Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008630.1 Hibiscus syriacus cultivar Beakdansim tig00111599_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: 385647
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:14856 original size:25 final size:23
Alignment explanation
Indices: 14826--14879 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
14816 GTGCTTCGAC
*
14826 AAAAGAAACAA-AAAGAGAAAAAGA
1 AAAAGAAA-AATAAAAAG-AAAAGA
14850 AAGAAGAAAAATAAAAAGAAAAGA
1 AA-AAGAAAAATAAAAAGAAAAGA
14874 AAAAGA
1 AAAAGA
14880 CTCCTACATC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 4 0.15
24 12 0.44
25 11 0.41
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAGAAAAATAAAAAGAAAAGA
Found at i:14865 original size:6 final size:6
Alignment explanation
Indices: 14826--14879 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
14816 GTGCTTCGAC
* *
14826 AAAAGA AACAA-A AAGAGA AAAAGA AAGAAGA AAAATA AAAAG- AAAAGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA
14874 AAAAGA
1 AAAAGA
14880 CTCCTACATC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 6 0.15
6 26 0.65
7 8 0.20
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:23162 original size:13 final size:12
Alignment explanation
Indices: 23143--23228 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
23133 ATATAGGCGT
23143 GATATGGTGATG
1 GATATGGTGATG
23155 GAATATGGTGAT-
1 G-ATATGGTGATG
*
23167 GATATAGGCG-T-
1 GATAT-GGTGATG
23178 GATAATGGTGATG
1 GAT-ATGGTGATG
23191 GACTATGGTGAT-
1 GA-TATGGTGATG
*
23203 GATATAGGCG-T-
1 GATAT-GGTGATG
23214 GATAATGGTGATG
1 GAT-ATGGTGATG
23227 GA
1 GA
23229 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:23198 original size:36 final size:36
Alignment explanation
Indices: 23125--23229 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
23115 ATTTATAAGT
* *
23125 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
23160 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
23196 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
23230 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:27138 original size:35 final size:36
Alignment explanation
Indices: 27091--27158 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
27081 ATTTATAAGT
*
27091 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGATGATGGAATA
* *
27126 TGGTGATGATATATGCGTGATAATGATGATGGA
1 TGGTGATAATATAGGCGTGATAATGATGATGGA
27159 CAGATTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGATGATGGAATA
Found at i:32467 original size:13 final size:13
Alignment explanation
Indices: 32444--32475 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
32434 TAATATATTG
32444 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
32456 GAAATAAAGAAAT
1 GAAATAAAGAAAT
32469 GAAATAA
1 GAAATAA
32476 TAAGAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:33064 original size:19 final size:20
Alignment explanation
Indices: 33017--33067 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
33007 GAAACCCCTT
**
33017 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
33037 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
33056 TGAAGATACATG
1 TGAAAATACATG
33068 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:37881 original size:143 final size:142
Alignment explanation
Indices: 37642--37925 Score: 423
Period size: 139 Copynumber: 2.0 Consensus size: 142
37632 ACTCTTCGCG
37642 AAAAGGTACGAATCCACAAAAATTGACCTAAACCATATTTGTAGTGTTTTGTGTGGTGAGATGAT
1 AAAAGGTACGAATCCACAAAAATT---CTAAACCATATTTGTAGTGTTTTGTGTGGTGAGATGAT
* *
37707 GGTGTAACTCTCCAGCTGAAATGAGGTTCTAGCTAGCTCAAAAGTCCAGCTCAAGTCAGCTATGA
63 GGTGTAACTCTCCAGCTAAAATGAGGTTCTAGCTA----AAAAGTCCAGCTCAAGTCAACTATGA
37772 GCTCGGGGGTAAGCTTGTA
124 GCTCGGGGGTAAGCTTGTA
37791 AAAAGGTACGAATCCACAAAAA-T-T-AACCATATTTGTAGTGTTTTGTGTGGTGAAGATGATGG
1 AAAAGGTACGAATCCACAAAAATTCTAAACCATATTTGTAGTGTTTTGTGTGGTG-AGATGATGG
* *
37853 TGTAACTGTCCAGCTAAAATGAGG-TCTAGCTAAAAAGTCCAGCTTAAGTCAACTATGAGCTCGG
65 TGTAACTCTCCAGCTAAAATGAGGTTCTAGCTAAAAAGTCCAGCTCAAGTCAACTATGAGCTCGG
*
37917 GGGTCAGCT
130 GGGTAAGCT
37926 AACAACTTTT
Statistics
Matches: 129, Mismatches: 5, Indels: 12
0.88 0.03 0.08
Matches are distributed among these distances:
139 38 0.29
143 36 0.28
144 32 0.25
148 1 0.01
149 22 0.17
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (142 bp):
AAAAGGTACGAATCCACAAAAATTCTAAACCATATTTGTAGTGTTTTGTGTGGTGAGATGATGGT
GTAACTCTCCAGCTAAAATGAGGTTCTAGCTAAAAAGTCCAGCTCAAGTCAACTATGAGCTCGGG
GGTAAGCTTGTA
Found at i:41367 original size:23 final size:25
Alignment explanation
Indices: 41341--41395 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
41331 AAATCCAGCA
41341 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
41364 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
41389 AAGAAAA
1 AAGAAAA
41396 AGAACAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:47131 original size:23 final size:25
Alignment explanation
Indices: 47105--47159 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
47095 AAATCCAGCA
*
47105 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGAACTCAAAGAGG
* *
47128 AAGAAATTGAAAGAACTCAAAGAGG
1 AAGAAAATCAAAGAACTCAAAGAGG
47153 AAGAAAA
1 AAGAAAA
47160 ATAACAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 18 0.69
24 1 0.04
25 7 0.27
ACGTcount: A:0.62, C:0.11, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGAACTCAAAGAGG
Found at i:52109 original size:7 final size:7
Alignment explanation
Indices: 52093--52161 Score: 64
Period size: 7 Copynumber: 10.7 Consensus size: 7
52083 GGGTCTTTTC
52093 TTTTGCT
1 TTTTGCT
52100 TTTTG-T
1 TTTTGCT
52106 TTTT-CT
1 TTTTGCT
52112 TCTTT-C-
1 T-TTTGCT
52118 TTTTGCT
1 TTTTGCT
52125 TTTTGCT
1 TTTTGCT
52132 TTTTG-T
1 TTTTGCT
52138 TTTT-CT
1 TTTTGCT
52144 TATTT-CT
1 T-TTTGCT
52151 TTTT-CT
1 TTTTGCT
52157 TTTTG
1 TTTTG
52162 TTGCAGCACT
Statistics
Matches: 55, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
5 3 0.05
6 25 0.45
7 27 0.49
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (7 bp):
TTTTGCT
Found at i:52132 original size:32 final size:31
Alignment explanation
Indices: 52086--52161 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 31
52076 GTTGTAGGGG
*
52086 TCTTTTC-TTTTGCTTTTTGTTTTTCTTCTT
1 TCTTTTCTTTTTGCTTTTTGTTTTTCTTATT
52116 TCTTTTGCTTTTTGCTTTTTGTTTTTCTTATT
1 TCTTTT-CTTTTTGCTTTTTGTTTTTCTTATT
52148 TCTTTTTCTTTTTG
1 TC-TTTTCTTTTTG
52162 TTGCAGCACT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 6 0.14
31 1 0.02
32 31 0.74
33 4 0.10
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.76
Consensus pattern (31 bp):
TCTTTTCTTTTTGCTTTTTGTTTTTCTTATT
Found at i:52159 original size:5 final size:6
Alignment explanation
Indices: 52088--52160 Score: 83
Period size: 6 Copynumber: 11.7 Consensus size: 6
52078 TGTAGGGGTC
* * * *
52088 TTTTCT TTTGCT TTTTGT TTTTCT TCTTTCT TTTGCT TTTTGCT TTTTGT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT-CT TTTTCT
52138 TTTTCT TATTTCT TTTTCT TTTT
1 TTTTCT T-TTTCT TTTTCT TTTT
52161 GTTGCAGCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
6 38 0.68
7 18 0.32
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:52161 original size:25 final size:24
Alignment explanation
Indices: 52088--52163 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 24
52078 TGTAGGGGTC
* *
52088 TTTTCTTTTGCTTTTTGTTTTTCT
1 TTTTCTTTTGCTTTTTCTTTTTGT
52112 TCTTTCTTTTGCTTTTTGCTTTTTGT
1 T-TTTCTTTTGCTTTTT-CTTTTTGT
*
52138 TTTTCTTATTTCTTTTTCTTTTTGT
1 TTTTCTT-TTGCTTTTTCTTTTTGT
52163 T
1 T
52164 GCAGCACTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.02
25 30 0.65
26 15 0.33
ACGTcount: A:0.01, C:0.13, G:0.08, T:0.78
Consensus pattern (24 bp):
TTTTCTTTTGCTTTTTCTTTTTGT
Found at i:52360 original size:12 final size:13
Alignment explanation
Indices: 52343--52371 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52333 TGATATATCG
52343 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
52355 GAAATAAAGAAAT
1 GAAATAAAGAAAT
52368 GAAA
1 GAAA
52372 GGATTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:56161 original size:18 final size:18
Alignment explanation
Indices: 56138--56180 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
56128 TTATCCTTCA
56138 TTCATCAACAAGGCATAC
1 TTCATCAACAAGGCATAC
56156 TTCATCAACAAGGCATAC
1 TTCATCAACAAGGCATAC
56174 TTCATCA
1 TTCATCA
56181 CCACCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (18 bp):
TTCATCAACAAGGCATAC
Found at i:61004 original size:12 final size:11
Alignment explanation
Indices: 60987--61033 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
60977 AAATTTTGGC
60987 TTTTTTGACTTT
1 TTTTTTG-CTTT
*
60999 TTTTTTGTTTT
1 TTTTTTGCTTT
*
61010 TTTTTTGC-CT
1 TTTTTTGCTTT
61020 TTTTTTG-TTT
1 TTTTTTGCTTT
61030 TTTT
1 TTTT
61034 GAAAAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
10 13 0.43
11 10 0.33
12 7 0.23
ACGTcount: A:0.02, C:0.06, G:0.09, T:0.83
Consensus pattern (11 bp):
TTTTTTGCTTT
Found at i:62545 original size:18 final size:17
Alignment explanation
Indices: 62496--62549 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
62486 GAGTTGTAAG
62496 TTATCTTCATTTTTCTTA
1 TTAT-TTCATTTTTCTTA
*
62514 CTATTTCA-TTTTCTTA
1 TTATTTCATTTTTCTTA
*
62530 TTCTTTCATCTTTTCTTA
1 TTATTTCAT-TTTTCTTA
62548 TT
1 TT
62550 TTCATTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 14 0.45
17 4 0.13
18 13 0.42
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTCATTTTTCTTA
Found at i:69916 original size:19 final size:19
Alignment explanation
Indices: 69893--69940 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
69883 CTTTTCTTCT
69893 TTTCTTTTTTCTGAATTTTC
1 TTTCTTTTTT-TGAATTTTC
**
69913 -TTCTTCTTTTTGTCTTTTC
1 TTTCTT-TTTTTGAATTTTC
69932 TTTCTTTTT
1 TTTCTTTTT
69941 GCACTCCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTCTTTTTTTGAATTTTC
Found at i:69920 original size:35 final size:33
Alignment explanation
Indices: 69866--69939 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 33
69856 GCTTGCTTTC
*
69866 TTTTTGAATTTCTTTTTCTTTTCT-TCTTTTCTT
1 TTTTTGAATTTCTTCTTCTTTT-TGTCTTTTCTT
69899 TTTTCTGAATTTTCTTCTTCTTTTTGTCTTTTCTT
1 TTTT-TGAA-TTTCTTCTTCTTTTTGTCTTTTCTT
69934 TCTTTT
1 T-TTTT
69940 TGCACTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 4 0.11
34 5 0.14
35 24 0.67
36 3 0.08
ACGTcount: A:0.05, C:0.16, G:0.04, T:0.74
Consensus pattern (33 bp):
TTTTTGAATTTCTTCTTCTTTTTGTCTTTTCTT
Found at i:74918 original size:6 final size:6
Alignment explanation
Indices: 74907--74972 Score: 87
Period size: 6 Copynumber: 10.7 Consensus size: 6
74897 TGTAGGAGTC
* *
74907 TTTTCT TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTTGT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT
*
74956 TCTTTCT TTTGCT TTTT
1 T-TTTCT TTTTCT TTTT
74973 GTTGCAGCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 40 0.77
7 12 0.23
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:74936 original size:25 final size:25
Alignment explanation
Indices: 74908--74975 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
74898 GTAGGAGTCT
74908 TTTCTTTTTCTTTTTGTTTTTCTTC
1 TTTCTTTTTCTTTTTGTTTTTCTTC
74933 TTTCTTTTTCTTTTTGTTTTTCTTC
1 TTTCTTTTTCTTTTTGTTTTTCTTC
*
74958 TTTCTTTTGCTTTTTGTT
1 TTTCTTTTTCTTTTTGTT
74976 GCAGCACTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (25 bp):
TTTCTTTTTCTTTTTGTTTTTCTTC
Found at i:74971 original size:19 final size:18
Alignment explanation
Indices: 74905--74972 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 18
74895 GTTGTAGGAG
74905 TCTTTT-CTTTTTCTTTT
1 TCTTTTGCTTTTTCTTTT
* *
74922 TGTTTTTCTTCTTTCTTTT
1 TCTTTTGCTT-TTTCTTTT
74941 TCTTTTTG-TTTTTCTTCTT
1 TC-TTTTGCTTTTTCTT-TT
74960 TCTTTTGCTTTTT
1 TCTTTTGCTTTTT
74973 GTTGCAGCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
17 5 0.12
18 14 0.33
19 20 0.47
20 4 0.09
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.79
Consensus pattern (18 bp):
TCTTTTGCTTTTTCTTTT
Found at i:75172 original size:12 final size:13
Alignment explanation
Indices: 75155--75183 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
75145 TGATATATCG
75155 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
75167 GAAATAAAGAAAT
1 GAAATAAAGAAAT
75180 GAAA
1 GAAA
75184 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:82004 original size:14 final size:14
Alignment explanation
Indices: 81985--82021 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
81975 AAATTTTGGC
81985 TTTTTTTGGCTCTTT
1 TTTTTTTGGC-CTTT
*
82000 TTTTTTTTGCCTTT
1 TTTTTTTGGCCTTT
82014 TTTTTTTG
1 TTTTTTTG
82022 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (14 bp):
TTTTTTTGGCCTTT
Found at i:90497 original size:15 final size:15
Alignment explanation
Indices: 90459--90497 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
90449 ACTTTCTTCA
90459 CTTCTTTTTTTTTCT
1 CTTCTTTTTTTTTCT
* **
90474 TTTAATTTTTTTTCT
1 CTTCTTTTTTTTTCT
90489 CTTCTTTTT
1 CTTCTTTTT
90498 CTTGTCGTTC
Statistics
Matches: 18, Mismatches: 6, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTCTTTTTTTTTCT
Found at i:90558 original size:7 final size:7
Alignment explanation
Indices: 90542--90616 Score: 53
Period size: 6 Copynumber: 11.7 Consensus size: 7
90532 GAGTCTTTTC
90542 TTTTGCT
1 TTTTGCT
90549 TTTTG-T
1 TTTTGCT
90555 TTTT-CT
1 TTTTGCT
90561 TCTTT-CT
1 T-TTTGCT
90568 TCTTT-C-
1 T-TTTGCT
90574 TTTTGC-
1 TTTTGCT
90580 TTTTGCT
1 TTTTGCT
90587 TTTTG-T
1 TTTTGCT
90593 TTTT-CT
1 TTTTGCT
90599 TCTTT-CT
1 T-TTTGCT
90606 TTTT-CT
1 TTTTGCT
90612 TTTTG
1 TTTTG
90617 TTGCAGCACT
Statistics
Matches: 61, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
5 3 0.05
6 31 0.51
7 27 0.44
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (7 bp):
TTTTGCT
Found at i:90598 original size:31 final size:31
Alignment explanation
Indices: 90538--90614 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
90528 GTAGGAGTCT
90538 TTTCTTTTGCTTTTTGTTTTTCTTCTTTCTTC
1 TTTCTTTTGC-TTTTGTTTTTCTTCTTTCTTC
*
90570 TTTCTTTTGCTTTTGCTTTTTGTT-TTTCTTC
1 TTTCTTTTGCTTTTG-TTTTTCTTCTTTCTTC
*
90601 TTTCTTTTTCTTTT
1 TTTCTTTTGCTTTT
90615 TGTTGCAGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
31 25 0.60
32 17 0.40
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (31 bp):
TTTCTTTTGCTTTTGTTTTTCTTCTTTCTTC
Found at i:90616 original size:38 final size:38
Alignment explanation
Indices: 90535--90614 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
90525 GTTGTAGGAG
90535 TCTTTT-CTTTTGCTTTTTGTTTTTCTTCTTTCTTCTT
1 TCTTTTGCTTTTGCTTTTTGTTTTTCTTCTTTCTTCTT
90572 TCTTTTGCTTTTGCTTTTTGTTTTTCTTCTTTCTT-TT
1 TCTTTTGCTTTTGCTTTTTGTTTTTCTTCTTTCTTCTT
90609 TCTTTT
1 TCTTTT
90615 TGTTGCAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 14 0.33
38 28 0.67
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.76
Consensus pattern (38 bp):
TCTTTTGCTTTTGCTTTTTGTTTTTCTTCTTTCTTCTT
Found at i:91408 original size:19 final size:20
Alignment explanation
Indices: 91370--91460 Score: 114
Period size: 19 Copynumber: 4.6 Consensus size: 20
91360 GAAACCCCTT
*
91370 TGAAAATACATGATTTTTTA
1 TGAAAATACATGAATTTTTA
91390 TGAAAATACAT-AATTTTTA
1 TGAAAATACATGAATTTTTA
*
91409 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-ATTTTTA
**
91430 TGAAAATACATG-ATTTAAA
1 TGAAAATACATGAATTTTTA
*
91449 TGAAGATACATG
1 TGAAAATACATG
91461 CTCTTGGCCG
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
19 33 0.52
20 12 0.19
21 18 0.29
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGAATTTTTA
Found at i:91427 original size:21 final size:20
Alignment explanation
Indices: 91370--91445 Score: 127
Period size: 21 Copynumber: 3.8 Consensus size: 20
91360 GAAACCCCTT
91370 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTTA
*
91390 TGAAAATACAT-AATTTTTA
1 TGAAAATACATGATTTTTTA
91409 TGAAAATACATGATTTTTTTA
1 TGAAAATACATGA-TTTTTTA
91430 TGAAAATACATGATTT
1 TGAAAATACATGATTT
91446 AAATGAAGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.35
20 15 0.29
21 19 0.37
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (20 bp):
TGAAAATACATGATTTTTTA
Found at i:91438 original size:40 final size:39
Alignment explanation
Indices: 91370--91460 Score: 137
Period size: 40 Copynumber: 2.3 Consensus size: 39
91360 GAAACCCCTT
**
91370 TGAAAATACATGATTTTTTATGAAAATACATAATTTTTA
1 TGAAAATACATGATTTTTTATGAAAATACATAATTTAAA
*
91409 TGAAAATACATGATTTTTTTATGAAAATACATGATTTAAA
1 TGAAAATACATGA-TTTTTTATGAAAATACATAATTTAAA
*
91449 TGAAGATACATG
1 TGAAAATACATG
91461 CTCTTGGCCG
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.28
40 34 0.72
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (39 bp):
TGAAAATACATGATTTTTTATGAAAATACATAATTTAAA
Found at i:102792 original size:19 final size:20
Alignment explanation
Indices: 102768--102807 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
102758 CTATCATTTC
102768 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
102787 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
102807 T
1 T
102808 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:105758 original size:33 final size:33
Alignment explanation
Indices: 105716--105784 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
105706 GTTGATGAAT
*
105716 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
105749 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
105782 GAA
1 GAA
105785 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:114307 original size:33 final size:33
Alignment explanation
Indices: 114263--114331 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
114253 CATCACCATA
*
114263 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
114296 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
114329 TTC
1 TTC
114332 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:115602 original size:36 final size:36
Alignment explanation
Indices: 115555--115655 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 36
115545 CAATTTGTCC
115555 ATCACCATTATCACGCCTATATCATCACCATAGTCA
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
* *
115591 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCA
* *
115627 ATCACCA-TATCATGCCTATATTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
115656 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 20 0.33
36 41 0.67
ACGTcount: A:0.33, C:0.34, G:0.04, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCA
Found at i:116076 original size:17 final size:17
Alignment explanation
Indices: 116037--116079 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
116027 GTGCTACAAC
116037 AAAA-AAAACAACAAGA
1 AAAAGAAAACAACAAGA
116053 AAGAAGAAAACAA-AAGA
1 AA-AAGAAAACAACAAGA
116070 GAAAAGAAAA
1 -AAAAGAAAA
116080 AGACTCCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAACAAGA
Found at i:121311 original size:13 final size:11
Alignment explanation
Indices: 121270--121354 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
121260 ACAATCTATC
121270 CATCACCATTAT
1 CATCACCA-TAT
*
121282 CA-CGCCTATAT
1 CATCACC-ATAT
121293 CATCACCATAGT
1 CATCACCATA-T
121305 CCATCACCATTAT
1 -CATCACCA-TAT
*
121318 CA-CGCCTATAT
1 CATCACC-ATAT
121329 CATCACCATATT
1 CATCACCATA-T
121341 CCATCACCATAT
1 -CATCACCATAT
121353 CA
1 CA
121355 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:121315 original size:36 final size:36
Alignment explanation
Indices: 121268--121371 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
121258 ATACAATCTA
121268 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
121304 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
121340 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
121372 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:123024 original size:13 final size:13
Alignment explanation
Indices: 123006--123030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
122996 GATACTATCT
123006 TTCCATCACCATA
1 TTCCATCACCATA
123019 TTCCATCACCAT
1 TTCCATCACCAT
123031 TCACGCCTAT
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATA
Found at i:128199 original size:20 final size:21
Alignment explanation
Indices: 128176--128228 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
128166 AAAAACAAAA
* *
128176 AAAAAAGGCAAAAAAA-AGGC
1 AAAAAAGACAAAAAAAGAGCC
128196 AAAAAA-ACAAAAAAAGAGCC
1 AAAAAAGACAAAAAAAGAGCC
*
128216 AAAAAAGCCAAAA
1 AAAAAAGACAAAA
128229 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.29
20 15 0.54
21 5 0.18
ACGTcount: A:0.74, C:0.13, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAAAGACAAAAAAAGAGCC
Found at i:128200 original size:12 final size:12
Alignment explanation
Indices: 128173--128202 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
128163 AAAAAAAACA
128173 AAAAAAAAAGGC
1 AAAAAAAAAGGC
128185 -AAAAAAAAGGC
1 AAAAAAAAAGGC
128196 AAAAAAA
1 AAAAAAA
128203 CAAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGGC
Found at i:135141 original size:10 final size:10
Alignment explanation
Indices: 135126--135163 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
135116 TTTTTTTTCA
135126 AAAAAAAAAC
1 AAAAAAAAAC
*
135136 AAAAAAAAGC
1 AAAAAAAAAC
135146 AAAAAAATAA-
1 AAAAAAA-AAC
135156 AAAAAAAA
1 AAAAAAAA
135164 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 1 0.04
10 23 0.92
11 1 0.04
ACGTcount: A:0.89, C:0.05, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:135151 original size:20 final size:21
Alignment explanation
Indices: 135124--135170 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
135114 ATTTTTTTTT
*
135124 CAAAAAAAAAACAAAAAAAAG-
1 CAAAAAAATAA-AAAAAAAAGC
135145 CAAAAAAATAAAAAAAAAAGC
1 CAAAAAAATAAAAAAAAAAGC
135166 CAAAA
1 CAAAA
135171 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.83, C:0.11, G:0.04, T:0.02
Consensus pattern (21 bp):
CAAAAAAATAAAAAAAAAAGC
Found at i:140015 original size:14 final size:15
Alignment explanation
Indices: 139981--140027 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
139971 AATTTGGAGT
139981 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
139996 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
140010 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
140027 G
1 G
140028 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:145603 original size:33 final size:33
Alignment explanation
Indices: 145561--145629 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
145551 GTTGATGAAT
*
145561 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
145594 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
145627 GAA
1 GAA
145630 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:151290 original size:33 final size:33
Alignment explanation
Indices: 151248--151316 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
151238 GTTGATGAAT
*
151248 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
151281 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
151314 GAA
1 GAA
151317 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:159075 original size:16 final size:18
Alignment explanation
Indices: 159054--159091 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
159044 TGTAGGGGTC
*
159054 TTTTCTT-TTTGTTTT-T
1 TTTTCTTCTTTCTTTTAT
159070 TTTTCTTCTTTCTTTTAT
1 TTTTCTTCTTTCTTTTAT
159088 TTTT
1 TTTT
159092 GTTGCAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 7 0.37
18 5 0.26
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (18 bp):
TTTTCTTCTTTCTTTTAT
Found at i:159309 original size:26 final size:28
Alignment explanation
Indices: 159271--159322 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
159261 GAAATATGAA
159271 ATAAGAAATGGAAAGATGG-AATGAAATG
1 ATAAGAAATGGAAA-ATGGAAATGAAATG
159299 ATAAG-AA-GGAAAATGGAAATGAAA
1 ATAAGAAATGGAAAATGGAAATGAAA
159323 GAAATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 2 0.09
28 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (28 bp):
ATAAGAAATGGAAAATGGAAATGAAATG
Found at i:182370 original size:664 final size:659
Alignment explanation
Indices: 181105--182429 Score: 2391
Period size: 664 Copynumber: 2.0 Consensus size: 659
181095 AAGAGAGCTC
181105 ATTATGATGAATTAAGTGAGATTATTTCTTTTAAGTCCTTGTGACTTTATCGACCAAACAAGTAA
1 ATTATGATGAATTAAGTGAGATTATTTCTTTTAAGTCCTTGTGACTTTATCGACCAAACAAGTAA
*
181170 CTTGTTACTTGTGGTGTCAATTCCTTCATTATGATAATTCTGGTTCCTATCTCTATATAGATAGG
66 CTTGTTACTTGTGGTGTCAATTCCTT-ATCATGATAATTCTGGTTCCTATCTCTATATAGATAGG
181235 GTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGGTCTTTGCTCTTTGTAGCA
130 GTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCT-GGGTCTTTGCTCTTTGTAGCA
181300 CTGTTCTCCTGGTTATTCTAAGATACTATCCATTCCTTATTACCATCCCTTATTGGAGTAATATA
194 CTGTTCTCCTGGTTATTCTAAGATACTATCCATTCCTTATTACCATCCCTTATTGGAGTAATATA
*
181365 AAGTATGGGTCTTTGTTCTTTAACATTGATTCTTCTTTGAGTCTTCCTTAGATACTATCTATTTA
259 AAGTATGGGTCTTTGTTCTTTAACATTGATTCTTCTTTGAGTCTTCCTTAGAGACTATCTATTTA
181430 CCATTCCATTAATTCGTAATCCACTTCATAACCACAACCAAGTCTTTCGCTACCATCTCTTATCC
324 CCATTCCATTAATTCGTAATCCACTTCATAACCACAACCAAGTCTTTCGCTACCATCTCTTATCC
181495 GACCATTTACCATCAAGTTTACCACTTAAACTATCCATTTCTTACCTTTCTTATGCAGGTTGTTT
389 GACCATTTACCATCAAGTTTACCACTTAAACTATCCATTTCTTACCTTTCTTATGCAGGTTGTTT
181560 TGCTTCCTTCCTAGATCCCAATCATTCGATAAGGCAGATCGGATCGTATCATACGATAATCAGAG
454 TGCTTCCTTCCTAGATCCCAATCATTCGATAAGGCAGATCGGATCGTATCATACGATAATCAGAG
181625 CTTTTGGTAGAAGAAGAATGTGCAACAGAAACAAAAAACAAAACGATACACTAAAGAGAAGTCAC
519 CTTTTGGTAGAAGAAGAATGTGCAACAGAAACAAAAAACAAAACGATACACTAAAGAGAAGTCAC
181690 CCTTCGATTTGAGGACAAATCGCCCAAAAGAAGGGGAGAATGATGTGATCCTGACTAGCACCAGT
584 CCTTCGATTTGAGGACAAATCGCCCAAAAGAAGGGGAGAATGATGTGATCCTGACTAGCACCAGT
181755 TTTATCCATTA
649 TTTATCCATTA
181766 ATTATGATGAATTAAGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTATCGACCAAACAA
1 ATTATGATGAATTAAGTGAGATTATT-TC-T-TTTAAGTCCTTGTGAC-TTTATCGACCAAACAA
181831 GTAACTTGTTACTTGTGGTGTCAATTCCTT-TCA-GATAATTCTGGTTCCTATCTCTATATAGAT
62 GTAACTTGTTACTTGTGGTGTCAATTCCTTATCATGATAATTCTGGTTCCTATCTCTATATAGAT
181894 AGTGGGTCAAATTCCTTG-TACCACCCCTTAGAACGATTTGTAAGGCT-GGTCTTTGCTCTTTGT
127 A--GGGTCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTTTGCTCTTTGT
181957 AGCACTGGTTCTTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATCCCTTATTGGA
190 AGCACT-GTTC-TCC-TGGTTATTCTAAGATACTATCCATTCCTTA-TTACCATCCCTTATTGGA
182022 GTAATATAAAGTATGGGTCTTTGTTCTTTAACATTGATTCTTCTTTGAGTC-TCCTTA-AGA-TA
251 GTAATATAAAGTATGGGTCTTTGTTCTTTAACATTGATTCTTCTTTGAGTCTTCCTTAGAGACTA
182084 TCATATTTACCATTCCATTAATTCGTAATCCA-TTCATAACCACAACCAAGTCTTTCGCTA-CAT
316 TC-TATTTACCATTCCATTAATTCGTAATCCACTTCATAACCACAACCAAGTCTTTCGCTACCAT
*
182147 CTCTTATCCGACCATTTACCATCAAGTTTACCACTTAAACTATCCATTTCTTACCCTTTTTCTAT
380 CTCTTATCCGACCATTTACCATCAAGTTTACCACTTAAACTATCCATTTCTTA-CCTTTCT-TAT
182212 GCAGGTTGTTTTGCTTCCTTCCTAGATCCACAATCATTCGATAAGGCAGATCGGATCGTATCATA
443 GCAGGTTGTTTTGCTTCCTTCCTAGATCC-CAATCATTCGATAAGGCAGATCGGATCGTATCATA
182277 CGATAATCAGAGCTTTTGGTAGAAGAAGAAATGTGCAACAGAAAC-AAAAACAAAACGATACACT
507 CGATAATCAGAGCTTTTGGTAGAAGAAG-AATGTGCAACAGAAACAAAAAACAAAACGATACACT
*
182341 AAAGAGAAGTCACCCTTCGATTTGAGGACAAATCGCCTAAAAGAAGGGGAGAATGATGTGATCCT
571 AAAGAGAAGTCACCCTTCGATTTGAGGACAAATCGCCCAAAAGAAGGGGAGAATGATGTGATCCT
182406 GACTAGCACCAGTTTTATCCATTA
636 GACTAGCACCAGTTTTATCCATTA
182430 TTTTATCACA
Statistics
Matches: 645, Mismatches: 4, Indels: 27
0.95 0.01 0.04
Matches are distributed among these distances:
661 104 0.16
662 75 0.12
663 98 0.15
664 237 0.37
665 131 0.20
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (659 bp):
ATTATGATGAATTAAGTGAGATTATTTCTTTTAAGTCCTTGTGACTTTATCGACCAAACAAGTAA
CTTGTTACTTGTGGTGTCAATTCCTTATCATGATAATTCTGGTTCCTATCTCTATATAGATAGGG
TCAAATTCCTTGTTACCACCCCTTAGAACGATTTGTAAGGCTGGGTCTTTGCTCTTTGTAGCACT
GTTCTCCTGGTTATTCTAAGATACTATCCATTCCTTATTACCATCCCTTATTGGAGTAATATAAA
GTATGGGTCTTTGTTCTTTAACATTGATTCTTCTTTGAGTCTTCCTTAGAGACTATCTATTTACC
ATTCCATTAATTCGTAATCCACTTCATAACCACAACCAAGTCTTTCGCTACCATCTCTTATCCGA
CCATTTACCATCAAGTTTACCACTTAAACTATCCATTTCTTACCTTTCTTATGCAGGTTGTTTTG
CTTCCTTCCTAGATCCCAATCATTCGATAAGGCAGATCGGATCGTATCATACGATAATCAGAGCT
TTTGGTAGAAGAAGAATGTGCAACAGAAACAAAAAACAAAACGATACACTAAAGAGAAGTCACCC
TTCGATTTGAGGACAAATCGCCCAAAAGAAGGGGAGAATGATGTGATCCTGACTAGCACCAGTTT
TATCCATTA
Found at i:186337 original size:53 final size:53
Alignment explanation
Indices: 186273--186379 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
186263 TTGTTTAAGT
*
186273 CCTTGTGACTTTTATCGACCAAACAAGTAACTTGTTACTTGTGGTGTCAATTC
1 CCTTGTGACTTTTATCGACCAAACAAGTAACTTGTTACTTGTGGGGTCAATTC
186326 CCTTGTGACTTTTATCGACCAAACAAGTAACTTGTTACTTGTGGGGTCAATTC
1 CCTTGTGACTTTTATCGACCAAACAAGTAACTTGTTACTTGTGGGGTCAATTC
186379 C
1 C
186380 TTTCATTATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (53 bp):
CCTTGTGACTTTTATCGACCAAACAAGTAACTTGTTACTTGTGGGGTCAATTC
Found at i:194422 original size:17 final size:19
Alignment explanation
Indices: 194388--194433 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
194378 CGGCCAAGAG
*
194388 CATGTATCTTCAT-TAAAAT
1 CATGTAT-TTCATCAAAAAT
194407 C-TGTATTTCATCAAAAAT
1 CATGTATTTCATCAAAAAT
194425 CATGTATTT
1 CATGTATTT
194434 TCAAAGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
19 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (19 bp):
CATGTATTTCATCAAAAAT
Found at i:198465 original size:19 final size:20
Alignment explanation
Indices: 198424--198466 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
198414 GAAACCCCTT
* *
198424 TGAAATTACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
198444 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
198463 TGAA
1 TGAA
198467 GACATGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:199371 original size:27 final size:27
Alignment explanation
Indices: 199339--199393 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
199329 CTGCCATGAT
**
199339 ATCTAAATGAAATGAAAACATAATATA
1 ATCTAAAACAAATGAAAACATAATATA
* *
199366 ATCTAAAACATATGTAAACATAATATA
1 ATCTAAAACAAATGAAAACATAATATA
199393 A
1 A
199394 AGCTAAGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.27
Consensus pattern (27 bp):
ATCTAAAACAAATGAAAACATAATATA
Found at i:199767 original size:21 final size:19
Alignment explanation
Indices: 199743--199812 Score: 81
Period size: 18 Copynumber: 3.6 Consensus size: 19
199733 CTTGGCTTTG
199743 CTTTCTTTTTGAATTCTTTTT
1 CTTTCTTTTTG--TTCTTTTT
*
199764 CTTTC-TTTTCTTCTTTTT
1 CTTTCTTTTTGTTCTTTTT
199782 CTTCTTCTTTTTG-TCTTTTT
1 C-T-TTCTTTTTGTTCTTTTT
199802 CTTTCTTTTTG
1 CTTTCTTTTTG
199813 CACTCCAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 18 0.41
19 2 0.05
20 15 0.34
21 9 0.20
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.74
Consensus pattern (19 bp):
CTTTCTTTTTGTTCTTTTT
Found at i:199777 original size:12 final size:11
Alignment explanation
Indices: 199762--199808 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
199752 TGAATTCTTT
199762 TTCTTTCTTTTC
1 TTCTTT-TTTTC
199774 TTCTTTTTCTTC
1 TTCTTTTT-TTC
*
199786 TTCTTTTTGTC
1 TTCTTTTTTTC
*
199797 TT-TTTCTTTC
1 TTCTTTTTTTC
199807 TT
1 TT
199809 TTTGCACTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 8 0.26
11 6 0.19
12 17 0.55
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (11 bp):
TTCTTTTTTTC
Found at i:205219 original size:19 final size:20
Alignment explanation
Indices: 205178--205228 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
205168 GAAACCCCTT
*
205178 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
205198 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
205217 TGAAGATACATG
1 TGAAAATACATG
205229 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:213746 original size:43 final size:43
Alignment explanation
Indices: 213699--213783 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
213689 TTTTGAAGGC
213699 TGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGTA
1 TGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGTA
213742 TGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGT
1 TGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGT
213784 CAAGGTTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
TGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGTA
Found at i:218543 original size:17 final size:18
Alignment explanation
Indices: 218503--218546 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
218493 TTCATGCATC
218503 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
218521 TAGTTCATT-AATTAAAG-
1 TAGTTCATTGAA-TAAAGT
218538 TAGTTCATT
1 TAGTTCATT
218547 CATCAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:220074 original size:19 final size:20
Alignment explanation
Indices: 220050--220088 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
220040 AGGTTAGTAA
220050 AAAAAGAAAAAAA-GAAAAT
1 AAAAAGAAAAAAAGGAAAAT
220069 AAAAAGAAAAAAAGGAAAAT
1 AAAAAGAAAAAAAGGAAAAT
220089 TTAAAGAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAGAAAAAAAGGAAAAT
Found at i:223782 original size:13 final size:13
Alignment explanation
Indices: 223764--223793 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
223754 TTTGTTTTTC
223764 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
223777 AAAAAAGAAACAA
1 AAAAAAAAAACAA
223790 AAAA
1 AAAA
223794 GGCAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.07, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:223803 original size:25 final size:25
Alignment explanation
Indices: 223775--223851 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
223765 AAAAAAAAAC
223775 AAAAAAAAGAAACAAAAAAGGCAAA
1 AAAAAAAAGAAACAAAAAAGGCAAA
223800 AAAATAAAA-ATAA-AAAAAAGGCAAAA
1 AAAA-AAAAGA-AACAAAAAAGGC-AAA
** *
223826 AAAAAAAAGAGCCAAAAAAGCCAAA
1 AAAAAAAAGAAACAAAAAAGGCAAA
223851 A
1 A
223852 TTTCAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
25 22 0.50
26 22 0.50
ACGTcount: A:0.78, C:0.09, G:0.10, T:0.03
Consensus pattern (25 bp):
AAAAAAAAGAAACAAAAAAGGCAAA
Found at i:223808 original size:15 final size:14
Alignment explanation
Indices: 223788--223832 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
223778 AAAAAGAAAC
223788 AAAAAAGGCAAAAA
1 AAAAAAGGCAAAAA
* *
223802 AATAAA---AATAA
1 AAAAAAGGCAAAAA
223813 AAAAAAGGCAAAAA
1 AAAAAAGGCAAAAA
223827 AAAAAA
1 AAAAAA
223833 AGAGCCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 9 0.38
14 15 0.62
ACGTcount: A:0.82, C:0.04, G:0.09, T:0.04
Consensus pattern (14 bp):
AAAAAAGGCAAAAA
Found at i:223825 original size:17 final size:17
Alignment explanation
Indices: 223805--223844 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
223795 GCAAAAAAAT
*
223805 AAAAATAAAAAAA-AGGC
1 AAAAA-AAAAAAAGAGCC
223822 AAAAAAAAAAAAGAGCC
1 AAAAAAAAAAAAGAGCC
223839 AAAAAA
1 AAAAAA
223845 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.80, C:0.07, G:0.10, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAAGAGCC
Found at i:228142 original size:16 final size:16
Alignment explanation
Indices: 228123--228162 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
228113 CTTTATTATC
228123 TTATTTTATCTTCCGT
1 TTATTTTATCTTCCGT
**
228139 TTA-TTTATCTTTTGT
1 TTATTTTATCTTCCGT
228154 TTATTTTAT
1 TTATTTTAT
228163 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTTATCTTCCGT
Found at i:229349 original size:35 final size:37
Alignment explanation
Indices: 229280--229359 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
229270 ATACTATTTC
*
229280 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
229317 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
229352 CATCACCA
1 CATCACCA
229360 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:230226 original size:19 final size:20
Alignment explanation
Indices: 230185--230235 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
230175 GAAACCCCTT
*
230185 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
230205 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
230224 TGAAGATACATG
1 TGAAAATACATG
230236 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:231184 original size:30 final size:31
Alignment explanation
Indices: 231144--231203 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
231134 ACATGCTGCC
**
231144 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
231175 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
231204 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:235619 original size:21 final size:22
Alignment explanation
Indices: 235560--235621 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
235550 CAGAACCCCA
*
235560 GGGGGTATCGATTCCC-CTATG
1 GGGGGGATCGATTCCCTCTATG
*
235581 GGGGGGAATCGGTTCCCTC-ATG
1 GGGGGG-ATCGATTCCCTCTATG
*
235603 GGGGGGATTGATTCCCTCT
1 GGGGGGATCGATTCCCTCT
235622 GCACCAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 15 0.44
22 18 0.53
23 1 0.03
ACGTcount: A:0.13, C:0.23, G:0.37, T:0.27
Consensus pattern (22 bp):
GGGGGGATCGATTCCCTCTATG
Found at i:243449 original size:14 final size:14
Alignment explanation
Indices: 243432--243486 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
243422 TTGGAGTGCA
243432 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
243446 AAAAAGACAA-AAAG
1 AAAAA-AAAAGAAAG
*
243460 AAGAAGAAAAG-AAG
1 AA-AAAAAAAGAAAG
*
243474 AAAAGAAAAGAAA
1 AAAAAAAAAGAAA
243487 AAGAATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 8 0.24
14 21 0.62
15 5 0.15
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:243457 original size:19 final size:18
Alignment explanation
Indices: 243434--243491 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
243424 GGAGTGCAAA
243434 AAAAAAAGAAAGAAAAAG
1 AAAAAAAGAAAGAAAAAG
*
243452 ACAAAAAG-AAGAAGAAAAG
1 AAAAAAAGAAAG-A-AAAAG
*
243471 AAGAAAAGAAAAGAAAAAG
1 AAAAAAAG-AAAGAAAAAG
243490 AA
1 AA
243492 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 8 0.24
19 18 0.55
20 1 0.03
21 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAGAAAAAG
Found at i:243463 original size:11 final size:10
Alignment explanation
Indices: 243432--243488 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
243422 TTGGAGTGCA
*
243432 AAAAAAAAAG
1 AAAAAAGAAG
243442 AAAGAAA-AAG
1 AAA-AAAGAAG
243452 ACAAAAAGAAG
1 A-AAAAAGAAG
243463 AAGAAAAGAAG
1 AA-AAAAGAAG
243474 AAAAGAA-AAG
1 AAAA-AAGAAG
243484 AAAAA
1 AAAAA
243489 GAATTCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.02
10 20 0.48
11 21 0.50
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:243508 original size:11 final size:10
Alignment explanation
Indices: 243436--243491 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
243426 AGTGCAAAAA
243436 AAAAAGAAAG
1 AAAAAGAAAG
243446 AAAAAGACAA-
1 AAAAAGA-AAG
243456 AAAGAAG-AAG
1 AAA-AAGAAAG
243466 -AAAAG-AAG
1 AAAAAGAAAG
243474 -AAAAGAAAAG
1 AAAAAG-AAAG
243484 AAAAAGAA
1 AAAAAGAA
243492 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
8 11 0.28
9 4 0.10
10 15 0.38
11 10 0.25
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:249810 original size:5 final size:5
Alignment explanation
Indices: 249800--249851 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
249790 AACTTCTCTT
*
249800 TTTTC TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TGATTTC TCTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC T--TTTC TTTTC
249848 TTTT
1 TTTT
249852 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 32 0.78
6 4 0.10
7 5 0.12
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:249825 original size:8 final size:8
Alignment explanation
Indices: 249796--249851 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
249786 TTTGAACTTC
249796 TCTTTT-T
1 TCTTTTCT
249803 TCTTTTCTTT
1 TCTTTTC--T
249813 TCTTTTCT
1 TCTTTTCT
249821 TCTTTTCT
1 TCTTTTCT
249829 TCTTTTCT
1 TCTTTTCT
**
249837 GATTTCTCT
1 TCTTT-TCT
249846 TCTTTT
1 TCTTTT
249852 TGCACTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 6 0.15
8 21 0.51
9 6 0.15
10 8 0.20
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (8 bp):
TCTTTTCT
Found at i:249825 original size:13 final size:13
Alignment explanation
Indices: 249796--249836 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
249786 TTTGAACTTC
249796 TCTTTT-TTCTTT
1 TCTTTTCTTCTTT
249808 TCTTTTCTT-TTCT
1 TCTTTTCTTCTT-T
249821 TCTTTTCTTCTTT
1 TCTTTTCTTCTTT
249834 TCT
1 TCT
249837 GATTTCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.31
13 16 0.62
14 2 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTTCTTCTTT
Found at i:249825 original size:18 final size:17
Alignment explanation
Indices: 249796--249829 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
249786 TTTGAACTTC
249796 TCTTTTTTCTTTTCTTT
1 TCTTTTTTCTTTTCTTT
249813 TCTTTTCTTCTTTTCTT
1 TCTTTT-TTCTTTTCTT
249830 CTTTTCTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TCTTTTTTCTTTTCTTT
Found at i:250613 original size:19 final size:20
Alignment explanation
Indices: 250572--250622 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
250562 GAAACCCCTT
*
250572 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
250592 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
250611 TGAAGATACATG
1 TGAAAATACATG
250623 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:251572 original size:30 final size:31
Alignment explanation
Indices: 251532--251591 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
251522 ACATGCTGCC
**
251532 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
251563 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
251592 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:253752 original size:26 final size:23
Alignment explanation
Indices: 253723--253769 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
253713 CAAGTGCTGC
253723 AACAAAAAGCAACAAGAAAGAAGAAA
1 AACAAAAAG-AA-AAGAAA-AAGAAA
253749 AACAAAAAGAAAAGAAAAAGA
1 AACAAAAAGAAAAGAAAAAGA
253770 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (23 bp):
AACAAAAAGAAAAGAAAAAGAAA
Found at i:253762 original size:20 final size:20
Alignment explanation
Indices: 253726--253768 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
253716 GTGCTGCAAC
*
253726 AAAAAGCAACAAGAAAGAAG
1 AAAAAGCAAAAAGAAAGAAG
253746 AAAAA-CAAAAAG-AA-AAG
1 AAAAAGCAAAAAGAAAGAAG
253763 AAAAAG
1 AAAAAG
253769 ACTCCTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 6 0.29
20 5 0.24
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAGCAAAAAGAAAGAAG
Found at i:258190 original size:18 final size:16
Alignment explanation
Indices: 258167--258234 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 16
258157 TTCATGCATC
258167 TAGTTCATTGAATAAAG
1 TAGTTCATT-AATAAAG
258184 TTAGTTCATTAATTAAAG
1 -TAGTTCATTAA-TAAAG
* *
258202 TAGTTCATTCATCAAG
1 TAGTTCATTAATAAAG
258218 CTAGTTCATTTAATAAA
1 -TAGTTCA-TTAATAAA
258235 CTAACTCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.09
17 19 0.44
18 20 0.47
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (16 bp):
TAGTTCATTAATAAAG
Found at i:258207 original size:17 final size:18
Alignment explanation
Indices: 258167--258234 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 18
258157 TTCATGCATC
258167 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
258185 TAGTTCATT-AATTAAAG-
1 TAGTTCATTGAA-TAAAGT
* * *
258202 TAGTTCATT-CATCAAGC
1 TAGTTCATTGAATAAAGT
*
258219 TAGTTCATTTAATAAA
1 TAGTTCATTGAATAAA
258235 CTAACTCTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.09
17 21 0.49
18 18 0.42
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:260099 original size:2 final size:2
Alignment explanation
Indices: 260088--260151 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
260078 TAACTATAGG
260088 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
260129 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
260152 GAAAATAACT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:263023 original size:5 final size:5
Alignment explanation
Indices: 263013--263068 Score: 51
Period size: 5 Copynumber: 10.6 Consensus size: 5
263003 CTCTTTTGAA
* *
263013 TTTCT TTTCT TTTCT TTT-T TTTGATT TTTCT TTTCT TTTCT CTTTTT
1 TTTCT TTTCT TTTCT TTTCT TTT--CT TTTCT TTTCT TTTCT -TTTCT
263060 CTTTCT TTT
1 -TTTCT TTT
263069 TGTACTCCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.09
5 27 0.61
6 9 0.20
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:263058 original size:17 final size:18
Alignment explanation
Indices: 263020--263068 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
263010 GAATTTCTTT
263020 TCTTTTCTTTT-TTTTGA
1 TCTTTTCTTTTCTTTTGA
*
263037 T-TTTTCTTTTCTTTT-C
1 TCTTTTCTTTTCTTTTGA
263053 TCTTTT-TCTTTCTTTT
1 TCTTTTCT-TTTCTTTT
263069 TGTACTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TCTTTTCTTTTCTTTTGA
Found at i:263428 original size:20 final size:21
Alignment explanation
Indices: 263391--263429 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
263381 GATGGTCTTG
*
263391 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
263412 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
263430 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:265340 original size:10 final size:10
Alignment explanation
Indices: 265325--265351 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
265315 TATTTTTTTC
265325 AAAAAAAACA
1 AAAAAAAACA
265335 AAAAAAAACA
1 AAAAAAAACA
265345 AAAAAAA
1 AAAAAAA
265352 GGCAAAAAAG
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:273556 original size:29 final size:29
Alignment explanation
Indices: 273514--273580 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
273504 TATGTTTATT
* *
273514 TATTTAATCGGTTTCTAATTTGTATCTTG
1 TATTTATTTGGTTTCTAATTTGTATCTTG
*
273543 TATTTATTTGGTTTCTAATTTGTATGTTG
1 TATTTATTTGGTTTCTAATTTGTATCTTG
273572 TATTTATTT
1 TATTTATTT
273581 CAGTCTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (29 bp):
TATTTATTTGGTTTCTAATTTGTATCTTG
Found at i:280425 original size:19 final size:19
Alignment explanation
Indices: 280401--280437 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
280391 TTCTTTTTCT
280401 TTCTTTTCT-TCTTTTCTTC
1 TTCTTTT-TGTCTTTTCTTC
280420 TTCTTTTTGTCTTTTCTT
1 TTCTTTTTGTCTTTTCTT
280438 TCTTTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.00, C:0.22, G:0.03, T:0.76
Consensus pattern (19 bp):
TTCTTTTTGTCTTTTCTTC
Found at i:280439 original size:23 final size:23
Alignment explanation
Indices: 280391--280441 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
280381 TCTTTTTGAA
* *
280391 TTCTTTTTCTTTCTTTTCTTCTT
1 TTCTTCTTCTTTCTTGTCTTCTT
*
280414 TTCTTCTTCTTT-TTGTCTTTTCT
1 TTCTTCTTCTTTCTTGTCTTCT-T
280437 TTCTT
1 TTCTT
280442 TTTACACTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (23 bp):
TTCTTCTTCTTTCTTGTCTTCTT
Found at i:285361 original size:14 final size:12
Alignment explanation
Indices: 285317--285374 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
285307 CTTTTTGAAC
285317 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
285330 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
285343 TTCTTCTTCTT-TT
1 TTCTT-TT-TTCTT
285356 TGTC-TTTTTC-T
1 T-TCTTTTTTCTT
285367 TTCTTTTT
1 TTCTTTTT
285375 GCACTCCAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.05
11 8 0.20
12 5 0.12
13 18 0.45
14 7 0.17
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.78
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:290278 original size:14 final size:12
Alignment explanation
Indices: 290234--290292 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
290224 CTTTTTGAAC
290234 TTCTCTTTTTCTT
1 TTCT-TTTTTCTT
290247 TTCTTTTCTTCTT
1 TTCTTTT-TTCTT
290260 TTCTTCTTCTT-TT
1 TTCTT-TT-TTCTT
290273 TGTC-TTTTTC-T
1 T-TCTTTTTTCTT
290284 TTCTTTTTT
1 TTCTTTTTT
290293 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
10 2 0.05
11 9 0.22
12 5 0.12
13 18 0.44
14 7 0.17
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTCTTTTTTCTT
Found at i:290279 original size:32 final size:31
Alignment explanation
Indices: 290233--290292 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
290223 TCTTTTTGAA
290233 CTTCTCTTTTTC-TTTTCTTTTCTTCTTTTCTT
1 CTTCTCTTTTTCTTTTTC-TTTCTT-TTTTCTT
290265 CTTCT-TTTTGTCTTTTTCTTTCTTTTTT
1 CTTCTCTTTT-TCTTTTTCTTTCTTTTTT
290293 GCACTCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
31 8 0.31
32 13 0.50
33 5 0.19
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (31 bp):
CTTCTCTTTTTCTTTTTCTTTCTTTTTTCTT
Found at i:290291 original size:19 final size:19
Alignment explanation
Indices: 290237--290293 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
290227 TTTGAACTTC
*
290237 TCTTTTTCTTTTCTTTTCT-
1 TCTTTTTC-TTTCTTTTTTG
290256 TC-TTTTC-TTCTTCTTTTTG
1 TCTTTTTCTTTC-T-TTTTTG
290275 TCTTTTTCTTTCTTTTTTG
1 TCTTTTTCTTTCTTTTTTG
290294 CACTCCAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 3 0.09
17 1 0.03
18 9 0.28
19 10 0.31
20 6 0.19
21 3 0.09
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (19 bp):
TCTTTTTCTTTCTTTTTTG
Found at i:290292 original size:11 final size:10
Alignment explanation
Indices: 290239--290292 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
290229 TGAACTTCTC
290239 TTTTTCTTTT
1 TTTTTCTTTT
*
290249 CTTTTCTTCTT
1 TTTTTCTT-TT
*
290260 TTCTTCTTCTT
1 TTTTTCTT-TT
*
290271 TTTGTCTTTT
1 TTTTTCTTTT
*
290281 TCTTTCTTTT
1 TTTTTCTTTT
290291 TT
1 TT
290293 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
10 18 0.51
11 17 0.49
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:294480 original size:4 final size:4
Alignment explanation
Indices: 294471--294519 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
294461 TGCTTCAACT
* *
294471 TTTC TTTC TTTC TTTTC TTTC TTTC TTT- TAT- TTTC TTTT TTTC -TTC
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
294517 TTT
1 TTT
294520 TTGAGTGCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
3 7 0.18
4 27 0.71
5 4 0.11
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:294487 original size:13 final size:13
Alignment explanation
Indices: 294469--294519 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
294459 AGTGCTTCAA
294469 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
294482 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
*
294495 CTTTTATTTTCTTT
1 CTTTT-CTTTCTTT
294509 -TTTTC-TTCTTT
1 CTTTTCTTTCTTT
294520 TTGAGTGCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 6 0.17
13 22 0.63
14 7 0.20
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:294545 original size:24 final size:25
Alignment explanation
Indices: 294508--294559 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
294498 TTATTTTCTT
*
294508 TTTTTCTTCTTTTTGAGTGCTTGAA
1 TTTTTCTTCTTTTTGAGTGCTTCAA
*
294533 TTTTTCTTC-TTTTGAGTGGTTCAA
1 TTTTTCTTCTTTTTGAGTGCTTCAA
294557 TTT
1 TTT
294560 CTTAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (25 bp):
TTTTTCTTCTTTTTGAGTGCTTCAA
Found at i:299026 original size:14 final size:14
Alignment explanation
Indices: 299007--299055 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
298997 TCTTTTTGAA
299007 CTTCTTTTTCTTTT
1 CTTCTTTTTCTTTT
*
299021 CTTCTTTTCCTTTT
1 CTTCTTTTTCTTTT
**
299035 C-TGATTTT-TTTT
1 CTTCTTTTTCTTTT
299047 CTTCTTTTT
1 CTTCTTTTT
299056 GTCTTTTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 5 0.18
13 9 0.32
14 14 0.50
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (14 bp):
CTTCTTTTTCTTTT
Found at i:311158 original size:34 final size:32
Alignment explanation
Indices: 311089--311160 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 32
311079 CTTGGCTTGC
* *
311089 TTTC-TTTTTGAATTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTTGAATTTCTTATTCTTTTCTTCA
311120 TTTCTTTTTCTGAATTTTCTTATTCTTTT-TGTCA
1 TTTCTTTTT-TGAA-TTTCTTATTCTTTTCT-TCA
311154 TTTCTTT
1 TTTCTTT
311161 CTTTTTGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 5 0.14
34 22 0.63
ACGTcount: A:0.08, C:0.15, G:0.04, T:0.72
Consensus pattern (32 bp):
TTTCTTTTTTGAATTTCTTATTCTTTTCTTCA
Found at i:324074 original size:275 final size:275
Alignment explanation
Indices: 323575--324132 Score: 990
Period size: 275 Copynumber: 2.0 Consensus size: 275
323565 ATGAAATGTG
* *
323575 CCATCTTTGAAAACCTATCAACAACAACAAAGATACTATCTCTGCCTGTTCTAGTTCTAGGCAAT
1 CCATCTTTGAAAAACTATCAACAACAACAAAGATACTATCTCTGCCTGTCCTAGTTCTAGGCAAT
* *
323640 CCCAACACAAAATCCATCGAGATATCCAGCCAAGGAGAATTAGTAATAGGTAAAGGCAAATAGAT
66 CCCAACACAAAATCCATCGAGATATCCAGCCAAGGAGAATTAGGAATAGGTAAAGGCAAATACAT
*
323705 ATCATGTGGTAGAACCTTTCATTTTGCTTTCTTACATGTTACACAACGTTCACATATTCTTTCAA
131 ATCATGTGGTAGAACCTTTCATTTTACTTTCTTACATGTTACACAACGTTCACATATTCTTTCAA
323770 CGTCCCTACGCATCTTAGGCAAGAATAGATGCTCCTTCAGAATGTGCAACGTCTTAGTAACTCCA
196 CGTCCCTACGCATCTTAGGCAAGAATAGATGCTCCTTCAGAATGTGCAACGTCTTAGTAACTCCA
323835 GAATGTCCCATAAGT
261 GAATGTCCCATAAGT
*
323850 CCATCTTTGAAAAACTATCAACGACAACAAAGATACTATCTCTGCCTGTCCTAGTTCTAGGCAAT
1 CCATCTTTGAAAAACTATCAACAACAACAAAGATACTATCTCTGCCTGTCCTAGTTCTAGGCAAT
* * *
323915 CCTAACACAAAATTCATCGAGATATCTAGCCAAGGAGAATTAGGAATAGGTAAAGGCAAATACAT
66 CCCAACACAAAATCCATCGAGATATCCAGCCAAGGAGAATTAGGAATAGGTAAAGGCAAATACAT
323980 ATCATGTGGTAGAACCTTTCATTTTACTTTCTTACATGTTACACAACGTTCACATATTCTTTCAA
131 ATCATGTGGTAGAACCTTTCATTTTACTTTCTTACATGTTACACAACGTTCACATATTCTTTCAA
* * **
324045 CGTCCCTACGCATCTTAGGCCATAATAGATGCTCCTTCAGAATGTGCAACGTCTTAGTAACTTTA
196 CGTCCCTACGCATCTTAGGCAAGAATAGATGCTCCTTCAGAATGTGCAACGTCTTAGTAACTCCA
324110 GAATGTCCCATAAGT
261 GAATGTCCCATAAGT
*
324125 CCACCTTT
1 CCATCTTT
324133 ATATGCTTTT
Statistics
Matches: 269, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
275 269 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (275 bp):
CCATCTTTGAAAAACTATCAACAACAACAAAGATACTATCTCTGCCTGTCCTAGTTCTAGGCAAT
CCCAACACAAAATCCATCGAGATATCCAGCCAAGGAGAATTAGGAATAGGTAAAGGCAAATACAT
ATCATGTGGTAGAACCTTTCATTTTACTTTCTTACATGTTACACAACGTTCACATATTCTTTCAA
CGTCCCTACGCATCTTAGGCAAGAATAGATGCTCCTTCAGAATGTGCAACGTCTTAGTAACTCCA
GAATGTCCCATAAGT
Found at i:326503 original size:34 final size:34
Alignment explanation
Indices: 326460--326529 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
326450 GTTGCATATG
326460 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
1 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
326494 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
1 TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
326528 TT
1 TT
326530 CAGACTAGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (34 bp):
TTGCTTTTTACGTCCAACTTCAACAATGGGAGGC
Found at i:366937 original size:13 final size:13
Alignment explanation
Indices: 366915--366944 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
366905 ACTAAACACC
366915 TTTC-ACATACCT
1 TTTCAACATACCT
366927 TTTCAACATACCT
1 TTTCAACATACCT
366940 TTTCA
1 TTTCA
366945 TCTTTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:384800 original size:17 final size:16
Alignment explanation
Indices: 384732--384802 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
384722 ATTCATGCAT
384732 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
384749 GTTAG-TCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
384766 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
384783 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
384800 CTA
1 CTA
384803 ACTCTTAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
16 6 0.14
17 31 0.70
18 7 0.16
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Done.