Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 23
Found at i:126628 original size:28 final size:27
Alignment explanation
Indices: 126543--126633 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
126533 TTTTAAATTT
* *
126543 TTAAAATAATTTTTGTCAAAATAAGTAA
1 TTAAAAT-ATTTTTGTCAAAATAGGTAC
* * *
126571 TT--AATTTTTTTGTCAAAATAGATGC
1 TTAAAATATTTTTGTCAAAATAGGTAC
*
126596 CTAAAATATTTTTAGTCAAAATAGGTAC
1 TTAAAATATTTTT-GTCAAAATAGGTAC
*
126624 TTAAAGTATT
1 TTAAAATATT
126634 CAATTTTTTA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
25 16 0.33
26 3 0.06
27 8 0.16
28 22 0.45
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (27 bp):
TTAAAATATTTTTGTCAAAATAGGTAC
Found at i:128052 original size:25 final size:25
Alignment explanation
Indices: 128024--128072 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
128014 CTCAAAAAAA
128024 TTTAATGTGAAAATAAAAGAGACTT
1 TTTAATGTGAAAATAAAAGAGACTT
*
128049 TTTAATTTGAAAATAAAAGAGACT
1 TTTAATGTGAAAATAAAAGAGACT
128073 ATATCCATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (25 bp):
TTTAATGTGAAAATAAAAGAGACTT
Found at i:130300 original size:12 final size:12
Alignment explanation
Indices: 130285--130310 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
130275 TCAAAGAAAT
130285 AAATAAAATAAA
1 AAATAAAATAAA
130297 AAATAAAATAAA
1 AAATAAAATAAA
130309 AA
1 AA
130311 TGTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:130355 original size:21 final size:20
Alignment explanation
Indices: 130329--130367 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
130319 TTCAAAGAAA
130329 AAAAAGGAAAGAAATAAAAAT
1 AAAAAGGAAAGAAA-AAAAAT
130350 AAAAAGGAAAGAAAAAAA
1 AAAAAGGAAAGAAAAAAA
130368 CGTTTAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (20 bp):
AAAAAGGAAAGAAAAAAAAT
Found at i:130504 original size:15 final size:14
Alignment explanation
Indices: 130482--130524 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
130472 TGGCTTACGA
130482 AAATATATTTAATAT
1 AAATATATTTAA-AT
* *
130497 ATATATATATAAAT
1 AAATATATTTAAAT
130511 AAATAATATTTAAA
1 AAAT-ATATTTAAA
130525 AGATAATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATATTTAAAT
Found at i:130558 original size:12 final size:13
Alignment explanation
Indices: 130522--130561 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
130512 AATAATATTT
*
130522 AAAAGATAATAACC
1 AAAAGA-AATAAAC
130536 AAAAGAAATAAAC
1 AAAAGAAATAAAC
130549 AAAA-AAATAAAC
1 AAAAGAAATAAAC
130561 A
1 A
130562 TATATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.36
13 10 0.40
14 6 0.24
ACGTcount: A:0.75, C:0.10, G:0.05, T:0.10
Consensus pattern (13 bp):
AAAAGAAATAAAC
Found at i:130610 original size:2 final size:2
Alignment explanation
Indices: 130603--130629 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
130593 AAATAAAAGA
130603 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
130630 ATAACAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134886 original size:24 final size:24
Alignment explanation
Indices: 134859--134907 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
134849 AAAAGAAAGA
134859 CAAATTAGTGGATTTGTGGAAAAT
1 CAAATTAGTGGATTTGTGGAAAAT
134883 CAAATTAGTGGATTTGTGGAAAAT
1 CAAATTAGTGGATTTGTGGAAAAT
134907 C
1 C
134908 CTTAGTGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (24 bp):
CAAATTAGTGGATTTGTGGAAAAT
Found at i:135856 original size:33 final size:34
Alignment explanation
Indices: 135819--135882 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
135809 AAATGAAAAT
*
135819 GGATTTTGAAA-ATC-AAAATGAAATCTTGAAGAA
1 GGATTTAGAAATATCAAAAATGAAAT-TTGAAGAA
*
135852 GGATTTAGAAATCTCAAAAATGAAATTTGAA
1 GGATTTAGAAATATCAAAAATGAAATTTGAA
135883 AGTATCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 10 0.37
34 7 0.26
35 10 0.37
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (34 bp):
GGATTTAGAAATATCAAAAATGAAATTTGAAGAA
Found at i:143361 original size:21 final size:22
Alignment explanation
Indices: 143330--143370 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
143320 ATATCCTTAT
143330 AAAATGAAATATGAGAAAGTTC
1 AAAATGAAATATGAGAAAGTTC
143352 AAAA-GAAATATGAGAAAGT
1 AAAATGAAATATGAGAAAGT
143371 AAAAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.20
Consensus pattern (22 bp):
AAAATGAAATATGAGAAAGTTC
Found at i:143376 original size:21 final size:21
Alignment explanation
Indices: 143330--143376 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
143320 ATATCCTTAT
* *
143330 AAAATGAAATATGAGAAAGTT
1 AAAAAGAAATATGAGAAAGTA
*
143351 CAAAAGAAATATGAGAAAGTA
1 AAAAAGAAATATGAGAAAGTA
143372 AAAAA
1 AAAAA
143377 AACAAGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAAAGAAATATGAGAAAGTA
Found at i:146645 original size:13 final size:13
Alignment explanation
Indices: 146627--146653 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
146617 ATTTTCAAAG
146627 AAATAAATAAATA
1 AAATAAATAAATA
146640 AAATAAATAAATA
1 AAATAAATAAATA
146653 A
1 A
146654 TGTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:150186 original size:54 final size:54
Alignment explanation
Indices: 150104--150208 Score: 210
Period size: 54 Copynumber: 1.9 Consensus size: 54
150094 CGACCTGCAG
150104 AAAGAAAATAATCATCCTCACAAACAGTTTCAAAAGTTCAAATGGGCATACACC
1 AAAGAAAATAATCATCCTCACAAACAGTTTCAAAAGTTCAAATGGGCATACACC
150158 AAAGAAAATAATCATCCTCACAAACAGTTTCAAAAGTTCAAATGGGCATAC
1 AAAGAAAATAATCATCCTCACAAACAGTTTCAAAAGTTCAAATGGGCATAC
150209 CCCCCCCCCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (54 bp):
AAAGAAAATAATCATCCTCACAAACAGTTTCAAAAGTTCAAATGGGCATACACC
Found at i:151676 original size:21 final size:21
Alignment explanation
Indices: 151650--151692 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
151640 GGGTTGTTGG
151650 TTAAGAATCAGGAGGAGACCC
1 TTAAGAATCAGGAGGAGACCC
151671 TTAAGAATCAGGAGGAGACCC
1 TTAAGAATCAGGAGGAGACCC
151692 T
1 T
151693 CCAGAAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (21 bp):
TTAAGAATCAGGAGGAGACCC
Found at i:151698 original size:21 final size:21
Alignment explanation
Indices: 151652--151698 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
151642 GTTGTTGGTT
*
151652 AAGAATCAGGAGGAGACCCTT
1 AAGAATCAGGAGGAGACCCTC
151673 AAGAATCAGGAGGAGACCCTC
1 AAGAATCAGGAGGAGACCCTC
*
151694 CAGAA
1 AAGAA
151699 GATGGATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.21, G:0.28, T:0.11
Consensus pattern (21 bp):
AAGAATCAGGAGGAGACCCTC
Found at i:154812 original size:46 final size:46
Alignment explanation
Indices: 154745--154842 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
154735 AAATTCCTCC
154745 ATGCTTTCCCATTTACAATTTGCAAATGACATTTTAATTTTCTGCA
1 ATGCTTTCCCATTTACAATTTGCAAATGACATTTTAATTTTCTGCA
154791 ATGCTTTCCCATTTACAATTTGCAAATGACATTTTAATTTTCTGCA
1 ATGCTTTCCCATTTACAATTTGCAAATGACATTTTAATTTTCTGCA
154837 ATGCTT
1 ATGCTT
154843 CCATCGGGGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (46 bp):
ATGCTTTCCCATTTACAATTTGCAAATGACATTTTAATTTTCTGCA
Found at i:158660 original size:12 final size:12
Alignment explanation
Indices: 158645--158673 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
158635 AAAGATATAA
158645 GGCGAGATTAGT
1 GGCGAGATTAGT
158657 GGCGAGATTAGT
1 GGCGAGATTAGT
158669 GGCGA
1 GGCGA
158674 AAGGATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.45, T:0.21
Consensus pattern (12 bp):
GGCGAGATTAGT
Found at i:164866 original size:2 final size:2
Alignment explanation
Indices: 164859--164887 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
164849 TTGCTTGATC
164859 GA GA 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 GA GA G
164888 TTGATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:165699 original size:6 final size:6
Alignment explanation
Indices: 165683--165727 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
165673 ATCGAATGGA
165683 CTCGA- CTCGAG CTCGAG CTCGA- CTCGAG CTCGAG CTCGA- CTCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
165728 TTCTTAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.41
6 22 0.59
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (6 bp):
CTCGAG
Found at i:165705 original size:17 final size:17
Alignment explanation
Indices: 165683--165727 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
165673 ATCGAATGGA
165683 CTCGACTCGAGCTCGAG
1 CTCGACTCGAGCTCGAG
165700 CTCGACTCGAGCTCGAG
1 CTCGACTCGAGCTCGAG
165717 CTCGACTCGAG
1 CTCGACTCGAG
165728 TTCTTAACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (17 bp):
CTCGACTCGAGCTCGAG
Found at i:165708 original size:11 final size:12
Alignment explanation
Indices: 165683--165727 Score: 69
Period size: 11 Copynumber: 4.0 Consensus size: 12
165673 ATCGAATGGA
165683 CTCGA-CTCGAG
1 CTCGAGCTCGAG
165694 CTCGAGCTCGA-
1 CTCGAGCTCGAG
165705 CTCGAGCTCGAG
1 CTCGAGCTCGAG
165717 CTCGA-CTCGAG
1 CTCGAGCTCGAG
165728 TTCTTAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (12 bp):
CTCGAGCTCGAG
Found at i:169350 original size:10 final size:10
Alignment explanation
Indices: 169335--169365 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
169325 ATGGAACGAG
*
169335 ATAAAATAAA
1 ATAAAACAAA
169345 ATAAAACAAA
1 ATAAAACAAA
169355 ATAAAACAAA
1 ATAAAACAAA
169365 A
1 A
169366 CAAGATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (10 bp):
ATAAAACAAA
Found at i:169355 original size:15 final size:15
Alignment explanation
Indices: 169337--169373 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
169327 GGAACGAGAT
*
169337 AAAATAAAATAAAAC
1 AAAATAAAACAAAAC
169352 AAAATAAAACAAAAC
1 AAAATAAAACAAAAC
*
169367 AAGATAA
1 AAAATAA
169374 TAAGGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.78, C:0.08, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAATAAAACAAAAC
Found at i:169861 original size:16 final size:16
Alignment explanation
Indices: 169820--169862 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
169810 ATGATAGCGG
**
169820 TTAGCAGTTAGAAATT
1 TTAGCAGTTAGAAACA
**
169836 TTAGTTGTTAGAAACA
1 TTAGCAGTTAGAAACA
169852 TTAGCAGTTAG
1 TTAGCAGTTAG
169863 TGGTTAGTAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (16 bp):
TTAGCAGTTAGAAACA
Found at i:170783 original size:16 final size:16
Alignment explanation
Indices: 170762--170806 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
170752 CAGTGATAGC
170762 AGTTAGCAGTTAGAAA
1 AGTTAGCAGTTAGAAA
** *
170778 TTTTAGCTGTTAGAAA
1 AGTTAGCAGTTAGAAA
170794 AGTTAGCAGTTAG
1 AGTTAGCAGTTAG
170807 TGGTTAGCAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (16 bp):
AGTTAGCAGTTAGAAA
Found at i:172885 original size:102 final size:101
Alignment explanation
Indices: 172722--173159 Score: 368
Period size: 103 Copynumber: 4.3 Consensus size: 101
172712 AAGTGGAAAG
* * * * * * *
172722 AAATTTGTTTCTAGAGAAGCTATCTCAGGTGAGATAAAATTTTGTTTCGAGTGAAAC-ATTTCAA
1 AAATTTGTTTTTAGAAAAACAATCTCA-ATGAGAT-TAATTTTGTTTCAAGTGAAACAATTTCAA
* *
172786 AATTTACTTTTC-AAGGGAAAAATGTCTCAAGCGAGACA
64 AATTT-GTTTTCTAAGGGAAAACTGTCTCAAGCGAGACA
* *
172824 AAATTTGTTTTTAGGAAAACAATCTTCAATGAGATTAATTTTGTTTCAAGTGAAACAATTTCACA
1 AAATTTGTTTTTAGAAAAACAATC-TCAATGAGATTAATTTTGTTTCAAGTGAAACAATTTCAAA
* * ** * *
172889 ATTTGTGTTTCGAA-TGAGGACTATCTCAAGCGAGACG
65 ATTTGT-TTTCTAAGGGAAAACTGTCTCAAGCGAGACA
*** * * *
172926 AAATTTGATGTTTT-TTTAAACATTCTCAAGTGAGATAAATTTTGTTTCAAGTGAAAGAATTTCA
1 AAATTTG-T-TTTTAGAAAAACAATCTCAA-TGAGATTAATTTTGTTTCAAGTGAAACAATTTCA
* * *
172990 AAATTTGTTTTTCTATGGG-AAACTGTATCAAGCGAGACG
63 AAATTTG-TTTTCTAAGGGAAAACTGTCTCAAGCGAGACA
* * * **
173029 AAATTTATTTTTAAGAAAAACAATCTCAAATGAGATTAATTTTGTTTCAAGTAAAATAGCTTCAA
1 AAATTTGTTTTT-AGAAAAACAATCTC-AATGAGATTAATTTTGTTTCAAGTGAAACAATTTCAA
* ** * * **
173094 AATTTGTGTTCTAAGGGACGATTGTCTTAAGAAAGACA
64 AATTTGTTTTCTAAGGGAAAACTGTCTCAAGCGAGACA
173132 AAATTTG-TTTT-GAAAGAATCAATCTCAA
1 AAATTTGTTTTTAGAAA-AA-CAATCTCAA
173160 ATGTTCGTGT
Statistics
Matches: 270, Mismatches: 51, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
100 4 0.01
101 28 0.10
102 89 0.33
103 141 0.52
104 8 0.03
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (101 bp):
AAATTTGTTTTTAGAAAAACAATCTCAATGAGATTAATTTTGTTTCAAGTGAAACAATTTCAAAA
TTTGTTTTCTAAGGGAAAACTGTCTCAAGCGAGACA
Found at i:173138 original size:206 final size:205
Alignment explanation
Indices: 172744--173138 Score: 492
Period size: 206 Copynumber: 1.9 Consensus size: 205
172734 AGAGAAGCTA
* * *
172744 TCTCAGGTGAGATAAAATTTTGTTTCGAGTGAAACATTTCAAAATTTACTTTTCAAGGGAAAAAT
1 TCTCAAGTGAGATAAAATTTTGTTTCAAGTGAAAAATTTCAAAATTTACTTTTCAAGGGAAAAAT
* * *
172809 GTCTCAAGCGAGACAAAATTTGTTTTTAGGAAAACAATCTTCAATGAGATTAATTTTGTTTCAAG
66 GTATCAAGCGAGACAAAATTTATTTTTAGAAAAACAATCTTCAATGAGATTAATTTTGTTTCAAG
* * * * * ** *
172874 TGAAACAATTTCACAATTTGTGTTTCGAATGAGGACTATCTCAAGCGAGACGAAATTTGATGTTT
131 TAAAACAACTTCAAAATTTGTGTTTCGAAGGACGACTATCTCAAGAAAGACAAAATTTGATGTTT
172939 TTTTAAACAT
196 TTTTAAACAT
** *
172949 TCTCAAGTGAGAT-AAATTTTGTTTCAAGTGAAAGAATTTCAAAATTTGTTTTTCTATGGG-AAA
1 TCTCAAGTGAGATAAAATTTTGTTTCAAGTGAAA-AATTTCAAAATTTACTTTTC-AAGGGAAAA
* *
173012 CTGTATCAAGCGAGACGAAATTTATTTTTAAGAAAAACAATC-TCAAATGAGATTAATTTTGTTT
64 ATGTATCAAGCGAGACAAAATTTATTTTT-AGAAAAACAATCTTC-AATGAGATTAATTTTGTTT
* * * * * *
173076 CAAGTAAAATAGCTTCAAAATTTGTG-TTCTAAGGGACGATTGTCTTAAGAAAGACAAAATTTG
127 CAAGTAAAACAACTTCAAAATTTGTGTTTCGAA-GGACGACTATCTCAAGAAAGACAAAATTTG
173139 TTTTGAAAGA
Statistics
Matches: 160, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
204 19 0.12
205 64 0.40
206 77 0.48
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (205 bp):
TCTCAAGTGAGATAAAATTTTGTTTCAAGTGAAAAATTTCAAAATTTACTTTTCAAGGGAAAAAT
GTATCAAGCGAGACAAAATTTATTTTTAGAAAAACAATCTTCAATGAGATTAATTTTGTTTCAAG
TAAAACAACTTCAAAATTTGTGTTTCGAAGGACGACTATCTCAAGAAAGACAAAATTTGATGTTT
TTTTAAACAT
Found at i:177288 original size:27 final size:27
Alignment explanation
Indices: 177255--177308 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
177245 TCCAATTTCT
177255 CCATAAAAAATGACCCCAAACAATCCC
1 CCATAAAAAATGACCCCAAACAATCCC
177282 CCATAAAAAATGACCCCAAACAATCCC
1 CCATAAAAAATGACCCCAAACAATCCC
177309 AAAGCAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.37, G:0.04, T:0.11
Consensus pattern (27 bp):
CCATAAAAAATGACCCCAAACAATCCC
Found at i:177662 original size:13 final size:13
Alignment explanation
Indices: 177644--177668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177634 TATTTATTGT
177644 TGGTGCAATTGGA
1 TGGTGCAATTGGA
177657 TGGTGCAATTGG
1 TGGTGCAATTGG
177669 CAGGGGATGG
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:0.20, C:0.08, G:0.40, T:0.32
Consensus pattern (13 bp):
TGGTGCAATTGGA
Found at i:178448 original size:39 final size:39
Alignment explanation
Indices: 178306--178545 Score: 349
Period size: 39 Copynumber: 6.1 Consensus size: 39
178296 AATCCTAAGT
*
178306 GAGAT-AAATCTTTTGTTTCGAGTGAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
* *
178344 GAGATAAAAATCTAT-TGTTTCAAGTGAAACTATCTCAAGT
1 GAGAT-AAAATCT-TCTGTTTCGAGTGAAACTATCTCAAGC
* *
178384 GAGATAAAAATCTTCTGGTTCGAGTGAAACTATCTCAAGT
1 GAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
* *
178424 GAGATAAAGTCTTCTGTTTTGAGTGAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
*
178463 GAGATAAAATCTTTTGTTTCGAGTGAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
* *
178502 GAGATAAAATCTTCTATTTCGAGTGAAACTATATCAAGC
1 GAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
178541 GAGAT
1 GAGAT
178546 GTTGATCCCT
Statistics
Matches: 184, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
38 5 0.03
39 108 0.59
40 70 0.38
41 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (39 bp):
GAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGC
Found at i:178853 original size:39 final size:39
Alignment explanation
Indices: 178753--178953 Score: 219
Period size: 38 Copynumber: 5.2 Consensus size: 39
178743 CTTAGTTTCT
* * * *
178753 TAAAATATTTTGTTTCGAGAGAAACTATCTCAAGCAAGA
1 TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
* * * *
178792 T-AAATCTTCTGTTTTGAATGAAACAATCTCAAGCAAGA
1 TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
* *
178830 TAAAATCTTATGTTTCGAGTGAAACTATCTTAAGCGAGA
1 TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
* * *
178869 TAAAATCTTCTGTTTCAAGTG-AACTATCTCATGCGATA
1 TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
* * * * *
178907 TGAAATATTCTGTTTCGATTGAAACAATATCAAGCGAGA
1 TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
178946 T-AAATCTT
1 TAAAATCTT
178954 GTTTTTAAAA
Statistics
Matches: 134, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
38 69 0.51
39 65 0.49
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (39 bp):
TAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGA
Found at i:178898 original size:77 final size:77
Alignment explanation
Indices: 178753--178953 Score: 235
Period size: 77 Copynumber: 2.6 Consensus size: 77
178743 CTTAGTTTCT
* * * *
178753 TAAAATATTTTGTTTCGAGAGAAACTATCTCAAGCAAGATAAATCTTCTGTTTTGAATGAAACAA
1 TAAAATATTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTTCAATGAAACAA
178818 TCTCAAGCAAGA
66 TCTCAAGCAAGA
* *
178830 TAAAATCTTATGTTTCGAGTGAAACTATCTTAAGCGAGATAAAATCTTCTG-TTTCAAGTG-AAC
1 TAAAATATTATGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATCTTCTGTTTTCAA-TGAAAC
* * * *
178893 TATCTCATGCGATA
64 AATCTCAAGCAAGA
* * * * *
178907 TGAAATATTCTGTTTCGATTGAAACAATATCAAGCGAGATAAATCTT
1 TAAAATATTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT
178954 GTTTTTAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
76 7 0.07
77 86 0.82
78 12 0.11
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (77 bp):
TAAAATATTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTCTGTTTTCAATGAAACAA
TCTCAAGCAAGA
Found at i:179041 original size:62 final size:62
Alignment explanation
Indices: 178938--179128 Score: 233
Period size: 71 Copynumber: 3.0 Consensus size: 62
178928 AAACAATATC
* * *
178938 AAGCGAGATAAATCTTGTTTT--TAAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCTA
1 AAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCTA
178998 AAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATCTCGAGTAAAAAC
1 AAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATCT----T-----C
*
179063 TTTCTC
57 TTTCTA
* *
179069 AAGCGAGACAAATCTTGTTTCAAGAAAAACAATCTTGAGTGAAATGAAATATCTTATTTC
1 AAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATCTTCTTTC
179129 GAGTAAAAAC
Statistics
Matches: 114, Mismatches: 6, Indels: 20
0.81 0.04 0.14
Matches are distributed among these distances:
60 20 0.18
62 33 0.29
66 1 0.01
67 1 0.01
71 59 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (62 bp):
AAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCTA
Found at i:179107 original size:71 final size:72
Alignment explanation
Indices: 178991--179194 Score: 261
Period size: 71 Copynumber: 2.8 Consensus size: 72
178981 GAAATGTCTT
* *
178991 CTTTCTAAAGCGAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATATC-TCGA
1 CTTTCTCAAGCGAGACAAATCTTGTTTAAAGAAAAACAATCTTGAGTGAAATGAAATATCTTCGA
179055 GTAAAAA
66 GTAAAAA
*
179062 CTTTCTCAAGCGAGACAAATCTTGTTTCAAGAAAAACAATCTTGAGTGAAATGAAATATCTTATT
1 CTTTCTCAAGCGAGACAAATCTTGTTTAAAGAAAAACAATCTTGAGTGAAATGAAATATC----T
179127 TCGAGTAAAAA
62 TCGAGTAAAAA
* * * * *
179138 CTGTCTCCAGCGAAACAAATCTGGTTTTAAAGAAAAACAAT-TTCAAGTGAAAT-AAAT
1 CTTTCTCAAGCGAGACAAATCTTG-TTTAAAGAAAAACAATCTT-GAGTGAAATGAAAT
179195 TTTCTGTATT
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
71 58 0.49
76 37 0.31
77 23 0.19
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (72 bp):
CTTTCTCAAGCGAGACAAATCTTGTTTAAAGAAAAACAATCTTGAGTGAAATGAAATATCTTCGA
GTAAAAA
Found at i:183799 original size:59 final size:59
Alignment explanation
Indices: 183691--183803 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
183681 ATGAAGGGTA
* *
183691 AAAAATAAAAGATCATAAATTTAAAGTACATAAAAAGTAAGGACTTAAATTAAATAAAG
1 AAAAATAAAAGATCATAAATTTAAAGTACATAAAAAGTAAGAACATAAATTAAATAAAG
* * * *
183750 AAAAGTAAAAGAT-ATAAATTTAAATGTGCAT-AAAATTAAATAACATAAATTAAA
1 AAAAATAAAAGATCATAAATTTAAA-GTACATAAAAAGT-AAGAACATAAATTAAA
183804 AGTGCAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 16 0.35
59 30 0.65
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.26
Consensus pattern (59 bp):
AAAAATAAAAGATCATAAATTTAAAGTACATAAAAAGTAAGAACATAAATTAAATAAAG
Found at i:184936 original size:22 final size:22
Alignment explanation
Indices: 184908--184965 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
184898 CAACAATGGT
184908 TGGTGGTAGCAGGCTCGGTTGG
1 TGGTGGTAGCAGGCTCGGTTGG
184930 TGGTGGTAGCAGGCTCGGTTGG
1 TGGTGGTAGCAGGCTCGGTTGG
*
184952 TGGTGGCAGCAGGC
1 TGGTGGTAGCAGGC
184966 ATGACAGGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.10, C:0.16, G:0.50, T:0.24
Consensus pattern (22 bp):
TGGTGGTAGCAGGCTCGGTTGG
Found at i:185948 original size:20 final size:21
Alignment explanation
Indices: 185901--185947 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
185891 TCTTTGCATG
*
185901 TGCTTCTTG-TTTTTTTCCTT
1 TGCTTTTTGCTTTTTTTCCTT
185921 TGCTTTTTGCTTTTTTT-CTT
1 TGCTTTTTGCTTTTTTTCCTT
185941 T-CTTTTT
1 TGCTTTTT
185948 TTCTCTTTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (21 bp):
TGCTTTTTGCTTTTTTTCCTT
Found at i:188921 original size:2 final size:2
Alignment explanation
Indices: 188916--188943 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
188906 ATTTGATTTA
188916 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
188944 TATTTTGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194280 original size:2 final size:2
Alignment explanation
Indices: 194273--194298 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
194263 AGTTCATTGC
194273 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
194299 AACTTACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:199959 original size:7 final size:7
Alignment explanation
Indices: 199947--199992 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
199937 TTATTTATAA
199947 AAATTTT
1 AAATTTT
199954 AAATTTT
1 AAATTTT
*
199961 AAA-TCT
1 AAATTTT
199967 AAATCTTT
1 AAAT-TTT
199975 AAATTTT
1 AAATTTT
*
199982 AAGTTTT
1 AAATTTT
199989 AAAT
1 AAAT
199993 GGATAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:202147 original size:9 final size:8
Alignment explanation
Indices: 202133--202184 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 8
202123 CACTATATCA
202133 AAATATATT
1 AAATAT-TT
202142 AAATATTT
1 AAATATTT
**
202150 ATTTATTT
1 AAATATTT
202158 ATAATATTT
1 A-AATATTT
202167 AATATATTT
1 AA-ATATTT
202176 AATATATTT
1 AA-ATATTT
202185 TGATATAACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 10 0.27
9 27 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
AAATATTT
Found at i:202182 original size:18 final size:18
Alignment explanation
Indices: 202134--202184 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
202124 ACTATATCAA
202134 AATATA-TTAA-ATATTT
1 AATATATTTAATATATTT
*
202150 -ATTTATTT-ATAATATTT
1 AATATATTTAAT-ATATTT
202167 AATATATTTAATATATTT
1 AATATATTTAATATATTT
202185 TGATATAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.18
16 2 0.07
17 6 0.21
18 13 0.46
19 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATATTTAATATATTT
Found at i:202190 original size:26 final size:26
Alignment explanation
Indices: 202134--202184 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
202124 ACTATATCAA
*
202134 AATATATTAAATATTTATTTATTTAT
1 AATATATTAAATATTTATATATTTAT
202160 AATAT-TTAATATATTTAATATATTT
1 AATATATTAA-ATATTT-ATATATTT
202185 TGATATAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 11 0.50
27 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATATTAAATATTTATATATTTAT
Found at i:202786 original size:24 final size:24
Alignment explanation
Indices: 202758--202803 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
202748 TTAAAAATCA
202758 AATTTAACAAAAACAATA-ATTATC
1 AATTTAACAAAAA-AATATATTATC
202782 AATTTAACAAAAAAATATATTA
1 AATTTAACAAAAAAATATATTA
202804 AGGACTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (24 bp):
AATTTAACAAAAAAATATATTATC
Found at i:208712 original size:22 final size:23
Alignment explanation
Indices: 208670--208713 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
208660 TATTCAGTCC
*
208670 TTGGTTTTTTGGTTGTTTTGTGA
1 TTGGTTTTTTGGTTGTCTTGTGA
208693 TTGG-TTTTTGCG-TGTCTTGTG
1 TTGGTTTTTTG-GTTGTCTTGTG
208714 GTTCTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.02, C:0.05, G:0.32, T:0.61
Consensus pattern (23 bp):
TTGGTTTTTTGGTTGTCTTGTGA
Found at i:209182 original size:22 final size:22
Alignment explanation
Indices: 209157--209220 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 22
209147 ACAAAAATTA
209157 AATAAACAAGATATAATATAAAAAT
1 AATAAA-AA-ATA-AATATAAAAAT
209182 AATAAAAAATAAATATAAAAAT
1 AATAAAAAATAAATATAAAAAT
* *
209204 AATAAAATATATATATA
1 AATAAAAAATAAATATA
209221 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 26 0.70
23 3 0.08
24 2 0.05
25 6 0.16
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAAAAAATAAATATAAAAAT
Found at i:209183 original size:11 final size:11
Alignment explanation
Indices: 209169--209220 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
209159 TAAACAAGAT
209169 ATAATATAAAA
1 ATAATATAAAA
209180 ATAATA-AAAA
1 ATAATATAAAA
209190 ATAAATATAAAA
1 AT-AATATAAAA
*
209202 ATAATA-AAAT
1 ATAATATAAAA
209212 ATATATATA
1 ATA-ATATA
209221 TATATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 12 0.33
11 17 0.47
12 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:209211 original size:16 final size:17
Alignment explanation
Indices: 209174--209214 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
209164 AAGATATAAT
209174 ATAAAA-ATAATAAAAA
1 ATAAAATATAATAAAAA
*
209190 AT-AAATATAA-AAATA
1 ATAAAATATAATAAAAA
209205 ATAAAATATA
1 ATAAAATATA
209215 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAATATAATAAAAA
Found at i:209217 original size:2 final size:2
Alignment explanation
Indices: 209210--209241 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
209200 AAATAATAAA
209210 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209242 TTCCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209356 original size:2 final size:2
Alignment explanation
Indices: 209347--209394 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
209337 TTTTAAAAAC
209347 TA TA -A 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
209388 TA TA TA T
1 TA TA TA T
209395 TTTCAAAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:209386 original size:145 final size:143
Alignment explanation
Indices: 209197--209464 Score: 346
Period size: 143 Copynumber: 1.9 Consensus size: 143
209187 AAAATAAATA
* *
209197 TAAAAATAATAAAATATATATATATATATATATATAATATTATATTTCCA-AAAATAAAAATATT
1 TAAAAATAATAAAATATATATATATATATATATATAATATTATATATACATAAAATAAAAATATT
*
209261 TTAAAAATTATAT-AT-TATATGTTTTCAAAAACCGATTTTAAAAACTATATAATATATATGTAT
66 TTAAAAACTATATAATATATATGTTTTC-AAAA-CG-TTTTAAAAACTATATAATATATATGTAT
209324 TTTCCAAACGTTTTTT
128 TTTCCAAACGTTTTTT
* * *** *
209340 TAAAAACT-ATAATATATATATATATATATATATATATATATATATATATATATATTTTCAAAAT
1 TAAAAA-TAATAAAATATATATATATATATATATATA-ATAT-TATATATACATAAAATAAAAAT
* * *
209404 GTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATAT
63 ATTTTAAAAACTATATAATATATATGTTTTCAAAACGTTTTAAAAACTATATAATATATAT
209465 ATTTTAAAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
143 33 0.31
144 5 0.05
145 30 0.28
146 22 0.21
147 6 0.06
148 11 0.10
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (143 bp):
TAAAAATAATAAAATATATATATATATATATATATAATATTATATATACATAAAATAAAAATATT
TTAAAAACTATATAATATATATGTTTTCAAAACGTTTTAAAAACTATATAATATATATGTATTTT
CCAAACGTTTTTT
Found at i:209425 original size:36 final size:36
Alignment explanation
Indices: 209253--209617 Score: 340
Period size: 36 Copynumber: 10.1 Consensus size: 36
209243 TCCAAAAATA
* * *
209253 AAAATATTTTAAAAATTATAT-AT-TATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
*
209287 AAAAACCGATTTTAAAAACTATATAATATATATGTATTTTCC
1 -AAAA-TG-TTTTAAAAACTATATAATATATA--TATTTT-C
* * *
209329 AAACGTTTTTTTAAAAAC--TATAATATATATA-TAT-
1 AAA--ATGTTTTAAAAACTATATAATATATATATTTTC
* * * * *
209363 ATATAT-ATATATATA-TATATATATATATATATTTTC
1 A-AAATGTTTTAAAAACTATATA-ATATATATATTTTC
*
209399 AAAATGTTTTAAAAACTATATAATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
*
209435 AAAATGTTTTAAAAACTATATATTATATATATTTT-
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
*
209470 AAAATGTTTTAAAAACTATATATTATATA-AGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATA-TTTTC
* * *
209506 CAAATGTTTTAAAAACTATAT-AT-TATATGTTTCC
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
*
209540 AAAATGTTTTAAAAACTATATAATATATATGTTTTC
1 AAAATGTTTTAAAAACTATATAATATATATATTTTC
* *
209576 AAAATGCTTTCAAAAACTATATATTATATATATATTTC
1 AAAATG-TTTTAAAAACTATATAATATATATAT-TTTC
209614 AAAA
1 AAAA
209618 ATCATTTGCA
Statistics
Matches: 274, Mismatches: 32, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
32 5 0.02
33 5 0.02
34 39 0.14
35 46 0.17
36 90 0.33
37 45 0.16
38 10 0.04
39 15 0.05
41 18 0.07
42 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATAATATATATATTTTC
Found at i:209455 original size:71 final size:72
Alignment explanation
Indices: 209378--209617 Score: 378
Period size: 71 Copynumber: 3.3 Consensus size: 72
209368 TATATATATA
209378 TATATATATATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTT
1 TATATAT-TATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTT
209443 TTAAAAAC
65 TTAAAAAC
* * *
209451 TATATATTATATATATTTT-AAAATGTTTTAAAAACTATATATTATATAAGTTTTCCAAATGTTT
1 TATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTT
209515 TAAAAAC
66 TAAAAAC
* *
209522 TATATA-T-TATATGTTTCCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGCTT
1 TATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATG-TT
*
209585 TCAAAAAC
65 TTAAAAAC
209593 TATATATTATATATATATTTCAAAA
1 TATATATTATATATAT-TTTCAAAA
209618 ATCATTTGCA
Statistics
Matches: 151, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
69 8 0.05
70 40 0.26
71 70 0.46
72 13 0.09
73 13 0.09
74 7 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTT
TAAAAAC
Found at i:209640 original size:71 final size:69
Alignment explanation
Indices: 209253--209617 Score: 321
Period size: 71 Copynumber: 5.1 Consensus size: 69
209243 TCCAAAAATA
* * *
209253 AAAATATTTTAAAAATTATATATTATATGTTTTCAAAAACCGATTTTAAAAACTATATAATATAT
1 AAAATGTTTTAAAAACTATATA-TATATGTTTTC-AAAA-TG-TTTTAAAAACTATAT-AT-TAT
*
209318 ATGTATTTTCC
60 ATATATTTT-C
* * * * * * * * *
209329 AAACGTTTTTTTAAAAACTATAATATATAT-ATAT-ATATAT-ATATATATA-TATATATATATA
1 AAA--ATGTTTTAAAAACTAT-ATATATATGTTTTCA-AAATGTTTTAAAAACTATATAT-TATA
209390 TATATTTTC
61 TATATTTTC
209399 AAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATA
1 AAAATGTTTTAAAAAC--TAT-ATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATA
209464 TATTTT-
63 TATTTTC
*
209470 AAAATGTTTTAAAAACTATATATTATATAAGTTTTCCAAATGTTTTAAAAACTATATA-T-TATA
1 AAAATGTTTTAAAAACTATATA-TATAT--GTTTTCAAAATGTTTTAAAAACTATATATTATATA
* *
209533 TGTTTCC
63 TATTTTC
*
209540 AAAATGTTTTAAAAACTATATAATATATATGTTTTCAAAATGCTTTCAAAAACTATATATTATAT
1 AAAATGTTTTAAAAAC--TAT-ATATATATGTTTTCAAAATG-TTTTAAAAACTATATATTATAT
209605 ATATATTTC
62 ATAT-TTTC
209614 AAAA
1 AAAA
209618 ATCATTTGCA
Statistics
Matches: 240, Mismatches: 28, Indels: 44
0.77 0.09 0.14
Matches are distributed among these distances:
68 14 0.06
69 16 0.07
70 44 0.18
71 77 0.32
72 32 0.13
73 21 0.09
74 7 0.03
75 1 0.00
76 5 0.02
77 2 0.01
78 18 0.08
79 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (69 bp):
AAAATGTTTTAAAAACTATATATATATGTTTTCAAAATGTTTTAAAAACTATATATTATATATAT
TTTC
Found at i:209642 original size:2 final size:2
Alignment explanation
Indices: 209631--209665 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
209621 ATTTGCAAAC
209631 TA TA -A 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
209666 ATAAATAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:210435 original size:22 final size:23
Alignment explanation
Indices: 210393--210436 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
210383 TATTTGGTCC
*
210393 TTGGTTTTTTAGTTGTTTTGTGA
1 TTGGTTTTTTAGTTGTCTTGTGA
210416 TTGG-TTTTT-GTGTGTCTTGTG
1 TTGGTTTTTTAGT-TGTCTTGTG
210437 GTTCTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 13 0.68
23 4 0.21
ACGTcount: A:0.05, C:0.02, G:0.30, T:0.64
Consensus pattern (23 bp):
TTGGTTTTTTAGTTGTCTTGTGA
Found at i:210916 original size:4 final size:4
Alignment explanation
Indices: 210907--210973 Score: 70
Period size: 4 Copynumber: 16.8 Consensus size: 4
210897 ACCCAAAAAT
210907 TAAA TAAA TAAGA TATAA TATAA -AAA T-AA TAAA -AAA TAAA TATAA
1 TAAA TAAA TAA-A TA-AA TA-AA TAAA TAAA TAAA TAAA TAAA TA-AA
210952 -AAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAA
210974 TATTATATTT
Statistics
Matches: 56, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
3 10 0.18
4 34 0.61
5 11 0.20
6 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:210933 original size:22 final size:21
Alignment explanation
Indices: 210908--210968 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
210898 CCCAAAAATT
210908 AAATAAATAAGATATAATATAA
1 AAATAAATAA-ATATAATATAA
*
210930 AAAT-AATAAAAAATAAATATAA
1 AAATAAAT-AAATAT-AATATAA
210952 AAATAAATAAATA-AATA
1 AAATAAATAAATATAATA
210969 AATAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 21 0.62
23 3 0.09
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AAATAAATAAATATAATATAA
Found at i:210973 original size:22 final size:22
Alignment explanation
Indices: 210901--210973 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 22
210891 GGAAAAACCC
210901 AAAAATTAAATAAATAAGATATAAT
1 AAAAA-TAAATAAATAA-ATA-AAT
210926 ATAAAA-ATAATAAA-AAATAAATAT
1 A-AAAATA-AATAAATAAAT-AA-AT
210950 AAAAATAAATAAATAAATAAAT
1 AAAAATAAATAAATAAATAAAT
210972 AA
1 AA
210974 TATTATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
22 4 0.10
23 15 0.36
24 12 0.29
25 7 0.17
26 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (22 bp):
AAAAATAAATAAATAAATAAAT
Found at i:211004 original size:38 final size:36
Alignment explanation
Indices: 210949--211019 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 36
210939 AAAATAAATA
210949 TAAAAATAAATAAATAAATAAATA-ATATTATATTTC
1 TAAAAATAAATAAATAAA-AAATATATATTATATTTC
* *
210985 TAAAAATAAAATATTATAAAAATTATATATTATAT
1 TAAAAAT-AAATA-AATAAAAAATATATATTATAT
211020 GTTTTCAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 9 0.30
38 14 0.47
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (36 bp):
TAAAAATAAATAAATAAAAAATATATATTATATTTC
Found at i:211006 original size:16 final size:16
Alignment explanation
Indices: 210985--211018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
210975 ATTATATTTC
210985 TAAAAATAAAATATTA
1 TAAAAATAAAATATTA
* *
211001 TAAAAATTATATATTA
1 TAAAAATAAAATATTA
211017 TA
1 TA
211019 TGTTTTCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAATAAAATATTA
Found at i:211852 original size:19 final size:21
Alignment explanation
Indices: 211819--211859 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
211809 GGCTAAAAAT
211819 ACTGTAGCAGTGTATCGATAC
1 ACTGTAGCAGTGTATCGATAC
211840 ACTGTAG-AG-GTATCGATAC
1 ACTGTAGCAGTGTATCGATAC
211859 A
1 A
211860 GTTTCACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 2 0.10
21 7 0.35
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (21 bp):
ACTGTAGCAGTGTATCGATAC
Found at i:212111 original size:2 final size:2
Alignment explanation
Indices: 212104--212172 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
212094 CAAAATTATT
212104 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
212146 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 T
212173 TTAAAATGTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:212202 original size:34 final size:35
Alignment explanation
Indices: 212156--212284 Score: 149
Period size: 34 Copynumber: 3.7 Consensus size: 35
212146 TATATATATA
212156 TATATATATATATATATTT-AAAATGTTTTAAAAAC
1 TATATAT-TATATATATTTCAAAATGTTTTAAAAAC
*
212191 TATATATTATATA-AGTTTTCCAAA-GTTTTTAAAAAC
1 TATATATTATATATA--TTTCAAAATG-TTTTAAAAAC
*
212227 TATATATTATATGT-TTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATTTCAAAATGTTTTAAAAAC
* *
212261 TATATAATATATATGTTTTCAAAA
1 TATATATTATATAT-ATTTCAAAA
212285 ACTATATATT
Statistics
Matches: 81, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
33 1 0.01
34 35 0.43
35 12 0.15
36 33 0.41
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (35 bp):
TATATATTATATATATTTCAAAATGTTTTAAAAAC
Found at i:212202 original size:36 final size:35
Alignment explanation
Indices: 212154--212284 Score: 142
Period size: 36 Copynumber: 3.7 Consensus size: 35
212144 TATATATATA
212154 TATATATATATATATATATTTAAAATGTTTTAAAAAC
1 TATATAT-TATATATAT-TTTAAAATGTTTTAAAAAC
*
212191 TATATATTATATA-AGTTTTCCAAA-GTTTTTAAAAAC
1 TATATATTATATATA-TTTT-AAAATG-TTTTAAAAAC
* *
212227 TATATATTATATGT-TTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTAAAATGTTTTAAAAAC
* *
212261 TATATAATATATATGTTTTCAAAA
1 TATATATTATATATATTTT-AAAA
212285 ACTATATATT
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
34 25 0.31
35 12 0.15
36 36 0.45
37 7 0.09
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (35 bp):
TATATATTATATATATTTTAAAATGTTTTAAAAAC
Found at i:212301 original size:28 final size:26
Alignment explanation
Indices: 212248--212312 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
212238 TGTTTTCAAA
212248 ATGTTTT-AAAAACTATATAATATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
212273 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
212299 ATATATTTCAAAAA
1 ATGT-TTTCAAAAA
212313 TCATTTGCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 7 0.19
26 20 0.56
27 9 0.25
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATAATATAT
Found at i:212761 original size:16 final size:17
Alignment explanation
Indices: 212740--212784 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
212730 ATACTAAAGC
212740 ATAAACATACAACCAAA
1 ATAAACATACAACCAAA
* *
212757 A-AAACAT-TAACTAAA
1 ATAAACATACAACCAAA
212772 ATAAACATACAAC
1 ATAAACATACAAC
212785 AAGTCGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (17 bp):
ATAAACATACAACCAAA
Found at i:212878 original size:3 final size:3
Alignment explanation
Indices: 212872--212939 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
212862 TGAATGATGA
212872 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
212920 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
212940 CTACTACTAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:215192 original size:68 final size:68
Alignment explanation
Indices: 215083--215224 Score: 266
Period size: 68 Copynumber: 2.1 Consensus size: 68
215073 ATTAACCCAC
*
215083 TTCTCTACCCAAATGGCCTATCCTTTCATTTACATCCATTAAGGAACCAACTTTGAGCCTTTACC
1 TTCTCTACCCAAATGGCCTATCATTTCATTTACATCCATTAAGGAACCAACTTTGAGCCTTTACC
215148 CTT
66 CTT
*
215151 TTCTCTACCCAAATGGCCTATCATTTCATTTATATCCATTAAGGAACCAACTTTGAGCCTTTACC
1 TTCTCTACCCAAATGGCCTATCATTTCATTTACATCCATTAAGGAACCAACTTTGAGCCTTTACC
215216 CTT
66 CTT
215219 TTCTCT
1 TTCTCT
215225 TTTTTTTTAC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 72 1.00
ACGTcount: A:0.25, C:0.30, G:0.08, T:0.37
Consensus pattern (68 bp):
TTCTCTACCCAAATGGCCTATCATTTCATTTACATCCATTAAGGAACCAACTTTGAGCCTTTACC
CTT
Found at i:228302 original size:20 final size:20
Alignment explanation
Indices: 228254--228315 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
228244 AACTTAAATC
*
228254 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
228274 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
228292 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
228311 AAAAT
1 AAAAT
228316 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:228355 original size:21 final size:21
Alignment explanation
Indices: 228331--228396 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
228321 ATCTATAATA
228331 TAATATTAAAAAAATAATATT
1 TAATATTAAAAAAATAATATT
* *
228352 TAATTTATTTAAAAAATTAATA-G
1 TAA--TA-TTAAAAAAATAATATT
* *
228375 TAATATCTATAAATATAATATT
1 TAATAT-TAAAAAAATAATATT
228397 AAAAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
20 1 0.03
21 15 0.44
23 5 0.15
24 13 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TAATATTAAAAAAATAATATT
Found at i:228408 original size:59 final size:58
Alignment explanation
Indices: 228318--228430 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 58
228308 TATAAAATTA
228318 AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATTAATAGT
1 AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATTAATAGT
**
228376 AATATCTATAAATATAATATTAAAAATTTAATATTTAATTTATTTAAAAAATTAA
1 AATATCTAT-AATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATTAA
228431 AATTAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 9 0.17
59 43 0.83
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (58 bp):
AATATCTATAATATAATATTAAAAAAATAATATTTAATTTATTTAAAAAATTAATAGT
Found at i:228460 original size:17 final size:17
Alignment explanation
Indices: 228430--228478 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
228420 TAAAAAATTA
228430 AAATTAAA-ATTAAAATC
1 AAATTAAATA-TAAAATC
228447 AAA-TATAATATAAAATC
1 AAATTA-AATATAAAATC
228464 AAATTAAATATAAAA
1 AAATTAAATATAAAA
228479 CCTCTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.07
17 24 0.83
18 3 0.10
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTAAATATAAAATC
Found at i:233085 original size:31 final size:31
Alignment explanation
Indices: 233049--233107 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
233039 AACTTAAAAG
*
233049 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
233080 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
233108 CCATGCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:233161 original size:22 final size:22
Alignment explanation
Indices: 233130--233252 Score: 210
Period size: 22 Copynumber: 5.5 Consensus size: 22
233120 AATAATAAAT
233130 TTTTGAAAATAAATCAATCCATA
1 TTTT-AAAATAAATCAATCCATA
233153 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
233175 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
233197 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
233219 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
233241 TTTTAAAATAAA
1 TTTTAAAATAAA
233253 ATTTTAAAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
22 90 0.96
23 4 0.04
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.39
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:237329 original size:35 final size:33
Alignment explanation
Indices: 237262--237341 Score: 90
Period size: 35 Copynumber: 2.4 Consensus size: 33
237252 CGTCATCAAA
* * *
237262 ATCAGAACATATAAGCACACACAGTGCTATCAC
1 ATCAGAACATATAAGAACACAAAGTGCAATCAC
*
237295 ATCAGAATCATAATATGAACACAAAGTGCAATCAC
1 ATCAGAA-CAT-ATAAGAACACAAAGTGCAATCAC
*
237330 ATC-GAAGATATA
1 ATCAGAACATATA
237342 CTAGTGTACC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.08
33 9 0.22
34 6 0.15
35 22 0.55
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.20
Consensus pattern (33 bp):
ATCAGAACATATAAGAACACAAAGTGCAATCAC
Found at i:245917 original size:3 final size:3
Alignment explanation
Indices: 245903--245978 Score: 84
Period size: 3 Copynumber: 25.7 Consensus size: 3
245893 ATATAATATG
* * *
245903 TAA TAT TAA TAA TAA TAA TAA TAA TAA TATA TTA TTA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
245948 TAG TTA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
245979 TTTATAACCC
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.90
4 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:246239 original size:56 final size:56
Alignment explanation
Indices: 246154--246530 Score: 383
Period size: 56 Copynumber: 6.9 Consensus size: 56
246144 TCGACTAGTT
* * * * * * *
246154 GGTTTGCTCCCTATTGC-TTCAGGGAGTATAGAACTCAAACAATCTTCTGCCTACT
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
* * * * * * * *
246209 AGTTCGTTTCCACTTTCTTTCAATGAGTATATAACTCGAATAATCTTCTGCAAACG
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
* * * *
246265 GGTTCGCTCCCTATTGC-TTCAGGGAGTATAGAACTC-AAGAAATCTTCTGCCAACG
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAA-CAATCTTCTGCCAACG
* * *
246320 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTTGAATAATCTTCTGCAAACG
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
* * *
246376 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATATAACTCGAAC-ATCTTCTTCCTACG
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
* * * * * *
246431 GGTTCACTCTCTCTTTCTTT-AGGGAGTATGGAACTCGAAC-ATCTTCTTCCCACG
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
* * *
246485 GGTTCACCCCCTCTTTCTTT-AGGGAGTATAGAACTCGAAC-ATCTTC
1 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTC
246531 AACAATCGTG
Statistics
Matches: 271, Mismatches: 47, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
54 75 0.28
55 84 0.31
56 110 0.41
57 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (56 bp):
GGTTCGCTCCCTCTTTCTTTCAAGGAGTATAGAACTCGAACAATCTTCTGCCAACG
Found at i:246361 original size:111 final size:111
Alignment explanation
Indices: 246154--246520 Score: 420
Period size: 111 Copynumber: 3.3 Consensus size: 111
246144 TCGACTAGTT
* ** * *
246154 GGTTTGCTCCCTATTGCTTCAGGGAGTATAGAACTCAA-ACAATCTTCTGCCTACTAGTTCGTTT
1 GGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAGA-AATCTTCTGCCTACGGGTTCGCTC
* * *
246218 CCACTTTCTTTCAATGAGTATATAACTCGAATAATCTTCTGCAAACG
65 CCTCTTTCTTTCAAGGAGTATAGAACTCGAATAATCTTCTGCAAACG
*
246265 GGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAGAAATCTTCTGCCAACGGGTTCGCTCC
1 GGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAGAAATCTTCTGCCTACGGGTTCGCTCC
*
246330 CTCTTTCTTTCAAGGAGTATAGAACTTGAATAATCTTCTGCAAACG
66 CTCTTTCTTTCAAGGAGTATAGAACTCGAATAATCTTCTGCAAACG
* * * * * *
246376 GGTTCGCTCCCTCTTTCTTTCAAGGAGTATATAACTC--GAACATCTTCTTCCTACGGGTTCACT
1 GGTTCGCTCCCTATTGC-TTCAGGGAGTATAGAACTCAAGAA-ATCTTCTGCCTACGGGTTCGCT
* * * * * **
246439 CTCTCTTTCTTT-AGGGAGTATGGAACTCGAA-CATCTTCTTCCCACG
64 CCCTCTTTCTTTCAAGGAGTATAGAACTCGAATAATCTTCTGCAAACG
* * * * *
246485 GGTTCACCCCCTCTTTCTTTAGGGAGTATAGAACTC
1 GGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTC
246521 GAACATCTTC
Statistics
Matches: 223, Mismatches: 30, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
108 16 0.07
109 26 0.12
110 19 0.09
111 144 0.65
112 18 0.08
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (111 bp):
GGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAGAAATCTTCTGCCTACGGGTTCGCTCC
CTCTTTCTTTCAAGGAGTATAGAACTCGAATAATCTTCTGCAAACG
Found at i:246594 original size:55 final size:55
Alignment explanation
Indices: 246508--246956 Score: 676
Period size: 55 Copynumber: 8.4 Consensus size: 55
246498 TTTCTTTAGG
*
246508 GAGTAT-AGAACTCGAAC-ATCTTCAACAATCGTGTCTTCTCCCTATTCCTTCAGA
1 GAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
** * *
246562 GAGTATAAGACTATAACAATCTCCAACAATCGTGTCTTCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
246617 GAGTATAAGATTTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
246672 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATT-CTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
246726 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
246781 GAGTATAAGACTCAAACAATCTTCAATAATCGTGTCTGCTCCCTA----TTC---
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
246829 ---TA-AA-ACTCGAACAATCTTCAACAATCTTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
246879 GAGTATAAGACTCGAAAAATCTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
246934 GAGTATAAGACTCGAACAATCTT
1 GAGTATAAGACTCGAACAATCTT
246957 GATGCTTCAA
Statistics
Matches: 361, Mismatches: 19, Indels: 29
0.88 0.05 0.07
Matches are distributed among these distances:
43 33 0.09
44 2 0.01
45 2 0.01
47 3 0.01
51 3 0.01
53 2 0.01
54 68 0.19
55 248 0.69
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
Found at i:246782 original size:109 final size:109
Alignment explanation
Indices: 246499--246956 Score: 672
Period size: 109 Copynumber: 4.3 Consensus size: 109
246489 CACCCCCTCT
* * *
246499 TTCTTTAGGGAGTAT-AGAACTCGAAC-ATCTTCAACAATCGTGTCTTCTCCCTATTCCTTCAGA
1 TTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
** * *
246562 GAGTATAAGACTATAACAATCTCCAACAATCGTGTCTTCTCCCTA
65 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
* *
246607 TTCCTTCAGAGAGTATAAGATTTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1 TT-CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
246672 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
65 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
246717 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAG
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAG
* *
246782 AGTATAAGACTCAAACAATCTTCAATAATCGTGTCTGCTCCCTA
66 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
*
246826 ---TTC------TA-AA-ACTCGAACAATCTTCAACAATCTTGTCTGCTCCCTATTCCTTCAGAG
1 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAG
* *
246880 AGTATAAGACTCGAAAAATCTTCAACAATCGTGTCCGCTCCCTA
66 AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
246924 TTCCTTCAGAGAGTATAAGACTCGAACAATCTT
1 TT-CTTCAGAGAGTATAAGACTCGAACAATCTT
246957 GATGCTTCAA
Statistics
Matches: 317, Mismatches: 18, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
98 86 0.27
99 2 0.01
100 2 0.01
102 3 0.01
106 3 0.01
108 4 0.01
109 122 0.38
110 95 0.30
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (109 bp):
TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAG
AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTA
Found at i:246844 original size:43 final size:43
Alignment explanation
Indices: 246790--246871 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
246780 AGAGTATAAG
*
246790 ACTCAAACAATCTTCAATAATCGTGTCTGCTCCCTATTCTAAA
1 ACTCAAACAATCTTCAACAATCGTGTCTGCTCCCTATTCTAAA
* *
246833 ACTCGAACAATCTTCAACAATCTTGTCTGCTCCCTATTC
1 ACTCAAACAATCTTCAACAATCGTGTCTGCTCCCTATTC
246872 CTTCAGAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.33
Consensus pattern (43 bp):
ACTCAAACAATCTTCAACAATCGTGTCTGCTCCCTATTCTAAA
Found at i:246904 original size:98 final size:98
Alignment explanation
Indices: 246735--246926 Score: 341
Period size: 98 Copynumber: 2.0 Consensus size: 98
246725 AGAGTATAAG
246735 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAA
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAA
* *
246800 TCTTCAATAATCGTGTCTGCTCCCTATTCTAAA
66 TCTTCAACAATCGTGTCCGCTCCCTATTCTAAA
*
246833 ACTCGAACAATCTTCAACAATCTTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAA-A
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC-AAACA
246897 ATCTTCAACAATCGTGTCCGCTCCCTATTC
65 ATCTTCAACAATCGTGTCCGCTCCCTATTC
246927 CTTCAGAGAG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
98 87 0.97
99 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (98 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAA
TCTTCAACAATCGTGTCCGCTCCCTATTCTAAA
Found at i:248013 original size:18 final size:18
Alignment explanation
Indices: 247992--248044 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
247982 TTGAACCCCC
* *
247992 TTTTATTCATTTTTTTTT
1 TTTTTTTCATTTTTTATT
248010 TTTTTTTCATTTTTTCATT
1 TTTTTTTCATTTTTT-ATT
248029 TTTTTTCTCATTTTTT
1 TTTTTT-TCATTTTTT
248045 CCTTTCCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 14 0.45
19 8 0.26
20 9 0.29
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCATTTTTTATT
Found at i:248024 original size:20 final size:20
Alignment explanation
Indices: 247998--248045 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
247988 CCCCTTTTAT
*
247998 TCATTTTTT--TTTTTTTTT
1 TCATTTTTTCATTTTTTTTC
248016 TCATTTTTTCATTTTTTTTC
1 TCATTTTTTCATTTTTTTTC
248036 TCATTTTTTC
1 TCATTTTTTC
248046 CTTTCCATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.33
20 18 0.67
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (20 bp):
TCATTTTTTCATTTTTTTTC
Found at i:248042 original size:26 final size:27
Alignment explanation
Indices: 247992--248042 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
247982 TTGAACCCCC
* **
247992 TTTTATTCATTTTTTTTTTTTTTTTCA
1 TTTTATTCATTTTTTTTCTCATTTTCA
248019 TTTT-TTCATTTTTTTTCTCATTTT
1 TTTTATTCATTTTTTTTCTCATTTT
248043 TTCCTTTCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTATTCATTTTTTTTCTCATTTTCA
Found at i:251556 original size:8 final size:8
Alignment explanation
Indices: 251543--251570 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
251533 AAGAGGATAT
251543 ATATATAC
1 ATATATAC
251551 ATATATAC
1 ATATATAC
251559 ATATATAC
1 ATATATAC
251567 ATAT
1 ATAT
251571 GGGAGACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:256145 original size:3 final size:3
Alignment explanation
Indices: 256137--256227 Score: 132
Period size: 3 Copynumber: 30.7 Consensus size: 3
256127 TATGTAACAT
*
256137 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* *
256182 TAA TAG TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
256228 TTTATAATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
2 4 0.05
3 73 0.92
4 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:257169 original size:21 final size:21
Alignment explanation
Indices: 257145--257238 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
257135 CACCGAAGTT
*
257145 CCACATAATTATCCCGAATGA
1 CCACATAATTATCCCAAATGA
* * * *
257166 CCACATAGGTTTGTACCGAAGTG-
1 CCACATA--ATTAT-CCCAAATGA
*
257189 CCACAT-ATTAGTCCCAAAGGA
1 CCACATAATTA-TCCCAAATGA
* *
257210 CCACATAATTGTCTCAAATGA
1 CCACATAATTATCCCAAATGA
257231 CCACATAA
1 CCACATAA
257239 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
20 7 0.13
21 30 0.56
22 3 0.06
23 9 0.17
24 5 0.09
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (21 bp):
CCACATAATTATCCCAAATGA
Found at i:257185 original size:44 final size:44
Alignment explanation
Indices: 257131--257216 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 44
257121 CAGCTCGTAA
* * *
257131 TTTGCACCGAAGTTCCACATAATTA-TCCCGAATGACCACATAGG
1 TTTGCACCGAAGTGCCACAT-ATTAGTCCCAAAGGACCACATAGG
*
257175 TTTGTACCGAAGTGCCACATATTAGTCCCAAAGGACCACATA
1 TTTGCACCGAAGTGCCACATATTAGTCCCAAAGGACCACATA
257217 ATTGTCTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATATTAGTCCCAAAGGACCACATAGG
Found at i:261390 original size:13 final size:14
Alignment explanation
Indices: 261360--261406 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
261350 TTTTTAAAGT
261360 AATTTATAAAATTA
1 AATTTATAAAATTA
261374 AATTTAT-AAA-TA
1 AATTTATAAAATTA
261386 GAATTTTAATAAAATTA
1 -AA-TTT-ATAAAATTA
261403 AATT
1 AATT
261407 AAATAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.07
13 5 0.18
14 10 0.36
15 4 0.14
16 5 0.18
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
AATTTATAAAATTA
Found at i:261474 original size:26 final size:26
Alignment explanation
Indices: 261423--261474 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
261413 ATAAATTAAT
*
261423 ATGACTAAATAATAATAATAACAATA
1 ATGACTAAATAATAATAATAAAAATA
* *
261449 ATGATTAAAGTAATAAT-TTAAAAATA
1 ATGACTAAA-TAATAATAATAAAAATA
261475 TTGAAATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
ATGACTAAATAATAATAATAAAAATA
Found at i:262112 original size:19 final size:22
Alignment explanation
Indices: 262070--262117 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 22
262060 ACCGTCGGTT
*
262070 ACTATTCCAAGCACTGTCGGTC
1 ACTATTCCAAGCACTGTCGATC
262092 ACTATTCC-AGC-C-GTCGATC
1 ACTATTCCAAGCACTGTCGATC
262111 ACTATTC
1 ACTATTC
262118 TGGTCGTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 1 0.04
21 3 0.12
22 8 0.32
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (22 bp):
ACTATTCCAAGCACTGTCGATC
Found at i:263019 original size:36 final size:35
Alignment explanation
Indices: 262925--263177 Score: 175
Period size: 36 Copynumber: 7.0 Consensus size: 35
262915 CTTCTGGAAA
*
262925 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGAAAAATT
* * ** * *
262960 GCTATTTTGAGTGAAACATTCTCAAGCGAGAAACAATT
1 --TGTTTTAAGAAAAACAATCTCAAGTGAGAAA-AATT
262998 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGA-AAAATT
* * ** ** *
263034 TATTTTATGTGAAACTTTCTCAAGTGAGAAACAGTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGAAA-AATT
* * *
263070 TTTTTTAAGAAAAACAATATCAAGTGAGATAAA-T
1 TGTTTTAAGAAAAACAATCTCAAGTGAGAAAAATT
* ** *** * * *
263104 TGTTATTTCGAGTGAAATTTTCTCAAGCGATAAACAGTT
1 TG-T-TTT-AAGAAAAACAATCTCAAGTGAGAAA-AATT
*
263143 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGAAAAATT
263178 GCTATTTTAA
Statistics
Matches: 157, Mismatches: 51, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
34 2 0.01
35 7 0.04
36 95 0.61
37 44 0.28
38 6 0.04
39 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGAAAAATT
Found at i:263143 original size:73 final size:72
Alignment explanation
Indices: 262925--263184 Score: 389
Period size: 73 Copynumber: 3.6 Consensus size: 72
262915 CTTCTGGAAA
*
262925 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTTGAGTGAAACATTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTA-TTTGAGTGAAACTTTCTCAAGCGAG
*
262990 AAACAATT
65 AAACAGTT
* *
262998 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT--TATTTTATGTGAAACTTTCTCAAGTGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATTGCTATTTGA-GTGAAACTTTCTCAAGCGA
263061 GAAACAGTT
64 GAAACAGTT
* * * * *
263070 TTTTTTAAGAAAAACAATATCAAGTGAGATAAATTGTTATTTCGAGTGAAATTTTCTCAAGCGAT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT-GAGTGAAACTTTCTCAAGCGAG
263135 AAACAGTT
65 AAACAGTT
263143 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
263185 TAAAACATCC
Statistics
Matches: 169, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
71 9 0.05
72 55 0.33
73 99 0.59
74 6 0.04
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTGAGTGAAACTTTCTCAAGCGAGA
AACAGTT
Found at i:263962 original size:22 final size:22
Alignment explanation
Indices: 263898--263949 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
263888 AATAAAGCGT
*
263898 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
263920 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATATA
263942 TCATCTTT
1 TCATCTTT
263950 AAAGAGTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:271577 original size:12 final size:13
Alignment explanation
Indices: 271553--271581 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
271543 AAAAATGCAA
271553 AAATGCAAAATGT
1 AAATGCAAAATGT
271566 AAATGC-AAATGT
1 AAATGCAAAATGT
271578 AAAT
1 AAAT
271582 ATATGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:271804 original size:40 final size:40
Alignment explanation
Indices: 271729--271809 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
271719 GTGCATCAAA
* * *
271729 CAAAACTTTATATATAGGGGATAACTTTCAGTCCTATCTT
1 CAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
*
271769 CAAAACTTTACATATAGGGGATAACTTTCCCTCCTAACTT
1 CAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
271809 C
1 C
271810 TCTGAAACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (40 bp):
CAAAACTTTACATATAGGGGATAACTTTCACTCCTAACTT
Found at i:275136 original size:23 final size:23
Alignment explanation
Indices: 275105--275150 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
275095 GGGAACATAA
*
275105 CGGCAGAGCAGTTGGAGTAGAGG
1 CGGCAGAGCAGCTGGAGTAGAGG
*
275128 CGGCGGAGCAGCTGGAGTAGAGG
1 CGGCAGAGCAGCTGGAGTAGAGG
275151 AACGGCTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.50, T:0.11
Consensus pattern (23 bp):
CGGCAGAGCAGCTGGAGTAGAGG
Found at i:279249 original size:20 final size:19
Alignment explanation
Indices: 279224--279278 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
279214 TATCTTGAAA
279224 ATGGTATCGATACCATACCC
1 ATGGTATCGATACC-TACCC
279244 ATGGTATCGATA-CTACCC
1 ATGGTATCGATACCTACCC
*
279262 ACTCAGTATCGATACCT
1 A-T-GGTATCGATACCT
279279 TCTTCAAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 6 0.19
19 2 0.06
20 21 0.68
21 2 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (19 bp):
ATGGTATCGATACCTACCC
Found at i:288150 original size:20 final size:20
Alignment explanation
Indices: 288125--288167 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
288115 TTTAAAAGCT
*
288125 CATTTAGAATCATATAGATG
1 CATTTAGAAGCATATAGATG
*
288145 CATTTAGAAGCATATAGTTG
1 CATTTAGAAGCATATAGATG
288165 CAT
1 CAT
288168 GTGGTGGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTTAGAAGCATATAGATG
Found at i:293467 original size:20 final size:20
Alignment explanation
Indices: 293442--293484 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
293432 TCTAAAAGCC
293442 CATTTAGGATCATATAGATG
1 CATTTAGGATCATATAGATG
*
293462 CATTTAGGATCATATAGTTG
1 CATTTAGGATCATATAGATG
293482 CAT
1 CAT
293485 GTGGTGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (20 bp):
CATTTAGGATCATATAGATG
Found at i:295686 original size:559 final size:559
Alignment explanation
Indices: 294384--295838 Score: 2579
Period size: 559 Copynumber: 2.6 Consensus size: 559
294374 CTAATCCACC
* * *
294384 TTAGACATAGAAGTAAGATCATTCTGAGAAGCGGACTTAAATTTCCTAAGTAACTCCTATCACTC
1 TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
294449 ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
66 ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
* * * * *
294514 TTTATATTGTCTTTGCATTTTCATTTGTTTACACTAAACACAATTTTATTTGTCACGATATCTTC
131 TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAACACAA-TTTATTTGTCACGACATCTCC
*
294579 ATCCATTTTGCCACAACATTCTCATTTATGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
195 ATCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
*
294644 TGCATAAACTTTACTCAAAATCTCTCCAATCCATGTGGATACGATACTCACTCATCGCTGTATTA
260 TGCATAAACTTTACTCAAAATCTCTCCAATCCATGTGGATACGATACTCACTCATCACTGTATTA
*
294709 CTTGTTCGATTATGCATAAGGCTAGGATTTCGTTCGACTAAAAGGAGTTGTGCATGAGCAATAGG
325 CTTGTTCGATTATGCATAAGGCTAGGATTTCATTCGACTAAAAGGAGTTGTGCATGAGCAATAGG
*
294774 TTAGATGTTAATGCAGCTGCAAAAAGGTATTGTCGAGACATATCTTGTTATTTGGACCAATAGGA
390 TTAGATGTTAATGCAGCCGCAAAAAGGTATTGTCGAGACATATCTTGTTATTTGGACCAATAGGA
* * * *
294839 TCACTATAGGGGTTTACGCCAACCGGTTTTTCCAAGGCATATTCACTCTGTCGAGTCTCTTACTA
455 TCACTACAGGGGTTTACGCCAACCGATTTTACCAAGGCATATTCACTCTGTCGAGTCCCTTACTA
* *
294904 GAGATAGCATAGGGCACCCTAGTAGATTTTGTCGGGCAGA
520 GAGATAGCATAGGGCACCCTAGTAGACTCTGTCGGGCAGA
294944 TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
1 TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
295009 ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
66 ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
295074 TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAACACAAGTTTATTTGTCACGACATCTCC
131 TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAACACAA-TTTATTTGTCACGACATCTCC
295139 ATCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
195 ATCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
*
295204 TGCATAAACTTTACTCAAGATCTCTCCAATCCATGTGGATACGATACTCACTCATCACTGTATTA
260 TGCATAAACTTTACTCAAAATCTCTCCAATCCATGTGGATACGATACTCACTCATCACTGTATTA
295269 CTTGTTCGATTATGCATAAGGCTAGGATTTCATTCGACTAAAAGGAGTTGTGCATGAGCAATAGG
325 CTTGTTCGATTATGCATAAGGCTAGGATTTCATTCGACTAAAAGGAGTTGTGCATGAGCAATAGG
295334 TTAGATGTTAATGCAGCCGCAAAAAGGTATTGTCGAGACATATCTTGTTA-TTGGACCAATAGGA
390 TTAGATGTTAATGCAGCCGCAAAAAGGTATTGTCGAGACATATCTTGTTATTTGGACCAATAGGA
* * *
295398 TCACTGCAGGGGTTTACGCCAACCGATTTTACCAAGGCGTCTTCACTCTGTCGAGTCCCTTACTA
455 TCACTACAGGGGTTTACGCCAACCGATTTTACCAAGGCATATTCACTCTGTCGAGTCCCTTACTA
*
295463 GAGATAGCATAGGGCACCCTAGTAGACTCTGTCGGGCATA
520 GAGATAGCATAGGGCACCCTAGTAGACTCTGTCGGGCAGA
295503 TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
1 TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
* * *
295568 ATTCTCATAGTAGCTTGTCGTATGAGGAAGTCTAAAGTCTTGATAATCAAATCCAGTATTTACAT
66 ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
*
295633 TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAAAACAATTTAATTTGTCACGACATCTCC
131 TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAACACAATTT-ATTTGTCACGACATCTCC
295698 ATCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
195 ATCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAG
* * * * *
295763 TTCATAAACTTTACTCAATATCTCTCCAATCCCTGTGGATATGATACTTACTCATCACTGTATTA
260 TGCATAAACTTTACTCAAAATCTCTCCAATCCATGTGGATACGATACTCACTCATCACTGTATTA
*
295828 CTTATTCGATT
325 CTTGTTCGATT
295839 GTGTATACTT
Statistics
Matches: 860, Mismatches: 34, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
558 3 0.00
559 431 0.50
560 426 0.50
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (559 bp):
TTAGGCATAGAAGTAAGATCATTCTAAGAAGTGGACTTAAATTTCCTAAGTAACTCCTATCACTC
ATTCCCATAGTAGCTTGTCGTGTGAGGAAGTCTAAAGTCCTGATAATCAAATCCAGTATTTACAT
TTTATATTGCCTTTGCATTTCCATTTGTTTGCACTAAACACAATTTATTTGTCACGACATCTCCA
TCCATTTTGCCACAACATTCTCATTTGTGAATATCATTAGCTATACTTAGTTACTTTAGAATAGT
GCATAAACTTTACTCAAAATCTCTCCAATCCATGTGGATACGATACTCACTCATCACTGTATTAC
TTGTTCGATTATGCATAAGGCTAGGATTTCATTCGACTAAAAGGAGTTGTGCATGAGCAATAGGT
TAGATGTTAATGCAGCCGCAAAAAGGTATTGTCGAGACATATCTTGTTATTTGGACCAATAGGAT
CACTACAGGGGTTTACGCCAACCGATTTTACCAAGGCATATTCACTCTGTCGAGTCCCTTACTAG
AGATAGCATAGGGCACCCTAGTAGACTCTGTCGGGCAGA
Found at i:296283 original size:2 final size:2
Alignment explanation
Indices: 296276--296306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
296266 CCAAAGATTA
296276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
296307 AAGAATGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:296337 original size:16 final size:16
Alignment explanation
Indices: 296316--296348 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
296306 AAAGAATGCT
296316 GTCAAAAAATAAGCAA
1 GTCAAAAAATAAGCAA
296332 GTCAAAAAATAAGCAA
1 GTCAAAAAATAAGCAA
296348 G
1 G
296349 AAACGTGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.12, G:0.15, T:0.12
Consensus pattern (16 bp):
GTCAAAAAATAAGCAA
Found at i:297399 original size:38 final size:37
Alignment explanation
Indices: 297274--297632 Score: 259
Period size: 37 Copynumber: 9.4 Consensus size: 37
297264 ATAGTCTAAT
297274 TTTTGAAAATATTTTTAAAAA-A-ATATAATATATAAG
1 TTTTGAAAATATTTTTAAAAATATATATAATATAT-AG
*** * ** *
297310 TTTTAGAAAACGGTTTT-GAAA-ACGTATAATATATTG
1 TTTT-GAAAATATTTTTAAAAATATATATAATATATAG
* * * *
297346 -TTTAAAAATTGGTTTTTAAAAATCTATATATTATATAG
1 TTTTGAAAA-T-ATTTTTAAAAATATATATAATATATAG
*
297384 TTTTGAAAATAGTTTTTGAATATATATATATATATATATATTATA
1 TTTTGAAAATA-TTTTT-AA-A-A-ATATATATA-ATATA-TA-G
*
297429 TTTTGCAAATGATTTTTGAAAAAAATATATATAATATATAG
1 TTTTGAAAAT-ATTTTT---AAAAATATATATAATATATAG
* *
297470 TTTTGAAAACATTTTGAAAAAATATATATAATATATAG
1 TTTTGAAAATATTTT-TAAAAATATATATAATATATAG
* *
297508 TTTTTGAAAACA-TTTTGAAAATATATATAATATATAAG
1 -TTTTGAAAATATTTTTAAAAATATATATAATATAT-AG
* * *
297546 TTTTGAAAACATTTTGAAAACT-TATATAATATATAG
1 TTTTGAAAATATTTTTAAAAATATATATAATATATAG
* * *
297582 TTTTGAAAACATTTTT-GAAACATATATAATATATA-
1 TTTTGAAAATATTTTTAAAAATATATATAATATATAG
* *
297617 TTTTTAAAACATTTTT
1 TTTTGAAAATATTTTT
297633 TATATATACT
Statistics
Matches: 264, Mismatches: 36, Indels: 47
0.76 0.10 0.14
Matches are distributed among these distances:
34 4 0.02
35 20 0.08
36 44 0.17
37 63 0.24
38 49 0.19
39 20 0.08
40 6 0.02
41 9 0.03
42 10 0.04
43 9 0.03
44 11 0.04
45 15 0.06
46 2 0.01
47 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATTTTTAAAAATATATATAATATATAG
Found at i:297429 original size:86 final size:81
Alignment explanation
Indices: 297334--297580 Score: 224
Period size: 86 Copynumber: 3.0 Consensus size: 81
297324 TTTGAAAACG
* * * *
297334 TATAATATATTGTTTAAAAATTGGTTTTT-AAAAATCTATATATTATATAGTTTTGAAAATAGTT
1 TATAATATA-T-TTTAAAAA-TGATTTTTAAAAAATATATATAATATATAGTTTTGAAAACA--T
* *
297398 TTTGAATATATATATATATATA
61 TTTGAAAAAATATATATA-ATA
* **
297420 TATATTATATTTTGCAAATGATTTTTGAAAAAAATATATATAATATATAGTTTTGAAAACATTTT
1 TATAATATATTTTAAAAATGATTTTT--AAAAAATATATATAATATATAGTTTTGAAAACATTTT
297485 GAAAAAATATATATAATA
64 GAAAAAATATATATAATA
* * * *
297503 TAT-A-GT-TTTTGAAAA-CA-TTTT-GAAAATATATATAATATATAAGTTTTGAAAACATTTTG
1 TATAATATATTTTAAAAATGATTTTTAAAAAATATATATAATATAT-AGTTTTGAAAACATTTTG
*
297562 -AAAACT-TATATAATA
65 AAAAAATATATATAATA
297577 TATA
1 TATA
297581 GTTTTGAAAA
Statistics
Matches: 141, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
74 12 0.09
75 23 0.16
76 18 0.13
78 4 0.03
79 1 0.01
80 8 0.06
81 1 0.01
83 13 0.09
84 23 0.16
85 1 0.01
86 37 0.26
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (81 bp):
TATAATATATTTTAAAAATGATTTTTAAAAAATATATATAATATATAGTTTTGAAAACATTTTGA
AAAAATATATATAATA
Found at i:297536 original size:37 final size:36
Alignment explanation
Indices: 297450--297631 Score: 271
Period size: 37 Copynumber: 5.0 Consensus size: 36
297440 ATTTTTGAAA
297450 AAAATATATATAATATATAGTTTTGAAAACATTTTG
1 AAAATATATATAATATATAGTTTTGAAAACATTTTG
297486 AAAAAATATATATAATATATAGTTTTTGAAAACATTTTG
1 --AAAATATATATAATATATAG-TTTTGAAAACATTTTG
297525 AAAATATATATAATATATAAGTTTTGAAAACATTTTG
1 AAAATATATATAATATAT-AGTTTTGAAAACATTTTG
297562 AAAACT-TATATAATATATAGTTTTGAAAACATTTTTG
1 AAAA-TATATATAATATATAGTTTTGAAAACA-TTTTG
* *
297599 -AAACATATATAATATATA-TTTTTAAAACATTTT
1 AAAATATATATAATATATAGTTTTGAAAACATTTT
297632 TTATATATAC
Statistics
Matches: 137, Mismatches: 2, Indels: 14
0.90 0.01 0.09
Matches are distributed among these distances:
34 4 0.03
35 10 0.07
36 29 0.21
37 55 0.40
38 23 0.17
39 16 0.12
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTGAAAACATTTTG
Found at i:297620 original size:24 final size:24
Alignment explanation
Indices: 297592--297650 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
297582 TTTTGAAAAC
297592 ATTTTTGAAACATATATAATATAT
1 ATTTTTGAAACATATATAATATAT
* * * *
297616 ATTTTTAAAACATTTTTTATATAT
1 ATTTTTGAAACATATATAATATAT
297640 ACTTTTTGAAA
1 A-TTTTTGAAA
297651 AAGTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (24 bp):
ATTTTTGAAACATATATAATATAT
Found at i:297646 original size:26 final size:24
Alignment explanation
Indices: 297610--297659 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
297600 AACATATATA
*
297610 ATATATATTTTTAAAACA-TTTTTT
1 ATATATATTTTGAAAA-AGTTTTTT
297634 ATATATACTTTTTGAAAAAGTTTTTT
1 ATATATA--TTTTGAAAAAGTTTTTT
297660 TGAAAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 7 0.32
25 1 0.05
26 14 0.64
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (24 bp):
ATATATATTTTGAAAAAGTTTTTT
Found at i:299004 original size:3 final size:3
Alignment explanation
Indices: 298998--299032 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
298988 ATTTTTTTAC
298998 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
299033 CACTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:299118 original size:26 final size:25
Alignment explanation
Indices: 299051--299141 Score: 76
Period size: 26 Copynumber: 3.5 Consensus size: 25
299041 AAATTTAATA
* * *
299051 TTTTTTTCATTTTCTTTTATTTTGT-T
1 TTTTTTT-ATTTTATTTAATTTT-TAC
* *
299077 TTTTCTTTAATTTATTTAATATTTTCC
1 TTTT-TTTATTTTATTTAAT-TTTTAC
*
299104 TTTTTTTATTTTATTTTATTTTTAC
1 TTTTTTTATTTTATTTAATTTTTAC
299129 TTTTTTTACTTTT
1 TTTTTTTA-TTTT
299142 TTTTTCCTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
25 13 0.24
26 31 0.57
27 10 0.19
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTTTTATTTTATTTAATTTTTAC
Found at i:299141 original size:6 final size:5
Alignment explanation
Indices: 299049--299125 Score: 50
Period size: 5 Copynumber: 15.2 Consensus size: 5
299039 TAAAATTTAA
* * * * *
299049 TATTT T-TTT CATTT TCTTT TATTT TGTTT TTTCTT TAATT TATTT AATATTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT --TATTT
**
299101 TCCTT T-TTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
299126 TACTTTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 6 0.11
5 41 0.75
6 3 0.05
7 5 0.09
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:299145 original size:20 final size:20
Alignment explanation
Indices: 299112--299189 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
299102 CCTTTTTTTA
299112 TTTTATTTTATTTTTACTTT
1 TTTTATTTTATTTTTACTTT
*
299132 TTTTACTTTT-TTTTTCCTTT
1 TTTTA-TTTTATTTTTACTTT
299152 TGATTTATTTAATATTTTT-CATTT
1 T--TTTATTT--TATTTTTAC-TTT
*
299176 TCTTATTTTATTTT
1 TTTTATTTTATTTT
299190 CTTTTCTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 21 0.43
21 7 0.14
22 10 0.20
23 2 0.04
24 9 0.18
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTATTTTATTTTTACTTT
Found at i:299164 original size:68 final size:68
Alignment explanation
Indices: 299065--299194 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 68
299055 TTTCATTTTC
* * *
299065 TTTTATTTTGTTTTTTCTTTAATTTATTTAATA-TTTTCCTTTTTTTATTTTATTTTATTTTTAC
1 TTTTATTTTGTTTTTCCTTTAATTTATTTAATATTTTTCATTTTCTTATTTTATTTTATTTTTAC
299129 TTT
66 TTT
* *
299132 TTTTACTTTT-TTTTTCCTTTTGATTTATTTAATATTTTTCATTTTCTTATTTTATTTTCTTTT
1 TTTTA-TTTTGTTTTTCC-TTTAATTTATTTAATATTTTTCATTTTCTTATTTTATTTTATTTT
299195 CTTTTTCCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 11 0.20
68 19 0.35
69 25 0.45
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (68 bp):
TTTTATTTTGTTTTTCCTTTAATTTATTTAATATTTTTCATTTTCTTATTTTATTTTATTTTTAC
TTT
Found at i:299194 original size:42 final size:42
Alignment explanation
Indices: 299113--299194 Score: 98
Period size: 44 Copynumber: 2.0 Consensus size: 42
299103 CTTTTTTTAT
* *
299113 TTTATTTTATTTTTACTTTTTTTACTTTTTTTTTCCTTTTGA
1 TTTATTTTATTTTTACTTTTCTTACTTTTATTTTCCTTTTGA
299155 TTTATTTAATATTTTT-CATTTTCTTA-TTTTATTTT-CTTTT
1 TTTATTT--TATTTTTAC-TTTTCTTACTTTTATTTTCCTTTT
299195 CTTTTTCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
42 12 0.34
43 9 0.26
44 14 0.40
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.76
Consensus pattern (42 bp):
TTTATTTTATTTTTACTTTTCTTACTTTTATTTTCCTTTTGA
Found at i:300500 original size:21 final size:21
Alignment explanation
Indices: 300476--300525 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
300466 ACACTTAGGG
300476 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
300497 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
300518 TACCGATT
1 AACCGATT
300526 ACCCCACGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:300745 original size:13 final size:13
Alignment explanation
Indices: 300724--300778 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
300714 AAGTTCGATA
*
300724 AATTCAAATACTT
1 AATTGAAATACTT
300737 AATTGAAATACTT
1 AATTGAAATACTT
* *
300750 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
300764 AATTGAAATACTT
1 AATTGAAATACTT
300777 AA
1 AA
300779 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:300860 original size:32 final size:33
Alignment explanation
Indices: 300764--300862 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
300754 AACTCAACAT
* * *
300764 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
300797 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
300830 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
300862 A
1 A
300863 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:300881 original size:21 final size:21
Alignment explanation
Indices: 300857--300896 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
300847 ACTTCAAGTT
300857 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
300878 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
300897 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Done.