Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007903.1 Hibiscus syriacus cultivar Beakdansim tig00110294_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: 402018
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3898 original size:37 final size:37
Alignment explanation
Indices: 3847--3924 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
3837 TTCGTTTGAA
* *
3847 TTGG-TTGTAGTAGATCTCTTGTACTAGTAATTCATT
1 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
3883 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
1 TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
3920 TTGGT
1 TTGGT
3925 CAAAGCGATC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 4 0.10
37 35 0.90
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (37 bp):
TTGGTTTGTACTAGATCTCTTGTACTAGCAATTCATT
Found at i:22240 original size:29 final size:29
Alignment explanation
Indices: 22198--22254 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
22188 AACACTCTAC
22198 GATATTGAGTCGATTATATTATTGTCTTT
1 GATATTGAGTCGATTATATTATTGTCTTT
22227 GATATTGAGTCGATTATATTATTGTCTT
1 GATATTGAGTCGATTATATTATTGTCTT
22255 ATCAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.51
Consensus pattern (29 bp):
GATATTGAGTCGATTATATTATTGTCTTT
Found at i:27802 original size:13 final size:13
Alignment explanation
Indices: 27798--27860 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
27788 CCGTTTACCC
27798 GACCCGACCCGTT
1 GACCCGACCCGTT
*
27811 TACCCGACCCGTT
1 GACCCGACCCGTT
27824 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
27842 GACCCGACCCGTT
1 GACCCGACCCGTT
27855 GACCCG
1 GACCCG
27861 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.26
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:27821 original size:18 final size:18
Alignment explanation
Indices: 27776--27821 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
27766 ACCGGTCACA
*
27776 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
27794 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
27812 ACCCGACCCG
1 ACCCGACCCG
27822 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:27821 original size:31 final size:31
Alignment explanation
Indices: 27780--27860 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
27770 GTCACAACCC
* *
27780 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
27811 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
27842 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
27861 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:27827 original size:8 final size:8
Alignment explanation
Indices: 27816--27887 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
27806 CCGTTTACCC
27816 GACCCGTT
1 GACCCGTT
*
27824 GACCCGACTC
1 GACCCG--TT
*
27834 GACTCGTT
1 GACCCGTT
27842 GACCC---
1 GACCCGTT
27847 GACCCGTT
1 GACCCGTT
27855 GACCCGTT
1 GACCCGTT
27863 GA-CCGTT
1 GACCCGTT
27870 GACCCGTT
1 GACCCGTT
27878 GA-CCGTT
1 GACCCGTT
27885 GAC
1 GAC
27888 TACTGTTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 5 0.09
7 14 0.26
8 28 0.53
10 6 0.11
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:27836 original size:18 final size:18
Alignment explanation
Indices: 27815--27849 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
27805 CCCGTTTACC
27815 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
27833 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
27850 CCGTTGACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:27870 original size:7 final size:7
Alignment explanation
Indices: 27850--27887 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
27840 TTGACCCGAC
27850 CCGTTGA
1 CCGTTGA
27857 CCCGTTGA
1 -CCGTTGA
27865 CCGTTGA
1 CCGTTGA
27872 CCCGTTGA
1 -CCGTTGA
27880 CCGTTGA
1 CCGTTGA
27887 C
1 C
27888 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:27870 original size:15 final size:15
Alignment explanation
Indices: 27850--27887 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
27840 TTGACCCGAC
27850 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
27865 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
27880 CCGTTGAC
1 CCGTTGAC
27888 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:29012 original size:18 final size:18
Alignment explanation
Indices: 28986--29020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28976 TCGAAAGGAC
*
28986 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
29004 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
29021 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:32802 original size:13 final size:13
Alignment explanation
Indices: 32798--32860 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
32788 CCGTTTACCC
32798 GACCCGACCCGTT
1 GACCCGACCCGTT
*
32811 TACCCGACCCGTT
1 GACCCGACCCGTT
32824 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
32842 GACCCGACCCGTT
1 GACCCGACCCGTT
32855 GACCCG
1 GACCCG
32861 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.26
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:32821 original size:18 final size:18
Alignment explanation
Indices: 32776--32821 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
32766 ACCGGTCACA
*
32776 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
32794 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
32812 ACCCGACCCG
1 ACCCGACCCG
32822 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:32821 original size:31 final size:31
Alignment explanation
Indices: 32780--32860 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
32770 GTCACAACCC
* *
32780 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
32811 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
32842 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
32861 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:32827 original size:8 final size:8
Alignment explanation
Indices: 32816--32886 Score: 64
Period size: 7 Copynumber: 9.4 Consensus size: 8
32806 CCGTTTACCC
32816 GACCCGTT
1 GACCCGTT
*
32824 GACCCGACTC
1 GACCCG--TT
*
32834 GACTCGTT
1 GACCCGTT
32842 GACCC---
1 GACCCGTT
32847 GACCCGTT
1 GACCCGTT
32855 GACCCGTT
1 GACCCGTT
32863 GA-CCGTT
1 GACCCGTT
32870 GA-CCGTT
1 GACCCGTT
32877 GA-CCGTT
1 GACCCGTT
32884 GAC
1 GAC
32887 TACTGTTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.09
7 21 0.40
8 21 0.40
10 6 0.11
ACGTcount: A:0.15, C:0.37, G:0.25, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:32836 original size:18 final size:18
Alignment explanation
Indices: 32815--32849 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32805 CCCGTTTACC
32815 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
32833 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
32850 CCGTTGACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:32870 original size:7 final size:7
Alignment explanation
Indices: 32850--32886 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
32840 TTGACCCGAC
32850 CCGTTGA
1 CCGTTGA
32857 CCCGTTGA
1 -CCGTTGA
32865 CCGTTGA
1 CCGTTGA
32872 CCGTTGA
1 CCGTTGA
32879 CCGTTGA
1 CCGTTGA
32886 C
1 C
32887 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:34014 original size:18 final size:18
Alignment explanation
Indices: 33988--34022 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33978 TCGAAAGGAC
*
33988 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
34006 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
34023 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:39524 original size:52 final size:52
Alignment explanation
Indices: 39452--39585 Score: 173
Period size: 52 Copynumber: 2.6 Consensus size: 52
39442 ACCCTTTTTA
* * *
39452 TATAATAAAGAGAATAAAATAAATTTTTAAATATAAT-GAAAAATAATATATT
1 TATAGTAAAGAGAATAAAATAAATTTTTAAATATAATAAAAAAATAACAT-TT
*
39504 TATAGTAAAGAGACTAAAATAAATTTTTAAATATAATAAAAAAATAACATTT
1 TATAGTAAAGAGAATAAAATAAATTTTTAAATATAATAAAAAAATAACATTT
* * *
39556 TTTGGTAAAG-GAATTAAAATAAACTTTTAA
1 TATAGTAAAGAGAA-TAAAATAAATTTTTAA
39586 TCCTTGAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
51 2 0.03
52 60 0.83
53 10 0.14
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (52 bp):
TATAGTAAAGAGAATAAAATAAATTTTTAAATATAATAAAAAAATAACATTT
Found at i:39547 original size:25 final size:26
Alignment explanation
Indices: 39467--39557 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 26
39457 TAAAGAGAAT
*
39467 AAAATAA-ATTTTTAAATATAAT-GA
1 AAAATAACATTTTTAAATATAATAAA
* * * * *
39491 AAAATAATATATTTATAGTA-AAGAGACT
1 AAAATAACATTTTTA-AATATAATA-A-A
39519 AAAATAA-ATTTTTAAATATAATAAA
1 AAAATAACATTTTTAAATATAATAAA
39544 AAAATAACATTTTT
1 AAAATAACATTTTT
39558 TGGTAAAGGA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
25 15 0.29
26 13 0.25
27 9 0.18
28 7 0.14
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
AAAATAACATTTTTAAATATAATAAA
Found at i:49184 original size:24 final size:24
Alignment explanation
Indices: 49155--49202 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
49145 GATTAAATTT
*
49155 TATCATACTTCAATTAGTAGATTA
1 TATCATACTTCAATCAGTAGATTA
49179 TATCATACTTCAATCAGTAGATTA
1 TATCATACTTCAATCAGTAGATTA
49203 ACGTCCAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (24 bp):
TATCATACTTCAATCAGTAGATTA
Found at i:53247 original size:25 final size:26
Alignment explanation
Indices: 53196--53258 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
53186 TTTATATAGA
53196 TTATAAAAAATATATAATTCTTAAAAT
1 TTAT-AAAAATATATAATTCTTAAAAT
53223 TTATGAAAAATATATAATT-TT-AAAT
1 TTAT-AAAAATATATAATTCTTAAAAT
53248 TT-TAAAAATAT
1 TTATAAAAATAT
53259 TCCAAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 8 0.23
24 1 0.03
25 6 0.17
26 2 0.06
27 18 0.51
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
TTATAAAAATATATAATTCTTAAAAT
Found at i:66516 original size:3 final size:3
Alignment explanation
Indices: 66508--66535 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66498 AGAGGAAGAG
66508 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
66536 TTACACCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:72000 original size:22 final size:21
Alignment explanation
Indices: 71966--72006 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
71956 ATAATTATTT
71966 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
71987 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
72007 TTTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:73434 original size:19 final size:19
Alignment explanation
Indices: 73410--73447 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
73400 AATTATGGTT
73410 TCTTGAGATACCTCATAGA
1 TCTTGAGATACCTCATAGA
73429 TCTTGAGATACCTCATAGA
1 TCTTGAGATACCTCATAGA
73448 CTCGAGATCT
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:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (19 bp):
TCTTGAGATACCTCATAGA
Found at i:74518 original size:21 final size:20
Alignment explanation
Indices: 74480--74541 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
74470 TTCGAGTTTT
74480 TATTTAAATTTAATTATAAA
1 TATTTAAATTTAATTATAAA
74500 TATTTATAATGTT-ATTAT--A
1 TATTTA-AAT-TTAATTATAAA
74519 T-TTT-AATTCTAATT-TAAA
1 TATTTAAATT-TAATTATAAA
74537 TATTT
1 TATTT
74542 TTCTATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 15
0.70 0.00 0.30
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 3 0.09
18 5 0.14
19 5 0.14
20 6 0.17
21 8 0.23
22 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTAAATTTAATTATAAA
Found at i:78948 original size:2 final size:2
Alignment explanation
Indices: 78937--78974 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
78927 TGAAATTCTT
78937 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78975 AAATTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:93419 original size:22 final size:22
Alignment explanation
Indices: 93394--93436 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
93384 AAAGGGGGGT
93394 AAAGGCAAGTGATCGGGAAACA
1 AAAGGCAAGTGATCGGGAAACA
93416 AAAGGCAAGTGATCGGGAAAC
1 AAAGGCAAGTGATCGGGAAAC
93437 TTTAGACGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.14, G:0.33, T:0.09
Consensus pattern (22 bp):
AAAGGCAAGTGATCGGGAAACA
Found at i:96996 original size:20 final size:20
Alignment explanation
Indices: 96971--97016 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
96961 GTATTTATAT
96971 TGTTAAAATTTTTAATATTA
1 TGTTAAAATTTTTAATATTA
96991 TGTTAAAATTTTTAATATTA
1 TGTTAAAATTTTTAATATTA
97011 TGTTAA
1 TGTTAA
97017 CATTCATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
TGTTAAAATTTTTAATATTA
Found at i:101003 original size:26 final size:25
Alignment explanation
Indices: 100955--101004 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
100945 TAAAATAATT
*
100955 TTATTTTTATTTTTTTCTCACTTAA
1 TTATTTTTATTTTTTACTCACTTAA
100980 TTATTTTCTATTTTTTCACT-ACTTA
1 TTATTTT-TATTTTTT-ACTCACTTA
101005 CATCTCCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 13 0.59
27 2 0.09
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTTTTATTTTTTACTCACTTAA
Found at i:107259 original size:29 final size:29
Alignment explanation
Indices: 107214--107307 Score: 127
Period size: 29 Copynumber: 3.2 Consensus size: 29
107204 CATTACGTAG
* *
107214 CTCCTTCGACCGA-TGTCTTAGTCTAATAT
1 CTCCTTCGACC-ACTGTCTTCGTCGAATAT
*
107243 CTCCTTCGACCACTGTCTTCGTCGAGTAT
1 CTCCTTCGACCACTGTCTTCGTCGAATAT
* *
107272 CTCCTTCTACCGCTGTCTTCGTCGAATAT
1 CTCCTTCGACCACTGTCTTCGTCGAATAT
107301 CTCCTTC
1 CTCCTTC
107308 AGCCTACACT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.15, C:0.34, G:0.14, T:0.37
Consensus pattern (29 bp):
CTCCTTCGACCACTGTCTTCGTCGAATAT
Found at i:109393 original size:27 final size:26
Alignment explanation
Indices: 109359--109409 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
109349 TATTTTAAAT
** *
109359 ATTTTTTATTATATTTATATTTATGA
1 ATTTTTTAAGATATCTATATTTATGA
109385 ATTTATTTAAGATATCTATATTTAT
1 ATTT-TTTAAGATATCTATATTTAT
109410 CACGTGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
ATTTTTTAAGATATCTATATTTATGA
Found at i:110402 original size:14 final size:14
Alignment explanation
Indices: 110385--110412 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
110375 CTTTTAAAAA
110385 TATAATTTATTAAT
1 TATAATTTATTAAT
110399 TATAATTTATTAAT
1 TATAATTTATTAAT
110413 GATTAACCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATAATTTATTAAT
Found at i:120396 original size:16 final size:16
Alignment explanation
Indices: 120375--120414 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
120365 TGTATGTCGT
120375 TTCATTGTCATATTTG
1 TTCATTGTCATATTTG
120391 TTCATTGTCATATTTG
1 TTCATTGTCATATTTG
*
120407 TTTATTGT
1 TTCATTGT
120415 TTGAGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.60
Consensus pattern (16 bp):
TTCATTGTCATATTTG
Found at i:124219 original size:15 final size:17
Alignment explanation
Indices: 124187--124226 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
124177 TGCACCAGCA
*
124187 ATAAAAAGAATAACTAG
1 ATAAAAAGAATAAATAG
124204 A-AAAAAGAA-AAATAG
1 ATAAAAAGAATAAATAG
124219 ATAAAAAG
1 ATAAAAAG
124227 GCATAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 14 0.67
17 1 0.05
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (17 bp):
ATAAAAAGAATAAATAG
Found at i:127380 original size:21 final size:21
Alignment explanation
Indices: 127337--127377 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
127327 TGTCGCCGTA
* *
127337 TTTCCTTCTCTTCTTTCTTTC
1 TTTCCTTCTCCTCATTCTTTC
127358 TTTCCTTCTTCCTCATTCTT
1 TTTCCTTC-TCCTCATTCTT
127378 CTTGTTGCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTCCTTCTCCTCATTCTTTC
Found at i:132219 original size:15 final size:15
Alignment explanation
Indices: 132185--132221 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
132175 TGAGACATTA
*
132185 CCCGCCCCACATCTG
1 CCCGCCCCACATCCG
132200 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
*
132215 TCCGCCC
1 CCCGCCC
132222 AGCTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.65, G:0.14, T:0.11
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:139938 original size:60 final size:61
Alignment explanation
Indices: 139886--140004 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 61
139876 AATTAATTTC
* * *
139886 TAAA-TTTCTAAATATTTTAATTTCACCCTTAAACTTTAAT-TATTATTCTAAATT-AGTCCT
1 TAAACTTT-TAAACATTTTAATTTCACCCTTAAACTATAATCT-TCATTCTAAATTAAGTCCT
* * *
139946 TAAACTTTTGAACATTTTAGTTTCATCCTTAAACTATAATCTTCATTCTAAATT-AGTCC
1 TAAACTTTTAAACATTTTAATTTCACCCTTAAACTATAATCTTCATTCTAAATTAAGTCC
140005 CCAAAGTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
60 47 0.92
61 4 0.08
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (61 bp):
TAAACTTTTAAACATTTTAATTTCACCCTTAAACTATAATCTTCATTCTAAATTAAGTCCT
Found at i:141539 original size:57 final size:57
Alignment explanation
Indices: 141472--141582 Score: 150
Period size: 57 Copynumber: 1.9 Consensus size: 57
141462 AGGTATGGAG
* * * * *
141472 GAAAATATAAATAATTCAGTAATTTGTTTATGTTGTAATATAATAAATAATGTGGCA
1 GAAAAAATAAATAATTCAGTAATTTATATAGGTTATAATATAATAAATAATGTGGCA
* * *
141529 GAAAAAATAAATAATTCTGTAATTTATATAGGTTATAATATAATATATTATGTG
1 GAAAAAATAAATAATTCAGTAATTTATATAGGTTATAATATAATAAATAATGTG
141583 ACAGGGAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 46 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.40
Consensus pattern (57 bp):
GAAAAAATAAATAATTCAGTAATTTATATAGGTTATAATATAATAAATAATGTGGCA
Found at i:151298 original size:309 final size:309
Alignment explanation
Indices: 150729--151333 Score: 944
Period size: 309 Copynumber: 2.0 Consensus size: 309
150719 CACAGTCGCA
*
150729 TTCAACAAGGAACGAGTAAACCTCCTTACAGGCTTCGCTTCCTTCACCACTTCCTCTATCTTACC
1 TTCAACAAGGAACGAGTAAACCTCCTTACAGGCTTCGCTTCCTTCACCACTTCCTCTATCTTAAC
* * * * *
150794 ATCATCTTTGCAACTAACCAAAACCGGCACCCCTAAATCCCCTTTGCATGACCCACTTTCTATCA
66 ATCACCCTTGCAACTAACAAAAAACGGCACCCCTAAATCCCCTTTGCAGGACCCACTTTCTATCA
* * *
150859 CCGAATCCTCCTTTAACTTTTCTTCGTCTACATTCTTCATTGTATTTTCCAGTTCACTTTCTTTC
131 CCAAATCCTCCTCTAACTTTTCTTCGTCTACATTCTTCATTGCATTTTCCAGTTCACTTTCTTTC
* * *
150924 TCTCCAATGTCAGCATTCATCTTCTCTACCTCCTGTTTTCCTGCTGGGGAGCCCGTTACAGCCAT
196 TCACCAATGTCAGCATTCATCTTCTCTACCTCCTGTTTTCCTGCTGGCGAGCCAGTTACAGCCAT
*
150989 TTC-GGTGTCAATTTTTTCCTCCCCTTCCTTGACAACCTCATCTTTAACT
261 TGCGGGT-TCAATTTTTTCCTCCCCTTCCTTGACAACCTCATCTTTAACT
* * * *
151038 TTCAACAAGGAACGAGTAAAGCTCCTTACAGGCTTCTCTTCCTTCACCGCTTCCTCTATCTTAAT
1 TTCAACAAGGAACGAGTAAACCTCCTTACAGGCTTCGCTTCCTTCACCACTTCCTCTATCTTAAC
* * *
151103 ATCACCCTTGCAACTAACAAAAAACGGCACCTCTAAATCCCCTTTGCAGGGCCCATTTTCTATCA
66 ATCACCCTTGCAACTAACAAAAAACGGCACCCCTAAATCCCCTTTGCAGGACCCACTTTCTATCA
151168 CCAAATCCTCCTCTAACTTTTCTTCGTCTACATTCTTCATTGCATTTTCCAGTTCACTTTCTTTC
131 CCAAATCCTCCTCTAACTTTTCTTCGTCTACATTCTTCATTGCATTTTCCAGTTCACTTTCTTTC
* * * *
151233 TCACCAATGTCAGCATTCATCTTCTCTTCC-CCGTGTTTTTCTTCTGGCGAGCCAGTTATAGCCA
196 TCACCAATGTCAGCATTCATCTTCTCTACCTCC-TGTTTTCCTGCTGGCGAGCCAGTTACAGCCA
* *
151297 TTGCGGGTTCACTTTTTTCCTCCCCTTGCTTGACAAC
260 TTGCGGGTTCAATTTTTTCCTCCCCTTCCTTGACAAC
151334 TTCAACTTCA
Statistics
Matches: 268, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
308 2 0.01
309 263 0.98
310 3 0.01
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.36
Consensus pattern (309 bp):
TTCAACAAGGAACGAGTAAACCTCCTTACAGGCTTCGCTTCCTTCACCACTTCCTCTATCTTAAC
ATCACCCTTGCAACTAACAAAAAACGGCACCCCTAAATCCCCTTTGCAGGACCCACTTTCTATCA
CCAAATCCTCCTCTAACTTTTCTTCGTCTACATTCTTCATTGCATTTTCCAGTTCACTTTCTTTC
TCACCAATGTCAGCATTCATCTTCTCTACCTCCTGTTTTCCTGCTGGCGAGCCAGTTACAGCCAT
TGCGGGTTCAATTTTTTCCTCCCCTTCCTTGACAACCTCATCTTTAACT
Found at i:153819 original size:143 final size:144
Alignment explanation
Indices: 153634--153921 Score: 533
Period size: 144 Copynumber: 2.0 Consensus size: 144
153624 TCTAGGTTGA
153634 TCCACATGCAAATATAAAGATCAACTTTGGATCGAATAATAAATTTTAAGTTATTTGAGTTGATA
1 TCCACATGCAAATATAAAGATCAACTTTGGATCGAATAATAAATTTTAAGTTATTTGAGTTGATA
153699 ACTC-TATTTTATAATTCAAATTTTATTTTAAAATATTAGTCAAGTTGAGTATATAAATTCGAGC
66 ACTCTTATTTTATAATTCAAATTTTATTTTAAAATATTAGTCAAGTTGAGTATATAAATTCGAGC
153763 CCAAGATGTTCGAG
131 CCAAGATGTTCGAG
*
153777 TCCACATGCAAATATAAAGATCAACTTTGGATCGAATCATAAATTTTAAGTTATTTGAGTTGATA
1 TCCACATGCAAATATAAAGATCAACTTTGGATCGAATAATAAATTTTAAGTTATTTGAGTTGATA
* *
153842 ACTCTTATTTTATAATTCAAATTTTATTTTAAAATATTAGTCAAGTTGAGTGTATAAATTCGAGT
66 ACTCTTATTTTATAATTCAAATTTTATTTTAAAATATTAGTCAAGTTGAGTATATAAATTCGAGC
*
153907 CCAATATGTTCGAG
131 CCAAGATGTTCGAG
153921 T
1 T
153922 TTTAATTTAA
Statistics
Matches: 140, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
143 68 0.49
144 72 0.51
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (144 bp):
TCCACATGCAAATATAAAGATCAACTTTGGATCGAATAATAAATTTTAAGTTATTTGAGTTGATA
ACTCTTATTTTATAATTCAAATTTTATTTTAAAATATTAGTCAAGTTGAGTATATAAATTCGAGC
CCAAGATGTTCGAG
Found at i:158061 original size:4 final size:4
Alignment explanation
Indices: 158054--158080 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
158044 ATTAATTAAT
158054 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
158081 TACTGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:163324 original size:95 final size:95
Alignment explanation
Indices: 163156--163346 Score: 287
Period size: 95 Copynumber: 2.0 Consensus size: 95
163146 CCTAGTTTTT
*
163156 TTCTTTATGCAAAATTAATTTCATAGGATAAATGTTATAAATGATCACTAAACTATGTCAAAATG
1 TTCTTTATGCAAAATTAATTTCATAGGATAAATGTTACAAATGATCACTAAACTATGTCAAAATG
** * *
163221 ATTTTTTGGACACTCAACTTTGAAAAATTA
66 ATCATTTGGACACTAAACTTTCAAAAATTA
* *
163251 TTCTTTATGCAACATTAATTTCATAGGATAAAT-TTCACAAATGCTCACTAAA-TCATGTCAAAA
1 TTCTTTATGCAAAATTAATTTCATAGGATAAATGTT-ACAAATGATCACTAAACT-ATGTCAAAA
163314 TGATCATTTGGACACTAAACTTTCAAAAATTA
64 TGATCATTTGGACACTAAACTTTCAAAAATTA
163346 T
1 T
163347 ATGGTGAACA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 3 0.03
95 84 0.97
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (95 bp):
TTCTTTATGCAAAATTAATTTCATAGGATAAATGTTACAAATGATCACTAAACTATGTCAAAATG
ATCATTTGGACACTAAACTTTCAAAAATTA
Found at i:171552 original size:58 final size:58
Alignment explanation
Indices: 171482--171597 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
171472 AATTATAACC
* * *
171482 TTTAATTTAAATTAGTCCTTAAACTTTTGAACATT-TCAATTTTATCCCCAAGCTATGA
1 TTTAATTTAAATTAGTACTTAAACTTTTGAACATTCT-AATTTCATCCCCAAACTATGA
* *
171540 TTTATTTTAAATTAGTACTTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATGA
1 TTTAATTTAAATTAGTACTTAAACTTTTGAACATTCTAATTTCATCCCCAAACTATGA
171598 ACCACTTTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 51 0.98
59 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (58 bp):
TTTAATTTAAATTAGTACTTAAACTTTTGAACATTCTAATTTCATCCCCAAACTATGA
Found at i:171924 original size:61 final size:60
Alignment explanation
Indices: 171811--171953 Score: 148
Period size: 61 Copynumber: 2.4 Consensus size: 60
171801 AAGTTTGTTG
* *
171811 ACCAGTTTAGAATGAATGTCATAGATCGGGGATGAAATTGAAATGTTCAAAAAGTTTAACA
1 ACCAATTTAGAATGAATGTCATAGATCAGGGATGAAATTGAAATGTTCAAAAA-TTTAACA
* * * **
171872 ACTAATTTAGAATG-ATAGTCATAGTTTAGGGATGAAATTGATACAT-TT-AAAAATTTAGGA
1 ACCAATTTAGAATGAAT-GTCATAGATCAGGGATGAAATTGA-A-ATGTTCAAAAATTTAACA
* *
171932 ACCAATTTAAAATGAAGGTCAT
1 ACCAATTTAGAATGAATGTCAT
171954 GCAGAACACG
Statistics
Matches: 68, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
60 24 0.35
61 39 0.57
62 3 0.04
63 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (60 bp):
ACCAATTTAGAATGAATGTCATAGATCAGGGATGAAATTGAAATGTTCAAAAATTTAACA
Found at i:172955 original size:2 final size:2
Alignment explanation
Indices: 172948--172974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
172938 ATGATTATTT
172948 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
172975 GCTCACTCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:173860 original size:13 final size:13
Alignment explanation
Indices: 173842--173867 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173832 AAGCTTAATT
173842 TGAACTTTAATCG
1 TGAACTTTAATCG
173855 TGAACTTTAATCG
1 TGAACTTTAATCG
173868 AGTAAGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGAACTTTAATCG
Found at i:176841 original size:22 final size:23
Alignment explanation
Indices: 176808--176855 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
176798 TTAATTTATA
176808 AAACGTCAAATTATAAAATA-TT
1 AAACGTCAAATTATAAAATAGTT
*
176830 AAACG-CATAATTATAAATTAGTT
1 AAACGTCA-AATTATAAAATAGTT
176853 AAA
1 AAA
176856 AATGTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.31
Consensus pattern (23 bp):
AAACGTCAAATTATAAAATAGTT
Found at i:186442 original size:21 final size:21
Alignment explanation
Indices: 186416--186537 Score: 64
Period size: 23 Copynumber: 5.8 Consensus size: 21
186406 TAATTATTAA
186416 AATATTTAA-AATATATTTATT
1 AATATTTAATAATATA-TTATT
186437 AATATTTCTAATAATATATTATT
1 AATA-TT-TAATAATATATTATT
*
186460 -ATATTT--TTA-ATATTA-T
1 AATATTTAATAATATATTATT
186476 AATATTATAATAAATTATATTA-T
1 AATATT-TAAT-AA-TATATTATT
* *
186499 AATAATATAAGATATTATATT-TT
1 AAT-AT-TTA-ATAATATATTATT
*
186522 TAT-TTTAATAATATAT
1 AATATTTAATAATATAT
186538 AATAAATTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
16 1 0.01
17 11 0.14
18 3 0.04
19 8 0.10
20 4 0.05
21 8 0.10
22 5 0.06
23 27 0.34
24 10 0.12
25 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
AATATTTAATAATATATTATT
Found at i:186463 original size:22 final size:22
Alignment explanation
Indices: 186425--186484 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
186415 AAATATTTAA
186425 AATATATTTATTAATATTTCTAAT
1 AATATA-TTATT-ATATTTCTAAT
*
186449 AATATATTATTATATTTTTAAT
1 AATATATTATTATATTTCTAAT
* *
186471 ATTATAATATTATA
1 AATATATTATTATA
186485 ATAAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 22 0.67
23 5 0.15
24 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AATATATTATTATATTTCTAAT
Found at i:186494 original size:18 final size:18
Alignment explanation
Indices: 186471--186505 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
186461 TATTTTTAAT
*
186471 ATTATAATATTATAATAA
1 ATTATAATATAATAATAA
*
186489 ATTATATTATAATAATA
1 ATTATAATATAATAATA
186506 TAAGATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATAATATAATAATAA
Found at i:186498 original size:23 final size:23
Alignment explanation
Indices: 186469--186565 Score: 78
Period size: 23 Copynumber: 4.3 Consensus size: 23
186459 TATATTTTTA
186469 ATATTATAATATTATAATAAATT
1 ATATTATAATATTATAATAAATT
* * *
186492 ATATTATAATAATATAAGATATT
1 ATATTATAATATTATAATAAATT
* *
186515 ATATT-T-TTATTTTAAT-AA-T
1 ATATTATAATATTATAATAAATT
*
186534 ATATAATAA-ATTATTAATAAAATTT
1 ATATTATAATATTA-TAAT-AAA-TT
186559 ATATTAT
1 ATATTAT
186566 TTATTAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
19 5 0.09
20 5 0.09
21 10 0.18
22 1 0.02
23 27 0.49
25 7 0.13
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
ATATTATAATATTATAATAAATT
Found at i:186620 original size:19 final size:18
Alignment explanation
Indices: 186596--186664 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
186586 ATATTATTAA
186596 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
186615 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
186633 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
186655 ATT-TTAATAA
1 ATTATTAATAA
186665 ATATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:186639 original size:27 final size:27
Alignment explanation
Indices: 186559--186644 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
186549 AATAAAATTT
* *
186559 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
186586 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
186613 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
186642 ATA
1 ATA
186645 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:186671 original size:54 final size:54
Alignment explanation
Indices: 186361--186671 Score: 135
Period size: 54 Copynumber: 5.9 Consensus size: 54
186351 TATTTTATGA
* * * *
186361 ATTTAATATTAATAAAATATTTTAAT-ATCATTTTAATCAAA-ATATTAATTAT-T
1 ATTTAATATTAATATAATA-ATTAATAAT-ATTTTAATAAAATATATTATTTATAT
* * * *
186414 A--AAATATTTAAAAT-ATATTTATTAATATTTCTAAT--AATATATTA-TTATAT
1 ATTTAATA-TTAATATAATAATTAATAATATTT-TAATAAAATATATTATTTATAT
* * * * * **
186464 TTTTAATATTATAATATTATAATAAATTATATTATAAT--AATATAAGATATTATAT
1 ATTTAATA-T-TAATATAATAATTAATAATATTTTAATAAAATATATTAT-TTATAT
* *
186519 -TTTTAT-TTTA-ATAAT-ATATAATAA-ATTATTAATAAAATTTATATTATTTAT-T
1 ATTTAATATTAATATAATAAT-TAATAATATT-TTAATAAAA--TATATTATTTATAT
* * *
186571 AATTTCATA-GAA-ATAAT-ATTATTAA-ATTATTAATAATGAATAATATTATTTATAT
1 -ATTTAATATTAATATAATAATTAATAATATT-TTAATAA--AAT-ATATTATTTATAT
186626 ATTTAATATTAATATAATAATCTAATAATATTTTAAT-AAATATATT
1 ATTTAATATTAATATAATAAT-TAATAATATTTTAATAAAATATATT
186672 TAAAATATAC
Statistics
Matches: 200, Mismatches: 29, Indels: 57
0.70 0.10 0.20
Matches are distributed among these distances:
49 11 0.05
50 28 0.14
51 15 0.08
52 15 0.08
53 38 0.19
54 58 0.29
55 14 0.07
56 5 0.03
57 3 0.01
58 10 0.05
59 3 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (54 bp):
ATTTAATATTAATATAATAATTAATAATATTTTAATAAAATATATTATTTATAT
Found at i:186678 original size:23 final size:23
Alignment explanation
Indices: 186631--186703 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
186621 TATATATTTA
*
186631 ATATTAATATAATA-ATCTAATAAT
1 ATATTAATA-AATATATTTAA-AAT
*
186655 ATTTTAATAAATATATTTAAAAT
1 ATATTAATAAATATATTTAAAAT
* * *
186678 ATACTAATTAATATTTTTAAAAT
1 ATATTAATAAATATATTTAAAAT
186701 ATA
1 ATA
186704 ATATAACACT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 29 0.69
24 13 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATAAATATATTTAAAAT
Found at i:187017 original size:37 final size:34
Alignment explanation
Indices: 186975--187057 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
186965 CATCGTAAAA
*
186975 CATTTTCCAGAAAATATTTT-TCAGAAAAAATATAATT
1 CATTTTCCAGAAAACATTTTCT-AG---AAATATAATT
* * *
187012 CATTTTACGGAAAACATTTTCTAGAAATGTAATT
1 CATTTTCCAGAAAACATTTTCTAGAAATATAATT
187046 CATTTTCCAGAA
1 CATTTTCCAGAA
187058 TTTAATTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
34 19 0.49
37 19 0.49
38 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.37
Consensus pattern (34 bp):
CATTTTCCAGAAAACATTTTCTAGAAATATAATT
Found at i:187215 original size:6 final size:6
Alignment explanation
Indices: 187204--187263 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
187194 AAATGTGCCA
* *
187204 TAAAAT TAAAAT TATTAA- -AAAAT TAAAAAT TAAAAT TAAAAT ATAATAT
1 TAAAAT TAAAAT TA-AAAT TAAAAT T-AAAAT TAAAAT TAAAAT -TAAAAT
*
187253 TAGAAT TAAAA
1 TAAAAT TAAAA
187264 GAAAAACAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.05
5 1 0.02
6 27 0.63
7 13 0.30
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (6 bp):
TAAAAT
Found at i:187254 original size:13 final size:12
Alignment explanation
Indices: 187204--187263 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
187194 AAATGTGCCA
187204 TAAAATTAAAAT
1 TAAAATTAAAAT
*
187216 TATTAA--AAAAT
1 TA-AAATTAAAAT
187227 TAAAAATTAAAAT
1 T-AAAATTAAAAT
*
187240 TAAAATATAATAT
1 TAAAAT-TAAAAT
*
187253 TAGAATTAAAA
1 TAAAATTAAAA
187264 GAAAAACAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 8 0.21
12 12 0.32
13 18 0.47
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TAAAATTAAAAT
Found at i:187708 original size:30 final size:29
Alignment explanation
Indices: 187647--187711 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
187637 GTTCCTTAAC
187647 ATTTTAAATTTTTATATAATTTAAATATTT
1 ATTTTAAATTTTTATATAATTT-AATATTT
* *
187677 ATTTTATATTTTTAATAATAATTT-ATTTTT
1 ATTTTAAATTTTT-AT-ATAATTTAATATTT
187707 ATTTT
1 ATTTT
187712 CTAAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 22 0.71
31 2 0.06
32 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTTAAATTTTTATATAATTTAATATTT
Found at i:188941 original size:27 final size:25
Alignment explanation
Indices: 188904--188953 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
188894 ACATGAGATC
*
188904 AAAATTTTAATTTCTTTTAAATTTTTA
1 AAAATCTTAATTT-TTTT-AATTTTTA
188931 AAAATCTTAATTTTTTTAATTTT
1 AAAATCTTAATTTTTTTAATTTT
188954 CTCAAACCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 4 0.18
27 12 0.55
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
AAAATCTTAATTTTTTTAATTTTTA
Found at i:194066 original size:17 final size:18
Alignment explanation
Indices: 194030--194064 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
194020 ACACACAATC
*
194030 AAAATTTTAATTTTTTTT
1 AAAATCTTAATTTTTTTT
194048 AAAATCTTAATTTTTTT
1 AAAATCTTAATTTTTTT
194065 AATTTTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
AAAATCTTAATTTTTTTT
Found at i:195166 original size:18 final size:17
Alignment explanation
Indices: 195143--195188 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
195133 TGTTTATGAG
195143 GGAATTGGAATATGTGAA
1 GGAATTGGAATATGT-AA
* *
195161 GGAATTGGAATCTGTCA
1 GGAATTGGAATATGTAA
195178 GGAATTGGAAT
1 GGAATTGGAAT
195189 TCAATTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATATGTAA
Found at i:208937 original size:60 final size:60
Alignment explanation
Indices: 208813--208927 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
208803 TAACATATGA
* * * * *
208813 ATAGTCGAGTGATCATTTTGTAACTTTAAATAGTTGAGGGACTCAACAGAACAACGACAT
1 ATAGTCGAGTGATCATTTTATAACTTTAAATAGTCGAGAGACTAAACAAAACAACGACAT
* *
208873 ATAGTCG-GATGATCATTTTATAACTTTTAATGGTCGAGAGACTAAACAAAACAAC
1 ATAGTCGAG-TGATCATTTTATAACTTTAAATAGTCGAGAGACTAAACAAAACAAC
208928 ACTCTATAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (60 bp):
ATAGTCGAGTGATCATTTTATAACTTTAAATAGTCGAGAGACTAAACAAAACAACGACAT
Found at i:220507 original size:3 final size:3
Alignment explanation
Indices: 220499--220523 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
220489 TTAAGTTAAA
220499 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
220524 CTAGTGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:221775 original size:17 final size:16
Alignment explanation
Indices: 221752--221798 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
221742 ACTCGGTTGA
221752 AAGTCAAACTCTAACTT
1 AAGTCAAACTCTAAC-T
** *
221769 ATTTCAAACTTTAACT
1 AAGTCAAACTCTAACT
221785 AAGTCAAACTCTAA
1 AAGTCAAACTCTAA
221799 TAACTTATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.32
Consensus pattern (16 bp):
AAGTCAAACTCTAACT
Found at i:222567 original size:24 final size:24
Alignment explanation
Indices: 222535--222587 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
222525 GTGCCTCCTT
222535 GCTCCGATGACTGCCCTGTTATTA
1 GCTCCGATGACTGCCCTGTTATTA
222559 GCTCCGATGACTGCCCTGTTATTA
1 GCTCCGATGACTGCCCTGTTATTA
222583 GCTCC
1 GCTCC
222588 AATATCAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.15, C:0.32, G:0.21, T:0.32
Consensus pattern (24 bp):
GCTCCGATGACTGCCCTGTTATTA
Found at i:231006 original size:90 final size:89
Alignment explanation
Indices: 230860--231028 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 89
230850 ATTTGTGACA
* * * * *
230860 AGTTTTAACTTAAAATATTATTTTTTTAACTCTAAAAAGTTACATAAGTGATAATAATTTTGATT
1 AGTTTTAACTTAAAATATTATATGTCTAACTCTAAAAAGTTACACAACTGATAATAATTTTGATT
*
230925 ACAACTGAGAATATTATATTGTGTCG
66 --AACTGAAAATATTATATTGTGTCG
* *
230951 AGTTTTAACTTAAAAT-TTATCATGTCT-ACTCTAAAAAGTTATACAACTGATAATAATTTTGGT
1 AGTTTTAACTTAAAATATTAT-ATGTCTAACTCTAAAAAGTTACACAACTGATAATAATTTTGAT
231014 TAACTGAAAATATTA
65 TAACTGAAAATATTA
231029 CATGAATTTC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 13 0.19
90 37 0.54
91 19 0.28
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (89 bp):
AGTTTTAACTTAAAATATTATATGTCTAACTCTAAAAAGTTACACAACTGATAATAATTTTGATT
AACTGAAAATATTATATTGTGTCG
Found at i:231983 original size:21 final size:21
Alignment explanation
Indices: 231950--231990 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
231940 CAAGAGAAAT
**
231950 AAAATATTTATATTTAATTAG
1 AAAATATAAATATTTAATTAG
*
231971 AAAATATAAATATTTTATTA
1 AAAATATAAATATTTAATTA
231991 ATATAATACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AAAATATAAATATTTAATTAG
Found at i:234711 original size:18 final size:18
Alignment explanation
Indices: 234688--234722 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
234678 CACAACGTCA
*
234688 TATCATTTCAATAACATT
1 TATCATATCAATAACATT
*
234706 TATCATATCACTAACAT
1 TATCATATCAATAACAT
234723 ATATTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
TATCATATCAATAACATT
Found at i:234862 original size:23 final size:23
Alignment explanation
Indices: 234828--234888 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
234818 CTCATATAAA
*
234828 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
234851 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
234874 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
234889 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:236128 original size:19 final size:20
Alignment explanation
Indices: 236091--236128 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
236081 TCTTTTATAT
236091 TCATATAATTTATTATCATA
1 TCATATAATTTATTATCATA
*
236111 TCATATGATTTA-TATCAT
1 TCATATAATTTATTATCAT
236129 CATAACATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
TCATATAATTTATTATCATA
Found at i:236137 original size:22 final size:20
Alignment explanation
Indices: 236092--236137 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
236082 CTTTTATATT
*
236092 CATATAATTTATTATCATAT
1 CATATAATTTATTATCATAA
*
236112 CATATGATTTATATCATCATAA
1 CATATAATTTAT-T-ATCATAA
236134 CATA
1 CATA
236138 GCACATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.43
Consensus pattern (20 bp):
CATATAATTTATTATCATAA
Found at i:236593 original size:21 final size:21
Alignment explanation
Indices: 236567--236610 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
236557 TTTTTATTCG
* *
236567 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
236588 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
236609 CT
1 CT
236611 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:239421 original size:18 final size:17
Alignment explanation
Indices: 239376--239425 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
239366 TGCCAACTTG
239376 TAAAATTTTAAAATATA
1 TAAAATTTTAAAATATA
*
239393 TAAAACATTTAAAATATA
1 TAAAA-TTTTAAAATATA
239411 -AGAGAATTTTAAAAT
1 TA-A-AATTTTAAAAT
239426 TTTAAGAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 20 0.71
19 2 0.07
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (17 bp):
TAAAATTTTAAAATATA
Found at i:239926 original size:6 final size:6
Alignment explanation
Indices: 239911--239951 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
239901 TGTATTTAAT
* * *
239911 GTTCAG GTTCAA GTTCAA GTTCAG GTTTAA GTTCAA GTTCA
1 GTTCAA GTTCAA GTTCAA GTTCAA GTTCAA GTTCAA GTTCA
239952 GTTTCAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (6 bp):
GTTCAA
Found at i:239934 original size:18 final size:18
Alignment explanation
Indices: 239911--239958 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
239901 TGTATTTAAT
239911 GTTCAGGTTCAAGTTCAA
1 GTTCAGGTTCAAGTTCAA
*
239929 GTTCAGGTTTAAGTTCAA
1 GTTCAGGTTCAAGTTCAA
*
239947 GTTCAGTTTCAA
1 GTTCAGGTTCAA
239959 TTTTCAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (18 bp):
GTTCAGGTTCAAGTTCAA
Found at i:248433 original size:111 final size:110
Alignment explanation
Indices: 248228--248573 Score: 532
Period size: 111 Copynumber: 3.1 Consensus size: 110
248218 TCGGTTTGTA
* * *
248228 TCGATACTTTATAAAAATATATTGAAT-CATAACAATATAACAAGTAAAAAAATGATAAAACCGG
1 TCGATACTTTATAAAAATGTATAG-ATCCATAACAATATAACAAGT-AAAAAATGACAAAA-CGG
*
248292 TCTATAAATGATAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
63 TCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
* *
248340 TCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAATGACAAAATCGGTC
1 TCGATACTTTATAAAAATGTATAGATCCATAACAATATAACAAGTAAAAAATGACAAAA-CGGTC
*
248405 TATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTG
65 TATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
*
248451 TCGATACTTTATAAAAATGTATAGATCCATAACAATATAACAGGTAAAAAATGACAAAACTGGTC
1 TCGATACTTTATAAAAATGTATAGATCCATAACAATATAACAAGTAAAAAATGACAAAAC-GGTC
** * *
248516 TATAAATGACAAAACAGGTAAAGCGCTACCAAATATGTTGATAGTG
65 TATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
248562 TCGATACTTTAT
1 TCGATACTTTAT
248574 TATAAGTATC
Statistics
Matches: 218, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
110 1 0.00
111 178 0.82
112 39 0.18
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (110 bp):
TCGATACTTTATAAAAATGTATAGATCCATAACAATATAACAAGTAAAAAATGACAAAACGGTCT
ATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG
Found at i:249742 original size:23 final size:23
Alignment explanation
Indices: 249696--249743 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
249686 AAATAGGTCA
* *
249696 ATATAAACGCTATCTATTACATT
1 ATATAAACGCTACCTAATACATT
* *
249719 ATATAATCGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
249742 AT
1 AT
249744 TGTACTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Found at i:250732 original size:249 final size:249
Alignment explanation
Indices: 250294--250792 Score: 989
Period size: 249 Copynumber: 2.0 Consensus size: 249
250284 CTTACACCAA
250294 TAGGTGAATTTTCCAACTTGTTTCTAATGGAGTTTAGGTTTCCTTTTTGTTGCAGAATTGGCTTA
1 TAGGTGAATTTTCCAACTTGTTTCTAATGGAGTTTAGGTTTCCTTTTTGTTGCAGAATTGGCTTA
250359 TTTTACATAGTTTATCATAGTTGTTGGGGTTTTCTTGGAAATTCTCACCTATTTCAAGCAGTTTT
66 TTTTACATAGTTTATCATAGTTGTTGGGGTTTTCTTGGAAATTCTCACCTATTTCAAGCAGTTTT
250424 TTCAGCACTTACGGTCAAAATATTTTACCATTTGTAATTTTGAGATCAGATCAGGACTATGTGAG
131 TTCAGCACTTACGGTCAAAATATTTTACCATTTGTAATTTTGAGATCAGATCAGGACTATGTGAG
250489 CCAAAGCCATCACCATTGAGTTACCTGCCAAATGAGCATATCTGCGGCCGACCT
196 CCAAAGCCATCACCATTGAGTTACCTGCCAAATGAGCATATCTGCGGCCGACCT
250543 TAGGTGAATTTTCCAACTTGTTTCTAATGGAGTTTAGGTTTCCTTTTTGTTGCAGAATTGGCTTA
1 TAGGTGAATTTTCCAACTTGTTTCTAATGGAGTTTAGGTTTCCTTTTTGTTGCAGAATTGGCTTA
250608 TTTTACATAGTTTATCATAGTTGTTGGGGTTTTCTTGGAAATTCTCACCTATTTCAAGCAGTTTT
66 TTTTACATAGTTTATCATAGTTGTTGGGGTTTTCTTGGAAATTCTCACCTATTTCAAGCAGTTTT
*
250673 TTCAGCACTTACGGTCAAAATATTTTACCATTTGTAATTTTGAGCTCAGATCAGGACTATGTGAG
131 TTCAGCACTTACGGTCAAAATATTTTACCATTTGTAATTTTGAGATCAGATCAGGACTATGTGAG
250738 CCAAAGCCATCACCATTGAGTTACCTGCCAAATGAGCATATCTGCGGCCGACCT
196 CCAAAGCCATCACCATTGAGTTACCTGCCAAATGAGCATATCTGCGGCCGACCT
250792 T
1 T
250793 TGGGACTCCG
Statistics
Matches: 249, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
249 249 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (249 bp):
TAGGTGAATTTTCCAACTTGTTTCTAATGGAGTTTAGGTTTCCTTTTTGTTGCAGAATTGGCTTA
TTTTACATAGTTTATCATAGTTGTTGGGGTTTTCTTGGAAATTCTCACCTATTTCAAGCAGTTTT
TTCAGCACTTACGGTCAAAATATTTTACCATTTGTAATTTTGAGATCAGATCAGGACTATGTGAG
CCAAAGCCATCACCATTGAGTTACCTGCCAAATGAGCATATCTGCGGCCGACCT
Found at i:253969 original size:9 final size:9
Alignment explanation
Indices: 253955--253984 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
253945 AGATTATCAC
253955 TAAAAAATA
1 TAAAAAATA
253964 TAAAAAATA
1 TAAAAAATA
*
253973 TAAAATATA
1 TAAAAAATA
253982 TAA
1 TAA
253985 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAAATA
Found at i:261361 original size:17 final size:17
Alignment explanation
Indices: 261334--261372 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
261324 AATTGCTGAC
261334 TTAAA-AACATAGAATA
1 TTAAATAACATAGAATA
261350 TTAAATAACATAGAATA
1 TTAAATAACATAGAATA
*
261367 TAAAAT
1 TTAAAT
261373 TATATATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (17 bp):
TTAAATAACATAGAATA
Found at i:282123 original size:10 final size:10
Alignment explanation
Indices: 282106--282144 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
282096 GTATTTCGAA
282106 AACTCTCTCT
1 AACTCTCTCT
**
282116 CTCTCTCTCT
1 AACTCTCTCT
282126 AACTCTCTCT
1 AACTCTCTCT
282136 AACTCTCTC
1 AACTCTCTC
282145 CATCCCTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (10 bp):
AACTCTCTCT
Found at i:288584 original size:17 final size:17
Alignment explanation
Indices: 288562--288597 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
288552 CTTAACAAGA
*
288562 GTTAGGTTGGCCTCTTG
1 GTTAGGCTGGCCTCTTG
288579 GTTAGGCTGGCCTCTTG
1 GTTAGGCTGGCCTCTTG
288596 GT
1 GT
288598 ATTTAGCAAA
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:0.06, C:0.19, G:0.36, T:0.39
Consensus pattern (17 bp):
GTTAGGCTGGCCTCTTG
Found at i:300661 original size:44 final size:44
Alignment explanation
Indices: 300598--300685 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
300588 GGTATACCAG
300598 CTCCAGGTTTCTATAACTTAAACATGTAAGAATAAGTGCAGGAT
1 CTCCAGGTTTCTATAACTTAAACATGTAAGAATAAGTGCAGGAT
300642 CTCCAGGTTTCTATAACTTAAACATGTAAGAATAAGTGCAGGAT
1 CTCCAGGTTTCTATAACTTAAACATGTAAGAATAAGTGCAGGAT
300686 TTACCTTCGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (44 bp):
CTCCAGGTTTCTATAACTTAAACATGTAAGAATAAGTGCAGGAT
Found at i:310267 original size:33 final size:35
Alignment explanation
Indices: 310203--310268 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
310193 TTATGATAAT
***
310203 AATTTGTTTAATGACTTTTTTTAACTCATATATTA
1 AATTTGTTTAATGACTTTTTTTAAAAAATATATTA
310238 AATTT-TTTAATGA-TTTTTTTAAAAAATATAT
1 AATTTGTTTAATGACTTTTTTTAAAAAATATAT
310269 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 15 0.54
34 8 0.29
35 5 0.18
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (35 bp):
AATTTGTTTAATGACTTTTTTTAAAAAATATATTA
Found at i:310455 original size:15 final size:14
Alignment explanation
Indices: 310428--310454 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
310418 AAATAAAATT
310428 ATTTTCTAAAAAAC
1 ATTTTCTAAAAAAC
310442 ATTTTCTAAAAAA
1 ATTTTCTAAAAAA
310455 AATTATTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTTCTAAAAAAC
Found at i:311395 original size:19 final size:19
Alignment explanation
Indices: 311371--311408 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
311361 ATAAGTCATG
311371 TACTTTTTGGATTTGTTTT
1 TACTTTTTGGATTTGTTTT
311390 TACTTTTTGGATTTGTTTT
1 TACTTTTTGGATTTGTTTT
311409 CTCTCTCTCT
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:0.11, C:0.05, G:0.16, T:0.68
Consensus pattern (19 bp):
TACTTTTTGGATTTGTTTT
Found at i:315678 original size:21 final size:21
Alignment explanation
Indices: 315645--315697 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
315635 ATTCTGACTA
315645 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
315666 TCGCGTTGTGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
315687 TCGCAATGCGA
1 TCGCATTGCGA
315698 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:315729 original size:20 final size:20
Alignment explanation
Indices: 315706--315819 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
315696 GAATATGTAA
* *
315706 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* * *
315726 ATCGAAACGCGATTCTAATT
1 ATCGCAACGCGATTCTGACT
*
315746 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
315766 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
315786 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
315806 ATCGCAATGCGATT
1 ATCGCAACGCGATT
315820 TTCAAAGCGC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:316019 original size:22 final size:22
Alignment explanation
Indices: 315994--316058 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
315984 GGCGACATCC
315994 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
316016 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
316038 GTCCCAATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
316059 CGCCTATCTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.28, C:0.40, G:0.14, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:316424 original size:19 final size:20
Alignment explanation
Indices: 316394--316431 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
316384 TTTAGTATTT
316394 GAAATCGAAAATCGCAACGC
1 GAAATCGAAAATCGCAACGC
316414 GAAAT-GAAAATCGCAACG
1 GAAATCGAAAATCGCAACG
316432 ACAGAATCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
GAAATCGAAAATCGCAACGC
Found at i:317230 original size:300 final size:300
Alignment explanation
Indices: 316639--317240 Score: 1125
Period size: 300 Copynumber: 2.0 Consensus size: 300
316629 TATTGTTCTT
*
316639 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTGTAGAACT
1 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
* *
316704 TTTATTCGGCTCAATTGACCTTAAGAAATAAAGTAAGCTTGGCCAAAACAATTGCGTCGAAGCTT
66 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
316769 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
131 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
316834 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
196 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
316899 ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
261 ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
*
316939 GGTATATCTTCACAGTGTAGTTTTTGGTATGTCTAACTTGGTATGTTTATTGTTTTTATAGAACT
1 GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
317004 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
66 TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
*
317069 TCACCTGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
131 TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
*
317134 GGGTGGAGATGCTATGTTGA-CCCATCTGTTTCTTCAAACCATGACTAGCGATCTACCAGAGACT
196 GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
*
317198 ATACAACGTCGTGATGAAGAGATATGGTTTGATTTTCCATC
261 ATACAACGTCGTAATGAAGAGATAT-GTTTGATTTTCCATC
317239 GG
1 GG
317241 CGTATACGTG
Statistics
Matches: 294, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
299 67 0.23
300 227 0.77
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (300 bp):
GGTATATCTTCACAGTGTAGTTTTTGGTATATCTAACTTGGTATGTTTATTGTTTTTATAGAACT
TTTATTCGACTCAATTGACCTTAAGAAATAAAGTAAGCCTGGCCAAAACAATTGCGTCGAAGCTT
TCACATGCACAAAGAAAAATATTTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACAACATCC
GGGTGGAGATGCTATGTTGACCCCATCTGTTTCTTCAAACCATGACTAGAGATCTACCAGAGACT
ATACAACGTCGTAATGAAGAGATATGTTTGATTTTCCATC
Found at i:318540 original size:18 final size:18
Alignment explanation
Indices: 318517--318566 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
318507 TTTACTCGTA
318517 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
318535 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
318553 ATTTCACTTAGATT
1 ATTTCACTTAGATT
318567 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:318813 original size:20 final size:21
Alignment explanation
Indices: 318784--318837 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
318774 GCGATTCTCT
*
318784 TGTTGGGATAGTCAAATTCG-
1 TGTTGCGATAGTCAAATTCGC
**
318804 TGTTGCGATAGTCATTTTCGC
1 TGTTGCGATAGTCAAATTCGC
318825 T-TTGCGATAGTCA
1 TGTTGCGATAGTCA
318838 CTCGTGTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (21 bp):
TGTTGCGATAGTCAAATTCGC
Found at i:319413 original size:21 final size:22
Alignment explanation
Indices: 319340--319415 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 22
319330 GACTCACTAG
**
319340 TCAT-CGTTCAAGAGGCCTCCCC
1 TCATCCGTTCAAGAGGCC-CCTA
319362 T-AT-CGTTCAAGAGGCCCCTA
1 TCATCCGTTCAAGAGGCCCCTA
* * *
319382 TCATCC-CTCAAGAGTCCCCTC
1 TCATCCGTTCAAGAGGCCCCTA
319403 TCA-CCGTTCAAGA
1 TCATCCGTTCAAGA
319416 CGCCACTGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.11
21 38 0.84
22 2 0.04
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (22 bp):
TCATCCGTTCAAGAGGCCCCTA
Found at i:319431 original size:21 final size:20
Alignment explanation
Indices: 319340--319436 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 20
319330 GACTCACTAG
**
319340 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGA-GCC-CCTA
319362 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGA-GCCCCTA
** *
319382 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-CCCCTA
* * *
319403 TCACCGTTCAAGACGCCACTG
1 TCATCGTTCAAGA-GCCCCTA
*
319424 TCATCGTTGAAGA
1 TCATCGTTCAAGA
319437 TGTCCCTCCC
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.07
21 54 0.90
22 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGCCCCTA
Found at i:321010 original size:20 final size:20
Alignment explanation
Indices: 320985--321038 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
320975 AGGTACAATT
*
320985 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
**
321005 TCGCAATACGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
321025 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
321039 TCAATTCGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:321158 original size:20 final size:20
Alignment explanation
Indices: 321081--321211 Score: 141
Period size: 20 Copynumber: 6.8 Consensus size: 20
321071 GCGATTTTCT
*
321081 CGTTGCGATAGTCAAATAC-
1 CGTTGCGATAGTCAAATTCG
* *
321100 CTGTTGCGATAATCAAATTCA
1 C-GTTGCGATAGTCAAATTCG
*
321121 CGTTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
*
321141 CGTTGCGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
321161 CGTTGC-A-A-T---TTTCG
1 CGTTGCGATAGTCAAATTCG
321175 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
321195 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
321212 GAATGTGTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 15
0.80 0.08 0.13
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 1 0.01
17 2 0.02
18 1 0.01
19 2 0.02
20 77 0.81
21 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:321179 original size:94 final size:93
Alignment explanation
Indices: 321032--321211 Score: 238
Period size: 94 Copynumber: 1.9 Consensus size: 93
321022 AAATCGCAAC
* * * *
321032 GCGAAAGTCAATTCGCGTTGCGATAGCCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAA
1 GCGAAAGTCAATTCGCGTTGCGATAGCCAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCAAA
321097 TAC-CTGTTGCGATAATCAAATTCACGTT
66 TACGC-GTTGCGATAATCAAATTCACGTT
* * *
321125 GCGATAGTCAAATTCTCGTTGCGATA-CTCAAATTCGCGTTGCAATTTTCGCGTTGCGATAGTCA
1 GCGAAAGTC-AATTCGCGTTGCGATAGC-CAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCA
* *
321189 AATTCGCGTTGCGATATTCAAAT
64 AATACGCGTTGCGATAATCAAAT
321212 GAATGTGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 9 0.12
94 65 0.87
95 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (93 bp):
GCGAAAGTCAATTCGCGTTGCGATAGCCAAATACGCGTTGCAATTTTCGCGTTGCGATAGTCAAA
TACGCGTTGCGATAATCAAATTCACGTT
Found at i:321405 original size:18 final size:18
Alignment explanation
Indices: 321382--321416 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
321372 AAGCAGGTTG
*
321382 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
321400 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
321417 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:323690 original size:24 final size:24
Alignment explanation
Indices: 323663--323716 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
323653 CTGAGACATC
*
323663 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
323687 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
323711 ATCAAA
1 ATCAAA
323717 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:323730 original size:24 final size:24
Alignment explanation
Indices: 323679--323730 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
323669 ATCTGAGTAT
** *
323679 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
323703 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
323727 TGAC
1 TGAC
323731 TAGTACTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:324606 original size:20 final size:20
Alignment explanation
Indices: 324583--324641 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
324573 ATCTCGCTGC
* * *
324583 GATAATCATAATCGCGTTGT
1 GATAGTCATAATCGCATTGA
*
324603 GATAGTCAGAATCGCATTGA
1 GATAGTCATAATCGCATTGA
324623 GATAGTCATAATCGCATTG
1 GATAGTCATAATCGCATTG
324642 CGATTTACAT
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:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (20 bp):
GATAGTCATAATCGCATTGA
Found at i:324632 original size:40 final size:40
Alignment explanation
Indices: 324546--324645 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
324536 GTGTTGCAAC
* * * * * *
324546 AGTCAAAATAGCGTTGCGATAGTTAGAATCTCGCTGCGAT
1 AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
* * *
324586 AATCATAATCGCGTTGTGATAGTCAGAATCGCATTGAGAT
1 AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
*
324626 AGTCATAATCGCATTGCGAT
1 AGTCATAATCGCGTTGCGAT
324646 TTACATATTC
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (40 bp):
AGTCATAATCGCGTTGCGATAGTCAGAATCGCACTGAGAT
Found at i:324685 original size:21 final size:21
Alignment explanation
Indices: 324661--324706 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
324651 TATTCGCATT
324661 GCGAATTCGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
* *
324682 GCGAATTTGGAAAATCGCAAT
1 GCGAATTCGGAAAATCGCAAC
324703 GCGA
1 GCGA
324707 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:325372 original size:14 final size:15
Alignment explanation
Indices: 325341--325374 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
325331 TTAAAGGATG
325341 AAATTTTAAAAATAA
1 AAATTTTAAAAATAA
*
325356 AAATTTT-AAATTAA
1 AAATTTTAAAAATAA
325370 AAATT
1 AAATT
325375 CGTTACGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATTTTAAAAATAA
Found at i:346192 original size:2 final size:2
Alignment explanation
Indices: 346185--346241 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
346175 ACAAATAATG
346185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
346227 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
346242 TAAATTGCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:346955 original size:21 final size:20
Alignment explanation
Indices: 346931--346995 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
346921 ATTTATAGTG
346931 TTGATGTGATGATTTAAAATA
1 TTGATGTGAT-ATTTAAAATA
** * *
346952 TTGATACGATAATATATAATA
1 TTGATGTGAT-ATTTAAAATA
346973 TTGATGTGATAGTTTAGAAATA
1 TTGATGTGATA-TTTA-AAATA
346995 T
1 T
346996 AATAGTATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 1 0.03
21 27 0.82
22 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.42
Consensus pattern (20 bp):
TTGATGTGATATTTAAAATA
Found at i:346977 original size:42 final size:43
Alignment explanation
Indices: 346907--346995 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 43
346897 GATCGTTATT
** * * *
346907 ATATTGATATTATAATTTATAGTGTTGATGTGAT-GATTTA-AA
1 ATATTGATACGATAATATATAATATTGATGTGATAG-TTTAGAA
346949 ATATTGATACGATAATATATAATATTGATGTGATAGTTTAGAA
1 ATATTGATACGATAATATATAATATTGATGTGATAGTTTAGAA
346992 ATAT
1 ATAT
346996 AATAGTATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 33 0.82
43 7 0.17
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (43 bp):
ATATTGATACGATAATATATAATATTGATGTGATAGTTTAGAA
Found at i:354843 original size:3 final size:3
Alignment explanation
Indices: 354835--354872 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
354825 AAACAAGAAA
354835 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
354873 ATCACCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:360736 original size:14 final size:14
Alignment explanation
Indices: 360719--360759 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
360709 TGAACGTTCA
360719 GTTATGTTCGTTTG
1 GTTATGTTCGTTTG
*
360733 GTTATGTTCGTTCG
1 GTTATGTTCGTTTG
360747 GTTATGTTCGTTT
1 GTTATGTTCGTTT
360760 ATGTTCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.10, G:0.27, T:0.56
Consensus pattern (14 bp):
GTTATGTTCGTTTG
Found at i:361914 original size:16 final size:16
Alignment explanation
Indices: 361893--361930 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
361883 GGTCTCCAAT
361893 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
361909 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
361925 GTTTAT
1 GTTTAT
361931 TTATTAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.11, G:0.24, T:0.58
Consensus pattern (16 bp):
GTTTATGTTCGTGTTC
Found at i:373188 original size:22 final size:20
Alignment explanation
Indices: 373149--373291 Score: 73
Period size: 20 Copynumber: 7.1 Consensus size: 20
373139 TTAAATATTT
*
373149 TTTTTAAATTAATCAAATTA
1 TTTTTAAATTAATAAAATTA
*
373169 TTTTTAAATTATTATAAAATAA
1 TTTTTAAATTA--ATAAAATTA
* * *
373191 ATATTAAATTTATCAAAATT-
1 TTTTTAAATTAAT-AAAATTA
* *
373211 TATATTAAATGTAA-ATAATTA
1 T-TTTTAAAT-TAATAAAATTA
*
373232 -TTTT-AATT-ATCAAA-TA
1 TTTTTAAATTAATAAAATTA
*
373248 TTTTTTAAATTAATCAAATTA
1 -TTTTTAAATTAATAAAATTA
* * *
373269 TTATTAAATGTTATTAAATTA
1 TTTTTAAAT-TAATAAAATTA
373290 TT
1 TT
373292 ATAAAATAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
16 3 0.03
17 3 0.03
18 7 0.07
19 7 0.07
20 32 0.34
21 26 0.27
22 17 0.18
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (20 bp):
TTTTTAAATTAATAAAATTA
Found at i:373218 original size:58 final size:58
Alignment explanation
Indices: 373151--373321 Score: 144
Period size: 58 Copynumber: 3.1 Consensus size: 58
373141 AAATATTTTT
* *
373151 TTTAAATTAATCAAATTATTTTTAAATTATTATAAAATAAATATTAAATTTATCAAAA
1 TTTATATTAATTAAATTATTTTTAAATTATTATAAAATAAATATTAAATTTATCAAAA
* * * ** * *
373209 TTTATATTAAATGTAAATAATTATTT---TAATTATCAAATATTTTTTAAATTAATC-AAA
1 TTTATATT-AAT-TAAATTATT-TTTAAATTATTATAAAATAAATATTAAATTTATCAAAA
* * *
373266 --T-TATT-ATTAAA-TGTTATTAAATTATTATAAAATAAACATTAAATTTATCAAAA
1 TTTATATTAATTAAATTATTTTTAAATTATTATAAAATAAATATTAAATTTATCAAAA
373319 TTT
1 TTT
373322 CATAGTTGTT
Statistics
Matches: 85, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
49 2 0.02
50 2 0.02
51 4 0.05
52 23 0.27
53 3 0.04
54 4 0.05
55 2 0.02
57 3 0.04
58 29 0.34
59 3 0.04
60 7 0.08
61 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (58 bp):
TTTATATTAATTAAATTATTTTTAAATTATTATAAAATAAATATTAAATTTATCAAAA
Found at i:376284 original size:30 final size:32
Alignment explanation
Indices: 376248--376337 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
376238 AGCAATATTT
376248 AAACTATTATATCATTCTA-A-ATTAATCCAC
1 AAACTATTATATCATTCTATATATTAATCCAC
* *
376278 AAACTATTATGT-ATTCTATATATTAATCCTC
1 AAACTATTATATCATTCTATATATTAATCCAC
* *
376309 AAACTATCATTATCA-T-TATATTTTAATCC
1 AAACTATTA-TATCATTCTATATATTAATCC
376338 TTCCACTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 6 0.12
30 12 0.24
31 29 0.57
32 3 0.06
33 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.01, T:0.42
Consensus pattern (32 bp):
AAACTATTATATCATTCTATATATTAATCCAC
Found at i:378228 original size:18 final size:18
Alignment explanation
Indices: 378205--378248 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
378195 GGCAATTGGT
378205 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
378223 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
378241 CCAGCAGA
1 CCAGCAGA
378249 AGCCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.09
Consensus pattern (18 bp):
CCAGCAGATACGGGTAGC
Found at i:382795 original size:18 final size:18
Alignment explanation
Indices: 382772--382815 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
382762 GGCAATTGGT
382772 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
382790 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
382808 CCAGCAGA
1 CCAGCAGA
382816 AGCCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.09
Consensus pattern (18 bp):
CCAGCAGATACGGGTAGC
Found at i:389582 original size:13 final size:15
Alignment explanation
Indices: 389550--389583 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
389540 CATCTCGAAA
389550 AGAGTTAATACTTAT
1 AGAGTTAATACTTAT
389565 AGAGTTAATA-TT-T
1 AGAGTTAATACTTAT
389578 AGAGTT
1 AGAGTT
389584 GAATTCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (15 bp):
AGAGTTAATACTTAT
Found at i:393094 original size:2 final size:2
Alignment explanation
Indices: 393087--393122 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
393077 ACTAAGTTTC
393087 AT AT AT AT A- 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 AT A
393123 AAACAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:397585 original size:73 final size:72
Alignment explanation
Indices: 397453--397587 Score: 198
Period size: 73 Copynumber: 1.9 Consensus size: 72
397443 AATGTCATAG
* * *
397453 CTTTGACATTGTGTCAAGCTTTGCTTTATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGAAAT
1 CTTTGACATTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGAAAT
397518 TCTATAC
66 TCTATAC
* * * *
397525 CTTTGGCATTTGTATCAAGCTCTGGTATATTTCTTCTTGTCATGCAGAGACTTTGGTTTAAGA
1 CTTTGACA-TTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGA
397588 CAAATCTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
72 7 0.13
73 48 0.87
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (72 bp):
CTTTGACATTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGAAAT
TCTATAC
Done.