Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003744.1 Hibiscus syriacus cultivar Beakdansim tig00008013_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: 2457414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:165881 original size:81 final size:79
Alignment explanation
Indices: 165735--165897 Score: 238
Period size: 81 Copynumber: 2.0 Consensus size: 79
165725 TCTTGAAACA
*
165735 CAAAACCTTCGATTTCGATTACACTCAGCTCAAGGGCACATCATTTACAGCATAGCTCAAGGCAA
1 CAAAACCTTCGATTTCGATTACACTCAGCTCAAGGGCACATCATTTACAACATAGCTCAAGGCAA
165800 GAAGGGCTATATGC
66 GAAGGGCTATATGC
* ** *
165814 CAAAGACCTTCGATTTCGATTACACTCAGTTTCTAA-GGCACATCATTTGTAACATAGCTCAATG
1 CAAA-ACCTTCGATTTCGATTACACTCAG-CTC-AAGGGCACATCATTTACAACATAGCTCAAGG
*
165878 CAAGAAGGGCTATTTGC
63 CAAGAAGGGCTATATGC
165895 CAA
1 CAA
165898 CCAAAGACCT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 4 0.05
80 24 0.32
81 45 0.60
82 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (79 bp):
CAAAACCTTCGATTTCGATTACACTCAGCTCAAGGGCACATCATTTACAACATAGCTCAAGGCAA
GAAGGGCTATATGC
Found at i:166228 original size:3 final size:3
Alignment explanation
Indices: 166216--166284 Score: 88
Period size: 3 Copynumber: 22.3 Consensus size: 3
166206 CAAAAACATT
166216 TTA TTA -TA TTA TTTA TTA TTA TTA TTTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA
166263 TTA TTA TTA TT- TTA TATA TTA T
1 TTA TTA TTA TTA TTA T-TA TTA T
166285 AATCATTTTT
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.07
3 44 0.73
4 12 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:166965 original size:12 final size:12
Alignment explanation
Indices: 166947--166976 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
166937 AGACTCGGAT
166947 GATGAATAAGAC
1 GATGAATAAGAC
*
166959 TATGAATAAGAC
1 GATGAATAAGAC
166971 GATGAA
1 GATGAA
166977 GTCGGGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.23, T:0.20
Consensus pattern (12 bp):
GATGAATAAGAC
Found at i:168019 original size:9 final size:9
Alignment explanation
Indices: 168005--168111 Score: 56
Period size: 9 Copynumber: 11.3 Consensus size: 9
167995 GGTCCTTCTA
168005 TTTATTTTT
1 TTTATTTTT
*
168014 TTTATTATT
1 TTTATTTTT
*
168023 TTTCTTTTT
1 TTTATTTTT
* *
168032 TACTAACTTTTA
1 T--TTA-TTTTT
*
168044 TTTATCTTT
1 TTTATTTTT
* * *
168053 GTTATCTGT
1 TTTATTTTT
168062 TTTATTTTAT
1 TTTATTTT-T
168072 TATTATTATATT
1 T-TTATT-T-TT
*
168084 TTT-TATTT
1 TTTATTTTT
168092 TTTA-TTTT
1 TTTATTTTT
168100 TTTATTTTT
1 TTTATTTTT
168109 TTT
1 TTT
168112 CATATTTATT
Statistics
Matches: 73, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
8 12 0.16
9 39 0.53
10 5 0.07
11 8 0.11
12 8 0.11
13 1 0.01
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTATTTTT
Found at i:168075 original size:30 final size:28
Alignment explanation
Indices: 168041--168106 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 28
168031 TTACTAACTT
*
168041 TTATTTATCTTTGTTATCTGTTTTATTTTA
1 TTATTTATATTTGTTAT-T-TTTTATTTTA
* *
168071 TTATTATTATATTTTTTATTTTTTATTTTT
1 TTA-T-TTATATTTGTTATTTTTTATTTTA
168101 TTATTT
1 TTATTT
168107 TTTTTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 2 0.06
29 1 0.03
30 15 0.48
31 2 0.06
32 11 0.35
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (28 bp):
TTATTTATATTTGTTATTTTTTATTTTA
Found at i:168080 original size:23 final size:22
Alignment explanation
Indices: 168054--168097 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
168044 TTTATCTTTG
*
168054 TTATCTGTTTTATTTTATTATTA
1 TTATATGTTTTATTTT-TTATTA
*
168077 TTATATTTTTTATTTTTTATT
1 TTATATGTTTTATTTTTTATT
168098 TTTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75
Consensus pattern (22 bp):
TTATATGTTTTATTTTTTATTA
Found at i:168100 original size:15 final size:15
Alignment explanation
Indices: 168061--168109 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
168051 TTGTTATCTG
*
168061 TTTTATTTTATTA-T
1 TTTTATTTTTTTATT
*
168075 TATTATATTTTTTATT
1 TTTTAT-TTTTTTATT
168091 TTTTATTTTTTTATT
1 TTTTATTTTTTTATT
168106 TTTT
1 TTTT
168110 TTCATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 5 0.17
15 19 0.63
16 6 0.20
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTTTTATT
Found at i:168104 original size:24 final size:24
Alignment explanation
Indices: 168066--168124 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
168056 ATCTGTTTTA
*
168066 TTTTATTATTATTATATTTTTT-ATT
1 TTTTATT-TTTTTATATTTTTTCA-T
*
168091 TTTTATTTTTTTATTTTTTTTCAT
1 TTTTATTTTTTTATATTTTTTCAT
*
168115 ATTTATTTTT
1 TTTTATTTTT
168125 ATTTTACAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTATTTTTTTATATTTTTTCAT
Found at i:168109 original size:22 final size:23
Alignment explanation
Indices: 168061--168109 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
168051 TTGTTATCTG
168061 TTTTATTTTATTATTATTATATT
1 TTTTATTTTATTATTATTATATT
* *
168084 TTTTATTTT-TTATTTTTTTATT
1 TTTTATTTTATTATTATTATATT
168106 TTTT
1 TTTT
168110 TTCATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTATTTTATTATTATTATATT
Found at i:171862 original size:163 final size:163
Alignment explanation
Indices: 171652--171977 Score: 559
Period size: 161 Copynumber: 2.0 Consensus size: 163
171642 CTGACCCGAA
*
171652 ATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAATTATATATAG
1 ATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG-AAAAAAATTATATATAA
*
171717 AGGGGTATTATTGTAATTATTCTTAAATATATAAGGAAAAATTATATAT-TTTTTGGGTCGGGTC
65 AGGGGTATTATTGTAATTATTCCT-AA-ATATAAGGAAAAATTATATATATTTTTGGGTCGGGTC
*
171781 GGGTATTTTTCACCCTAAACCCGAACCCGACACGAC
128 GGGTATTTTTCACCCTAAACCCGAACACGACACGAC
171817 ATAAT-AAAAAAA-TATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAAA
1 ATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAAA
*
171880 GGGGTATTATTGTAATTATTCCTAAATATAAGGTAAAATTATATATATTTTTGGGTCGGGTCGGG
66 GGGGTATTATTGTAATTATTCCTAAATATAAGGAAAAATTATATATATTTTTGGGTCGGGTCGGG
*
171945 TATTTTTCACCCTAAACCCGAACACGACCCGAC
131 TATTTTTCACCCTAAACCCGAACACGACACGAC
171978 CCGAATATTA
Statistics
Matches: 155, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
160 20 0.13
161 51 0.33
162 39 0.25
163 33 0.21
164 7 0.05
165 5 0.03
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (163 bp):
ATAATAAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAAA
GGGGTATTATTGTAATTATTCCTAAATATAAGGAAAAATTATATATATTTTTGGGTCGGGTCGGG
TATTTTTCACCCTAAACCCGAACACGACACGAC
Found at i:172991 original size:145 final size:145
Alignment explanation
Indices: 172728--173015 Score: 513
Period size: 145 Copynumber: 2.0 Consensus size: 145
172718 TTACTTGCAA
172728 GGAATTGTAATGAGGGTTGAAGTAAGTTTGTTTTATATTTTCAAATCAAATTACATCTCCAATAC
1 GGAATTGTAATGAGGGTTGAAGTAAGTTTGTTTTATATTTTCAAATCAAATTACATCTCCAATAC
* * * *
172793 AATGTTGTTTGTATGAACTCAGGAAACTAGAAGCACATTGCTAACAAGAAAATATTTAGGACATG
66 AATGTTGTTTATATGAACTCAGGAAACTAGAAGCACATTACCAACAAGAAAATATTTAGGACATA
172858 TATTGAGAAATGTAC
131 TATTGAGAAATGTAC
* *
172873 GGAATTGTAATGAGGGTTGAAGTAAGTTTGTTTTATATTTTCGAATCAAATTACATCTTCAATAC
1 GGAATTGTAATGAGGGTTGAAGTAAGTTTGTTTTATATTTTCAAATCAAATTACATCTCCAATAC
*
172938 AATGTTGTTTATATGAATTCAGGAAACTAGAAGCACATTACCAACAAGAAAATATTTAGGACATA
66 AATGTTGTTTATATGAACTCAGGAAACTAGAAGCACATTACCAACAAGAAAATATTTAGGACATA
173003 TATTGAGAAATGT
131 TATTGAGAAATGT
173016 TTCTGATACA
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 136 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (145 bp):
GGAATTGTAATGAGGGTTGAAGTAAGTTTGTTTTATATTTTCAAATCAAATTACATCTCCAATAC
AATGTTGTTTATATGAACTCAGGAAACTAGAAGCACATTACCAACAAGAAAATATTTAGGACATA
TATTGAGAAATGTAC
Found at i:178791 original size:15 final size:15
Alignment explanation
Indices: 178771--178801 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
178761 TAGCCTGGGA
178771 TTGCTTTACTTTCGT
1 TTGCTTTACTTTCGT
178786 TTGCTTTACTTTCGT
1 TTGCTTTACTTTCGT
178801 T
1 T
178802 GAATTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.13, T:0.61
Consensus pattern (15 bp):
TTGCTTTACTTTCGT
Found at i:185854 original size:20 final size:20
Alignment explanation
Indices: 185829--185866 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
185819 CACATGTTAA
185829 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
185849 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
185867 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:187861 original size:22 final size:20
Alignment explanation
Indices: 187836--187878 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
187826 TTTTCTTTAA
187836 TTTAAAAAAAATTCACAATTTT
1 TTTAAAAAAAATT-A-AATTTT
*
187858 TTTATAAAAAATTAAATTTT
1 TTTAAAAAAAATTAAATTTT
187878 T
1 T
187879 CTACTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAAAAAAATTAAATTTT
Found at i:189410 original size:28 final size:26
Alignment explanation
Indices: 189373--189437 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
189363 ATTTAAAATT
* *
189373 TAAAATAAATTTATTTTTTTAATATTTC
1 TAAAATAAA-TTAATTATTT-ATATTTC
*
189401 TAAATTAAATTAATTATTTATATTTC
1 TAAAATAAATTAATTATTTATATTTC
189427 TAAAGATAAAT
1 TAAA-ATAAAT
189438 ATAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 11 0.34
27 13 0.41
28 8 0.25
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (26 bp):
TAAAATAAATTAATTATTTATATTTC
Found at i:189446 original size:27 final size:26
Alignment explanation
Indices: 189394--189446 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
189384 TATTTTTTTA
* *
189394 ATATTTCTAAATTAAATTAATTATTT
1 ATATTTCTAAAATAAATTAATAATTT
189420 ATATTTCTAAAGATAAATATAA-AATTT
1 ATATTTCTAAA-ATAAAT-TAATAATTT
189447 TAAAAATAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 11 0.48
27 9 0.39
28 3 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
ATATTTCTAAAATAAATTAATAATTT
Found at i:191149 original size:17 final size:18
Alignment explanation
Indices: 191108--191146 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
191098 ATTATATAAG
191108 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
191125 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
191143 TAAA
1 TAAA
191147 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:198954 original size:15 final size:15
Alignment explanation
Indices: 198934--198963 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
198924 ATGTGGTACC
*
198934 TTTTAACATCGAGAT
1 TTTTAACACCGAGAT
198949 TTTTAACACCGAGAT
1 TTTTAACACCGAGAT
198964 CACTTGATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (15 bp):
TTTTAACACCGAGAT
Found at i:207142 original size:19 final size:19
Alignment explanation
Indices: 207110--207178 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
207100 TTCATTGAAA
207110 AACCGAAAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
207128 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
*
207147 TTA---AAAAACCCGAACCG
1 -AACCGAAAAACCCGAACCG
*
207164 AACCGAAAAAACCGA
1 AACCGAAAAACCCGA
207179 TTTCAGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 1 0.02
17 14 0.33
18 10 0.23
19 17 0.40
20 1 0.02
ACGTcount: A:0.51, C:0.32, G:0.14, T:0.03
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:207144 original size:14 final size:14
Alignment explanation
Indices: 207125--207165 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
207115 AAAAACCGAA
207125 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
207139 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
207156 CCGAACCGAA
1 CCGAACCGAA
207166 CCGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:213987 original size:66 final size:66
Alignment explanation
Indices: 213910--214034 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
213900 GTCCATTTTT
* * * *
213910 TTCTTCTGGTTGGTGGGTGCAGCTTCTCTCCCACGTTCCTCAGTAACAGTCGACTCGTTGGTGCT
1 TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTTGGTGCT
213975 C
66 C
* * * *
213976 TTCTTCGGGTTGGTGGGTGCAATTTCTTTCCCACGTCCCTCGGTAGCAGTCAACTCGTT
1 TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTT
214035 CGAGTTTTCG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (66 bp):
TTCTTCGGGTTGGTGGGTGCAACTTCTCTCCCACGTCCCTCAGTAACAGTCAACTCGTTGGTGCT
C
Found at i:215296 original size:5 final size:5
Alignment explanation
Indices: 215286--215316 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
215276 AGGGTTCTCC
215286 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
215317 ATATGACTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:221778 original size:23 final size:23
Alignment explanation
Indices: 221728--221782 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
221718 AAACATGTTT
**
221728 GTTTAACGTTCACGAATATGTTC
1 GTTTAACGTTCACGAATATGAGC
* * *
221751 ATTTAATGTTCATGAATATGAGC
1 GTTTAACGTTCACGAATATGAGC
221774 GTTTAACGT
1 GTTTAACGT
221783 CGTTTAATGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
GTTTAACGTTCACGAATATGAGC
Found at i:222620 original size:34 final size:34
Alignment explanation
Indices: 222579--222652 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
222569 TGAAATACTT
*
222579 TTATTATAAAGGATACTT-AACTTATTTATGTTTA
1 TTATTATAAA-GATACTTAAAATTATTTATGTTTA
* *
222613 TTATTATAAATATGCTTAAAATTATTTATGTTTA
1 TTATTATAAAGATACTTAAAATTATTTATGTTTA
222647 TT-TTAT
1 TTATTAT
222653 TTATTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
33 9 0.25
34 27 0.75
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (34 bp):
TTATTATAAAGATACTTAAAATTATTTATGTTTA
Found at i:223140 original size:43 final size:41
Alignment explanation
Indices: 223092--223244 Score: 166
Period size: 43 Copynumber: 3.7 Consensus size: 41
223082 TTGCATTTCG
*
223092 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTT-AAAAT-TCGTTGCGATAGTCTACAGTTGT
* * *
223135 CGTTGCGAT-TTTCAAATTCTTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTTAAAATTCGTTGCGATAGTCTACAGTTGT
* * *
223175 TGTTGCGATAGATTACAAATTTGTTGCGATAGTCTACCGTTGT
1 CGTTGCGATAG-TTA-AAATTCGTTGCGATAGTCTACAGTTGT
* *
223218 CGTTGCGAT-TTTCCAAATTCGTTGCGA
1 CGTTGCGATAGTT-AAAATTCGTTGCGA
223245 AAATTTGTTG
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
40 29 0.32
41 18 0.20
42 4 0.04
43 41 0.45
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATAGTTAAAATTCGTTGCGATAGTCTACAGTTGT
Found at i:223163 original size:40 final size:40
Alignment explanation
Indices: 223115--223244 Score: 172
Period size: 43 Copynumber: 3.1 Consensus size: 40
223105 GAAAATCGCG
223115 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCAAATTCT
1 TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCAAATTCT
* *
223155 TTGCGATAGTCTACAGTTGTTGTTGCGATAGATTACAAATT-T
1 TTGCGATAGTCTACAGTTGTCGTTGCGAT---TTTCAAATTCT
* *
223197 GTTGCGATAGTCTACCGTTGTCGTTGCGATTTTCCAAATTCG
1 -TTGCGATAGTCTACAGTTGTCGTTGCGATTTT-CAAATTCT
223239 TTGCGA
1 TTGCGA
223245 AAATTTGTTG
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
40 30 0.38
41 12 0.15
42 1 0.01
43 35 0.45
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCTACAGTTGTCGTTGCGATTTTCAAATTCT
Found at i:224295 original size:39 final size:41
Alignment explanation
Indices: 224164--224344 Score: 217
Period size: 41 Copynumber: 4.5 Consensus size: 41
224154 CCATTTTAAA
* **
224164 ACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
* *
224205 ACTATCGCAACGCGAAATGGAAAACCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
*
224246 ACTATTGCAACGCGAAATGG-AAATCACAACGAC-CTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
* * * * *
224285 ACTATCGCAACGCGAAATGAAAAACCGCAACG-CGATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCACAACGAC-ACTGT-AG
224326 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
224345 CAGCGTGAAT
Statistics
Matches: 122, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
39 25 0.20
40 20 0.16
41 76 0.62
42 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
Found at i:224301 original size:80 final size:82
Alignment explanation
Indices: 224164--224316 Score: 265
Period size: 80 Copynumber: 1.9 Consensus size: 82
224154 CCATTTTAAA
** *
224164 ACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
224229 CCGCAACGACACTGTAG
66 CCGCAACGACACTGTAG
224246 ACTATTGCAACGCGAAATGG-AAATCACAACGAC-CTGTAGACTATCGCAACGCGAAATGAAAAA
1 ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
224309 CCGCAACG
66 CCGCAACG
224317 CGATTTTCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
80 37 0.54
81 11 0.16
82 20 0.29
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (82 bp):
ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAAA
CCGCAACGACACTGTAG
Found at i:224330 original size:80 final size:81
Alignment explanation
Indices: 224163--224344 Score: 262
Period size: 80 Copynumber: 2.2 Consensus size: 81
224153 ACCATTTTAA
** *
224163 AACTATTGCAACGCGAAATGGAAAATCATGACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 AACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
224228 ACCGCAACGACACTGT
66 ACCGCAACGACACTGT
224244 AGACTATTGCAACGCGAAATGG-AAATCACAACGAC-CTGTAGACTATCGCAACGCGAAATGAAA
1 A-ACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAA
* *
224307 AACCGCAACG-CGATTTT
65 AACCGCAACGAC-ACTGT
*
224324 CAACTATCGCAACGCGAAATG
1 -AACTATTGCAACGCGAAATG
224345 CAGCGTGAAT
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
79 1 0.01
80 58 0.63
81 13 0.14
82 20 0.22
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (81 bp):
AACTATTGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGAAAA
ACCGCAACGACACTGT
Found at i:225943 original size:14 final size:16
Alignment explanation
Indices: 225912--225953 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
225902 TCATAAAATA
225912 AATAAATTAATTTCAAT
1 AATAAATT-ATTTCAAT
225929 AATAAATT-TTT-AAT
1 AATAAATTATTTCAAT
*
225943 AATAATTTATT
1 AATAAATTATT
225954 AAACCCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
15 5 0.22
17 8 0.35
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTATTTCAAT
Found at i:233542 original size:70 final size:70
Alignment explanation
Indices: 233429--233568 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
233419 TTTCCTCTTG
233429 CCTGAGGTTTTCTTTGCAAGAACATAGCCTACGAAAGCAGAATTTTATGTTAAGAAAGTAAATTT
1 CCTGAGGTTTTCTTTGCAAGAACATAGCCTACGAAAGCAGAATTTTATGTTAAGAAAGTAAATTT
233494 CTAAA
66 CTAAA
233499 CCTGAGGTTTTCTTTGCAAGAACATAGCCTACGAAAGCAGAATTTTATGTTAAGAAAGTAAATTT
1 CCTGAGGTTTTCTTTGCAAGAACATAGCCTACGAAAGCAGAATTTTATGTTAAGAAAGTAAATTT
233564 CTAAA
66 CTAAA
233569 ACTTTAAGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (70 bp):
CCTGAGGTTTTCTTTGCAAGAACATAGCCTACGAAAGCAGAATTTTATGTTAAGAAAGTAAATTT
CTAAA
Found at i:233554 original size:34 final size:34
Alignment explanation
Indices: 233446--233554 Score: 87
Period size: 34 Copynumber: 3.1 Consensus size: 34
233436 TTTTCTTTGC
233446 AAGAACATAGCCTACGAAAGCAGAATTTTATGTT
1 AAGAACATAGCCTACGAAAGCAGAATTTTATGTT
*** * * * * * *
233480 AAGAA-AGTAAATTTCTAAACCTGAGGTTTTCT-TT
1 AAGAACA-TAGCCTACGAAAGCAGA-ATTTTATGTT
233514 GCAAGAACATAGCCTACGAAAGCAGAATTTTATGTT
1 --AAGAACATAGCCTACGAAAGCAGAATTTTATGTT
233550 AAGAA
1 AAGAA
233555 AGTAAATTTC
Statistics
Matches: 51, Mismatches: 18, Indels: 12
0.63 0.22 0.15
Matches are distributed among these distances:
33 1 0.02
34 22 0.43
35 10 0.20
36 17 0.33
37 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (34 bp):
AAGAACATAGCCTACGAAAGCAGAATTTTATGTT
Found at i:235287 original size:20 final size:21
Alignment explanation
Indices: 235252--235297 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
235242 AATTAAGAGC
235252 TCAATTAATTATTTATAAAAAATT
1 TCAATTAATTA--T-TAAAAAATT
*
235276 TCAATTAATTATTATAAAATT
1 TCAATTAATTATTAAAAAATT
235297 T
1 T
235298 GAGAGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
24 11 0.52
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TCAATTAATTATTAAAAAATT
Found at i:235377 original size:21 final size:21
Alignment explanation
Indices: 235331--235381 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
235321 ATATTTAAAA
*
235331 TTTAAAT-AATTATTTAATTT
1 TTTAAATAAAATATTTAATTT
*
235351 TATAAATAAAATA-TTAATATT
1 TTTAAATAAAATATTTAAT-TT
235372 TTTAAATAAA
1 TTTAAATAAA
235382 TGAATAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAATAAAATATTTAATTT
Found at i:235382 original size:20 final size:20
Alignment explanation
Indices: 235311--235382 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
235301 AGTTTATCTA
* *
235311 TTTTAAGTAAATATTTAA-A
1 TTTTAAATAAATATTTAATT
* *
235330 ATTTAAATAATTATTTAATT
1 TTTTAAATAAATATTTAATT
*
235350 TTATAAATAAA-ATATTAATAT
1 TTTTAAATAAATAT-TTAAT-T
235371 TTTTAAATAAAT
1 TTTTAAATAAAT
235383 GAATAATTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 17 0.41
20 13 0.32
21 11 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (20 bp):
TTTTAAATAAATATTTAATT
Found at i:235389 original size:21 final size:22
Alignment explanation
Indices: 235347--235389 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
235337 TAATTATTTA
*
235347 ATTTTATAAATAAAATATTAAT
1 ATTTTATAAATAAAATAATAAT
235369 ATTTT-TAAAT-AAATGAATAAT
1 ATTTTATAAATAAAAT-AATAAT
235390 TAACATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATTTTATAAATAAAATAATAAT
Found at i:236028 original size:18 final size:19
Alignment explanation
Indices: 235989--236057 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
235979 TTATCTATTT
*
235989 TTTAAGTAAATATTTAAAA
1 TTTAAATAAATATTTAAAA
* *
236008 TTTAAATAATTATTTAAAT
1 TTTAAATAAATATTTAAAA
**
236027 TTATAAATAAA-ATATTAATT
1 TT-TAAATAAATAT-TTAAAA
236047 TTTAAATAAAT
1 TTTAAATAAAT
236058 GAATAATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
19 28 0.67
20 14 0.33
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (19 bp):
TTTAAATAAATATTTAAAA
Found at i:236064 original size:19 final size:19
Alignment explanation
Indices: 236024--236065 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
236014 TAATTATTTA
*
236024 AATTTATAAATAAAATATT
1 AATTTATAAATAAAATAAT
*
236043 AATTTTTAAAT-AAATGAAT
1 AATTTATAAATAAAAT-AAT
236062 AATT
1 AATT
236066 AACATTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTTATAAATAAAATAAT
Found at i:240527 original size:50 final size:50
Alignment explanation
Indices: 240464--240584 Score: 233
Period size: 50 Copynumber: 2.4 Consensus size: 50
240454 GTTTTAACTC
*
240464 TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTTAACCCAACCT
240514 TAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTTAACCCAACCT
240564 TAATTCCTAATAAAATAATAA
1 TAATTCCTAATAAAATAATAA
240585 ATCTGATCCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.33
Consensus pattern (50 bp):
TAATTCCTAATAAAATAATAACAACTAAAAATATTGTTTTAACCCAACCT
Found at i:244995 original size:43 final size:47
Alignment explanation
Indices: 244947--245102 Score: 171
Period size: 50 Copynumber: 3.3 Consensus size: 47
244937 ATAACTAAAG
*
244947 AATAAAATAATAATAAACTAAACA-TGTTTTAA-C-TC-TAATTCCT
1 AATAAAATAATAATAAACTAAACATTGTTTTAACCACCTTAATTCCT
*
244990 AATAAAATAATAAT-AACTAAAAATATTGTTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAAACT--AAACATTGTTTTAA-CC-ACCTTAATTCCT
*
245040 AATAAAATAATAATAAA-TAAAAATATTGTTTTAACCCAACCTTAATTCCT
1 AATAAAATAATAATAAACT--AAACATTGTTTTAA-CC-ACCTTAATTCCT
245090 AATAAAATAATAA
1 AATAAAATAATAA
245103 ATCTGATCCT
Statistics
Matches: 102, Mismatches: 2, Indels: 11
0.89 0.02 0.10
Matches are distributed among these distances:
42 4 0.04
43 14 0.14
44 4 0.04
45 8 0.08
47 1 0.01
49 1 0.01
50 68 0.67
51 2 0.02
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.33
Consensus pattern (47 bp):
AATAAAATAATAATAAACTAAACATTGTTTTAACCACCTTAATTCCT
Found at i:245041 original size:50 final size:50
Alignment explanation
Indices: 244982--245102 Score: 233
Period size: 50 Copynumber: 2.4 Consensus size: 50
244972 GTTTTAACTC
*
244982 TAATTCCTAATAAAATAATAATAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAATAAATAAAAATATTGTTTTAACCCAACCT
245032 TAATTCCTAATAAAATAATAATAAATAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAATAAATAAAAATATTGTTTTAACCCAACCT
245082 TAATTCCTAATAAAATAATAA
1 TAATTCCTAATAAAATAATAA
245103 ATCTGATCCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (50 bp):
TAATTCCTAATAAAATAATAATAAATAAAAATATTGTTTTAACCCAACCT
Found at i:247189 original size:21 final size:22
Alignment explanation
Indices: 247151--247191 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
247141 AAGACTCTAT
247151 TTTCAAAATTACAAAAATGATA
1 TTTCAAAATTACAAAAATGATA
*
247173 TTTCAAAATT-GAAAAATGA
1 TTTCAAAATTACAAAAATGA
247192 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (22 bp):
TTTCAAAATTACAAAAATGATA
Found at i:251065 original size:21 final size:22
Alignment explanation
Indices: 251007--251077 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
250997 GAATCAATAC
*
251007 CCCCCTTGAAGGGGAAATGATT
1 CCCCCTTGAAGGGGAAACGATT
*
251029 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTGAAGGGGAAACGATT
* * *
251052 CCCCC-TGTAGGGGAATCGATA
1 CCCCCTTGAAGGGGAAACGATT
251073 CCCCC
1 CCCCC
251078 CTGGGGTTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.42
22 5 0.12
23 20 0.47
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAAACGATT
Found at i:251080 original size:22 final size:22
Alignment explanation
Indices: 250995--251080 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 22
250985 TTAGTGCAGA
*
250995 GGGAATCAATACCCCCCTTGAAG
1 GGGAATCGATACCCCCC-TGAAG
* *
251018 GGGAAAT-GATTCCCCCTTTGAAG
1 GGG-AATCGATACCCCC-CTGAAG
* * *
251041 GGGAACCGAT-TCCCCCTGTAG
1 GGGAATCGATACCCCCCTGAAG
251062 GGGAATCGATACCCCCCTG
1 GGGAATCGATACCCCCCTG
251081 GGGTTCTGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 13 0.26
22 13 0.26
23 21 0.42
24 3 0.06
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCCTGAAG
Found at i:252681 original size:18 final size:18
Alignment explanation
Indices: 252658--252698 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
252648 AGAACAACAC
*
252658 GAGGAATAAGCACGAG-CA
1 GAGGAACAAGCAC-AGCCA
252676 GAGGAACAAGCACAGCCA
1 GAGGAACAAGCACAGCCA
252694 GAGGA
1 GAGGA
252699 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.44, C:0.20, G:0.34, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACAGCCA
Found at i:253232 original size:2 final size:2
Alignment explanation
Indices: 253225--253263 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
253215 GCAGCTTAAG
253225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
253264 ATCAATTGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:253538 original size:13 final size:13
Alignment explanation
Indices: 253520--253544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
253510 AATAAATTTT
253520 AAGATTTTCTAAA
1 AAGATTTTCTAAA
253533 AAGATTTTCTAA
1 AAGATTTTCTAA
253545 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:254594 original size:30 final size:32
Alignment explanation
Indices: 254530--254595 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
254520 TAACTCAACA
* * *
254530 CAAGACAATTCTCGGGGCCACAAAGGCTTACC
1 CAAGACAAATCTCAGGGCCACAAAGGCCTACC
*
254562 CAAGA-AAATCTCAGGGCCCCAAA-GCCTACC
1 CAAGACAAATCTCAGGGCCACAAAGGCCTACC
254592 CAAG
1 CAAG
254596 GGTCTCTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 10 0.33
31 15 0.50
32 5 0.17
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.12
Consensus pattern (32 bp):
CAAGACAAATCTCAGGGCCACAAAGGCCTACC
Found at i:261658 original size:41 final size:41
Alignment explanation
Indices: 261596--261684 Score: 169
Period size: 41 Copynumber: 2.1 Consensus size: 41
261586 TTTCGAACAT
261596 GTTTCTAGCCTTTGATTCTTTACTAATTATTTATGCTTAATG
1 GTTT-TAGCCTTTGATTCTTTACTAATTATTTATGCTTAATG
261638 GTTTTAGCCTTTGATTCTTTACTAATTATTTATGCTTAATG
1 GTTTTAGCCTTTGATTCTTTACTAATTATTTATGCTTAATG
261679 GTTTTA
1 GTTTTA
261685 TAGGAAAACG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 43 0.91
42 4 0.09
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (41 bp):
GTTTTAGCCTTTGATTCTTTACTAATTATTTATGCTTAATG
Found at i:262121 original size:17 final size:16
Alignment explanation
Indices: 262092--262139 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
262082 ATATTTTGTT
262092 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
262109 TTTAACTTT-TTTAATA
1 TTTAA-TTTATTTAATA
* *
262125 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
262140 TTTTTTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 10 0.37
18 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:267723 original size:14 final size:15
Alignment explanation
Indices: 267699--267727 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
267689 ATAATCATAT
267699 ATAATTATAAAAAAA
1 ATAATTATAAAAAAA
267714 ATAA-TATAAAAAAA
1 ATAATTATAAAAAAA
267728 TTACCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAATTATAAAAAAA
Found at i:270140 original size:17 final size:17
Alignment explanation
Indices: 270118--270151 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
270108 TTTATATAAA
*
270118 TTATTATTATTATTATT
1 TTATTAATATTATTATT
*
270135 TTATTAATATTTTTATT
1 TTATTAATATTATTATT
270152 GCACCCCATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTAATATTATTATT
Found at i:271876 original size:17 final size:19
Alignment explanation
Indices: 271850--271891 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
271840 AACGTCTTTT
*
271850 AAAAACAATTTT-TAAGA-
1 AAAAATAATTTTATAAGAC
271867 AAAAATAATTTTATAAGAC
1 AAAAATAATTTTATAAGAC
271886 AAAAAT
1 AAAAAT
271892 TTGGTCTACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 5 0.23
19 6 0.27
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAATAATTTTATAAGAC
Found at i:272346 original size:14 final size:14
Alignment explanation
Indices: 272327--272354 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
272317 ATGTTAGTTA
272327 AAATAAATAAAAAT
1 AAATAAATAAAAAT
272341 AAATAAATAAAAAT
1 AAATAAATAAAAAT
272355 CCTTTGCTCG
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:272620 original size:17 final size:16
Alignment explanation
Indices: 272594--272635 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
272584 TAAATTAATC
272594 AAAA-AAAATAAAAAAT
1 AAAATAAAAT-AAAAAT
*
272610 AAAATAAAATAACAAT
1 AAAATAAAATAAAAAT
272626 AACAATAAAA
1 AA-AATAAAA
272636 ATAATTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:274492 original size:25 final size:25
Alignment explanation
Indices: 274458--274555 Score: 187
Period size: 25 Copynumber: 3.9 Consensus size: 25
274448 GAGTAGGGAA
274458 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
274483 TTAGGGTTTGAAACCCTAATTTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
274508 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
274533 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
274556 CTAGGTTGGG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:274716 original size:10 final size:10
Alignment explanation
Indices: 274689--274729 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
274679 TAATATGTAA
274689 AATTAATAAT
1 AATTAATAAT
274699 AA-TAATAAT
1 AATTAATAAT
274708 AATTAATAAT
1 AATTAATAAT
*
274718 AATTAAAAAT
1 AATTAATAAT
274728 AA
1 AA
274730 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTAATAAT
Found at i:275176 original size:141 final size:141
Alignment explanation
Indices: 274972--275242 Score: 386
Period size: 141 Copynumber: 1.9 Consensus size: 141
274962 CTGGTCCAGG
* ** *
274972 GATGACACGGCTCATACGCGATGAAGAGTTCTGGTCATGTTTAAGAAGGGTGATAACTCGGTTCC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCATGTTTAAGAAGGGTGATAACTCGGTTCC
275037 TACGTGATGAGGACGGCTGATTAT-CTAAGGTTGACACGGCTCCTACGTGATGAGGA-AGTCTGG
66 TACGTGATGAGGACGGCTGATTATCCTAAGGTTGACAC-GCTCCTACGTGATGAGGAGA-TCTGG
275100 TCGTCTAAGGGTA
129 TCGTCTAAGGGTA
* * * * *
275113 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCG-TTAGGAAGGGTGATAACTTGGTTC
1 GATGACACGGCTCATACACGATGAAGAACTCTGGCCAT-GTTTAAGAAGGGTGATAACTCGGTTC
* * *
275177 CTACGTGATGAGGACGGCTGGTTATCCTAATGTTGACACTCTCCTACGTGATGAGGAGATCTGGT
65 CTACGTGATGAGGACGGCTGATTATCCTAAGGTTGACACGCTCCTACGTGATGAGGAGATCTGGT
275242 C
130 C
275243 AGTTGATGTT
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
141 101 0.88
142 14 0.12
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (141 bp):
GATGACACGGCTCATACACGATGAAGAACTCTGGCCATGTTTAAGAAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGGCTGATTATCCTAAGGTTGACACGCTCCTACGTGATGAGGAGATCTGGTC
GTCTAAGGGTA
Found at i:276218 original size:15 final size:15
Alignment explanation
Indices: 276198--276232 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
276188 CTTTATTTAT
276198 TTTTTC-TTCTTTTCA
1 TTTTTCATT-TTTTCA
276213 TTTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
276228 TTTTT
1 TTTTT
276233 TTTAAGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.89
16 2 0.11
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:276224 original size:8 final size:8
Alignment explanation
Indices: 276196--276233 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
276186 TCCTTTATTT
276196 ATTTTTTC
1 ATTTTTTC
276204 -TTCTTTTC
1 ATT-TTTTC
276212 A-TTTTTC
1 ATTTTTTC
276219 ATTTTTTC
1 ATTTTTTC
276227 ATTTTTT
1 ATTTTTT
276234 TTAAGTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 8 0.30
8 19 0.70
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Found at i:287182 original size:16 final size:16
Alignment explanation
Indices: 287157--287199 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
287147 AACGTCTTTT
287157 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
287173 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
287190 ACAAAAATTT
1 AAAAAAATTT
287200 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:287654 original size:14 final size:14
Alignment explanation
Indices: 287635--287662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
287625 ATGTTAGTTA
287635 AAATAAATAAAAAT
1 AAATAAATAAAAAT
287649 AAATAAATAAAAAT
1 AAATAAATAAAAAT
287663 CCTTTGCTCG
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATAAAAAT
Found at i:287922 original size:5 final size:5
Alignment explanation
Indices: 287914--287943 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
287904 AAAAAAATAA
287914 AAAAT AAAAT AAAAT AAAAT AACAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAA
287944 ATAATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:287944 original size:17 final size:17
Alignment explanation
Indices: 287890--287947 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
287880 TATGAACATC
* *
287890 AAATAAATTAATCAAAAA
1 AAATAAAATAA-CAATAA
287908 AAATAAAAAATAA-AAT-A
1 AAAT--AAAATAACAATAA
287925 AAATAAAATAACAATAA
1 AAATAAAATAACAATAA
287942 AAATAA
1 AAATAA
287948 TTTCTATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 12 0.35
18 6 0.18
20 6 0.18
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAAAATAACAATAA
Found at i:287947 original size:22 final size:21
Alignment explanation
Indices: 287903--287943 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
287893 TAAATTAATC
287903 AAAAAAAATAAAAAATAAAAT
1 AAAAAAAATAAAAAATAAAAT
*
287924 AAAATAAAAT-AACAATAAAA
1 AAAA-AAAATAAAAAATAAAA
287944 ATAATTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAAAATAAAAAATAAAAT
Found at i:289418 original size:11 final size:11
Alignment explanation
Indices: 289402--289426 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
289392 CTTTCTCTCC
289402 TTTTTTTCTGT
1 TTTTTTTCTGT
289413 TTTTTTTCTGT
1 TTTTTTTCTGT
289424 TTT
1 TTT
289427 GAATCCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTGT
Found at i:289807 original size:25 final size:25
Alignment explanation
Indices: 289773--289895 Score: 219
Period size: 25 Copynumber: 4.9 Consensus size: 25
289763 GAGTAGGGAA
* *
289773 TTAGGGTTTGAAACCCTAATATGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
289798 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
*
289823 TTAGGGTTTGAAACCCTAATTTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
289848 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
289873 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
289896 CTAGGTTGGG
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 94 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:290057 original size:10 final size:10
Alignment explanation
Indices: 290030--290070 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
290020 AATATGTAAA
290030 AATTAATAAT
1 AATTAATAAT
290040 AA-TAATAAT
1 AATTAATAAT
290049 AATTAATAAT
1 AATTAATAAT
*
290059 AATTAAAAAT
1 AATTAATAAT
290069 AA
1 AA
290071 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AATTAATAAT
Found at i:294076 original size:31 final size:31
Alignment explanation
Indices: 294002--294079 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
293992 CATGACTGAG
*
294002 GGACTAAAATCGAACGGACCGATAACATTAT
1 GGACTAAAATCGGACGGACCGATAACATTAT
* *
294033 GGACTGAAATCGGATGGACCGATAACATTA-
1 GGACTAAAATCGGACGGACCGATAACATTAT
*
294063 GAGACTTAAATCGGACG
1 G-GACTAAAATCGGACG
294080 TAGTGATGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.19
Consensus pattern (31 bp):
GGACTAAAATCGGACGGACCGATAACATTAT
Found at i:296385 original size:24 final size:24
Alignment explanation
Indices: 296358--296419 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
296348 CGTTCATGAA
*
296358 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
296382 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
296406 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
296420 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:297965 original size:16 final size:16
Alignment explanation
Indices: 297944--298010 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
297934 TTATGTTCGT
297944 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
297960 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
297976 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
297992 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
298006 TTTAT
1 TTTAT
298011 TAAATGAACG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:297989 original size:32 final size:33
Alignment explanation
Indices: 297937--298002 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
297927 CCAACGTTTA
297937 TGTTCGTTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTTATGTTCGTGTTCATTTATGTTCG
* *
297970 TGTTCG-TTTATGTTTGTGTTCGTTTATGTTCG
1 TGTTCGTTTTATGTTCGTGTTCATTTATGTTCG
298002 T
1 T
298003 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.59
Consensus pattern (33 bp):
TGTTCGTTTTATGTTCGTGTTCATTTATGTTCG
Found at i:299735 original size:21 final size:21
Alignment explanation
Indices: 299705--299756 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
299695 AAACTAAATT
*
299705 TGAATCAAATCTAACCCGACC
1 TGAATAAAATCTAACCCGACC
*
299726 TGAATAAAATCTAACCTGACC
1 TGAATAAAATCTAACCCGACC
*
299747 TAAATCAAAA
1 TGAAT-AAAA
299757 CAAAGCGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.46, C:0.25, G:0.08, T:0.21
Consensus pattern (21 bp):
TGAATAAAATCTAACCCGACC
Found at i:300439 original size:29 final size:29
Alignment explanation
Indices: 300405--300463 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
300395 CCTAAATTAA
300405 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
**
300434 TTTGATGTCATTGCTTATGTCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
300463 T
1 T
300464 ATGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.15, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:305095 original size:29 final size:29
Alignment explanation
Indices: 305061--305119 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
305051 CCTAAATTAA
305061 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
305090 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
305119 T
1 T
305120 ATGTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:311070 original size:23 final size:23
Alignment explanation
Indices: 311004--311080 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
310994 TGCATGTGTT
* *
311004 GCACGTTTATCTCTGATTATGTT
1 GCACGTTTATCTCTGATTTTGTG
** *
311027 ATACGTTTATCTATGCA-TTTGTG
1 GCACGTTTATCTCTG-ATTTTGTG
*
311050 GCACGTTTATCTCTGTTTTTGTG
1 GCACGTTTATCTCTGATTTTGTG
*
311073 GTACGTTT
1 GCACGTTT
311081 TTTAGTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (23 bp):
GCACGTTTATCTCTGATTTTGTG
Found at i:311078 original size:46 final size:46
Alignment explanation
Indices: 310992--311080 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
310982 TAAGAATAAT
* *
310992 TATGCATGTGTTGCACGTTTATCTCTGATTATGTTATACGTTTATC
1 TATGCATGTGTGGCACGTTTATCTCTGATTATGTGATACGTTTATC
* * * *
311038 TATGCATTTGTGGCACGTTTATCTCTGTTTTTGTGGTACGTTT
1 TATGCATGTGTGGCACGTTTATCTCTGATTATGTGATACGTTT
311081 TTTAGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.16, C:0.15, G:0.20, T:0.49
Consensus pattern (46 bp):
TATGCATGTGTGGCACGTTTATCTCTGATTATGTGATACGTTTATC
Found at i:311670 original size:16 final size:17
Alignment explanation
Indices: 311649--311685 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
311639 GCGTTCAAAT
*
311649 TTTTTAATACTTT-TTA
1 TTTTTAATAATTTATTA
311665 TTTTTAATAATTTATTA
1 TTTTTAATAATTTATTA
311682 TTTT
1 TTTT
311686 ATAGCTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAATAATTTATTA
Found at i:320165 original size:2 final size:2
Alignment explanation
Indices: 320158--320204 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
320148 ATCGAATACT
320158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
320200 TA TA T
1 TA TA T
320205 TGAATACAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:320332 original size:33 final size:34
Alignment explanation
Indices: 320289--320353 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
320279 TCAGAAGGAC
*
320289 AAGTTTATTTAT-TTTTAAATATTATAATAGTGT
1 AAGTTCATTTATATTTTAAATATTATAATAGTGT
320322 AAGTTCATTTATATTTTAAATATTATAATAGT
1 AAGTTCATTTATATTTTAAATATTATAATAGT
320354 TACCAAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.37
34 19 0.63
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (34 bp):
AAGTTCATTTATATTTTAAATATTATAATAGTGT
Found at i:326911 original size:17 final size:18
Alignment explanation
Indices: 326889--326928 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
326879 GAAAATGGAT
326889 TCCTTTAA-AACGCTTGG
1 TCCTTTAAGAACGCTTGG
*
326906 TCCTTTAAGTACGCTTGG
1 TCCTTTAAGAACGCTTGG
326924 TCCTT
1 TCCTT
326929 GAATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (18 bp):
TCCTTTAAGAACGCTTGG
Found at i:327249 original size:18 final size:18
Alignment explanation
Indices: 327226--327265 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
327216 TCTAAATATA
327226 TAATATGTATTTAATTAT
1 TAATATGTATTTAATTAT
* *
327244 TAATATTTATTTAATTGT
1 TAATATGTATTTAATTAT
327262 TAAT
1 TAAT
327266 TAATAATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TAATATGTATTTAATTAT
Found at i:328496 original size:98 final size:97
Alignment explanation
Indices: 328389--328568 Score: 333
Period size: 98 Copynumber: 1.8 Consensus size: 97
328379 TAAATCATAG
328389 AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATTT
1 AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATTT
328454 CATAACGGTTAACCAACAATTAACCGTTCATC
66 CATAACGGTTAACCAACAATTAACCGTTCATC
*
328486 AAAACTTATATTAGGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATT
1 AAAA-TTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATT
*
328551 TCTTAACGGTTAACCAAC
65 TCATAACGGTTAACCAAC
328569 GACGTTCATC
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
97 4 0.05
98 76 0.95
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (97 bp):
AAAATTATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAACATAATTATAAATTTAATTT
CATAACGGTTAACCAACAATTAACCGTTCATC
Found at i:329579 original size:51 final size:51
Alignment explanation
Indices: 329519--329622 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
329509 TCGTGCAAAG
* * * *
329519 AAAGCTTTAGGATGTTTCTCTTTTCCCATTTTCCATCTGTTGGCCTTTTGT
1 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
329570 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
1 AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
329621 AA
1 AA
329623 GAAGTTTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.45
Consensus pattern (51 bp):
AAAGCTTTAGGAAGTTTCCCTTTTCCCATTTTCCATCGGTTGACCTTTTGT
Found at i:334801 original size:16 final size:16
Alignment explanation
Indices: 334780--334811 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
334770 CGACGATCGG
334780 CGATGAGTACCATTAA
1 CGATGAGTACCATTAA
334796 CGATGAGTACCATTAA
1 CGATGAGTACCATTAA
334812 TTTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
CGATGAGTACCATTAA
Found at i:336693 original size:18 final size:18
Alignment explanation
Indices: 336666--336704 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
336656 ATATACATAT
*
336666 ATATACACTTTAAAGAGC
1 ATATACACTTTAAAAAGC
*
336684 ATATATACTTTAAAAAGC
1 ATATACACTTTAAAAAGC
336702 ATA
1 ATA
336705 ATGTGCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (18 bp):
ATATACACTTTAAAAAGC
Found at i:336928 original size:2 final size:2
Alignment explanation
Indices: 336921--336979 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
336911 TTTACATGGT
336921 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
336963 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
336980 TTATTTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:349692 original size:17 final size:19
Alignment explanation
Indices: 349657--349697 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
349647 ATTTCCATTA
349657 TATTTATATATATTAATAT
1 TATTTATATATATTAATAT
*
349676 TATTTATA-AT-TTTATAT
1 TATTTATATATATTAATAT
349693 TATTT
1 TATTT
349698 TAAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 2 0.10
19 8 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTATATATATTAATAT
Found at i:355129 original size:2 final size:2
Alignment explanation
Indices: 355122--355146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
355112 TTTACTCGAA
355122 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
355147 GTAAAATTTA
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:358760 original size:50 final size:49
Alignment explanation
Indices: 358678--358845 Score: 147
Period size: 52 Copynumber: 3.3 Consensus size: 49
358668 GTGTTCATTG
* * * *
358678 AACTCATCACGTCAAGGTGACAAGTTTCAATAAAAAATATTTTTTATTCA
1 AACTCATCACCTCGAGATGACAAGTTT-AATAAAAAATATTTTTTATTAA
* *
358728 AACTCATCACCTCGAGATGACGAGTTCTAATAAAATATAATTTTTTTATTAA
1 AACTCATCACCTCGAGATGACAAGTT-TAATAAAAAAT-A-TTTTTTATTAA
* * ** * * * *
358780 AATTTATCATATCGAGATAAAAAGTTAAAATAAAAAAATATTTTTTATTGA
1 AACTCATCACCTCGAGATGACAAGTT-TAAT-AAAAAATATTTTTTATTAA
*
358831 AACTCATCATCTCGA
1 AACTCATCACCTCGA
358846 CGTGACGAGT
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
50 31 0.33
51 24 0.26
52 33 0.35
53 6 0.06
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (49 bp):
AACTCATCACCTCGAGATGACAAGTTTAATAAAAAATATTTTTTATTAA
Found at i:359323 original size:54 final size:52
Alignment explanation
Indices: 359224--359342 Score: 123
Period size: 54 Copynumber: 2.2 Consensus size: 52
359214 TGATGATGAA
* *
359224 TCCTCAAGTGTTGTTACAAAATGTGTCATCAAGACGTCTTCTTGGTAACAAC
1 TCCTCAAGTGTTGTTACAAAATGTGTCATCAAGACATATTCTTGGTAACAAC
* * * *** *
359276 TCCTCAAGTGTTGTTGCAGAATTGGTGTCGTCAAGACAATATT-TTGGTGGTAGC
1 TCCTCAAGTGTTGTTACA-AAAT-GTGTCATCAAGAC-ATATTCTTGGTAACAAC
359330 TCCTCAAGTGTTG
1 TCCTCAAGTGTTG
359343 CGACTACTAC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 17 0.31
53 3 0.05
54 32 0.58
55 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (52 bp):
TCCTCAAGTGTTGTTACAAAATGTGTCATCAAGACATATTCTTGGTAACAAC
Found at i:360497 original size:34 final size:34
Alignment explanation
Indices: 360459--360523 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
360449 ATTAAACAAA
* * *
360459 TAAATCTAGTATAGATTTATTACTATAATAGCGT
1 TAAATCTAGTACAAATCTATTACTATAATAGCGT
360493 TAAATCTAGTACAAATCTATTACTATAATAG
1 TAAATCTAGTACAAATCTATTACTATAATAG
360524 TGGTGAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (34 bp):
TAAATCTAGTACAAATCTATTACTATAATAGCGT
Found at i:362758 original size:20 final size:20
Alignment explanation
Indices: 362729--362766 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
362719 ATAAAGAAAA
*
362729 TGATAAAATTTTTGTATAAG
1 TGATAAAATTTATGTATAAG
*
362749 TGATAGAATTTATGTATA
1 TGATAAAATTTATGTATA
362767 GTTAAGCCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (20 bp):
TGATAAAATTTATGTATAAG
Found at i:363108 original size:3 final size:3
Alignment explanation
Indices: 363102--363127 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
363092 TTGATGCTGC
363102 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
363128 CTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:363135 original size:3 final size:3
Alignment explanation
Indices: 363129--363170 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
363119 ATAATAATAC
363129 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
363171 AGTAAAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:365417 original size:28 final size:28
Alignment explanation
Indices: 365391--365499 Score: 146
Period size: 28 Copynumber: 3.9 Consensus size: 28
365381 TATTTTTTTG
* * *
365391 GTCAAAATAAGTACCTAAAGTTTTTTTT
1 GTCAAAATAGGTACCTAAAGTATTTTAT
* * * *
365419 ATCAAAATATGCACATAAAGTATTTTAT
1 GTCAAAATAGGTACCTAAAGTATTTTAT
365447 GTCAAAATAGGTACCTAAAGTATTTTAT
1 GTCAAAATAGGTACCTAAAGTATTTTAT
*
365475 GTCAAAATAGGTACCTAAATTATTT
1 GTCAAAATAGGTACCTAAAGTATTT
365500 AAACTTTTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 70 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (28 bp):
GTCAAAATAGGTACCTAAAGTATTTTAT
Found at i:367123 original size:20 final size:21
Alignment explanation
Indices: 367098--367136 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
367088 AATTAAATTT
*
367098 AAAATTATA-CTCAAACCCAA
1 AAAATTATATCACAAACCCAA
367118 AAAATTATATCACAAACCC
1 AAAATTATATCACAAACCC
367137 TAAACCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAATTATATCACAAACCCAA
Found at i:371121 original size:34 final size:33
Alignment explanation
Indices: 371078--371260 Score: 105
Period size: 34 Copynumber: 5.5 Consensus size: 33
371068 TCCAAAATAG
*
371078 ATATATTTTAATATTCAAATTTAAACAGATAATA
1 ATATCTTTTAATATTCAAATTTAAACAGAT-ATA
* *
371112 ATATCTTTTAA-CTTAAAATATTCAAA-AGATATA
1 ATATCTTTTAATATTCAAAT-TT-AAACAGATATA
* *
371145 GATAT-TTTATACTATTCAAACTTAAACAGATAT-
1 -ATATCTTT-TAATATTCAAATTTAAACAGATATA
* * * *
371178 -TA--TTTTAAT-TTGAGATTCAAACTGATATA
1 ATATCTTTTAATATTCAAATTTAAACAGATATA
* * *
371207 ATTATCTTTTAATATTTAAAATTAAATAGATAATA
1 A-TATCTTTTAATATTCAAATTTAAACAGAT-ATA
371242 A-ATGCCTTTTAAATATTCA
1 ATAT--CTTTT-AATATTCA
371261 TAAGAATAGT
Statistics
Matches: 113, Mismatches: 20, Indels: 30
0.69 0.12 0.18
Matches are distributed among these distances:
28 14 0.12
29 3 0.03
30 3 0.03
31 4 0.04
33 24 0.21
34 41 0.36
35 17 0.15
36 7 0.06
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (33 bp):
ATATCTTTTAATATTCAAATTTAAACAGATATA
Found at i:371959 original size:11 final size:11
Alignment explanation
Indices: 371945--371977 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
371935 GATCATAAAT
371945 AGAATATATAA
1 AGAATATATAA
*
371956 AGAAAATATAA
1 AGAATATATAA
371967 A-AATATATAA
1 AGAATATATAA
371977 A
1 A
371978 AATTCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
AGAATATATAA
Found at i:371976 original size:10 final size:10
Alignment explanation
Indices: 371947--371980 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
371937 TCATAAATAG
371947 AATATATAAA
1 AATATATAAA
*
371957 GAAAATATAAA
1 -AATATATAAA
371968 AATATATAAA
1 AATATATAAA
371978 AAT
1 AAT
371981 TCGAAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
AATATATAAA
Found at i:375369 original size:16 final size:18
Alignment explanation
Indices: 375344--375379 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
375334 TTAAAAAATA
375344 TTATT-TTTTT-AGATAT
1 TTATTCTTTTTCAGATAT
375360 TTATTCTTTTTCAGATAT
1 TTATTCTTTTTCAGATAT
375378 TT
1 TT
375380 TCAGATAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
18 8 0.44
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (18 bp):
TTATTCTTTTTCAGATAT
Found at i:376281 original size:24 final size:25
Alignment explanation
Indices: 376240--376287 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
376230 CTATGTTTTT
376240 ATTTTATTTTCTAATTTT-AAAATA
1 ATTTTATTTTCTAATTTTGAAAATA
*
376264 ATTTTATTTT-TATTTTTTGAAAAT
1 ATTTTATTTTCTA-ATTTTGAAAAT
376288 TAAAACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 14 0.67
25 5 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
ATTTTATTTTCTAATTTTGAAAATA
Found at i:376524 original size:30 final size:31
Alignment explanation
Indices: 376490--376567 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 31
376480 TATTATACTC
* *
376490 TTTTTCCTGTTTTACTTATCATACTTTC-AA
1 TTTTTCCTGTTTTACTCATCAAACTTTCGAA
**
376520 TTTTT-CTAATTTACTCATCAAACTTTCGAA
1 TTTTTCCTGTTTTACTCATCAAACTTTCGAA
* * *
376550 TTGTTCATGTTTTGCTCA
1 TTTTTCCTGTTTTACTCA
376568 CTCCAAATTA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 18 0.49
30 11 0.30
31 8 0.22
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (31 bp):
TTTTTCCTGTTTTACTCATCAAACTTTCGAA
Found at i:377835 original size:21 final size:21
Alignment explanation
Indices: 377809--377879 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
377799 AAGCTAAAGC
377809 TCTTTAGGTGTACTGCTTTCT
1 TCTTTAGGTGTACTGCTTTCT
* * **
377830 TCTTTA-CTGATACAAGCTAAAGC-
1 TCTTTAGGTG-TAC-TGCT--TTCT
377853 TCTTTAGGTGTACTGCTTTCT
1 TCTTTAGGTGTACTGCTTTCT
377874 TCTTTA
1 TCTTTA
377880 CTGATACAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 3 0.08
21 15 0.42
22 6 0.17
23 9 0.25
24 3 0.08
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (21 bp):
TCTTTAGGTGTACTGCTTTCT
Found at i:377835 original size:44 final size:44
Alignment explanation
Indices: 377772--377923 Score: 277
Period size: 44 Copynumber: 3.5 Consensus size: 44
377762 TATGAAAATA
377772 GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
1 GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
377816 GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
1 GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
* *
377860 GTGTACTGCTTTCTTCTTTACTGATACAAGATCAAGCTCTTTAG
1 GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
*
377904 GTGTACCGCTTTCTTCTTTA
1 GTGTACTGCTTTCTTCTTTA
377924 TTCAAAAATA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (44 bp):
GTGTACTGCTTTCTTCTTTACTGATACAAGCTAAAGCTCTTTAG
Found at i:393006 original size:85 final size:85
Alignment explanation
Indices: 392871--393043 Score: 319
Period size: 85 Copynumber: 2.0 Consensus size: 85
392861 CTCCCAGCTC
*
392871 AATCGATATTATCATAAATTTGTCTTTTCCACAATGAGGAAGTTGGCTATGGTCTTGGGATGCAT
1 AATCGATATTATCATAAATTTGTCTTTTCCACAATGAGGAAGTTGACTATGGTCTTGGGATGCAT
*
392936 TTATCGGTCGCTCCCCACTA
66 TTATCGATCGCTCCCCACTA
*
392956 AATCGATATTATCATAAATTTGTCTTTTCCACATTGAGGAAGTTGACTATGGTCTTGGGATGCAT
1 AATCGATATTATCATAAATTTGTCTTTTCCACAATGAGGAAGTTGACTATGGTCTTGGGATGCAT
393021 TTATCGATCGCTCCCCACTA
66 TTATCGATCGCTCCCCACTA
393041 AAT
1 AAT
393044 ACATCCTTGC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (85 bp):
AATCGATATTATCATAAATTTGTCTTTTCCACAATGAGGAAGTTGACTATGGTCTTGGGATGCAT
TTATCGATCGCTCCCCACTA
Found at i:398021 original size:3 final size:3
Alignment explanation
Indices: 398013--398040 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
398003 TTGGAATCAT
398013 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
398041 AACCCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:405270 original size:20 final size:20
Alignment explanation
Indices: 405214--405271 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
405204 TTTTGGTGCA
* *
405214 GAGGGAATCGATAACCCCAT
1 GAGGGAACCGATACCCCCAT
405234 GAGGGAACCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
405254 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
405272 CTTTGAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.29, C:0.33, G:0.26, T:0.12
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:417006 original size:43 final size:42
Alignment explanation
Indices: 416880--417036 Score: 122
Period size: 43 Copynumber: 3.7 Consensus size: 42
416870 AAAAATGCCG
* *
416880 CAATAGGTGTTGATGTTTAGCGGCATTTTTCCTACAAACG-T-
1 CAATAGGTGTTGATATTTAGCGGC-GTTTTCCTACAAACGCTA
* * * * *
416921 CGTAGTAGGTGTTGAGATTTAGCGGTGTTTTACTTACGAACGCTA
1 C--AATAGGTGTTGATATTTAGCGGCGTTTT-CCTACAAACGCTA
* * *
416966 CAATAGGTGTTGATATTTTGCGGCGTCTTTCCCACAAACGCCA
1 CAATAGGTGTTGATATTTAGCGGCGT-TTTCCTACAAACGCTA
* * *
417009 CAGTAGGTTTTCG-GATTTAGCGGCGTTT
1 CAATAGGTGTT-GATATTTAGCGGCGTTT
417037 GTAGCGGAAA
Statistics
Matches: 90, Mismatches: 19, Indels: 13
0.74 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 6 0.07
43 77 0.86
44 5 0.06
45 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (42 bp):
CAATAGGTGTTGATATTTAGCGGCGTTTTCCTACAAACGCTA
Found at i:424989 original size:41 final size:41
Alignment explanation
Indices: 424892--425005 Score: 113
Period size: 41 Copynumber: 2.7 Consensus size: 41
424882 TTAAAGGACA
* * **
424892 ATTGCGGCGTTTATATTAAAAACGCCGCAAAGGAACTATTTT
1 ATTGCGGCGTTTAT-TTAAAAACGCCACTAAGGAACTATACT
* * * *
424934 ATTGAGGTGTTTATTGTGAAAACGCCACTAAGGGAC-ATACT
1 ATTGCGGCGTTTATT-TAAAAACGCCACTAAGGAACTATACT
*
424975 ATTGCGGCGTTTATTACAAAAACGCCACTAA
1 ATTGCGGCGTTTATT-TAAAAACGCCACTAA
425006 ATTACAACTC
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 30 0.52
42 28 0.48
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (41 bp):
ATTGCGGCGTTTATTTAAAAACGCCACTAAGGAACTATACT
Found at i:425030 original size:42 final size:42
Alignment explanation
Indices: 424952--425056 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
424942 GTTTATTGTG
* * *
424952 AAAACGCCACTAAGGGAC-A-TACTATTGCGGCGTTTAT-TACA
1 AAAACGCCACTAAAGTACAACT-CTATTACGGCGTTTATGT-CA
*
424993 AAAACGCCACTAAATTACAACTCTATTACGGCGTTTATGTCA
1 AAAACGCCACTAAAGTACAACTCTATTACGGCGTTTATGTCA
*
425035 AAAACGCCATTAAAGTACAACT
1 AAAACGCCACTAAAGTACAACT
425057 TTTTAGCGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 15 0.27
42 38 0.69
43 2 0.04
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (42 bp):
AAAACGCCACTAAAGTACAACTCTATTACGGCGTTTATGTCA
Found at i:426503 original size:42 final size:41
Alignment explanation
Indices: 426449--426583 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
426439 GACTATATAT
* *
426449 TTAACA-TTTTGTGACGTTTATACAAAAAAACGCCACTATTGA
1 TTAACACTATTGTGGCGTTT-T-CAAAAAAACGCCACTATTGA
* **
426491 TT-ACACTATTGTGGCGTTTGTTAAAAAAATACCACTATTGA
1 TTAACACTATTGTGGCGTTT-TCAAAAAAACGCCACTATTGA
* * * * *
426532 TTAAAACTATTGCGGCATTTTTC-TAAAAACGTCACTATTGA
1 TTAACACTATTGTGGC-GTTTTCAAAAAAACGCCACTATTGA
426573 TTAACACTATT
1 TTAACACTATT
426584 ACGGTGTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
41 46 0.61
42 26 0.35
43 3 0.04
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (41 bp):
TTAACACTATTGTGGCGTTTTCAAAAAAACGCCACTATTGA
Found at i:426749 original size:42 final size:42
Alignment explanation
Indices: 426611--426758 Score: 126
Period size: 42 Copynumber: 3.6 Consensus size: 42
426601 AACGCCACTA
* * * *
426611 TATATGT-AA-TCTATTGCGGCGTTTGTGGTATAAACACCGC
1 TATATGTCAACTCTATTGCAGCGTTTGTTGTAAAAACGCCGC
* * * *
426651 TA-ATTTACCACTCTATTGCGGCGTTTGTT-AAAAAACGCCGC
1 TATATGT-CAACTCTATTGCAGCGTTTGTTGTAAAAACGCCGC
* ** * * *
426692 AATA-AACCACCCTATTGCAACGTTTGTTGTAAAAACGCCGC
1 TATATGTCAACTCTATTGCAGCGTTTGTTGTAAAAACGCCGC
426733 TATATGTCAACTCTATTGCAGCGTTT
1 TATATGTCAACTCTATTGCAGCGTTT
426759 TTACAACAAA
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
39 3 0.04
40 21 0.25
41 25 0.30
42 34 0.41
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
TATATGTCAACTCTATTGCAGCGTTTGTTGTAAAAACGCCGC
Found at i:426770 original size:42 final size:40
Alignment explanation
Indices: 426660--426776 Score: 110
Period size: 42 Copynumber: 2.9 Consensus size: 40
426650 CTAATTTACC
* * *
426660 ACTCTATTGCGGCGTTTGTTAAAAAACGCCGCAATAAACC
1 ACTCTATTGCAGCGTTTGTTAAAAAACGCCGCTATAAACA
* * * **
426700 ACCCTATTGCAACGTTTGTTGTAAAAACGCCGCTATATGTCA
1 ACTCTATTGCAGCGTTTGTT-AAAAAACGCCGCTATA-AACA
*
426742 ACTCTATTGCAGCGTTT-TTACAACAAACGCTGCTA
1 ACTCTATTGCAGCGTTTGTTA-AA-AAACGCCGCTA
426777 AAGTATCAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
40 17 0.28
41 18 0.30
42 26 0.43
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (40 bp):
ACTCTATTGCAGCGTTTGTTAAAAAACGCCGCTATAAACA
Found at i:432636 original size:18 final size:18
Alignment explanation
Indices: 432613--432658 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
432603 TTCACGAAAT
*
432613 ATAAGATTACCAGTGGGA
1 ATAAGATTACCAGCGGGA
** *
432631 ATAAGATTTTCGGCGGGA
1 ATAAGATTACCAGCGGGA
432649 ATAAGATTAC
1 ATAAGATTAC
432659 TAAGAATGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (18 bp):
ATAAGATTACCAGCGGGA
Found at i:435169 original size:15 final size:14
Alignment explanation
Indices: 435144--435195 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
435134 AAACATGTCA
*
435144 TAAAGATAAAATTAT
1 TAAA-ATAAAAATAT
* *
435159 TAAAATAAAAAAAA
1 TAAAATAAAAATAT
435173 TAAAA-AAAAATAT
1 TAAAATAAAAATAT
*
435186 TATAATAAAA
1 TAAAATAAAA
435196 TAAAGGAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 10 0.33
14 16 0.53
15 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAAATAAAAATAT
Found at i:435205 original size:27 final size:27
Alignment explanation
Indices: 435151--435206 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
435141 TCATAAAGAT
* *
435151 AAAATTATTAAAATAAAAAAAATAAAA
1 AAAAATATTAAAATAAAAAAAAGAAAA
* * *
435178 AAAAATATTATAATAAAATAAAGGAAA
1 AAAAATATTAAAATAAAAAAAAGAAAA
435205 AA
1 AA
435207 CAATGAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (27 bp):
AAAAATATTAAAATAAAAAAAAGAAAA
Found at i:455781 original size:16 final size:16
Alignment explanation
Indices: 455760--455813 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
455750 TTTAGGAAAA
455760 TAAAATAATACAATTT
1 TAAAATAATACAATTT
* **
455776 TAAAAT-ATAAAAGAT
1 TAAAATAATACAATTT
455791 TAAAATAATACAATTT
1 TAAAATAATACAATTT
455807 TAAAATA
1 TAAAATA
455814 TATTGTATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (16 bp):
TAAAATAATACAATTT
Found at i:458777 original size:17 final size:18
Alignment explanation
Indices: 458741--458781 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
458731 ATATTATGTA
*
458741 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
458759 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
458776 TTTACT
1 TTTACT
458782 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:460457 original size:18 final size:18
Alignment explanation
Indices: 460431--460465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
460421 CAGCAGTCAC
* *
460431 CGCAGCCATTTATGATGT
1 CGCAACCATATATGATGT
460449 CGCAACCATATATGATG
1 CGCAACCATATATGATG
460466 CCGTCGCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (18 bp):
CGCAACCATATATGATGT
Done.