Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004640.1 Hibiscus syriacus cultivar Beakdansim tig00010390_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88878
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:9519 original size:23 final size:23
Alignment explanation
Indices: 9489--9565 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
9479 AGCTGAGCTA
*
9489 GAGCATGGGCATGGGTAACAGTG
1 GAGCATGGGCGTGGGTAACAGTG
9512 GAGCATGGGCGTGGGTAACAGTG
1 GAGCATGGGCGTGGGTAACAGTG
* * * *
9535 GAACACGAGCGTGGGTGACAGTG
1 GAGCATGGGCGTGGGTAACAGTG
9558 GAGCATGG
1 GAGCATGG
9566 TGCTTCACAT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.25, C:0.14, G:0.45, T:0.16
Consensus pattern (23 bp):
GAGCATGGGCGTGGGTAACAGTG
Found at i:9861 original size:22 final size:23
Alignment explanation
Indices: 9827--9892 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 23
9817 TACACAATAT
*
9827 TAATACTAATAATAATTATAAT-
1 TAATAATAATAATAATTATAATC
* *
9849 TTATAATAATAATTATTATAATC
1 TAATAATAATAATAATTATAATC
* *
9872 TAATAATTATTATAA-TATAAT
1 TAATAATAATAATAATTATAAT
9893 ATTTAATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAATAATAATAATTATAATC
Found at i:9877 original size:17 final size:17
Alignment explanation
Indices: 9835--9893 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
9825 ATTAATACTA
* *
9835 ATAATAATTATAATTTAT
1 ATAATAATTATTA-TAAT
9853 AATAATAATTATTATAAT
1 -ATAATAATTATTATAAT
*
9871 CTAATAATTATTATAAT
1 ATAATAATTATTATAAT
9888 ATAATA
1 ATAATA
9894 TTTAATTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
17 21 0.58
18 3 0.08
19 12 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATAATTATTATAAT
Found at i:11195 original size:81 final size:81
Alignment explanation
Indices: 11097--11508 Score: 565
Period size: 81 Copynumber: 5.1 Consensus size: 81
11087 ATGTTTTAAA
* *
11097 TAAAAGATTAATGGCCTAGTTGTGCATTTAACAGAAATGTGCCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
11162 GTTAAATAACTTTGTG
66 GTTAAATACCTTTGAG
* *
11178 TAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
11243 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
11259 TAAAAGATTAATGGTCTAGCTATGCATCTGATAGAAAAGTGTCAATTATGCCAGTTGGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
11324 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
11340 TAAAATATTAATGGCCTAGTTGTGCATTTGAAAGAAA-GATGTCATTTATGCTAGTTATATGAAA
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
11404 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * *
11421 TAAACGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTTTCAATCATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* * * *
11486 GCTAAATTCTTTTGGG
66 GTTAAATACCTTTGAG
11502 TAAAAGA
1 TAAAAGA
11509 ATAAATGTTT
Statistics
Matches: 291, Mismatches: 38, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
80 1 0.00
81 289 0.99
82 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:13064 original size:23 final size:23
Alignment explanation
Indices: 13038--13128 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
13028 GTGCCACGTA
* *
13038 TTTGTCCCAAAGGACCACATAGT
1 TTTGTCCCGAAGGACCACATAGG
** *
13061 TTTGTATCGAAGGAACACATAGG
1 TTTGTCCCGAAGGACCACATAGG
* * * * *
13084 ATTATCCTGAATGATCACATAGG
1 TTTGTCCCGAAGGACCACATAGG
13107 TTTGTCCCGAAGGACCACATAG
1 TTTGTCCCGAAGGACCACATAG
13129 AACCCTTGAC
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
TTTGTCCCGAAGGACCACATAGG
Found at i:16372 original size:17 final size:17
Alignment explanation
Indices: 16350--16385 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
16340 ATAAAGTTCA
*
16350 TCCATACTTATTTTGTT
1 TCCATACTTATTTCGTT
16367 TCCATACTTATTTCGTT
1 TCCATACTTATTTCGTT
16384 TC
1 TC
16386 TAAGCCCACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (17 bp):
TCCATACTTATTTCGTT
Found at i:23454 original size:62 final size:62
Alignment explanation
Indices: 23332--23454 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 62
23322 ACTCAAAGTT
* * * * *
23332 ACATAACAATGTCAAAATGAATATTTAAGTAACATATATTTAAATGACAACAAGTTTATTTA
1 ACATAACAATGGCAAAATAAATATTTAAGAAACATATATTTAAATAACAACAAGTATATTTA
*
23394 ACATAACAATGGCAGAATAAATATTTAAGAAACATATATTTAAATAACAACCAA-TATATTT
1 ACATAACAATGGCAAAATAAATATTTAAGAAACATATATTTAAATAACAA-CAAGTATATTT
23455 GATAACATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 51 0.94
63 3 0.06
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (62 bp):
ACATAACAATGGCAAAATAAATATTTAAGAAACATATATTTAAATAACAACAAGTATATTTA
Found at i:24861 original size:25 final size:25
Alignment explanation
Indices: 24817--24866 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
24807 ATTGTTTAAA
*
24817 TTATATTTGTTGATCAAGTCTATGT
1 TTATATTTGTTGATCAAGTCAATGT
*
24842 TTATATTATGTTG-TCCAGTCAATGT
1 TTATATT-TGTTGATCAAGTCAATGT
24867 CTGAGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (25 bp):
TTATATTTGTTGATCAAGTCAATGT
Found at i:25703 original size:2 final size:2
Alignment explanation
Indices: 25696--25730 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25686 AACAAAAATA
25696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25731 ACAAACGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39569 original size:35 final size:35
Alignment explanation
Indices: 39512--39645 Score: 169
Period size: 35 Copynumber: 3.8 Consensus size: 35
39502 TGTTTTTCTC
* *
39512 AAAACACAATTTTGTTTCGCTTGAGACAGTTTTATA
1 AAAACA-AATTTTGTCTCACTTGAGACAGTTTTATA
**
39548 AAAACAAATTTTGTCTTGCTTGAGACAGTTTTATA
1 AAAACAAATTTTGTCTCACTTGAGACAGTTTTATA
* * * *
39583 AAAACAAATTTTGTCTCATTTGAGACAATTTCTCTC
1 AAAACAAATTTTGTCTCACTTGAGACAGTTT-TATA
*
39619 AAAATAAATTTTGTCTCACTTGAGACA
1 AAAACAAATTTTGTCTCACTTGAGACA
39646 ATTTATCTCA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
35 54 0.62
36 33 0.38
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCACTTGAGACAGTTTTATA
Found at i:39633 original size:36 final size:35
Alignment explanation
Indices: 39505--39655 Score: 167
Period size: 35 Copynumber: 4.2 Consensus size: 35
39495 TTGAGGGTGT
* * *
39505 TTTTCTCAAAACACAATTTTGTTTCGCTTGAGACAG
1 TTTTCTCAAAACA-AATTTTGTCTCACTTGAGACAA
* * ** *
39541 TTTTATAAAAACAAATTTTGTCTTGCTTGAGACAG
1 TTTTCTCAAAACAAATTTTGTCTCACTTGAGACAA
* * *
39576 TTTTATAAAAACAAATTTTGTCTCATTTGAGACAA
1 TTTTCTCAAAACAAATTTTGTCTCACTTGAGACAA
*
39611 TTTCTCTCAAAATAAATTTTGTCTCACTTGAGACAA
1 TTT-TCTCAAAACAAATTTTGTCTCACTTGAGACAA
39647 TTTATCTCA
1 TTT-TCTCA
39656 GAATATAAAT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 54 0.53
36 47 0.47
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (35 bp):
TTTTCTCAAAACAAATTTTGTCTCACTTGAGACAA
Found at i:39633 original size:71 final size:71
Alignment explanation
Indices: 39512--39645 Score: 171
Period size: 71 Copynumber: 1.9 Consensus size: 71
39502 TGTTTTTCTC
* * * **
39512 AAAACACAATTTTGTTTCGCTTGAGACAGTTTTATAAAAACAAATTTTGTCTTGCTTGAGACAGT
1 AAAACACAATTTTGTCTCACTTGAGACAATTTTATAAAAACAAATTTTGTCTCACTTGAGACAGT
39577 TTTATA
66 TTTATA
* * * *
39583 AAAACA-AATTTTGTCTCATTTGAGACAATTTCTCTCAAAATAAATTTTGTCTCACTTGAGACA
1 AAAACACAATTTTGTCTCACTTGAGACAATTT-TATAAAAACAAATTTTGTCTCACTTGAGACA
39646 ATTTATCTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
70 21 0.40
71 32 0.60
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (71 bp):
AAAACACAATTTTGTCTCACTTGAGACAATTTTATAAAAACAAATTTTGTCTCACTTGAGACAGT
TTTATA
Found at i:39982 original size:66 final size:66
Alignment explanation
Indices: 39795--39988 Score: 248
Period size: 66 Copynumber: 2.9 Consensus size: 66
39785 AAAATTTATA
* * * * * *
39795 ATCTTCGAGTATGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACCGTTTCTCATGAAACACC
1 ATCTTTGAGTATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAC
39860 C
66 C
* *
39861 ATCTTTGAG-ATTGTTTCCCTCGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAT
1 ATCTTTGAGTA-TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-
*
39925 ATC
64 ACC
* * *
39928 ATCTTTGAGTATGTTTCCCTTGAAAC-AAGTTTGTCTCTCTTGAGACGGTTTCTCTTCAAAC
1 ATCTTTGAGTATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
39989 CAAAATCCCT
Statistics
Matches: 111, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 85 0.77
67 24 0.22
68 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (66 bp):
ATCTTTGAGTATGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAC
C
Found at i:40321 original size:131 final size:130
Alignment explanation
Indices: 40044--40350 Score: 350
Period size: 134 Copynumber: 2.3 Consensus size: 130
40034 GCTATCCTCT
* *
40044 GACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCTTCATCATATA
1 GACCAGA-CTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATCATATA
* ** * *
40109 GGAATCGTGTTATCATCCATAAAGATAGCTTGCCATCCTTATCGCGTAGGAACCGTGTCATCCAT
65 GGAACCGTGTTATCATCCATAAAGATAGCTAACCATCCTCATCGCGTAGGAACCGTATCATCCAT
40174 C
130 C
* * *
40175 GACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAATCAGTCGTCCTCATCGA-AT
1 GACCAGA-CTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATC-ATAT
* * * * *
40239 AGGAACCGTGTTATCACCCTCCCTAAAG-TTGGTCAACCATCCTCATTGCGTAGGAACTGTATCA
64 AGGAACCGTGTTATCA---TCCATAAAGATAGCT-AACCATCCTCATCGCGTAGGAACCGTATCA
40303 TCCA-C
125 TCCATC
* * *
40308 TGACCATATCTCATCATCACGTAGGAGCTGTGTCACCCATAGA
1 -GACCAGA-CTCCTCATCACGTAGGAGCTGTGTCACCCCTAGA
40351 GGACCAAAAC
Statistics
Matches: 150, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
131 71 0.47
132 1 0.01
133 4 0.03
134 74 0.49
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (130 bp):
GACCAGACTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCATCATATAG
GAACCGTGTTATCATCCATAAAGATAGCTAACCATCCTCATCGCGTAGGAACCGTATCATCCATC
Found at i:40332 original size:134 final size:131
Alignment explanation
Indices: 40037--40350 Score: 373
Period size: 131 Copynumber: 2.4 Consensus size: 131
40027 AAACCGTGCT
* * *
40037 ATCCTCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCCATCTTCA
1 ATCCACTGACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCA
* ** * *
40102 TCATATAGGAATCGTGTTATCATCCATAAAGATAGCTTGCCATCCTTATCGCGTAGGAACCGTGT
66 TCATATAGGAACCGTGTTATCATCCATAAAGATAGCTAACCATCCTCATCGCGTAGGAACCGTAT
40167 C
131 C
* * * *
40168 ATCCA-TCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAATCAGTCGTCCTC
1 ATCCACT-GACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTC
* * * *
40232 ATCGA-ATAGGAACCGTGTTATCACCCTCCCTAAAG-TTGGTCAACCATCCTCATTGCGTAGGAA
65 ATC-ATATAGGAACCGTGTTATCA---TCCATAAAGATAGCT-AACCATCCTCATCGCGTAGGAA
*
40295 CTGTATC
125 CCGTATC
* * *
40302 ATCCACTGACCATATCTCATCATCACGTAGGAGCTGTGTCACCCATAGA
1 ATCCACTGACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGA
40351 GGACCAAAAC
Statistics
Matches: 155, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
130 1 0.01
131 75 0.48
132 1 0.01
133 3 0.02
134 74 0.48
135 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (131 bp):
ATCCACTGACCAGATCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATAACCAGCCATCCTCA
TCATATAGGAACCGTGTTATCATCCATAAAGATAGCTAACCATCCTCATCGCGTAGGAACCGTAT
C
Found at i:43837 original size:19 final size:19
Alignment explanation
Indices: 43815--43852 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43805 TTTTTATATT
43815 TTTAAATAATTAATTTTAA
1 TTTAAATAATTAATTTTAA
43834 TTTAAATAATTAATTTTAA
1 TTTAAATAATTAATTTTAA
43853 AAGTCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTAAATAATTAATTTTAA
Found at i:45234 original size:17 final size:16
Alignment explanation
Indices: 45206--45237 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
45196 TGGGATCATA
45206 ATATTAATTTTATATT
1 ATATTAATTTTATATT
45222 ATATTATATTTTATAT
1 ATATTA-ATTTTATAT
45238 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTAATTTTATATT
Found at i:45412 original size:49 final size:47
Alignment explanation
Indices: 45337--45435 Score: 144
Period size: 49 Copynumber: 2.1 Consensus size: 47
45327 GATAGTATAA
45337 TAATTAAAATATTTTTAATTTTTATTCAAATATTTATAATTTAATAT
1 TAATTAAAATATTTTTAATTTTTATTCAAATATTTATAATTTAATAT
* * * *
45384 TAATTAAATTTTTTTATAAATTTTTATTCAATTTTTTATAATTTAATAT
1 TAATTAAAATATTTT-T-AATTTTTATTCAAATATTTATAATTTAATAT
45433 TAA
1 TAA
45436 ATTTTTACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 13 0.28
48 1 0.02
49 32 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (47 bp):
TAATTAAAATATTTTTAATTTTTATTCAAATATTTATAATTTAATAT
Found at i:45421 original size:22 final size:22
Alignment explanation
Indices: 45386--45441 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
45376 TTTAATATTA
*
45386 ATTAAATTTTTTTATAAATTT-TT
1 ATTAAA-TTTTTTAT-AATTTAAT
*
45409 ATTCAATTTTTTATAATTTAAT
1 ATTAAATTTTTTATAATTTAAT
45431 ATTAAATTTTT
1 ATTAAATTTTT
45442 ACTTGTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.17
22 19 0.66
23 5 0.17
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTAAATTTTTTATAATTTAAT
Found at i:45442 original size:21 final size:22
Alignment explanation
Indices: 45394--45442 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
45384 TAATTAAATT
* *
45394 TTTTTATAAATTTTTATTCAAT
1 TTTTTATAAATTTATATTCAAA
45416 TTTTTAT-AATTTAATATT-AAA
1 TTTTTATAAATTT-ATATTCAAA
45437 TTTTTA
1 TTTTTA
45443 CTTGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTATAAATTTATATTCAAA
Found at i:45570 original size:18 final size:18
Alignment explanation
Indices: 45547--45599 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
45537 AATACAACAT
45547 TCTTAAAATAATATTATA
1 TCTTAAAATAATATTATA
*
45565 TCTT--AATAATTTTAT-
1 TCTTAAAATAATATTATA
*
45580 TCTCAAATATAATATTATA
1 TCTTAAA-ATAATATTATA
45599 T
1 T
45600 TCTATAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 1 0.04
18 13 0.46
19 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TCTTAAAATAATATTATA
Found at i:46340 original size:37 final size:37
Alignment explanation
Indices: 46290--46393 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
46280 CTTTTCGTCC
* *
46290 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
*
46327 TACTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
46364 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
46394 CCACAAGCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:46825 original size:15 final size:13
Alignment explanation
Indices: 46790--46851 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 13
46780 TTAACCCTTA
*
46790 TTATTTATATGTAT
1 TTATTTA-ATTTAT
*
46804 ATATTTAATTATATT
1 TTATTTAATT-TA-T
46819 TTATTT-ATTTAT
1 TTATTTAATTTAT
46831 TTATTATAATTTTAT
1 TTATT-TAA-TTTAT
46846 TTATTT
1 TTATTT
46852 TTCTTTGCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 6 0.15
13 5 0.12
14 13 0.32
15 16 0.40
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTATTTAATTTAT
Found at i:46842 original size:23 final size:23
Alignment explanation
Indices: 46791--46851 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
46781 TAACCCTTAT
* *
46791 TATTTATATGTATATATTTAATTA
1 TATTT-TATTTATTTATTTAATTA
46815 TATTTTATTTATTTATTT-ATTA
1 TATTTTATTTATTTATTTAATTA
46837 TAATTTTATTTATTT
1 T-ATTTTATTTATTT
46852 TTCTTTGCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 5 0.15
23 24 0.71
24 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTTTATTTATTTATTTAATTA
Found at i:47121 original size:24 final size:22
Alignment explanation
Indices: 47091--47146 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
47081 CTATTTAGCA
47091 TTTTATTATATTATACATACATT
1 TTTTATTAT-TTATACATACATT
* *
47114 TTTATATT-TTTATATATATATT
1 TTT-TATTATTTATACATACATT
47136 TTTTATTATTT
1 TTTTATTATTT
47147 TATTTATACT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.59
23 4 0.14
24 4 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTATACATACATT
Found at i:47126 original size:22 final size:21
Alignment explanation
Indices: 47091--47169 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 21
47081 CTATTTAGCA
47091 TTTTATTATATTATACATACATT
1 TTTTATT-T-TTATACATACATT
* *
47114 TTTATATTTTTATATATATATT
1 TTT-TATTTTTATACATACATT
**
47136 TTTTATTATTTTATTTATACTATT
1 TTTTA-T-TTTTATACATAC-ATT
47160 TATTTATTTT
1 T-TTTATTTT
47170 CATTATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 15 0.32
23 17 0.36
24 9 0.19
25 4 0.09
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTTATACATACATT
Found at i:47142 original size:21 final size:21
Alignment explanation
Indices: 47112--47181 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 21
47102 TATACATACA
47112 TTTTTATATTTTTATATATATAT
1 TTTTTATA-TTTTAT-TATATAT
47135 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTTA-TTATA-TAT
*
47159 TTATTTAT-TTTCATTATAT-T
1 TT-TTTATATTTTATTATATAT
47179 TTT
1 TTT
47182 AGTTTCTTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 1 0.02
22 5 0.12
23 19 0.45
24 9 0.21
25 4 0.10
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATTTTATTATATAT
Found at i:47177 original size:45 final size:44
Alignment explanation
Indices: 47091--47181 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 44
47081 CTATTTAGCA
*
47091 TTTTATTATATTATACATACATTTTTATATTTTTATATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-TT
* **
47136 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATTT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATTT
47180 TT
1 TT
47182 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 22 0.55
46 12 0.30
47 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (44 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATTT
Found at i:47178 original size:28 final size:27
Alignment explanation
Indices: 47122--47179 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
47112 TTTTTATATT
* *
47122 TTTATATATATATTTTTTATTATTTTA
1 TTTATATATATATTTTTTATCATTATA
*
47149 TTTATACTATTTATTTATTT-TCATTATA
1 TTTATA-TATATATTT-TTTATCATTATA
47177 TTT
1 TTT
47180 TTAGTTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 6 0.23
28 17 0.65
29 3 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (27 bp):
TTTATATATATATTTTTTATCATTATA
Found at i:48301 original size:4 final size:4
Alignment explanation
Indices: 48288--48324 Score: 65
Period size: 4 Copynumber: 9.0 Consensus size: 4
48278 TCCTTTCGTC
48288 ATTT ATTTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
48325 TACTAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:50726 original size:21 final size:21
Alignment explanation
Indices: 50700--50745 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
50690 CCTCTGAATA
50700 TTAAATGAATTAATGATTCTT
1 TTAAATGAATTAATGATTCTT
50721 TTAAATGAATTAATGATTCTT
1 TTAAATGAATTAATGATTCTT
50742 TTAA
1 TTAA
50746 TTCTTCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (21 bp):
TTAAATGAATTAATGATTCTT
Found at i:51485 original size:21 final size:20
Alignment explanation
Indices: 51459--51541 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 20
51449 ATTCAATCAG
*
51459 AACAAAAAGGGCAAAAATAAA
1 AACAAAAAGAGCAAAAA-AAA
51480 AACAAAAAGAAGCAAAAAAGAA
1 AACAAAAAG-AGCAAAAAA-AA
* *
51502 CAAAAAAAAGAACAAAAAAAA
1 -AACAAAAAGAGCAAAAAAAA
* *
51523 AAGAAAAAGGGACAAAAAA
1 AACAAAAAGAG-CAAAAAA
51542 GCACATGCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 8 0.15
21 19 0.37
22 17 0.33
23 8 0.15
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.01
Consensus pattern (20 bp):
AACAAAAAGAGCAAAAAAAA
Found at i:51497 original size:11 final size:10
Alignment explanation
Indices: 51483--51542 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
51473 AAATAAAAAC
51483 AAAAAGAAGCA
1 AAAAAGAA-CA
51494 AAAAAGAACAAA
1 AAAAAGAAC--A
51506 AAAAAGAACA
1 AAAAAGAACA
*
51516 AAAAA-AAAA
1 AAAAAGAACA
*
51525 GAAAAAGGGACA
1 -AAAAA-GAACA
51537 AAAAAG
1 AAAAAG
51543 CACATGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
9 3 0.07
10 13 0.32
11 13 0.32
12 12 0.29
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAACA
Found at i:51498 original size:12 final size:11
Alignment explanation
Indices: 51483--51521 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
51473 AAATAAAAAC
51483 AAAAAGAAGC-A
1 AAAAAGAA-CAA
51494 AAAAAGAACAAA
1 AAAAAGAAC-AA
51506 AAAAAGAACAA
1 AAAAAGAACAA
51517 AAAAA
1 AAAAA
51522 AAAGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.04
11 15 0.58
12 10 0.38
ACGTcount: A:0.82, C:0.08, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGAACAA
Found at i:51527 original size:14 final size:12
Alignment explanation
Indices: 51493--51522 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
51483 AAAAAGAAGC
51493 AAAAAAGAACAA
1 AAAAAAGAACAA
51505 AAAAAAGAACAA
1 AAAAAAGAACAA
51517 AAAAAA
1 AAAAAA
51523 AAGAAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.07, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAACAA
Found at i:51530 original size:12 final size:12
Alignment explanation
Indices: 51471--51530 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
51461 CAAAAAGGGC
* *
51471 AAAAATAAAAAC
1 AAAAAGAAAAAA
**
51483 AAAAAG-AAGCA
1 AAAAAGAAAAAA
*
51494 AAAAAGAACAAA
1 AAAAAGAAAAAA
51506 AAAAAGAACAAAAA
1 AAAAAG-A-AAAAA
51520 AAAAAGAAAAA
1 AAAAAGAAAAA
51531 GGGACAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.83, C:0.07, G:0.08, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:51530 original size:23 final size:23
Alignment explanation
Indices: 51469--51523 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
51459 AACAAAAAGG
* *
51469 GCAAAAATAAA-AACAAAAAGAA
1 GCAAAAAAAAACAAAAAAAAGAA
*
51491 GCAAAAAAGAACAAAAAAAAGAA
1 GCAAAAAAAAACAAAAAAAAGAA
51514 -CAAAAAAAAA
1 GCAAAAAAAAA
51524 AGAAAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (23 bp):
GCAAAAAAAAACAAAAAAAAGAA
Found at i:52156 original size:22 final size:22
Alignment explanation
Indices: 52131--52185 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
52121 AAGCACCCAT
52131 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
52153 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
52175 TACACCTTTGA
1 CAAACCTTTGA
52186 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:53274 original size:106 final size:106
Alignment explanation
Indices: 53148--54423 Score: 2016
Period size: 106 Copynumber: 12.0 Consensus size: 106
53138 ATATCGGGCC
* * * * *
53148 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
53213 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53254 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
53319 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53360 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
53425 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * ** * ** *
53466 ACTCAAGACAACGAAAGTTCAACTTCATAACGAAGGGACCACAAGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
53531 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
53572 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
53637 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
53678 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
53743 AATTTTGGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
53784 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTAAACAAACAATTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
53849 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
53890 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
53955 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
53996 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
54061 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
54102 ACTCCAGACAATGCAAATTCAACTTCACGACGAAGGGACCGCTTGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
54167 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
54208 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
54273 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
54314 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
54379 GA-TTCTAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
54420 ACTC
1 ACTC
54424 GGAACAATGC
Statistics
Matches: 1092, Mismatches: 76, Indels: 4
0.93 0.06 0.00
Matches are distributed among these distances:
105 3 0.00
106 1089 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:55263 original size:37 final size:37
Alignment explanation
Indices: 55174--55277 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
55164 CTTTTCGTCC
* * *
55174 TACTAGGATTCAAACTCCTAAAAATATGATATAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
55211 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
55248 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
55278 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:55711 original size:23 final size:23
Alignment explanation
Indices: 55660--55721 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
55650 TAGCCCTTAT
* *
55660 TATTTATATGTATATATTTAATTA
1 TATTT-TATTTATTTATTTAATTA
55684 TATTTTATTTATTTATTT-ATTA
1 TATTTTATTTATTTATTTAATTA
*
55706 TAATTTTTTTTCATTT
1 T-ATTTTATTT-ATTT
55722 TTCTTTGCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 5 0.15
23 19 0.58
24 9 0.27
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTTATTTATTTATTTAATTA
Found at i:55974 original size:21 final size:20
Alignment explanation
Indices: 55950--56000 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
55940 ACTATTTAGT
55950 ATTTTATTATATTATACATAC
1 ATTTT-TTATATTATACATAC
* * *
55971 ATTTTTATATTTTATATATAT
1 ATTTTT-TATATTATACATAC
55992 ATTTTTTAT
1 ATTTTTTAT
56001 TATTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTTATATTATACATAC
Found at i:55997 original size:22 final size:22
Alignment explanation
Indices: 55972--56040 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
55962 TATACATACA
55972 TTTTTATATTTTATATATATAT
1 TTTTTATATTTTATATATATAT
*
55994 TTTTTATTATTTTATTTATATTAT
1 TTTTTA-TATTTTATATATA-TAT
* *
56018 TTATT-TATTTT-CAT-TATAT
1 TTTTTATATTTTATATATATAT
56037 TTTT
1 TTTT
56041 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.15
20 2 0.05
21 1 0.03
22 12 0.30
23 12 0.30
24 7 0.17
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTATATTTTATATATATAT
Found at i:56037 original size:28 final size:28
Alignment explanation
Indices: 55975--56039 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
55965 ACATACATTT
*
55975 TTATATTTTATATATATATTTTTTATTA
1 TTATATTTTATATATATATTTTTTATCA
* *
56003 TTTTA-TTTATATTATTTATTTATTT-TCA
1 TTATATTTTATA-TATATATTT-TTTATCA
56031 TTATATTTT
1 TTATATTTT
56040 TAGTTTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
27 6 0.20
28 18 0.60
29 6 0.20
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATATTTTATATATATATTTTTTATCA
Found at i:56147 original size:20 final size:19
Alignment explanation
Indices: 56123--56178 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
56113 TTTTATCTTC
56123 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
56142 ATTTTATTTT-TTTTCA-TCA
1 A-TTTATTTTATTTT-ATTCA
*
56161 AATTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
56179 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
18 7 0.23
19 11 0.35
20 13 0.42
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:56925 original size:24 final size:24
Alignment explanation
Indices: 56885--56941 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
56875 ACCAACCAAA
*
56885 CATAGGAATGTGGGATTCCCTTCC
1 CATAGGAATGTGAGATTCCCTTCC
*
56909 CATGGGAATGTGAGATTCCCTTCC
1 CATAGGAATGTGAGATTCCCTTCC
56933 CATAGGAAT
1 CATAGGAAT
56942 CCCACAATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (24 bp):
CATAGGAATGTGAGATTCCCTTCC
Found at i:58823 original size:180 final size:180
Alignment explanation
Indices: 58514--58873 Score: 711
Period size: 180 Copynumber: 2.0 Consensus size: 180
58504 TTGATCCTTC
*
58514 AATTTCCTTCGTAATTGTGGATTTGACAACTAATCTTCAAAAATTGTTGTTTCCATTAATCATCG
1 AATTTCATTCGTAATTGTGGATTTGACAACTAATCTTCAAAAATTGTTGTTTCCATTAATCATCG
58579 TTTGTGAGATGCTTAAACTCACAGTTGTATATGATGTGCATAGTATGCAGACTATAACAATCATC
66 TTTGTGAGATGCTTAAACTCACAGTTGTATATGATGTGCATAGTATGCAGACTATAACAATCATC
58644 AACATAGGAGTATGAGTCAACATTAACATATATACATGTAACAACAGCGT
131 AACATAGGAGTATGAGTCAACATTAACATATATACATGTAACAACAGCGT
58694 AATTTCATTCGTAATTGTGGATTTGACAACTAATCTTCAAAAATTGTTGTTTCCATTAATCATCG
1 AATTTCATTCGTAATTGTGGATTTGACAACTAATCTTCAAAAATTGTTGTTTCCATTAATCATCG
58759 TTTGTGAGATGCTTAAACTCACAGTTGTATATGATGTGCATAGTATGCAGACTATAACAATCATC
66 TTTGTGAGATGCTTAAACTCACAGTTGTATATGATGTGCATAGTATGCAGACTATAACAATCATC
58824 AACATAGGAGTATGAGTCAACATTAACATATATACATGTAACAACAGCGT
131 AACATAGGAGTATGAGTCAACATTAACATATATACATGTAACAACAGCGT
58874 GAACGCATAA
Statistics
Matches: 179, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 179 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (180 bp):
AATTTCATTCGTAATTGTGGATTTGACAACTAATCTTCAAAAATTGTTGTTTCCATTAATCATCG
TTTGTGAGATGCTTAAACTCACAGTTGTATATGATGTGCATAGTATGCAGACTATAACAATCATC
AACATAGGAGTATGAGTCAACATTAACATATATACATGTAACAACAGCGT
Found at i:59040 original size:74 final size:74
Alignment explanation
Indices: 58953--59101 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
58943 GAATGATCAC
58953 TCACTCAAAGGTAGTCAAACAAGTGCTTGAACAATACAATCAGATGTAAATATGATAAAATTATG
1 TCACTCAAAGGTAGTCAAACAAGTGCTTGAACAATACAATCAGATGTAAATATGATAAAATTATG
59018 AACAAATAT
66 AACAAATAT
59027 TCACTCAAAGGTAGTCAAACAAGTGCTTGAACAATACAATCAGATGTAAATATGATAAAATTATG
1 TCACTCAAAGGTAGTCAAACAAGTGCTTGAACAATACAATCAGATGTAAATATGATAAAATTATG
59092 AACAAATAT
66 AACAAATAT
59101 T
1 T
59102 GATGTTGCAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (74 bp):
TCACTCAAAGGTAGTCAAACAAGTGCTTGAACAATACAATCAGATGTAAATATGATAAAATTATG
AACAAATAT
Found at i:59249 original size:27 final size:27
Alignment explanation
Indices: 59219--59274 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
59209 GATATCAAAT
*
59219 ATATTA-TAGTATAGTA-TTATATTTATA
1 ATATTATTA-TATAGCATTTATATTT-TA
59246 ATATTATTATATAGCATTTATATTTTA
1 ATATTATTATATAGCATTTATATTTTA
59273 AT
1 AT
59275 TATAGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (27 bp):
ATATTATTATATAGCATTTATATTTTA
Found at i:60036 original size:18 final size:17
Alignment explanation
Indices: 60009--60043 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
59999 TCAAGGGGCA
60009 ATGATTTTTTTAAAACC
1 ATGATTTTTTTAAAACC
60026 ATGATTTTTTTAAAACC
1 ATGATTTTTTTAAAACC
60043 A
1 A
60044 AATCTTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (17 bp):
ATGATTTTTTTAAAACC
Found at i:60306 original size:7 final size:7
Alignment explanation
Indices: 60296--60362 Score: 52
Period size: 7 Copynumber: 9.7 Consensus size: 7
60286 TTTTACTGTA
60296 TTTAATT
1 TTTAATT
60303 TTTAATT
1 TTTAATT
60310 ATTT-ATAT
1 -TTTAAT-T
*
60318 TTTATTT
1 TTTAATT
*
60325 TATTTATT
1 T-TTAATT
60333 TTT-ATT
1 TTTAATT
60339 TTTAA-T
1 TTTAATT
*
60345 GTTAATT
1 TTTAATT
60352 TTT-ATT
1 TTTAATT
60358 TTTAA
1 TTTAA
60363 GGAATCAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 17 0.35
7 21 0.44
8 10 0.21
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:60327 original size:16 final size:15
Alignment explanation
Indices: 60294--60359 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 15
60284 TATTTTACTG
*
60294 TATTTAATTTTTA-AT
1 TATTT-ATTTTTATTT
60309 TATTTATATTTTATTT
1 TATTTAT-TTTTATTT
60325 TATTTATTTTTATTTT
1 TATTTATTTTTA-TTT
60341 TAATGTTAATTTTTATTT
1 T-AT-TT-ATTTTTATTT
60359 T
1 T
60360 TAAGGAATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.05
15 15 0.34
16 12 0.27
17 2 0.05
18 6 0.14
19 7 0.16
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
TATTTATTTTTATTT
Found at i:60331 original size:20 final size:20
Alignment explanation
Indices: 60302--60361 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
60292 TGTATTTAAT
60302 TTTTAATTATTTATATTTTA
1 TTTTAATTATTTATATTTTA
* *
60322 TTTTATTTATTTTTATTTTTAA
1 TTTTAATTATTTATA-TTTT-A
*
60344 TGTTAATT-TTTAT-TTTTA
1 TTTTAATTATTTATATTTTA
60362 AGGAATCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 13 0.39
21 8 0.24
22 7 0.21
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTAATTATTTATATTTTA
Found at i:63204 original size:106 final size:106
Alignment explanation
Indices: 62870--63220 Score: 537
Period size: 105 Copynumber: 3.3 Consensus size: 106
62860 TCGATGACAA
*
62870 AAACTTTTCAGTGATATATCATTTCATTTCAGAAAAACGCCATTTTCTCATAGACCATTTAATGC
1 AAACTTTTCAGTGATATATCATTTCATTTCAGAAAAACGTCATTTTCTCATAGACCATTTAATGC
62935 ACAATG-AAAAAACTTTCAGTGCCCAATTAATTCACTTTAG
66 ACAATGAAAAAAACTTTCAGTGCCCAATTAATTCACTTTAG
* * * *
62975 AAACTGTTCAGTGATATATCATTTCATTTTAGAAAAACGTTATTTTCTCATGGACCATTTAATGC
1 AAACTTTTCAGTGATATATCATTTCATTTCAGAAAAACGTCATTTTCTCATAGACCATTTAATGC
* *
63040 ACAATGAAAAAAA-ATTCAGTTCCCAATTAATTCACTTTAG
66 ACAATGAAAAAAACTTTCAGTGCCCAATTAATTCACTTTAG
* * *
63080 AGACTTTTCAGTGATATATCATTTCATTTCAG-AAAACGTCATTTTCTCATATATCATTTAATGC
1 AAACTTTTCAGTGATATATCATTTCATTTCAGAAAAACGTCATTTTCTCATAGACCATTTAATGC
* *
63144 ACAATGAAAAAAACTCTTTAGTGCCCAATTACTTCACTTTAG
66 ACAATGAAAAAAACT-TTCAGTGCCCAATTAATTCACTTTAG
* * *
63186 AAACTTTTCAATGATATATAACTTCATTTCAGAAA
1 AAACTTTTCAGTGATATATCATTTCATTTCAGAAA
63221 CTTTTCAGTG
Statistics
Matches: 220, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
104 41 0.19
105 120 0.55
106 57 0.26
107 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (106 bp):
AAACTTTTCAGTGATATATCATTTCATTTCAGAAAAACGTCATTTTCTCATAGACCATTTAATGC
ACAATGAAAAAAACTTTCAGTGCCCAATTAATTCACTTTAG
Found at i:63252 original size:32 final size:31
Alignment explanation
Indices: 63174--63252 Score: 113
Period size: 32 Copynumber: 2.5 Consensus size: 31
63164 GTGCCCAATT
63174 ACTTCACTTTAGAAACTTTTCAATGATATATA
1 ACTTCA-TTTAGAAACTTTTCAATGATATATA
*
63206 ACTTCATTTCAGAAACTTTTCAGTGATATATA
1 ACTTCATTT-AGAAACTTTTCAATGATATATA
*
63238 ACTTTATTGTAGAAA
1 ACTTCATT-TAGAAA
63253 AACTTCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.07
32 39 0.91
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
ACTTCATTTAGAAACTTTTCAATGATATATA
Found at i:66707 original size:29 final size:29
Alignment explanation
Indices: 66663--66736 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
66653 TGCATATTTG
* ** *
66663 CATTCTGCACCTGCATTTTATTTATTTAAA
1 CATTCT-CACATGCATTCAATTTATTCAAA
* *
66693 CATTTTCACATGCATTCAATTTATTCAAG
1 CATTCTCACATGCATTCAATTTATTCAAA
66722 CATTCTCACATGCAT
1 CATTCTCACATGCAT
66737 CATTCATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (29 bp):
CATTCTCACATGCATTCAATTTATTCAAA
Found at i:68152 original size:7 final size:6
Alignment explanation
Indices: 68142--68255 Score: 56
Period size: 7 Copynumber: 17.3 Consensus size: 6
68132 AGTTCAAATC
*
68142 AAAGCAA AAAGAA AAA-AA GAAAGAA AGAA-AA AAAGCAA AGAAAAA AATAGAA
1 AAAG-AA AAAGAA AAAGAA -AAAGAA A-AAGAA AAAG-AA A-AAGAA AA-AGAA
*
68194 TAAAGAA AAA-AGA AAAGAGC AAAGAA AAA-AA AAGCAGAAA GAAAGAA
1 -AAAGAA AAAGA-A AAAGA-A AAAGAA AAAGAA AA--AG-AA -AAAGAA
68241 AAAGAA GAAAGAA AA
1 AAAGAA -AAAGAA AA
68256 TGTATCAAGA
Statistics
Matches: 87, Mismatches: 4, Indels: 33
0.70 0.03 0.27
Matches are distributed among these distances:
5 9 0.10
6 31 0.36
7 37 0.43
8 6 0.07
9 2 0.02
10 2 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:68175 original size:17 final size:16
Alignment explanation
Indices: 68148--68255 Score: 99
Period size: 17 Copynumber: 6.2 Consensus size: 16
68138 AATCAAAGCA
68148 AAAAGAAAAAAAGAAAG
1 AAAA-AAAAAAAGAAAG
*
68165 AAAGAAAAAAAGCAAAG
1 AAAAAAAAAAAG-AAAG
* *
68182 AAAAAAATAGAATAAAG
1 AAAAAAA-AAAAGAAAG
68199 AAAAAAGAAAAGAGCAAAG
1 AAAAAA-AAAA-AG-AAAG
*
68218 AAAAAAAAAGCAGAAAG
1 AAAAAAAAA-AAGAAAG
*
68235 AAAGAAAAAGAAGAAAG
1 AAA-AAAAAAAAGAAAG
68252 AAAA
1 AAAA
68256 TGTATCAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.12
17 41 0.55
18 15 0.20
19 10 0.13
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAAAGAAAG
Found at i:68205 original size:29 final size:29
Alignment explanation
Indices: 68148--68254 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 29
68138 AATCAAAGCA
68148 AAAAGAAAAAAAGAAAGAAAGAAAAAAAG
1 AAAAGAAAAAAAGAAAGAAAGAAAAAAAG
* * *
68177 CAAAGAAAAAAATAGAATAAAG-AAAAAAG
1 AAAAGAAAAAAAGA-AAGAAAGAAAAAAAG
* *
68206 AAAAGAGCAAAGAAA-AAA-AAAG-CAGAAAG
1 AAAAGA--AAA-AAAGAAAGAAAGAAAAAAAG
68235 -AAAGAAAAAGAAGAAAGAAA
1 AAAAGAAAAA-AAGAAAGAAA
68255 ATGTATCAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.02
26 5 0.08
27 3 0.05
28 8 0.12
29 33 0.51
30 8 0.12
31 4 0.06
32 3 0.05
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.02
Consensus pattern (29 bp):
AAAAGAAAAAAAGAAAGAAAGAAAAAAAG
Found at i:68209 original size:53 final size:52
Alignment explanation
Indices: 68142--68255 Score: 135
Period size: 53 Copynumber: 2.2 Consensus size: 52
68132 AGTTCAAATC
* *
68142 AAAGCAAAAAGAAAAAAAG-AAAGAAAGAAAAAAAGC-AAAGAAA-AAAATAGAAT
1 AAAGAAAAAAG-AAAAAAGCAAAG-AA-AAAAAAAGCAAAAGAAAGAAAA-AGAAG
*
68195 AAAGAAAAAAGAAAAGAGCAAAGAAAAAAAAAGCAGAAAGAAAGAAAAAGAAG
1 AAAGAAAAAAGAAAAAAGCAAAGAAAAAAAAAGCA-AAAGAAAGAAAAAGAAG
68248 AAAGAAAA
1 AAAGAAAA
68256 TGTATCAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
51 9 0.17
52 8 0.15
53 33 0.61
54 4 0.07
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (52 bp):
AAAGAAAAAAGAAAAAAGCAAAGAAAAAAAAAGCAAAAGAAAGAAAAAGAAG
Found at i:68235 original size:36 final size:38
Alignment explanation
Indices: 68147--68241 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 38
68137 AAATCAAAGC
*
68147 AAAAAGAAAAAAAGAAAGAAAGAAAAAAAGCAAAGAAAA
1 AAAAAG-AAGAAAGAAAGAAAGAAAAAAAGCAAAGAAAA
* * *
68186 AAATAGAATAAAGAAA-AAAG-AAAAGAGCAAAGAAAA
1 AAAAAGAAGAAAGAAAGAAAGAAAAAAAGCAAAGAAAA
*
68222 AAAAAGCAGAAAGAAAGAAA
1 AAAAAGAAGAAAGAAAGAAA
68242 AAGAAGAAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
36 28 0.57
37 7 0.14
38 9 0.18
39 5 0.10
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (38 bp):
AAAAAGAAGAAAGAAAGAAAGAAAAAAAGCAAAGAAAA
Found at i:69825 original size:24 final size:23
Alignment explanation
Indices: 69791--69865 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
69781 TTTTTTAATA
69791 ATAAAAAAATTCTTTAATATTCA-
1 ATAAAAAAATTCTTTAATATT-AT
*
69814 ATAAAAAAAATTCTTTAA-AATAT
1 AT-AAAAAAATTCTTTAATATTAT
*
69837 ATTAAAAAATTCTTTAATA-TAT
1 ATAAAAAAATTCTTTAATATTAT
*
69859 ATTAAAA
1 ATAAAAA
69866 TACATTTTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 25 0.53
23 7 0.15
24 15 0.32
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAAAAAAATTCTTTAATATTAT
Found at i:69846 original size:22 final size:22
Alignment explanation
Indices: 69818--69865 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
69808 TATTCAATAA
69818 AAAAAATTCTTTAAAATATATT
1 AAAAAATTCTTTAAAATATATT
*
69840 AAAAAATTCTTTAATATATATT
1 AAAAAATTCTTTAAAATATATT
69862 AAAA
1 AAAA
69866 TACATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATTCTTTAAAATATATT
Found at i:71772 original size:2 final size:2
Alignment explanation
Indices: 71765--71791 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71755 CAGACTATTC
71765 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
71792 AGTTTGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73898 original size:194 final size:193
Alignment explanation
Indices: 73541--73951 Score: 461
Period size: 194 Copynumber: 2.1 Consensus size: 193
73531 GTGTTTTGCT
* * * *
73541 ACAATATCTATTTCGTCACATATAAGTTGATTTTAATGCATTAATTGTGACAATATAAATTATCA
1 ACAATATTTCTTTCGTCACATATAAGTTGATTTTAATGCATTAATCGCGACAATATAAATTATCA
**
73606 ATAACGAAATCTTATTTAATTTAGTGACTTAACCAACTGTCATAGAATATAAATTATAAAGTGAC
66 ATAACGAAATCTTACATAATTTAGTGACTTAACCAACTGTCATAGAATATAAATTATAAAGTGAC
* * * * * *
73671 GTTATGCATAGACGTCATTCATAATATTATTAGGTAAC-ATTTATATTATGTCACTAAAAATGTG
131 GTTATACATAAACGTCATCCATAATACTATTAGGTAACGA--TATACTACGTCACTAAAAATGTG
* * *
73735 ACAATATTTCTTTCGTCACATATAGGTTGATTTTAATGTATT-ATCCGCGACGATATAAATTATC
1 ACAATATTTCTTTCGTCACATATAAGTTGATTTTAATGCATTAAT-CGCGACAATATAAATTATC
* ** ** * * *
73799 AATAACGAAATTTTACATAATTTAGTGA-TATAATTAGTTGTCATTGAATATTAATTATATAGTG
65 AATAACGAAATCTTACATAATTTAGTGACT-TAACCAACTGTCATAGAATATAAATTATAAAGTG
* * ** * * *
73863 ACGTTATATATAAATGTCATCCATGCTACTATTAGGTGACGATATACTACGTTACTAACAATGTG
129 ACGTTATACATAAACGTCATCCATAATACTATTAGGTAACGATATACTACGTCACTAAAAATGTG
* *
73928 AAAAT-TTTCTTTTCGTCACGTATA
1 ACAATATTTC-TTTCGTCACATATA
73952 CAATGAAATT
Statistics
Matches: 181, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
192 4 0.02
193 39 0.22
194 137 0.76
195 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (193 bp):
ACAATATTTCTTTCGTCACATATAAGTTGATTTTAATGCATTAATCGCGACAATATAAATTATCA
ATAACGAAATCTTACATAATTTAGTGACTTAACCAACTGTCATAGAATATAAATTATAAAGTGAC
GTTATACATAAACGTCATCCATAATACTATTAGGTAACGATATACTACGTCACTAAAAATGTG
Found at i:74607 original size:21 final size:20
Alignment explanation
Indices: 74575--74614 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
74565 GAGGCAATAG
74575 TTTTTCATTTTTCAAAATTC
1 TTTTTCATTTTTCAAAATTC
* *
74595 TTTTTGATATTTTTAAAATT
1 TTTTTCAT-TTTTCAAAATT
74615 TTTGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTCATTTTTCAAAATTC
Found at i:74793 original size:44 final size:44
Alignment explanation
Indices: 74730--74818 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
74720 TATTGGAGCA
*
74730 AGAAATGATAAATGTTGGGGAATTTTTTAAGGCCCATACCATCC
1 AGAAATGATAAATGTTGGGGAATTTTTGAAGGCCCATACCATCC
* *
74774 AGAAATGATAAATGTTGGGGCATTTTTGAAGGCCCATATCATCC
1 AGAAATGATAAATGTTGGGGAATTTTTGAAGGCCCATACCATCC
74818 A
1 A
74819 AGAATACAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (44 bp):
AGAAATGATAAATGTTGGGGAATTTTTGAAGGCCCATACCATCC
Found at i:77076 original size:167 final size:168
Alignment explanation
Indices: 76650--77076 Score: 418
Period size: 167 Copynumber: 2.5 Consensus size: 168
76640 AAATTTTGAA
* * * * * *
76650 AAAATTGATCTTATTTGAGATTGTTGCTCTCCAAACAAAATTTCGTCTCGCTTGAGAC-ATTTTC
1 AAAATTGATCTCACTTGAGATTGTTTCTTTCAAAAC-AAACTTCGTCTCGCTTGAGACAATTTTC
** * *
76714 TTTTAAAACATAAGCCTTTGAGATT-ATTTATCTAAAAAAAAATTTCGTCTCGCTTGAGACAATT
65 CCTTAAAACATAA-CATTTGAGATTGTTTTATCTAAAAAAAAATTTCGTCTCGCTTGAGACAATT
* ** ** ** *
76778 TCCCTTGAGATGCAAATTTTGAATTTGTTTTACTTGAAAC
129 CCCCCGGAGACACAAATTTCAAAGTTGTTTTACTTGAAAC
* * * * * * * * *
76818 AAAGTTGACCTCACTTGAGATT-ATT-TTTCATTAAATAAACTTTGTCTCACTTAAGACAGTCTT
1 AAAATTGATCTCACTTGAGATTGTTTCTTTCA--AAACAAACTTCGTCTCGCTTGAGACAATTTT
* * * * * *
76881 -CCTTAAGACACGAACATTTGAGATTGTTTTTTCTCAAAACAAATTTCGTCTCGCTTGAGATAAT
64 CCCTTAAAACA-TAACATTTGAGATTGTTTTATCTAAAAAAAAATTTCGTCTCGCTTGAGACAAT
76945 TCCCCCGGA-ACACAAATTTCAAAGTTGTTTTACTTGAAAC
128 TCCCCCGGAGACACAAATTTCAAAGTTGTTTTACTTGAAAC
*
76985 AAAATTAATCTCACTTGAGATTGTTTCTTTCAAAACAAA-TTCGTCTCGCTTGAGACAATTTTCC
1 AAAATTGATCTCACTTGAGATTGTTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACAATTTTCC
* * *
77049 CTCAAAACATAAAATTTAGAAATTGTTT
66 CTTAAAACATAACATTT-GAGATTGTTT
77077 CACTTGAAAC
Statistics
Matches: 202, Mismatches: 48, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
166 27 0.13
167 103 0.51
168 67 0.33
169 5 0.02
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (168 bp):
AAAATTGATCTCACTTGAGATTGTTTCTTTCAAAACAAACTTCGTCTCGCTTGAGACAATTTTCC
CTTAAAACATAACATTTGAGATTGTTTTATCTAAAAAAAAATTTCGTCTCGCTTGAGACAATTCC
CCCGGAGACACAAATTTCAAAGTTGTTTTACTTGAAAC
Found at i:77082 original size:102 final size:101
Alignment explanation
Indices: 76898--77092 Score: 261
Period size: 102 Copynumber: 1.9 Consensus size: 101
76888 ACACGAACAT
* * ** *
76898 TTGAGATTGTTTTTTCTCAAAACAAATTTCGTCTCGCTTGAGATAATTCCCCCGGAACACAAATT
1 TTGAGATTGTTTCTTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTCCCCCAAAACAAAAATT
* *
76963 TCAAAGTTGTTTTACTTGAAACAAAATTAATCTCAC
66 TCAAAATTGTTTCACTTGAAACAAAATTAATCTCAC
*
76999 TTGAGATTGTTTCTT-TCAAAACAAA-TTCGTCTCGCTTGAGACAATTTTCCCTCAAAACATAAA
1 TTGAGATTGTTTCTTCTCAAAACAAATTTCGTCTCGCTTGAGACAA--TTCCCCCAAAACA-AAA
77062 ATTT-AGAAATTGTTTCACTTGAAACAAAATT
63 ATTTCA-AAATTGTTTCACTTGAAACAAAATT
77093 GATAACATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
99 18 0.22
100 10 0.12
101 25 0.30
102 29 0.35
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (101 bp):
TTGAGATTGTTTCTTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTCCCCCAAAACAAAAATT
TCAAAATTGTTTCACTTGAAACAAAATTAATCTCAC
Found at i:77482 original size:61 final size:61
Alignment explanation
Indices: 77406--77528 Score: 174
Period size: 61 Copynumber: 2.0 Consensus size: 61
77396 TTATCTTCAG
* * * *
77406 ACAATTAAACTTCCTCAACAAGAAGGAACATCATTGTCTTCAGATTCACTATCCTTCAAGA
1 ACAATTAAACTTCCTCAACAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGA
* * * *
77467 ACAATTAGACTTCCTCATCAAGAAGGAATAACATTATCTTCAGATTCCCAATCCTACAAGA
1 ACAATTAAACTTCCTCAACAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGA
77528 A
1 A
77529 TGACTAGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (61 bp):
ACAATTAAACTTCCTCAACAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGA
Found at i:77542 original size:61 final size:60
Alignment explanation
Indices: 77414--77556 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 60
77404 AGACAATTAA
* * * * *
77414 ACTTCCTCAACAAGAAGGAACATCATTGTCTTCAGATTCACTATCCTTCAAGAACAATTAG
1 ACTTCCTC-ACAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGAACAACTAG
* * **
77475 ACTTCCTCATCAAGAAGGAATAACATTATCTTCAGATTCCCAATCCTACAAGAATGACTAG
1 ACTTCCTCA-CAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGAACAACTAG
**
77536 TTTTCCTCACAAAGAAGGAAC
1 ACTTCCTCAC-AAGAAGGAAC
77557 CATGTCAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
60 2 0.03
61 66 0.97
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (60 bp):
ACTTCCTCACAAGAAGGAACAACATTATCTTCAGATTCACAATCCTACAAGAACAACTAG
Found at i:81872 original size:15 final size:15
Alignment explanation
Indices: 81852--81886 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
81842 CTTGTAGAGA
81852 AGCTTAGACCAAATT
1 AGCTTAGACCAAATT
81867 AGCTTAGACCAAATT
1 AGCTTAGACCAAATT
81882 AGCTT
1 AGCTT
81887 TGAGTTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (15 bp):
AGCTTAGACCAAATT
Found at i:82731 original size:50 final size:50
Alignment explanation
Indices: 82656--82752 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
82646 TTGTTAAAAC
* * * *
82656 AAAGAGTAAATTCAATAGGGAGTATCGATACGCCTTCAAGGAGTATCGAT
1 AAAGAGTAAATTCAACAAGGAGTATCGATACACATTCAAGGAGTATCGAT
82706 AAAGAGTAAATTCAACAAGGAGTATCGATACACATTCAAGGAGTATC
1 AAAGAGTAAATTCAACAAGGAGTATCGATACACATTCAAGGAGTATC
82753 AATACTGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (50 bp):
AAAGAGTAAATTCAACAAGGAGTATCGATACACATTCAAGGAGTATCGAT
Found at i:84059 original size:36 final size:37
Alignment explanation
Indices: 84019--84096 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 37
84009 TGTCCTGAAC
* * *
84019 GTAATGCGTTA-GGTTTGTCGTTTTTATCTTCTTAAT
1 GTAATGCGTTATGGTTTGTCATTATTATCTCCTTAAT
** *
84055 GTAAT-TTTTATGGTTTGTTATTATTATCTCCTTAAT
1 GTAATGCGTTATGGTTTGTCATTATTATCTCCTTAAT
84091 GTAATG
1 GTAATG
84097 TTTTATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
35 3 0.09
36 31 0.91
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.54
Consensus pattern (37 bp):
GTAATGCGTTATGGTTTGTCATTATTATCTCCTTAAT
Found at i:88061 original size:182 final size:182
Alignment explanation
Indices: 87783--88177 Score: 551
Period size: 182 Copynumber: 2.2 Consensus size: 182
87773 AAAGCGCTAT
*
87783 CGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTGTGTGAATTTAAAAGAGAAA
1 CGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTGTGTGAATTTAAAAAAGAAA
* * * *
87848 CAATTTTAGCGCCTACAAAGTGTCTATACTTTATAACAATGTATCGATCCACAATGATATAACAG
66 CAATTTTAGCGCCTACAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAG
* * *
87913 GTAAAAATATGACAAAA-CATGTCTCTAAAGGACAAAATCGATATAGAGCGAC
131 GTAAAAATATGACAAAATC-GGTCTCGAAAGGACAAAATCGATAAAGAGCGAC
*
87965 CGAATATATTGAAAGTGTCGATATTTTAATATAAGTATCGACACAT-TGTGAATTTAAAAAAGAA
1 CGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC-TGTGTGAATTTAAAAAAGAA
** * * *
88029 GTAATTTTAGTGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCATAACGATATAACA
65 ACAATTTTAGCGCCTACAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACGATATAACA
* * * * * *
88094 GGTAAAAATATGATAAAATCGGTCTCGAAATGACAAAATCGGTAAAGCGCTAT
130 GGTAAAAATATGACAAAATCGGTCTCGAAAGGACAAAATCGATAAAGAGCGAC
* * *
88147 CGGATATATTGAAATTGTTGATACTTTAATA
1 CGAATATATTGAAAGTGTCGATACTTTAATA
88178 AATACGCGTA
Statistics
Matches: 187, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
182 185 0.99
183 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.30
Consensus pattern (182 bp):
CGAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTGTGTGAATTTAAAAAAGAAA
CAATTTTAGCGCCTACAAAGTATCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAG
GTAAAAATATGACAAAATCGGTCTCGAAAGGACAAAATCGATAAAGAGCGAC
Done.