAATACA
Found at i:472201 original size:13 final size:14
Alignment explanation
Indices: 472170--472207 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
472160 ACTTTTTATT
*
472170 ATAAAAAATTAATA
1 ATAAATAATTAATA
*
472184 ATAAATTATTAA-A
1 ATAAATAATTAATA
472197 ATAAATAATTA
1 ATAAATAATTA
472208 TCATTCGAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAATAATTAATA
Found at i:472516 original size:52 final size:52
Alignment explanation
Indices: 472435--472542 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 52
472425 ATAAAATATT
** * **
472435 AAAA-ATTATTTTTAATTATATTTATATATTTTTA-TAATTAAAATTTAAATA
1 AAAATATTATTTTTAATTATAAATAAATATTTAAATTAA-TAAAATTTAAATA
*
472486 AAAATATTA-TTTTAATTAATAAATAAATATTTAAATTAATCAAATTTAAATA
1 AAAATATTATTTTTAATT-ATAAATAAATATTTAAATTAATAAAATTTAAATA
472538 AAAAT
1 AAAAT
472543 TAAAATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
51 12 0.25
52 33 0.69
53 3 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (52 bp):
AAAATATTATTTTTAATTATAAATAAATATTTAAATTAATAAAATTTAAATA
Found at i:472522 original size:20 final size:20
Alignment explanation
Indices: 472468--472530 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
472458 ATATATTTTT
*
472468 ATAATTAAA-ATTTAAA-TA
1 ATAAATAAATATTTAAATTA
* *
472486 A-AAAT-ATTATTTTAATTA
1 ATAAATAAATATTTAAATTA
472504 ATAAATAAATATTTAAATTA
1 ATAAATAAATATTTAAATTA
472524 ATCAAAT
1 AT-AAAT
472531 TTAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 4 0.11
19 4 0.11
20 13 0.37
21 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAATAAATATTTAAATTA
Found at i:472556 original size:22 final size:20
Alignment explanation
Indices: 472528--472576 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
472518 AAATTAATCA
472528 AATTTAAATAAAAATTAAAATT
1 AATTTAAATAAAAA-T-AAATT
*
472550 AATTTAAATCAAAATAAATT
1 AATTTAAATAAAAATAAATT
*
472570 TATTTAA
1 AATTTAA
472577 CTGTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTAAATAAAAATAAATT
Found at i:472838 original size:16 final size:15
Alignment explanation
Indices: 472817--472849 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
472807 TTAAAAGGAC
472817 AAAAAGAGAGAAAAAA
1 AAAAAGAGA-AAAAAA
472833 AAAAAGAGAAAAAAA
1 AAAAAGAGAAAAAAA
472848 AA
1 AA
472850 CATTTTCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAGAAAAAAA
Found at i:472840 original size:14 final size:14
Alignment explanation
Indices: 472817--472849 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
472807 TTAAAAGGAC
*
472817 AAAAAGAGAGAAAA
1 AAAAAAAGAGAAAA
472831 AAAAAAAGAGAAAA
1 AAAAAAAGAGAAAA
472845 AAAAA
1 AAAAA
472850 CATTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAGAAAA
Found at i:475768 original size:16 final size:16
Alignment explanation
Indices: 475744--475777 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
475734 TTACTGTATG
*
475744 ATTTGTTTTTATATTT
1 ATTTGTTTTGATATTT
*
475760 ATTTTTTTTGATATTT
1 ATTTGTTTTGATATTT
475776 AT
1 AT
475778 ACCATCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
ATTTGTTTTGATATTT
Found at i:485264 original size:18 final size:18
Alignment explanation
Indices: 485241--485275 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
485231 TCATTTAATT
485241 ATTAAAAA-AGAAAAAATA
1 ATTAAAAATA-AAAAAATA
485259 ATTAAAAATAAAAAAAT
1 ATTAAAAATAAAAAAAT
485276 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
ATTAAAAATAAAAAAATA
Found at i:487169 original size:17 final size:18
Alignment explanation
Indices: 487137--487173 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
487127 GTATCGATGC
487137 ATGAACAGTATGAAAAATG
1 ATGAACAG-ATGAAAAATG
487156 ATGAACAG-TGAAAAATG
1 ATGAACAGATGAAAAATG
487173 A
1 A
487174 GATTTAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (18 bp):
ATGAACAGATGAAAAATG
Found at i:487625 original size:39 final size:39
Alignment explanation
Indices: 487595--487677 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 39
487585 TTAGATTTTG
* * * *
487595 AAAGATATTAGTAATGTATAAATTACTTATTGGAATCTA
1 AAAGATATAACTAATATATAAATTACTTATTAGAATCTA
** * *
487634 AAAGATATAACTAATATATAAATTTTTTATTAAAATTTA
1 AAAGATATAACTAATATATAAATTACTTATTAGAATCTA
487673 AAAGA
1 AAAGA
487678 GGAGACTAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (39 bp):
AAAGATATAACTAATATATAAATTACTTATTAGAATCTA
Found at i:487960 original size:165 final size:163
Alignment explanation
Indices: 487673--488125 Score: 457
Period size: 172 Copynumber: 2.7 Consensus size: 163
487663 TTAAAATTTA
* * *
487673 AAAGAGGAGACTAATGCATATATTCTGTTTTTGAATAAATATGATAAATGTATAGATTCTTAATG
1 AAAGAGGAGACTAATGCAT-GATTCTG-TTTGGAATAAATATGAT-AATGTATAAATTC-TAATG
* * * *
487738 GAAAATCAGATTCTTTCTT-ATATGAAAGAAGTTGATAAGACTAATGCATGGA-TTGTAAATGTT
62 G-GAATCAGATTCTTT-TTGATATGAAAAAAGTTGATAAGACTAATGCATGAATTTGTAAATGTC
* * * *
487801 AGACTACAAATAA-AAGACTGATTCATGGATT-AGAGTTCG
125 AGACTACAAAGAATAA-ACTAATGCATGGATTGA-AATTCG
*
487840 AAAGAAGGA-ACTAATGCATGGATTCTGTTTGGAATAAATATGATAACTGCATAAATTCATAATG
1 AAAG-AGGAGACTAATGCAT-GATTCTGTTTGGAATAAATATGATAA-TGTATAAATTC-TAATG
*
487904 GGAATCAGATTCTTTTTGATATAAAAAAAGTTGATAAGACTAATGCATGAATTGTAATTTGTAAA
62 GGAATCAGATTCTTTTTGATATGAAAAAAGTTGATAAGACTAATGC----A-TG-AATTTGTAAA
** *
487969 TGTCAGACTGTAAAGAATAAACTAATGCGTGGATTGAAATTCG
121 TGTCAGACTACAAAGAATAAACTAATGCATGGATTGAAATTCG
* * * * * * * *
488012 AAAGATGAGACTAATGTATGATTTTATTTTGAAATAAATGTGATTAATGTATACATTGCTAATGA
1 AAAGAGGAGACTAATGCATGATTCT-GTTTGGAATAAATATGA-TAATGTATAAATT-CTAATGG
*
488077 GAATCAGATTCTCTTTGATATGAAAAAAGTTGATAAGACTAATGCATGA
63 GAATCAGATTCTTTTTGATATGAAAAAAGTTGATAAGACTAATGCATGA
488126 TGTACAGATT
Statistics
Matches: 241, Mismatches: 29, Indels: 33
0.80 0.10 0.11
Matches are distributed among these distances:
164 2 0.01
165 41 0.17
166 32 0.13
167 22 0.09
168 5 0.02
169 1 0.00
170 2 0.01
171 9 0.04
172 120 0.50
173 7 0.03
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (163 bp):
AAAGAGGAGACTAATGCATGATTCTGTTTGGAATAAATATGATAATGTATAAATTCTAATGGGAA
TCAGATTCTTTTTGATATGAAAAAAGTTGATAAGACTAATGCATGAATTTGTAAATGTCAGACTA
CAAAGAATAAACTAATGCATGGATTGAAATTCG
Found at i:490845 original size:19 final size:20
Alignment explanation
Indices: 490821--490870 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
490811 TTCCATCGAC
490821 TTTTTTGGAGATTCAAG-GT
1 TTTTTTGGAGATTCAAGTGT
490840 TTTTTTGGAGATTCAAGTGT
1 TTTTTTGGAGATTCAAGTGT
490860 TTTTTT-GAGAT
1 TTTTTTGGAGAT
490871 ACAGAACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (20 bp):
TTTTTTGGAGATTCAAGTGT
Found at i:491078 original size:271 final size:271
Alignment explanation
Indices: 490595--491108 Score: 911
Period size: 271 Copynumber: 1.9 Consensus size: 271
490585 TTTGATTATC
* *
490595 GAGATACAGAACAGGCATAAATACATGACTTTTTATAAGAAGGCATGGATAGTTAAGCAAAAGGC
1 GAGATACAGAACAAGCATAAATACATGACTTTTTATAAGAAGGCATGGATAGTCAAGCAAAAGGC
* *
490660 AATTGCTTGAGTGTTTGGCGATTAGGTTAAATAATACAATGGTCTGCCAAAATGGTTAGTTGTAA
66 AATTGCTTGAGTGTTTGGCGATTAGGTTAAATAATACAATGGTCTGCCAAAATGGTTAGCTATAA
* *
490725 TGCAACATTTTGTTCTTGCTATAATTGTGGATTTGTAAACCATACCTACATATAATGGTCCTAAA
131 TGCAACATTTTGTTCTTGCTATAATTGTGGATTTGCAAACCATACCTACATACAATGGTCCTAAA
490790 ATGATGCATGATAAGTGTTTTTTCCATCGACTTTTTTGGAGATTCAAGGTTTTTTTGGAGATTCA
196 ATGATGCATGATAAGTGTTTTTTCCATCGACTTTTTTGGAGATTCAAGGTTTTTTTGGAGATTCA
490855 AGTGTTTTTTT
261 AGTGTTTTTTT
* * *
490866 GAGATACAGAACAAGTATAAATATATGACTTTTTATAAGGAGGCATGGATAGTCAAGCAAAAGGC
1 GAGATACAGAACAAGCATAAATACATGACTTTTTATAAGAAGGCATGGATAGTCAAGCAAAAGGC
* *
490931 AATTGCTTGAGTGTTTGGCGATTGGGTTAAATATTACAATGGTCTGCCAAAATGGTTAGCTATAA
66 AATTGCTTGAGTGTTTGGCGATTAGGTTAAATAATACAATGGTCTGCCAAAATGGTTAGCTATAA
* *
490996 TGCAACATTTTGTTCTTGGTATAATTGTGGATTTGCAAACCATACCTATATACAATGGTCCTAAA
131 TGCAACATTTTGTTCTTGCTATAATTGTGGATTTGCAAACCATACCTACATACAATGGTCCTAAA
491061 ATGATGCATGATAAGTGTTTTTTCCATCGACTTTTTTGGAGATTCAAG
196 ATGATGCATGATAAGTGTTTTTTCCATCGACTTTTTTGGAGATTCAAG
491109 TCTTGCATTG
Statistics
Matches: 230, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
271 230 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (271 bp):
GAGATACAGAACAAGCATAAATACATGACTTTTTATAAGAAGGCATGGATAGTCAAGCAAAAGGC
AATTGCTTGAGTGTTTGGCGATTAGGTTAAATAATACAATGGTCTGCCAAAATGGTTAGCTATAA
TGCAACATTTTGTTCTTGCTATAATTGTGGATTTGCAAACCATACCTACATACAATGGTCCTAAA
ATGATGCATGATAAGTGTTTTTTCCATCGACTTTTTTGGAGATTCAAGGTTTTTTTGGAGATTCA
AGTGTTTTTTT
Found at i:493048 original size:7 final size:7
Alignment explanation
Indices: 493030--493084 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
493020 TATATTTTAA
*
493030 TTATTTT
1 TTATATT
493037 TTATATT
1 TTATATT
*
493044 GTATATT
1 TTATATT
*
493051 TTTTATT
1 TTATATT
493058 TTATATT
1 TTATATT
493065 TTA-ATT
1 TTATATT
493071 ATTAT-TT
1 -TTATATT
*
493078 TAATATT
1 TTATATT
493085 GATAATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TTATATT
Found at i:493052 original size:16 final size:14
Alignment explanation
Indices: 493031--493066 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
493021 ATATTTTAAT
493031 TATTTTTTATATTGTA
1 TATTTTTTAT-TT-TA
493047 TATTTTTTATTTTA
1 TATTTTTTATTTTA
493061 TATTTT
1 TATTTT
493067 AATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 2 0.10
16 10 0.50
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (14 bp):
TATTTTTTATTTTA
Found at i:493084 original size:11 final size:12
Alignment explanation
Indices: 493022--493081 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
493012 CTAAATGCTA
493022 TATTTTAATTAT
1 TATTTTAATTAT
*
493034 T-TTTTATATTGT
1 TATTTTA-ATTAT
* *
493046 ATATTTTTTATTTT
1 -TA-TTTTAATTAT
493060 ATATTTTAATTAT
1 -TATTTTAATTAT
493073 TATTTTAAT
1 TATTTTAAT
493082 ATTGATAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 5 0.13
12 14 0.36
13 9 0.23
14 7 0.18
15 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:495071 original size:68 final size:67
Alignment explanation
Indices: 494931--495071 Score: 146
Period size: 64 Copynumber: 2.1 Consensus size: 67
494921 TGGCAGAAAC
* * *
494931 AAGAAGAAGAAATGAGAAAAATAAGCAATTAAGCTGCTGAAAATAAATAAGAAAGAAACGACAAC
1 AAGAAGAAGAAAT-AGAAAAATAAGCAATTAAGCTGCTGAAAACAAATAAGAAAGAAACAACAAA
*
494996 AAG
65 AAA
* *
494999 AAGAAGAAGAAAT-G-AAAA-AGGCAATTAA-CTTGCTGAAAACAAATAAGAAAAAGAAATTAAC
1 AAGAAGAAGAAATAGAAAAATAAGCAATTAAGC-TGCTGAAAACAAATAAG--AAAGAAA-CAA-
495060 CAAAAAA
61 CAAAAAA
495067 AAGAA
1 AAGAA
495072 AAAAAAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
63 1 0.02
64 25 0.40
65 4 0.06
66 8 0.13
67 1 0.02
68 23 0.37
ACGTcount: A:0.62, C:0.09, G:0.17, T:0.12
Consensus pattern (67 bp):
AAGAAGAAGAAATAGAAAAATAAGCAATTAAGCTGCTGAAAACAAATAAGAAAGAAACAACAAAA
AA
Found at i:495255 original size:22 final size:22
Alignment explanation
Indices: 495215--495256 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
495205 ACACAACAGT
*
495215 AGCAACAACAACAGCAGCAAGC
1 AGCAACAACAACAGAAGCAAGC
495237 AGCAACAACAATC-GAAGCAA
1 AGCAACAACAA-CAGAAGCAA
495257 CAAACACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.52, C:0.29, G:0.17, T:0.02
Consensus pattern (22 bp):
AGCAACAACAACAGAAGCAAGC
Found at i:495484 original size:23 final size:23
Alignment explanation
Indices: 495441--495486 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
495431 TCTCCATTTT
* *
495441 GAGTTGCATGAGGAGTGGATTAA
1 GAGTTGCATGAGGAATAGATTAA
*
495464 GAGTTGCATGATGAATAGATTAA
1 GAGTTGCATGAGGAATAGATTAA
495487 TGGAGAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.28
Consensus pattern (23 bp):
GAGTTGCATGAGGAATAGATTAA
Found at i:499779 original size:159 final size:158
Alignment explanation
Indices: 499565--500451 Score: 730
Period size: 157 Copynumber: 5.7 Consensus size: 158
499555 TATTAAATAT
* * *
499565 AAAAAATTAATAATATCAGAAATCTCAAACAACATGAAGAAGCATCTAAATGAGCATTTCATATT
1 AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACGAGCATTTCATATT
** * *
499630 AATTAAAAAATATAACCTAAAACCATGTTAAACTAAATCTTTTTATTTTTGATATCTTAAACATA
66 AATTAAAAAATATAACCTAAAACCACATTAAACTAAGTCTTTTTATTTTTGATATATTAAACATA
* * *
499695 TTTTGGCATAATAAACAAGCATGCCATAA
131 TTTTGACATATTAAATAAGCATGCCAT-A
* * *
499724 AAAAAATTAATAATATCAGAAATTTCAAACAACATCAAGAGGTATTTAAACGAGCATTTCATATT
1 AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACGAGCATTTCATATT
* * *
499789 AATTAAAAAATATAATCC-AAAACCACGTTAAACTAAGTCTTTTAATTTTTGACATATTAAACA-
66 AATTAAAAAATATAA-CCTAAAACCACATTAAACTAAGTCTTTTTATTTTTGATATATTAAACAT
*** * ** **
499852 AGCATGTCATAAAAAATTAATAAT---ATCA
130 ATTTTGACATATTAAA-TAAGCATGCCAT-A
* ** * * * *** *
499880 GAAATCTTAAATAATATCAAGAGGTATCT-AAACGAATATTTC-ATATTAAT-TAAA--A-AATT
1 AAAAAATT-AATAATATC-AGA--AATCTCAAAC-AACA--TCAAGAGGCATCTAAACGAGCATT
* * * * **** *** * * * *
499939 ACA-A-CACA--AAACCAAGT-TAAACT--AA-GTTTTTATTTTTA-T-TTTTGATCTATT-AGA
59 TCATATTA-ATTAAA--AAATATAACCTAAAACCACATTAAACTAAGTCTTTTTAT-TTTTGATA
*
499993 TA-T------ATTTTGACATATTAAATAAGCATGTCATA
120 TATTAAACATATTTTGACATATTAAATAAGCATGCCATA
* *
500025 AAAAAATTAATAATATCAAAAATCTCAAACAATATCAAGAGGCATCTAAACGAGCA-TTCATATT
1 AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACGAGCATTTCATATT
* *
500089 AATTAAAAAATATAACCTAAAA-CATATTAAACTAAGTCTTTTTATTTTTGATATGTTAAACATA
66 AATTAAAAAATATAACCTAAAACCACATTAAACTAAGTCTTTTTATTTTTGATATATTAAACATA
* * *
500153 TTTTGACATATTAAACAAGTATGCTATA
131 TTTTGACATATTAAATAAGCATGCCATA
* * * *
500181 AAAAAATTAATAATAT-TGAAATCTCAAACAATATCAAGAGGCATCTAAACGATCATTTCATAAT
1 AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACGAGCATTTCATATT
* * * *
500245 AATTAAAAAA-AGTAACCTAAAATCACATTAAACTAAGTCTTTTTATTTTTTACATATTAAATAT
66 AATTAAAAAATA-TAACCTAAAACCACATTAAACTAAGTCTTTTTATTTTTGATATATTAAACAT
500309 ATTTTGACATATTAAATAAGCATGCCAT-
130 ATTTTGACATATTAAATAAGCATGCCATA
* *
500337 AAAAAATTAATAGTATCAGAAATCTCAAACAACATCAAGAGGTATCTAAA-GTAGCAGTTT-ATA
1 AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACG-AGCA-TTTCATA
* * *
500400 TTAATTACAAAATATAACCCAAAACCACATTAAACTAAGTTTTTTTATTTTT
64 TTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGTCTTTTTATTTTT
500452 TTAGCTTAAT
Statistics
Matches: 576, Mismatches: 105, Indels: 96
0.74 0.14 0.12
Matches are distributed among these distances:
139 2 0.00
140 4 0.01
141 12 0.02
142 4 0.01
143 11 0.02
144 25 0.04
145 12 0.02
146 5 0.01
147 8 0.01
148 4 0.01
149 10 0.02
150 11 0.02
151 4 0.01
152 5 0.01
153 2 0.00
154 4 0.01
155 41 0.07
156 97 0.17
157 156 0.27
158 19 0.03
159 122 0.21
160 12 0.02
161 4 0.01
162 2 0.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (158 bp):
AAAAAATTAATAATATCAGAAATCTCAAACAACATCAAGAGGCATCTAAACGAGCATTTCATATT
AATTAAAAAATATAACCTAAAACCACATTAAACTAAGTCTTTTTATTTTTGATATATTAAACATA
TTTTGACATATTAAATAAGCATGCCATA
Found at i:499899 original size:138 final size:138
Alignment explanation
Indices: 499695--499975 Score: 399
Period size: 138 Copynumber: 2.0 Consensus size: 138
499685 CTTAAACATA
*
499695 TTTTGGCATAATAAACAAGCATGCCATAAAAAAAATTAATAATATCAGAAATTTCAAACAACATC
1 TTTTGACATAATAAACAAGCATGCCAT-AAAAAAATTAATAATATCAGAAATTTCAAACAACATC
* * * *
499760 AAGAGGTATTTAAACGAGCATTTCATATTAATTAAAAAATATA-ATC-CAAAACCACGTTAAACT
65 AAGAGGTATCTAAACGAACATTTCATATTAATTAAAAAAT-TACAACACAAAACCAAGTTAAACT
499823 AAGTCTTTTAAT
129 AAGT-TTTT-AT
* * * *
499835 TTTTGACATATTAAACAAGCATGTCAT-AAAAAATTAATAATATCAGAAATCTT-AAATAATATC
1 TTTTGACATAATAAACAAGCATGCCATAAAAAAATTAATAATATCAGAAAT-TTCAAACAACATC
*
499898 AAGAGGTATCTAAACGAATATTTCATATTAATTAAAAAATTACAACACAAAACCAAGTTAAACTA
65 AAGAGGTATCTAAACGAACATTTCATATTAATTAAAAAATTACAACACAAAACCAAGTTAAACTA
499963 AGTTTTTAT
130 AGTTTTTAT
499972 TTTT
1 TTTT
499976 ATTTTTGATC
Statistics
Matches: 128, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
137 8 0.06
138 74 0.58
139 22 0.17
140 24 0.19
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.32
Consensus pattern (138 bp):
TTTTGACATAATAAACAAGCATGCCATAAAAAAATTAATAATATCAGAAATTTCAAACAACATCA
AGAGGTATCTAAACGAACATTTCATATTAATTAAAAAATTACAACACAAAACCAAGTTAAACTAA
GTTTTTAT
Found at i:500191 original size:156 final size:157
Alignment explanation
Indices: 499835--500451 Score: 793
Period size: 157 Copynumber: 3.9 Consensus size: 157
499825 GTCTTTTAAT
* *
499835 TTTTGACATATTAAACAAGCATGTCATAAAAAATTAATAATATCAGAAATCTTAAATAATATCAA
1 TTTTGACATATTAAACAAGCATGTCATAAAAAATTAATAATATCAGAAATCTCAAACAATATCAA
* ** *
499900 GAGGTATCTAAACGAATATTTCATATTAATTAAAAAATTACAACAC-AAAACCA-AGTTAAACTA
66 GAGGCATCTAAACGAGCATTTCATATTAATTAAAAAA-TATAAC-CTAAAACCACA-TTAAACTA
* * *
499963 AGTTTTTATTTTTATTTTTGATCTATTAGATATA
128 AG----TCTTTTTATTTTTGATATATTAAATATA
* *
499997 TTTTGACATATTAAATAAGCATGTCATAAAAAAATTAATAATATCAAAAATCTCAAACAATATCA
1 TTTTGACATATTAAACAAGCATGTCAT-AAAAAATTAATAATATCAGAAATCTCAAACAATATCA
*
500062 AGAGGCATCTAAACGAGCA-TTCATATTAATTAAAAAATATAACCTAAAA-CATATTAAACTAAG
65 AGAGGCATCTAAACGAGCATTTCATATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAG
* *
500125 TCTTTTTATTTTTGATATGTTAAACATA
130 TCTTTTTATTTTTGATATATTAAATATA
* *
500153 TTTTGACATATTAAACAAGTATG-CTATAAAAAAATTAATAATAT-TGAAATCTCAAACAATATC
1 TTTTGACATATTAAACAAGCATGTC-AT-AAAAAATTAATAATATCAGAAATCTCAAACAATATC
* * *
500216 AAGAGGCATCTAAACGATCATTTCATAATAATTAAAAAA-AGTAACCTAAAATCACATTAAACTA
64 AAGAGGCATCTAAACGAGCATTTCATATTAATTAAAAAATA-TAACCTAAAACCACATTAAACTA
* *
500280 AGTCTTTTTATTTTTTACATATTAAATATA
128 AGTCTTTTTATTTTTGATATATTAAATATA
* * * *
500310 TTTTGACATATTAAATAAGCATGCCATAAAAAATTAATAGTATCAGAAATCTCAAACAACATCAA
1 TTTTGACATATTAAACAAGCATGTCATAAAAAATTAATAATATCAGAAATCTCAAACAATATCAA
* * *
500375 GAGGTATCTAAA-GTAGCAGTTT-ATATTAATTACAAAATATAACCCAAAACCACATTAAACTAA
66 GAGGCATCTAAACG-AGCA-TTTCATATTAATTAAAAAATATAACCTAAAACCACATTAAACTAA
*
500438 GTTTTTTTATTTTT
129 GTCTTTTTATTTTT
500452 TTAGCTTAAT
Statistics
Matches: 407, Mismatches: 36, Indels: 29
0.86 0.08 0.06
Matches are distributed among these distances:
155 38 0.09
156 106 0.26
157 141 0.35
158 5 0.01
160 13 0.03
161 10 0.02
162 44 0.11
163 50 0.12
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (157 bp):
TTTTGACATATTAAACAAGCATGTCATAAAAAATTAATAATATCAGAAATCTCAAACAATATCAA
GAGGCATCTAAACGAGCATTTCATATTAATTAAAAAATATAACCTAAAACCACATTAAACTAAGT
CTTTTTATTTTTGATATATTAAATATA
Found at i:500604 original size:4 final size:4
Alignment explanation
Indices: 500586--500651 Score: 57
Period size: 4 Copynumber: 16.0 Consensus size: 4
500576 AGGCACCTAC
*
500586 CTTT -TTT CTTT -TTT CTTT CTTT CTTATT CTCTT CTTATT CTTT CCTT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-T-TT CT-TT C-T-TT CTTT CTTT
500633 CTTT CTTT -TTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT
500652 TTTTTGCCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
3 9 0.17
4 30 0.58
5 6 0.12
6 7 0.13
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:500606 original size:11 final size:11
Alignment explanation
Indices: 500590--500654 Score: 55
Period size: 11 Copynumber: 5.9 Consensus size: 11
500580 ACCTACCTTT
500590 TTTCTTTTTTC
1 TTTCTTTTTTC
* *
500601 TTTCTTTCTTA
1 TTTCTTTTTTC
500612 TTCTCTTCTTATTC
1 TT-TCTT-TT-TTC
*
500626 TTTC---CTTC
1 TTTCTTTTTTC
500634 TTTCTTTTTTC
1 TTTCTTTTTTC
500645 TTTCTTTTTT
1 TTTCTTTTTT
500655 TTGCCTTCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
8 7 0.17
11 24 0.57
12 4 0.10
13 3 0.07
14 4 0.10
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:500661 original size:29 final size:29
Alignment explanation
Indices: 500594--500662 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
500584 ACCTTTTTTC
*
500594 TTTTTTCTTTCTTTCTTATTCTCTTCTTA
1 TTTTTTCCTTCTTTCTTATTCTCTTCTTA
* *
500623 TTCTTTCCTTCTTTCTT-TTTTCTTTCTT-
1 TTTTTTCCTTCTTTCTTATTCTC-TTCTTA
500651 TTTTTTGCCTTC
1 TTTTTT-CCTTC
500663 CTCCCTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 9 0.26
29 25 0.74
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.72
Consensus pattern (29 bp):
TTTTTTCCTTCTTTCTTATTCTCTTCTTA
Found at i:501210 original size:109 final size:109
Alignment explanation
Indices: 501096--501469 Score: 264
Period size: 109 Copynumber: 3.2 Consensus size: 109
501086 AAGTTGCTTC
*
501096 TACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTTAAA
1 TACAAATAAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTTAAA
501161 CTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCT
66 CTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCT
* * * * ** ***
501205 TACAAATAAAAATAAATCACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGG
1 TACAAATAAAAATAAATTATA--TT---CT-AA--AAATTTAAAC-AGC-ATAATCAAA-T-AAA
* * * * * * * * *** * *
501270 GATAAACTCGTATAA-TTATATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAA
54 AATAAA-T-TTA-AACTTCTA-CAAATA-GAAATAAATA-ATA-CTTTTAATCA-A-ATT---AA
501334 GTTGCTT
107 --T-C-T
*
501341 CTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTTAA
1 -TACAAATAAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTTAA
501406 ACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCT
65 ACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCT
501451 TACAAATAAAAATAAATTA
1 TACAAATAAAAATAAATTA
501470 CACTTTAAAA
Statistics
Matches: 188, Mismatches: 47, Indels: 60
0.64 0.16 0.20
Matches are distributed among these distances:
109 36 0.19
110 1 0.01
111 3 0.02
112 1 0.01
114 3 0.02
115 2 0.01
117 12 0.06
118 3 0.02
119 13 0.07
120 3 0.02
121 12 0.06
122 8 0.04
123 12 0.06
124 8 0.04
125 12 0.06
126 3 0.02
127 13 0.07
128 3 0.02
129 12 0.06
131 2 0.01
132 3 0.02
134 1 0.01
135 3 0.02
136 1 0.01
137 18 0.10
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (109 bp):
TACAAATAAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTTAAA
CTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCT
Found at i:501260 original size:246 final size:246
Alignment explanation
Indices: 500847--501587 Score: 1401
Period size: 246 Copynumber: 3.0 Consensus size: 246
500837 AAATATAAAT
* *
500847 TTCTATAAATCAAAATAAATTATATTCTAAAAATTTAAATAGCATAATCAAATAAAAATAAATTT
1 TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
500912 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
66 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
500977 ACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGGGATAAACTCGTATAATTA
131 ACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGGGATAAACTCGTATAATTA
501042 TATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
196 TATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
501093 TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
1 TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
501158 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
66 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
501223 ACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGGGATAAACTCGTATAATTA
131 ACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGGGATAAACTCGTATAATTA
501288 TATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
196 TATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
501339 TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
1 TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
*
501404 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATT
66 AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
* * *
501469 ACACTTTAAAATAAAGTAAATTTAAACTATCTACAAAAAAAAGTGGGGGATAAACTCGTATAATT
131 ACACTTTAAAATAAAGCAAATTTAAACTACCTA-TAAAAAAAGTGGGGGATAAACTCGTATAATT
* *
501534 ACATCAAAAACTAATTTAATAGTTAAAAATAAATCATACCTTAAAAAGTTGC
195 ATATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
501586 TT
1 TT
501588 GATAAATTTT
Statistics
Matches: 486, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
246 404 0.83
247 82 0.17
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (246 bp):
TTCTACAAATCAAAATAAATTATATTCTAAAAATTTAAACAGCATAATCAAATAAAAATAAATTT
AAACTTCTACAAATAGAAATAAATAATACTTTTAATCAAATTAATCTTACAAATAAAAATAAATC
ACACTTTAAAATAAAGCAAATTTAAACTACCTATAAAAAAAGTGGGGGATAAACTCGTATAATTA
TATCAAAAACTAATTTAATAGTTAGAAATAAATCATACCTTAAAAAGTTGC
Found at i:502987 original size:21 final size:20
Alignment explanation
Indices: 502959--502999 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
502949 GACAAAAATA
*
502959 CCTAATGTATTAATACATTT
1 CCTAATGTATCAATACATTT
*
502979 CCTATATGTATCGATACATTT
1 CCTA-ATGTATCAATACATTT
503000 AGGCAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (20 bp):
CCTAATGTATCAATACATTT
Found at i:514006 original size:23 final size:23
Alignment explanation
Indices: 513980--514024 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
513970 GCATTCTCCA
*
513980 TTAATCTACTCATCATGCAACTT
1 TTAATCCACTCATCATGCAACTT
* *
514003 TTAATCCATTCCTCATGCAACT
1 TTAATCCACTCATCATGCAACT
514025 CAAAATGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.38
Consensus pattern (23 bp):
TTAATCCACTCATCATGCAACTT
Found at i:515112 original size:21 final size:19
Alignment explanation
Indices: 515088--515140 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
515078 TTCAACAATT
515088 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* * *
515109 TGTATCAATACATAAGTAT
1 TGTATCGATACAAAAGTAA
515128 TGTATCGATACAA
1 TGTATCGATACAA
515141 TGTATCGTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.44
20 3 0.11
21 12 0.44
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:515209 original size:13 final size:13
Alignment explanation
Indices: 515191--515217 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
515181 CATTATTTAA
515191 TGTATCGATACAT
1 TGTATCGATACAT
515204 TGTATCGATACAT
1 TGTATCGATACAT
515217 T
1 T
515218 ATTCGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:515225 original size:12 final size:13
Alignment explanation
Indices: 515193--515225 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
515183 TTATTTAATG
*
515193 TATCGATACATTG
1 TATCGATACATTA
515206 TATCGATACATTA
1 TATCGATACATTA
515219 T-TCGATA
1 TATCGATA
515226 TATCTGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:518412 original size:13 final size:13
Alignment explanation
Indices: 518394--518421 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
518384 ATTACTCAAA
518394 TGTATCGATACAT
1 TGTATCGATACAT
518407 TGTATCGATACAT
1 TGTATCGATACAT
518420 TG
1 TG
518422 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:518490 original size:51 final size:52
Alignment explanation
Indices: 518427--518554 Score: 240
Period size: 51 Copynumber: 2.5 Consensus size: 52
518417 CATTGATCTT
518427 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACT-TGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
518478 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
518530 TATATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
518555 TCATATTTTG
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 46 0.61
52 29 0.39
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:527149 original size:20 final size:20
Alignment explanation
Indices: 527124--527178 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
527114 GTTGGGCTCA
*
527124 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
* **
527144 ATGTATTGATACAATTCATT
1 ATGTATCGATACAATTCACC
527164 ATGTATCGATACAAT
1 ATGTATCGATACAAT
527179 GTATCGATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:527857 original size:31 final size:32
Alignment explanation
Indices: 527806--527867 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
527796 CAAGCAAAGG
527806 TAAACTTATCCCTTCATGTGTCTTAATTTCGA
1 TAAACTTATCCCTTCATGTGTCTTAATTTCGA
*
527838 TAAACTTTTCCC-TCATGTGTCTTAATTTCG
1 TAAACTTATCCCTTCATGTGTCTTAATTTCG
527868 GGGACAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (32 bp):
TAAACTTATCCCTTCATGTGTCTTAATTTCGA
Found at i:528344 original size:22 final size:21
Alignment explanation
Indices: 528319--528363 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
528309 GCATGACATT
528319 AAAAAGAATTAAATAACAATTG
1 AAAAAGAATTAAATAA-AATTG
* *
528341 AAAATGAATTAATTAAAATTG
1 AAAAAGAATTAAATAAAATTG
528362 AA
1 AA
528364 TTAACATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAAGAATTAAATAAAATTG
Found at i:531387 original size:3 final size:3
Alignment explanation
Indices: 531379--531407 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
531369 TAACTAAAAT
531379 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
531408 TATTTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:534360 original size:21 final size:21
Alignment explanation
Indices: 534331--534392 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
534321 TATGCGTAAA
*
534331 TTAATTATTTTGATAATTAAT
1 TTAAATATTTTGATAATTAAT
*
534352 TTAAATA-TTTGAATAATCTTAT
1 TTAAATATTTTG-ATAAT-TAAT
*
534374 TTAAATATTTGTGAGAATT
1 TTAAATATTT-TGATAATT
534393 GTTATGGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 11 0.32
23 6 0.18
24 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.52
Consensus pattern (21 bp):
TTAAATATTTTGATAATTAAT
Found at i:541709 original size:30 final size:30
Alignment explanation
Indices: 541671--541845 Score: 185
Period size: 30 Copynumber: 5.9 Consensus size: 30
541661 GTGGTATTCC
* *
541671 TCTCAAAGTCTACGACTCAGTGGCATCTTT
1 TCTCAAAGTCAACGACTCAATGGCATCTTT
* * **
541701 TTTCAAAGTCCACGACT-AATGGCATCCCT
1 TCTCAAAGTCAACGACTCAATGGCATCTTT
*
541730 TCTCAAAGTCAATGACTCAATGGCATCTTT
1 TCTCAAAGTCAACGACTCAATGGCATCTTT
* * **
541760 TGTCAAAGTCCACGACT-AATGGCATCCCT
1 TCTCAAAGTCAACGACTCAATGGCATCTTT
*
541789 TCTCAAAGTCAATGACTCAATGGCATCTTT
1 TCTCAAAGTCAACGACTCAATGGCATCTTT
* * *
541819 TTTCAAAGTTC-ACAACTCAGTGGCATC
1 TCTCAAAG-TCAACGACTCAATGGCATC
541846 CCTTTTTTTT
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
29 47 0.40
30 69 0.58
31 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (30 bp):
TCTCAAAGTCAACGACTCAATGGCATCTTT
Found at i:541739 original size:59 final size:59
Alignment explanation
Indices: 541671--541849 Score: 286
Period size: 59 Copynumber: 3.0 Consensus size: 59
541661 GTGGTATTCC
* * *
541671 TCTCAAAGTCTACGACTCAGTGGCATCTTTTTTCAAAGTCCACGACTAATGGCATCCCT
1 TCTCAAAGTCAATGACTCAATGGCATCTTTTTTCAAAGTCCACGACTAATGGCATCCCT
*
541730 TCTCAAAGTCAATGACTCAATGGCATCTTTTGTCAAAGTCCACGACTAATGGCATCCCT
1 TCTCAAAGTCAATGACTCAATGGCATCTTTTTTCAAAGTCCACGACTAATGGCATCCCT
* * *
541789 TCTCAAAGTCAATGACTCAATGGCATCTTTTTTCAAAGTTCACAACTCAGTGGCATCCCT
1 TCTCAAAGTCAATGACTCAATGGCATCTTTTTTCAAAGTCCACGACT-AATGGCATCCCT
541849 T
1 T
541850 TTTTTTAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
59 99 0.89
60 12 0.11
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (59 bp):
TCTCAAAGTCAATGACTCAATGGCATCTTTTTTCAAAGTCCACGACTAATGGCATCCCT
Found at i:541914 original size:31 final size:31
Alignment explanation
Indices: 541875--542506 Score: 471
Period size: 31 Copynumber: 19.8 Consensus size: 31
541865 CACAACTCTA
*
541875 TGGC-ACCCTTCTAAAGCCCGCACAAGTCGG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* * * *
541905 TGGAAACCCTTATAAAGTCCATACAAGTCGG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
** * *
541936 TGGTGACCCTTCTAAAGCCCACACAAATCAG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
** * *
541967 TGGTGACCCTTTTAAAGCCCACACAAGTTGG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* * * *
541998 TGACAATCCTTTTCTAAAGCTCACACAAGTTGG
1 TGGCAA-CC-CTTCTAAAGCCCACACAAGTCGG
* *
542031 TGTCAACCCTTCTAAAGCCCACACAAGTTGG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* * *
542062 TGGTAACCCTTCTAAAGCCTACACAAGTCGT
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
542093 TGGCAACCCTTCTCTAAA-CTCCACACAAGTCGG
1 TGGCAACCC-T-TCTAAAGC-CCACACAAGTCGG
** * * **
542126 TGATAGCCCTTCTCTAAAGCCCGCACAAGTCAA
1 TGGCAACCC-T-TCTAAAGCCCACACAAGTCGG
* *
542159 T--CATAGCCCTTCTAAAGCCTACACAAGTCAG
1 TGGCA-A-CCCTTCTAAAGCCCACACAAGTCGG
* * ** **
542190 TCGTAACATTTCTCTAAAGCCCACACAAGTCAA
1 TGGCAAC-CCT-TCTAAAGCCCACACAAGTCGG
*** * *
542223 TGGCAATATTTCTCTAAAGTCCACGCAAGTCGG
1 TGGCAA-CCCT-TCTAAAGCCCACACAAGTCGG
* * * *
542256 TGGCAACCCTTCTAAAGCCCATATAGGTCAG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* * **
542287 TGGAAACCCTTCTCTAAAGCCCACATAAGTTAG
1 TGGCAACCC-T-TCTAAAGCCCACACAAGTCGG
* * * *
542320 TGGCAACCTTTCTAAAGCACATACAAGTCAG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* **
542351 TGGCAACCCTTCTAAAGGCCACACAAGTTAG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
*
542382 TGGCAACCCTTCTAAAGCCCACACAAGTCAG
1 TGGCAACCCTTCTAAAGCCCACACAAGTCGG
* * * *
542413 TGACAACCCTTTTCAAAAACCCACACAAGTCGA
1 TGGCAACCC--TTCTAAAGCCCACACAAGTCGG
*
542446 TGGCAACCCTTCTCGAAAGTCCACACAAGTCGG
1 TGGCAACCCTTCT--AAAGCCCACACAAGTCGG
* *
542479 TGGCAACCTTTCTTCAAAGCCCATACAA
1 TGGCAACCCTTC-T-AAAGCCCACACAA
542507 ACTAGTGGCA
Statistics
Matches: 485, Mismatches: 96, Indels: 39
0.78 0.15 0.06
Matches are distributed among these distances:
30 3 0.01
31 258 0.53
32 12 0.02
33 210 0.43
34 2 0.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (31 bp):
TGGCAACCCTTCTAAAGCCCACACAAGTCGG
Found at i:541950 original size:62 final size:62
Alignment explanation
Indices: 541879--542506 Score: 418
Period size: 64 Copynumber: 9.8 Consensus size: 62
541869 ACTCTATGGC
* * * * * * *
541879 ACCCTTCTAAAGCCCGCACAAGTCGGTGGAAACCCTTATAAAGTCCATACAAGTCGGTGGTG
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGATA
* * ** * * *
541941 ACCCTTCTAAAGCCCACACAAATCAGTGGTGACCCTTTTAAAGCCCACACAAGTTGGTGACA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGATA
* * * * * *
542003 ATCCTTTTCTAAAGCTCACACAAGTTGGTGTCAACCCTTCTAAAGCCCACACAAGTTGGTGGTA
1 A-CC-CTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGATA
* *
542067 ACCCTTCTAAAGCCTACACAAGTCGTTGGCAACCCTTCTCTAAA-CTCCACACAAGTCGGTGATA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCC-T-TCTAAAGC-CCACACAAGTCGGTGATA
* * ** * *
542131 GCCCTTCTCTAAAGCCCGCACAAGTCAAT--CATAGCCCTTCTAAAGCCTACACAAGTCAGTCG-
1 ACCC-T-TCTAAAGCCCACACAAGTCGGTGGCA-A-CCCTTCTAAAGCCCACACAAGTCGGT-GA
542193 TA
61 TA
** ** *** * * **
542195 ACATTTCTCTAAAGCCCACACAAGTCAATGGCAATATTTCTCTAAAGTCCACGCAAGTCGGTGGC
1 AC-CCT-TCTAAAGCCCACACAAGTCGGTGGCAA-CCCT-TCTAAAGCCCACACAAGTCGGTGAT
542260 A
62 A
* * * * * * ** **
542261 ACCCTTCTAAAGCCCATATAGGTCAGTGGAAACCCTTCTCTAAAGCCCACATAAGTTAGTGGCA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCC-T-TCTAAAGCCCACACAAGTCGGTGATA
* * * * * ** **
542325 ACCTTTCTAAAGCACATACAAGTCAGTGGCAACCCTTCTAAAGGCCACACAAGTTAGTGGCA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGATA
* * * * * **
542387 ACCCTTCTAAAGCCCACACAAGTCAGTGACAACCCTTTTCAAAAACCCACACAAGTCGATGGCA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCC--TTCTAAAGCCCACACAAGTCGGTGATA
* * *
542451 ACCCTTCTCGAAAGTCCACACAAGTCGGTGGCAACCTTTCTTCAAAGCCCATACAA
1 ACCCTTCT--AAAGCCCACACAAGTCGGTGGCAACCCTTC-T-AAAGCCCACACAA
542507 ACTAGTGGCA
Statistics
Matches: 453, Mismatches: 90, Indels: 42
0.77 0.15 0.07
Matches are distributed among these distances:
62 132 0.29
63 7 0.02
64 227 0.50
65 9 0.02
66 78 0.17
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (62 bp):
ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTAAAGCCCACACAAGTCGGTGATA
Found at i:542023 original size:33 final size:32
Alignment explanation
Indices: 541945--542506 Score: 227
Period size: 33 Copynumber: 17.5 Consensus size: 32
541935 GTGGTGACCC
*
541945 TTCTAAAGCCCACACAAATCAGTGGTGAC--CC-T
1 TTCTAAAGCCCACACAAGT---TGGTGACAACCTT
541977 TT-TAAAGCCCACACAAGTTGGTGACAATCCTT
1 TTCTAAAGCCCACACAAGTTGGTGACAA-CCTT
* * *
542009 TTCTAAAGCTCACACAAGTTGGTGTCAACC-C
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
** *
542040 TTCTAAAGCCCACACAAGTTGGTGGTAACC-C
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
* * * *
542071 TTCTAAAGCCTACACAAGTCGTTGGCAACCCTT
1 TTCTAAAGCCCACACAAGTTGGTGACAA-CCTT
* * * *
542104 CTCTAAA-CTCCACACAAGTCGGTGATAGCCCTT
1 TTCTAAAGC-CCACACAAGTTGGTGACA-ACCTT
* * *** * * * *
542137 CTCTAAAGCCCGCACAAGTCAATCATAGCC-C
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
* ** * *
542168 TTCTAAAGCCTACACAAGTCAGTCG-TAACATT
1 TTCTAAAGCCCACACAAGTTGGT-GACAACCTT
*** * **
542200 TCTCTAAAGCCCACACAAGTCAATGGCAATATT
1 T-TCTAAAGCCCACACAAGTTGGTGACAACCTT
* * * * *
542233 TCTCTAAAGTCCACGCAAGTCGGTGGCAACC-C
1 T-TCTAAAGCCCACACAAGTTGGTGACAACCTT
* * * **
542265 TTCTAAAGCCCATATAGGTCAGTGGA-AACCCTT
1 TTCTAAAGCCCACACAAGTTGGT-GACAA-CCTT
* * * *
542298 CTCTAAAGCCCACATAAGTTAGTGGCAACC-T
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
* * ** * *
542329 TTCTAAAGCACATACAAGTCAGTGGCAACC-C
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
* * * *
542360 TTCTAAAGGCCACACAAGTTAGTGGCAACC-C
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
**
542391 TTCTAAAGCCCACACAAGTCAGTGACAACCCTT
1 TTCTAAAGCCCACACAAGTTGGTGACAA-CCTT
* * * * *
542424 TTCAAAAACCCACACAAGTCGATGGCAACCCTT
1 TTCTAAAGCCCACACAAGTTGGTGACAA-CCTT
* * * * *
542457 CTCGAAAGTCCACACAAGTCGGTGGCAACC-T
1 TTCTAAAGCCCACACAAGTTGGTGACAACCTT
*
542488 TTCTTCAAAGCCCATACAA
1 TTC-T-AAAGCCCACACAA
542507 ACTAGTGGCA
Statistics
Matches: 424, Mismatches: 84, Indels: 43
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.02
31 190 0.45
32 25 0.06
33 201 0.47
34 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (32 bp):
TTCTAAAGCCCACACAAGTTGGTGACAACCTT
Found at i:542045 original size:95 final size:95
Alignment explanation
Indices: 541879--542491 Score: 363
Period size: 95 Copynumber: 6.4 Consensus size: 95
541869 ACTCTATGGC
* * * * * *
541879 ACCCTTCTAAAGCCCGCACAAGTCGGTGGA-AACCC-T-TATAAAGTCCATACAAGTCGGTGGTG
1 ACCCTTCTAAAGCCCACACAAGTCGGT-GACAACCCTTCTCTAAACTCCACACAAGTCGGTGATA
*
541941 ACCCTTCTAAAGCCCACACAAATCAGTGGTG
65 ACCCTTCTAAAGCCCACACAAATCAGTGGTA
* * * * *
541972 ACCCTTTTAAAGCCCACACAAGTTGGTGACAATCCTTTTCTAAAGCT-CACACAAGTTGGTG-TC
1 ACCCTTCTAAAGCCCACACAAGTCGGTGACAACCCTTCTCTAAA-CTCCACACAAGTCGGTGAT-
* **
542035 AACCCTTCTAAAGCCCACACAAGTTGGTGGTA
64 AACCCTTCTAAAGCCCACACAAATCAGTGGTA
* * * *
542067 ACCCTTCTAAAGCCTACACAAGTCGTTGGCAACCCTTCTCTAAACTCCACACAAGTCGGTGATAG
1 ACCCTTCTAAAGCCCACACAAGTCGGTGACAACCCTTCTCTAAACTCCACACAAGTCGGTGATAA
* * * **
542132 CCCTTCTCTAAAGCCCGCACAAGTCAATCATA
66 CCC-T-TCTAAAGCCCACACAAATCAGTGGTA
* * * * ** *
542164 GCCCTTCTAAAGCCTACACAAGTCAGTCG-TAACATTTCTCTAAAGC-CCACACAAGTCAATGGC
1 ACCCTTCTAAAGCCCACACAAGTCGGT-GACAACCCTTCTCTAAA-CTCCACACAAGTC---GGT
* *** * * * * *
542227 AATATTTC-TCTAAAGTCCACGCAAGTCGGTGGCA
61 GATAACCCTTCTAAAGCCCACACAAATCAGTGGTA
* * * * * ** **
542261 ACCCTTCTAAAGCCCATATAGGTCAGTGGA-AACCCTTCTCTAAAGC-CCACATAAGTTAGTGGC
1 ACCCTTCTAAAGCCCACACAAGTCGGT-GACAACCCTTCTCTAAA-CTCCACACAAGTCGGTGAT
* * * * *
542324 AACCTTTCTAAAGCACATACAAGTCAGTGGCA
64 AACCCTTCTAAAGCCCACACAAATCAGTGGTA
* ** * * *
542356 ACCCTTCTAAAGGCCACACAAGTTAGTGGCAACCC-T-TCTAAAGC-CCACACAAGTCAGTGACA
1 ACCCTTCTAAAGCCCACACAAGTCGGTGACAACCCTTCTCTAAA-CTCCACACAAGTCGGTGATA
* * * *
542418 ACCCTTTTCAAAAACCCACACAAGTC-GATGGCA
65 ACCC--TTCTAAAGCCCACACAAATCAG-TGGTA
* * *
542451 ACCCTTCTCGAAAGTCCACACAAGTCGGTGGCAACCTTTCT
1 ACCCTTCT--AAAGCCCACACAAGTCGGTGACAACCCTTCT
542492 TCAAAGCCCA
Statistics
Matches: 407, Mismatches: 89, Indels: 42
0.76 0.17 0.08
Matches are distributed among these distances:
92 2 0.00
93 54 0.13
94 9 0.02
95 175 0.43
96 3 0.01
97 154 0.38
98 3 0.01
99 1 0.00
100 6 0.01
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (95 bp):
ACCCTTCTAAAGCCCACACAAGTCGGTGACAACCCTTCTCTAAACTCCACACAAGTCGGTGATAA
CCCTTCTAAAGCCCACACAAATCAGTGGTA
Found at i:553122 original size:20 final size:21
Alignment explanation
Indices: 553073--553126 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
553063 ATAATGAATA
553073 ATGTATCGATACATTACAAGC
1 ATGTATCGATACATTACAAGC
* ***
553094 ATATATCGATACATT-CACTT
1 ATGTATCGATACATTACAAGC
553114 ATGTATCGATACA
1 ATGTATCGATACA
553127 ATTTTTCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTACAAGC
Found at i:553195 original size:20 final size:20
Alignment explanation
Indices: 553167--553225 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
553157 CATGGTCCAA
*
553167 TATTAATACATTCACTTATG
1 TATTAATACATTAACTTATG
* *
553187 TATTGATACATTTACTTATG
1 TATTAATACATTAACTTATG
*
553207 TATCAATACATTAACTTAT
1 TATTAATACATTAACTTAT
553226 TATATCAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.46
Consensus pattern (20 bp):
TATTAATACATTAACTTATG
Found at i:554118 original size:13 final size:13
Alignment explanation
Indices: 554100--554124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
554090 ATATTGCTTA
554100 GTATCGATACATT
1 GTATCGATACATT
554113 GTATCGATACAT
1 GTATCGATACAT
554125 ATTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:554123 original size:33 final size:32
Alignment explanation
Indices: 554079--554142 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
554069 CACACCCAGA
*
554079 TGTATCAATACATATTGCTTAGTATCGATACAT
1 TGTATCAATACATATT-CATAGTATCGATACAT
*
554112 TGTATCGATACATATTCATAGTATCGATACA
1 TGTATCAATACATATTCATAGTATCGATACA
554143 CCTTGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (32 bp):
TGTATCAATACATATTCATAGTATCGATACAT
Found at i:559909 original size:28 final size:27
Alignment explanation
Indices: 559851--559912 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
559841 AACGGGGTTG
* * *
559851 GAGTATCCCTCAAAAATAACGGGGTTG
1 GAGTATCCCTCAAAAATAACAGAGTTA
* *
559878 GAGTATCCCTGATGAAATAACAGAGTTA
1 GAGTATCCCTCA-AAAATAACAGAGTTA
559906 GAGTATC
1 GAGTATC
559913 TCCGATTGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.24
Consensus pattern (27 bp):
GAGTATCCCTCAAAAATAACAGAGTTA
Found at i:559958 original size:51 final size:51
Alignment explanation
Indices: 559900--560015 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
559890 TGAAATAACA
* * *
559900 GAGTTAGAGTATCTCCGATTGTGAAAAATTGATGTTTT-GAAAATAAAATCG
1 GAGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTTAG-AAATAAAATCG
* * *
559951 GAGTTAGAATATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAATTG
1 GAGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAATCG
* *
560002 GGGTTGGAGTATCC
1 GAGTTAGAGTATCC
560016 TCTTGGAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 54 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (51 bp):
GAGTTAGAGTATCCCCGATTATGAAAAATTAATGTTTTAGAAATAAAATCG
Found at i:560043 original size:79 final size:79
Alignment explanation
Indices: 559953--560206 Score: 278
Period size: 79 Copynumber: 3.2 Consensus size: 79
559943 TAAAATCGGA
* * * *
559953 GTTAGAATATCCCCGATTATGGAAAATTAATGTTTTAGAAATAAAATTGGGGTTGGAGTATCCTC
1 GTTAGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
*
560018 TTGGAAATAACAGG
66 TTGAAAATAACAGG
* * *
560032 GTTAGAGTATCCCTGATTATAGAAAATTGGTGTTTT-GAAAATAAAATCGGGGTTGGAGTATCCC
1 GTTAGAGTATCCCCGATTATGGAAAATTGATGTTTTAG-AAATAAAATCGGGGTTGGAGTATCCC
** *
560096 CTCAAAAATAACGGG
65 CTTGAAAATAACAGG
* * * * * ***
560111 GTTGGAGTATCCTCGATTGTGGAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCCCC
1 GTTAGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
* *
560176 GTGAAAATAA-TGAG
66 TTGAAAATAACAG-G
*
560190 GTTAGAGTATCTCCGAT
1 GTTAGAGTATCCCCGAT
560207 GAAATAACGG
Statistics
Matches: 143, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
78 2 0.01
79 140 0.98
80 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (79 bp):
GTTAGAGTATCCCCGATTATGGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
TTGAAAATAACAGG
Found at i:560197 original size:28 final size:28
Alignment explanation
Indices: 560161--560230 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
560151 ATAAGGCCGG
*
560161 GGTTGGAGTATCCCCG-TGAAAATAATGA
1 GGTTGGAGTATCCCCGATG-AAATAACGA
* * *
560189 GGTTAGAGTATCTCCGATGAAATAACGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
560217 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
560231 TAATTGTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:560287 original size:51 final size:51
Alignment explanation
Indices: 560221--560361 Score: 147
Period size: 51 Copynumber: 2.8 Consensus size: 51
560211 TAACGGGGTT
* * * *
560221 GGAGTATCCCTAATTGTGAAAAATTGGTGTTTTGGAAATAAAATTGGAGTA
1 GGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTA
* * ** * * * *
560272 GGGGTATCCCCAATTGCGGTAAATCGATGCTTTAGAAATAAAATCGGAGTT
1 GGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTA
* * *
560323 GGAGTATCCCCGATTAAGAAAATTTGATGTTTTGGAAAT
1 GGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAAT
560362 GGAACCGGGA
Statistics
Matches: 69, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GGAGTATCCCCAATTGAGAAAAATTGATGTTTTGGAAATAAAATCGGAGTA
Found at i:562705 original size:20 final size:20
Alignment explanation
Indices: 562680--562754 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
562670 AAAAATGCCT
562680 AATGTATCGATACATTATAA
1 AATGTATCGATACATTATAA
562700 AATGTATCGATACA--ATAA
1 AATGTATCGATACATTATAA
* * **
562718 GCAATGTATCGATATAATGCAA
1 --AATGTATCGATACATTATAA
562740 AATGTATCGATACAT
1 AATGTATCGATACAT
562755 CTGGGTAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.09
20 40 0.87
22 2 0.04
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTATAA
Found at i:562787 original size:13 final size:13
Alignment explanation
Indices: 562769--562798 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
562759 GTAAACCTAG
562769 AATGTATCGATAC
1 AATGTATCGATAC
562782 AATGTATCGATAC
1 AATGTATCGATAC
562795 AATG
1 AATG
562799 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:565202 original size:19 final size:18
Alignment explanation
Indices: 565178--565238 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
565168 CGATATAATG
565178 TATCGATACATAAGTGTT
1 TATCGATACATAAGTGTT
565196 CTATCGATAC--AA-TG--
1 -TATCGATACATAAGTGTT
*
565210 TATCGATACATAAGTTTT
1 TATCGATACATAAGTGTT
565228 GTATCGATACA
1 -TATCGATACA
565239 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 9 0.26
15 2 0.06
16 3 0.09
17 2 0.06
19 19 0.54
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (18 bp):
TATCGATACATAAGTGTT
Found at i:565210 original size:32 final size:32
Alignment explanation
Indices: 565165--565251 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
565155 CAACGATTTG
*
565165 TATCGATATAATGTATCGATACATAAGTGTTC
1 TATCGATACAATGTATCGATACATAAGTGTTC
* *
565197 TATCGATACAATGTATCGATACATAAGTTTTG
1 TATCGATACAATGTATCGATACATAAGTGTTC
*
565229 TATCGATACAATGTATCGCTACA
1 TATCGATACAATGTATCGATACA
565252 AAGCTACTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (32 bp):
TATCGATACAATGTATCGATACATAAGTGTTC
Found at i:565218 original size:13 final size:13
Alignment explanation
Indices: 565163--565252 Score: 54
Period size: 13 Copynumber: 6.0 Consensus size: 13
565153 TTCAACGATT
*
565163 TGTATCGATATAA
1 TGTATCGATACAA
565176 TGTATCGATACATAA
1 TGTATCGATAC--AA
565191 GTGTTCTATCGATACAA
1 -TG---TATCGATACAA
565208 TGTATCGATACATAA
1 TGTATCGATAC--AA
565223 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
*
565240 TGTATCGCTACAA
1 TGTATCGATACAA
565253 AGCTACTGCC
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
13 31 0.49
15 4 0.06
16 4 0.06
17 4 0.06
19 20 0.32
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:565309 original size:13 final size:13
Alignment explanation
Indices: 565291--565315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
565281 ATTACTCAAA
565291 TGTATCGATACAT
1 TGTATCGATACAT
565304 TGTATCGATACA
1 TGTATCGATACA
565316 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:565369 original size:52 final size:52
Alignment explanation
Indices: 565324--565452 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
565314 CACTGATCTT
* *
565324 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
565376 TGTATCGATACATACAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
565428 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
565453 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:573727 original size:17 final size:17
Alignment explanation
Indices: 573705--573741 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
573695 TATGTAATGT
573705 TTATTTATGTTTGATAG
1 TTATTTATGTTTGATAG
573722 TTATTTATGTTTGATAG
1 TTATTTATGTTTGATAG
573739 TTA
1 TTA
573742 CCATATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (17 bp):
TTATTTATGTTTGATAG
Found at i:576025 original size:77 final size:77
Alignment explanation
Indices: 575887--576029 Score: 196
Period size: 77 Copynumber: 1.9 Consensus size: 77
575877 AGATAAGGTG
* * * * * * *
575887 TTCGAGAGGCGAAAAGTATGAAAAATTCACATTTTTGCCTACATGTATTGATATATTCCTTCCAT
1 TTCGAGAGGCAAAAAGTATGAAAAAGTCACATTTTTACCTACAAGTATCGATACATGCCTTCCAT
575952 GTATCAATACTA
66 GTATCAATACTA
* * *
575964 TTCGGGAGGCAAAAAGTATGAAAAAGTCACCTTTTTACTTACAAGTATCGATACATGCCTTCCAT
1 TTCGAGAGGCAAAAAGTATGAAAAAGTCACATTTTTACCTACAAGTATCGATACATGCCTTCCAT
576029 G
66 G
576030 CATCGATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 56 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (77 bp):
TTCGAGAGGCAAAAAGTATGAAAAAGTCACATTTTTACCTACAAGTATCGATACATGCCTTCCAT
GTATCAATACTA
Found at i:576273 original size:52 final size:52
Alignment explanation
Indices: 576196--576335 Score: 210
Period size: 52 Copynumber: 2.7 Consensus size: 52
576186 TTCTGGACAG
*
576196 CAAAT-TATCAATATATTTTTCATTGTATCGATACATTCTGGGTTTTTGACC
1 CAAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTTGACC
* * *
576247 CAAATGTATCGATACATTTTTCATTGTATCGATATAATCTGGGTTTTTGACC
1 CAAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTTGACC
* * *
576299 CAAATGTATCAATACATTCTTCAATGTACCGATACAT
1 CAAATGTATCAATACATTTTTCATTGTATCGATACAT
576336 GTAGGCAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
51 5 0.06
52 73 0.94
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (52 bp):
CAAATGTATCAATACATTTTTCATTGTATCGATACATTCTGGGTTTTTGACC
Found at i:583965 original size:52 final size:52
Alignment explanation
Indices: 583903--584028 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
583893 CACTGATCTT
* *
583903 TGTATCGATACACGCAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
583955 TGTATTGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
584007 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
584029 ATTTCATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:590886 original size:10 final size:10
Alignment explanation
Indices: 590867--590901 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
590857 AACAAAAGTC
*
590867 AAAAAGAAAA
1 AAAAACAAAA
590877 AAAAACAAAA
1 AAAAACAAAA
*
590887 CAAAACAAAA
1 AAAAACAAAA
590897 AAAAA
1 AAAAA
590902 ACCCAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:590897 original size:21 final size:22
Alignment explanation
Indices: 590856--590903 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
590846 GTAAACACAC
590856 AAACAAAAGTCAAAAAGAAAAAA
1 AAACAAAAG-CAAAAAGAAAAAA
590879 AAACAAAA-CAAAACA-AAAAAA
1 AAACAAAAGCAAAA-AGAAAAAA
590900 AAAC
1 AAAC
590904 CCAGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 15 0.62
22 1 0.04
23 8 0.33
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.02
Consensus pattern (22 bp):
AAACAAAAGCAAAAAGAAAAAA
Found at i:591175 original size:13 final size:13
Alignment explanation
Indices: 591152--591188 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
591142 TATTCCTTTC
591152 CAAACACAAAAAAA
1 CAAA-ACAAAAAAA
591166 CAAAAC-AAAAAA
1 CAAAACAAAAAAA
591178 CAAAA-AAAAAA
1 CAAAACAAAAAA
591189 GGGAAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 16 0.73
13 2 0.09
14 4 0.18
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAACAAAAAAA
Found at i:592164 original size:30 final size:31
Alignment explanation
Indices: 592123--592645 Score: 163
Period size: 34 Copynumber: 16.6 Consensus size: 31
592113 CTTCAAATAC
* *
592123 CTTTTCAAAGTCCACAATTTAGTGGCA-TCT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTCT
* * *
592153 CTTTCCAAAGTCCACGACTCAGTGGCATTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCATTCT
* *
592184 CTTTTCAAAGTCCACGACTCCGTGGCA----
1 CTTTTCAAAGTCCACAACTCAGTGGCATTCT
* * *
592211 ----TCAAAGTCCACAACCCCGTGGCACCTTGTT
1 CTTTTCAAAGTCCACAACTCAGTGGCA--TT-CT
* * *
592241 CCTTTT--AAGTCCACGACTTAGTGGCATCCT
1 -CTTTTCAAAGTCCACAACTCAGTGGCATTCT
* *
592271 TTTCTTCAAAGTCCACGACTCAGTGGCATT-T
1 CTT-TTCAAAGTCCACAACTCAGTGGCATTCT
* * *
592302 -TGTCTCAAAGTCCACGACTCAGTGGCATCCT
1 CT-TTTCAAAGTCCACAACTCAGTGGCATTCT
* * *
592333 TTTCTTTAAAGTCCACGACTCAGTGGCATT-T
1 CTT-TTCAAAGTCCACAACTCAGTGGCATTCT
* **
592364 -TGTCTCAAAGTCCATGACTCAGTGGCATT-T
1 CT-TTTCAAAGTCCACAACTCAGTGGCATTCT
* * * *
592394 TTTCTTCAAAGTCCACGACTCTGTGGCA--CC
1 CTT-TTCAAAGTCCACAACTCAGTGGCATTCT
* * *
592424 CTTTT--AAGCCCACAACTCCGTGGCACCTTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCA--TTCT
* * *
592455 CCTTTTCAAAGCCCAAAACTTC-GTGGCACCTTTTT
1 -CTTTTCAAAGTCCACAAC-TCAGTGGCA---TTCT
** * * * *
592490 CTTTTTGAAGCCCACAACTCCGTGACACCTTTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCA---TTCT
* *
592524 CTTTTCAAAG-CTCACAACTCCGTGGCACCTTTTT
1 CTTTTCAAAGTC-CACAACTCAGTGGCA---TTCT
** * * *
592558 CTTTTTGAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCA---TTCT
* * * *
592592 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTTTCAAAGTCCACAACTCAGTGGCA---TTCT
*
592626 CTTTTCAAAGCCCACAACTC
1 CTTTTCAAAGTCCACAACTC
592646 CATGGCACCT
Statistics
Matches: 408, Mismatches: 49, Indels: 68
0.78 0.09 0.13
Matches are distributed among these distances:
23 21 0.05
27 17 0.04
29 4 0.01
30 79 0.19
31 56 0.14
32 49 0.12
33 19 0.05
34 154 0.38
35 9 0.02
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.33
Consensus pattern (31 bp):
CTTTTCAAAGTCCACAACTCAGTGGCATTCT
Found at i:592218 original size:23 final size:23
Alignment explanation
Indices: 592188--592233 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
592178 CATTTTCTTT
* *
592188 TCAAAGTCCACGACTCCGTGGCA
1 TCAAAGTCCACAACCCCGTGGCA
592211 TCAAAGTCCACAACCCCGTGGCA
1 TCAAAGTCCACAACCCCGTGGCA
592234 CCTTGTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.37, G:0.20, T:0.15
Consensus pattern (23 bp):
TCAAAGTCCACAACCCCGTGGCA
Found at i:592287 original size:32 final size:31
Alignment explanation
Indices: 592211--592421 Score: 241
Period size: 30 Copynumber: 6.7 Consensus size: 31
592201 CTCCGTGGCA
* * * *
592211 TCAAAGTCCACAACCCCGTGGCACCTTGTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTT-TT-CT
** *
592244 TTTAAGTCCACGACTTAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCT
592276 TCAAAGTCCACGACTCAGTGGCAT-TTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTT-TCT
592306 TCAAAGTCCACGACTCAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCT
*
592338 TTAAAGTCCACGACTCAGTGGCAT-TTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTT-TCT
* *
592368 TCAAAGTCCATGACTCAGTGGCATTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
*
592399 TCAAAGTCCACGACTCTGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
592422 CCCTTTTAAG
Statistics
Matches: 155, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
30 54 0.35
31 30 0.19
32 49 0.32
33 19 0.12
34 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.32
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:592326 original size:62 final size:62
Alignment explanation
Indices: 592247--592421 Score: 298
Period size: 62 Copynumber: 2.8 Consensus size: 62
592237 TGTTCCTTTT
*
592247 AAGTCCACGACTTAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCA
1 AAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCA
*
592309 AAGTCCACGACTCAGTGGCATCCTTTTCTTTAAAGTCCACGACTCAGTGGCATTTTGTCTCA
1 AAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCA
* * *
592371 AAGTCCATGACTCAGTGGCAT-TTTTTCTTCAAAGTCCACGACTCTGTGGCA
1 AAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA
592422 CCCTTTTAAG
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 27 0.25
62 80 0.75
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (62 bp):
AAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTCA
Found at i:592468 original size:34 final size:34
Alignment explanation
Indices: 592429--592675 Score: 395
Period size: 34 Copynumber: 7.3 Consensus size: 34
592419 GCACCCTTTT
*
592429 AAGCCCACAACTCCGTGGCACCTTTTCCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* * **
592463 AAGCCCAAAACTTCGTGGCACCTTTTTCTTTTTG
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
*
592497 AAGCCCACAACTCCGTGACACCTTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
* **
592531 AAGCTCACAACTCCGTGGCACCTTTTTCTTTTTG
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
*
592565 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
592599 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
*
592633 AAGCCCACAACTCCATGGCACCTTTTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
592667 AAGCCCACA
1 AAGCCCACA
592676 CAAGTCGATG
Statistics
Matches: 195, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 195 1.00
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCA
Found at i:592721 original size:31 final size:32
Alignment explanation
Indices: 592664--592744 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 32
592654 CTTTTTCTTT
**
592664 TCAAAGCCCACACAAGTCGATGGCAACC-CCC
1 TCAAAGCCCACACAAGTCGACCGCAACCTCCC
* * *
592695 TCAAAGCCCACACAAGTCGGCCGCAACCTTCT
1 TCAAAGCCCACACAAGTCGACCGCAACCTCCC
592727 TCAAAAGCCCACACAAGT
1 TC-AAAGCCCACACAAGT
592745 TGGTGGCACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 25 0.58
32 3 0.07
33 15 0.35
ACGTcount: A:0.33, C:0.40, G:0.15, T:0.12
Consensus pattern (32 bp):
TCAAAGCCCACACAAGTCGACCGCAACCTCCC
Found at i:592827 original size:22 final size:22
Alignment explanation
Indices: 592760--592827 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
592750 GCACTTTCAT
*
592760 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
592782 CTTGAA-T-CAACACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
592803 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
592825 CTT
1 CTT
592828 AAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:592875 original size:49 final size:43
Alignment explanation
Indices: 592760--592941 Score: 229
Period size: 43 Copynumber: 4.1 Consensus size: 43
592750 GCACTTTCAT
*
592760 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
* * *
592803 CTTTAAGTCCAATATAGCTGGCCTTAAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCA----C
* * *
592850 TTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCAC
1 --CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
* *
592895 CTTTAAGTCCAACATAGCTGGCCTTGAATCAACATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
592938 CTTT
1 CTTT
592942 TCCATCTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
43 80 0.67
45 1 0.01
47 1 0.01
49 38 0.32
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAACACATTGGCAC
Found at i:592905 original size:92 final size:94
Alignment explanation
Indices: 592748--592981 Score: 329
Period size: 92 Copynumber: 2.6 Consensus size: 94
592738 CACAAGTTGG
* *
592748 TGGCACT-TT-CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCACCTTTAAGT
1 TGGCACTCTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTTAAGT
* *
592811 CCAATATAGCTGGCCTTAAATCAGCATAT
66 CCAACATAGCTGGCCTTAAATCAACATAT
*
592840 TGGCA-TCTT-CTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTTAAGT
1 TGGCACTCTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTTAAGT
*
592903 CCAACATAGCTGGCCTTGAATCAACATAT
66 CCAACATAGCTGGCCTTAAATCAACATAT
* * *
592932 TGGCACCTTTTCCATCTTTAAGTTCAA---CGCTGGCCTTGAATCAGCACATT
1 TGGCA-CTCTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT
592982 GACATCCTTT
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
91 1 0.01
92 111 0.87
94 3 0.02
95 13 0.10
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (94 bp):
TGGCACTCTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTAGCACCTTTAAGT
CCAACATAGCTGGCCTTAAATCAACATAT
Found at i:592970 original size:49 final size:55
Alignment explanation
Indices: 592911--593039 Score: 162
Period size: 49 Copynumber: 2.5 Consensus size: 55
592901 GTCCAACATA
*
592911 GCTGGCCTTGAATCAACATATTGGCA-CC-TTTTC-CATCTTTAAGTTC-A-A-C
1 GCTGGCCTTGAATCAACATATTGGCATCCTTTTTCTCATCTTTAAGCTCAATATC
* * *
592960 GCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCTCAATATC
1 GCTGGCCTTGAATCAACATATTGGCATCCTTTTTCTCATCTTTAAGCTCAATATC
* *
593015 GTTGGCCGTGAATCAACATATTGGC
1 GCTGGCCTTGAATCAACATATTGGC
593040 GTCTTTATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 23 0.35
50 2 0.03
51 5 0.08
52 12 0.18
53 1 0.02
54 1 0.02
55 21 0.32
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (55 bp):
GCTGGCCTTGAATCAACATATTGGCATCCTTTTTCTCATCTTTAAGCTCAATATC
Found at i:593753 original size:32 final size:33
Alignment explanation
Indices: 593688--593754 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
593678 TTCAATAATT
593688 TGTATCGATACATAAAGTGTTGTATCGACACAA
1 TGTATCGATACATAAAGTGTTGTATCGACACAA
* *
593721 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGACACAA
593753 TG
1 TG
593755 AAGCTACTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGACACAA
Found at i:593812 original size:13 final size:13
Alignment explanation
Indices: 593794--593818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593784 ATTACTCAAA
593794 TGTATCGATACAT
1 TGTATCGATACAT
593807 TGTATCGATACA
1 TGTATCGATACA
593819 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:597235 original size:23 final size:23
Alignment explanation
Indices: 597209--597259 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
597199 AAAAATGCTC
* * *
597209 AAAAAGTTAAAAACAAAAGCACA
1 AAAAAGATAAAAACAAAAGAAAA
* *
597232 AAAATGATAAACACAAAAGAAAA
1 AAAAAGATAAAAACAAAAGAAAA
597255 AAAAA
1 AAAAA
597260 ACAAAGGCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.75, C:0.10, G:0.08, T:0.08
Consensus pattern (23 bp):
AAAAAGATAAAAACAAAAGAAAA
Found at i:598588 original size:30 final size:30
Alignment explanation
Indices: 598548--598621 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
598538 AATGGACTAA
*
598548 CCTTC-TCAAAGTCCATGACTCAATAGTAC
1 CCTTCTTCAAAGTCCATGACTCAATAGCAC
* *
598577 CCTTCTTCAAAGTCCATGACTTAATGGCAC
1 CCTTCTTCAAAGTCCATGACTCAATAGCAC
*
598607 CTTTCTT-AAAGTCCA
1 CCTTCTTCAAAGTCCA
598622 CTTTGTGGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (30 bp):
CCTTCTTCAAAGTCCATGACTCAATAGCAC
Found at i:598662 original size:30 final size:30
Alignment explanation
Indices: 598626--598814 Score: 256
Period size: 30 Copynumber: 6.3 Consensus size: 30
598616 AGTCCACTTT
* * *
598626 GTGGCACCATTTTCTATAGTCCACAACTCC
1 GTGGCACCCTTTTTTAAAGTCCACAACTCC
* *
598656 GTGGCACCCTTTTTTAAAGTCTACAACTCT
1 GTGGCACCCTTTTTTAAAGTCCACAACTCC
* * *
598686 GTGACACCTTTCTTTTAAAGTCCATAACTCC
1 GTGGCACCCTT-TTTTAAAGTCCACAACTCC
598717 GTGGCACCC--TTTTAAAGTCCACAACTCC
1 GTGGCACCCTTTTTTAAAGTCCACAACTCC
*
598745 ATGGCACCCTTTTTTAAAGTCCACAACTCC
1 GTGGCACCCTTTTTTAAAGTCCACAACTCC
* *
598775 GTGGCACCCCTTTTTAAAGTCCAAAACTCC
1 GTGGCACCCTTTTTTAAAGTCCACAACTCC
598805 GTGGCACCCT
1 GTGGCACCCT
598815 GTAAACACCT
Statistics
Matches: 138, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 26 0.19
30 89 0.64
31 23 0.17
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.30
Consensus pattern (30 bp):
GTGGCACCCTTTTTTAAAGTCCACAACTCC
Found at i:598752 original size:89 final size:88
Alignment explanation
Indices: 598643--598814 Score: 272
Period size: 89 Copynumber: 1.9 Consensus size: 88
598633 CATTTTCTAT
* * * **
598643 AGTCCACAACTCCGTGGCACCCTTTTTTAAAGTCTACAACTCTGTGACACCTTTCTTTTAAAGTC
1 AGTCCACAACTCCATGGCACCCTTTTTTAAAGTCCACAACTCCGTGACACCCCT-TTTTAAAGTC
*
598708 CATAACTCCGTGGCACCCTTTTAA
65 CAAAACTCCGTGGCACCCTTTTAA
*
598732 AGTCCACAACTCCATGGCACCCTTTTTTAAAGTCCACAACTCCGTGGCACCCCTTTTTAAAGTCC
1 AGTCCACAACTCCATGGCACCCTTTTTTAAAGTCCACAACTCCGTGACACCCCTTTTTAAAGTCC
598797 AAAACTCCGTGGCACCCT
66 AAAACTCCGTGGCACCCT
598815 GTAAACACCT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
88 28 0.37
89 48 0.63
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (88 bp):
AGTCCACAACTCCATGGCACCCTTTTTTAAAGTCCACAACTCCGTGACACCCCTTTTTAAAGTCC
AAAACTCCGTGGCACCCTTTTAA
Found at i:599065 original size:13 final size:13
Alignment explanation
Indices: 599047--599071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
599037 TTCAACAATT
599047 TGTATCGATACAA
1 TGTATCGATACAA
599060 TGTATCGATACA
1 TGTATCGATACA
599072 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:599084 original size:19 final size:19
Alignment explanation
Indices: 599060--599109 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
599050 ATCGATACAA
599060 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
599079 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
599098 TGTATCGATACA
1 TGTATCGATACA
599110 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:606511 original size:33 final size:33
Alignment explanation
Indices: 606474--607101 Score: 394
Period size: 33 Copynumber: 19.5 Consensus size: 33
606464 AACCATTTTT
* * *
606474 AAAGCCCACACAAGTCGGTGGTAACCATTTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
*
606507 AAAGCCCACAC-AGATTGGTGGCAGCCCTTTT--
1 AAAGCCCACACAAG-TTGGTGGCAACCCTTTTCA
* * **
606538 AAAGCCCATACAAGTTGGTGGCATCGTTTTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * **
606571 AAAGCCCACAAAAGTTGATGGC-AGCCTTTTTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * *
606603 AAAGCCTACACAAGTTGCTGGCAATCCTTTTTTA
1 AAAGCCCACACAAGTTGGTGGCAA-CCCTTTTCA
*
606637 AAAGCCCACACAAGTCGGTGGCAACCCTTTT--
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * * *
606668 AAAGCCCACAAAAGTTAGTGGCATCCTTTTTTA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* ** *
606701 AAAG-CC-CATAA-TTCCATGGCAACCCTTTT-T
1 AAAGCCCACACAAGTT-GGTGGCAACCCTTTTCA
* * ** * **
606731 AAAGCCCACACAAGTCGATGATAA-TCTTTTTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * **
606763 AAAGCCCACACAAGTCGATGGCAACCCTTTTTT
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * *
606796 AAGGCCTACACAAGTTGGTGGCAATCTTTTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
** * **
606829 AAAATCCACAGAAGTCAGTGGCAACCCTTTT--
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* **** *
606860 AAAGCCCACACAAGTTAGTGGC-TTTTTTTTAAA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTT-CA
* * * *
606893 AAAACACACACAAGTTTGTGACAACCC-TTTC-
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * *
606924 AAAGCCCACACCAGTTAGTGGCATCCTTTTTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * *
606957 AAAGCCCACATAAGTTGGTGACAACCC-TCTCA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* ** *
606989 AAAGCCTACACAAGTCAGTGGCAACCCTTTTTA
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * *
607022 TAAAGCTCACACAAATTGGTAGCAACCCTTTTAA
1 -AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
* * * *
607056 AAAACCCATACAAGTCGATGGCAACCC-TTTC-
1 AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
607087 AAAGCCCACACAAGT
1 AAAGCCCACACAAGT
607102 ACCATCTTTT
Statistics
Matches: 454, Mismatches: 119, Indels: 46
0.73 0.19 0.07
Matches are distributed among these distances:
30 10 0.02
31 123 0.27
32 94 0.21
33 174 0.38
34 53 0.12
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (33 bp):
AAAGCCCACACAAGTTGGTGGCAACCCTTTTCA
Found at i:606571 original size:64 final size:64
Alignment explanation
Indices: 606470--607101 Score: 485
Period size: 64 Copynumber: 9.8 Consensus size: 64
606460 TGGTAACCAT
* * * * *
606470 TTTTAAAGCCCACACAAGTCGGTGGTAACCATTTTCAAAAGCCCACAC-AGATTGGTGGCAGCCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAG-TTGGTGGCAACCC
* * * * * *
606534 TTTTAAAGCCCATACAAGTTGGTGGCATCGTTTTTCAAAAGCCCACAAAAGTTGATGGCAGCCTT
1 TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACC-C
* * * *
606599 TTTTAAAGCCTACACAAGTTGCTGGCAATCCTTTTTTAAAAGCCCACACAAGTCGGTGGCAACCC
1 TTTTAAAGCCCACACAAGTTGGTGGC-ATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACCC
* * * * **
606664 TTTTAAAGCCCACAAAAGTTAGTGGCATCCTTTTTTAAAAG-CC-CATAA-TTCCATGGCAACCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAGTT-GGTGGCAACCC
* * ** * * *
606726 TTTTTAAAGCCCACACAAGTCGATGATAAT-CTTTTT-TAAAGCCCACACAAGTCGATGGCAACC
1 -TTTTAAAGCCCACACAAGTTGGTG-GCATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACC
606789 C
64 C
* * ** * **
606790 TTTTTTAAGGCCTACACAAGTTGGTGGCAAT-CTTTTTCAAAAATCCACAGAAGTCAGTGGCAAC
1 --TTTTAAAGCCCACACAAGTTGGTGGC-ATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAAC
606854 CC
63 CC
* ** * * * * *
606856 TTTTAAAGCCCACACAAGTTAGTGGC-TTTTTTTTAAAAAAACACACACAAGTTTGTGACAACCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTT-CAAAAGCCCACACAAGTTGGTGGCAACCC
* * * * *
606920 TTTCAAAGCCCACACCAGTTAGTGGCATCCTTTTTCAAAAGCCCACATAAGTTGGTGACAACCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACCC
** * ** * * * *
606984 TCTCAAAAGCCTACACAAGTCAGTGGCAACCCTTTTT-ATAAAGCTCACACAAATTGGTAGCAAC
1 T-TTTAAAGCCCACACAAGTTGGTGGC-ATCCTTTTTCA-AAAGCCCACACAAGTTGGTGGCAAC
607048 CC
63 CC
* * * * * *
607050 TTTTAAAAAACCCATACAAGTCGATGGCAACC-CTTTC-AAAGCCCACACAAGT
1 TTTT--AAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAGT
607102 ACCATCTTTT
Statistics
Matches: 456, Mismatches: 91, Indels: 42
0.77 0.15 0.07
Matches are distributed among these distances:
61 1 0.00
62 18 0.04
63 35 0.08
64 190 0.42
65 108 0.24
66 87 0.19
67 17 0.04
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (64 bp):
TTTTAAAGCCCACACAAGTTGGTGGCATCCTTTTTCAAAAGCCCACACAAGTTGGTGGCAACCC
Found at i:606615 original size:34 final size:32
Alignment explanation
Indices: 606534--606826 Score: 195
Period size: 32 Copynumber: 9.1 Consensus size: 32
606524 GTGGCAGCCC
* * * *
606534 TTTTAAAGCCCATACAAGTTGGTGGCATCGTT
1 TTTTAAAGCCCACAAAAGTTGATGGCATCCTT
* *
606566 TTTCAAAAGCCCACAAAAGTTGATGGCAGCCTT
1 TTT-TAAAGCCCACAAAAGTTGATGGCATCCTT
* * *
606599 TTTTAAAGCCTACACAAGTTGCTGGCAATCCTT
1 TTTTAAAGCCCACAAAAGTTGATGGC-ATCCTT
* * * * *
606632 TTTTAAAAGCCCACACAAGTCGGTGGCAACC-C
1 TTTT-AAAGCCCACAAAAGTTGATGGCATCCTT
606664 TTTTAAAGCCCACAAAAGTT-AGTGGCATCCTT
1 TTTTAAAGCCCACAAAAGTTGA-TGGCATCCTT
* * * *
606696 TTTTAAAAG-CC-CATAA-TTCCATGGCAACCCT
1 TTTT-AAAGCCCACAAAAGTT-GATGGCATCCTT
* * **
606727 TTTTAAAGCCCACACAAGTCGATGATAAT-CTT
1 TTTTAAAGCCCACAAAAGTTGATG-GCATCCTT
* * *
606759 TTTTAAAGCCCACACAAGTCGATGGCAACCCTT
1 TTTTAAAGCCCACAAAAGTTGATGGC-ATCCTT
* * * *
606792 TTTTAAGGCCTACACAAGTTGGTGGCAAT-CTT
1 TTTTAAAGCCCACAAAAGTTGATGGC-ATCCTT
606824 TTT
1 TTT
606827 CAAAAATCCA
Statistics
Matches: 208, Mismatches: 39, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
30 6 0.03
31 39 0.19
32 73 0.35
33 71 0.34
34 19 0.09
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (32 bp):
TTTTAAAGCCCACAAAAGTTGATGGCATCCTT
Found at i:606966 original size:128 final size:128
Alignment explanation
Indices: 606501--607056 Score: 440
Period size: 130 Copynumber: 4.3 Consensus size: 128
606491 GTGGTAACCA
* * * * * *
606501 TTTTCAAAAGCCCACAC-AGATTGGTGGCAGCCCTTTTAAAGCCCATACAAGTTGGTGGCATCGT
1 TTTTTAAAAGCCCACACAAG-TTCGTGGCAACCCTTTTAAAGCCCACACAAGTTAGTGGCATCCT
* * * * * * *
606565 TTTTCAAAAGCCCACAAAAGT-TGATGGCAGCCTTTTTTAAAGCCTACACAAGTT-GCTGGCAAT
65 TTTTCAAAAGCCCACATAAGTCAG-TGGCAACC-CTTTTAAAGCCCACACAAGTTAGATGGCTAT
606628 CCT
128 --T
*
606631 TTTTTAAAAGCCCACACAAG-TCGGTGGCAACCCTTTTAAAGCCCACAAAAGTTAGTGGCATCCT
1 TTTTTAAAAGCCCACACAAGTTC-GTGGCAACCCTTTTAAAGCCCACACAAGTTAGTGGCATCCT
* * * *
606695 TTTTTAAAAG-CC-CATAATTCCA-TGGCAACCCTTTTTAAAGCCCACACAAG-TCGAT-GATAA
65 TTTTCAAAAGCCCACATAAGT-CAGTGGCAACCC-TTTTAAAGCCCACACAAGTTAGATGGCT-A
606755 TCT
127 T-T
* * *
606758 TTTTT-AAAGCCCACACAAG-TCGATGGCAACCCTTTTTTAAGGCCTACACAAGTTGGTGGCAAT
1 TTTTTAAAAGCCCACACAAGTTCG-TGGCAACCC--TTTTAAAGCCCACACAAGTTAGTGGC-AT
** *
606821 -CTTTTTCAAAAATCCACAGAAGTCAGTGGCAACCCTTTTAAAGCCCACACAAGTTAG-TGGCT-
62 CCTTTTTCAAAAGCCCACATAAGTCAGTGGCAACCCTTTTAAAGCCCACACAAGTTAGATGGCTA
606883 TT
127 TT
* * * * * *
606885 TTTTTAAAAAAACACACACAAGTTTGTGACAACCCTTTCAAAGCCCACACCAGTTAGTGGCATCC
1 TTTTT--AAAAGCCCACACAAGTTCGTGGCAACCCTTTTAAAGCCCACACAAGTTAGTGGCATCC
** * ** * * *
606950 TTTTTCAAAAGCCCACATAAGTTGGTGACAACCCTCTCAAAAGCCTACACAAGTCAG-TGGCAAC
64 TTTTTCAAAAGCCCACATAAGTCAGTGGCAACCCT-TTTAAAGCCCACACAAGTTAGATGGCTA-
**
607014 CC
127 TT
* * * *
607016 TTTTTATAAAGCTCACACAAATTGGTAGCAACCCTTTTAAA
1 TTTTTA-AAAGCCCACACAAGTTCGTGGCAACCCTTTTAAA
607057 AAACCCATAC
Statistics
Matches: 345, Mismatches: 56, Indels: 50
0.76 0.12 0.11
Matches are distributed among these distances:
125 1 0.00
126 25 0.07
127 17 0.05
128 117 0.34
129 50 0.14
130 126 0.37
131 9 0.03
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (128 bp):
TTTTTAAAAGCCCACACAAGTTCGTGGCAACCCTTTTAAAGCCCACACAAGTTAGTGGCATCCTT
TTTCAAAAGCCCACATAAGTCAGTGGCAACCCTTTTAAAGCCCACACAAGTTAGATGGCTATT
Found at i:607482 original size:52 final size:52
Alignment explanation
Indices: 607278--607503 Score: 229
Period size: 52 Copynumber: 4.3 Consensus size: 52
607268 AATGTTAGTA
* * * * * *
607278 GCCTTAAATCAGTACATTGGCATTCTTCTCACCTTTAAGTCTAATGTCGCTA
1 GCCTTAAATCAGCATATTGGCACTCTTCTCATCTTTAAGTCCAATGTCGCTG
* * * * * * * *
607330 GCCTTGAATTAGTACATTGGCACTTTTCTCATTTTTAAGTCCGATGTCACTG
1 GCCTTAAATCAGCATATTGGCACTCTTCTCATCTTTAAGTCCAATGTCGCTG
* * * *
607382 GCCTTAAACCAGCATATTGGCATTCTTCTCATATTTAAGTCTAATGTCGCTG
1 GCCTTAAATCAGCATATTGGCACTCTTCTCATCTTTAAGTCCAATGTCGCTG
* * *
607434 GCCTTAAATCAGCATATTGGCACCCTTATCATCTTTAAGTCCAGTGTCG-TAG
1 GCCTTAAATCAGCATATTGGCACTCTTCTCATCTTTAAGTCCAATGTCGCT-G
* *
607486 GCTTTAAATCTGCATATT
1 GCCTTAAATCAGCATATT
607504 AGCCAAGAAA
Statistics
Matches: 143, Mismatches: 30, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
51 1 0.01
52 142 0.99
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (52 bp):
GCCTTAAATCAGCATATTGGCACTCTTCTCATCTTTAAGTCCAATGTCGCTG
Found at i:607503 original size:104 final size:104
Alignment explanation
Indices: 607278--607475 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 104
607268 AATGTTAGTA
* * * * * * *
607278 GCCTTAAATCAGTACATTGGCATTCTTCTCACCTTTAAGTCTAATGTCGCTAGCCTTGAATTAGT
1 GCCTTAAACCAGCATATTGGCATTCTTCTCACATTTAAGTCTAATGTCGCTAGCCTTAAATCAGC
** * *
607343 ACATTGGCACTTTTCTCATTTTTAAGTCCGATGTCACTG
66 ACATTGGCACCCTTATCATCTTTAAGTCCGATGTCACTG
* *
607382 GCCTTAAACCAGCATATTGGCATTCTTCTCATATTTAAGTCTAATGTCGCTGGCCTTAAATCAGC
1 GCCTTAAACCAGCATATTGGCATTCTTCTCACATTTAAGTCTAATGTCGCTAGCCTTAAATCAGC
*
607447 ATATTGGCACCCTTATCATCTTTAAGTCC
66 ACATTGGCACCCTTATCATCTTTAAGTCC
607476 AGTGTCGTAG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 80 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (104 bp):
GCCTTAAACCAGCATATTGGCATTCTTCTCACATTTAAGTCTAATGTCGCTAGCCTTAAATCAGC
ACATTGGCACCCTTATCATCTTTAAGTCCGATGTCACTG
Found at i:609411 original size:12 final size:12
Alignment explanation
Indices: 609394--609427 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
609384 CTTGCATCTT
**
609394 TGTCATAACCCA
1 TGTCATAAAACA
609406 TGTCATAAAACA
1 TGTCATAAAACA
609418 TGTCATAAAA
1 TGTCATAAAA
609428 TTTCCAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (12 bp):
TGTCATAAAACA
Found at i:613273 original size:21 final size:21
Alignment explanation
Indices: 613222--613288 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 21
613212 CTGAAAAAAT
* *
613222 TGTATCGATATATAAGTG-AA
1 TGTATCGATACATAATTGCAA
* * *
613242 TATATCAATACATGATTGCAA
1 TGTATCGATACATAATTGCAA
* *
613263 TGTATCGATACATTATT-CAT
1 TGTATCGATACATAATTGCAA
613283 TGTATC
1 TGTATC
613289 AATAAATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATAATTGCAA
Found at i:613288 original size:20 final size:21
Alignment explanation
Indices: 613244--613292 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
613234 TAAGTGAATA
613244 TATCAATACATGATTGCAATG
1 TATCAATACATGATTGCAATG
* * *
613265 TATCGATACATTATT-CATTG
1 TATCAATACATGATTGCAATG
613285 TATCAATA
1 TATCAATA
613293 AATTTTGAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCAATACATGATTGCAATG
Found at i:619874 original size:32 final size:31
Alignment explanation
Indices: 619834--619899 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
619824 ACCATTCCTT
*
619834 TTTGTTTTTTACTTT-TTCTTTTGTATTTTTA
1 TTTGTTTTTTA-TTTATTCTTTTATATTTTTA
619865 TTTGATTTTTTATTTATTCTTTTATATTTTTA
1 TTTG-TTTTTTATTTATTCTTTTATATTTTTA
619897 TTT
1 TTT
619900 AGTAAATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 7 0.22
32 25 0.78
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (31 bp):
TTTGTTTTTTATTTATTCTTTTATATTTTTA
Found at i:620997 original size:9 final size:9
Alignment explanation
Indices: 620971--620998 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
620961 ATTTTCATGA
620971 TTTTTTAAT
1 TTTTTTAAT
620980 TTTTTTAAT
1 TTTTTTAAT
620989 TTTTTTAAT
1 TTTTTTAAT
620998 T
1 T
620999 AATATCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:621222 original size:16 final size:18
Alignment explanation
Indices: 621203--621244 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
621193 TATTATATCG
621203 TATTTAAATT-A-TTTTA
1 TATTTAAATTAATTTTTA
*
621219 TATTTATATTAATTTTTA
1 TATTTAAATTAATTTTTA
621237 TATATTAA
1 TAT-TTAA
621245 TAATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 8 0.38
19 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTAAATTAATTTTTA
Found at i:621248 original size:17 final size:18
Alignment explanation
Indices: 621214--621266 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
621204 ATTTAAATTA
621214 TTTTATATTTATATTAAT
1 TTTTATATTTATATTAAT
621232 TTTTATATATTA-A-TAA-
1 TTTTATAT-TTATATTAAT
*
621248 -TTTATA-TTATATAAAT
1 TTTTATATTTATATTAAT
621264 TTT
1 TTT
621267 AAATCATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.10
14 1 0.03
15 8 0.28
17 5 0.17
18 9 0.31
19 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATTTATATTAAT
Found at i:621890 original size:20 final size:20
Alignment explanation
Indices: 621865--621911 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
621855 TAAATGAGTA
*
621865 AAAATTATAATTTTATATTT
1 AAAATTATAATTTGATATTT
*
621885 AAAATTATGATTTGATATTT
1 AAAATTATAATTTGATATTT
*
621905 TAAATTA
1 AAAATTA
621912 AAAAGATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
AAAATTATAATTTGATATTT
Done.