Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007802.1 Hibiscus syriacus cultivar Beakdansim tig00110120_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: 449556
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 3
Found at i:157699 original size:29 final size:29
Alignment explanation
Indices: 157671--157918 Score: 211
Period size: 29 Copynumber: 8.4 Consensus size: 29
157661 GTTATGGTGT
* * *
157671 TATTTTCGTAATTATTTTTAAAAGTGTGT
1 TATTTTGGTAATTATTGTTAAAAGTGTGA
* * *
157700 TATTTTCGT-ATTGATTTTTAAAAAAAG-GTGT
1 TATTTTGGTAATT-ATTGTT---AAAAGTGTGA
**
157731 TATTTTCATAATTAATT-TTAAAACG-GTGA
1 TATTTTGGTAATT-ATTGTTAAAA-GTGTGA
* **
157760 TATTTTGGCAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAAGTGTGA
* ***
157789 TATTTTGGCAATTATTGTTAAAACAATGA
1 TATTTTGGTAATTATTGTTAAAAGTGTGA
*
157818 TATTTTGGTAATTATTGTTAAAA-TGATGC
1 TATTTTGGTAATTATTGTTAAAAGTG-TGA
157847 TATTTTGGTAATTATTGTTAAAA-TGGTGA
1 TATTTTGGTAATTATTGTTAAAAGT-GTGA
**
157876 TATTTTGGTAATTATTGTTAAAAACAGTGA
1 TATTTTGGTAATTATTGTT-AAAAGTGTGA
157906 TATTTTGGTAATT
1 TATTTTGGTAATT
157919 GTTTAAAAAA
Statistics
Matches: 193, Mismatches: 14, Indels: 23
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.05
29 136 0.70
30 22 0.11
31 14 0.07
32 11 0.06
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAAGTGTGA
Found at i:157819 original size:58 final size:58
Alignment explanation
Indices: 157671--157918 Score: 261
Period size: 58 Copynumber: 4.2 Consensus size: 58
157661 GTTATGGTGT
* * * * * * *
157671 TATTTTCGTAATTATTTTTAAAA-GTGTGTTATTTTCGT-ATTGATTTTTAAAAAAAGGTGT
1 TATTTTGGTAATTATTGTTAAAACG-GTGATATTTTGGTAATT-ATTGTT-AAAACA-GTGA
** *
157731 TATTTTCATAATTAATT-TTAAAACGGTGATATTTTGGCAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATT-ATTGTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACAGTGA
* ** * *
157789 TATTTTGGCAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAAA-TGATGC
1 TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACAG-TGA
*
157847 TATTTTGGTAATTATTGTTAAAATGGTGATATTTTGGTAATTATTGTTAAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGTAATTATTGTT-AAAACAGTGA
157906 TATTTTGGTAATT
1 TATTTTGGTAATT
157919 GTTTAAAAAA
Statistics
Matches: 160, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
57 4 0.03
58 91 0.57
59 24 0.15
60 34 0.21
61 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (58 bp):
TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACAGTGA
Found at i:160830 original size:10 final size:10
Alignment explanation
Indices: 160815--160841 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
160805 ACGTGGGAAT
160815 AAAAGAAAGG
1 AAAAGAAAGG
160825 AAAAGAAAGG
1 AAAAGAAAGG
160835 AAAAGAA
1 AAAAGAA
160842 TTTTAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGG
Found at i:161234 original size:21 final size:22
Alignment explanation
Indices: 161191--161234 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
161181 TGTTGAACAC
*
161191 AAAATAAAAATAAAAAAGTAAT
1 AAAATAAAAATAAAAAAGAAAT
161213 AAAAT-AAAATAAAACAA-AAAT
1 AAAATAAAAATAAAA-AAGAAAT
161234 A
1 A
161235 GATCGGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAATAAAAATAAAAAAGAAAT
Found at i:162440 original size:13 final size:14
Alignment explanation
Indices: 162390--162440 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
162380 ACATAATAAT
162390 AATA-ATAATAATTA
1 AATATATAA-AATTA
*
162404 AATATATTAAAAATA
1 AATATA-TAAAATTA
*
162419 AACATATAAAATTA
1 AATATATAAAATTA
162433 AATA-ATAA
1 AATATATAA
162441 CTAAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
15 10 0.32
16 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AATATATAAAATTA
Found at i:163858 original size:8 final size:7
Alignment explanation
Indices: 163844--163926 Score: 70
Period size: 6 Copynumber: 12.1 Consensus size: 7
163834 ATATGTAATG
163844 ATAATAA
1 ATAATAA
163851 ATTAAT-A
1 A-TAATAA
163858 ATAA-AA
1 ATAATAA
163864 ATAATAA
1 ATAATAA
163871 TATAAT-A
1 -ATAATAA
163878 ATAATAA
1 ATAATAA
*
163885 ACAAATAAA
1 A-TAAT-AA
163894 ATAATAA
1 ATAATAA
163901 A-AATAA
1 ATAATAA
163907 A-AATAA
1 ATAATAA
163913 A-AATAA
1 ATAATAA
*
163919 AAAATAA
1 ATAATAA
163926 A
1 A
163927 ATGAAAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
6 31 0.47
7 17 0.26
8 15 0.23
9 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (7 bp):
ATAATAA
Found at i:163859 original size:3 final size:3
Alignment explanation
Indices: 163839--163918 Score: 62
Period size: 3 Copynumber: 28.0 Consensus size: 3
163829 CAGTAATATG
* * *
163839 TAA TGA TAA TAA -AT TAA TAA TAA AAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
163885 -ACA -AA TAA -AA TAA TAA AAA TAA AAA TAA AAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
163919 AAAATAAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
2 7 0.12
3 53 0.88
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:163884 original size:34 final size:32
Alignment explanation
Indices: 163839--163927 Score: 92
Period size: 34 Copynumber: 2.8 Consensus size: 32
163829 CAGTAATATG
* *
163839 TAATGATAATAAATTAATAATAAAAATAATAATA
1 TAATAATAATAAATAAATAATAAAAATAA-AA-A
* *
163873 TAATAATAATAAACAAATAA-AATAATAAAAA
1 TAATAATAATAAATAAATAATAAAAATAAAAA
* *
163904 TAAAAATAA-AAATAAAAAATAAAA
1 TAATAATAATAAATAAATAATAAAA
163928 TGAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
30 8 0.17
31 12 0.26
32 2 0.04
33 7 0.15
34 17 0.37
ACGTcount: A:0.73, C:0.01, G:0.01, T:0.25
Consensus pattern (32 bp):
TAATAATAATAAATAAATAATAAAAATAAAAA
Found at i:163933 original size:25 final size:24
Alignment explanation
Indices: 163846--163934 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 24
163836 ATGTAATGAT
* *
163846 AATAAATTAATAATAAAAATAATAA
1 AATAAAATAAAAATAAAAATAA-AA
* * *
163871 TATAATAATAATAA-ACAAATAAAA
1 AATAA-AATAAAAATAAAAATAAAA
163895 TAATAAAAATAAAAATAAAAATAAAA
1 -AAT-AAAATAAAAATAAAAATAAAA
163921 AATAAAATGAAAAA
1 AATAAAAT-AAAAA
163935 AAACTAGTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
24 7 0.13
25 28 0.53
26 18 0.34
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (24 bp):
AATAAAATAAAAATAAAAATAAAA
Found at i:163935 original size:13 final size:13
Alignment explanation
Indices: 163857--163927 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
163847 ATAAATTAAT
163857 AATAAAAATAATAA
1 AATAAAAATAA-AA
* * *
163871 TATAATAAT-AAT
1 AATAAAAATAAAA
*
163883 AA-ACAAATAAAA
1 AATAAAAATAAAA
163895 TAATAAAAAT-AAA
1 -AATAAAAATAAAA
163908 AATAAAAATAAAA
1 AATAAAAATAAAA
163921 AATAAAA
1 AATAAAA
163928 TGAAAAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
11 4 0.09
12 13 0.29
13 16 0.36
14 12 0.27
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAAATAAAA
Found at i:164431 original size:123 final size:114
Alignment explanation
Indices: 164283--165065 Score: 696
Period size: 112 Copynumber: 6.8 Consensus size: 114
164273 AAATTAAGGC
** *
164283 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTAATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
164347 TGAACTCCT-TGTGGAAATGTTGATGCTAACCTATCTCCTTCTGTGATAGAGTTACA-CAA
66 TGAACT-CTAT-TGGCAATGTTGAT--T--CCTA--T-C-TCAGTGAT-GAATT-CAGCAA
* * * *
164406 AAGGTTGAACAAGCTCTTCTTATTATGAACTTCATCTTCC-TGTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* ** * * ** *
164470 TGAACTTTCTCTTGAAAATTGTATG-TTGATCTATCTCTTTCTGTGAT-AGCGTCGAGAAA
66 TGAAC--TCTATTGGCAA-TGT-TGATT--CCTA--TC--TCAGTGATGA-ATTC-AGCAA
* *
164529 AAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
164593 TGAACTTTCT-TTAGCAATGTTGATT--TATCT-AGTGATGAATTCGAGCAA
66 TGAAC--TCTATTGGCAATGTTGATTCCTATCTCAGTGATGAATTC-AGCAA
* * *
164641 AAAGTTGAACAAGCTCTTCTCATTATGAACTTATTC-TCCTTATTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
164705 TGAACTCTACCTGGCAAT-TTGA-TCC-ATC-GAGTGATGAATTTGAGCAA
66 TGAACTCTA-TTGGCAATGTTGATTCCTATCTCAGTGATGAA-TTCAGCAA
*
164752 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
164817 TGAACTCTACCTGGCAATGCTGA-TCC-ATC-AAGTGATGAATTCGAGCAA
66 TGAACTCTA-TTGGCAATGTTGATTCCTATCTCAGTGATGAATTC-AGCAA
* *
164865 AAGGTTGAACAAGTTCTTCTCATTATGAACTTATTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
164929 TGAACTCTACCCTGGCTATGCTGA-TCC-ATC-GAGTGATGAATTCGAGCAA
66 TGAACTCTA--TTGGCAATGTTGATTCCTATCTCAGTGATGAATTC-AGCAA
* * * *
164978 AAGGTTGAAGAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
165043 TGAACTTCT-CTGGAAATGTTGAT
66 TGAAC-TCTATTGGCAATGTTGAT
165066 CCATTGAGTG
Statistics
Matches: 587, Mismatches: 47, Indels: 62
0.84 0.07 0.09
Matches are distributed among these distances:
110 4 0.01
111 57 0.10
112 174 0.30
113 131 0.22
114 31 0.05
115 5 0.01
117 2 0.00
120 2 0.00
121 7 0.01
122 7 0.01
123 149 0.25
124 10 0.02
125 6 0.01
126 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (114 bp):
AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTATTGGCAATGTTGATTCCTATCTCAGTGATGAATTCAGCAA
Found at i:164883 original size:113 final size:113
Alignment explanation
Indices: 164521--165078 Score: 815
Period size: 112 Copynumber: 5.0 Consensus size: 113
164511 TGTGATAGCG
* * * *
164521 TCGAGAAAAAGGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * ** *
164585 TCTCATTATGAACT-TTCTTTAGCAATGTTGATTTATCTAGTGATGAAT
66 TCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCGAGTGATGAAT
* * * *
164633 TCGAGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTATTC-TCCTTATTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
164697 TCTCATTATGAACTCTACCTGGCAAT-TTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
*
164744 TTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
164809 TCTCATTATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAAT
66 TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
*
164857 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTC-TCCTTCTTCAGATGAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
164921 TCTCATTATGAACTCTACCCTGGCTATGCTGATCCATCGAGTGATGAAT
66 TCTCATTATGAACTCTA-CCTGGCAATGTTGATCCATCGAGTGATGAAT
* * *
164970 TCGAGCAAAAGGTTGAAGAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATAAGTTCT
1 TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
165035 TCTCATTATGAACT-T-CTCTGGAAATGTTGATCCATTGAGTGATG
66 TCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCGAGTGATG
165079 GATTTGAATC
Statistics
Matches: 408, Mismatches: 31, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
111 62 0.15
112 179 0.44
113 135 0.33
114 32 0.08
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (113 bp):
TCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACTCTACCTGGCAATGTTGATCCATCGAGTGATGAAT
Found at i:165487 original size:22 final size:22
Alignment explanation
Indices: 165437--165491 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
165427 AATAAGGCTT
* *
165437 TCATCTATAAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
*
165459 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATATA
165481 TCATCTTTGAA
1 TCATCTTTGAA
165492 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:165946 original size:54 final size:54
Alignment explanation
Indices: 165859--165966 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
165849 ATAATCACTG
* * *
165859 GTTCGTAAAACACTTAACAACACATTCATCATTTCTTGTGGCTTCTGCTCAGAT
1 GTTCATAAAACACTTAACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
* * *
165913 GTTCATAAAACATTTGACAACATATTCATCATTTCCTGTGGCTTCTGCCCAGAT
1 GTTCATAAAACACTTAACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
165967 TTCTTGTTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (54 bp):
GTTCATAAAACACTTAACAACACATTCATCATTTCCTGTGGCTTCTGCCCAGAT
Found at i:166294 original size:27 final size:27
Alignment explanation
Indices: 166256--166311 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
166246 GGTTCGTGGA
166256 ATTCTTGTTGTTGTAAATGAAACGCAC
1 ATTCTTGTTGTTGTAAATGAAACGCAC
166283 ATTCTTGTTGTTGTAAATGAAACGCAC
1 ATTCTTGTTGTTGTAAATGAAACGCAC
166310 AT
1 AT
166312 GATAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (27 bp):
ATTCTTGTTGTTGTAAATGAAACGCAC
Found at i:166927 original size:75 final size:75
Alignment explanation
Indices: 166799--166967 Score: 248
Period size: 75 Copynumber: 2.3 Consensus size: 75
166789 AATATGGATC
*
166799 TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTATGATT
*
166864 GAAAGGGGTT
66 GAAAGGGGCT
* *** *
166874 TTCAGCATGCCCCAGCATTGGCTAATACAAACATTCAAAATGTGTCAATATTCCTGATTATGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTATGATT
*
166939 GAAATGGGCT
66 GAAAGGGGCT
* *
166949 TTCAGCATGCTCCATCATT
1 TTCAGCATGCCCCAACATT
166968 TGCTTCTTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAACATTCAAAATACATCAACATTCCTGATTATGATT
GAAAGGGGCT
Found at i:170725 original size:8 final size:8
Alignment explanation
Indices: 170712--170741 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
170702 ATTAAGGGAT
170712 ATATATAC
1 ATATATAC
*
170720 ATATATAT
1 ATATATAC
170728 ATATATAC
1 ATATATAC
170736 ATATAT
1 ATATAT
170742 TTGCAAGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAC
Found at i:174330 original size:36 final size:36
Alignment explanation
Indices: 174270--174338 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
174260 TCTTACCATA
* *
174270 GAATGCTTTTGGTATCAATCTAACA-AGATCTTTTTG
1 GAATACTTTTGGTATCAATATAACAGA-ATCTTTTTG
*
174306 GAATACTTTTGGTATTAATATAACAGAATCTTT
1 GAATACTTTTGGTATCAATATAACAGAATCTTT
174339 GTGTGCATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGAATCTTTTTG
Found at i:175222 original size:22 final size:23
Alignment explanation
Indices: 175194--175236 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
175184 TTAATACTTG
*
175194 AAAATAAAATA-ATATTAATAAA
1 AAAATAAAATACATATAAATAAA
*
175216 AAAATAATATACATATAAATA
1 AAAATAAAATACATATAAATA
175237 TTATGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATAAAATACATATAAATAAA
Found at i:175245 original size:29 final size:29
Alignment explanation
Indices: 175204--175300 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
175194 AAAATAAAAT
175204 AATATTAAT-AAAAAAATAA-TATACATATA
1 AATATT-ATGAAAAAAATAAGTATA-ATATA
*
175233 AATATTATGAAAATAATAAGTAT-ATATA
1 AATATTATGAAAAAAATAAGTATAATATA
* * * *
175261 AAAATTTTGAAAAGAAAGAATTATAA-ATTA
1 AATATTATGAAAA-AAATAAGTATAATA-TA
175291 AATA-TATGAA
1 AATATTATGAA
175301 TTTCTAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 18 0.33
29 28 0.51
30 9 0.16
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (29 bp):
AATATTATGAAAAAAATAAGTATAATATA
Found at i:175259 original size:28 final size:26
Alignment explanation
Indices: 175216--175273 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
175206 TATTAATAAA
*
175216 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
175242 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
175270 AAAA
1 AAAA
175274 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:176175 original size:13 final size:14
Alignment explanation
Indices: 176125--176175 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
176115 ACATAATAAT
176125 AATA-ATAATAATTA
1 AATATATAA-AATTA
*
176139 AATATATTAAAAATA
1 AATATA-TAAAATTA
*
176154 AACATATAAAATTA
1 AATATATAAAATTA
176168 AATA-ATAA
1 AATATATAA
176176 CTAAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
15 10 0.32
16 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AATATATAAAATTA
Found at i:177535 original size:3 final size:3
Alignment explanation
Indices: 177527--177597 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
177517 CTGTAATATG
*
177527 TAA TAA TAA TAA -AT TAA TAA T-A TAA -AA -AA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
177570 TAA TAA TAA -ACA -AA TAA -AA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
177598 AAAACAAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
2 13 0.22
3 46 0.78
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:177546 original size:8 final size:8
Alignment explanation
Indices: 177531--177594 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
177521 AATATGTAAT
177531 AATAATAA
1 AATAATAA
*
177539 ATTAATAA
1 AATAATAA
*
177547 TATAA-AA
1 AATAATAA
177554 AATAATAA
1 AATAATAA
*
177562 TATAATAA
1 AATAATAA
177570 TAATAATAA
1 -AATAATAA
177579 ACA-AATAA
1 A-ATAATAA
177587 AATAATAA
1 AATAATAA
177595 TAAAAAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 7 0.15
8 31 0.67
9 8 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAATAA
Found at i:177559 original size:26 final size:27
Alignment explanation
Indices: 177528--177597 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
177518 TGTAATATGT
177528 AATAATAATAAATTAATAAT-ATAAA-A
1 AATAATAATAAA-TAATAATAATAAACA
177554 AATAATAATATAATAATAATAATAAACA
1 AATAATAATA-AATAATAATAATAAACA
177582 AATAA-AAT-AATAATAA
1 AATAATAATAAATAATAA
177598 AAAACAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
25 8 0.20
26 17 0.41
27 10 0.24
28 6 0.15
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (27 bp):
AATAATAATAAATAATAATAATAAACA
Found at i:177592 original size:19 final size:18
Alignment explanation
Indices: 177528--177607 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 18
177518 TGTAATATGT
*
177528 AATAATAATAAATTAATAA
1 AATAATAATAAA-AAATAA
* * *
177547 TATAAAAAATAATAATATAA
1 AAT-AATAATAA-AAAATAA
177567 TAATAATAATAAACAAATAA
1 -AATAATAATAAA-AAATAA
*
177587 AATAATAATAAAAAACAA
1 AATAATAATAAAAAATAA
177605 AAT
1 AAT
177608 GAAAAAAAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 8 0.16
19 15 0.31
20 23 0.47
21 3 0.06
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAATAATAAAAAATAA
Found at i:177597 original size:11 final size:11
Alignment explanation
Indices: 177528--177599 Score: 72
Period size: 11 Copynumber: 6.2 Consensus size: 11
177518 TGTAATATGT
177528 AATAATAATAA
1 AATAATAATAA
*
177539 ATTAATAATATA
1 AATAATAATA-A
*
177551 AAAAATAATAA
1 AATAATAATAA
*
177562 TATAATAATAA
1 AATAATAATAA
*
177573 TAATAAACAAATAA
1 -AAT-AA-TAATAA
177587 AATAATAATAA
1 AATAATAATAA
177598 AA
1 AA
177600 AACAAAATGA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
11 26 0.53
12 13 0.27
13 5 0.10
14 5 0.10
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:182953 original size:17 final size:18
Alignment explanation
Indices: 182917--182958 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
182907 GTTGTTTTTA
182917 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
182935 AAATAAAATA-AATAATT
1 AAATAAAAGATAAGAATT
182952 AAATAAA
1 AAATAAA
182959 TAATTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:184132 original size:19 final size:19
Alignment explanation
Indices: 184093--184146 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
184083 CTGCACATGT
*
184093 AGTTTCGAAACTTTTGAGAA
1 AGTTTC-AAAATTTTGAGAA
*
184113 AGTTTCAAAATTTTGTGAA
1 AGTTTCAAAATTTTGAGAA
*
184132 AGTATCAAAACTTTT
1 AGTTTCAAAA-TTTT
184147 AAACACACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (19 bp):
AGTTTCAAAATTTTGAGAA
Found at i:184211 original size:20 final size:20
Alignment explanation
Indices: 184162--184214 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
184152 CACTGTTCTT
*
184162 GAAAGTTTCAAAACTTTGAC
1 GAAAGTTTCGAAACTTTGAC
184182 GAAAGTTTCGAAACTTTGAC
1 GAAAGTTTCGAAACTTTGAC
184202 GAAAGTTTCGAAA
1 GAAAGTTTCGAAA
184215 GTTTCGAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (20 bp):
GAAAGTTTCGAAACTTTGAC
Found at i:184213 original size:9 final size:9
Alignment explanation
Indices: 184162--184223 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
184152 CACTGTTCTT
184162 GAAAGTTTC
1 GAAAGTTTC
* *
184171 AAAACTTTGAC
1 GAAAGTTT--C
184182 GAAAGTTTC
1 GAAAGTTTC
*
184191 GAAACTTTGAC
1 GAAAGTTT--C
184202 GAAAGTTTC
1 GAAAGTTTC
184211 GAAAGTTTC
1 GAAAGTTTC
184220 GAAA
1 GAAA
184224 CTCTTACTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 28 0.65
11 15 0.35
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (9 bp):
GAAAGTTTC
Found at i:184330 original size:19 final size:20
Alignment explanation
Indices: 184282--184336 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
184272 GTTCTAGGTG
*
184282 CAAAGTTTCGAAACTCTTAA
1 CAAAGTTTCCAAACTCTTAA
*
184302 TAAGAGTTTCCAAACTCTT-A
1 CAA-AGTTTCCAAACTCTTAA
184322 CAAAGTTTCCAAACT
1 CAAAGTTTCCAAACT
184337 ATGAACAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.39
20 5 0.16
21 14 0.45
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (20 bp):
CAAAGTTTCCAAACTCTTAA
Found at i:192154 original size:15 final size:15
Alignment explanation
Indices: 192136--192178 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
192126 ACAGCAACTC
192136 CCACAACAGCCTTAT
1 CCACAACAGCCTTAT
192151 CCACAACAGCCTTAT
1 CCACAACAGCCTTAT
*
192166 CCACAACATCCTT
1 CCACAACAGCCTT
192179 CTTCTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.33, C:0.42, G:0.05, T:0.21
Consensus pattern (15 bp):
CCACAACAGCCTTAT
Found at i:196318 original size:21 final size:20
Alignment explanation
Indices: 196254--196329 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
196244 TTCGGTTTGC
196254 AAAAAACCGG--TTTTTAAA
1 AAAAAACCGGTTTTTTTAAA
****
196272 AAAAAACCGGATTTTTTCGGT
1 AAAAAACCGG-TTTTTTTAAA
*
196293 TAAAAACCGGTTTTTTTAAAA
1 AAAAAACCGGTTTTTTT-AAA
196314 AAAAAACCGGTTTTTT
1 AAAAAACCGGTTTTTT
196330 ATCCGGATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
18 10 0.23
20 6 0.14
21 28 0.64
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (20 bp):
AAAAAACCGGTTTTTTTAAA
Found at i:196366 original size:24 final size:23
Alignment explanation
Indices: 196273--196358 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 23
196263 GTTTTTAAAA
* *
196273 AAAAACCGGATTTTT-T-CGGTT
1 AAAAACCGGTTTTTTATCCGGAT
*** *
196294 AAAAACCGGTTTTTT-T-AAAAA
1 AAAAACCGGTTTTTTATCCGGAT
196315 AAAAACCGGTTTTTTATCCGGAT
1 AAAAACCGGTTTTTTATCCGGAT
196338 AAAAACCGGTTTTTTATCCGG
1 AAAAACCGGTTTTTTATCCGG
196359 TTTGAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 30 0.57
22 1 0.02
23 22 0.42
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (23 bp):
AAAAACCGGTTTTTTATCCGGAT
Found at i:205343 original size:22 final size:24
Alignment explanation
Indices: 205303--205346 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
205293 TTAACAGAAT
205303 AATAGATGAAACGAGAAAGAAGAG
1 AATAGATGAAACGAGAAAGAAGAG
*
205327 AATAGAT-AAACTA-AAAGAAG
1 AATAGATGAAACGAGAAAGAAG
205347 CACCATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.61, C:0.05, G:0.23, T:0.11
Consensus pattern (24 bp):
AATAGATGAAACGAGAAAGAAGAG
Found at i:206051 original size:66 final size:66
Alignment explanation
Indices: 205970--206102 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
205960 TTTATCACAT
205970 CCATATTCAACTCTTTGATTTCTCTCTGCCAGTTTTTGATTTTGTTTCGTTTCCTCTGTCAAGAG
1 CCATATTCAACTCTTTGATTTCTCTCTGCCAGTTTTTGATTTTGTTTCGTTTCCTCTGTCAAGAG
206035 A
66 A
206036 CCATATTCAACTCTTTGATTTCTCTCTGCCAGTTTTTGATTTTGTTTCGTTTCCTCTGTCAAGAG
1 CCATATTCAACTCTTTGATTTCTCTCTGCCAGTTTTTGATTTTGTTTCGTTTCCTCTGTCAAGAG
206101 A
66 A
206102 C
1 C
206103 GTATTTCTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.47
Consensus pattern (66 bp):
CCATATTCAACTCTTTGATTTCTCTCTGCCAGTTTTTGATTTTGTTTCGTTTCCTCTGTCAAGAG
A
Found at i:212013 original size:24 final size:25
Alignment explanation
Indices: 211968--212016 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
211958 AATTTCCTTA
* *
211968 ATTATTCTATATCTTTAAGAAAATT
1 ATTAATCTATATCCTTAAGAAAATT
211993 ATTAATCTA-ATCCTTAAGAAAATT
1 ATTAATCTATATCCTTAAGAAAATT
212017 TACGTGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (25 bp):
ATTAATCTATATCCTTAAGAAAATT
Found at i:214591 original size:31 final size:31
Alignment explanation
Indices: 214554--214623 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
214544 AGTTTCAAAA
* *
214554 GTAACAAAATAGTCACTAATGTTATTAGTTT
1 GTAACAAAATAGTCACTAATGTTATCAATTT
*
214585 GTAACAAAATGGTCACTAATGTTATCAATTT
1 GTAACAAAATAGTCACTAATGTTATCAATTT
214616 GTAACAAA
1 GTAACAAA
214624 CTGATCACTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.34
Consensus pattern (31 bp):
GTAACAAAATAGTCACTAATGTTATCAATTT
Found at i:214632 original size:31 final size:31
Alignment explanation
Indices: 214554--214632 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
214544 AGTTTCAAAA
* *
214554 GTAACAAAAT-AGTCACTAATGTTATTAGTTT
1 GTAACAAAATGA-TCACTAATGTTATCAATTT
*
214585 GTAACAAAATGGTCACTAATGTTATCAATTT
1 GTAACAAAATGATCACTAATGTTATCAATTT
*
214616 GTAACAAACTGATCACT
1 GTAACAAAATGATCACT
214633 CCACCATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (31 bp):
GTAACAAAATGATCACTAATGTTATCAATTT
Found at i:215300 original size:31 final size:31
Alignment explanation
Indices: 215233--215304 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
215223 GTGGAGTGAT
* * * *
215233 AATTTTCTTATAAATCGATAACGTTAGTGAC
1 AATTTTGTTAAAAATCGATAACGTTACTAAC
*
215264 AATTTTGTTAAAAATCGATAATGTTACTAAC
1 AATTTTGTTAAAAATCGATAACGTTACTAAC
*
215295 CATTTTGTTA
1 AATTTTGTTA
215305 CTTTTGAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (31 bp):
AATTTTGTTAAAAATCGATAACGTTACTAAC
Found at i:219856 original size:12 final size:12
Alignment explanation
Indices: 219839--219877 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
219829 ACAACCCGAC
*
219839 CCGACCTGTTGA
1 CCGACCCGTTGA
219851 CCGACCCGTTGA
1 CCGACCCGTTGA
*
219863 CCCCACCCGTTGA
1 -CCGACCCGTTGA
219876 CC
1 CC
219878 CGTTGACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.15, C:0.46, G:0.21, T:0.18
Consensus pattern (12 bp):
CCGACCCGTTGA
Found at i:219870 original size:13 final size:13
Alignment explanation
Indices: 219836--219879 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
219826 GTCACAACCC
*
219836 GACCCGACCTGTT
1 GACCCGACCCGTT
219849 GA-CCGACCCGTT
1 GACCCGACCCGTT
*
219861 GACCCCACCCGTT
1 GACCCGACCCGTT
219874 GACCCG
1 GACCCG
219880 TTGACTGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 11 0.41
13 16 0.59
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:221224 original size:18 final size:18
Alignment explanation
Indices: 221198--221232 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
221188 TCAAAAGGAC
*
221198 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
221216 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
221233 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:222362 original size:24 final size:24
Alignment explanation
Indices: 222335--222396 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
222325 GATACGTTAC
* *
222335 CTGAATTCTGATCTGGATTCTGTT
1 CTGAATTCTGATATGAATTCTGTT
222359 CTG-ATATCTGATATGAATTCTGTT
1 CTGAAT-TCTGATATGAATTCTGTT
* *
222383 TTGATTTCTGATAT
1 CTGAATTCTGATAT
222397 CTCCGTTTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (24 bp):
CTGAATTCTGATATGAATTCTGTT
Found at i:224962 original size:64 final size:64
Alignment explanation
Indices: 224824--224984 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
224814 ATTGTTCAAG
* * * *
224824 GTGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAAATAAAAACATTGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
* * ** *
224888 GTGTATCGATGCACAAGTAGTGCATCAATGCACTCGC-TTAAAATATAAACATCGAATGGGATTT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACTC-CTTTAAAATAAAAACATCGAATGCCA-TC
224952 A
64 A
* *
224953 -TGTACCGATGCA-TAGATAGTGCATCGATGCAC
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCAC
224985 CCGTCAAGGG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.02
64 77 0.94
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
Found at i:225581 original size:18 final size:18
Alignment explanation
Indices: 225558--225592 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
225548 AGGGATTATC
*
225558 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
225576 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
225593 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:231870 original size:63 final size:63
Alignment explanation
Indices: 231740--231858 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
231730 TTGTTCAAGT
* * *
231740 TGTATCGATGCACATGAAGTGTATCGATGCACTCCTTTAAATAAAAACATCGAATGCCATCAG
1 TGTATCGATGCACAAGAAGTGCATCGATGCACTCCTTTAAATAAAAACATCAAATGCCATCAG
* * *
231803 TGTATCGATGCACAAGTAGTGCATCGATGCACCTGC-TTAAATACAAACATCAAATG
1 TGTATCGATGCACAAGAAGTGCATCGATGCA-CTCCTTTAAATAAAAACATCAAATG
231859 GGATTTATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 46 0.94
64 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (63 bp):
TGTATCGATGCACAAGAAGTGCATCGATGCACTCCTTTAAATAAAAACATCAAATGCCATCAG
Found at i:233353 original size:3 final size:3
Alignment explanation
Indices: 233347--233382 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
233337 GATGATGATG
233347 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
233383 TATTAAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:251477 original size:21 final size:21
Alignment explanation
Indices: 251453--251492 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
251443 ATGTTTAATG
251453 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
251474 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
251493 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:254654 original size:23 final size:20
Alignment explanation
Indices: 254601--254658 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
254591 TCGAAATAGA
254601 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTACATG
*
254621 GTGCATCGATGCACTAGTGGCAT-
1 GTGCATGGATGCACTA----CATG
254644 GTGCATGGATGCACT
1 GTGCATGGATGCACT
254659 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 15 0.47
23 14 0.44
24 3 0.09
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (20 bp):
GTGCATGGATGCACTACATG
Found at i:255316 original size:23 final size:23
Alignment explanation
Indices: 255290--255334 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
255280 CACCACAGCT
*
255290 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
255313 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
255335 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:255583 original size:149 final size:149
Alignment explanation
Indices: 255313--255616 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
255303 CGAAGTGCCC
*
255313 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
255378 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
255443 CATATGTCCCAAAGAACTG
131 CATATGTCCCAAAGAACCG
255462 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
255527 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
255592 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
255611 CGTAGA
1 CGTAGA
255617 CCCTCTACCA
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:256121 original size:21 final size:21
Alignment explanation
Indices: 256095--256135 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
256085 TTTTTTCTCA
* *
256095 TGGGGGAATTGGTTCCCCCCC
1 TGGGGGAATCGATTCCCCCCC
*
256116 TGGGGGTATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
256136 TAGCATTCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.34, G:0.32, T:0.24
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCCCC
Found at i:256206 original size:67 final size:67
Alignment explanation
Indices: 256096--256247 Score: 259
Period size: 67 Copynumber: 2.3 Consensus size: 67
256086 TTTTTCTCAT
* * *
256096 GGGGGAATTGGTTCCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAATTTCATATTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGT
256161 TGA
65 TGA
*
256164 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
256229 GA
66 GA
256231 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
256248 TTGAATGGGT
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
67 69 0.86
68 11 0.14
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
GA
Found at i:259011 original size:15 final size:15
Alignment explanation
Indices: 258988--259021 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
258978 AACTTTTATT
*
258988 ATTATTTTGTAATAA
1 ATTAGTTTGTAATAA
259003 ATTAGTTTGTAATAA
1 ATTAGTTTGTAATAA
259018 ATTA
1 ATTA
259022 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
ATTAGTTTGTAATAA
Found at i:259500 original size:2 final size:2
Alignment explanation
Indices: 259493--259525 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
259483 ATCTCTAAAC
259493 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
259526 TGCTTAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:259523 original size:60 final size:60
Alignment explanation
Indices: 259404--259526 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
259394 TTTAAGCCCA
* * * * *
259404 TATTTTTTTGTCAAAATAAATATTTAAATTATAAAATATAATTATTTTAAATATTTATAT
1 TATTTGTTTGTCAAAATAAATATCTAAACTATAAAATATAATTATTATAAATATATATAT
* * *
259464 TATTTGTTTGTCAAAATAAATCTCTAAACTAT-ATATATATATATATATATATATATATATAT
1 TATTTGTTTGTCAAAATAAATATCTAAACTATAAAATATA-AT-TAT-TATAAATATATATAT
259526 T
1 T
259527 GCTTAGTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
59 6 0.12
60 30 0.58
61 3 0.06
62 13 0.25
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (60 bp):
TATTTGTTTGTCAAAATAAATATCTAAACTATAAAATATAATTATTATAAATATATATAT
Found at i:267772 original size:28 final size:28
Alignment explanation
Indices: 267732--267789 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
267722 TTGCACTTAA
*
267732 GAATGTTTTCAATTGGCTTGTGTAATTG
1 GAATGCTTTCAATTGGCTTGTGTAATTG
267760 GAATGCTTTCAATTGGCTTGTGTAATTG
1 GAATGCTTTCAATTGGCTTGTGTAATTG
267788 GA
1 GA
267790 TTATATCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (28 bp):
GAATGCTTTCAATTGGCTTGTGTAATTG
Found at i:270530 original size:23 final size:23
Alignment explanation
Indices: 270504--270548 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
270494 TTTAATATGG
270504 ATTTATGA-ATATATGTTTATAAT
1 ATTT-TGATATATATGTTTATAAT
* *
270527 ATTTTGATTTATATTTTTATAA
1 ATTTTGATATATATGTTTATAA
270549 AATAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTTGATATATATGTTTATAAT
Found at i:273559 original size:19 final size:17
Alignment explanation
Indices: 273535--273573 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
273525 AGCAATGTTG
273535 TTTTAATAAAATTATTATT
1 TTTTAAT-AAATTATT-TT
*
273554 TTTTAATTAATTATTTT
1 TTTTAATAAATTATTTT
273571 TTT
1 TTT
273574 AATTTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 7 0.37
19 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATAAATTATTTT
Found at i:273565 original size:18 final size:16
Alignment explanation
Indices: 273544--273577 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
273534 GTTTTAATAA
273544 AATT-ATTA-TTTTTT
1 AATTAATTATTTTTTT
273558 AATTAATTATTTTTTT
1 AATTAATTATTTTTTT
273574 AATT
1 AATT
273578 TAACTCGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTAATTATTTTTTT
Found at i:277807 original size:11 final size:11
Alignment explanation
Indices: 277785--277814 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
277775 AATCCCATGA
277785 AAAGAA-AAAT
1 AAAGAAGAAAT
277795 AAAGAAGAAAT
1 AAAGAAGAAAT
277806 AAAGAAGAA
1 AAAGAAGAA
277815 TATCGTGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (11 bp):
AAAGAAGAAAT
Found at i:279095 original size:16 final size:17
Alignment explanation
Indices: 279074--279105 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
279064 TTTATCTGTA
279074 TAAATGTCAT-GAAAAG
1 TAAATGTCATGGAAAAG
279090 TAAATGTCATGGAAAA
1 TAAATGTCATGGAAAA
279106 CTTGACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
TAAATGTCATGGAAAAG
Found at i:279560 original size:19 final size:19
Alignment explanation
Indices: 279536--279572 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
279526 AGTAAATGCT
*
279536 AAAATAAAGGAATAAAATA
1 AAAATAAAGGAAAAAAATA
279555 AAAATAAAGGAAAAAAAT
1 AAAATAAAGGAAAAAAAT
279573 TCAACAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.14
Consensus pattern (19 bp):
AAAATAAAGGAAAAAAATA
Found at i:280116 original size:154 final size:154
Alignment explanation
Indices: 279831--280138 Score: 607
Period size: 154 Copynumber: 2.0 Consensus size: 154
279821 CTTGTTGAAT
279831 TATATTTTGATATAACAATTTAAGGAAAAATGTTTTTGGACTTGAATTGAATTTATTCAAAGTTT
1 TATATTTTGATATAACAATTTAAGGAAAAATGTTTTTGGACTTGAATTGAATTTATTCAAAGTTT
*
279896 TCAAAAATAATTCAAAGTCCTTAAAAGTTTGGAATTAAGCACAAAATAATTTTCTGTACAATTAG
66 TCAAAAATAATTCAAAGTCCTTAAAAGTTTGGAATTAAGCACAAAATAATTTTCTGTACAAGTAG
279961 TACCGATACTGTTCCTACAATATC
131 TACCGATACTGTTCCTACAATATC
279985 TATATTTTGATATAACAATTTAAGGAAAAATGTTTTTGGACTTGAATTGAATTTATTCAAAGTTT
1 TATATTTTGATATAACAATTTAAGGAAAAATGTTTTTGGACTTGAATTGAATTTATTCAAAGTTT
280050 TCAAAAATAATTCAAAGTCCTTAAAAGTTTGGAATTAAGCACAAAATAATTTTCTGTACAAGTAG
66 TCAAAAATAATTCAAAGTCCTTAAAAGTTTGGAATTAAGCACAAAATAATTTTCTGTACAAGTAG
280115 TACCGATACTGTTCCTACAATATC
131 TACCGATACTGTTCCTACAATATC
280139 GATACCAATT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (154 bp):
TATATTTTGATATAACAATTTAAGGAAAAATGTTTTTGGACTTGAATTGAATTTATTCAAAGTTT
TCAAAAATAATTCAAAGTCCTTAAAAGTTTGGAATTAAGCACAAAATAATTTTCTGTACAAGTAG
TACCGATACTGTTCCTACAATATC
Found at i:280239 original size:65 final size:65
Alignment explanation
Indices: 280135--280274 Score: 253
Period size: 65 Copynumber: 2.2 Consensus size: 65
280125 GTTCCTACAA
* *
280135 TATCGATACCAATTGAACAAGTATCGATACTGTTCATATGATATCGATATCAAAGGTAAGGGAAG
1 TATCGATACTAATTGAACAAGTACCGATACTGTTCATATGATATCGATATCAAAGGTAAGGGAAG
280200 TATCGATACTAATTGAACAAGTACCGATACTGTTCATATGATATCGATATCAAAGGTAAGGGAAG
1 TATCGATACTAATTGAACAAGTACCGATACTGTTCATATGATATCGATATCAAAGGTAAGGGAAG
*
280265 TATCAATACT
1 TATCGATACT
280275 CACTAGGTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 72 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (65 bp):
TATCGATACTAATTGAACAAGTACCGATACTGTTCATATGATATCGATATCAAAGGTAAGGGAAG
Found at i:285949 original size:20 final size:22
Alignment explanation
Indices: 285924--285981 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
285914 TTCCCCTTGA
285924 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
285944 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
285967 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
285982 CTACTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:286047 original size:64 final size:62
Alignment explanation
Indices: 285969--286109 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 62
285959 TCTTTAACAT
* *
285969 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTATTAAAGA
* * * * *
286032 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCATTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTT-ATTAAAGA
286096 GTGCATCGATGCAC
1 GTGCATCGATGCAC
286110 ATTTAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 2 0.03
63 18 0.26
64 48 0.71
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTATTAAAGA
Found at i:289474 original size:30 final size:30
Alignment explanation
Indices: 289440--289512 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
289430 CCTGAAGGAC
289440 CTATCCAAAGGTCATAAAGATCATCGGTAA
1 CTATCCAAAGGTCATAAAGATCATCGGTAA
* *
289470 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAAAGGTCATAAAGATCATCGGTAA
*
289500 CTATCCATAGGTC
1 CTATCCAAAGGTC
289513 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAAAGGTCATAAAGATCATCGGTAA
Found at i:289529 original size:30 final size:30
Alignment explanation
Indices: 289440--289539 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
289430 CCTGAAGGAC
* * * * *
289440 CTATCCAAAGGTCATAAAGATCATCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* * * *
289470 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* *
289500 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGAACCTAGGT-AA
289531 CTATCCATA
1 CTATCCATA
289540 TGTTCCTTAG
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
30 50 0.82
31 11 0.18
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTAGGTAA
Found at i:289552 original size:31 final size:31
Alignment explanation
Indices: 289498--289590 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
289488 GATCCTCGGT
* *
289498 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
289529 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * * *
289560 TACTGTTCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
289591 GACCCTCGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:290332 original size:24 final size:20
Alignment explanation
Indices: 290278--290315 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
290268 TTCCCCTTGA
290278 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
290298 AATGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
290316 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:290407 original size:64 final size:62
Alignment explanation
Indices: 290323--290463 Score: 176
Period size: 64 Copynumber: 2.2 Consensus size: 62
290313 TCTTTAACAT
* * *
290323 GTGCATCGATACACTACTTATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTAAAGG
1 GTGCATCGATGCACTACTTATGCATCGATACACAAATTACATTCGATG-TTTC-TTATTAAAGA
* * * *
290386 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCATTAAAGA
1 G-TGCATCGATGCACTACTTATGCATCGATACACAAATTACATTCGATGTTTCTT-ATTAAAGA
290450 GTGCATCGATGCAC
1 GTGCATCGATGCAC
290464 ATTTAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
62 2 0.03
63 18 0.26
64 48 0.71
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (62 bp):
GTGCATCGATGCACTACTTATGCATCGATACACAAATTACATTCGATGTTTCTTATTAAAGA
Found at i:290951 original size:3 final size:3
Alignment explanation
Indices: 290943--290968 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
290933 GCTTACGGGG
290943 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
290969 GAAATAAGCT
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:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:293837 original size:30 final size:30
Alignment explanation
Indices: 293803--293875 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
293793 CCTGAAGGAC
293803 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
293833 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
293863 CTGTCCATAGGTC
1 CTATCCAGAGGTC
293876 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:293892 original size:30 final size:30
Alignment explanation
Indices: 293849--293942 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
293839 AGAGGTCATA
* * *
293849 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * *
293879 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
293910 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
293941 AA
1 AA
293943 AGACATAGGT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 11 0.22
31 38 0.78
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:293949 original size:31 final size:30
Alignment explanation
Indices: 293858--293953 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
293848 AAAGATCCTC
* * *
293858 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
293888 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
293919 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
293950 GGTA
1 GGTA
293954 GACTCTCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:294669 original size:20 final size:20
Alignment explanation
Indices: 294644--294681 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
294634 TTCCCCTTGA
294644 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAT
294664 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
294682 TTAACATGTG
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:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAT
Found at i:294697 original size:24 final size:20
Alignment explanation
Indices: 294644--294701 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
294634 TTCCCCTTGA
*
294644 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
294664 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
294687 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
294702 CTACTCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:295314 original size:3 final size:3
Alignment explanation
Indices: 295306--295336 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
295296 GCTTACGGGG
295306 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
295337 AAATAAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:296055 original size:11 final size:11
Alignment explanation
Indices: 296033--296062 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
296023 AATCCCATGA
296033 AAAGAA-AAAT
1 AAAGAAGAAAT
296043 AAAGAAGAAAT
1 AAAGAAGAAAT
296054 AAAGAAGAA
1 AAAGAAGAA
296063 GAAGAAGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.32
11 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (11 bp):
AAAGAAGAAAT
Found at i:296224 original size:27 final size:25
Alignment explanation
Indices: 296180--296254 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 25
296170 TTTTTATTCC
*
296180 AATAAAAGAGCTATTAAATTTCTTCTA
1 AATAAAAGAG-TAATAAATTTCTT-TA
* * *
296207 AATAAAAGATGTAATAAATCTATTTT
1 AATAAAAGA-GTAATAAATTTCTTTA
296233 AATAAAAGA--AATAAATTTCTTT
1 AATAAAAGAGTAATAAATTTCTTT
296255 TTATCTTTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
23 11 0.27
26 10 0.24
27 19 0.46
28 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (25 bp):
AATAAAAGAGTAATAAATTTCTTTA
Found at i:298981 original size:64 final size:64
Alignment explanation
Indices: 298880--299004 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 64
298870 TTTTTTTTTT
* * *
298880 CATTTAGGATTAGGGTGGTTTTTAATGAGGTCCTCGAGGTGGTGTACTTTGTAATCGTTCTATC
1 CATTTAGGATTAGGGAGGTTTTTAATGAGGTCCTCGAGATGATGTACTTTGTAATCGTTCTATC
*
298944 CATTTAGGATTATGGAGGTTTTTAATGAGGTCCTCGAGATGATGTACTTTGTAATCGTTCT
1 CATTTAGGATTAGGGAGGTTTTTAATGAGGTCCTCGAGATGATGTACTTTGTAATCGTTCT
299005 TAATACAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (64 bp):
CATTTAGGATTAGGGAGGTTTTTAATGAGGTCCTCGAGATGATGTACTTTGTAATCGTTCTATC
Found at i:307477 original size:27 final size:27
Alignment explanation
Indices: 307442--307500 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
307432 ACCAAGAAAG
307442 AAAGT-TTCTACTGATTCTGTCAGTTT
1 AAAGTCTTCTACTGATTCTGTCAGTTT
307468 AAAGTCTTCTACTGATTCTGTCAGTTT
1 AAAGTCTTCTACTGATTCTGTCAGTTT
307495 AAAGTC
1 AAAGTC
307501 ATTCAGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (27 bp):
AAAGTCTTCTACTGATTCTGTCAGTTT
Found at i:316668 original size:14 final size:14
Alignment explanation
Indices: 316627--316699 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 14
316617 CAGAGAGTTC
*
316627 GTTCGTTCGTTCAT
1 GTTCGTTCGTTTAT
* *
316641 -TTATGTTTGTTTAT
1 GTT-CGTTCGTTTAT
316655 GTTCGTTCGTTTAT
1 GTTCGTTCGTTTAT
*
316669 GTTTGTTCGTTTAT
1 GTTCGTTCGTTTAT
* *
316683 GTGCGTTCATTTAT
1 GTTCGTTCGTTTAT
316697 GTT
1 GTT
316700 TAGCCTGATC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
13 2 0.04
14 43 0.91
15 2 0.04
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.59
Consensus pattern (14 bp):
GTTCGTTCGTTTAT
Found at i:316675 original size:28 final size:28
Alignment explanation
Indices: 316627--316700 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
316617 CAGAGAGTTC
* *
316627 GTTCGTTCGTTCAT-TTATGTTTGTTTAT
1 GTTCGTTCGTTTATGTT-TGTTCGTTTAT
316655 GTTCGTTCGTTTATGTTTGTTCGTTTAT
1 GTTCGTTCGTTTATGTTTGTTCGTTTAT
* *
316683 GTGCGTTCATTTATGTTT
1 GTTCGTTCGTTTATGTTT
316701 AGCCTGATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.09, C:0.11, G:0.20, T:0.59
Consensus pattern (28 bp):
GTTCGTTCGTTTATGTTTGTTCGTTTAT
Found at i:316948 original size:23 final size:23
Alignment explanation
Indices: 316901--316948 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
316891 TTTATATTTA
* * *
316901 TTTATTGTTTTCGTTTACGTTCG
1 TTTATTGTGTTCGTTTACATCCG
316924 TTTATTGTGTTCGTTTACATCCG
1 TTTATTGTGTTCGTTTACATCCG
316947 TT
1 TT
316949 CGTTTACGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.17, T:0.58
Consensus pattern (23 bp):
TTTATTGTGTTCGTTTACATCCG
Found at i:317763 original size:2 final size:2
Alignment explanation
Indices: 317756--317806 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
317746 ATCTTGTCCC
317756 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
317798 TA TA TA TA T
1 TA TA TA TA T
317807 TGAAGTTAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:318766 original size:185 final size:181
Alignment explanation
Indices: 318389--318775 Score: 591
Period size: 185 Copynumber: 2.1 Consensus size: 181
318379 TTTTCTAATT
* *
318389 TATATAA-AAATTAAATATTTTTTAATTAAAAAACAGTTTCTAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATA-TTTTTAATTAAAAAACAGTTTCTAATTAATTTAAATAATATATAAT
*
318453 TATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTAATTTAGGTTTAAAAGTTATTG
65 TATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTG
* * * *
318518 GATCTAAATTATTAATTAGATTTTAAATGGTTTGTGCTAAGCCCATATGTTG
130 AATCTAAATTATTAATTAGATTTTAAATAGTTTGAGCTAAGCCCATATGTTA
*
318570 TATATAATATATTTAATATTTTTAATTCAAAAAAATAGTTTAC-AATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTAATT--AAAAAACAGTTT-CTAATTAATTTAAATAATATATA
* *
318634 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTA
63 ATTATAAAATAAAAATTTTATATAAA-ATTTTAATTAATTAATATTAATTTAGGTTTAAAAATTA
*
318699 TTGAATCTTAAATTATTAATT-GAGTTTTAAATAGTTTGAGTTAAGCCCATATGTTA
127 TTGAATC-TAAATTATTAATTAGA-TTTTAAATAGTTTGAGCTAAGCCCATATGTTA
318755 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
318776 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
181 16 0.09
182 8 0.04
183 58 0.31
184 44 0.23
185 62 0.33
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (181 bp):
TATATAATATATTTAATATTTTTAATTAAAAAACAGTTTCTAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTAATTTAGGTTTAAAAATTATTGA
ATCTAAATTATTAATTAGATTTTAAATAGTTTGAGCTAAGCCCATATGTTA
Found at i:326615 original size:64 final size:65
Alignment explanation
Indices: 326542--326669 Score: 204
Period size: 65 Copynumber: 2.0 Consensus size: 65
326532 TATCTTTTTA
* * * *
326542 TGCTATGCAT-GGAAAGATTAGCACAAGTCATTCAAAGGAGTTTTAGGAATCAAGGATGAAAATT
1 TGCTATGCATGGGAAAGACTAGCACAAGCCATTCAAAGGAGTATTACGAATCAAGGATGAAAATT
*
326606 TGCTATGCATGGGAAAGACTAGCACAAGCCATTCAAAGGAGTATTACGAATCAAGGATGGAAAT
1 TGCTATGCATGGGAAAGACTAGCACAAGCCATTCAAAGGAGTATTACGAATCAAGGATGAAAAT
326670 CAGTTCACCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 10 0.17
65 48 0.83
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.23
Consensus pattern (65 bp):
TGCTATGCATGGGAAAGACTAGCACAAGCCATTCAAAGGAGTATTACGAATCAAGGATGAAAATT
Found at i:327148 original size:89 final size:89
Alignment explanation
Indices: 326997--327177 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
326987 AGAGCTCGAG
326997 ACAGGCTGACCAGATGGGTAGCAAAGACCAAGGATGGTAACGGGTAAGGATTTTGATCAACCCGA
1 ACAGGCTGACCAGATGGGTAGCAAAGACCAAGGATGGTAACGGGTAAGGATTTTGATCAACCCGA
327062 TCAGATCCAAAAATTTTATATCCT
66 TCAGATCCAAAAATTTTATATCCT
* *
327086 ACAGGCTGACCTGATGGGTAGCAAAGACCAAGGATGGTAACGGGTCAGGATTTTGATCAACCCGA
1 ACAGGCTGACCAGATGGGTAGCAAAGACCAAGGATGGTAACGGGTAAGGATTTTGATCAACCCGA
327151 TCAGATCCAAAAATTTTATATCCT
66 TCAGATCCAAAAATTTTATATCCT
327175 ACA
1 ACA
327178 TCGATCCGAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (89 bp):
ACAGGCTGACCAGATGGGTAGCAAAGACCAAGGATGGTAACGGGTAAGGATTTTGATCAACCCGA
TCAGATCCAAAAATTTTATATCCT
Found at i:328765 original size:23 final size:23
Alignment explanation
Indices: 328722--328767 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
328712 ATATTCATTT
*
328722 TACATAACTTAGAAAGAAAAAAA
1 TACATAACTTACAAAGAAAAAAA
* *
328745 TACATAA-TTACAAATATAAAAA
1 TACATAACTTACAAAGAAAAAAA
328767 T
1 T
328768 TCTATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (23 bp):
TACATAACTTACAAAGAAAAAAA
Found at i:330803 original size:18 final size:20
Alignment explanation
Indices: 330774--330813 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
330764 TTTTGAACCT
*
330774 GACAAGCCCTTT-TTGAGTC
1 GACAAGCCCTTTATCGAGTC
330793 GACAA-CCCTTTATCGAGTC
1 GACAAGCCCTTTATCGAGTC
330812 GA
1 GA
330814 ACCCCCGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (20 bp):
GACAAGCCCTTTATCGAGTC
Found at i:331159 original size:35 final size:34
Alignment explanation
Indices: 331120--331197 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 34
331110 AATACAATCC
331120 TCAATTTCATTCTAAACCCCAAATT-ACAAAATAAT
1 TCAATTT-ATTCTAAACCCCAAATTCA-AAAATAAT
* * *
331155 TCAATTATATTTTAAACTCCAAATTCAAAAATACT
1 TCAATT-TATTCTAAACCCCAAATTCAAAAATAAT
331190 TCAATTTA
1 TCAATTTA
331198 GGGTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 2 0.05
35 34 0.89
36 2 0.05
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (34 bp):
TCAATTTATTCTAAACCCCAAATTCAAAAATAAT
Found at i:331238 original size:35 final size:35
Alignment explanation
Indices: 331199--331266 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
331189 TTCAATTTAG
* *
331199 GGTTTATAATATAATTGAAGTGTTTTGGAATTTGA
1 GGTTTAGAATATAATTGAAGTGTTTTGAAATTTGA
*
331234 GGTTTAGAATGTAATTGAAGTGTTTTGAAATTT
1 GGTTTAGAATATAATTGAAGTGTTTTGAAATTT
331267 TGAACACGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.46
Consensus pattern (35 bp):
GGTTTAGAATATAATTGAAGTGTTTTGAAATTTGA
Found at i:335309 original size:17 final size:17
Alignment explanation
Indices: 335273--335342 Score: 86
Period size: 18 Copynumber: 4.0 Consensus size: 17
335263 AGTATCCTCT
*
335273 TTCATTAAATAAAGCTAG
1 TTCATTAATTAAA-CTAG
*
335291 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* *
335308 TTCATTCATTTAAACTGG
1 TTCATT-AATTAAACTAG
335326 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAG
335343 CTCTTTATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 18 0.41
18 26 0.59
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:335313 original size:35 final size:35
Alignment explanation
Indices: 335273--335342 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
335263 AGTATCCTCT
335273 TTCATT-AAATAAAGCTAGTTCACTAATTAAACTAG
1 TTCATTCAAATAAA-CTAGTTCACTAATTAAACTAG
** * *
335308 TTCATTCATTTAAACTGGTTCATTAATTAAACTAG
1 TTCATTCAAATAAACTAGTTCACTAATTAAACTAG
335343 CTCTTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 25 0.83
36 5 0.17
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (35 bp):
TTCATTCAAATAAACTAGTTCACTAATTAAACTAG
Found at i:335766 original size:24 final size:24
Alignment explanation
Indices: 335739--335784 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
335729 TTATTCACCT
335739 AATTCAAAGCTGATTTAATCATCC
1 AATTCAAAGCTGATTTAATCATCC
* *
335763 AATTCAAGGTTGATTTAATCAT
1 AATTCAAAGCTGATTTAATCAT
335785 TCAAACCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (24 bp):
AATTCAAAGCTGATTTAATCATCC
Found at i:335794 original size:24 final size:24
Alignment explanation
Indices: 335749--335795 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
335739 AATTCAAAGC
**
335749 TGATTTAATCATCCAATTCAAGGT
1 TGATTTAATCATCCAAACCAAGGT
*
335773 TGATTTAATCATTCAAACCAAGG
1 TGATTTAATCATCCAAACCAAGG
335796 GCTGTTCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (24 bp):
TGATTTAATCATCCAAACCAAGGT
Found at i:336531 original size:74 final size:74
Alignment explanation
Indices: 336410--336590 Score: 328
Period size: 74 Copynumber: 2.5 Consensus size: 74
336400 TTTTATAACG
336410 TTGGTTCCTAGCTCACCTATAGCTAGTGGGTCACGTTCCACCCTCTATCACTTGGATTCCATCTT
1 TTGGTTCCTAGCTCACCTATAGCTAGTGGGTCACGTTCCACCCTCTATCACTTGGATTCCATCTT
336475 TGTATATTA
66 TGTATATTA
* *
336484 TTGGTTCCTAGCTCACCTATAGCTAGCGGGTCATGTTCCACCCTCTATCACTTGGATTCCATCTT
1 TTGGTTCCTAGCTCACCTATAGCTAGTGGGTCACGTTCCACCCTCTATCACTTGGATTCCATCTT
336549 TGTATATTA
66 TGTATATTA
*
336558 TTGGTTCCTAGCTC-CATATAGCTAGTGGGTCAC
1 TTGGTTCCTAGCTCACCTATAGCTAGTGGGTCAC
336591 AATCCATACT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 16 0.16
74 86 0.84
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.37
Consensus pattern (74 bp):
TTGGTTCCTAGCTCACCTATAGCTAGTGGGTCACGTTCCACCCTCTATCACTTGGATTCCATCTT
TGTATATTA
Found at i:336857 original size:3 final size:3
Alignment explanation
Indices: 336849--336914 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
336839 TCATTTAAAT
* *
336849 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
336895 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
336915 AATATATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:336887 original size:27 final size:26
Alignment explanation
Indices: 336849--336925 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 26
336839 TCATTTAAAT
336849 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
336873 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
336898 TTAGTATATTATTATTAAA-TATATATTA
1 TTA-T-TATTATTATTAAATTAT-TATTA
336926 CAAGCCCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.37
25 9 0.18
26 1 0.02
27 16 0.33
28 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:337665 original size:13 final size:13
Alignment explanation
Indices: 337647--337671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337637 CCACCGTTAC
337647 GGTGGCCGGCGGT
1 GGTGGCCGGCGGT
337660 GGTGGCCGGCGG
1 GGTGGCCGGCGG
337672 CGGAGTACGG
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:0.00, C:0.24, G:0.64, T:0.12
Consensus pattern (13 bp):
GGTGGCCGGCGGT
Found at i:339194 original size:17 final size:16
Alignment explanation
Indices: 339162--339208 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
339152 TTTCTTTCAA
339162 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
339178 ATTTTTA-TATTAATATT
1 ATTTTTATTATT--TATT
* *
339195 GTTTTTTTTATTTA
1 ATTTTTATTATTTA
339209 GGTATTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.15
16 9 0.35
17 9 0.35
18 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATTTTTATTATTTATT
Found at i:343560 original size:2 final size:2
Alignment explanation
Indices: 343553--343598 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
343543 TTATCCTTTA
343553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
343595 AT AT
1 AT AT
343599 CCTTTGTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343901 original size:4 final size:4
Alignment explanation
Indices: 343892--343954 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
343882 CTCATCCAAC
* *
343892 AAAG AAAG AAAG AAAG AAAG AAAAA AAAG AGAA- AAAG AAA- AAAA AGAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG A-AAG AAAG AAAG AAAG A-AAG
*
343941 AAA- AAAA AAAG AAA
1 AAAG AAAG AAAG AAA
343955 AAGGAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
3 8 0.16
4 33 0.67
5 8 0.16
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:343926 original size:11 final size:10
Alignment explanation
Indices: 343896--343956 Score: 54
Period size: 11 Copynumber: 5.9 Consensus size: 10
343886 TCCAACAAAG
343896 AAAGAAAGAAA
1 AAAGAAA-AAA
343907 GAAAG-AAAAA
1 -AAAGAAAAAA
343917 AAAGAGAAAAA
1 AAAGA-AAAAA
*
343928 GAA-AAAAAA
1 AAAGAAAAAA
*
343937 GAAGAAAAAAA
1 AAAG-AAAAAA
343948 AAAGAAAAA
1 AAAGAAAAA
343957 GGAAAAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
9 12 0.28
10 9 0.21
11 18 0.42
12 4 0.09
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:343928 original size:17 final size:18
Alignment explanation
Indices: 343908--343963 Score: 73
Period size: 17 Copynumber: 3.2 Consensus size: 18
343898 AGAAAGAAAG
343908 AAAGAAAAAAAAG-AGAA
1 AAAGAAAAAAAAGAAGAA
343925 AAAGAAAAAAAAGAAGAA
1 AAAGAAAAAAAAGAAGAA
343943 AAA-AAAAAGAAA-AAGGAA
1 AAAGAAAAA-AAAGAA-GAA
343961 AAA
1 AAA
343964 TTGAATCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 20 0.56
18 16 0.44
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAGAAGAA
Found at i:343955 original size:8 final size:8
Alignment explanation
Indices: 343892--343956 Score: 62
Period size: 8 Copynumber: 8.1 Consensus size: 8
343882 CTCATCCAAC
*
343892 AAAGAAAG
1 AAAGAAAA
*
343900 AAAGAAAG
1 AAAGAAAA
343908 AAAGAAAAA
1 AAAG-AAAA
*
343917 AAAGAGAA
1 AAAGAAAA
343925 AAAGAAAA
1 AAAGAAAA
*
343933 AAA-AGAAG
1 AAAGA-AAA
343941 AAA-AAAA
1 AAAGAAAA
343948 AAAGAAAA
1 AAAGAAAA
343956 A
1 A
343957 GGAAAAATTG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
7 6 0.12
8 36 0.73
9 7 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:343962 original size:29 final size:30
Alignment explanation
Indices: 343899--343963 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
343889 AACAAAGAAA
* *
343899 GAAAGAAAGAAAGAAAAAAAAGAGAAAAAG
1 GAAAAAAAGAAAGAAAAAAAAAAGAAAAAG
*
343929 AAAAAAAAG-AAGAAAAAAAAAAGAAAAAG
1 GAAAAAAAGAAAGAAAAAAAAAAGAAAAAG
343958 GAAAAA
1 GAAAAA
343964 TTGAATCAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (30 bp):
GAAAAAAAGAAAGAAAAAAAAAAGAAAAAG
Found at i:346444 original size:93 final size:94
Alignment explanation
Indices: 346287--346505 Score: 347
Period size: 93 Copynumber: 2.4 Consensus size: 94
346277 GATTTGGTAA
* * * *
346287 AATCAATCATTGAATTTGGAAGA-GGA-G-ACTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTT
1 AATCAATCATTGAATTTGGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAATT
346349 ATCTGATCTGGTTTGGTATGAAACCACAG
66 ATCTGATCTGGTTTGGTATGAAACCACAG
*
346378 AATCAATCATTGAATTTGGAAGATGAATGTGCT-TATAGCATCTTCTGGAAGTGTTCTTTGAATT
1 AATCAATCATTGAATTTGGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAATT
346442 ATCTGATCTGGTTTGGTATGAAACCACAG
66 ATCTGATCTGGTTTGGTATGAAACCACAG
* *
346471 AATCAATCATTGAATTTGAAAGATGAATTTGCTCA
1 AATCAATCATTGAATTTGGAAGATGAATGTGCTCA
346506 TGGTAGAAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
91 23 0.20
92 2 0.02
93 89 0.77
94 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (94 bp):
AATCAATCATTGAATTTGGAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAATT
ATCTGATCTGGTTTGGTATGAAACCACAG
Found at i:349166 original size:22 final size:22
Alignment explanation
Indices: 349137--349191 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
349127 ATCTACACTC
349137 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
349159 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
349181 TTCAAAGATGA
1 TTCAAAGATGA
349192 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:350103 original size:112 final size:113
Alignment explanation
Indices: 349608--350270 Score: 829
Period size: 112 Copynumber: 5.9 Consensus size: 113
349598 CCATCATTCA
* * *
349608 ATGGATCAACATTTCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 ATGGATCAGCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* ** *
349671 TTCATAATGAGAAGAACTTGTTCAACTTTTTTGTTTGAATTCATCATTTG
65 TTCATAATGAGAAGAACTTGTTCAAC-TTTTTGCTCAAATTCATCACTTG
* * * * * *
349721 ATGAATCAACATTGT-CAG-GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAA
1 ATGGATCAGC-TTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* * * *
349784 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTCAAATCCATAAC--A
64 GTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACTTG
* *
349832 ATGGATCAACTTTGCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAA
1 ATGGATCAGCTTTTCCAGA-GAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAA
**
349897 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACCCG
61 GAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACTTG
* ** * ** * *
349950 GTGGATCAGCAGTGCCAGTTAAAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGT
1 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
350015 TCATAATGAGAAGAGCTTGTTCAAC-CTTTGCTCAAATTCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACTTG
*
350062 ATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * *
350127 TCATAATAAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACTTG
* *
350175 ATGGAGCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGT
1 ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* *
350239 TCATAATAAGAAGAATTTGTTCAACTTTTTGC
66 TCATAATGAGAAGAACTTGTTCAACTTTTTGC
350271 ATAATTCTAT
Statistics
Matches: 484, Mismatches: 53, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
110 2 0.00
111 12 0.02
112 172 0.36
113 129 0.27
114 70 0.14
115 2 0.00
116 81 0.17
117 2 0.00
118 14 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (113 bp):
ATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATTCATCACTTG
Found at i:350926 original size:76 final size:76
Alignment explanation
Indices: 350678--351011 Score: 609
Period size: 76 Copynumber: 4.4 Consensus size: 76
350668 TTCTCACATA
350678 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
*
350743 TTCAGGTCATC
66 TTCGGGTCATC
*
350754 TGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCAAAGC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGC
350819 CTTCGGGTCATC
65 CTTCGGGTCATC
*
350831 TGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
350896 TTCGGGTCATC
66 TTCGGGTCATC
350907 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
350971 TTCGGGTCATC
66 TTCGGGTCATC
*
350982 TGTAAG-CCTTCAGTGCATGATGTTTTCAAA
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAA
351012 CATTTGCATC
Statistics
Matches: 253, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
74 23 0.09
75 27 0.11
76 128 0.51
77 75 0.30
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
TTCGGGTCATC
Found at i:350956 original size:153 final size:151
Alignment explanation
Indices: 350678--351011 Score: 607
Period size: 153 Copynumber: 2.2 Consensus size: 151
350668 TTCTCACATA
350678 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
350743 TTCAGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGAT
66 TTCAGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGAT
350808 GTTTTCAAAGCCTTCGGGTCATC
130 G-TTTCAAAGCCTTCGGGTCATC
*
350831 TGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
* *
350896 TTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
66 TTCAGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
350961 TTTCAAAGCCTTCGGGTCATC
131 TTTCAAAGCCTTCGGGTCATC
*
350982 TGTAAG-CCTTCAGTGCATGATGTTTTCAAA
1 TGTAAGTCCTTCAGTGCATGATGTTTCCAAA
351012 CATTTGCATC
Statistics
Matches: 176, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
150 22 0.12
151 27 0.15
152 9 0.05
153 118 0.67
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (151 bp):
TGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
TTCAGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
TTTCAAAGCCTTCGGGTCATC
Found at i:351144 original size:3 final size:3
Alignment explanation
Indices: 351136--351201 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
351126 TCATTTAAAT
* * *
351136 TTA TTA TTA TGA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
351182 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
351202 AATATATATT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 3 0.06
3 46 0.88
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:351153 original size:18 final size:18
Alignment explanation
Indices: 351130--351168 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
351120 ATTTTTTCAT
351130 TTAAATTTATTATTATGA
1 TTAAATTTATTATTATGA
*
351148 TTAAATTTATTATTATTA
1 TTAAATTTATTATTATGA
351166 TTA
1 TTA
351169 TTATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTAAATTTATTATTATGA
Found at i:351194 original size:27 final size:25
Alignment explanation
Indices: 351136--351212 Score: 111
Period size: 24 Copynumber: 3.0 Consensus size: 25
351126 TCATTTAAAT
*
351136 TTATTATTATGATTAAAT-TTATTA
1 TTATTATTATTATTAAATATTATTA
351160 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAATATTATTA
351185 TTAGTATATTATTATTAAATATATATTA
1 TTA-T-TATTATTATTAAATAT-TATTA
351213 CAAGCCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 17 0.35
25 9 0.19
26 1 0.02
27 16 0.33
28 5 0.10
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (25 bp):
TTATTATTATTATTAAATATTATTA
Found at i:356714 original size:25 final size:26
Alignment explanation
Indices: 356686--356738 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
356676 GTCATAAATC
*
356686 TATGACGCGCATTTATGA-ACTCATT
1 TATGACGCACATTTATGACACTCATT
356711 TATGACGCACATTTATGACACTCATT
1 TATGACGCACATTTATGACACTCATT
356737 TA
1 TA
356739 GCATCATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (26 bp):
TATGACGCACATTTATGACACTCATT
Done.