Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007915.1 Hibiscus syriacus cultivar Beakdansim tig00110318_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: 1667290
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:229207 original size:23 final size:24
Alignment explanation
Indices: 229157--229207 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
229147 ATCATAACCA
* *
229157 TTTTTTTTAAAAACAATTAAGTAT
1 TTTTTTTAAAAAACAATTAAGTAC
*
229181 TTTTTTTAAAAAACAATTATG-AC
1 TTTTTTTAAAAAACAATTAAGTAC
229204 TTTT
1 TTTT
229208 ATTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTTTTAAAAAACAATTAAGTAC
Found at i:231782 original size:25 final size:25
Alignment explanation
Indices: 231751--231949 Score: 373
Period size: 25 Copynumber: 8.0 Consensus size: 25
231741 AGTTAGGGGA
231751 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231776 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231801 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231826 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231851 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
231876 TTAGGATTTGAAACCCT-AACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231900 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
231925 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
231950 GGGTGTTGGG
Statistics
Matches: 170, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
24 23 0.14
25 147 0.86
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:232293 original size:32 final size:32
Alignment explanation
Indices: 232257--232328 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
232247 TTTGAGGTTT
232257 CGAAAAAGCTATTTTTTTGTGTCAACTTTCAA
1 CGAAAAAGCTATTTTTTTGTGTCAACTTTCAA
232289 CGAAAAAGCTATTTTTTTGTGTCAACTTTCAA
1 CGAAAAAGCTATTTTTTTGTGTCAACTTTCAA
232321 CTGAAAAA
1 C-GAAAAA
232329 ACTTCGATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
32 33 0.85
33 6 0.15
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (32 bp):
CGAAAAAGCTATTTTTTTGTGTCAACTTTCAA
Found at i:238081 original size:19 final size:20
Alignment explanation
Indices: 238050--238090 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
238040 AAAATATTAA
*
238050 AAAATATTAATATTTTAGAT
1 AAAATATTAATATTTTAAAT
238070 AAAATA-TAATATTTTAAAT
1 AAAATATTAATATTTTAAAT
238089 AA
1 AA
238091 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAATATTAATATTTTAAAT
Found at i:245562 original size:19 final size:18
Alignment explanation
Indices: 245535--245570 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
245525 AACGCTGTAT
245535 TTATATTAAATTATATTTA
1 TTATATTAAATTA-ATTTA
*
245554 TTATTTTAAATTAATTT
1 TTATATTAAATTAATTT
245571 CTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTAAATTAATTTA
Found at i:249791 original size:19 final size:18
Alignment explanation
Indices: 249768--249814 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
249758 ATGTAAGAAA
* *
249768 TAAATAAATAAATAAAAT
1 TAAATAAAGAAAAAAAAT
*
249786 TAAAATGAAGAAAAAAAAT
1 T-AAATAAAGAAAAAAAAT
249805 TAAATAAAGA
1 TAAATAAAGA
249815 TAAGATAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
TAAATAAAGAAAAAAAAT
Found at i:249825 original size:29 final size:31
Alignment explanation
Indices: 249762--249832 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 31
249752 ATAAAAATGT
*
249762 AAGAAATAAATAAATAAATAAAATTAAAATG
1 AAGAAATAAATAAATAAATAAAATTAAAATA
* *
249793 AAGAAA-AAA-AATTAAATAAAGA-TAAGATA
1 AAGAAATAAATAAATAAATAAA-ATTAAAATA
249822 AAGAAAGTAAA
1 AAGAAA-TAAA
249833 GATAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 21 0.62
30 4 0.12
31 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (31 bp):
AAGAAATAAATAAATAAATAAAATTAAAATA
Found at i:249891 original size:82 final size:80
Alignment explanation
Indices: 249750--249918 Score: 195
Period size: 82 Copynumber: 2.1 Consensus size: 80
249740 AAATCATGTT
*
249750 AGATAAAAATGTAAGAAATAAATAAATAAATAAAATTAAAATGAAGAAAAAAAATTAAATAAAGA
1 AGATAAAAATGTAAGAAAAAAATAAATAAATAAAA-TAAAATGAAGAAAAAAAATTAAATAAA-A
*
249815 TAA-GATAAAGAAAGTAA
64 TAATAATAAA-AAAGTAA
*
249832 AGAT-AAAATAGTAAGTAAAAAAATAAA-AAATAAAGA-ATAAT-AAGAAAAAAATATATAAATA
1 AGATAAAAAT-GTAAG-AAAAAAATAAATAAATAAA-ATAAAATGAAGAAAAAAA-AT-TAAATA
249893 AAATAATAATAAAAAAGTAA
61 AAATAATAATAAAAAAGTAA
*
249913 AAATAA
1 AGATAA
249919 TATATATATA
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
80 10 0.13
81 25 0.33
82 30 0.39
83 11 0.14
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (80 bp):
AGATAAAAATGTAAGAAAAAAATAAATAAATAAAATAAAATGAAGAAAAAAAATTAAATAAAATA
ATAATAAAAAAGTAA
Found at i:249901 original size:44 final size:44
Alignment explanation
Indices: 249847--249959 Score: 102
Period size: 44 Copynumber: 2.5 Consensus size: 44
249837 AAATAGTAAG
*
249847 TAAAAAAATAAAAAATAAAGAATAATAAGAAAAAAATATATAAA
1 TAAAATAATAAAAAATAAAGAATAATAAGAAAAAAATATATAAA
* * * * * * *
249891 TAAAATAATAATAAA-AAAGTAAAAATAATATATATATATATATA
1 TAAAATAATAAAAAATAAAG-AATAATAAGAAAAAAATATATAAA
* * *
249935 TATAATAAATAAATAATAAAAAATA
1 TAAAAT-AATAAAAAATAAAGAATA
249960 GTATATATAT
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
43 4 0.08
44 36 0.68
45 10 0.19
46 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (44 bp):
TAAAATAATAAAAAATAAAGAATAATAAGAAAAAAATATATAAA
Found at i:249940 original size:38 final size:37
Alignment explanation
Indices: 249876--250037 Score: 140
Period size: 38 Copynumber: 4.4 Consensus size: 37
249866 GAATAATAAG
* *
249876 AAAAAAATATATAAATA-AAATA-ATAATAAAAAAGT
1 AAAAAAATATATATATATATATATATAATAAAAAAGT
249911 AAAAATAATATATATATATATATATATAATAAATAAA-T
1 AAAAA-AATATATATATATATATATATAATAAA-AAAGT
* **
249949 AATAAAAA-ATAGTATATATATAAAT-TAATAAAACTGAT
1 AA-AAAAATATA-TATATATATATATATAATAAAAAAG-T
* *
249987 AATAAAAAAATA-ATATATATATATATAATCTAAAAAAAT
1 AA-AAAAATATATATATATATATATATAA--TAAAAAAGT
250026 -AAAAAATATATA
1 AAAAAAATATATA
250038 CTAAAGTAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
35 5 0.05
36 12 0.12
37 33 0.32
38 39 0.38
39 10 0.10
40 5 0.05
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (37 bp):
AAAAAAATATATATATATATATATATAATAAAAAAGT
Found at i:249946 original size:42 final size:40
Alignment explanation
Indices: 249882--250033 Score: 132
Period size: 42 Copynumber: 3.8 Consensus size: 40
249872 TAAGAAAAAA
*
249882 ATATATAAATAAAATAAT-AATAAAAAAGTAAAAATAATAT
1 ATATATAAATAATATAATAAATAAAAAA-TAAAAATAATAT
* * *
249922 ATATATATATATATATAATAAATAAATAATAAAAAATAGTAT
1 ATATATAAATA-ATATAATAAATAAAAAAT-AAAAATAATAT
* * *
249964 ATATATAAATTA-ATAA-AACTGATAATAA-AAAAATAATAT
1 ATATATAAATAATATAATAAAT-A-AAAAATAAAAATAATAT
* * *
250003 ATATATATATAATCTAAAAAAATAAAAAATA
1 ATATATAAATAATAT-AATAAATAAAAAATA
250034 TATACTAAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
39 23 0.26
40 20 0.22
41 17 0.19
42 30 0.33
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (40 bp):
ATATATAAATAATATAATAAATAAAAAATAAAAATAATAT
Found at i:249953 original size:14 final size:14
Alignment explanation
Indices: 249853--249959 Score: 64
Period size: 14 Copynumber: 7.8 Consensus size: 14
249843 TAAGTAAAAA
* *
249853 AATAAAAAATAAAG
1 AATAATAAATAAAT
*
249867 AATAATAAGA-AAAA
1 AATAATAA-ATAAAT
249881 AATATATAAATAAAAT
1 AATA-ATAAAT-AAAT
249897 AATAATAAA-AAAGT
1 AATAATAAATAAA-T
* *
249911 AAAAAT-AATATAT
1 AATAATAAATAAAT
* *
249924 -AT-ATATATATAT
1 AATAATAAATAAAT
249936 -ATAATAAATAAAT
1 AATAATAAATAAAT
*
249949 AATAAAAAATA
1 AATAATAAATA
249960 GTATATATAT
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
11 2 0.03
12 9 0.12
13 14 0.19
14 32 0.43
15 10 0.14
16 7 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAATAAATAAAT
Found at i:251223 original size:39 final size:36
Alignment explanation
Indices: 251169--251259 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 36
251159 CGAGGGTTTG
*
251169 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-T-T-T
* * *
251208 GTGTTTGAAGAGAAACAATTTCGAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
251244 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
251260 TGTCTCAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
36 16 0.34
37 1 0.02
38 1 0.02
39 29 0.62
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTT
Found at i:251285 original size:36 final size:36
Alignment explanation
Indices: 251245--251478 Score: 227
Period size: 36 Copynumber: 6.6 Consensus size: 36
251235 TTTTTTTTTG
*
251245 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
251281 TGTTTCAAAAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
251318 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
251354 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
251383 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
251419 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
251456 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
251479 AACTCGTTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 29
0.78 0.08 0.14
Matches are distributed among these distances:
29 14 0.08
30 6 0.04
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 6 0.04
36 76 0.46
37 57 0.34
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:251479 original size:102 final size:102
Alignment explanation
Indices: 251279--251465 Score: 263
Period size: 102 Copynumber: 1.8 Consensus size: 102
251269 TGAGACAAAA
* *
251279 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
251344 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
251381 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAGA
251444 GAGAC-AAGATTTTGTTTCAAGG
65 GAGACGAA-A-TTTGTTTCAAGG
251466 GAAACTGTCT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 3 0.04
101 27 0.36
102 45 0.60
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:251594 original size:37 final size:37
Alignment explanation
Indices: 251543--251615 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
251533 TCAAGGTTTA
*
251543 TGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATTT
* *
251580 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATT
251616 AATTTCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCACAAGAGAGACAAAATTT
Found at i:251629 original size:36 final size:37
Alignment explanation
Indices: 251545--251629 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
251535 AAGGTTTATG
* **
251545 TTTC-AAGAGAAACTATCACAAGGGAGACAAAATTTTG
1 TTTCAAAG-GAAACTATCACAAGAGAGACAAAATTTAA
* *
251582 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAAGGAAACTATCACAAGAGAGACAAAATTTAA
251618 TTTCAAAGGAAA
1 TTTCAAAGGAAA
251630 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 13 0.32
37 26 0.63
38 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (37 bp):
TTTCAAAGGAAACTATCACAAGAGAGACAAAATTTAA
Found at i:251637 original size:102 final size:102
Alignment explanation
Indices: 251516--251755 Score: 365
Period size: 102 Copynumber: 2.4 Consensus size: 102
251506 ATATTTTGTG
* *
251516 TTTCAAGGGAAAAGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
* * *
251581 GTTTCAAGGGAAACTATCTCAAG-AGAGACAAAATTAA
66 ATTTCAAGGGAAACTACCCCAAGCA-AGACAAAATTAA
* * * *
251618 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
* *
251683 ATTTCAAGGGAAACTACCCCAAGCAAGATAAAATTTA
66 ATTTCAAGGGAAACTACCCCAAGCAAGACAAAATTAA
251720 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
251756 GGAGACAAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
102 123 0.99
103 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCACAAGGGAGACAAAATTTT
ATTTCAAGGGAAACTACCCCAAGCAAGACAAAATTAA
Found at i:252189 original size:106 final size:106
Alignment explanation
Indices: 252001--252319 Score: 417
Period size: 106 Copynumber: 3.0 Consensus size: 106
251991 TTGTTCCGAA
* * * ** *
252001 TCCAATATCC-TCTGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACAGCC
1 TCCAATATCCTTC-GCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACC
* * * * * *
252065 AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAG
65 AGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
* * *
252107 TCCAATATCCTTCACCGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACCA
1 TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
*
252172 GCTGTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
66 GCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
* * * *
252213 TCTAATATCCTTCGCTGTGAATTTGAAATTGGCTATGAAATTGGGAAATTGTTTGTTGACAACCA
1 TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
*
252278 G-TCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTATCTCGAG
66 GCT-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
252319 T
1 T
252320 GGCACGATAT
Statistics
Matches: 186, Mismatches: 25, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
105 1 0.01
106 183 0.98
107 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (106 bp):
TCCAATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCA
GCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCGAG
Found at i:252953 original size:31 final size:32
Alignment explanation
Indices: 252917--253002 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
252907 CCCAAAGATG
* * *
252917 CCCCAATATTCAATG-TGAATCTCAAAAAATG
1 CCCCAATATTCAATGTTAAATCTAAAAAAATA
* * **
252948 TCCCAACATTTGATGTTAAATCTAAAAAAATA
1 CCCCAATATTCAATGTTAAATCTAAAAAAATA
**
252980 CCCCAATATTTGATGTTAAATCT
1 CCCCAATATTCAATGTTAAATCT
253003 TCAAAGATGC
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 11 0.24
32 34 0.76
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (32 bp):
CCCCAATATTCAATGTTAAATCTAAAAAAATA
Found at i:252970 original size:32 final size:32
Alignment explanation
Indices: 252934--253007 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
252924 ATTCAATGTG
**
252934 AATCTCAAAAAATGTCCCAACATTTGATGTTA
1 AATCTCAAAAAATACCCCAACATTTGATGTTA
* *
252966 AATCTAAAAAAATACCCCAATATTTGATGTTA
1 AATCTCAAAAAATACCCCAACATTTGATGTTA
252998 AATCTTCAAA
1 AATC-TCAAA
253008 GATGCCCTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.31
Consensus pattern (32 bp):
AATCTCAAAAAATACCCCAACATTTGATGTTA
Found at i:254046 original size:69 final size:69
Alignment explanation
Indices: 253942--254072 Score: 226
Period size: 69 Copynumber: 1.9 Consensus size: 69
253932 CTCTTGATTT
* *
253942 TCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
1 TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
254007 ATGC
66 ATGC
* *
254011 TCTATGATCTTCGAGTGAAGGGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCAT
254073 AGTTTGAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (69 bp):
TCTATGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATAATTGTGCTTGATCAATCTCATTTG
ATGC
Found at i:254188 original size:15 final size:13
Alignment explanation
Indices: 254145--254196 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
254135 TTTTCTTCAA
*
254145 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
254157 TTTTCTCTTTTTA
1 TTTTCTCTTTTTT
254170 TTTTCTCTTTACTTT
1 TTTTCTCTTT--TTT
*
254185 TTTTTTCTTTTT
1 TTTTCTCTTTTT
254197 GTTCTGATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 5 0.15
13 17 0.52
15 11 0.33
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:258509 original size:5 final size:4
Alignment explanation
Indices: 258488--258737 Score: 54
Period size: 4 Copynumber: 61.8 Consensus size: 4
258478 AAATGGTAAG
* * *
258488 AAAT AAAT AAAT AAATT AAATT AAAAT GAAG AAA- AAAC AAATT AAAT
1 AAAT AAAT AAAT AAA-T AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * * * * *
258535 AAA- AGAT AAGAT AAAGA AAAT AAAG ATA- AAAT -AGT AAGT AAAAA AAAT
1 AAAT AAAT AA-AT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT
* * * * *
258583 AAA- AAAT AAAG AAAA AGAAG AAA- AATAT ATAT AAAT AAAAC AAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AA-AT AAAT AAAT -AAAT AAAT AAAT
* * * *
258632 AAA- ATAAT -AAT AAA- AAAGT AAAA ATAAT ATAT ATAT ATAT ATAAT
1 AAAT A-AAT AAAT AAAT AAA-T AAAT A-AAT AAAT AAAT AAAT A-AAT
* * * * * * *
258677 AAAT AAAA AAAT AAA- AAAT -AGT AAAT ATAT ATAT ATAT ATAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
258723 AAAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAA
258738 ACTGATAATA
Statistics
Matches: 188, Mismatches: 34, Indels: 48
0.70 0.13 0.18
Matches are distributed among these distances:
3 26 0.14
4 124 0.66
5 35 0.19
6 3 0.02
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:258555 original size:26 final size:25
Alignment explanation
Indices: 258488--258582 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 25
258478 AAATGGTAAG
* *
258488 AAATAA-AT-AAATAAATTAAATTA
1 AAATAAGATAAAAAAAATTAAATAA
258511 AAATGAAGA-AAAAACAAATTAAATAA
1 AAAT-AAGATAAAAA-AAATTAAATAA
* *
258537 AAGATAAGATAAAGAAAATAAAGATAA
1 AA-ATAAGATAAAAAAAATTAA-ATAA
258564 AATAGTAAG-TAAAAAAAAT
1 AA-A-TAAGATAAAAAAAAT
258583 AAAAAATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.07
24 2 0.03
25 4 0.07
26 22 0.38
27 22 0.38
28 4 0.07
ACGTcount: A:0.71, C:0.01, G:0.08, T:0.20
Consensus pattern (25 bp):
AAATAAGATAAAAAAAATTAAATAA
Found at i:258576 original size:27 final size:27
Alignment explanation
Indices: 258516--258585 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
258506 AATTAAAATG
*
258516 AAGA-AAAAACAAATTAA-ATAAAAGAT
1 AAGATAAAAA-AAATAAAGATAAAAGAT
* *
258542 AAGATAAAGAAAATAAAGATAAAATAGT
1 AAGATAAAAAAAATAAAGATAAAAGA-T
258570 AAG-TAAAAAAAATAAA
1 AAGATAAAAAAAATAAA
258586 AAATAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.27
27 23 0.62
28 4 0.11
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (27 bp):
AAGATAAAAAAAATAAAGATAAAAGAT
Found at i:258592 original size:43 final size:42
Alignment explanation
Indices: 258540--258634 Score: 106
Period size: 42 Copynumber: 2.2 Consensus size: 42
258530 TAAATAAAAG
*
258540 ATAAGATAAAGAAAATA-AAGATAAAATAGTA-AGTAAAAAAAATAA
1 ATAA-ATAAAGAAAA-AGAAGA-AAAATA-TATA-TAAAAAAAACAA
*
258585 A-AAATAAAGAAAAAGAAGAAAAATATATATAAATAAAACAA
1 ATAAATAAAGAAAAAGAAGAAAAATATATATAAAAAAAACAA
258626 ATAAATAAA
1 ATAAATAAA
258635 ATAATAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
41 13 0.29
42 15 0.33
43 14 0.31
44 2 0.04
45 1 0.02
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (42 bp):
ATAAATAAAGAAAAAGAAGAAAAATATATATAAAAAAAACAA
Found at i:258633 original size:49 final size:47
Alignment explanation
Indices: 258574--258730 Score: 149
Period size: 49 Copynumber: 3.2 Consensus size: 47
258564 AATAGTAAGT
258574 AAAAA-AAATAAAAAATAAAGAAAAAG-AAGAAA-AATATATATAAATAA
1 AAAAATAAATAAAAAATAAA-AAAAAGTAA-AAATAATATATATAAAT-A
*
258621 AACAAATAAATAAAATAATAATAAAAAAGTAAAAATAATATATATATATA
1 AA-AAATAAATAAAA-AATAA-AAAAAAGTAAAAATAATATATATAAATA
* * * * *
258671 TATAATAAATAAAAAAATAAAAAATAGTAAATATATATATATATATATA
1 AAAAATAAAT-AAAAAATAAAAAAAAGTAAAAATA-ATATATATAAATA
*
258720 TATAAATAAAT
1 -AAAAATAAAT
258731 TAATAAAACT
Statistics
Matches: 93, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
47 2 0.02
48 16 0.17
49 33 0.35
50 27 0.29
51 15 0.16
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (47 bp):
AAAAATAAATAAAAAATAAAAAAAAGTAAAAATAATATATATAAATA
Found at i:258657 original size:38 final size:38
Alignment explanation
Indices: 258615--258693 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
258605 AAATATATAT
*
258615 AAATAAAACAAATAAATAAAATAAT-AATAAAAAAGTAA
1 AAATAAAACAAATAAAT-AAATAATAAATAAAAAAATAA
* * * * *
258653 AAATAATATATATATATATATAATAAATAAAAAAATAA
1 AAATAAAACAAATAAATAAATAATAAATAAAAAAATAA
258691 AAA
1 AAA
258694 ATAGTAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 6 0.18
38 28 0.82
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.24
Consensus pattern (38 bp):
AAATAAAACAAATAAATAAATAATAAATAAAAAAATAA
Found at i:258705 original size:39 final size:37
Alignment explanation
Indices: 258635--258713 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 37
258625 AATAAATAAA
* *
258635 ATAATAATAAAAAAGTAAAAATAATATATATATATAT
1 ATAATAATAAAAAAATAAAAATAATAAATATATATAT
*
258672 ATAATAAATAAAAAAATAAAAAATAGTAAATATATATAT
1 ATAAT-AATAAAAAAAT-AAAAATAATAAATATATATAT
258711 ATA
1 ATA
258714 TATATATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 5 0.14
38 10 0.27
39 22 0.59
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (37 bp):
ATAATAATAAAAAAATAAAAATAATAAATATATATAT
Found at i:258706 original size:2 final size:2
Alignment explanation
Indices: 258701--258776 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
258691 AAAATAGTAA
* * *
258701 AT AT AT AT AT AT AT AT AT AT AT AA AT AA AT -T A- AT A- AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
258741 GAT A- AT AA AA AT A- AT AT AT AT AT AT AT AT AT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
258777 ATCTAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
1 5 0.08
2 53 0.88
3 1 0.02
4 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:259157 original size:17 final size:17
Alignment explanation
Indices: 259128--259170 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
259118 TAACTATTTT
*
259128 TAGAATACTATTAACAA
1 TAGAATCCTATTAACAA
*
259145 TATAATCCTATTAACAA
1 TAGAATCCTATTAACAA
259162 TAGAATCCT
1 TAGAATCCT
259171 TATGCAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (17 bp):
TAGAATCCTATTAACAA
Found at i:263852 original size:18 final size:18
Alignment explanation
Indices: 263828--263875 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
263818 GAGTTGTTAT
*
263828 TATTATTTTTATCA-TCA
1 TATTATTTTTATCACTAA
*
263845 TCATTATTATTATCACTAA
1 T-ATTATTTTTATCACTAA
263864 TATTATTTTTAT
1 TATTATTTTTAT
263876 TATTTTCAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 1 0.04
18 22 0.85
19 3 0.12
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTTTTATCACTAA
Found at i:265343 original size:34 final size:33
Alignment explanation
Indices: 265275--265343 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 33
265265 ATCCTCCCAA
265275 ATTTATGGTTTATCTTATTTTAGTCCTTAATATT
1 ATTTATGGTTTATCTTATTTTAGTCCTT-ATATT
* *
265309 ATTTATGGTTTTTTTTATTTCTAGTACCTT-TATT
1 ATTTATGGTTTATCTTATTT-TAGT-CCTTATATT
265343 A
1 A
265344 ATTAATATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 23 0.74
35 4 0.13
36 4 0.13
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.61
Consensus pattern (33 bp):
ATTTATGGTTTATCTTATTTTAGTCCTTATATT
Found at i:265675 original size:2 final size:2
Alignment explanation
Indices: 265668--265705 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
265658 CCTAATAAGC
*
265668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265706 GTAAATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:269949 original size:3 final size:3
Alignment explanation
Indices: 269941--269965 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
269931 GAATTGGGTT
269941 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
269966 ACTCATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:270246 original size:90 final size:88
Alignment explanation
Indices: 270132--270305 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 88
270122 TCCCGAATAT
* * * * *
270132 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAA-CCCTAATATGACTAG
270197 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
270221 TTAAATTCTAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAACCCTAATATGACTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAACCCTAATATGACTAG
*
270286 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
270306 GTGTGTTAGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 38 0.49
90 40 0.51
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAACTAATTTGAAATAATAAAACCCTAATATGACTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:274143 original size:17 final size:17
Alignment explanation
Indices: 274117--274164 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
274107 AACAAAGTAT
*
274117 TTTTTGCTCGAACAG-GAG
1 TTTTT-CTCGAA-AGAGAA
274135 TTTTTCTCGAAAGAGAA
1 TTTTTCTCGAAAGAGAA
274152 TTTTTCTC-AAAGA
1 TTTTTCTCGAAAGA
274165 AAGGGAAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 7 0.25
17 16 0.57
18 5 0.18
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.38
Consensus pattern (17 bp):
TTTTTCTCGAAAGAGAA
Found at i:277084 original size:90 final size:88
Alignment explanation
Indices: 276975--277148 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 88
276965 TCCTGAATAT
* * *
276975 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-TCTATGATATGATTA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTA--ATATGACTA
277039 GGGTAACTTGGATATAAAAGGATTA
64 GGGTAACTTGGATATAAAAGGATTA
277064 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAG
*
277129 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
277149 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
89 35 0.44
90 41 0.52
91 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:284817 original size:16 final size:16
Alignment explanation
Indices: 284796--284832 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
284786 CGAGTTTATT
284796 TTAATAAAAATGATAA
1 TTAATAAAAATGATAA
284812 TTAATAAAAATGATAA
1 TTAATAAAAATGATAA
284828 TTAAT
1 TTAAT
284833 TCATTTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
TTAATAAAAATGATAA
Found at i:287086 original size:20 final size:21
Alignment explanation
Indices: 287048--287091 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
287038 AAACCATTCA
* *
287048 GGGGGGTATCGGTTCCCCTTT
1 GGGGGGAATCGGTTCCCCTCT
287069 GGGGGGAATCGGTT-CCCTCT
1 GGGGGGAATCGGTTCCCCTCT
287089 GGG
1 GGG
287092 TAATATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.07, C:0.23, G:0.43, T:0.27
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCCTCT
Found at i:287747 original size:16 final size:16
Alignment explanation
Indices: 287722--287752 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
287712 ATCTAAAAAA
*
287722 AAATTTAAACATCCAC
1 AAATTCAAACATCCAC
287738 AAATTCAAACATCCA
1 AAATTCAAACATCCA
287753 TAAGCATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATTCAAACATCCAC
Found at i:295249 original size:20 final size:21
Alignment explanation
Indices: 295212--295254 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
295202 AAACCATTTA
* *
295212 GGGGGTATCAGTTCCCCTTTG
1 GGGGGAATCAGTTCCCCTCTG
*
295233 GGGGGAATCGGTT-CCCTCTG
1 GGGGGAATCAGTTCCCCTCTG
295253 GG
1 GG
295255 CAATCTGCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.09, C:0.23, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGAATCAGTTCCCCTCTG
Found at i:297925 original size:23 final size:23
Alignment explanation
Indices: 297895--297939 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
297885 TTCACAGATT
297895 GAATAGTTGGGTAGATGAATTTG
1 GAATAGTTGGGTAGATGAATTTG
297918 GAATAGTTGGGTAGATGAATTT
1 GAATAGTTGGGTAGATGAATTT
297940 AGTTTAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (23 bp):
GAATAGTTGGGTAGATGAATTTG
Found at i:299815 original size:65 final size:67
Alignment explanation
Indices: 299701--299976 Score: 285
Period size: 67 Copynumber: 4.2 Consensus size: 67
299691 AGATTGTATG
* * * * *
299701 TCTCCCTTGAGACGGTTTCCCTTAAAACATAAACCTTTGAGATTATTTCTCTTGAAA-AAAATTT
1 TCTCGCTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAATTT
299765 -A
66 CA
* * * *
299766 TCTCACTTGAGACAGTTTCTCTTGAATCATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTT
1 TCTCGCTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAATTT
299831 CGA
66 C-A
* * * * *
299834 -CTCGTTTAAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTT
1 TCTCGCTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAATTT
*
299898 CG
66 CA
* ** * * *
299900 TCTCGCTTGAGACAGTTTCCCTTGAAGCCCAAA-TTTTG-GAGTTGTTTCACTTGAAACAAAA-T
1 TCTCGCTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGA-TTGTTTCTCTCGAAACAAAATT
*
299962 TGA
65 TCA
*
299965 TCTCTCTTGAGA
1 TCTCGCTTGAGA
299977 TTGTTTTCCT
Statistics
Matches: 178, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
65 65 0.37
66 27 0.15
67 85 0.48
68 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (67 bp):
TCTCGCTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAATTT
CA
Found at i:299867 original size:67 final size:67
Alignment explanation
Indices: 299706--299925 Score: 293
Period size: 67 Copynumber: 3.3 Consensus size: 67
299696 GTATGTCTCC
* * * * *
299706 CTTGAGACGGTTTCCCTTAAAACATAAACCTTTGAGATTATTTCTCTTGAAA-AAAATTT--ATC
1 CTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGA-C
*
299768 TCA
65 TCG
* *
299771 CTTGAGACAGTTTCTCTTGAATCATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGACT
1 CTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGACT
299836 CG
66 CG
* * * * *
299838 TTTAAGACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCT
1 CTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGACT
299903 CG
66 CG
299905 CTTGAGACAGTTTCCCTTGAA
1 CTTGAGACAGTTTCCCTTGAA
299926 GCCCAAATTT
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
65 46 0.34
66 6 0.04
67 82 0.61
68 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (67 bp):
CTTGAGACAGTTTCCCTTGAAACATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTCGACT
CG
Found at i:301121 original size:64 final size:66
Alignment explanation
Indices: 301053--301191 Score: 146
Period size: 65 Copynumber: 2.2 Consensus size: 66
301043 TGCACTAAGG
* *
301053 GTGCATCGATGTG-TGAAATGCATTCGATGTTTCAA-ACA-AGC-CTGAGTGCATCGATGCATGG
1 GTGCATCGATGTGATAAAATGAATTCGATGTTTCAATA-ATA-CACTGAGTGCATCGATGCATGG
*
301114 TTT
64 TAT
* * * *
301117 GTGCATC-A-GTGCATAAAATTAATTCGATGTTTTAATAATACATTGAGTTCATCGATGCATGGT
1 GTGCATCGATGTG-ATAAAATGAATTCGATGTTTCAATAATACACTGAGTGCATCGATGCATGGT
301180 AT
65 AT
301182 GTGCATCGAT
1 GTGCATCGAT
301192 ACATAAAAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
62 3 0.05
63 1 0.02
64 27 0.44
65 29 0.48
66 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (66 bp):
GTGCATCGATGTGATAAAATGAATTCGATGTTTCAATAATACACTGAGTGCATCGATGCATGGTA
T
Found at i:303771 original size:21 final size:21
Alignment explanation
Indices: 303747--303810 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
303737 TCGGTGCATC
303747 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* *
303768 TTCATAGGGATGCATCGATGCACC
1 TTCAT---GATGTATCGATGCACA
303792 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
303811 TTATGCACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 16 0.44
24 19 0.53
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:303784 original size:24 final size:24
Alignment explanation
Indices: 303752--303798 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
303742 GCATCTTCAT
*
303752 GATGTATCGATGCACATTCATAGG
1 GATGCATCGATGCACATTCATAGG
*
303776 GATGCATCGATGCACCTTCATAG
1 GATGCATCGATGCACATTCATAG
303799 TGTATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (24 bp):
GATGCATCGATGCACATTCATAGG
Found at i:303795 original size:45 final size:44
Alignment explanation
Indices: 303715--303810 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 44
303705 CATTGTGCAC
* * *
303715 CGATGTACATTCAAGGAGTGCATCGGTGCATCTTCAT-GATGTAT
1 CGATGCACATTCAAGGAGTGCATCGATGCACCTTCATAG-TGTAT
303759 CGATGCACATTCATAGG-GATGCATCGATGCACCTTCATAGTGTAT
1 CGATGCACATTCA-AGGAG-TGCATCGATGCACCTTCATAGTGTAT
303804 CGATGCA
1 CGATGCA
303811 TTATGCACGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
44 13 0.28
45 32 0.70
46 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (44 bp):
CGATGCACATTCAAGGAGTGCATCGATGCACCTTCATAGTGTAT
Found at i:309635 original size:64 final size:65
Alignment explanation
Indices: 309567--309726 Score: 175
Period size: 65 Copynumber: 2.5 Consensus size: 65
309557 TGCACTAAGG
* * *
309567 GTGCATCGATGCGTGAAATGC-ATTCGATGTTTCAAACAAT-CCT-GAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAAT-CAATTCGATGTTT-AAACAATACATGGAGTGCATCGATGCATGGT
*
309629 TT
64 AT
* * *
309631 GTGCATCGGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATCAATTCGATGTTTAAACAATACATGGAGTGCATCGATGCATGGTAT
* * *
309696 GTGCATCGGTACATAAAAGT-TATTCGATGTT
1 GTGCATCGATGCATAAAA-TCAATTCGATGTT
309727 CAATTAAAAC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 6 0.07
64 29 0.35
65 47 0.57
66 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATCAATTCGATGTTTAAACAATACATGGAGTGCATCGATGCATGGTAT
Found at i:309693 original size:65 final size:65
Alignment explanation
Indices: 309609--309771 Score: 199
Period size: 65 Copynumber: 2.5 Consensus size: 65
309599 CAAACAATCC
* * *
309609 TGAGTGCATCGATGCATGGTTTGTGCATCGGTGCATAAAA-TCAATTCGATGTTTTAA-TAATAC
1 TGAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGT-AATTCGATG-TTCAATTAAAAC
309672 -A
64 AA
* *
309673 TGGAGTGCATCGATGCATGGTATGTGCATCGGTACATAAAAGTTATTCGATGTTCAATTAAAACA
1 T-GAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGTAATTCGATGTTCAATTAAAACA
309738 A
65 A
* *
309739 TG-GTGCATCGATGCATTGATTTATGCATCGGTA
1 TGAGTGCATCGATGCA-TGGTTTGTGCATCGGTA
309772 AACTTACCTA
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 18 0.21
65 65 0.76
66 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (65 bp):
TGAGTGCATCGATGCATGGTTTGTGCATCGGTACATAAAAGTAATTCGATGTTCAATTAAAACAA
Found at i:313041 original size:41 final size:41
Alignment explanation
Indices: 312930--313041 Score: 120
Period size: 40 Copynumber: 2.7 Consensus size: 41
312920 ATAAATTAGA
* * *
312930 GGCGTTTTTAAACACAAACGCTGCTATAGATTGTACTTTAGC
1 GGCGTTTTTATA-ACAAACGCTGCAATAGATTGTACTATAGC
* * * *
312972 GGCGTTTTTATAA-AAACACCGCAATAGATTCGTTC-ATAGT
1 GGCGTTTTTATAACAAACGCTGCAATAGATT-GTACTATAGC
*
313012 GGCGTTTTTCTAACAAACGCTGCAATAGAT
1 GGCGTTTTTATAACAAACGCTGCAATAGAT
313042 GTAATCTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 29 0.50
41 18 0.31
42 11 0.19
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (41 bp):
GGCGTTTTTATAACAAACGCTGCAATAGATTGTACTATAGC
Found at i:322321 original size:86 final size:86
Alignment explanation
Indices: 322191--322349 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 86
322181 CAACACATAT
* * * * *
322191 TGCGGCGTGTGTGGAAAAAACGCCGCTAAATCTCAACAATTATTACGGCGTTTGCGATAAAAACG
1 TGCGGCGTGTGTGGAAAAAACGCCGCTAAATCTCAACAACTATTACAGCATTTGCAAGAAAAACG
*
322256 CTGCTAAATATAAACAACTAC
66 CCGCTAAATATAAACAACTAC
* * * *
322277 TGCGGCGTTTGTGGGAAAAACGCCGCTAAA-CATCAACACCTATTACAGCATTTGTAAGAAAAAC
1 TGCGGCGTGTGTGGAAAAAACGCCGCTAAATC-TCAACAACTATTACAGCATTTGCAAGAAAAAC
322341 GCCGCTAAA
65 GCCGCTAAA
322350 AATCAACACC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 1 0.02
86 61 0.98
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (86 bp):
TGCGGCGTGTGTGGAAAAAACGCCGCTAAATCTCAACAACTATTACAGCATTTGCAAGAAAAACG
CCGCTAAATATAAACAACTAC
Found at i:322331 original size:43 final size:43
Alignment explanation
Indices: 322149--322357 Score: 167
Period size: 43 Copynumber: 4.8 Consensus size: 43
322139 GATACTTTAG
** *
322149 CGGCGTTTGT-ATGAAAAAACGCCGGGAAATC-TCAAC-ACATATTG
1 CGGCGTTTGTGA-G-AAAAACGCCGCTAAA-CATCAACAAC-TATTA
* *
322193 CGGCGTGTGTG-GAAAAAACGCCGCTAAATC-TCAACAATTATTA
1 CGGCGTTTGTGAG-AAAAACGCCGCTAAA-CATCAACAACTATTA
* * * * * * *
322236 CGGCGTTTGCGATAAAAACGCTGCTAAATATAAACAACTACTG
1 CGGCGTTTGTGAGAAAAACGCCGCTAAACATCAACAACTATTA
* *
322279 CGGCGTTTGTGGGAAAAACGCCGCTAAACATCAACACCTATTA
1 CGGCGTTTGTGAGAAAAACGCCGCTAAACATCAACAACTATTA
* * * *
322322 CAGCATTTGTAAGAAAAACGCCGCTAAAAATCAACA
1 CGGCGTTTGTGAGAAAAACGCCGCTAAACATCAACA
322358 CCCTATGGCG
Statistics
Matches: 133, Mismatches: 28, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
43 123 0.92
44 10 0.08
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
CGGCGTTTGTGAGAAAAACGCCGCTAAACATCAACAACTATTA
Found at i:329331 original size:19 final size:20
Alignment explanation
Indices: 329307--329358 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
329297 TATATGTTTT
**
329307 TATGAACAGTAA-AATATGG
1 TATGAACAGTAACAATACCG
*
329326 TATGAACAGTCAACAGTACCG
1 TATGAACAGT-AACAATACCG
329347 TATGAACAGTAA
1 TATGAACAGTAA
329359 TGAATAGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.36
20 4 0.14
21 14 0.50
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.23
Consensus pattern (20 bp):
TATGAACAGTAACAATACCG
Found at i:330105 original size:31 final size:31
Alignment explanation
Indices: 330067--330504 Score: 284
Period size: 31 Copynumber: 13.9 Consensus size: 31
330057 CCTCGACAAC
* *
330067 TGTCCATAGGTCCCGAAGAACCTAGGTAAAG
1 TGTCCATATGTCCCGAAGAACATAGGTAAAG
* ** * *
330098 TGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATATGTCCCGAAGAACATAGGTAAAG
**
330129 TGTCCATATGTCCCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AG
** * *
330161 TGTCCATATGTTTC-ATAGAACATAGGTATAC
1 TGTCCATATGTCCCGA-AGAACATAGGTAAAG
* **
330192 TGTCCATATGTCTCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AG
** * * *
330224 TGTCCATATGTTACGTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAG
* **
330255 TGTCCATATGTCTCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AG
** * * *
330287 TGTCCATATGTTACGTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAG
**
330318 TGTCCATATGTCCCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AG
* * * *
330350 TATCCATATATTCCGTAGAACATAGGTATAA-
1 TGTCCATATGTCCCGAAGAACATAGGTA-AAG
**
330381 TGTCCATATGTCCCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AG
* * * *
330413 TGTCCATATGTTCCGTAGAACATAGGTATAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAG
330444 TGTCCATATGTCCCGAA-AGACATAGGTAATTA-
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA--AG
*
330476 TGTCCATATGTTCC-ATAGAACATAGGTAA
1 TGTCCATATGTCCCGA-AGAACATAGGTAA
330505 TTCTTCGACT
Statistics
Matches: 325, Mismatches: 58, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
30 7 0.02
31 168 0.52
32 142 0.44
33 8 0.02
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAG
Found at i:330186 original size:63 final size:63
Alignment explanation
Indices: 330065--330503 Score: 702
Period size: 63 Copynumber: 7.0 Consensus size: 63
330055 AACCTCGACA
* * ** *
330065 ACTGTCCATAGGTCCCG-AAGAACCTAGGTAA-AGTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
330127 ATTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTTCATAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
330190 ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTACGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
330253 ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTACGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
330316 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTATCCATATATTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
*
330379 AATGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
330442 ACTGTCCATATGTCCCGAAAGACATAGGTAATTATGTCCATATGTTCCATAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
330504 ATTCTTCGAC
Statistics
Matches: 354, Mismatches: 21, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
62 24 0.07
63 330 0.93
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (63 bp):
ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:333133 original size:136 final size:136
Alignment explanation
Indices: 332779--333136 Score: 396
Period size: 136 Copynumber: 2.6 Consensus size: 136
332769 AATATGGAAA
* * * * * * * * *
332779 ATTTAAAGATAACATGGTTCCTTTGCGTTGAGGAAGTCTGATTGTTTGAGGATAACACTGCTCCA
1 ATTTAGAGATAACATCGTTCCTTCGTGTTGAAGAAATCTGATTGTCTGAGGATGACACTGCTCCT
* * * * * *
332844 TCGCGTTGAGGAGATCTGGTCTATGGATGACATTGTTCATTCATATTGAGGACGTCTAGCTGTAT
66 TTGCATTGAGGAGATCTAGTCGATGGATAACATTGTTCATTCATATTGAGGACATCTAGCTGTAT
332909 TTGGAG
131 TTGGAG
* * * *
332915 ATTTGGAGATAACA-CGATTCATTCGTGGTGAAGAAATCTGATTGTCTGAGGATGACACTGCTTC
1 ATTTAGAGATAACATCG-TTCCTTCGTGTTGAAGAAATCTGATTGTCTGAGGATGACACTGCTCC
* * * * * *
332979 TTTGCATTGAGAATATCTAGTCGGTGGATAACATTGTTCCTTCGTGTTGAGGACATCTAGCCT-T
65 TTTGCATTGAGGAGATCTAGTCGATGGATAACATTGTTCATTCATATTGAGGACATCTAG-CTGT
333043 ATTTGGAG
129 ATTTGGAG
* * * * *
333051 ATTTAGAGACAACATTGTTCCTTCGTGTTGATGAAATCTGATTGTCTGATGATGACACTACTCCT
1 ATTTAGAGATAACATCGTTCCTTCGTGTTGAAGAAATCTGATTGTCTGAGGATGACACTGCTCCT
* *
333116 TTTCATTGAGGGGATCTAGTC
66 TTGCATTGAGGAGATCTAGTC
333137 TTAGTTGCCA
Statistics
Matches: 181, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
135 1 0.01
136 177 0.98
137 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (136 bp):
ATTTAGAGATAACATCGTTCCTTCGTGTTGAAGAAATCTGATTGTCTGAGGATGACACTGCTCCT
TTGCATTGAGGAGATCTAGTCGATGGATAACATTGTTCATTCATATTGAGGACATCTAGCTGTAT
TTGGAG
Found at i:337864 original size:12 final size:13
Alignment explanation
Indices: 337849--337898 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
337839 ATTGGATCTG
337849 AAATAAT-TAATT
1 AAATAATATAATT
337861 AAATAATATAA-T
1 AAATAATATAATT
*
337873 ATAATAATACTATAAT
1 A-AATAATA-TA-ATT
337889 AAATAATATA
1 AAATAATATA
337899 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 9 0.27
13 10 0.30
14 4 0.12
15 8 0.24
16 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAATATAATT
Found at i:337906 original size:28 final size:28
Alignment explanation
Indices: 337860--337914 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
337850 AATAATTAAT
*
337860 TAAATAATATAATATAATAATACTATAA
1 TAAATAATATAATAAAATAATACTATAA
*
337888 TAAATAATAT-ATAAAAATAATATTATA
1 TAAATAATATAAT-AAAATAATACTATA
337915 TACTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
TAAATAATATAATAAAATAATACTATAA
Found at i:337916 original size:2 final size:2
Alignment explanation
Indices: 337866--338216 Score: 161
Period size: 2 Copynumber: 189.5 Consensus size: 2
337856 TAATTAAATA
* * *
337866 AT AT A- AT AT A- AT A- AT ACT AT A- AT AA AT A- AT AT AT AA AA
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
337904 AT A- AT AT -T AT AT ACT AT AT AT AT -T GT A- AT AT AA AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
337943 AT TT ACT AT A- AT AT A- ACT A- AT AT A- AT AT AT AC AT A- AA AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
337982 AT AT A- AT AT AT AT -T A- 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
* * * *
338021 AA AT AT AT AT AT -T AC AT ACC AT AT A- AT AT AT AT ACC AT AT A-
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
**
338062 AT AT ACT AT AT AT A- AT A- AT AT -T CC AT AT A- AT AT A- AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
338100 AT AT A- AT AT ACT AT -T AT AT A- AT A- AT AT ACC AT A- AT AT ACT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T
*
338140 AT AT A- AT AT AT -T AT AT A- AT AT AT AT A- AC AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
338177 AT -T AT AT A- AT A- AT AT ACT AA AT AT ACT AT AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
338216 A
1 A
338217 CTAAATGTGT
Statistics
Matches: 269, Mismatches: 28, Indels: 104
0.67 0.07 0.26
Matches are distributed among these distances:
1 40 0.15
2 209 0.78
3 20 0.07
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:342137 original size:9 final size:9
Alignment explanation
Indices: 342123--342179 Score: 73
Period size: 9 Copynumber: 6.6 Consensus size: 9
342113 TTTCGTCCTA
342123 AATATTATT
1 AATATTATT
342132 AATATTATT
1 AATATTATT
*
342141 ATTATTATT
1 AATATTATT
*
342150 ATTATTATT
1 AATATTATT
342159 -ATA-TATT
1 AATATTATT
*
342166 ATTATTATT
1 AATATTATT
342175 AATAT
1 AATAT
342180 AATTGTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 4 0.10
8 4 0.10
9 34 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
AATATTATT
Found at i:342140 original size:3 final size:3
Alignment explanation
Indices: 342125--342175 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
342115 TCGTCCTAAA
*
342125 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
342171 TAT TA
1 TAT TA
342176 ATATAATTGT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:342233 original size:13 final size:13
Alignment explanation
Indices: 342196--342234 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
342186 TTTTGTTACA
342196 GGTTACAAGACCC
1 GGTTACAAGACCC
* *
342209 GGAT-CCAGACCC
1 GGTTACAAGACCC
342221 GGTTACAAGACCC
1 GGTTACAAGACCC
342234 G
1 G
342235 ACCCGATAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (13 bp):
GGTTACAAGACCC
Found at i:344206 original size:2 final size:2
Alignment explanation
Indices: 344194--344238 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
344184 TTCCATGTTA
344194 AT AT A- 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
344235 AT AT
1 AT AT
344239 TGTAACACCC
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):
AT
Found at i:344680 original size:20 final size:20
Alignment explanation
Indices: 344645--344685 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
344635 TTTGATCATG
*
344645 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
344665 ATATTTC-ATATGGCATATAT
1 ATATTTCAATAT-GCATATAT
344685 A
1 A
344686 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:349820 original size:6 final size:6
Alignment explanation
Indices: 349811--349835 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
349801 CTGACTTCTT
349811 CCTCTA CCTCTA CCTCTA CCTCTA C
1 CCTCTA CCTCTA CCTCTA CCTCTA C
349836 ATCTTCCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTCTA
Found at i:351414 original size:20 final size:20
Alignment explanation
Indices: 351374--351414 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
351364 TTTGATCATG
*
351374 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
351394 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
351414 A
1 A
351415 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:353150 original size:2 final size:2
Alignment explanation
Indices: 353143--353174 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
353133 AAGGAATTTA
353143 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
353175 GTGATCATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355125 original size:37 final size:37
Alignment explanation
Indices: 355035--355131 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
355025 CCTTTTCGTC
*
355035 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
* * * *
355072 TTGCTAGGATTCAAACTCCTATAAATAAGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
** *
355109 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
355132 GATAGGATCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAAGATAGAATT
Found at i:355491 original size:22 final size:22
Alignment explanation
Indices: 355466--355539 Score: 103
Period size: 22 Copynumber: 3.1 Consensus size: 22
355456 ACGTTATATA
355466 TATATATATTCTTACTTTATTT
1 TATATATATTCTTACTTTATTT
355488 TATATATATTCTTACTTTATTTATAT
1 TATATATATTCTTACTTTA--T-T-T
355514 ATATATATATTCTTACTTTATTT
1 -TATATATATTCTTACTTTATTT
355537 TAT
1 TAT
355540 TTTATATTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
22 22 0.47
23 1 0.02
24 2 0.04
25 2 0.04
26 1 0.02
27 19 0.40
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (22 bp):
TATATATATTCTTACTTTATTT
Found at i:355583 original size:56 final size:56
Alignment explanation
Indices: 355508--355616 Score: 218
Period size: 56 Copynumber: 1.9 Consensus size: 56
355498 CTTACTTTAT
355508 TTATATATATATATATTCTTACTTTATTTTATTTTATATTTCTATGATTACTAACG
1 TTATATATATATATATTCTTACTTTATTTTATTTTATATTTCTATGATTACTAACG
355564 TTATATATATATATATTCTTACTTTATTTTATTTTATATTTCTATGATTACTA
1 TTATATATATATATATTCTTACTTTATTTTATTTTATATTTCTATGATTACTA
355617 TTTTTTTAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (56 bp):
TTATATATATATATATTCTTACTTTATTTTATTTTATATTTCTATGATTACTAACG
Found at i:355601 original size:27 final size:27
Alignment explanation
Indices: 355481--355602 Score: 122
Period size: 27 Copynumber: 4.4 Consensus size: 27
355471 ATATTCTTAC
355481 TTTATTTTATATATATTCTTACTTTA-
1 TTTATTTTATATATATTCTTACTTTAT
*
355507 TTTATATATATATATATTCTTACTTTAT
1 TTTAT-TTTATATATATTCTTACTTTAT
* ** * *
355535 TTTATTTTATATTTCTATGATTAC-TAAC
1 TTTATTTTATA--TATATTCTTACTTTAT
* *
355563 GTTATATATATATATATTCTTACTTTAT
1 TTTAT-TTTATATATATTCTTACTTTAT
355591 TTTATTTTATAT
1 TTTATTTTATAT
355603 TTCTATGATT
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
26 5 0.07
27 39 0.53
28 17 0.23
29 13 0.18
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATTTTATATATATTCTTACTTTAT
Found at i:355614 original size:29 final size:29
Alignment explanation
Indices: 355526--355633 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 29
355516 ATATATATTC
355526 TTACTTTATTTTATTTTATATTTCTATGA
1 TTACTTTATTTTATTTTATATTTCTATGA
* ** * * * **
355555 TTAC-TAACGTTA-TATATATATATATTC
1 TTACTTTATTTTATTTTATATTTCTATGA
355582 TTACTTTATTTTATTTTATATTTCTATGA
1 TTACTTTATTTTATTTTATATTTCTATGA
* * *
355611 TTACTATTTTTTTAGTTAATATT
1 TTACT-TTATTTTATTTTATATT
355634 ATATGTATAT
Statistics
Matches: 57, Mismatches: 19, Indels: 5
0.70 0.23 0.06
Matches are distributed among these distances:
27 14 0.25
28 10 0.18
29 19 0.33
30 14 0.25
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (29 bp):
TTACTTTATTTTATTTTATATTTCTATGA
Found at i:355618 original size:27 final size:27
Alignment explanation
Indices: 355532--355620 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
355522 ATTCTTACTT
355532 TATTTTATTTTATATTTCTATGATTAC
1 TATTTTATTTTATATTTCTATGATTAC
** * * * **
355559 TAACGTTA-TATATATATATATTCTTAC
1 T-ATTTTATTTTATATTTCTATGATTAC
355586 TTTATTTTATTTTATATTTCTATGATTAC
1 --TATTTTATTTTATATTTCTATGATTAC
355615 TATTTT
1 TATTTT
355621 TTTAGTTAAT
Statistics
Matches: 44, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
27 21 0.48
28 8 0.18
29 15 0.34
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.61
Consensus pattern (27 bp):
TATTTTATTTTATATTTCTATGATTAC
Found at i:355730 original size:14 final size:14
Alignment explanation
Indices: 355715--355758 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
355705 TTTTTATATT
*
355715 TTTATATATATTTT
1 TTTATATATATTTA
355729 TTTAT-TAT-TTTA
1 TTTATATATATTTA
355741 TTTATAT-TATTTA
1 TTTATATATATTTA
355754 TTTAT
1 TTTAT
355759 TTTCATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 9 0.33
13 13 0.48
14 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATATATTTA
Found at i:355740 original size:22 final size:22
Alignment explanation
Indices: 355684--355773 Score: 78
Period size: 22 Copynumber: 4.1 Consensus size: 22
355674 CTATTTAGTA
* * **
355684 TTTTATTATATTATACATACAT
1 TTTTATTATTTTATATATATTT
355706 TTTTA-TATTTTTATATATATTT
1 TTTTATTA-TTTTATATATATTT
*
355728 TTTTATTATTTTATTTATA-TT
1 TTTTATTATTTTATATATATTT
*
355749 ATTTATTTATTTTCAT-TATATTT
1 TTTTA-TTATTTT-ATATATATTT
355772 TT
1 TT
355774 AGTTTCTTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.14
22 41 0.73
23 7 0.12
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTATTTTATATATATTT
Found at i:355774 original size:34 final size:34
Alignment explanation
Indices: 355707--355772 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
355697 TACATACATT
*
355707 TTTATATTTTTATATATATTTTTTTATTATTTTA
1 TTTATATTTTTATATATATTTTATTATTATTTTA
355741 TTTATATTATTTAT-T-TATTTTCATTA-TATTTT
1 TTTATATT-TTTATATATATTTT-ATTATTATTTT
355773 TAGTTTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 12 0.41
34 12 0.41
35 5 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (34 bp):
TTTATATTTTTATATATATTTTATTATTATTTTA
Found at i:355884 original size:20 final size:19
Alignment explanation
Indices: 355857--355913 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
355847 TTTTATCTTC
355857 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
355876 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
355897 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
355914 ATTATTAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:360252 original size:18 final size:18
Alignment explanation
Indices: 360224--360277 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
360214 AAAAAGGGCA
*
360224 AAAACAAAAAAGAAAAGAAG
1 AAAA-AAAAAAG-AAAGAAC
360244 AAAAAAAAAAGAAAGAAC
1 AAAAAAAAAAGAAAGAAC
360262 AAAAATCAAAAAGAAA
1 AAAAA--AAAAAGAAA
360278 AAGGGACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 11 0.35
19 7 0.23
20 13 0.42
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAGAAAGAAC
Found at i:360259 original size:15 final size:15
Alignment explanation
Indices: 360229--360279 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
360219 GGGCAAAAAC
360229 AAAAAAGAAAAG-AAG
1 AAAAAA-AAAAGAAAG
360244 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
*
360259 AACAAAAATCAA-AAAG
1 AA-AAAAA-AAAGAAAG
360275 AAAAA
1 AAAAA
360280 GGGACAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 14 0.44
16 11 0.34
17 2 0.06
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:361809 original size:22 final size:22
Alignment explanation
Indices: 361779--361823 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
361769 TACAATACTT
*
361779 GGATTTC-AACTTCACGACGAA
1 GGATTTCAAACTTCACAACGAA
*
361800 GGATATTCAAACTTTACAACGAA
1 GGAT-TTCAAACTTCACAACGAA
361823 G
1 G
361824 TGGCTATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 13 0.65
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (22 bp):
GGATTTCAAACTTCACAACGAA
Found at i:362024 original size:106 final size:106
Alignment explanation
Indices: 361867--362706 Score: 1186
Period size: 106 Copynumber: 8.0 Consensus size: 106
361857 ATATCGTGCC
* * * *
361867 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
361932 AAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
361973 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
362038 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
362079 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
362144 AATTTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
362185 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
362250 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
362291 ACTCCAGACAA-AGCAAGTTCAACTTCACGACGAAGGGCCCGCAGGTTGTCAACAAACAACTTCT
1 ACTCCAGACAACA-CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
*
362355 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
362397 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACTGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
362462 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
362503 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC--A-AA-----C
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
362560 AATTTC----CCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * ***
362597 ACTCGATACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTTTT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
362662 GATTCCACAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
362703 ACTC
1 ACTC
362707 GAAACAATGC
Statistics
Matches: 666, Mismatches: 53, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
94 77 0.12
96 1 0.00
97 2 0.00
98 7 0.01
102 4 0.01
103 2 0.00
104 1 0.00
106 572 0.86
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:363509 original size:37 final size:37
Alignment explanation
Indices: 363456--363560 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
363446 CATTTTCGTC
*
363456 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
* * * *
363493 TTGCTAGGATTTAAACTCCTATAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
** *
363530 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
363561 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAGAATT
Found at i:364060 original size:24 final size:24
Alignment explanation
Indices: 364033--364082 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
364023 TTTCTTTGCG
* *
364033 TTATAT-TATATTATTTTCCTATTA
1 TTATATATATA-TATTATACTATTA
364057 TTATATATATATATTATACTATTA
1 TTATATATATATATTATACTATTA
364081 TT
1 TT
364083 TTTTTATCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATATATATATATTATACTATTA
Found at i:364282 original size:29 final size:27
Alignment explanation
Indices: 364226--364319 Score: 72
Period size: 27 Copynumber: 3.5 Consensus size: 27
364216 TTTTCATTTA
* *
364226 TTTATTATTATTAT-TACTATTTAGTAT
1 TTTATTA-TATTATATAATTTTTAGTAT
364253 TTTATTATATTATACATACATTTTTA-TA-
1 TTTATTATATTAT--ATA-ATTTTTAGTAT
* *
364281 TTT-TTATA-TATATATTTTTTATTAT
1 TTTATTATATTATATAATTTTTAGTAT
364306 TTTATTTATATTAT
1 TTTA-TTATATTAT
364320 TTATTTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
23 6 0.11
24 5 0.09
25 3 0.05
26 9 0.16
27 17 0.31
28 6 0.11
29 4 0.07
30 5 0.09
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTATTATATTATATAATTTTTAGTAT
Found at i:364294 original size:14 final size:14
Alignment explanation
Indices: 364277--364343 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
364267 CATACATTTT
364277 TATATTTTTATATA
1 TATATTTTTATATA
364291 TATATTTTT-TAT-
1 TATATTTTTATATA
*
364303 TATTTTATTTATATTA
1 TATATT-TTTATA-TA
*
364319 TTTATTTATT-TATA
1 TATATTT-TTATATA
364333 TTATATTTTTA
1 -TATATTTTTA
364344 GTTTCTTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
12 5 0.12
13 6 0.14
14 15 0.36
15 10 0.24
16 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTTTTATATA
Found at i:364303 original size:21 final size:20
Alignment explanation
Indices: 364272--364342 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 20
364262 TTATACATAC
364272 ATTTTTATATTTTTATATATAT
1 ATTTTT-TATTTTT-TATATAT
*
364294 ATTTTTTATTATTTTATTTAT
1 ATTTTTTATT-TTTTATATAT
*
364315 ATTATTTATTTATTTATATTAT
1 ATTTTTTATTT-TTTATA-TAT
364337 ATTTTT
1 ATTTTT
364343 AGTTTCTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 24 0.57
22 17 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTTATTTTTTATATAT
Found at i:364326 original size:17 final size:17
Alignment explanation
Indices: 364275--364336 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
364265 TACATACATT
*
364275 TTTATATT-TTTATATA
1 TTTATATTATTTATTTA
* * *
364291 TATATTTTTTATTATTTTA
1 TTTATATTAT-TTA-TTTA
364310 TTTATATTATTTATTTA
1 TTTATATTATTTATTTA
364327 TTTATATTAT
1 TTTATATTAT
364337 ATTTTTAGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 6 0.16
17 15 0.41
18 6 0.16
19 10 0.27
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATATTATTTATTTA
Found at i:364330 original size:29 final size:29
Alignment explanation
Indices: 364222--364340 Score: 99
Period size: 28 Copynumber: 4.2 Consensus size: 29
364212 ATTTTTTTCA
*
364222 TTTATTTATTATTAT-TATTACTATTTAGTAT
1 TTTATTTA-TATTATATATT--TATTTATTAT
* **
364253 TTTA-TTATATTATACATACATTT-TTAT
1 TTTATTTATATTATATATTTATTTATTAT
*
364280 ATT-TTTATA-TATATATTT-TTTATTAT
1 TTTATTTATATTATATATTTATTTATTAT
*
364306 TTTATTTATATTATTTATTTATTTA-TAT
1 TTTATTTATATTATATATTTATTTATTAT
*
364334 TATATTT
1 TTTATTT
364341 TTAGTTTCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
25 3 0.04
26 12 0.17
27 16 0.23
28 21 0.30
29 10 0.14
30 5 0.07
31 4 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTATTTATATTATATATTTATTTATTAT
Found at i:364343 original size:17 final size:16
Alignment explanation
Indices: 364299--364343 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 16
364289 TATATATTTT
364299 TTATTATTTTATTTATA
1 TTATT-TTTTATTTATA
364316 TTATTTATTTATTTATA
1 TTATTT-TTTATTTATA
364333 TTATATTTTTA
1 TTAT-TTTTTA
364344 GTTTCTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.88
18 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTTTATTTATA
Found at i:364343 original size:21 final size:21
Alignment explanation
Indices: 364202--364343 Score: 79
Period size: 22 Copynumber: 6.8 Consensus size: 21
364192 TTAGTTAATA
*
364202 TTATATGTATATTTTT-TTCAT
1 TTATAT-TATATTTTTATTTAT
*
364223 TTAT-TTATTATTATTA-TTA-
1 TTATATTA-TATTTTTATTTAT
*
364242 CTAT-TTAGTA-TTTTA-TTAT
1 TTATATTA-TATTTTTATTTAT
* *
364261 ATTATACATACATTTTTATATT-T
1 -TTATA-TTATATTTTTAT-TTAT
364284 TTATATATATATTTTT-TATTAT
1 TTATAT-TATATTTTTAT-TTAT
364306 TT-TATTTATATTATTTATTTAT
1 TTATA-TTATATT-TTTATTTAT
364328 TTATATTATATTTTTA
1 TTATATTATATTTTTA
364344 GTTTCTTTGC
Statistics
Matches: 96, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
18 7 0.07
19 10 0.10
20 12 0.12
21 21 0.22
22 40 0.42
23 4 0.04
24 2 0.02
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TTATATTATATTTTTATTTAT
Found at i:364459 original size:20 final size:19
Alignment explanation
Indices: 364432--364487 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
364422 TTTTATCTTC
364432 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
364451 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
364471 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
364488 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:367190 original size:6 final size:6
Alignment explanation
Indices: 367179--367204 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
367169 GTCGGTTTTG
367179 GTCACC GTCACC GTCACC GTCACC GT
1 GTCACC GTCACC GTCACC GTCACC GT
367205 GAATTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.46, G:0.19, T:0.19
Consensus pattern (6 bp):
GTCACC
Found at i:367697 original size:15 final size:15
Alignment explanation
Indices: 367679--367719 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
367669 CCCCCACAGT
367679 GTCTGAAATCACAAC
1 GTCTGAAATCACAAC
*
367694 GTCTGAAATCACAGC
1 GTCTGAAATCACAAC
*
367709 GTCCGAAATCA
1 GTCTGAAATCA
367720 GTACTTAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (15 bp):
GTCTGAAATCACAAC
Found at i:367924 original size:2 final size:2
Alignment explanation
Indices: 367917--367952 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
367907 TTTAATAAAT
*
367917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
367953 AACTCGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:371604 original size:19 final size:19
Alignment explanation
Indices: 371572--371608 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
371562 ATGACCAATA
* *
371572 AAATCGCAATGCGATCTCT
1 AAATCACAACGCGATCTCT
371591 AAATCACAACGCGATCTC
1 AAATCACAACGCGATCTC
371609 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCACAACGCGATCTCT
Found at i:371659 original size:20 final size:20
Alignment explanation
Indices: 371607--371651 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
371597 CAACGCGATC
371607 TCCAGTATCGCAAATCAGTT
1 TCCAGTATCGCAAATCAGTT
371627 TCCAGTATCGCAAATCAGTT
1 TCCAGTATCGCAAATCAGTT
371647 TCCAG
1 TCCAG
371652 ATTCGCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TCCAGTATCGCAAATCAGTT
Found at i:371751 original size:20 final size:19
Alignment explanation
Indices: 371713--371767 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
371703 CAATTTTAGA
* * *
371713 AAATCGCAATGAGAATATG
1 AAATCGCAACGCGATTATG
371732 TAAATCGCAACGCGATTATG
1 -AAATCGCAACGCGATTATG
*
371752 ACTATCGCAACGCGAT
1 A-AATCGCAACGCGAT
371768 CTCCAGTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATTATG
Found at i:371798 original size:142 final size:142
Alignment explanation
Indices: 371627--371909 Score: 460
Period size: 142 Copynumber: 2.0 Consensus size: 142
371617 CAAATCAGTT
* * * *
371627 TCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGGGATTTTAACTATCGTATTGCGATTTTTCA
1 TCCAGTATCACAAATCAGTTTCCAGATTCGCAACGCGATTTTAACTATCGCATTGCGATTTTCCA
*
371692 AATTCGCGTTGCAATTTTAGAA-AATCGCAATGAGAATATGTAAATCGCAACGCGATTATGACTA
66 AATTCCCGTTGCAATTTTA-AATAATCGCAATGAGAATATGTAAATCGCAACGCGATTATGACTA
371756 TCGCAACGCGATC
130 TCGCAACGCGATC
* *
371769 TCCAGTATCACAAATCAGTTTCCAGATTCGCAGCGCGATTTTGACTATCGCATTGCGATTTTCCA
1 TCCAGTATCACAAATCAGTTTCCAGATTCGCAACGCGATTTTAACTATCGCATTGCGATTTTCCA
* * *
371834 AATTCCCGTTGCGATTTTAAATAATCGCAATGTGAATATGTAAATCGCAACGCGATTCTGACTAT
66 AATTCCCGTTGCAATTTTAAATAATCGCAATGAGAATATGTAAATCGCAACGCGATTATGACTAT
371899 CGCAACGCGAT
131 CGCAACGCGAT
371910 AATACAAAAT
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 2 0.02
142 128 0.98
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (142 bp):
TCCAGTATCACAAATCAGTTTCCAGATTCGCAACGCGATTTTAACTATCGCATTGCGATTTTCCA
AATTCCCGTTGCAATTTTAAATAATCGCAATGAGAATATGTAAATCGCAACGCGATTATGACTAT
CGCAACGCGATC
Found at i:371923 original size:21 final size:21
Alignment explanation
Indices: 371897--372033 Score: 138
Period size: 21 Copynumber: 6.6 Consensus size: 21
371887 GATTCTGACT
371897 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
371918 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* ** *
371939 ATCACAACGCGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
371959 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
** *
371980 ATCGCAACGCGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
* *
372000 ATCGCAATGTGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
372021 ATCGCAATGCGAT
1 ATCGCAACGCGAT
372034 TTTCCAAGTT
Statistics
Matches: 93, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.04
20 25 0.27
21 60 0.65
22 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:371941 original size:62 final size:62
Alignment explanation
Indices: 371875--371992 Score: 227
Period size: 62 Copynumber: 1.9 Consensus size: 62
371865 GTGAATATGT
*
371875 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATAATACA
1 AAATCACAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATAATACA
371937 AAATCACAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGAT
1 AAATCACAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGAT
371993 TCTGACTATC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (62 bp):
AAATCACAACGCGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATAATACA
Found at i:371963 original size:41 final size:41
Alignment explanation
Indices: 371918--372034 Score: 198
Period size: 41 Copynumber: 2.9 Consensus size: 41
371908 ATAATACAAA
*
371918 ATCGCAACGCGATAATACAAAATCACAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
371959 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
* * *
372000 ATCGCAATGTGATAATACAAAATCGCAATGCGATT
1 ATCGCAACGCGATAATACAAAATCGCAACGCGATT
372035 TTCCAAGTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
Found at i:372514 original size:19 final size:19
Alignment explanation
Indices: 372421--372515 Score: 91
Period size: 19 Copynumber: 4.7 Consensus size: 19
372411 TATTTTGGAT
* * *
372421 TTTTCACTATCACAACACT
1 TTTTAACTATCGCAACACA
*
372440 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
*
372460 CGTTTTTCAAACTCTCGCAACACA
1 ---TTTT--AACTATCGCAACACA
372484 TTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACA
372503 TTTTAACTATCGC
1 TTTTAACTATCGC
372516 GTTGCGAATC
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
19 42 0.65
20 2 0.03
21 4 0.06
23 4 0.06
24 3 0.05
25 10 0.15
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:373533 original size:31 final size:31
Alignment explanation
Indices: 373462--373540 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
373452 TAAGTATTTA
* *
373462 ATTTTTTTTAGTCAAAATAAGTATTTAAAGT
1 ATTTTTTTTGGTCAAAATAAGTATATAAAGT
** *
373493 -TATCATTTTGGTCAAAATATGTATATAAAGT
1 AT-TTTTTTTGGTCAAAATAAGTATATAAAGT
*
373524 ATTTTTTTTGGTTAAAA
1 ATTTTTTTTGGTCAAAA
373541 CAGTTACATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTTTTTTTGGTCAAAATAAGTATATAAAGT
Found at i:375936 original size:13 final size:14
Alignment explanation
Indices: 375907--375937 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
375897 ATCTTTTAAA
375907 ATAATTTTAAGAAG
1 ATAATTTTAAGAAG
375921 ATAATTTTAA-AAG
1 ATAATTTTAAGAAG
375934 ATAA
1 ATAA
375938 AAAGTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (14 bp):
ATAATTTTAAGAAG
Found at i:377384 original size:21 final size:21
Alignment explanation
Indices: 377358--377412 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
377348 ATTTACCGTG
*
377358 ATTGCGGTCGTCGCGGGCGCT
1 ATTGCGGTCGTCGCGGACGCT
377379 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGTCGTCGCGGACGCT
* *
377400 ATTACGGCCGTCG
1 ATTGCGGTCGTCG
377413 TAGGTAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (21 bp):
ATTGCGGTCGTCGCGGACGCT
Found at i:378621 original size:21 final size:21
Alignment explanation
Indices: 378597--378636 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
378587 GTTTCGGGTA
*
378597 CGGGA-ACGGTACGGGGACGGC
1 CGGGATAC-GTACCGGGACGGC
378618 CGGGATACGTACCGGGACG
1 CGGGATACGTACCGGGACG
378637 TGCCACGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.20, C:0.25, G:0.47, T:0.07
Consensus pattern (21 bp):
CGGGATACGTACCGGGACGGC
Found at i:378770 original size:21 final size:21
Alignment explanation
Indices: 378740--378780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
378730 GGGCGGAGAA
378740 GAGGAAGAGGAA-AAGTAAGAG
1 GAGGAAGAGGAAGAAG-AAGAG
*
378761 GAGGAGGAGGAAGAAGAAGA
1 GAGGAAGAGGAAGAAGAAGA
378781 TGCAGAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.02
Consensus pattern (21 bp):
GAGGAAGAGGAAGAAGAAGAG
Found at i:382174 original size:22 final size:22
Alignment explanation
Indices: 382149--382200 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
382139 AATCGAAATC
*
382149 AATCAGAATCGAAATTAACCCT
1 AATCAAAATCGAAATTAACCCT
382171 AATCAAAATCGAAATTAA-CCT
1 AATCAAAATCGAAATTAACCCT
382192 GAATCAAAA
1 -AATCAAAA
382201 GCAACACGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (22 bp):
AATCAAAATCGAAATTAACCCT
Found at i:383803 original size:26 final size:23
Alignment explanation
Indices: 383774--383836 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 23
383764 TATTCTCTCT
* *
383774 AGTTTTATTCTTTTCTTTTCTTTTCA
1 AGTTTTATT-TTTACTTTAC-TTT-A
*
383800 AGTTCTTGTTTTTACTTTACTTTA
1 AGTT-TTATTTTTACTTTACTTTA
383824 AGTTTTATTTTTA
1 AGTTTTATTTTTA
383837 AACATGTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 8 0.25
24 5 0.16
25 3 0.09
26 12 0.38
27 4 0.12
ACGTcount: A:0.16, C:0.11, G:0.06, T:0.67
Consensus pattern (23 bp):
AGTTTTATTTTTACTTTACTTTA
Found at i:399330 original size:16 final size:16
Alignment explanation
Indices: 399290--399332 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
399280 TTTAATTTGG
* *
399290 GTTGTTTTCGGTTCTA
1 GTTGATTTCGGTTCGA
*
399306 GTTAATTTCGGTTCGA
1 GTTGATTTCGGTTCGA
*
399322 GTTGCTTTCGG
1 GTTGATTTCGG
399333 CTTATGTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (16 bp):
GTTGATTTCGGTTCGA
Found at i:401782 original size:30 final size:30
Alignment explanation
Indices: 401748--401838 Score: 157
Period size: 30 Copynumber: 3.0 Consensus size: 30
401738 TAAAACTAAC
401748 AGACATTTAAAGGACTAAAATAGCAAAAAT
1 AGACATTTAAAGGACTAAAATAGCAAAAAT
401778 AGACATTTAAAGGACTAAAATAGCAAAAAT
1 AGACATTTAAAGGACTAAAATAGCAAAAAT
*
401808 AGA-ACTTTAAAGGACTAAAATAGAAAAAAT
1 AGACA-TTTAAAGGACTAAAATAGCAAAAAT
401838 A
1 A
401839 AAAAATTTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
29 1 0.02
30 58 0.98
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (30 bp):
AGACATTTAAAGGACTAAAATAGCAAAAAT
Found at i:402319 original size:2 final size:2
Alignment explanation
Indices: 402314--402338 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
402304 TGAAGGGGGG
402314 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
402339 CTTTATAGAG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:403580 original size:21 final size:21
Alignment explanation
Indices: 403554--403616 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
403544 TGTAAAATTT
* *
403554 TGTCCCGAAGAACCTCATGTA
1 TGTCCCGAAGGACCTCATATA
* *
403575 TGTCCCGATGGACCTCGTATA
1 TGTCCCGAAGGACCTCATATA
*
403596 TGTCCCAAAGGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
403617 ATCCCTCGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:411712 original size:21 final size:21
Alignment explanation
Indices: 411695--411750 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
411685 TTTTGTCCTA
*
411695 AAGGACCTCATGTATGTCCCG
1 AAGGACCTCATATATGTCCCG
* *
411716 AATGACCTCTTATATGTCCCG
1 AAGGACCTCATATATGTCCCG
411737 AAGGACCTCATATA
1 AAGGACCTCATATA
411751 ATCCCTCGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (21 bp):
AAGGACCTCATATATGTCCCG
Found at i:413578 original size:3 final size:3
Alignment explanation
Indices: 413559--413605 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
413549 TAATATGTAT
* *
413559 TAA TAA TTA TAA TTAA TAA TAA TAG TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
413604 TA
1 TA
413606 TTTTTGTAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:413843 original size:43 final size:40
Alignment explanation
Indices: 413774--413918 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 40
413764 GGACAACACT
* *
413774 GCTCATACGTGATGAAGAGTTCTGGTCGTCTAAGGGTGACATG
1 GCTCCTACGTGATGAGGAGTT-TGGTC-TCT-AGGGTGACATG
* *
413817 GCTCCTACGTGATGAGGAGATTTGGTCTGT-GGATGACATG
1 GCTCCTACGTGATGAGGAG-TTTGGTCTCTAGGGTGACATG
* * * * *
413857 GTTCCTACGCGATGAGGATGGTTGGTTATCTAGGGGTGACACG
1 GCTCCTACGTGATGAGGA-GTTTGG-TCTCTA-GGGTGACATG
413900 GCTCCTACGTGATGAGGAG
1 GCTCCTACGTGATGAGGAG
413919 GTCTGGTCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
40 29 0.35
41 4 0.05
42 3 0.04
43 46 0.55
44 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.35, T:0.28
Consensus pattern (40 bp):
GCTCCTACGTGATGAGGAGTTTGGTCTCTAGGGTGACATG
Found at i:413865 original size:40 final size:39
Alignment explanation
Indices: 413769--413957 Score: 128
Period size: 40 Copynumber: 4.6 Consensus size: 39
413759 GTCGGGGACA
* * * * *
413769 ACACTGCTCATACGTGATGAAGAGTTCTGGTCGTCTAAGGGTG
1 ACACGGCTCCTACGTGATGAGGAGTT-TGGTC-TGT--GGATG
*
413812 ACATGGCTCCTACGTGATGAGGAGATTTGGTCTGTGGATG
1 ACACGGCTCCTACGTGATGAGGAG-TTTGGTCTGTGGATG
* * * * *
413852 ACATGGTTCCTACGCGATGAGGATGGTTGGTTATCTAG-GGGTG
1 ACACGGCTCCTACGTGATGAGGA-GTTTGG---TCT-GTGGATG
* **
413895 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCAATGGATG
1 ACACGGCTCCTACGTGATGAGGA-GTTTGGTCTGTGGATG
* *
413935 AGACGGTTCCTACGTGATGAGGA
1 ACACGGCTCCTACGTGATGAGGA
413958 TGGTAGGTCA
Statistics
Matches: 118, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
40 56 0.47
41 1 0.01
42 2 0.02
43 56 0.47
44 3 0.03
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (39 bp):
ACACGGCTCCTACGTGATGAGGAGTTTGGTCTGTGGATG
Done.