Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005853.1 Hibiscus syriacus cultivar Beakdansim tig00013738_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: 876857
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:364938 original size:12 final size:11
Alignment explanation
Indices: 364921--364987 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 11
364911 GAACCTGGAC
364921 AATAAAACAAAA
1 AATAAAA-AAAA
364933 AATAAAAATAAA
1 AATAAAAA-AAA
*
364945 ATTAATAATAAATA
1 AATAA-AA-AAA-A
*
364959 AATAAATAAATA
1 AATAAA-AAAAA
364971 AATAAAAAAAA
1 AATAAAAAAAA
364982 CAATAA
1 -AATAA
364988 TATTATTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
11 5 0.11
12 26 0.58
13 7 0.16
14 7 0.16
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:364960 original size:4 final size:4
Alignment explanation
Indices: 364938--364976 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
364928 CAAAAAATAA
*
364938 AAAT AAAAT TAAT -AAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
364977 AAAAACAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:365173 original size:38 final size:37
Alignment explanation
Indices: 365120--365339 Score: 172
Period size: 38 Copynumber: 6.0 Consensus size: 37
365110 TAAAACTATG
*
365120 TTTTC-AAAACTATATATTATATGTATTTTCAAAATGT
1 TTTTCAAAAACCATATATTATAT-TATTTTCAAAATGT
* * *
365157 TTTTCAAAAACCATATAATATATACATTTTTAAAATGT
1 TTTTCAAAAACCATATATTATAT-TATTTTCAAAATGT
* *
365195 TTTT-AAAAAAC-TATA-TA-A-TATTTTC-AAACGT
1 TTTTCAAAAACCATATATTATATTATTTTCAAAATGT
* *
365226 TTTTCAAAAACTATATATTATATATATATATTTCAAAAT-A
1 TTTTCAAAAACCATATA-T-TATAT-TAT-TTTCAAAATGT
* * *
365266 TTTTC-AAAACCATATGTTATATAAGTTTTCTAAAAATAT
1 TTTTCAAAAACCATATATTATATTA-TTTTC--AAAATGT
* *
365305 TTTT-AAAAACCATATATTATATAATTTCCAAAATG
1 TTTTCAAAAACCATATATTATATTATTTTCAAAATG
365340 ATTTCGAACT
Statistics
Matches: 147, Mismatches: 20, Indels: 33
0.74 0.10 0.17
Matches are distributed among these distances:
31 9 0.06
32 10 0.07
33 4 0.03
34 1 0.01
35 2 0.01
36 16 0.11
37 18 0.12
38 41 0.28
39 34 0.23
40 9 0.06
41 3 0.02
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACCATATATTATATTATTTTCAAAATGT
Found at i:365210 original size:31 final size:31
Alignment explanation
Indices: 365175--365242 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
365165 AACCATATAA
*
365175 TATATACAT-TTTTAAAATGTTTTTAAAAAAC
1 TATATA-ATATTTTAAAACGTTTTTAAAAAAC
* *
365206 TATATAATATTTTCAAACGTTTTTCAAAAAC
1 TATATAATATTTTAAAACGTTTTTAAAAAAC
365237 TATATA
1 TATATA
365243 TTATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (31 bp):
TATATAATATTTTAAAACGTTTTTAAAAAAC
Found at i:365286 original size:39 final size:37
Alignment explanation
Indices: 365120--365329 Score: 152
Period size: 39 Copynumber: 5.7 Consensus size: 37
365110 TAAAACTATG
* * *
365120 TTTTCAAAACTATATATTATAT-GTATTTTCAAAATGT
1 TTTTCAAAACCATATATTATATAATATTTTCAAAAT-A
* *
365157 TTTTCAAAAACCATATAATATATACAT-TTTT-AAAATG
1 TTTTC-AAAACCATATATTATATA-ATATTTTCAAAATA
* * *
365194 TTTT-TAAA--A-A-ACTATATAATATTTTCAAACGT-
1 TTTTCAAAACCATATATTATATAATATTTTCAAA-ATA
*
365226 TTTTCAAAAACTATATATTATATATATATATTTCAAAATA
1 TTTTC-AAAACCATATATTATATA-ATAT-TTTCAAAATA
* *
365266 TTTTCAAAACCATATGTTATATAAGT-TTTCTAAAAATA
1 TTTTCAAAACCATATATTATATAA-TATTT-TCAAAATA
*
365304 TTTTTAAAAACCATATATTATATAAT
1 -TTTTCAAAACCATATATTATATAAT
365330 TTCCAAAATG
Statistics
Matches: 140, Mismatches: 15, Indels: 35
0.74 0.08 0.18
Matches are distributed among these distances:
30 2 0.01
31 11 0.08
32 8 0.06
33 2 0.01
34 3 0.02
35 3 0.02
36 1 0.01
37 12 0.09
38 37 0.26
39 48 0.34
40 13 0.09
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTCAAAACCATATATTATATAATATTTTCAAAATA
Found at i:365877 original size:36 final size:36
Alignment explanation
Indices: 365827--366389 Score: 501
Period size: 36 Copynumber: 16.1 Consensus size: 36
365817 CAAAGATTGG
* *
365827 TGTTTCAAGAGAAACTGTCTCTAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
365863 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
365899 TGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** *
365935 TGTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*** * *
365971 TGTTTCAACAAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* *
366000 TGTTTCAAGGGAAACTGTCTTAAGAGTGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
366036 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
366072 TGTTTTAAGAGAAACAGTCTCAAGGGAGACAAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
366108 TGTTTCAAGGAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
*
366137 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
366173 TGTTTCAGGGGGAAACTGCCACAAGAGAGACAAAATT
1 TGTTTCA-AGGGAAACTGTCTCAAGAGAGACAAAATT
*
366210 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * ** * * * *
366247 AGTTCCAAAAGAAACTGTCTCAGGGGAGACGAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * **
366283 AGTTTCAA-GGAAA-------AA-AAATTCAAAGATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-A-TT
* *
366312 TGTTTCAAGGGAAACTGTCTCAAAAGATACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
366348 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
366385 TGTTT
1 TGTTT
366390 TGAGTAAATT
Statistics
Matches: 426, Mismatches: 69, Indels: 63
0.76 0.12 0.11
Matches are distributed among these distances:
27 4 0.01
28 4 0.01
29 43 0.10
30 7 0.02
31 2 0.00
32 3 0.01
33 4 0.01
34 1 0.00
35 6 0.01
36 272 0.64
37 73 0.17
38 7 0.02
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:365978 original size:21 final size:21
Alignment explanation
Indices: 365849--365978 Score: 80
Period size: 21 Copynumber: 7.0 Consensus size: 21
365839 AACTGTCTCT
365849 AGAGAGACAAAATTTGTTTCA
1 AGAGAGACAAAATTTGTTTCA
* *
365870 AG-G-G---AAA-CTGTCTCA
1 AGAGAGACAAAATTTGTTTCA
365885 AGAGAGACAAAATTTGTTTCA
1 AGAGAGACAAAATTTGTTTCA
* *
365906 AG-G-G---AAA-CTGTCTCA
1 AGAGAGACAAAATTTGTTTCA
*
365921 AGAGAAACAAAATTTGTTTCA
1 AGAGAGACAAAATTTGTTTCA
*
365942 A-A-AG---AAA-TTGTCTCA
1 AGAGAGACAAAATTTGTTTCA
365957 AGAGAGACAAAATTTGTTTCA
1 AGAGAGACAAAATTTGTTTCA
365978 A
1 A
365979 CAAAAACAGA
Statistics
Matches: 79, Mismatches: 12, Indels: 36
0.62 0.09 0.28
Matches are distributed among these distances:
15 24 0.30
16 12 0.15
17 3 0.04
19 3 0.04
20 12 0.15
21 25 0.32
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (21 bp):
AGAGAGACAAAATTTGTTTCA
Found at i:366015 original size:137 final size:137
Alignment explanation
Indices: 365861--366243 Score: 586
Period size: 137 Copynumber: 2.8 Consensus size: 137
365851 AGAGACAAAA
365861 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * * *
365926 AACAAAATTTGTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAACAAAAACAGATT
66 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTCAACAAAAACAGATT
365991 CAAAGAT
131 CAAAGAT
* * * * *
365998 TTTGTTTCAAGGGAAACTGTCTTAAGAGTGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * * ** *
366063 GACAAAATTTGTTTTAAGAGAAACAGTCTCAAGGGAGACAAAAATTGTTTCAAGGAAAACATATT
66 GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTCAACAAAAACAGATT
366128 CAAAGAT
131 CAAAGAT
* * * *
366135 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAGGGGGAAACTGCCACAAGAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA-AGGGAAACTGTCTCAAGAG
366200 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
65 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
366244 CTTAGTTCCA
Statistics
Matches: 218, Mismatches: 27, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
137 163 0.75
138 55 0.25
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (137 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTGTTTCAACAAAAACAGATT
CAAAGAT
Found at i:366049 original size:101 final size:101
Alignment explanation
Indices: 365827--366389 Score: 414
Period size: 101 Copynumber: 5.4 Consensus size: 101
365817 CAAAGATTGG
* ** *
365827 TGTTTCAAGAGAAACTGTCTCTAGAGAGACAAAATTTGTTTCAAGGGAAACTG-TCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGAT-TC-A-A-AG
* *
365891 ACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAATT
62 ----ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
365935 TGTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAACAAAAACAGATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGATTCAAAGATTT
* *
366000 TGTTTCAAGGGAAACTGTCTTAAGAGTGACAAAATT
66 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * * *
366036 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACAG-TCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGAT-TCAA---AG
** * * *
366100 ACAAAAATTGTTTCAAGGAAAACATAT-TC-A-A-AG----ATTT
62 ----ATTTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
* * * * *
366137 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAGGGGGAAACTGCCACAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA---AG-AA-----A-AACAGAT
* *
366202 ACAAA-A-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
56 TCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * * * *
366247 AGTTCCAAAAGAAACTGTCTCAGGGGAGACGAAGTTAGTTTCAAGGAAAAA-AAATTCAAAGATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GAAAAACAGATTCAAAGATT
* *
366311 TTGTTTCAAGGGAAACTGTCTCAAAAGATACAAAATT
65 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
*
366348 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
366390 TGAGTAAATT
Statistics
Matches: 357, Mismatches: 64, Indels: 74
0.72 0.13 0.15
Matches are distributed among these distances:
100 7 0.02
101 162 0.45
102 56 0.16
103 2 0.01
104 4 0.01
105 6 0.02
106 2 0.01
107 4 0.01
108 67 0.19
109 4 0.01
110 36 0.10
111 7 0.02
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGATTCAAAGATTT
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:366082 original size:19 final size:19
Alignment explanation
Indices: 366027--366083 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
366017 TCTTAAGAGT
366027 GACAAAATTTGTTTTAAGA
1 GACAAAATTTGTTTTAAGA
**
366046 G--AAAA--TGTCTCAAGAGA
1 GACAAAATTTGT-TTTA-AGA
366063 GACAAAATTTGTTTTAAGA
1 GACAAAATTTGTTTTAAGA
366082 GA
1 GA
366084 AACAGTCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 12
0.64 0.09 0.27
Matches are distributed among these distances:
15 3 0.11
16 2 0.07
17 8 0.29
19 10 0.36
20 2 0.07
21 3 0.11
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (19 bp):
GACAAAATTTGTTTTAAGA
Found at i:366083 original size:21 final size:21
Alignment explanation
Indices: 366019--366083 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
366009 GGAAACTGTC
*
366019 TTAAGAGTGACAAAATTTGTT
1 TTAAGAGAGACAAAATTTGTT
*
366040 TT-A-AGAG--AAAA--TGTC
1 TTAAGAGAGACAAAATTTGTT
*
366055 TCAAGAGAGACAAAATTTGTT
1 TTAAGAGAGACAAAATTTGTT
366076 TTAAGAGA
1 TTAAGAGA
366084 AACAGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 8 0.24
19 7 0.21
20 1 0.03
21 12 0.36
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (21 bp):
TTAAGAGAGACAAAATTTGTT
Found at i:366276 original size:73 final size:72
Alignment explanation
Indices: 366135--366295 Score: 171
Period size: 73 Copynumber: 2.2 Consensus size: 72
366125 ATTCAAAGAT
* * * ***
366135 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAGGGGGAAACTGCCACAAGAG
1 TTTGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAGAAAGAAACTGCCACAAGAG
366200 AGACAAAA
65 AGACAAAA
* * * *
366208 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA-AAAGAAACTGTCTCAGGG
1 TTTGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAGAAAGAAACTGCCACAAGA
* *
366272 GAGACGAAG
64 GAGACAAAA
*
366281 TTAGTTTCAAGGAAA
1 TTTGTTTCAAGGAAA
366296 AAAAATTCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
72 5 0.07
73 61 0.84
74 7 0.10
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.24
Consensus pattern (72 bp):
TTTGTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAGAAAGAAACTGCCACAAGAGA
GACAAAA
Found at i:366333 original size:175 final size:173
Alignment explanation
Indices: 365998--366389 Score: 561
Period size: 175 Copynumber: 2.2 Consensus size: 173
365988 ATTCAAAGAT
* * *
365998 TTTGTTTCAAGGGAAACTGTCTTAAGAGTGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGA
* ** * * *
366063 GACAAAATTTGTTTTAAGAGAAACAGTCTCAAGGGAGACAAAAATTGTTTCAAGGAAAACATATT
66 GACAAAATTAGTTCCAAAAGAAACAGTCTCAAGGGAGACAAAAATTGTTTCAAGGAAAAAAAATT
* *
366128 CAAAGATTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
131 CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
* * * *
366171 TTTGTTTCAGGGGGAAACTGCCACAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
1 TTTGTTTCA-AGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAG
* * * *
366236 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAGGGGAGAC-GAAGTTAGTTTCAAGGAAAAAAA
65 AGACAAAA-TTAGTTCCAAAAGAAACAGTCTCAAGGGAGACAAAAATT-GTTTCAAGGAAAAAAA
*
366300 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAAAGATACAAAA
128 ATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
366346 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
366390 TGAGTAAATT
Statistics
Matches: 192, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
173 9 0.05
174 84 0.44
175 99 0.52
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (173 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAATGTCTCAAGAGA
GACAAAATTAGTTCCAAAAGAAACAGTCTCAAGGGAGACAAAAATTGTTTCAAGGAAAAAAAATT
CAAAGATTTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAA
Found at i:367830 original size:95 final size:95
Alignment explanation
Indices: 367622--367872 Score: 279
Period size: 95 Copynumber: 2.6 Consensus size: 95
367612 GGCTAGCTGA
* ** * * * ** *
367622 ATCCATAAAGCCGGGGCGTTTAACCAATTGTTCTAGAGGGACAGCTCAATATCATTGTA-TAAAT
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAAC-CCA-AGC-TT-TATTGCAC
** *
367686 ATTATAATTGCCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTGATCAGGCTAGCTGAATATT
* * * *
367720 ATCCATAAAGCCGGGGTGTTTAACTAATTGCTCTAGAGGGACAACCCAAGCTTTATTGCACATTA
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACCCAAGCTTTATTGCACATTA
*
367785 TAATCACCTTGATCAGGCTAGCTGAATCTT
66 TAATCACCTTGATCAGGCTAGCTGAATATT
* * *
367815 ATCCATAAAGACGGGGCGTTTAACCAATTACTTTAGAGGGACATCTCAAGCTTTATTG
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACCCAAGCTTTATTG
367873 TATATATATA
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
94 2 0.02
95 85 0.64
96 2 0.02
97 2 0.02
98 41 0.31
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACCCAAGCTTTATTGCACATTA
TAATCACCTTGATCAGGCTAGCTGAATATT
Found at i:373199 original size:25 final size:25
Alignment explanation
Indices: 373170--373237 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
373160 ACAATAAAAC
*
373170 AAAAAATAAAAATAAAATTAAT-AAT
1 AAAAAATAAAAAT-AAATAAATAAAT
373195 AAAAAATAAAAATAAATAAATAAAT
1 AAAAAATAAAAATAAATAAATAAAT
*
373220 AAAACAATAATAA-AAATA
1 AAAA-AATAAAAATAAATA
373238 TTATTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 7 0.18
25 25 0.64
26 7 0.18
ACGTcount: A:0.78, C:0.01, G:0.00, T:0.21
Consensus pattern (25 bp):
AAAAAATAAAAATAAATAAATAAAT
Found at i:373201 original size:19 final size:18
Alignment explanation
Indices: 373177--373235 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
373167 AACAAAAAAT
373177 AAAAATAAAATTAATAATA
1 AAAAATAAAA-TAATAATA
373196 AAAAAT-AAA-AATAAATA
1 AAAAATAAAATAAT-AATA
*
373213 AATAAATAAAACAATAATA
1 AA-AAATAAAATAATAATA
373232 AAAA
1 AAAA
373236 TATTATTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 3 0.08
17 6 0.17
18 9 0.25
19 15 0.42
20 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATAAAATAATAATA
Found at i:373206 original size:20 final size:20
Alignment explanation
Indices: 373162--373218 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
373152 GGATCTGGAC
*
373162 AATAAAACAAA-AAAT-AAA
1 AATAAAATAAATAAATAAAA
*
373180 AATAAAATTAAT-AATAAAA
1 AATAAAATAAATAAATAAAA
373199 AATAAAAATAAATAAATAAA
1 AAT-AAAATAAATAAATAAA
373219 TAAAACAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.38
19 6 0.19
20 8 0.25
21 6 0.19
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AATAAAATAAATAAATAAAA
Found at i:373286 original size:37 final size:34
Alignment explanation
Indices: 373245--373342 Score: 88
Period size: 37 Copynumber: 2.6 Consensus size: 34
373235 ATATTATTAT
373245 AAAAATATTTTCCAAAAATCTATATAATATATATTTCAA
1 AAAAATATTTT---AAAAT-TATATAATATATATTTC-A
* **
373284 AAAAATATTTTAAAATTATATATTATATATTTTTTT
1 AAAAATATTTTAAAATTATATA--ATATATATTTCA
*
373320 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTT-AAAATTATATA
373343 GTTTTCAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
35 6 0.12
36 15 0.29
37 20 0.38
39 11 0.21
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (34 bp):
AAAAATATTTTAAAATTATATAATATATATTTCA
Found at i:373311 original size:35 final size:37
Alignment explanation
Indices: 373245--373342 Score: 110
Period size: 36 Copynumber: 2.6 Consensus size: 37
373235 ATATTATTAT
373245 AAAAATATTTTCCAAAAATCTATATAATATATA-TTTCAA
1 AAAAATATTTT-C-AAAAT-TATATAATATATATTTTCAA
* ***
373284 AAAAATATTTT-AAAATTATATATTATATATTTTTTT
1 AAAAATATTTTCAAAATTATATAATATATATTTTCAA
*
373320 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
373343 GTTTTCAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
35 12 0.23
36 18 0.35
37 11 0.21
39 11 0.21
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAATATTTTCAAAATTATATAATATATATTTTCAA
Found at i:373375 original size:25 final size:25
Alignment explanation
Indices: 373316--373392 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
373306 TTATATATTT
* * *
373316 TTTTAAAAATGTTTTCAAAATTATATAG
1 TTTTCAAAATGATTTCAAAA--CTAT-G
*
373344 TTTTCAAGAATG-TTTTAAAACTATG
1 TTTTCAA-AATGATTTCAAAACTATG
373369 TTTTCAAAATGATTTCAAAACTAT
1 TTTTCAAAATGATTTCAAAACTAT
373393 ATATTATATG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 4 0.09
25 19 0.44
26 3 0.07
28 13 0.30
29 4 0.09
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTTCAAAATGATTTCAAAACTATG
Found at i:373483 original size:37 final size:36
Alignment explanation
Indices: 373442--373570 Score: 115
Period size: 37 Copynumber: 3.6 Consensus size: 36
373432 ACGTTTGTAA
*
373442 AAAACTATATATTATGTATATTTTTCAAAATATTTTC
1 AAAACCATATATTA-GTATATTTTTCAAAATATTTTC
* *
373479 AAAACCATATATTA-TATAAGTTTTCTAAAAATATTTTTA
1 AAAACCATATATTAGTAT-A-TTTT-TCAAAATA-TTTTC
* *
373518 AAAACCATATATTA-TATAATTTCCAAAATGA-TTTC
1 AAAACCATATATTAGTATATTTTTCAAAAT-ATTTTC
*
373553 -AAACTATATA-TAGTATAT
1 AAAACCATATATTAGTATAT
373571 AATAAAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.03
34 13 0.17
35 6 0.08
36 6 0.08
37 21 0.27
38 8 0.10
39 21 0.27
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (36 bp):
AAAACCATATATTAGTATATTTTTCAAAATATTTTC
Found at i:373522 original size:39 final size:36
Alignment explanation
Indices: 373441--373539 Score: 126
Period size: 39 Copynumber: 2.6 Consensus size: 36
373431 AACGTTTGTA
* * *
373441 AAAAACTATATATTATGTATATTTTTCAAAATATTTT
1 AAAAACCATATATTATATA-ATTTTTAAAAATATTTT
*
373478 CAAAACCATATATTATATAAGTTTTCTAAAAATATTTTT
1 AAAAACCATATATTATATAA-TTTT-TAAAAATA-TTTT
373517 AAAAACCATATATTATATAATTT
1 AAAAACCATATATTATATAATTT
373540 CCAAAATGAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.02
37 20 0.37
38 10 0.19
39 23 0.43
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (36 bp):
AAAAACCATATATTATATAATTTTTAAAAATATTTT
Found at i:379524 original size:20 final size:20
Alignment explanation
Indices: 379501--379552 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
379491 AACGCGATCC
379501 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
379521 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
379541 CCAAAATCGCAA
1 CCAGAATCGCAA
379553 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:379633 original size:20 final size:20
Alignment explanation
Indices: 379608--379801 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
379598 GATTTTCCAT
* *
379608 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
379628 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
379648 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
379668 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
379688 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
379708 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
379728 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
379748 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
379769 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
379789 AATCGCAACGCGA
1 AATCGCAACGCGA
379802 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:379653 original size:40 final size:39
Alignment explanation
Indices: 379604--379801 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
379594 TTGCGATTTT
* ** *
379604 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
379642 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
379683 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
379723 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
379762 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
379802 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:379691 original size:60 final size:60
Alignment explanation
Indices: 379608--379800 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
379598 GATTTTCCAT
* ** * *
379608 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
379668 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
379728 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
379789 AATCGCAACGCG
1 AATCGCAACGCG
379801 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:380218 original size:33 final size:33
Alignment explanation
Indices: 380179--380249 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
380169 TTCACTTAGA
*
380179 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
380212 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
380245 TTTCA
1 TTTCA
380250 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:380389 original size:14 final size:14
Alignment explanation
Indices: 380370--380424 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
380360 AGAATGACTG
380370 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
380384 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
380403 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
380417 TCGCAACG
1 TCGCAACG
380425 CGAAACCAAA
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:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:380407 original size:33 final size:33
Alignment explanation
Indices: 380370--380440 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
380360 AGAATGACTG
**
380370 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
380403 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
380436 TCGCA
1 TCGCA
380441 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:380458 original size:19 final size:19
Alignment explanation
Indices: 380436--380533 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
380426 GAAACCAAAA
*
380436 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
380455 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
380469 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
380488 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
380502 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
380521 TCGCGTTGCGATT
1 TCGCGTTGCGATT
380534 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:380477 original size:14 final size:14
Alignment explanation
Indices: 380458--380547 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
380448 TTTCATTTCG
380458 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
380472 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
380491 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
380505 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
380522 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
380538 CGTTGCGATT
1 CGTTGCGATT
380548 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:380483 original size:33 final size:33
Alignment explanation
Indices: 380441--380555 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
380431 CAAAATCGCA
380441 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
380474 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
380507 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
380540 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
380556 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:382621 original size:93 final size:93
Alignment explanation
Indices: 382245--382710 Score: 900
Period size: 93 Copynumber: 5.0 Consensus size: 93
382235 TAGATTGCTT
*
382245 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
382310 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
382338 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
382402 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
382430 AGTAAATTTGTTCGGTTGATGCCAATTCTGCTAAA-TGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
382494 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
382522 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
382587 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
382615 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
382680 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
382708 AGT
1 AGT
382711 TTCAATTTGC
Statistics
Matches: 368, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 26 0.07
92 128 0.35
93 214 0.58
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:382761 original size:16 final size:16
Alignment explanation
Indices: 382740--382853 Score: 74
Period size: 19 Copynumber: 6.8 Consensus size: 16
382730 TAGTTTACTT
*
382740 TCGCAACACGAAAAAA
1 TCGCAACGCGAAAAAA
382756 TCGCAACGCGAAACCAAAA
1 TCGCAACGCG-AA--AAAA
382775 TCGCAACGCGAAATGAAAA
1 TCGCAACGCG-AA--AAAA
* *
382794 TCGCAA--CGACAGAA
1 TCGCAACGCGAAAAAA
382808 TCGCAACGCGAAACCAAAA
1 TCGCAACGCG-AA--AAAA
* *
382827 TCGCAA--CGACAAGA
1 TCGCAACGCGAAAAAA
382841 TCGCAACGCGAAA
1 TCGCAACGCGAAA
382854 CCAAAATCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
14 18 0.23
16 17 0.22
17 7 0.09
19 36 0.46
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.07
Consensus pattern (16 bp):
TCGCAACGCGAAAAAA
Found at i:382776 original size:19 final size:19
Alignment explanation
Indices: 382752--382864 Score: 120
Period size: 19 Copynumber: 6.5 Consensus size: 19
382742 GCAACACGAA
382752 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
382771 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
382790 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
382804 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
382823 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
382837 AAGATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
382856 AAAATCGCA
1 AAAATCGCA
382865 TTGCGATTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
14 19 0.25
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 46 0.60
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:382815 original size:33 final size:32
Alignment explanation
Indices: 382772--382864 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
382762 CGCGAAACCA
**
382772 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
382804 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
382837 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
382865 TTGCGATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:382862 original size:52 final size:51
Alignment explanation
Indices: 382752--382864 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 51
382742 GCAACACGAA
* *
382752 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAAC-AC
* * *
382804 AGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGATCGCAACGCGAAAC-C
1 AAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-AT-GAAAAGCGAAACAC
382856 AAAATCGCA
1 AAAATCGCA
382865 TTGCGATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
52 41 0.79
53 3 0.06
54 8 0.15
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAAGCGAAACAC
Found at i:382900 original size:14 final size:14
Alignment explanation
Indices: 382881--382936 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
382871 TTTCATTTCG
382881 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
382895 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
382911 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
382927 CGTTGCGATT
1 CGTTGCGATT
382937 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:382945 original size:33 final size:32
Alignment explanation
Indices: 382865--382955 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
382855 CAAAATCGCA
*
382865 TTGCGATTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
*
382897 TTGCGATTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
382929 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGA-TTTCATTTCGCGTTGCGATT
382956 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 36 0.65
33 19 0.35
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
Found at i:382951 original size:19 final size:18
Alignment explanation
Indices: 382860--382975 Score: 113
Period size: 19 Copynumber: 6.8 Consensus size: 18
382850 GAAACCAAAA
*
382860 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
382878 TCGCGTTGCGA-TTC-TT
1 TCGCGTTGCGATTTCATT
382894 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
382910 TCGCATTGCGA-TTC-TG
1 TCGCGTTGCGATTTCATT
382926 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
**
382943 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGA-TTTCATT
382962 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
382976 TAAGTTTCGT
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
14 15 0.18
15 3 0.04
16 11 0.13
17 8 0.10
18 20 0.24
19 25 0.30
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:382984 original size:20 final size:19
Alignment explanation
Indices: 382927--382992 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
382917 GCGATTCTGT
382927 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
382946 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
382965 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
382985 TGTTGCGA
1 CGTTGCGA
382993 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:384926 original size:14 final size:14
Alignment explanation
Indices: 384907--384942 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
384897 ATTGTTTAAT
384907 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
384921 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
384935 TGATTTGT
1 TGATTTGT
384943 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:385072 original size:18 final size:18
Alignment explanation
Indices: 385049--385148 Score: 136
Period size: 18 Copynumber: 5.6 Consensus size: 18
385039 AAAAATGACT
385049 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
385067 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
385086 ATCGCAA--CGAGA-G-A
1 ATCGCAATGCGAAATGAA
385100 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
385118 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATG-AA
385138 ATCGCAATGCG
1 ATCGCAATGCG
385149 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 5 0.07
18 27 0.37
19 16 0.22
20 12 0.16
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:385141 original size:38 final size:38
Alignment explanation
Indices: 385049--385148 Score: 133
Period size: 33 Copynumber: 2.8 Consensus size: 38
385039 AAAAATGACT
385049 ATCGCAATGCGAAATG-AAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
*
385086 ATCGCAA--CG--A-GAGAATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
385118 ATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGC-GAAATGAAAATCGCAATGCG
385149 TTTATAATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
32 10 0.19
33 18 0.33
34 1 0.02
35 3 0.06
37 8 0.15
38 14 0.26
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
Found at i:385195 original size:52 final size:52
Alignment explanation
Indices: 385155--385365 Score: 297
Period size: 52 Copynumber: 4.0 Consensus size: 52
385145 TGCGTTTATA
385155 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
385207 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
385257 -TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
385311 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
385364 AT
1 AT
385366 GTTGGGATTT
Statistics
Matches: 143, Mismatches: 5, Indels: 21
0.85 0.03 0.12
Matches are distributed among these distances:
47 6 0.04
49 7 0.05
50 8 0.06
52 85 0.59
53 17 0.12
54 7 0.05
55 7 0.05
57 6 0.04
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:385201 original size:19 final size:19
Alignment explanation
Indices: 385177--385393 Score: 258
Period size: 19 Copynumber: 12.4 Consensus size: 19
385167 GATTATCTCG
385177 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
385196 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
385215 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
385229 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
385248 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
385262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
385281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
385300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
385319 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
385333 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
385353 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
385367 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
385386 TTGCGATT
1 TTGCGATT
385394 GTATTTTCCG
Statistics
Matches: 173, Mismatches: 4, Indels: 42
0.79 0.02 0.19
Matches are distributed among these distances:
14 29 0.17
16 25 0.14
17 22 0.13
18 3 0.02
19 82 0.47
20 12 0.07
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:385233 original size:33 final size:33
Alignment explanation
Indices: 385196--385393 Score: 283
Period size: 33 Copynumber: 5.8 Consensus size: 33
385186 TCATTTCGCA
385196 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
385229 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
385262 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG
*
385298 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
385333 TTGCGATTTTCATTTCCGCATTGCGA-T-TTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTTTC--G
* *
385367 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
385394 GTATTTTCCG
Statistics
Matches: 152, Mismatches: 4, Indels: 17
0.88 0.02 0.10
Matches are distributed among these distances:
32 3 0.02
33 83 0.55
34 26 0.17
35 7 0.05
36 8 0.05
38 25 0.16
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
Found at i:385234 original size:14 final size:14
Alignment explanation
Indices: 385215--385269 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
385205 TCATTTCGCA
385215 TTGCGATTCTTTCG
1 TTGCGATTCTTTCG
385229 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
385246 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
385262 TTGCGATT
1 TTGCGATT
385270 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.39
16 8 0.22
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:385298 original size:104 final size:104
Alignment explanation
Indices: 385177--385393 Score: 366
Period size: 104 Copynumber: 2.1 Consensus size: 104
385167 GATTATCTCG
*
385177 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
385242 TT-CGCATTGCGATTCTTTC-GTTGCGATTTTCATTTCGCA
66 TTCCGCATTGCGA-T-TTTCAGTTGCGATTTTCATTTCGCA
385281 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
385346 TTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCG
66 TTCCGCATTGCGATTTTCA-GTTGCGATTTTCATTTCGCA
385386 TTGCGATT
1 TTGCGATT
385394 GTATTTTCCG
Statistics
Matches: 107, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
103 4 0.04
104 67 0.63
105 36 0.34
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (104 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCCGCATTGCGATTTTCAGTTGCGATTTTCATTTCGCA
Found at i:387488 original size:250 final size:246
Alignment explanation
Indices: 387021--387516 Score: 908
Period size: 250 Copynumber: 2.0 Consensus size: 246
387011 AAACAGCAAC
387021 TCAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGATTTTCAGCTTTAAATTG
1 TCAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGATTTTCAGCTTTAAATTG
387086 TGACAATAAGCCGGCAGTTGGGCAAACGATGCTTCTGGCCCCCTCAACAATTCCAAGGCATAACA
66 TGACAATAAGCCGGCAGTTGGGCAAACGATGCTTCTGGCCCCCTCAACAATTCCAAGGCATAACA
387151 TTTGGCTCTCCAAGCTTGAGAATATGATATAACTAATCTTGAACCGAGCATTGTCAGTCATAATT
131 TTTGGCTCTCCAAGCTTGAGAATATGATATAACTAATCTTGAACCGAGCATTGTCAGTCATAATT
387216 TCATGTCCCCGATATAACCCTGCCATTCAAAAACATTAACTCAGCCAGAAA
196 TCATGTCCCCGATATAACCCTGCCATTCAAAAACATTAACTCAGCCAGAAA
387267 TCAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGATTTTTCAGCTTTAAATT
1 TCAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGA-TTTTCAGCTTTAAATT
387332 GTGACAATAAGCCGGCAGTTGGGCAAACGATGCTTCTGGCGACCCCCTCAACAATTCCAAGGCAT
65 GTGACAATAAGCCGGCAGTTGGGCAAACGATGCTTCT-G-G-CCCCCTCAACAATTCCAAGGCAT
387397 AACATTTGGCTCTCCAAGCTTGAGAATATGATAT-ACTAATCTTGAACCGAGCATTCATGTCAGT
127 AACATTTGGCTCTCCAAGCTTGAGAATATGATATAACTAATCTTGAACCGAGCA-T--TGTCAGT
387461 CATAATTTCATGT-CCCGATAT-ACCCTGCCATTCAAAAACATTAACTCAGCCAGAAA
189 CATAATTTCATGTCCCCGATATAACCCTGCCATTCAAAAACATTAACTCAGCCAGAAA
387517 ACCACCCAAC
Statistics
Matches: 243, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
246 48 0.20
247 53 0.22
248 1 0.00
249 20 0.08
250 93 0.38
251 8 0.03
252 20 0.08
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (246 bp):
TCAAAGCGTCCATCTCTATCTGTTTTGATATGAGTTACCGACCCAGGATTTTCAGCTTTAAATTG
TGACAATAAGCCGGCAGTTGGGCAAACGATGCTTCTGGCCCCCTCAACAATTCCAAGGCATAACA
TTTGGCTCTCCAAGCTTGAGAATATGATATAACTAATCTTGAACCGAGCATTGTCAGTCATAATT
TCATGTCCCCGATATAACCCTGCCATTCAAAAACATTAACTCAGCCAGAAA
Found at i:388136 original size:24 final size:24
Alignment explanation
Indices: 388102--388148 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
388092 CTGAAACATC
388102 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
388126 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
388149 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:388851 original size:20 final size:20
Alignment explanation
Indices: 388823--389157 Score: 312
Period size: 20 Copynumber: 17.4 Consensus size: 20
388813 AAATTTCAGT
* * * *
388823 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
388843 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* *
388863 GTTGCGATTTACAGAT--TC
1 GTTGCGATTTACGGATACGC
*
388881 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
388901 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
388921 GTTGCGA-TTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
388940 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
388960 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
388980 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
389000 GGTTGCGATTTACGGATACAC
1 -GTTGCGATTTACGGATACGC
*
389021 GTTGCGGTTTACGGAT-CGC
1 GTTGCGATTTACGGATACGC
389040 GTTGCGATTTAC-GATACGC
1 GTTGCGATTTACGGATACGC
389059 GTTGCG----A---ATACG-
1 GTTGCGATTTACGGATACGC
* *
389071 GAT--GATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
389089 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
389109 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
389129 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
389149 GTTGCGATT
1 GTTGCGATT
389158 ATGGAAAATC
Statistics
Matches: 270, Mismatches: 24, Indels: 42
0.80 0.07 0.12
Matches are distributed among these distances:
10 1 0.00
12 2 0.01
13 5 0.02
14 1 0.00
15 1 0.00
17 4 0.01
18 21 0.08
19 43 0.16
20 172 0.64
21 20 0.07
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:389092 original size:30 final size:30
Alignment explanation
Indices: 389045--389104 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
389035 ATCGCGTTGC
*
389045 GATTTACGATACGCGTTGCGA-ATACGGAT
1 GATTTACGATACACGTTGCGATATACGGAT
*
389074 GATTTACGGATACACGTTGCGATTTACGGAT
1 GATTTAC-GATACACGTTGCGATATACGGAT
389105 ACGCGTTGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 7 0.26
30 13 0.48
31 7 0.26
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (30 bp):
GATTTACGATACACGTTGCGATATACGGAT
Found at i:403436 original size:43 final size:42
Alignment explanation
Indices: 403371--403510 Score: 154
Period size: 43 Copynumber: 3.3 Consensus size: 42
403361 TATATTGAAC
403371 AAACGCCGCAACAAGTTCTGATATTTAGCGGCGTTTTTCTTAA
1 AAACGCCGCAACAAGTT-TGATATTTAGCGGCGTTTTTCTTAA
* * * *
403414 AAATGCCGCAACATGTTGTGATATTTAGCGGCGTTTTTATTAC
1 AAACGCCGCAACAAGTT-TGATATTTAGCGGCGTTTTTCTTAA
* * * * * *
403457 AAACGCCGTAATAGGTTTGGACATTTAGTGGCGTTTTTCTTAC
1 AAACGCCGCAACAAGTTT-GATATTTAGCGGCGTTTTTCTTAA
*
403500 AAACGCAGCAA
1 AAACGCCGCAA
403511 TATGATCTGG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 1 0.01
43 81 0.99
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
AAACGCCGCAACAAGTTTGATATTTAGCGGCGTTTTTCTTAA
Found at i:412701 original size:41 final size:40
Alignment explanation
Indices: 412637--412772 Score: 114
Period size: 41 Copynumber: 3.3 Consensus size: 40
412627 CGACGTTTAG
* * *
412637 GTAAAAAACACCAATATTGTTCAACTCTATTACGGTGTTT
1 GTAAAAAACGCCTATATTATTCAACTCTATTACGGTGTTT
* * *
412677 GTAGAAAAACGCCTATATTATTCAACTATATTATGGCGTTT
1 GTA-AAAAACGCCTATATTATTCAACTCTATTACGGTGTTT
* * * *
412718 ACATAAAAAATGCCTCTATATATT-ACAC-CTATTACGGTATTT
1 --GTAAAAAACGCCTATAT-TATTCA-ACTCTATTACGGTGTTT
412760 GTACAAAAACGCC
1 GTA-AAAAACGCC
412773 GCTAATGTAT
Statistics
Matches: 75, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
40 5 0.07
41 39 0.52
42 23 0.31
43 8 0.11
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (40 bp):
GTAAAAAACGCCTATATTATTCAACTCTATTACGGTGTTT
Found at i:414004 original size:22 final size:22
Alignment explanation
Indices: 413979--414024 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
413969 ACGTTTTCAG
* *
413979 AAGCTATTATTTTCCTATTCGA
1 AAGCAATTATTTTCCTATTAGA
*
414001 AAGCAATTATTTTTCTATTAGA
1 AAGCAATTATTTTCCTATTAGA
414023 AA
1 AA
414025 ACAAAAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
AAGCAATTATTTTCCTATTAGA
Found at i:414474 original size:39 final size:39
Alignment explanation
Indices: 414431--414559 Score: 105
Period size: 42 Copynumber: 3.2 Consensus size: 39
414421 ATATTTTTGT
414431 GGCGTTTTTATAAAAACGCCACTATAAACAACATATTGC
1 GGCGTTTTTATAAAAACGCCACTATAAACAACATATTGC
* * * ** *
414470 GGCGTTTGTATGAAAAACGCCGCTATATTATTACTCTATTGC
1 GGCGTTTTTAT-AAAAACGCCACTATA-AACAAC-ATATTGC
*** * *
414512 GGCGTTTTGCGCACAAACGCCACTATAAACAATACTATTGC
1 GGCGTTTT-TATAAAAACGCCACTATAAACAACA-TATTGC
*
414553 GGTGTTT
1 GGCGTTT
414560 GTTTAGTAAA
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
39 10 0.15
40 14 0.21
41 17 0.25
42 26 0.39
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (39 bp):
GGCGTTTTTATAAAAACGCCACTATAAACAACATATTGC
Found at i:414538 original size:82 final size:80
Alignment explanation
Indices: 414444--414649 Score: 234
Period size: 83 Copynumber: 2.5 Consensus size: 80
414434 GTTTTTATAA
* * * *
414444 AAACGCCACTATAAACAACATATTGCGGCGTTTGTATGAAAAACGCCGCTATATTATTACTCTAT
1 AAACGCCACTATAAACAACATATTGCGGTGTTTGT-TGAAAAACGCCGATAAATTACTACTCTAT
*
414509 TGCGGCGTTT-TGCGCAC
65 AGCGGCGTTTGT-CG-AC
* * * *
414526 AAACGCCACTATAAACAATACTATTGCGGTGTTTGTTTAGTAAACGCCGATAAATTACTCCTCTA
1 AAACGCCACTATAAACAACA-TATTGCGGTGTTTGTTGA-AAAACGCCGATAAATTACTACTCTA
* * *
414591 TAGCGTCGTTTGTTGAT
64 TAGCGGCGTTTGTCGAC
* *
414608 AAACGCCACTATAAACAACATCTTACGGTGTTTGTTGAAAAA
1 AAACGCCACTATAAACAACATATTGCGGTGTTTGTTGAAAAA
414650 ATGCCACTAT
Statistics
Matches: 104, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
80 3 0.03
81 15 0.14
82 41 0.39
83 44 0.42
84 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (80 bp):
AAACGCCACTATAAACAACATATTGCGGTGTTTGTTGAAAAACGCCGATAAATTACTACTCTATA
GCGGCGTTTGTCGAC
Found at i:414775 original size:39 final size:40
Alignment explanation
Indices: 414686--414777 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 40
414676 CCGTTTTAGC
*
414686 TATAAACGCCGCTAAATTACACTCTATTACGGCGTTTGTT
1 TATAAACGCCGCTAAAGTACACTCTATTACGGCGTTTGTT
* *
414726 TAAAAGACGCCGCTAAAGTATCA-T-T-TTATGGCGTTTGTAT
1 TATAA-ACGCCGCTAAAGTA-CACTCTATTACGGCGTTTGT-T
*
414766 TGTAAACGCCGC
1 TATAAACGCCGC
414778 GATATACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
39 19 0.43
40 9 0.20
41 14 0.32
42 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (40 bp):
TATAAACGCCGCTAAAGTACACTCTATTACGGCGTTTGTT
Found at i:424789 original size:19 final size:19
Alignment explanation
Indices: 424764--424814 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
424754 TCTAGAAATG
424764 GTATCGATACTAGGGGTC-
1 GTATCGATACTAGGGGTCA
424782 GATATCGATACTCAGGGGTCA
1 G-TATCGATACT-AGGGGTCA
*
424803 GTACCGATACTA
1 GTATCGATACTA
424815 AAGGCTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.38
20 16 0.55
21 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (19 bp):
GTATCGATACTAGGGGTCA
Found at i:429567 original size:22 final size:19
Alignment explanation
Indices: 429521--429591 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 19
429511 TGCAAAAATG
*
429521 GTATCGATACCAAAGTAGA
1 GTATCGATACCATAGTAGA
429540 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG--TAG-A
* *
429562 GTATCGATACCATGGTAGG
1 GTATCGATACCATAGTAGA
429581 GATATCGATAC
1 G-TATCGATAC
429592 TATGGAGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.33
20 12 0.27
21 3 0.07
22 15 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (19 bp):
GTATCGATACCATAGTAGA
Found at i:430062 original size:45 final size:44
Alignment explanation
Indices: 430006--430145 Score: 165
Period size: 45 Copynumber: 3.4 Consensus size: 44
429996 ATAAAAGAAT
430006 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT-A
* * *
430051 AATGAATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T-
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTA
430085 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT-A
430130 AATGCATATGGGTGCA
1 AATGCATATGGGTGCA
430146 ATATCGACAT
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
34 23 0.29
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 1 0.01
43 1 0.01
44 3 0.04
45 39 0.50
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (44 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTA
Found at i:430099 original size:34 final size:34
Alignment explanation
Indices: 430051--430183 Score: 122
Period size: 34 Copynumber: 3.6 Consensus size: 34
430041 CCATAGCTGA
*
430051 AATGAATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGACATAAAAGAAT
* *
430085 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T
*
430128 AAAATGCATATGGGTGCAATATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGACATAAAAGAAT
*
430164 AATGCATATAGGTGCATTAT
1 AATGCATATGGGTGCATTAT
430184 TGCCATGAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
34 41 0.51
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 1 0.01
43 1 0.01
44 3 0.04
45 23 0.29
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGACATAAAAGAAT
Found at i:430210 original size:79 final size:79
Alignment explanation
Indices: 429996--430215 Score: 368
Period size: 79 Copynumber: 2.8 Consensus size: 79
429986 GAATGAATGA
* *
429996 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGAATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATG
*
430061 GGTGCATTATCGAC
66 GGTGCAATATCGAC
430075 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATG
430140 GGTGCAATATCGAC
66 GGTGCAATATCGAC
* * * **
430154 ATAAAAGAATAATGCATATAGGTGCATTATTGCCATGAAAGGATGCTATAAATAAAATGCAT
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCAT
430216 GAAAGGATGC
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 133 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATG
GGTGCAATATCGAC
Found at i:436042 original size:2 final size:2
Alignment explanation
Indices: 436035--436079 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
436025 CAATTACTAT
436035 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
436076 TA TA
1 TA TA
436080 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:436663 original size:105 final size:107
Alignment explanation
Indices: 436542--436783 Score: 265
Period size: 107 Copynumber: 2.3 Consensus size: 107
436532 GTGATGAAGT
* * *
436542 TATTGTTAATAGTATCGAATATTTGGTCACT-GAAAAACATTTATTGTGACAACATTGGTGGTCA
1 TATTGATAATAGTATCGAATATTTGGTCACTAGAAAAACATTTAGTGTGACAACATTGATGGTCA
* * * * * *
436606 CAAAA-TATACTTTCAGTGT-CAAATATATTTATCACAATTTC
66 AAAAATTATACTTTCAATGTAAAAAAATA-TCATCACAATTTA
* ** * * *
436647 TATTGATAATAGTATCGAACATTAAGTCACTATAAAAATATTTAGTGTGACAATATTGATGGTCA
1 TATTGATAATAGTATCGAATATTTGGTCACTAGAAAAACATTTAGTGTGACAACATTGATGGTCA
* *
436712 AAAAATTATATTTTTAATGTAAAAAAATATCATCACAATTTA
66 AAAAATTATACTTTCAATGTAAAAAAATATCATCACAATTTA
* * **
436754 TATTGATAATTGTGTCGAATAGATGGTCAC
1 TATTGATAATAGTATCGAATATTTGGTCAC
436784 AAAAAAAAAC
Statistics
Matches: 110, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
105 27 0.25
106 32 0.29
107 45 0.41
108 6 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (107 bp):
TATTGATAATAGTATCGAATATTTGGTCACTAGAAAAACATTTAGTGTGACAACATTGATGGTCA
AAAAATTATACTTTCAATGTAAAAAAATATCATCACAATTTA
Found at i:437420 original size:44 final size:44
Alignment explanation
Indices: 437353--437436 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
437343 ATAACAAAAG
437353 CAAAGAGAATATATATTTGAACAAATACAAGCTTGTGAAGCTTA
1 CAAAGAGAATATATATTTGAACAAATACAAGCTTGTGAAGCTTA
* **
437397 CAAAGAGAATATATATTTTAACAAATGTAAGCTTGTGAAG
1 CAAAGAGAATATATATTTGAACAAATACAAGCTTGTGAAG
437437 TTTGCTCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (44 bp):
CAAAGAGAATATATATTTGAACAAATACAAGCTTGTGAAGCTTA
Found at i:437845 original size:68 final size:67
Alignment explanation
Indices: 437736--437864 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 67
437726 TATTGGCAGT
** * *
437736 TTGAGTGCGTTGGGCATGTGGAGTGTCTATGTGCTTTATGGTTTGCATGACAATGTGGTTCTTGG
1 TTGAGTGCGTAAGCCATGTGGAGTGTCTACGTGCTTTATGG-TTGCATGACAATGTGGTTCTTGG
437801 TCG
65 TCG
*
437804 TTGAGTGCGTAAGCCATGTGGAGTGTCTACGTGTTTTATGGTTGCATGACAATGTGGTTCT
1 TTGAGTGCGTAAGCCATGTGGAGTGTCTACGTGCTTTATGGTTGCATGACAATGTGGTTCT
437865 ATCTTTAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 20 0.36
68 36 0.64
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (67 bp):
TTGAGTGCGTAAGCCATGTGGAGTGTCTACGTGCTTTATGGTTGCATGACAATGTGGTTCTTGGT
CG
Found at i:439788 original size:175 final size:176
Alignment explanation
Indices: 439482--439834 Score: 690
Period size: 175 Copynumber: 2.0 Consensus size: 176
439472 GCATCGATAG
439482 TGCATCAATGCACTGTAGAATGTATCGATACACTTCAAGGGGAAAATAGAATTAGACCTTTCTTT
1 TGCATCAATGCAC-GTAGAATGTATCGATACACTTCAAGGGGAAAATAGAATTAGACCTTTCTTT
439547 TGGTCTAAGAAATGATAGATTAGAATACATCAATTGGATACTGATATGTATCAATGTATGATTAT
65 TGGTCTAAGAAATGATAGATTAGAATACATCAATTGGATACTGATATGTATCAATGTATGATTAT
439612 GTAGATATCAAGCACGAACAAGTTCCGTGACGACTATCAGATTAAGA
130 GTAGATATCAAGCACGAACAAGTTCCGTGACGACTATCAGATTAAGA
439659 TGCATCAATGCAC-TAGAATGTATCGATACACTTCAAGGGGAAAATAGAATTAGACCTTTCTTTT
1 TGCATCAATGCACGTAGAATGTATCGATACACTTCAAGGGGAAAATAGAATTAGACCTTTCTTTT
439723 GGTCTAAGAAATGATAGATTAGAATACATCAATTGGATACTGATATGTATCAATGTATGATTATG
66 GGTCTAAGAAATGATAGATTAGAATACATCAATTGGATACTGATATGTATCAATGTATGATTATG
439788 TAGATATCAAGCACGAACAAGTTCCGTGACGACTATCAGATTAAGA
131 TAGATATCAAGCACGAACAAGTTCCGTGACGACTATCAGATTAAGA
439834 T
1 T
439835 TCGATCGAAA
Statistics
Matches: 176, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
175 163 0.93
177 13 0.07
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (176 bp):
TGCATCAATGCACGTAGAATGTATCGATACACTTCAAGGGGAAAATAGAATTAGACCTTTCTTTT
GGTCTAAGAAATGATAGATTAGAATACATCAATTGGATACTGATATGTATCAATGTATGATTATG
TAGATATCAAGCACGAACAAGTTCCGTGACGACTATCAGATTAAGA
Found at i:440497 original size:18 final size:18
Alignment explanation
Indices: 440474--440526 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
440464 AGGGATTAAG
440474 AGTGGTCCTTCGGGACAC
1 AGTGGTCCTTCGGGACAC
* *
440492 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAC
*
440510 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
440527 AATTCTACGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAC
Found at i:444744 original size:36 final size:34
Alignment explanation
Indices: 444610--444790 Score: 124
Period size: 31 Copynumber: 5.6 Consensus size: 34
444600 AGAAGGGATT
* *
444610 TTAAATAAAATATTAATTTAGTTTGAGTTTTAAATA
1 TTAAATAAAATATTAATTTAATTTGA-TATT-AATA
444646 TTAAAT--AATA-T-A-TTAATTTGATATTAATA
1 TTAAATAAAATATTAATTTAATTTGATATTAATA
* * *
444675 --AAGGTAAATTATTAATTTAATCT-ATATT--T-
1 TTAA-ATAAAATATTAATTTAATTTGATATTAATA
444704 TTAAATAAAATATTAATTTAATTTGAGTATTAAATA
1 TTAAATAAAATATTAATTTAATTTGA-TATT-AATA
* * *
444740 TTAAAT--AATATTAATTTAATCT-CTA--AATT
1 TTAAATAAAATATTAATTTAATTTGATATTAATA
*
444769 TTAAATAAAATATTATTTTAAT
1 TTAAATAAAATATTAATTTAAT
444791 CTTTAAATTA
Statistics
Matches: 117, Mismatches: 12, Indels: 37
0.70 0.07 0.22
Matches are distributed among these distances:
27 2 0.02
28 1 0.01
29 13 0.11
30 24 0.21
31 25 0.21
32 13 0.11
33 7 0.06
34 19 0.16
35 1 0.01
36 12 0.10
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (34 bp):
TTAAATAAAATATTAATTTAATTTGATATTAATA
Found at i:444780 original size:34 final size:32
Alignment explanation
Indices: 444684--444785 Score: 86
Period size: 34 Copynumber: 3.1 Consensus size: 32
444674 AAAGGTAAAT
*
444684 TATTAATTTAATCTATATTTTTAAAT--AA-AA
1 TATTAATTTAATCT-TAATTTTAAATAAAATAA
* *
444714 TATTAATTTAAT-TTGAGTATTAAATATTAAATAA
1 TATTAATTTAATCTT-AATTTTAAATA--AAATAA
*
444748 TATTAATTTAATCTCTAAATTTTAAATAAAATAT
1 TATTAATTTAATCT-T-AATTTTAAATAAAATAA
444782 TATT
1 TATT
444786 TTAATCTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
28 1 0.02
29 9 0.16
30 12 0.21
33 2 0.03
34 23 0.40
35 1 0.02
36 10 0.17
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (32 bp):
TATTAATTTAATCTTAATTTTAAATAAAATAA
Found at i:444789 original size:31 final size:29
Alignment explanation
Indices: 444734--444799 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 29
444724 ATTTGAGTAT
*
444734 TAAATATTAAATAATATTAATTTAATCTC
1 TAAATTTTAAATAATATTAATTTAATCTC
* *
444763 TAAATTTTAAATAAAATATTATTTTAATCTT
1 TAAATTTTAAAT--AATATTAATTTAATCTC
444794 TAAATT
1 TAAATT
444800 AATCAAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 11 0.34
31 21 0.66
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (29 bp):
TAAATTTTAAATAATATTAATTTAATCTC
Found at i:444789 original size:65 final size:63
Alignment explanation
Indices: 444637--444790 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 63
444627 TTAGTTTGAG
* * *
444637 TTTTAAATATTAAATAATATATTAATTTGATATTAATAAAGGTAAATTATTAATTTAATCTATAT
1 TTTTAAATA--AAATATTATTTTAATTTGATATTAATAAAGGTAAATTATTAATTTAATCTATAA
* * * *
444702 TTTTAAATAAAATATTAATTTAATTTGAGTATTAA-ATA-TTAAATAATATTAATTTAATCTCTA
1 TTTTAAATAAAATATTATTTTAATTTGA-TATTAATAAAGGTAAAT--TATTAATTTAATCTAT-
444765 AA
62 AA
444767 TTTTAAATAAAATATTATTTTAAT
1 TTTTAAATAAAATATTATTTTAAT
444791 CTTTAAATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
62 5 0.06
63 18 0.23
64 21 0.27
65 33 0.43
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (63 bp):
TTTTAAATAAAATATTATTTTAATTTGATATTAATAAAGGTAAATTATTAATTTAATCTATAA
Found at i:444912 original size:14 final size:14
Alignment explanation
Indices: 444893--444920 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
444883 AACTCATTCA
444893 TATTTAATTAATTG
1 TATTTAATTAATTG
444907 TATTTAATTAATTG
1 TATTTAATTAATTG
444921 AATGTGAATC
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:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTAATTAATTG
Found at i:450753 original size:25 final size:26
Alignment explanation
Indices: 450725--450775 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
450715 AAAGTTATTT
450725 TTAACGGACAACTA-ATTGTCTAGTG
1 TTAACGGACAACTAGATTGTCTAGTG
* * *
450750 TTAACTGACAATTAGTTTGTCTAGTG
1 TTAACGGACAACTAGATTGTCTAGTG
450776 AGATAAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (26 bp):
TTAACGGACAACTAGATTGTCTAGTG
Found at i:455303 original size:17 final size:18
Alignment explanation
Indices: 455264--455309 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
455254 TGTTTATGAG
*
455264 GGAATTAGAATCTGTGAA
1 GGAATTAGAATATGTGAA
*
455282 GGAATTAGAATATGT-CA
1 GGAATTAGAATATGTGAA
*
455299 GGAATTGGAAT
1 GGAATTAGAAT
455310 CCAATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTAGAATATGTGAA
Found at i:458456 original size:17 final size:18
Alignment explanation
Indices: 458423--458456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
458413 TCAATTCTGT
*
458423 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
458441 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
458457 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:467010 original size:262 final size:257
Alignment explanation
Indices: 466629--467216 Score: 855
Period size: 262 Copynumber: 2.3 Consensus size: 257
466619 AAGTTTTACT
*
466629 CGACCCGAATATATGAATTAGAAAAT-CGACCCGA-CCGAAAATAATAAAAAATTATTTTTATTC
1 CGACCCGAATATATGAATTAG-AAATCCGACCCGACCCG-AAATAATAAAAAAATATTTTTATTC
* * * *
466692 AACAAAAACATTGACTTAATTGAAAATATATATATATAGGGGTATTATTATAATTATTCCTAAAT
64 AATAAAAACAGTGACTTAATTGAAAATATATATAGAGAGGGGTATTATTATAATTATTCCTAAAT
* *
466757 ATA-AATGGTAAAATTATATAT-TTTTTGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACC
129 ATATAA-GGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCCG-A----ACC
* *
466820 CGACCCGACCCGAATATCACACTTAAAAAA-A-CCGACTCGACACGACCAAAATAAAGTTTTACC
188 CGACCCGACCCGAATATCACACTTAAAAAACACCCGACCCGACACGACCAAAATAAAGTTTCACC
466883 CGACC
253 CGACC
*
466888 CGACCCGAATATATGAATCAGAAATCCGACCCGACCCGAAATAATAATAAAAATATTTTTATTCA
1 CGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAA-AAAAATATTTTTATTCA
* *
466953 ATAAAAACAGTGACTTAATTGAAAAAATTTATATAGAGAGGGGTATTATTGTAATTATTCCTAAA
65 ATAAAAACAGTGACTTAATTG--AAAATATATATAGAGAGGGGTATTATTATAATTATTCCTAAA
*
467018 TATATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACTCGACC
128 TATATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACCCGACC
* * *
467083 CGACCTGAATATCACACTTAAAAAACCGACCCGACCCGACCCGACCAAAATAAAGTTTCACTCGA
193 CGACCCGAATATCACACTTAAAAAA-C-ACCCGACCCGACACGACCAAAATAAAGTTTCACCCGA
467148 CC
256 CC
* *
467150 CGACCCGAATATATGAATTAGAAACCCGACTCGACCCGAAATAATAAAAAAATATTTTTATTCAA
1 CGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAA
467215 TA
66 TA
467217 TATGAAATAA
Statistics
Matches: 299, Mismatches: 19, Indels: 20
0.88 0.06 0.06
Matches are distributed among these distances:
258 35 0.12
259 37 0.12
260 38 0.13
261 21 0.07
262 135 0.45
263 33 0.11
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (257 bp):
CGACCCGAATATATGAATTAGAAATCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAA
TAAAAACAGTGACTTAATTGAAAATATATATAGAGAGGGGTATTATTATAATTATTCCTAAATAT
ATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACCCGACCCGA
CCCGAATATCACACTTAAAAAACACCCGACCCGACACGACCAAAATAAAGTTTCACCCGACC
Found at i:471766 original size:15 final size:15
Alignment explanation
Indices: 471741--471773 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
471731 GAGGAAAGAT
471741 AAATTTAATTT-TTA
1 AAATTTAATTTCTTA
471755 AAATTATAATTTCTTA
1 AAATT-TAATTTCTTA
471771 AAA
1 AAA
471774 AATGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTAATTTCTTA
Found at i:474934 original size:2 final size:2
Alignment explanation
Indices: 474927--474980 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
474917 AGTCACATTA
474927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474969 AT AT AT AT AT AT
1 AT AT AT AT AT AT
474981 GAAAGATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:475821 original size:26 final size:25
Alignment explanation
Indices: 475782--475831 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
475772 TAAGAATTCA
475782 GATTTATTTAATTTATGATTCTTTT
1 GATTTATTTAATTTATGATTCTTTT
* * *
475807 GATTTCTTTCAATTTTTTATTCTTT
1 GATTTATTT-AATTTATGATTCTTT
475832 ATTATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.66
Consensus pattern (25 bp):
GATTTATTTAATTTATGATTCTTTT
Found at i:476109 original size:17 final size:17
Alignment explanation
Indices: 476087--476128 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
476077 ATACCCTATG
476087 TCTTCGTGAGGATTTAT
1 TCTTCGTGAGGATTTAT
476104 TCTTCGTGAGGATTTAT
1 TCTTCGTGAGGATTTAT
476121 TCTTCGTG
1 TCTTCGTG
476129 TCAGGCATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (17 bp):
TCTTCGTGAGGATTTAT
Found at i:480288 original size:86 final size:81
Alignment explanation
Indices: 480171--480370 Score: 231
Period size: 86 Copynumber: 2.4 Consensus size: 81
480161 GAGTTATCGT
* * * *
480171 CCTAAAACAATTGGTTAATCACTCCGACTTTATGTATAATATTCAGCTAACCTA-TATTATTATA
1 CCTAAAGCAATTGGTTAATCGCCCCGACTTTATGAATAATATTCAGCTAACCTATTA-TA-T-TA
480235 TATACAATAAAGCTTTTGTCCC
63 TATACAATAAAG---TTGTCCC
* * *
480257 CCTAAAGCAATTGGTTAATCGCCCCGTCTTTATGAATAATATTCAGCTAGCCTGTTATATTATAT
1 CCTAAAGCAATTGGTTAATCGCCCCGACTTTATGAATAATATTCAGCTAACCTATTATATTATAT
480322 ACAATAAAGTTGTCCC
66 ACAATAAAGTTGTCCC
* * * * *
480338 TCTAGAGCAATTGGTTAATAGCCTCGGCTTTAT
1 CCTAAAGCAATTGGTTAATCGCCCCGACTTTAT
480371 AGATAAGTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
81 35 0.35
84 14 0.14
85 1 0.01
86 49 0.49
87 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (81 bp):
CCTAAAGCAATTGGTTAATCGCCCCGACTTTATGAATAATATTCAGCTAACCTATTATATTATAT
ACAATAAAGTTGTCCC
Found at i:480369 original size:81 final size:85
Alignment explanation
Indices: 480171--480393 Score: 237
Period size: 81 Copynumber: 2.7 Consensus size: 85
480161 GAGTTATCGT
* * * * *
480171 CCTAAAACAATTGGTTAATCA-CTCCGACTTTATGTATAATATTCAGCTAACCT-ATATTATTAT
1 CCTAAAGCAATTGGTTAAT-AGCCCCGGCTTTATGAATAATATTCAGCTAGCCTGATATTATTAT
480234 ATATACAATAAAGCTTTTGTCCC
65 ATATACAATAAAG--TTTGTCCC
* * *
480257 CCTAAAGCAATTGGTTAATCGCCCCGTCTTTATGAATAATATTCAGCTAGCCTGTTA-TA-T-TA
1 CCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGAATAATATTCAGCTAGCCTGATATTATTATA
480319 TATACAATAAAG-TTGTCCC
66 TATACAATAAAGTTTGTCCC
* * * *
480338 TCTAGAGCAATTGGTTAATAGCCTCGGCTTTAT-AGATAAGT-TTCAACTAGCCTGAT
1 CCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGA-ATAA-TATTCAGCTAGCCTGAT
480394 TGAGGCAAAT
Statistics
Matches: 119, Mismatches: 14, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
80 1 0.01
81 52 0.44
82 1 0.01
84 14 0.12
85 1 0.01
86 48 0.40
87 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (85 bp):
CCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGAATAATATTCAGCTAGCCTGATATTATTATA
TATACAATAAAGTTTGTCCC
Found at i:483095 original size:42 final size:41
Alignment explanation
Indices: 483048--483142 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
483038 CCCGAATTTG
* * *
483048 TAAATCCTTCGGGTCATC-AGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCTA-TAAGCCTTTCGAGCAAGATG-A
*
483090 TAAATCCTTTGGGTCATCTATAAGCCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA
*
483131 TAAGTCCTTCGG
1 TAAATCCTTCGG
483143 TCCATTTCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 10 0.22
42 35 0.76
43 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGA
Found at i:483415 original size:118 final size:118
Alignment explanation
Indices: 483228--483498 Score: 354
Period size: 118 Copynumber: 2.3 Consensus size: 118
483218 AAGAGGGAAG
*
483228 AAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTCGACTCTATCACAGAAGGATAGATCAGC
1 AAGTTCA-AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGATAGATCAAC
* *
483292 ATCAACATTTCTGAA-G-GAGTTCATAATGAGAAAAAACTCA-TGAATAGGAAGAAA
65 ATCAACA-TTC-AAAGGAGAGTTCATAATGA-AAAAAACTCACTAAATAGGAAGAAA
* * *
483346 AAGTTC-AGTGAGAAGAACTTGTTCAACCTTTTTCTTGACTCTATCACAGAAGGAATAGATCAAC
1 AAGTTCAAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGG-ATAGATCAAC
* *
483410 ATCAACATTCAAAGGAAGAGTTCATAATGAAAAGAACTCACTAAATAGGAAGAAG
65 ATCAACATTCAAAGG-AGAGTTCATAATGAAAAAAACTCACTAAATAGGAAGAAA
* *
483465 AAGTTCATAATGAGAAGAACTTGTTTAACATTTT
1 AAGTTCA-AATGAGAAGAACTTGTTCAACCTTTT
483499 ACATCCCATC
Statistics
Matches: 134, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
116 21 0.16
117 28 0.21
118 31 0.23
119 31 0.23
121 23 0.17
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.27
Consensus pattern (118 bp):
AAGTTCAAATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGATAGATCAACA
TCAACATTCAAAGGAGAGTTCATAATGAAAAAAACTCACTAAATAGGAAGAAA
Found at i:483470 original size:119 final size:118
Alignment explanation
Indices: 483197--483601 Score: 395
Period size: 116 Copynumber: 3.4 Consensus size: 118
483187 GAAGGAATTA
* *
483197 ATAATGAGAAGAACTCATCTGAAGAGG--GAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTT
1 ATAATGAAAAGAACTCA-CTAAAGAGGAAGAAGAAGTTCA-AATGAGAAGAACTTGTTCAACCTT
* * * *
483259 TTGCTCGACTCTATCACAGAAGG-ATAGATCAGCATCAACATTTC-TGAAGGAGTTC
64 TTACTTGACTCTATCACAGAAGGAATAGATCAACATCAACA-TTCAGGAA-GAGTTC
* * * * *
483314 ATAATGAGAAAAAACTCA-TGAATAGGAAGAAAAAGTTC-AGTGAGAAGAACTTGTTCAACCTTT
1 ATAATGA-AAAGAACTCACTAAAGAGGAAGAAGAAGTTCAAATGAGAAGAACTTGTTCAACCTTT
*
483377 TTCTTGACTCTATCACAGAAGGAATAGATCAACATCAACATTCAAAGGAAGAGTTC
65 TACTTGACTCTATCACAGAAGGAATAGATCAACATCAACATTC--AGGAAGAGTTC
* * *
483433 ATAATGAAAAGAACTCACTAAATAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACATTT
1 ATAATGAAAAGAACTCACTAAAGAGGAAGAAGAAGTTCA-AATGAGAAGAACTTGTTCAACCTTT
* * * * * *
483498 TACAT--C-CCATCACAGAAGGAGATGGATCGACATTC-TCAGT--GGAAGAGTTC
65 TACTTGACTCTATCACAGAAGGA-ATAGATCAACA-TCAACATTCAGGAAGAGTTC
* * *
483548 ATAATGAGAAGAACTCGTCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 ATAATGAAAAGAACTC-ACTAAAGAGGAAGAAGAAGTTCA-AATGAGAAGAACT
483602 CGTCTGAAGA
Statistics
Matches: 248, Mismatches: 26, Indels: 29
0.82 0.09 0.10
Matches are distributed among these distances:
115 25 0.10
116 60 0.24
117 34 0.14
118 55 0.22
119 44 0.18
120 5 0.02
121 25 0.10
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (118 bp):
ATAATGAAAAGAACTCACTAAAGAGGAAGAAGAAGTTCAAATGAGAAGAACTTGTTCAACCTTTT
ACTTGACTCTATCACAGAAGGAATAGATCAACATCAACATTCAGGAAGAGTTC
Found at i:483587 original size:39 final size:39
Alignment explanation
Indices: 483539--483679 Score: 230
Period size: 39 Copynumber: 3.6 Consensus size: 39
483529 ATTCTCAGTG
**
483539 GAAG-AGTTCATAATGAGAAGAACTCGTCCAAAGAGGAA
1 GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAA
*
483577 GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAAGAA
1 GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAA
483616 GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAA
1 GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAA
* *
483655 GAATAAATTCATAATGAGAAGAACT
1 GAAGAAGTTCATAATGAGAAGAACT
483680 TGTTCAACAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 4 0.04
39 92 0.96
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.18
Consensus pattern (39 bp):
GAAGAAGTTCATAATGAGAAGAACTCGTCTGAAGAGGAA
Found at i:486322 original size:2 final size:2
Alignment explanation
Indices: 486315--486339 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
486305 AAGTCAAGCA
486315 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 A
486340 CTCAGCCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:487245 original size:22 final size:22
Alignment explanation
Indices: 487220--487263 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
487210 GTCTTTTATC
487220 ATCGCAGTCAGTCAGTAGGGGA
1 ATCGCAGTCAGTCAGTAGGGGA
* *
487242 ATCGTAGTCAGTCATTAGGGGA
1 ATCGCAGTCAGTCAGTAGGGGA
487264 GTTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.34, T:0.23
Consensus pattern (22 bp):
ATCGCAGTCAGTCAGTAGGGGA
Found at i:496893 original size:37 final size:37
Alignment explanation
Indices: 496843--496957 Score: 230
Period size: 37 Copynumber: 3.1 Consensus size: 37
496833 GACTGCAGAA
496843 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
1 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
496880 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
1 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
496917 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
1 GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
496954 GAAT
1 GAAT
496958 AAAAACTTTC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 78 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (37 bp):
GAATTACGTGTAGCTTACAAAACTTTTTCAGAGTAAT
Found at i:498888 original size:21 final size:21
Alignment explanation
Indices: 498864--498944 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
498854 CATATGAAAT
* *
498864 TTGTCCTGAAAGGCCACTGTA
1 TTGTCCCGAAAGACCACTGTA
498885 TTGTCCCGAAAGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
** *
498906 TTACCCCGAATGACCACTGTA
1 TTGTCCCGAAAGACCACTGTA
* * *
498927 TTATCTCGAAGGACCACT
1 TTGTCCCGAAAGACCACT
498945 ATAACCCTCG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
TTGTCCCGAAAGACCACTGTA
Found at i:501972 original size:31 final size:31
Alignment explanation
Indices: 501909--501972 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
501899 TAGGTCCATA
** *
501909 AGGAATTACCAATCAGTGCTGAACCTATCAG
1 AGGAATTACCAATCAGAACTGAACCTACCAG
*
501940 AGGAATTACCAA-CAGCAACTGAACCTGCCAG
1 AGGAATTACCAATCAG-AACTGAACCTACCAG
501971 AG
1 AG
501973 TCTTCATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (31 bp):
AGGAATTACCAATCAGAACTGAACCTACCAG
Found at i:502839 original size:58 final size:58
Alignment explanation
Indices: 502749--502876 Score: 195
Period size: 58 Copynumber: 2.2 Consensus size: 58
502739 ACAGTCAACT
* * *
502749 TTTACAAAAATAGCATCGAACAGAAATTAATTACGTATTAGGCACTATTTTCAAAATA
1 TTTACAAAAATAGCACCGAACAGAAATTAATTACGTATTAGGCACTATTTTAAAAACA
* *
502807 TTTACAAAAATAGCACCGACCA-AAATTTAATTACGTATTAGGCACTCTTTTAAAAACA
1 TTTACAAAAATAGCACCGAACAGAAA-TTAATTACGTATTAGGCACTATTTTAAAAACA
502865 TTTACAAAAATA
1 TTTACAAAAATA
502877 TTACCCTAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 3 0.05
58 61 0.95
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (58 bp):
TTTACAAAAATAGCACCGAACAGAAATTAATTACGTATTAGGCACTATTTTAAAAACA
Found at i:506987 original size:29 final size:29
Alignment explanation
Indices: 506955--507085 Score: 192
Period size: 29 Copynumber: 4.5 Consensus size: 29
506945 CAGAAATTAA
**
506955 TTACAAAACTAACACTATTTTAAAAATAT
1 TTACAAAACTAACACCCTTTTAAAAATAT
*
506984 TTACGAAACTAACACCCTTTTAAAAATAT
1 TTACAAAACTAACACCCTTTTAAAAATAT
* *
507013 TTACGAAGCTAACACCCTTTTAAAAATAT
1 TTACAAAACTAACACCCTTTTAAAAATAT
507042 TTA-AGAAACTAACACCCTTTTAAAAATAT
1 TTACA-AAACTAACACCCTTTTAAAAATAT
*
507071 TTACAAAAATAACAC
1 TTACAAAACTAACAC
507086 AGAATAGAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (29 bp):
TTACAAAACTAACACCCTTTTAAAAATAT
Found at i:507121 original size:58 final size:58
Alignment explanation
Indices: 507059--507197 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
507049 ACTAACACCC
* *
507059 TTTTAAAAATATTTACAAAAATAACACAGAATAGAAATTAATTACGTATTAGGCATTA
1 TTTTAAAAATATTTACAAAAATAACACAGAACAGAAATTAATTACGTATTAGGCACTA
* * * * *
507117 TTTTAAAAATATTCACAAAAATAGCACTGAACATAAATTAATTACGTATTAGGCACTC
1 TTTTAAAAATATTTACAAAAATAACACAGAACAGAAATTAATTACGTATTAGGCACTA
507175 TTTTAAAAATATTTACAAAAATA
1 TTTTAAAAATATTTACAAAAATA
507198 TCACCCGAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (58 bp):
TTTTAAAAATATTTACAAAAATAACACAGAACAGAAATTAATTACGTATTAGGCACTA
Found at i:510395 original size:21 final size:21
Alignment explanation
Indices: 510371--510421 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
510361 TTGAATTTGA
510371 AACTAAATTTGACTTGTCATC
1 AACTAAATTTGACTTGTCATC
* *
510392 AACTAAATTTTACTTGTCATG
1 AACTAAATTTGACTTGTCATC
*
510413 AACTTAATT
1 AACTAAATT
510422 AAGAGATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (21 bp):
AACTAAATTTGACTTGTCATC
Found at i:511333 original size:12 final size:12
Alignment explanation
Indices: 511316--511341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
511306 ATTAATGGTG
511316 ATAATAAGAATA
1 ATAATAAGAATA
511328 ATAATAAGAATA
1 ATAATAAGAATA
511340 AT
1 AT
511342 GAAATGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
ATAATAAGAATA
Found at i:512127 original size:31 final size:31
Alignment explanation
Indices: 512059--512279 Score: 261
Period size: 31 Copynumber: 7.1 Consensus size: 31
512049 GAGTCGAGGG
*
512059 TTACCTATGTCTTTCGGGACATATGAACATGA
1 TTACCTATGTCTTTCGGGACATATGGACA-GA
* * *
512091 TTACCTATGTCTTTCGAGACATTTAGACAGA
1 TTACCTATGTCTTTCGGGACATATGGACAGA
** *
512122 TTACCTATGTCTTTCAAGACATATGGACAGT
1 TTACCTATGTCTTTCGGGACATATGGACAGA
* *
512153 TTACCTATGT-TCTTCGGGACATATGAACAGT
1 TTACCTATGTCT-TTCGGGACATATGGACAGA
* *
512184 TTACCTATGTCTTTCGGGACCTATAGACA-A
1 TTACCTATGTCTTTCGGGACATATGGACAGA
*
512214 TTTACCTATGT-TCTTCGGGACATATGGA-AAA
1 -TTACCTATGTCT-TTCGGGACATATGGACAGA
512245 TTTACCTATGTCTTTCGGGACATATGGACAGA
1 -TTACCTATGTCTTTCGGGACATATGGACAGA
512277 TTA
1 TTA
512280 TTATACGAGC
Statistics
Matches: 164, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
30 3 0.02
31 132 0.80
32 29 0.18
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (31 bp):
TTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:512219 original size:93 final size:93
Alignment explanation
Indices: 512059--512279 Score: 304
Period size: 93 Copynumber: 2.4 Consensus size: 93
512049 GAGTCGAGGG
*
512059 TTACCTATGTCTTTCGGGACATATGAACATGATTACCTATGTCTTTCGAGACATTTAGACAGATT
1 TTACCTATGTCTTTCGGGACATATGAACA-GATTACCTATGTCTTTCGAGACATATAGACAGATT
* *
512124 ACCTATG-TCTTTCAAGACATATGGACAGT
65 ACCTATGTTC-TTCAAGACATATGGAAAAT
* * *
512153 TTACCTATGT-TCTTCGGGACATATGAACAGTTTACCTATGTCTTTCGGGACCTATAGACA-ATT
1 TTACCTATGTCT-TTCGGGACATATGAACAGATTACCTATGTCTTTCGAGACATATAGACAGA-T
**
512216 TACCTATGTTCTTCGGGACATATGGAAAAT
64 TACCTATGTTCTTCAAGACATATGGAAAAT
*
512246 TTACCTATGTCTTTCGGGACATATGGACAGATTA
1 TTACCTATGTCTTTCGGGACATATGAACAGATTA
512280 TTATACGAGC
Statistics
Matches: 113, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
92 1 0.01
93 82 0.73
94 30 0.27
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (93 bp):
TTACCTATGTCTTTCGGGACATATGAACAGATTACCTATGTCTTTCGAGACATATAGACAGATTA
CCTATGTTCTTCAAGACATATGGAAAAT
Found at i:512514 original size:31 final size:31
Alignment explanation
Indices: 512479--512557 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
512469 AAAAGATAAG
*
512479 TATACATTATTGTTCATGGTATTGTTCATAT
1 TATACATTATTGTTCATGGTATTGTTCATAC
* *
512510 TATACATTATTATTCACGGTATTGTTCATAC
1 TATACATTATTGTTCATGGTATTGTTCATAC
* * *
512541 CATATATTACTGTTCAT
1 TATACATTATTGTTCAT
512558 AAAAACGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (31 bp):
TATACATTATTGTTCATGGTATTGTTCATAC
Found at i:512959 original size:24 final size:24
Alignment explanation
Indices: 512931--513019 Score: 151
Period size: 24 Copynumber: 3.7 Consensus size: 24
512921 AAAAATTCAG
* *
512931 GAGCTCGATTGATGCTCGAGAGTC
1 GAGCTCGATTGAAGCTCGAGAATC
512955 GAGCTCGATTGAAGCTCGAGAATC
1 GAGCTCGATTGAAGCTCGAGAATC
*
512979 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGAGAATC
513003 GAGCTCGATTGAAGCTC
1 GAGCTCGATTGAAGCTC
513020 AATTTTGAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTGAAGCTCGAGAATC
Found at i:513457 original size:30 final size:29
Alignment explanation
Indices: 513423--513513 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
513413 AAATGATAGA
* *
513423 AACAAGTTAAGCTTACTTATAAAAGATGAC
1 AACAAGTCAAGTTTACTTATAAAAGATG-C
513453 AACAAAATGTCAAGTTTACTTATAAAAGATTGC
1 AAC--AA-GTCAAGTTTACTTATAAAAGA-TGC
* *
513486 AACATGTCAAGTTTACTTACAAAAGATG
1 AACAAGTCAAGTTTACTTATAAAAGATG
513514 GTAGTTGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 2 0.04
30 23 0.43
31 1 0.02
32 2 0.04
33 23 0.43
34 2 0.04
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (29 bp):
AACAAGTCAAGTTTACTTATAAAAGATGC
Found at i:513472 original size:33 final size:29
Alignment explanation
Indices: 513435--513513 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
513425 CAAGTTAAGC
513435 TTACTTATAAAAGATGACAACAAAATGTCAAGT
1 TTACTTATAAAAGATG-CAAC---ATGTCAAGT
513468 TTACTTATAAAAGATTGCAACATGTCAAGT
1 TTACTTATAAAAGA-TGCAACATGTCAAGT
*
513498 TTACTTACAAAAGATG
1 TTACTTATAAAAGATG
513514 GTAGTTGCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 2 0.05
30 22 0.50
33 18 0.41
34 2 0.05
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (29 bp):
TTACTTATAAAAGATGCAACATGTCAAGT
Found at i:517082 original size:35 final size:35
Alignment explanation
Indices: 517027--517230 Score: 106
Period size: 35 Copynumber: 5.5 Consensus size: 35
517017 AAATAAGAAT
*
517027 AACGAAAGGAAGCATCGCACTTTCGATTCAAGTTG
1 AACGAAAGGAAGCATAGCACTTTCGATTCAAGTTG
* * *
517062 AACGAAATGAGGCATAGCACTTTCGATTCTCGTATAAAGTAG
1 AACGAAAGGAAGCATAGCACTTTCGA-T-TC-----AAGTTG
* * * *
517104 AATGGAATGAAGCATCGCACTTTCGATTCAA-TTAG
1 AACGAAAGGAAGCATAGCACTTTCGATTCAAGTT-G
* * *
517139 AACGAAAGGAGGCATAACACTTT-GATTCTCCTTTAAAGTAG
1 AACGAAAGGAAGCATAGCACTTTCGA-T-T-C----AAGTTG
* * * * *
517180 AATGGAAGGAAACATCGCACTTTCGATTCAAGTAG
1 AACGAAAGGAAGCATAGCACTTTCGATTCAAGTTG
*
517215 AACGAAAGGAGGCATA
1 AACGAAAGGAAGCATA
517231 ATACTTTTGA
Statistics
Matches: 125, Mismatches: 27, Indels: 34
0.67 0.15 0.18
Matches are distributed among these distances:
34 3 0.02
35 61 0.49
36 2 0.02
37 3 0.02
39 1 0.01
40 3 0.02
41 22 0.18
42 30 0.24
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (35 bp):
AACGAAAGGAAGCATAGCACTTTCGATTCAAGTTG
Found at i:517216 original size:76 final size:76
Alignment explanation
Indices: 517032--517245 Score: 329
Period size: 76 Copynumber: 2.8 Consensus size: 76
517022 AGAATAACGA
* * * *
517032 AAGGAAGCATCGCACTTTCGATTCAAGTTGAACGAAATGAGGCATAGCACTTTCGATTCTCGTAT
1 AAGGAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTT-GATTCTCCTAT
517097 AAAGTAGAATGG
65 AAAGTAGAATGG
* * *
517109 AATGAAGCATCGCACTTTCGATTCAATTAGAACGAAAGGAGGCATAACACTTTGATTCTCCTTTA
1 AAGGAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTGATTCTCCTATA
517174 AAGTAGAATGG
66 AAGTAGAATGG
* *
517185 AAGGAAACATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAATACTTTTGATTCTC
1 AAGGAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACAC-TTTGATTCTC
517246 ATTGATAGAA
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
76 67 0.54
77 58 0.46
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (76 bp):
AAGGAAGCATCGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTGATTCTCCTATA
AAGTAGAATGG
Found at i:518338 original size:17 final size:17
Alignment explanation
Indices: 518295--518346 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
518285 TTTACAGTAG
*
518295 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
518312 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
518327 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
518344 AAA
1 AAA
518347 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:519593 original size:17 final size:18
Alignment explanation
Indices: 519571--519607 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
519561 ATGCAACAAT
519571 TATATATTTTAAA-AAAA
1 TATATATTTTAAATAAAA
519588 TATATATTTTAAATAAAA
1 TATATATTTTAAATAAAA
519606 TA
1 TA
519608 CAATTTGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TATATATTTTAAATAAAA
Found at i:519613 original size:17 final size:17
Alignment explanation
Indices: 519574--519613 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
519564 CAACAATTAT
*
519574 ATATTTTAAAAAAATAT
1 ATATTTTAAAAAAATAC
519591 ATATTTTAAATAAAATAC
1 ATATTTTAAA-AAAATAC
519609 A-ATTT
1 ATATTT
519614 GAGGGTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTTAAAAAAATAC
Found at i:519687 original size:11 final size:11
Alignment explanation
Indices: 519635--519694 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
519625 TATTATAGAA
519635 TTTAATATATT
1 TTTAATATATT
*
519646 TTTAA-AAATT
1 TTTAATATATT
* *
519656 TATAAT-TATC
1 TTTAATATATT
** *
519666 AATAATGTATT
1 TTTAATATATT
519677 TTTAATATATT
1 TTTAATATATT
519688 TTTAATA
1 TTTAATA
519695 ATGTAATTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
10 15 0.39
11 23 0.61
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATATATT
Found at i:519950 original size:4 final size:4
Alignment explanation
Indices: 519941--520040 Score: 66
Period size: 4 Copynumber: 24.5 Consensus size: 4
519931 ACTTTGCCTG
* * *
519941 AAGA AAGA AAAA TAAAA AAGAA AAGA AAGA ACGA AAGA AAGA AAGA AAGA
1 AAGA AAGA AAGA -AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
519991 AA-A AA-A ATGA AAGA AA-A AA-A AGAGA AATGGAA AAGA GAA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA A-AGA AA--G-A AAGA -AAGA AAGA
520035 AAGA AA
1 AAGA AA
520041 AAATAAAATA
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
3 12 0.15
4 51 0.64
5 13 0.16
6 1 0.01
7 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:519979 original size:34 final size:32
Alignment explanation
Indices: 519941--520042 Score: 93
Period size: 34 Copynumber: 3.1 Consensus size: 32
519931 ACTTTGCCTG
519941 AAGAAAGAAAAATAAAAAAGAAAAGAAAGAACGA
1 AAGAAAGAAAAATAAAAAAGAAAAGAAAGAA--A
*
519975 AAGAAAGAAAGAA-AGAAAAA-AAATGAAAGAAA
1 AAGAAAGAAA-AATA-AAAAAGAAAAGAAAGAAA
* *
520007 AA-AAAGAGAAATGGAAAAGAGAAAAAGAAAGAAA
1 AAGAAAGAAAAAT--AAAAAAG-AAAAGAAAGAAA
520041 AA
1 AA
520043 ATAAAATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
30 2 0.04
31 6 0.11
32 7 0.12
33 1 0.02
34 34 0.60
35 7 0.12
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (32 bp):
AAGAAAGAAAAATAAAAAAGAAAAGAAAGAAA
Found at i:521396 original size:92 final size:91
Alignment explanation
Indices: 521276--521550 Score: 345
Period size: 92 Copynumber: 3.0 Consensus size: 91
521266 AATCCAACTC
* * ** *
521276 GATTCAATCTTCTCTGAAGAACAGTGGAACGAATCAATGTCCCCAGATATGATTTTCCCTCAAGA
1 GATTCAATCTTC-CTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTCAAGA
*
521341 AGTAGCAGAACATATCCCTCTTTTTCA
65 AGCAGCAGAACATATCCCTCTTTTTCA
* * * *
521368 GATTCAATCTTCACTGAAGAACAATGGAATGAATCAACATTTTCAGATCTAATTTTCCCTCAAGA
1 GATTCAATCTTC-CTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTCAAGA
* * * *
521433 AGCAACAGAATAGATCCCTCTCTTTCA
65 AGCAGCAGAACATATCCCTCTTTTTCA
* * *
521460 TATTTAATCTTCCTTGAAGAACAGTGGAATTAATCAACGTTTCCAGATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCC-TGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTCAAGA
*
521525 AGCAGCGGAACATATCCCAT-TTTTTC
65 AGCAGCAGAACATATCCC-TCTTTTTC
521551 CAAATTTGAT
Statistics
Matches: 154, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
91 1 0.01
92 152 0.99
93 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (91 bp):
GATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTCAAGAA
GCAGCAGAACATATCCCTCTTTTTCA
Found at i:521433 original size:45 final size:44
Alignment explanation
Indices: 521362--521525 Score: 107
Period size: 45 Copynumber: 3.6 Consensus size: 44
521352 ATATCCCTCT
* *
521362 TTTTCAGAT-TCAATCTTCACTGAAGAACAATGGAATGAATCAACA
1 TTTTCAGATCT-AATCTTCCCTCAAGAACAATGGAAT-AATCAACA
* ** * *
521407 TTTTCAGATCTAATTTTCCCTCAAGAAGCAACAGAATAGATC-CCTC
1 TTTTCAGATCTAATCTTCCCTCAAGAA-CAATGGAATA-ATCAAC-A
* * * * * *
521453 TCTTTCATATTTAATCTTCCTTGAAGAACAGTGGAATTAATCAACG
1 T-TTTCAGATCTAATCTTCCCTCAAGAACAATGGAA-TAATCAACA
* * *
521499 TTTCCAGATCTGATTTTCCCTCAAGAA
1 TTTTCAGATCTAATCTTCCCTCAAGAA
521526 GCAGCGGAAC
Statistics
Matches: 88, Mismatches: 24, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
45 43 0.49
46 21 0.24
47 24 0.27
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (44 bp):
TTTTCAGATCTAATCTTCCCTCAAGAACAATGGAATAATCAACA
Found at i:521708 original size:132 final size:133
Alignment explanation
Indices: 521465--521766 Score: 412
Period size: 132 Copynumber: 2.3 Consensus size: 133
521455 TTTCATATTT
* * * *
521465 AATCTTCCTTGAAGAACAGTGGAATTAATCAACGTTTCCAGATCTGATTTTCCCTCAAGAAGCAG
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAAC-ATTCCAGATCTGATTTTCCCTCAAGAAGCAA
* *
521530 CGGAACATATCCCATTTTTTCCAAATTTGATATTCCATGAGGAATAGGGGAACAAGTCTACCTCG
65 CGGAACAGATCCCATTCTTTCCAAATTTGATATTCCATGAGGAATAGGGGAACAAGTCTACCTCG
521595 ATTC
130 ATTC
* * * *
521599 AATCTTCCCTAAAGAACAGTGGTATGAATCAACATTCCATATCTGATTTT-CTTCAAGAAGCAAC
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACATTCCAGATCTGATTTTCCCTCAAGAAGCAAC
* * * * *
521663 GGAACAGATCCC-TCTCTTT-CAAGATTTGATCTTCCCTGAGTAATAGTGGAACAAGTCTGCCTC
66 GGAACAGATCCCAT-TCTTTCCAA-ATTTGATATTCCATGAGGAATAGGGGAACAAGTCTACCTC
521726 GATTC
129 GATTC
*
521731 AATCTTCCCTGAAGAAAAGTGGAATGAATCAACATT
1 AATCTTCCCTGAAGAACAGTGGAATGAATCAACATT
521767 TCTCAATATG
Statistics
Matches: 148, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
131 4 0.03
132 100 0.68
133 15 0.10
134 29 0.20
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (133 bp):
AATCTTCCCTGAAGAACAGTGGAATGAATCAACATTCCAGATCTGATTTTCCCTCAAGAAGCAAC
GGAACAGATCCCATTCTTTCCAAATTTGATATTCCATGAGGAATAGGGGAACAAGTCTACCTCGA
TTC
Found at i:521939 original size:3 final size:3
Alignment explanation
Indices: 521931--522012 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
521921 TTTCGTTCCA
521931 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
521978 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
522013 CAGGCCTTAA
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:524143 original size:131 final size:131
Alignment explanation
Indices: 523942--524440 Score: 665
Period size: 131 Copynumber: 3.8 Consensus size: 131
523932 CGATATTAAG
* * * * *
523942 AATAGTAATATCTTTTTATTTCGGTTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
1 AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
* * * * * *
524007 TATTCTTGATTGAAAATAATTCGATATTACCGTTTTCTCTCGAACCAATATTGATTTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGATTTTTAAGACG
524072 A
131 A
* * * *
524073 AATAGTGATATCTCTTCATTTCGATTAGAGCAATAAATGTATGCTTAAAGGTATGAGAGGTCATT
1 AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
* * * * *
524138 CATTCTCGATTGTAAATCATTAGATATTATCATTTTCTCTCGAATCACTATTAATTTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGATTTTTAAGACG
*
524203 T
131 A
* *
524204 AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCATT
1 AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
* ** * * * *
524269 TATTCTCGATTGGAAATCATTAGATATTATTGTTTTCACTCGAATCGATATAGAATTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGATTTTTAAGACG
524334 A
131 A
* * * *
524335 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGAATACTTTAAGGCATGAGAGGTAATT
1 AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
* * *
524400 TATTATCAATTGGAAATAATTAGAAATTATCATTTTCTCTC
66 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTC
524441 TTAGAATTAT
Statistics
Matches: 320, Mismatches: 48, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 320 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (131 bp):
AATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCGAATCAATATTGATTTTTAAGACG
A
Found at i:526251 original size:31 final size:31
Alignment explanation
Indices: 526215--526273 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
526205 AACTTAAAAG
*
526215 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
526246 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
526274 CCATACAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:527961 original size:22 final size:22
Alignment explanation
Indices: 526297--527960 Score: 2383
Period size: 22 Copynumber: 75.6 Consensus size: 22
526287 ATAATAAATT
*
526297 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
526319 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
526341 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
526363 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
526385 TTTTAAAATGAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
526407 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
526429 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
526451 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
526473 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
526495 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
526517 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
526539 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
526561 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
**
526583 TTTTAAAATAAAT-TTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
526604 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
526626 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
526648 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
526670 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
526692 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
526714 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
526736 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
526758 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
526780 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
526802 TTTTAAAATAAATCAAACCATA
1 TTTTAAAATAAATCAATCCATA
526824 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
526846 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
526868 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
526890 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
526912 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
526934 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
526956 TTTTAAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
526979 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
527001 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
527023 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
527045 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
527067 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
527089 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
527111 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
* *
527133 TTTTAAAATAAATTAATTCATA
1 TTTTAAAATAAATCAATCCATA
527155 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
527177 TTTCAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
527199 TTTTATAAATAAATCAATCCATA
1 TTTTA-AAATAAATCAATCCATA
527222 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
527244 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
527266 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
527288 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
527310 TTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
527332 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* ***
527354 TTTTAAACTAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
527376 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
527398 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
527420 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
527442 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*
527464 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
527486 TTTTAAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
527509 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
527531 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
527553 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
527575 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
527597 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
527619 TTTTAAAATAAATTTTTCTATA
1 TTTTAAAATAAATCAATCCATA
* *
527641 TTTTAAAATAAATTAATTCATA
1 TTTTAAAATAAATCAATCCATA
**
527663 TTTTAAAATAAAGT-TTTCCATA
1 TTTTAAAATAAA-TCAATCCATA
*
527685 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
*
527707 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCCATA
527729 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
527751 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
527773 TTTTAAAATAAATCAATCCTTA
1 TTTTAAAATAAATCAATCCATA
**
527795 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
527817 TTTTAAAATAAATCAATCCTTA
1 TTTTAAAATAAATCAATCCATA
**
527839 TTTTAAAATAAAAT-TTTCCAT-
1 TTTTAAAAT-AAATCAATCCATA
**
527860 TTTTAAAATAAATCAATTTATA
1 TTTTAAAATAAATCAATCCATA
527882 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
527904 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
527926 TTTTAAAATAAATTAATCTATA
1 TTTTAAAATAAATCAATCCATA
527948 TTTTAAAATAAAT
1 TTTTAAAATAAAT
527961 TTTAAAATAG
Statistics
Matches: 1467, Mismatches: 157, Indels: 36
0.88 0.09 0.02
Matches are distributed among these distances:
20 4 0.00
21 54 0.04
22 1325 0.90
23 84 0.06
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Done.