Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002616.1 Hibiscus syriacus cultivar Beakdansim tig00005294_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: 1287628
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:249646 original size:77 final size:77
Alignment explanation
Indices: 249519--249684 Score: 269
Period size: 77 Copynumber: 2.2 Consensus size: 77
249509 TGGAGTGGAT
*
249519 GCAACGCGATTTACAAATTCGAAACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTA
1 GCAACGCGATTTACAAATTCGAAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTA
249584 AACACTACTATC
66 AACACTACTATC
* * *
249596 GCAACACGATTTACAAATTCGCAACGCGATTTACAAATTTGCAACGCTAATTACCGATATAGGTA
1 GCAACGCGATTTACAAATTCGAAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTA
* **
249661 AACAGTGTTATC
66 AACACTACTATC
249673 GCAACGCGATTT
1 GCAACGCGATTT
249685 TCCAAAATCG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (77 bp):
GCAACGCGATTTACAAATTCGAAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTA
AACACTACTATC
Found at i:249649 original size:20 final size:20
Alignment explanation
Indices: 249594--249649 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
249584 AACACTACTA
* *
249594 TCGCAACACGATTTACAAAT
1 TCGCAACGCGAATTACAAAT
*
249614 TCGCAACGCGATTTACAAAT
1 TCGCAACGCGAATTACAAAT
* *
249634 TTGCAACGCTAATTAC
1 TCGCAACGCGAATTAC
249650 CGATATAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTACAAAT
Found at i:249675 original size:57 final size:57
Alignment explanation
Indices: 249614--249751 Score: 188
Period size: 58 Copynumber: 2.4 Consensus size: 57
249604 ATTTACAAAT
* **
249614 TCGCAACGCGATTTACAAATTTGCAAC-GCTAATTACCGATATAGGTAAACAGTGTTA
1 TCGCAACGCGATTTACAAATTCGC-ACTGCTAATTACCGATATAGGTAAACAGTACTA
* *
249671 TCGCAACGCGATTTTCCAAAATCGCACTGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGCGA-TTTACAAATTCGCACTGCTAATTACCGATATAGGTAAACAGTACTA
* *
249729 TCGCAACACGATTTTCAAATTCG
1 TCGCAACGCGATTTACAAATTCG
249752 TAACGAGATT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
57 23 0.32
58 48 0.68
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (57 bp):
TCGCAACGCGATTTACAAATTCGCACTGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:249776 original size:20 final size:20
Alignment explanation
Indices: 249738--249776 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
249728 ATCGCAACAC
**
249738 GATTTTCAAATTCGTAACGA
1 GATTTTCAAATTCACAACGA
249758 GATTTTCAAATTCACAACG
1 GATTTTCAAATTCACAACG
249777 CTAATTACCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
GATTTTCAAATTCACAACGA
Found at i:249799 original size:135 final size:135
Alignment explanation
Indices: 249541--249838 Score: 451
Period size: 135 Copynumber: 2.2 Consensus size: 135
249531 ACAAATTCGA
*
249541 AACGCGATTTT-CAAATTCGCAACGCTAATTACCGATATAGGTAAACACTACTATCGCAACACGA
1 AACGCGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACACTACTATCGCAACACGA
* **
249605 TTTACAAATTCGCAACGCGATTTACAAATTTGCAACGCTAATTACCGATATAGGTAAACAGTGTT
66 TTTACAAATTCGCAACGAGATTTACAAATTCACAACGCTAATTACCGATATAGGTAAACAGTGTT
249670 ATCGC
131 ATCGC
*
249675 AACGCGATTTTCCAAAATCGC-ACTGCTAATTACCGATATAGGTAAACAGTACTATCGCAACACG
1 AACGCGATTTTCCAAAATCGCAAC-GCTAATTACCGATATAGGTAAACACTACTATCGCAACACG
* * *
249739 ATTTTCAAATTCGTAACGAGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAGTGT
65 ATTTACAAATTCGCAACGAGATTTACAAATTCACAACGCTAATTACCGATATAGGTAAACAGTGT
249804 TATCGC
130 TATCGC
* * * *
249810 AACACAATTTT-CAAATTTGCAACGC-AATT
1 AACGCGATTTTCCAAAATCGCAACGCTAATT
249839 TTCAAATTCG
Statistics
Matches: 149, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
133 4 0.03
134 22 0.15
135 123 0.83
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (135 bp):
AACGCGATTTTCCAAAATCGCAACGCTAATTACCGATATAGGTAAACACTACTATCGCAACACGA
TTTACAAATTCGCAACGAGATTTACAAATTCACAACGCTAATTACCGATATAGGTAAACAGTGTT
ATCGC
Found at i:249826 original size:77 final size:77
Alignment explanation
Indices: 249671--249854 Score: 246
Period size: 77 Copynumber: 2.4 Consensus size: 77
249661 AACAGTGTTA
* * *
249671 TCGCAACGCGATTTTCCAAAATCGC-ACTGCTAATTACCGATATAGGTAAACAGTACTATCGCAA
1 TCGCAACGCAATTTT-CAAATTCACAAC-GCTAATTACCGATATAGGTAAACAGTACTATCGCAA
*
249735 CACGATTTTCAAAT
64 CACAATTTTCAAAT
* **
249749 TCGTAACG-AGATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAGTGTTATCGCAAC
1 TCGCAACGCA-ATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAAC
249813 ACAATTTTCAAAT
65 ACAATTTTCAAAT
* *
249826 TTGCAACGCAATTTTCAAATTCGCAACGC
1 TCGCAACGCAATTTTCAAATTCACAACGC
249855 GATTTTCAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
77 78 0.84
78 15 0.16
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (77 bp):
TCGCAACGCAATTTTCAAATTCACAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACA
CAATTTTCAAAT
Found at i:249837 original size:20 final size:20
Alignment explanation
Indices: 249806--249879 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
249796 AACAGTGTTA
*
249806 TCGCAACACAATTTTCAAAT
1 TCGCAACGCAATTTTCAAAT
*
249826 TTGCAACGCAATTTTCAAAT
1 TCGCAACGCAATTTTCAAAT
*
249846 TCGCAACGCGATTTTCAAAT
1 TCGCAACGCAATTTTCAAAT
249866 TCGCAACGCTAATT
1 TCGCAACGC-AATT
249880 ACCGATATAG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 45 0.94
21 3 0.06
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (20 bp):
TCGCAACGCAATTTTCAAAT
Found at i:249974 original size:20 final size:20
Alignment explanation
Indices: 249910--249978 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
249900 CTATCGCAAC
* *
249910 GCGATTTTGGAAACTATGTT
1 GCGATTTTGAAAACTGTGTT
* *
249930 GCGA-TTT-ACAAATTCGCGTT
1 GCGATTTTGA-AAACT-GTGTT
*
249950 ACGATTTTGAAAACTGTGTT
1 GCGATTTTGAAAACTGTGTT
249970 GCGATTTTG
1 GCGATTTTG
249979 GAGCCTGTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 7 0.19
20 22 0.59
21 7 0.19
22 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (20 bp):
GCGATTTTGAAAACTGTGTT
Found at i:252091 original size:22 final size:22
Alignment explanation
Indices: 252063--252113 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
252053 AGCATTCAAT
252063 TGAGGCTGCAACTACTGGTCCA
1 TGAGGCTGCAACTACTGGTCCA
252085 TGAGGCTGCAACTACTGGTCCA
1 TGAGGCTGCAACTACTGGTCCA
252107 TGAGGCT
1 TGAGGCT
252114 TATATTTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (22 bp):
TGAGGCTGCAACTACTGGTCCA
Found at i:257811 original size:19 final size:21
Alignment explanation
Indices: 257775--257817 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
257765 ATTCAGTGTA
*
257775 AAAAAATTCCATTATATATTC
1 AAAAAATTCCATTATATATAC
*
257796 AAAAAATT-TATT-TATATAC
1 AAAAAATTCCATTATATATAC
257815 AAA
1 AAA
257818 CTCACTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATTCCATTATATATAC
Found at i:258558 original size:24 final size:23
Alignment explanation
Indices: 258510--258557 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
258500 TTCACCTATT
* *
258510 ATATAAATAATATACAAATTAAA
1 ATATAAATAATATAAAAAATAAA
258533 ATATAAACTAATACTAAAAAATAAA
1 ATATAAA-TAATA-TAAAAAATAAA
258558 TGAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 5 0.24
25 9 0.43
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (23 bp):
ATATAAATAATATAAAAAATAAA
Found at i:259215 original size:21 final size:22
Alignment explanation
Indices: 259191--259231 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
259181 ATTGAGAAGA
259191 TAATTTT-TTAATAA-AAATAGT
1 TAATTTTATTAA-AAGAAATAGT
259212 TAATTTTATTAAAAGAAATA
1 TAATTTTATTAAAAGAAATA
259232 CACCCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TAATTTTATTAAAAGAAATAGT
Found at i:264170 original size:40 final size:40
Alignment explanation
Indices: 264079--264163 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
264069 ACCGATCACT
264079 AAATTAATGATTGAGAAGGTTTTTCTCTCTTCCTAGTGGC
1 AAATTAATGATTGAGAAGGTTTTTCTCTCTTCCTAGTGGC
*
264119 AAATTAATGATTGAGAAGGTTTTTCTTTCTTCCTAGTGGC
1 AAATTAATGATTGAGAAGGTTTTTCTCTCTTCCTAGTGGC
264159 AAATT
1 AAATT
264164 GTTGATTTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (40 bp):
AAATTAATGATTGAGAAGGTTTTTCTCTCTTCCTAGTGGC
Found at i:265010 original size:13 final size:13
Alignment explanation
Indices: 264978--265003 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
264968 ATTTTAGTTT
264978 TAAATAATTAAAA
1 TAAATAATTAAAA
264991 TAAATAATTAAAA
1 TAAATAATTAAAA
265004 GTGATAAATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAATTAAAA
Found at i:266875 original size:3 final size:3
Alignment explanation
Indices: 266867--266898 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
266857 ATATACATAT
266867 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
266899 TGAAGCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:268311 original size:31 final size:32
Alignment explanation
Indices: 268268--268353 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
268258 TCCAACATTT
* *
268268 ACTTTTTATTTCATTTTAATACCCAT-C-GTTA
1 ACTTTTTGTTTCATTTTAGTACCC-TGCTGTTA
*
268299 ATTTTTTGTTTCATTTTAGTACCCTGCTGTTA
1 ACTTTTTGTTTCATTTTAGTACCCTGCTGTTA
268331 ACTTTTTGTTTCATTTTAGTACC
1 ACTTTTTGTTTCATTTTAGTACC
268354 TAATTTTTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.02
31 22 0.45
32 26 0.53
ACGTcount: A:0.20, C:0.17, G:0.08, T:0.55
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTTAGTACCCTGCTGTTA
Found at i:268846 original size:2 final size:2
Alignment explanation
Indices: 268839--268870 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
268829 TCATATCACA
268839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
268871 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269068 original size:23 final size:23
Alignment explanation
Indices: 269042--269085 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
269032 TTTTAATAAG
* *
269042 TCTACCTTTATGTCATGTTTTCA
1 TCTACCTTTATGACACGTTTTCA
*
269065 TCTATCTTTATGACACGTTTT
1 TCTACCTTTATGACACGTTTT
269086 TTCTTTGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.52
Consensus pattern (23 bp):
TCTACCTTTATGACACGTTTTCA
Found at i:270878 original size:23 final size:23
Alignment explanation
Indices: 270826--270879 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
270816 CATAAAAAAT
* *
270826 TGTCATAAGAGCAGAGAAAAATA
1 TGTCACAAGAGCAGAGAAAAACA
* * *
270849 TGCCACAAGAGTAGAGAAAAACG
1 TGTCACAAGAGCAGAGAAAAACA
270872 TGTCACAA
1 TGTCACAA
270880 AGACAACGAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (23 bp):
TGTCACAAGAGCAGAGAAAAACA
Found at i:277148 original size:23 final size:23
Alignment explanation
Indices: 277122--277171 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
277112 GATCACTGAG
*
277122 TTTATTTTTTAAAATTTAATTAC
1 TTTATTTTTTAAAATTCAATTAC
277145 TTTATTTTTTAAAATTCAATTAC
1 TTTATTTTTTAAAATTCAATTAC
277168 TTTA
1 TTTA
277172 CTCCAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTATTTTTTAAAATTCAATTAC
Found at i:277542 original size:5 final size:5
Alignment explanation
Indices: 277532--277560 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
277522 GAACTCCAAA
277532 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
277561 AAGAAAGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:278884 original size:35 final size:36
Alignment explanation
Indices: 278829--278900 Score: 137
Period size: 35 Copynumber: 2.0 Consensus size: 36
278819 TAAACTAATC
278829 TAACAGTCTTAGTTTCATTACAGACTCCAAGTTATT
1 TAACAGTCTTAGTTTCATTACAGACTCCAAGTTATT
278865 TAACAGTCTT-GTTTCATTACAGACTCCAAGTTATT
1 TAACAGTCTTAGTTTCATTACAGACTCCAAGTTATT
278900 T
1 T
278901 CTCTTTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 26 0.72
36 10 0.28
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
TAACAGTCTTAGTTTCATTACAGACTCCAAGTTATT
Found at i:287354 original size:14 final size:14
Alignment explanation
Indices: 287337--287366 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
287327 ATGTTTGTAA
287337 TTAAATTTTTTATT
1 TTAAATTTTTTATT
287351 TTAAATTTTTTATT
1 TTAAATTTTTTATT
287365 TT
1 TT
287367 TAGTGTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTAAATTTTTTATT
Found at i:291867 original size:12 final size:12
Alignment explanation
Indices: 291852--291920 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
291842 GATACATAAC
291852 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
291864 CTGATTTCTGAT
1 CTGAATTCTGTT
*
291876 CTGGATTCTGTT
1 CTGAATTCTGTT
291888 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
*
291900 CTAAATTCTGTT
1 CTGAATTCTGTT
*
291912 -TGATTTCTG
1 CTGAATTCTG
291921 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
11 9 0.19
12 36 0.77
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.17, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:291883 original size:24 final size:24
Alignment explanation
Indices: 291855--291922 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
291845 ACATAACCTG
*
291855 AATTCTGTTCTGATTTCTGATCTG
1 AATTCTGTTCTGATTTCTGATCTA
* * *
291879 GATTCTGTTCTGATATCTGTTCTA
1 AATTCTGTTCTGATTTCTGATCTA
291903 AATTCTGTT-TGATTTCTGAT
1 AATTCTGTTCTGATTTCTGAT
291923 ATCTCCGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 9 0.24
24 28 0.76
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (24 bp):
AATTCTGTTCTGATTTCTGATCTA
Found at i:295934 original size:18 final size:18
Alignment explanation
Indices: 295900--295935 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
295890 TTGAAAGGAC
*
295900 TAAAGTAAATTACAAGAT
1 TAAAGTAAATAACAAGAT
*
295918 TAAAGTAAATAATAAGAT
1 TAAAGTAAATAACAAGAT
295936 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAAGTAAATAACAAGAT
Found at i:297143 original size:48 final size:48
Alignment explanation
Indices: 297091--297184 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
297081 TTCGACTTGA
297091 ATTCTGTTCTGATA-CATGACCTGAATTATGTTCTGATTTCTGATATGG
1 ATTCTGTTCTGATATC-TGACCTGAATTATGTTCTGATTTCTGATATGG
* ** * *
297139 ATTCTGTTTTGATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTGATATCTGACCTGAATTATGTTCTGATTTCTGATAT
297185 CTCCGTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTATGTTCTGATTTCTGATATGG
Found at i:297146 original size:24 final size:24
Alignment explanation
Indices: 297112--297184 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
297102 ATACATGACC
* *
297112 TGAATTATGTTCTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
* * * *
297136 TGGATTCTGTTTTGATATCTGTTC
1 TGAATTCTGTTTTGATTTCTGATA
297160 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTTTGATTTCTGATA
297184 T
1 T
297185 CTCCGTTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATA
Found at i:298064 original size:26 final size:27
Alignment explanation
Indices: 298013--298064 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
298003 AATTAATAGT
* *
298013 TTTTTTAATATAATAATATTTTTAATA
1 TTTTTTAAGATAATAATATTTATAATA
298040 TTTTTTAAGA-AATAA-ATTTCATAAT
1 TTTTTTAAGATAATAATATTT-ATAAT
298065 TATCATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 9 0.41
27 9 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTTTAAGATAATAATATTTATAATA
Found at i:301750 original size:27 final size:27
Alignment explanation
Indices: 301688--301753 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
301678 TAAACAATAC
*
301688 AATCACAAATCATAACCTAAAACCCAA
1 AATCACAACTCATAACCTAAAACCCAA
*
301715 AATCGCAACTCATAACCTAAAACCCAA
1 AATCACAACTCATAACCTAAAACCCAA
301742 AATCACAACTCA
1 AATCACAACTCA
301754 GTCCCATCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.52, C:0.32, G:0.02, T:0.15
Consensus pattern (27 bp):
AATCACAACTCATAACCTAAAACCCAA
Found at i:301896 original size:22 final size:22
Alignment explanation
Indices: 301780--301886 Score: 196
Period size: 22 Copynumber: 4.9 Consensus size: 22
301770 TCACTCTCTG
*
301780 CGGCGACATCCGTCCCCATCTG
1 CGGCGACATCCGTCCCCATCTC
301802 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATCTC
301824 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATCTC
301846 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATCTC
*
301868 CGACGACATCCGTCCCCAT
1 CGGCGACATCCGTCCCCAT
301887 ATCTGACGAC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 83 1.00
ACGTcount: A:0.15, C:0.49, G:0.19, T:0.18
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATCTC
Found at i:302263 original size:20 final size:20
Alignment explanation
Indices: 302223--302282 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
302213 TTTGAAACTT
302223 AAATTCGCAACACGAAAAATG
1 AAATTCGCAACACG-AAAATG
302244 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
302264 AAATTCGTAACACGAAAAT
1 AAATTCGCAACACGAAAAT
302283 CTCAAAGTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:308676 original size:22 final size:23
Alignment explanation
Indices: 308644--308699 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
308634 TATAGGGCAG
*
308644 AGGGAATCGATACCCCC-ATGAA
1 AGGGAACCGATACCCCCTATGAA
* *
308666 AGGGAACCGATTCCCCCTTTGAA
1 AGGGAACCGATACCCCCTATGAA
*
308689 TGGGAACCGAT
1 AGGGAACCGAT
308700 TCCTCCCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
AGGGAACCGATACCCCCTATGAA
Found at i:308688 original size:23 final size:23
Alignment explanation
Indices: 308644--308708 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
308634 TATAGGGCAG
* * *
308644 AGGGAATCGATACCCCC-ATGAA
1 AGGGAACCGATTCCCCCTTTGAA
308666 AGGGAACCGATTCCCCCTTTGAA
1 AGGGAACCGATTCCCCCTTTGAA
*
308689 TGGGAACCGATTCCTCCCTT
1 AGGGAACCGATTCC-CCCTT
308709 AGGGGAATCG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.41
23 17 0.46
24 5 0.14
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (23 bp):
AGGGAACCGATTCCCCCTTTGAA
Found at i:311238 original size:22 final size:23
Alignment explanation
Indices: 311213--311256 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
311203 AATTAAGTTT
311213 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
311235 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
311257 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:313477 original size:16 final size:16
Alignment explanation
Indices: 313455--313493 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
313445 GAAATCATTG
*
313455 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
313471 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
313487 AAAAATT
1 AAAAATT
313494 TGAGATGGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:313680 original size:20 final size:20
Alignment explanation
Indices: 313645--313721 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
313635 TTGTGAAATT
*
313645 AAAATTCGTATTGCGAATTCG
1 AAAA-TCGTGTTGCGAATTCG
* **
313666 AAAATCGAGTTGCGAAAAC-
1 AAAATCGTGTTGCGAATTCG
* *
313685 AAAATTCGTGTTGCGATTTAG
1 AAAA-TCGTGTTGCGAATTCG
*
313706 AAAATCTTGTTGCGAA
1 AAAATCGTGTTGCGAA
313722 AAGGAAACTT
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
19 4 0.09
20 31 0.72
21 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (20 bp):
AAAATCGTGTTGCGAATTCG
Found at i:313700 original size:40 final size:40
Alignment explanation
Indices: 313645--313723 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
313635 TTGTGAAATT
*
313645 AAAATTCGTATTGCGAATTCGAAAATCGAGTTGCGAAAAC
1 AAAATTCGTATTGCGAATTAGAAAATCGAGTTGCGAAAAC
* * **
313685 AAAATTCGTGTTGCGATTTAGAAAATCTTGTTGCGAAAA
1 AAAATTCGTATTGCGAATTAGAAAATCGAGTTGCGAAAA
313724 GGAAACTTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (40 bp):
AAAATTCGTATTGCGAATTAGAAAATCGAGTTGCGAAAAC
Found at i:313770 original size:20 final size:20
Alignment explanation
Indices: 313745--313804 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
313735 TATGAAAAAT
313745 AAATTCACGTTGCGAATTTG
1 AAATTCACGTTGCGAATTTG
313765 AAATTCACGTTGCGAATTTG
1 AAATTCACGTTGCGAATTTG
313785 AAATTC-CGTGTTGCGAATTT
1 AAATTCAC--GTTGCGAATTT
313805 AACTTTTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.03
20 26 0.68
21 11 0.29
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (20 bp):
AAATTCACGTTGCGAATTTG
Found at i:313817 original size:20 final size:20
Alignment explanation
Indices: 313773--313844 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
313763 TGAAATTCAC
* *
313773 GTTGCGAATTTGAAATTCCGT
1 GTTGCGAATTT-AACTTCTGT
*
313794 GTTGCGAATTTAACTTTTGT
1 GTTGCGAATTTAACTTCTGT
* *
313814 GTTGCGATTTTGACTTCTGT
1 GTTGCGAATTTAACTTCTGT
313834 GTTGCG-ATTTA
1 GTTGCGAATTTA
313845 CATATTCGCG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.07
20 29 0.67
21 11 0.26
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.46
Consensus pattern (20 bp):
GTTGCGAATTTAACTTCTGT
Found at i:323220 original size:19 final size:20
Alignment explanation
Indices: 323178--323235 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
323168 TTTAAAATAT
* *
323178 TAAAACATACAAT-TTTTTTT
1 TAAAA-ATACAATATTTTATC
*
323198 TAAAAATGC-ATATTTTATC
1 TAAAAATACAATATTTTATC
323217 TAAAAATACAATATTTTAT
1 TAAAAATACAATATTTTAT
323236 TTAGAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.06
19 16 0.50
20 14 0.44
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (20 bp):
TAAAAATACAATATTTTATC
Found at i:348730 original size:22 final size:22
Alignment explanation
Indices: 348699--348767 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
348689 CACCTCACTC
348699 CATGAATCATGTCATGTTTAAG
1 CATGAATCATGTCATGTTTAAG
*
348721 CATGAGTCATGTCATGTTTAAG
1 CATGAATCATGTCATGTTTAAG
* *
348743 CATGATTCATGTCATGTTCAAG
1 CATGAATCATGTCATGTTTAAG
348765 CAT
1 CAT
348768 AACCTTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (22 bp):
CATGAATCATGTCATGTTTAAG
Found at i:356159 original size:24 final size:24
Alignment explanation
Indices: 356132--356185 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
356122 GTATTCGAAA
356132 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
356156 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
356180 TTTGAT
1 TTTGAT
356186 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:356404 original size:14 final size:14
Alignment explanation
Indices: 356375--356411 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
356365 AGAAAAAGAA
356375 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
356390 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
356404 GAAGAAAA
1 GAAGAAAA
356412 TGCAACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:358431 original size:18 final size:18
Alignment explanation
Indices: 358408--358442 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
358398 AGCAAAAGGC
358408 AATCAAAATCGCAATCAA
1 AATCAAAATCGCAATCAA
*
358426 AATCAAAATCTCAATCA
1 AATCAAAATCGCAATCA
358443 CAACCGGCTT
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:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCGCAATCAA
Found at i:358750 original size:140 final size:140
Alignment explanation
Indices: 358498--358773 Score: 480
Period size: 140 Copynumber: 2.0 Consensus size: 140
358488 ATGCAAACGT
* *
358498 TGTATTATGTGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACA
1 TGTATTATATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACA
* *
358563 TTGCTATGATTTGTTCAGTTATTATCACTTGTTACACATTCATTTGAATATCGCAACGCGAATTT
66 TTGCTATGATCTGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTT
358628 GACTATTATG
131 GACTATTATG
* *
358638 TGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAATA
1 TGTATTATATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACA
* *
358703 TTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATGCGAATTT
66 TTGCTATGATCTGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTT
358768 GACTAT
131 GACTAT
358774 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TGTATTATATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGTTTGAACA
TTGCTATGATCTGTTCAGTTATTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTT
GACTATTATG
Found at i:358769 original size:20 final size:20
Alignment explanation
Indices: 358744--358940 Score: 304
Period size: 20 Copynumber: 9.8 Consensus size: 20
358734 TTACACATTC
* *
358744 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
358764 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
358784 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
358804 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
358824 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
358844 ATATGACTATCACAACGTGA
1 ATTTGACTATCGCAACGCGA
*
358864 ATTTGACTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
358884 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
358904 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
358924 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
358941 AGAAAATTGC
Statistics
Matches: 163, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 163 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:359016 original size:20 final size:20
Alignment explanation
Indices: 358991--359042 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
358981 GACAGGGGCC
*
358991 TTGCGATTTTGGCTTTCGCA
1 TTGCGATTTTGACTTTCGCA
* *
359011 TTGCGATTTTAACTTTCTCA
1 TTGCGATTTTGACTTTCGCA
*
359031 TTGCTATTTTGA
1 TTGCGATTTTGA
359043 GTTTAGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCGCA
Found at i:359220 original size:67 final size:67
Alignment explanation
Indices: 359108--359285 Score: 195
Period size: 71 Copynumber: 2.6 Consensus size: 67
359098 GATTGAAATC
*
359108 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAA-AA-ATTA-TTTACACATC
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAATAATATTATTTTACACATC
359170 AATTA
63 AATTA
* *
359175 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAGAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGCAA-AAATAATAAT-A---TTATTTTACACA
359239 TCAATTA
61 TCAATTA
* *
359246 AACAAATCACACTTTTA-AGAATCAATTAAACAATCAAAAA
1 AACAAATCA-ACTTTTACATAATCAATTAAACAAGCAAAAA
359286 AAGTGTACCC
Statistics
Matches: 97, Mismatches: 4, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
63 17 0.18
64 6 0.06
65 2 0.02
67 19 0.20
70 3 0.03
71 26 0.27
72 24 0.25
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (67 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAATAATATTATTTTACACATCAAT
TA
Found at i:360618 original size:21 final size:21
Alignment explanation
Indices: 360569--360627 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
360559 TTTAAAATGG
* *
360569 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGACCTCTTGAACAA
** *
360590 TGACAGGGGCCTCTTGAACAA
1 TGGGAGGGACCTCTTGAACAA
*
360611 TGGGAGGGAACTCTTGA
1 TGGGAGGGACCTCTTGA
360628 GGGATGATAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.20
Consensus pattern (21 bp):
TGGGAGGGACCTCTTGAACAA
Found at i:360634 original size:42 final size:42
Alignment explanation
Indices: 360569--360680 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
360559 TTTAAAATGG
*
360569 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACAA
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACAA
* ** * **
360611 TGGGAGGGAACTCTTGAGGGATGATAGGGGCCTCTTGAATGA
1 TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACAA
* * *
360653 TAGGAGAGGCA-TCTTGAACGATGACAGG
1 TGGGAG-GGAACTCTTCAACGATGACAGG
360681 TGAGTCAGGC
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 54 0.95
43 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.36, T:0.21
Consensus pattern (42 bp):
TGGGAGGGAACTCTTCAACGATGACAGGGGCCTCTTGAACAA
Found at i:361212 original size:20 final size:20
Alignment explanation
Indices: 361189--361259 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
361179 ACTTAAAATT
*
361189 GCAACGCAAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
361209 GCAACGCGGAAATGACTATC
1 GCAACGCGAAAATGACTATC
**
361229 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
361249 GCAACGCGAAA
1 GCAACGCGAAA
361260 CCAAAATCGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:361313 original size:20 final size:20
Alignment explanation
Indices: 361284--361321 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361274 CGAAACTAAA
*
361284 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
361304 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATTTTCA
361322 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:361345 original size:33 final size:34
Alignment explanation
Indices: 361288--361383 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 34
361278 ACTAAATTCG
*
361288 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
361322 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
** **
361355 CGTTGCGATAGTCAAATTCGCATTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
361384 AGTCATTTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:361382 original size:20 final size:20
Alignment explanation
Indices: 361355--361423 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
361345 GCGATTATCC
*
361355 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
361375 CATTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
361395 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
361415 CGTTGCGAT
1 CGTTGCGAT
361424 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:361433 original size:20 final size:20
Alignment explanation
Indices: 361410--361454 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
361400 CGATAGTCAT
*
361410 TTTCGCGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
* *
361430 TTTCATGTTGTGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
361450 TTTCA
1 TTTCA
361455 AAAACTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTAAG
Found at i:361743 original size:21 final size:21
Alignment explanation
Indices: 361719--361764 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
361709 GTTACCATCT
* *
361719 CACGTAGAGCCGCTACCTCAC
1 CACGTAAAGCCGATACCTCAC
* *
361740 CACGTAAAGTCGATACCTCAT
1 CACGTAAAGCCGATACCTCAC
361761 CACG
1 CACG
361765 CCATGCACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.17
Consensus pattern (21 bp):
CACGTAAAGCCGATACCTCAC
Found at i:363822 original size:22 final size:22
Alignment explanation
Indices: 363788--363852 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
363778 TCTGAGAGAT
363788 GGAGAT-A-GACGGATTTCGCC
1 GGAGATGAGGACGGATTTCGCC
*
363808 GGAGATGAGGACGGATTTCGTC
1 GGAGATGAGGACGGATTTCGCC
* * *
363830 GGAGATGGGGACGAATGTCGCC
1 GGAGATGAGGACGGATTTCGCC
363852 G
1 G
363853 TAGAGAGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 6 0.16
21 1 0.03
22 31 0.82
ACGTcount: A:0.23, C:0.17, G:0.42, T:0.18
Consensus pattern (22 bp):
GGAGATGAGGACGGATTTCGCC
Found at i:363987 original size:20 final size:19
Alignment explanation
Indices: 363962--364030 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
363952 AAATAAAATA
* *
363962 CGCGTTGTGATAATGGAGAT
1 CGCGTTGCGAT-ATAGAGAT
*
363982 CGCGTTGCGATTTAGAGAT
1 CGCGTTGCGATATAGAGAT
*
364001 CGCGTTGCGATTTAGAGAT
1 CGCGTTGCGATATAGAGAT
*
364020 CGCATTGCGAT
1 CGCGTTGCGAT
364031 TTTGTTGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 35 0.78
20 10 0.22
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (19 bp):
CGCGTTGCGATATAGAGAT
Found at i:364001 original size:19 final size:19
Alignment explanation
Indices: 363977--364032 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
363967 TGTGATAATG
363977 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
363996 GAGATCGCGTTGCGATTTA
1 GAGATCGCGTTGCGATTTA
*
364015 GAGATCGCATTGCGATTT
1 GAGATCGCGTTGCGATTT
364033 TGTTGGTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCGTTGCGATTTA
Found at i:371114 original size:30 final size:29
Alignment explanation
Indices: 371064--371144 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
371054 TCAAATATGT
* *
371064 AACTTTTAAAA-TTACAATTTTGATC-CCTA
1 AACTTTTAAAACTTA-TATTTT-ATCTACTA
**
371093 AACTTTTTAAAGTTTATATTTTATCTACTA
1 AAC-TTTTAAAACTTATATTTTATCTACTA
371123 AACTTTTAAAACTTATATTTTA
1 AACTTTTAAAACTTATATTTTA
371145 GTCACTAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 23 0.52
30 18 0.41
31 3 0.07
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.48
Consensus pattern (29 bp):
AACTTTTAAAACTTATATTTTATCTACTA
Found at i:372059 original size:12 final size:12
Alignment explanation
Indices: 372042--372066 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
372032 TCATGGGTTG
372042 AAGAAGAAGAAA
1 AAGAAGAAGAAA
372054 AAGAAGAAGAAA
1 AAGAAGAAGAAA
372066 A
1 A
372067 GTCAAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:373426 original size:19 final size:19
Alignment explanation
Indices: 373399--373435 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
373389 ATGACCAACA
*
373399 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
373418 AAATTGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
373436 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:373578 original size:21 final size:21
Alignment explanation
Indices: 373549--373671 Score: 128
Period size: 21 Copynumber: 6.0 Consensus size: 21
373539 TAAATCACAA
373549 CGCGATTGCGATAGTCCAAATT
1 CGCG-TTGCGATAGTCCAAATT
* *
373571 CGCGTTGCGATAGTTCGAATT
1 CGCGTTGCGATAGTCCAAATT
* *
373592 CGCTTTGCGATAGTCCAAAAT
1 CGCGTTGCGATAGTCCAAATT
* *
373613 --CGTTGCAATAGTCCGAATT
1 CGCGTTGCGATAGTCCAAATT
*
373632 CGCGTTGCGATAGTCCAAAAT
1 CGCGTTGCGATAGTCCAAATT
* *
373653 --CATTGCGATAGTCCGAATT
1 CGCGTTGCGATAGTCCAAATT
373672 TTTACGTTAT
Statistics
Matches: 83, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
19 31 0.37
21 48 0.58
22 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (21 bp):
CGCGTTGCGATAGTCCAAATT
Found at i:373630 original size:40 final size:40
Alignment explanation
Indices: 373549--373671 Score: 174
Period size: 40 Copynumber: 3.0 Consensus size: 40
373539 TAAATCACAA
* *
373549 CGCGATTGCGATAGTCCAAATTCGCGTTGCGATAGTTCGAATT
1 CGCG-TTGCGATAGTCCAAAAT--CGTTGCGATAGTCCGAATT
* *
373592 CGCTTTGCGATAGTCCAAAATCGTTGCAATAGTCCGAATT
1 CGCGTTGCGATAGTCCAAAATCGTTGCGATAGTCCGAATT
*
373632 CGCGTTGCGATAGTCCAAAATCATTGCGATAGTCCGAATT
1 CGCGTTGCGATAGTCCAAAATCGTTGCGATAGTCCGAATT
373672 TTTACGTTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
40 54 0.74
42 16 0.22
43 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (40 bp):
CGCGTTGCGATAGTCCAAAATCGTTGCGATAGTCCGAATT
Found at i:373833 original size:6 final size:6
Alignment explanation
Indices: 373824--373862 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
373814 CATTACCATT
* *
373824 ACCACG ACCACG ACCACG ACCACG ACCATG ACCATG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
373863 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.46, G:0.15, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:373839 original size:18 final size:18
Alignment explanation
Indices: 373818--373862 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
373808 TATTACCATT
*
373818 ACCATTACCACGACCACG
1 ACCATGACCACGACCACG
* *
373836 ACCACGACCACGACCATG
1 ACCATGACCACGACCACG
373854 ACCATGACC
1 ACCATGACC
373863 CGAGACGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.44, G:0.13, T:0.09
Consensus pattern (18 bp):
ACCATGACCACGACCACG
Found at i:374554 original size:6 final size:6
Alignment explanation
Indices: 374538--374569 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
374528 GGTCGGTTCG
374538 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
374570 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:377786 original size:16 final size:16
Alignment explanation
Indices: 377765--377795 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
377755 TAATATTGAA
377765 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
377781 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
377796 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:378323 original size:21 final size:20
Alignment explanation
Indices: 378296--378394 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
378286 AATCAGTTTC
378296 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
378317 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
378338 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
378358 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
378379 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
378395 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:378423 original size:20 final size:20
Alignment explanation
Indices: 378362--378590 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
378352 GATTTTCAAG
* ** *
378362 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
378382 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
378402 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
378422 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
378442 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
378462 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
378482 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
378502 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
378522 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
378542 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
378562 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
378582 AATCACAAC
1 AATCGCAAC
378591 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:379322 original size:24 final size:24
Alignment explanation
Indices: 379283--379329 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
379273 AAATTTGGTC
379283 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
379307 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
379330 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:379521 original size:12 final size:12
Alignment explanation
Indices: 379504--379528 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
379494 ATATAATCCT
379504 GAAGAAGAAAAA
1 GAAGAAGAAAAA
379516 GAAGAAGAAAAA
1 GAAGAAGAAAAA
379528 G
1 G
379529 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:381864 original size:33 final size:33
Alignment explanation
Indices: 381813--382025 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
381803 CGGAAATTAT
* *
381813 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
381846 AATCCCAACAAGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
381879 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
381918 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
381951 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
381984 AATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
382018 AATCGCAA
1 AATCGCAA
382026 TGCGAAATGA
Statistics
Matches: 153, Mismatches: 16, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
32 5 0.03
33 89 0.58
34 30 0.20
35 2 0.01
37 2 0.01
38 14 0.09
39 6 0.04
40 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:381970 original size:14 final size:14
Alignment explanation
Indices: 381951--382005 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
381941 GCGAAATGAA
381951 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
381965 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
381984 AATCGCAACGAGAG
1 AATCGCAACGAGAG
381998 AATCGCAA
1 AATCGCAA
382006 TGCGGAAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:381979 original size:86 final size:89
Alignment explanation
Indices: 381813--382043 Score: 363
Period size: 86 Copynumber: 2.7 Consensus size: 89
381803 CGGAAATTAT
*
381813 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG
381872 AAATGAAAATCGCAATGCGAAATGAA
65 -AATGAAAATCGCAATGCGAAATGAA
381898 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CG-
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
*
381961 A-GAGAATCGCAATGCGAAATGAA
66 ATGAAAATCGCAATGCGAAATGAA
381984 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
382044 TTGCGATTCT
Statistics
Matches: 138, Mismatches: 2, Indels: 11
0.91 0.01 0.07
Matches are distributed among these distances:
85 25 0.18
86 96 0.70
87 1 0.01
88 1 0.01
89 2 0.01
90 2 0.01
91 11 0.08
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (89 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA
ATGAAAATCGCAATGCGAAATGAA
Found at i:382022 original size:53 final size:51
Alignment explanation
Indices: 381827--382049 Score: 288
Period size: 53 Copynumber: 4.3 Consensus size: 51
381817 GCAACGAGAG
*
381827 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-AGAAAATCGCAATGCGAAATGAA
*
381879 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-AGAAAATCGCAATGC-GAAATGAA
*
381932 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-AGAAAATCGCAATGCGAAATGAA
* * * *
381984 AATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACA-GAAAATCGCAATGCGAAATGAA
*
382037 AATCGCATTGCGA
1 AATCGCAATGCGA
382050 TTCTCTCGTT
Statistics
Matches: 155, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
52 61 0.39
53 89 0.57
54 5 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (51 bp):
AATCGCAATGCGAAATGAAAATCGCAACAGAAAATCGCAATGCGAAATGAA
Found at i:382083 original size:53 final size:52
Alignment explanation
Indices: 382020--382135 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
382010 GAAATGAAAA
*
382020 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
382072 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
382125 TCGCATTGCGA
1 TCGCATTGCGA
382136 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:382098 original size:19 final size:19
Alignment explanation
Indices: 382058--382145 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
382048 GATTCTCTCG
382058 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
382078 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
382097 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
382111 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
382130 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
382146 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:382255 original size:14 final size:14
Alignment explanation
Indices: 382236--382272 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
382226 CATCAATTAC
382236 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
382250 ACAAATCATCTTTT
1 ACAAATCAACTTTT
382264 ACAAATCAA
1 ACAAATCAA
382273 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:384239 original size:19 final size:19
Alignment explanation
Indices: 384197--384314 Score: 129
Period size: 19 Copynumber: 6.4 Consensus size: 19
384187 TAGTTTACTT
* *
384197 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
384217 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
**
384236 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
384255 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
384274 TCGCAA--CGACAT---AA
1 TCGCAACGCGAAATGAAAA
*
384288 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
384307 TCGCAACG
1 TCGCAACG
384315 AGAGAATTGT
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 5 0.06
19 52 0.63
20 12 0.15
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:384263 original size:38 final size:38
Alignment explanation
Indices: 384197--384314 Score: 147
Period size: 33 Copynumber: 3.2 Consensus size: 38
384187 TAGTTTACTT
* * *
384197 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAA
384236 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
* *
384274 TCGCAA--CG--A-CATAATCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
384307 TCGCAACG
1 TCGCAACG
384315 AGAGAATTGT
Statistics
Matches: 72, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
33 28 0.39
34 1 0.01
36 2 0.03
38 28 0.39
39 13 0.18
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.12
Consensus pattern (38 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
Found at i:384299 original size:33 final size:33
Alignment explanation
Indices: 384213--384345 Score: 149
Period size: 33 Copynumber: 3.9 Consensus size: 33
384203 CACGAAACTT
*
384213 AAAATCGCAACGCGAAATGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAA--CG--A-C
384251 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
* * *
384284 ATAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
* * * *
384317 AGAATTGTAACGTGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
384346 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
33 55 0.64
34 1 0.01
36 2 0.02
38 28 0.33
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:384368 original size:19 final size:18
Alignment explanation
Indices: 384346--384437 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
384336 AAAATCGCAA
384346 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
384365 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
384379 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
384398 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
384412 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
384431 TGCGATT
1 TGCGATT
384438 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:384381 original size:14 final size:14
Alignment explanation
Indices: 384362--384420 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
384352 TTTGGTTTCG
384362 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
384376 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
384393 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
384409 CGTTGCGATTTT
1 CGTTGCGATTTT
384421 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:384388 original size:33 final size:33
Alignment explanation
Indices: 384346--384469 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
384336 AAAATCGCAA
*
384346 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
384379 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
384412 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
384445 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
384470 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:384447 original size:14 final size:14
Alignment explanation
Indices: 384395--384451 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
384385 TTTGGTTTCG
*
384395 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
384409 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
384428 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
384442 CGTTGCGATT
1 CGTTGCGATT
384452 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:384726 original size:93 final size:93
Alignment explanation
Indices: 384567--384882 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
384557 TCAGGGTATT
384567 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
384632 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
384660 AGTTTAGCAGAATTAGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
384725 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
384753 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
384818 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
384846 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
384883 AAGCAATCTA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:386600 original size:20 final size:20
Alignment explanation
Indices: 386569--386665 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
386559 TTTTGGTTGA
386569 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
386589 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
386609 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
386628 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
386643 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
386663 AAT
1 AAT
386666 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:386621 original size:21 final size:21
Alignment explanation
Indices: 386567--386631 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
386557 TCTTTTGGTT
386567 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
386588 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
386608 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
386629 GAA
1 GAA
386632 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:386635 original size:14 final size:14
Alignment explanation
Indices: 386616--386672 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
386606 GAGAAATGAA
386616 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
386630 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
386649 AATCGCAACGAGAG
1 AATCGCAACGAGAG
386663 AATCGCAACG
1 AATCGCAACG
386673 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:386648 original size:33 final size:33
Alignment explanation
Indices: 386567--386689 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
386557 TCTTTTGGTT
*
386567 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
386608 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
386641 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
386674 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
386690 TGCGATTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:386725 original size:14 final size:14
Alignment explanation
Indices: 386706--386762 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
386696 TTTTGTTTCA
386706 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
386720 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
386739 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
386753 CGTTCCGATT
1 CGTTGCGATT
386763 TTCATTTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:386743 original size:33 final size:33
Alignment explanation
Indices: 386690--386769 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
386680 AAAATCGCAA
**
386690 TGCGATTTTTGTTTCACGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
*
386723 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
*
386756 TCCGATTTTCATTT
1 TGCGATTTTCATTT
386770 TTCTCGTTGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
Found at i:386820 original size:21 final size:20
Alignment explanation
Indices: 386717--386823 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
386707 GTTGCGATTC
386717 TCTCGTTGCGATTTTCA-TT
1 TCTCGTTGCGATTTTCATTT
*
386736 TCGCGTTGCGA--TTC----
1 TCTCGTTGCGATTTTCATTT
*
386750 TCTCGTTCCGATTTTCATTTT
1 TCTCGTTGCGATTTTCA-TTT
**
386771 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCATTT
*
386792 TCACGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
386812 ATCTCGTTGCGA
1 -TCTCGTTGCGA
386824 CTCTTCTGCA
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 10 0.14
20 9 0.13
21 29 0.42
22 6 0.09
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:386945 original size:33 final size:33
Alignment explanation
Indices: 386903--386973 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
386893 AATACTAACT
*
386903 TGAAAATCGCAACGAGATAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
386936 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
386969 TGAAA
1 TGAAA
386974 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:387379 original size:20 final size:20
Alignment explanation
Indices: 387354--387504 Score: 196
Period size: 20 Copynumber: 7.5 Consensus size: 20
387344 TTTAAAAATT
387354 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
*
387374 GCGTTGCGATATACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
387394 GCATTGCGATTTATGGATAC
1 GCGTTGCGATTTACGGATAC
387414 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
*
387434 ACGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
387454 GCGTTGCGATTTATGTG-TTC
1 GCGTTGCGATTTACG-GATAC
* ** *
387474 GCGTTGCGATTTTCATATTC
1 GCGTTGCGATTTACGGATAC
387494 GCGTTGCGATT
1 GCGTTGCGATT
387505 CTGGAAAATC
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
20 114 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:389489 original size:21 final size:21
Alignment explanation
Indices: 389463--389560 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
389453 CAGTTTCAAG
*
389463 AATCGCAACGCGATTATGGAA
1 AATCGCAATGCGATTATGGAA
*
389484 AATCGCAATGCGA-TA-GTACA
1 AATCGCAATGCGATTATGGA-A
* * ** *
389504 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAATGCGATTATGGAA
*
389526 AATCGCAATGCGAATAT-GAA
1 AATCGCAATGCGATTATGGAA
*
389546 AATCGCAACGCGATT
1 AATCGCAATGCGATT
389561 CTGACTATCG
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.03
20 19 0.32
21 34 0.58
22 3 0.05
23 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
AATCGCAATGCGATTATGGAA
Found at i:389612 original size:20 final size:20
Alignment explanation
Indices: 389567--389839 Score: 213
Period size: 20 Copynumber: 13.4 Consensus size: 20
389557 GATTCTGACT
389567 ATCGCAACG-AGTATCCGTAAAA
1 ATCGCAACGCA-TATCCGT--AA
389589 ATCGCAACGCATATCCGTAA
1 ATCGCAACGCATATCCGTAA
*
389609 ATCGCAACGACA-ATACGTAAA
1 ATCGCAACG-CATATCCGT-AA
*
389630 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCATATCCGTAA
* * * *
389650 ATCGTAACGAAAATACGTAA
1 ATCGCAACGCATATCCGTAA
*
389670 ATCGCAACGCGAT-TCTG-AA
1 ATCGCAACGC-ATATCCGTAA
*
389689 TATCGCAACG-AGAATCCGTAAA
1 -ATCGCAACGCA-TATCCGT-AA
*
389711 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCATATCCGTAA
* *
389731 ATAGCAACGACA-ATACGTAAA
1 ATCGCAACG-CATATCCGT-AA
*
389752 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCATATCCGTAA
* *
389772 ATCGCAACG-AGAATCTGTAA
1 ATCGCAACGCA-TATCCGTAA
389792 ATCGCAACG-ATAATCCGTAA
1 ATCGCAACGCAT-ATCCGTAA
* *
389812 ATCGCAACG-AGAATCTGTAA
1 ATCGCAACGCA-TATCCGTAA
389832 ATCGCAAC
1 ATCGCAAC
389840 ACTGAAATTT
Statistics
Matches: 204, Mismatches: 30, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 132 0.65
21 50 0.25
22 18 0.09
23 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCATATCCGTAA
Found at i:389645 original size:41 final size:41
Alignment explanation
Indices: 389567--389839 Score: 337
Period size: 41 Copynumber: 6.7 Consensus size: 41
389557 GATTCTGACT
* * *
389567 ATCGCAACGAGTATCCGTAAAAATCGCAACGCATATCCGTAA
1 ATCGCAACGAGAATACGT-AAAATCGCAACGCGTATCCGTAA
*
389609 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
389650 ATCGTAACGAAAATACGT-AAATCGCAACGCG-ATTC-TGAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-AA
*
389689 TATCGCAACGAGAATCCGTAAAATCGCAACGCGTATCCGTAA
1 -ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
389731 ATAGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
389772 ATCGCAACGAGAAT-CTGT-AAATCGCAACG-ATAATCCGTAA
1 ATCGCAACGAGAATAC-GTAAAATCGCAACGCGT-ATCCGTAA
389812 ATCGCAACGAGAAT-CTGT-AAATCGCAAC
1 ATCGCAACGAGAATAC-GTAAAATCGCAAC
389840 ACTGAAATTT
Statistics
Matches: 207, Mismatches: 17, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
38 1 0.00
39 6 0.03
40 76 0.37
41 103 0.50
42 20 0.10
43 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:389756 original size:122 final size:122
Alignment explanation
Indices: 389545--389839 Score: 443
Period size: 122 Copynumber: 2.4 Consensus size: 122
389535 GCGAATATGA
* *
389545 AAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGTAAAAATCGCAACGCATATCCGTAAA
1 AAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGT-AAAATCGCAACGCATATCCGTAAA
* *
389610 TCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGTAACGAAAATAC-GT
65 TAGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAAAAT-CTGT
*
389668 AAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAATCGCAACGCATATCCGTAAAT
*
389733 AGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTGT
66 AGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAAAATCTGT
** * * *
389790 AAATCGCAACGATAATCCGTAA-ATCGCAACGAGAATCTGT-AAATCGCAAC
1 AAATCGCAACGCGATTCTG-AATATCGCAACGAGAATCCGTAAAATCGCAAC
389840 ACTGAAATTT
Statistics
Matches: 159, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
121 11 0.07
122 108 0.68
123 40 0.25
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (122 bp):
AAATCGCAACGCGATTCTGAATATCGCAACGAGAATCCGTAAAATCGCAACGCATATCCGTAAAT
AGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAAAATCTGT
Found at i:393280 original size:33 final size:33
Alignment explanation
Indices: 393243--393390 Score: 188
Period size: 33 Copynumber: 4.3 Consensus size: 33
393233 CGGAAATTAC
393243 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * *
393276 AATCGCAACGTGAAAATCGCAACGCGAATATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAA-ATGAA
* *
393310 TATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAA
1 AATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAA
393349 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
393382 AATCGCAAC
1 AATCGCAAC
393391 ATAATGCAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
33 52 0.53
34 12 0.12
35 2 0.02
36 4 0.04
37 3 0.03
38 1 0.01
39 12 0.12
40 12 0.12
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:393291 original size:14 final size:14
Alignment explanation
Indices: 393272--393299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
393262 CAATGCGAAA
393272 TGAAAATCGCAACG
1 TGAAAATCGCAACG
393286 TGAAAATCGCAACG
1 TGAAAATCGCAACG
393300 CGAATATGAA
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:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:393309 original size:20 final size:19
Alignment explanation
Indices: 393257--393390 Score: 117
Period size: 19 Copynumber: 7.5 Consensus size: 19
393247 GCAACGAGAG
*
393257 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
393276 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
393290 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
393310 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
393330 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
393349 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
393363 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
393382 AATCGCAAC
1 AATCGCAAC
393391 ATAATGCAGA
Statistics
Matches: 95, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 32 0.34
20 28 0.29
21 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:393497 original size:14 final size:14
Alignment explanation
Indices: 393478--393514 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
393468 CATCAATTAA
393478 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
393492 ACAAATCATCTTTT
1 ACAAATCAACTTTT
393506 ACAAATCAA
1 ACAAATCAA
393515 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:395462 original size:14 final size:14
Alignment explanation
Indices: 395439--395476 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
395429 GCGAAATAAA
* *
395439 AATCGTAACGAGAG
1 AATCGCAACGACAG
395453 AATCGCAACGACAG
1 AATCGCAACGACAG
395467 AATCGCAACG
1 AATCGCAACG
395477 CGAAATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:395527 original size:14 final size:14
Alignment explanation
Indices: 395508--395564 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
395498 AAAATTTTCG
395508 CGTTGCGATTATGT
1 CGTTGCGATTATGT
*
395522 CGTTGCGATTTTCATTT
1 CGTTGCGA--TT-ATGT
*
395539 CGCGTTGCGATTCTGT
1 --CGTTGCGATTATGT
395555 CGTTGCGATT
1 CGTTGCGATT
395565 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATGT
Found at i:395545 original size:33 final size:33
Alignment explanation
Indices: 395503--395648 Score: 238
Period size: 33 Copynumber: 4.4 Consensus size: 33
395493 ATGACAAAAT
*
395503 TTTCGCGTTGCGATTATGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
395536 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
* *
395569 TTTCGCGTTGCGATTCTGTCATTGCAATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
* * *
395602 TTTCTCGTTGCGATTCTCTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
395635 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
395649 AGTCATTTTT
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 104 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTGTCGTTGCGATTTTCA
Found at i:395546 original size:19 final size:19
Alignment explanation
Indices: 395522--395688 Score: 94
Period size: 19 Copynumber: 9.4 Consensus size: 19
395512 GCGATTATGT
395522 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
395541 CGTTGCGA--TTC-TGT--
1 CGTTGCGATTTTCATTTCG
395555 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
395574 CGTTGCGA--TTC-TGT--
1 CGTTGCGATTTTCATTTCG
* * *
395588 CATTGCAATTTTCATTTCT
1 CGTTGCGATTTTCATTTCG
*
395607 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
395621 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
395640 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
*
395661 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
395681 TGTTGCGA
1 CGTTGCGA
395689 AAGTAAACTA
Statistics
Matches: 111, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
14 24 0.22
16 13 0.12
17 13 0.12
19 35 0.32
20 11 0.10
21 15 0.14
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:395905 original size:93 final size:93
Alignment explanation
Indices: 395736--396155 Score: 700
Period size: 93 Copynumber: 4.5 Consensus size: 93
395726 ATGGATTGCA
* * *
395736 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
*
395800 TTAGCAAAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
395829 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
395894 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
395922 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
395987 TAACAGAATTGACAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
396015 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAATGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
396080 TAGCAGAATTGGCAACAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
396108 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGT
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACT-ATTTCACAGT
396156 ATTGGCAGCA
Statistics
Matches: 309, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
92 19 0.06
93 251 0.81
94 39 0.13
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:395985 original size:17 final size:17
Alignment explanation
Indices: 395963--395995 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
395953 AATACTATTT
395963 CACAGTGTTAA-AGAATA
1 CACAGT-TTAACAGAATA
395980 CACAGTTTAACAGAAT
1 CACAGTTTAACAGAAT
395996 TGACAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CACAGTTTAACAGAATA
Found at i:397788 original size:26 final size:25
Alignment explanation
Indices: 397735--397788 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
397725 ATACAAAGTT
* *
397735 AGATATACCAAAAACTACACTATGA
1 AGATATACCAAAAACTAAACTATAA
397760 AGATATACCAAAAACAATAAAC-ATAA
1 AGATATACCAAAAAC--TAAACTATAA
397786 AGA
1 AGA
397789 GTAGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (25 bp):
AGATATACCAAAAACTAAACTATAA
Found at i:397874 original size:20 final size:20
Alignment explanation
Indices: 397844--397906 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
397834 TTTTGGTTGA
397844 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
** *
397864 AATGACTATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
*
397883 AAATGAAAATCGTAACGAGAG
1 -AATGAAAATCGCAACGAGAG
397904 AAT
1 AAT
397907 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:398541 original size:20 final size:20
Alignment explanation
Indices: 398516--398734 Score: 194
Period size: 20 Copynumber: 10.7 Consensus size: 20
398506 CTTTAAAAAT
398516 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
398536 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
398556 TGTCGTTGCGATTTACGGATG
1 CG-CGTTGCGATTTACGGATA
* *
398577 CGCGTTGAGATTTTACGGATT
1 CGCGTTGCGA-TTTACGGATA
* *
398598 CTCGTTGCGATATT-CAGA-A
1 CGCGTTGCGAT-TTACGGATA
* *
398617 TCGCGTTGCGATTTACGTATT
1 -CGCGTTGCGATTTACGGATA
*
398638 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
398658 CGCGTTGCGATTTTACTTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
398678 TGTCGTTGCGATTTAGGGATA
1 CG-CGTTGCGATTTACGGATA
398699 CGCGTTGCGATTTTTACGGATA
1 CGCGTTGCGA--TTTACGGATA
*
398721 CTCGTTGCGATTTA
1 CGCGTTGCGATTTA
398735 TATGTTCGCG
Statistics
Matches: 159, Mismatches: 27, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
19 2 0.01
20 87 0.55
21 52 0.33
22 18 0.11
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:398575 original size:41 final size:41
Alignment explanation
Indices: 398518--398734 Score: 296
Period size: 41 Copynumber: 5.3 Consensus size: 41
398508 TTAAAAATCG
*
398518 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
398559 CGTTGCGATTTACGGATGCGCGTTGAGATTTTACGGATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
398600 CGTTGCGATATT-CAGA-ATCGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTTACGTATTCT
* *
398640 CGTTGCGATTTACGGATACGCGTTGCGATTTTACTTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
398681 CGTTGCGATTTAGGGATACGCGTTGCGATTTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTTACGTATTCT
398723 CGTTGCGATTTA
1 CGTTGCGATTTA
398735 TATGTTCGCG
Statistics
Matches: 154, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 2 0.01
40 33 0.21
41 96 0.62
42 23 0.15
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:398654 original size:81 final size:82
Alignment explanation
Indices: 398518--398734 Score: 289
Period size: 81 Copynumber: 2.6 Consensus size: 82
398508 TTAAAAATCG
* *
398518 CGTTGCGATTTACGG-ATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATGCGCGT
1 CGTTGCGATTTA-GGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGT
398582 TGAGATTTTACGGATTCT
65 TGAGATTTTACGGATTCT
398600 CGTTGCGATATTCA-GAAT-CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 CGTTGCGAT-TT-AGGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCG
* ** *
398662 TTGCGATTTTACTTATTGT
64 TTGAGATTTTACGGATTCT
* * *
398681 CGTTGCGATTTAGGGATACGCGTTGCGATTTTTACGGATACTCGTTGCGATTTA
1 CGTTGCGATTTAGGAATACGCGTTGCGA-TTTTACGTATTCTCGTTGCGATTTA
398735 TATGTTCGCG
Statistics
Matches: 119, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 66 0.55
82 20 0.17
83 26 0.22
84 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (82 bp):
CGTTGCGATTTAGGAATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
GAGATTTTACGGATTCT
Found at i:398771 original size:20 final size:20
Alignment explanation
Indices: 398515--398772 Score: 173
Period size: 20 Copynumber: 12.7 Consensus size: 20
398505 GCTTTAAAAA
*
398515 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCGGAT
* *
398535 ACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTT-CGGAT
*
398556 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTTCGGAT
* *
398576 GCGCGTTGAGATTTTACGGAT
1 TCGCGTTGCGATTTT-CGGAT
* * * *
398597 TCTCGTTGCGATATTCAGAA
1 TCGCGTTGCGATTTTCGGAT
* *
398617 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTTCGGAT
* *
398637 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCGGAT
* **
398657 ACGCGTTGCGATTTTACTTAT
1 TCGCGTTGCGATTTT-CGGAT
**
398678 T-GTCGTTGCGATTTAGGGAT
1 TCG-CGTTGCGATTTTCGGAT
*
398698 ACGCGTTGCGATTTTTACGGAT
1 TCGCGTTGCGA-TTTT-CGGAT
* * **
398720 ACTCGTTGCGATTTATATG-T
1 TCGCGTTGCGATTT-TCGGAT
**
398740 TCGCGTAT-CGATTTTCATAT
1 TCGCGT-TGCGATTTTCGGAT
398760 TCGCGTTGCGATT
1 TCGCGTTGCGATT
398773 CTGGAAAATC
Statistics
Matches: 181, Mismatches: 44, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
19 2 0.01
20 109 0.60
21 55 0.30
22 15 0.08
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCGGAT
Found at i:400035 original size:18 final size:18
Alignment explanation
Indices: 400012--400050 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
400002 AATTTGAATA
*
400012 CTTATTTTATA-ATTAAAC
1 CTTATTTT-TACATGAAAC
400030 CTTATTTTTACATGAAAC
1 CTTATTTTTACATGAAAC
400048 CTT
1 CTT
400051 TAAGAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (18 bp):
CTTATTTTTACATGAAAC
Found at i:400184 original size:12 final size:12
Alignment explanation
Indices: 400167--400191 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
400157 GTCTATTATT
400167 GATCTTTTAAAA
1 GATCTTTTAAAA
400179 GATCTTTTAAAA
1 GATCTTTTAAAA
400191 G
1 G
400192 TTAAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (12 bp):
GATCTTTTAAAA
Found at i:400695 original size:14 final size:15
Alignment explanation
Indices: 400670--400698 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
400660 AAATATTTTT
400670 ATATTATATTATTAA
1 ATATTATATTATTAA
400685 ATATT-TATTATTAA
1 ATATTATATTATTAA
400699 CTTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATTATTAA
Done.