Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008238.1 Hibiscus syriacus cultivar Beakdansim tig00110885_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: 622934
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 3
Found at i:30688 original size:23 final size:23
Alignment explanation
Indices: 30620--30680 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
30610 CAATCATAGA
30620 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
30643 TGGCAATACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
30666 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
30681 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:33214 original size:68 final size:68
Alignment explanation
Indices: 33119--33249 Score: 172
Period size: 68 Copynumber: 1.9 Consensus size: 68
33109 TGACTCAATC
* * * * * *
33119 CATAACAGACAAAATCAAAAACAAAATCCTGAACTTCCGCACGAATAGAAAACCAGAAACAACAT
1 CATAAAAGACAAAAGCAAAAACAAAATCCTGAACATCCACACGAACAGAAAACAAGAAACAACAT
33184 TCG
66 TCG
* * * *
33187 CATAAAAGACGAAAGCAAAAGCAAAATCCTGAACATCCACACGAACAGAGAACAAGAATCAAC
1 CATAAAAGACAAAAGCAAAAACAAAATCCTGAACATCCACACGAACAGAAAACAAGAAACAAC
33250 TTCCGCCTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 53 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.11
Consensus pattern (68 bp):
CATAAAAGACAAAAGCAAAAACAAAATCCTGAACATCCACACGAACAGAAAACAAGAAACAACAT
TCG
Found at i:43421 original size:21 final size:21
Alignment explanation
Indices: 43397--43437 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43387 AAGGACAAGA
43397 AGACCCTTCACAAAGACATGC
1 AGACCCTTCACAAAGACATGC
*
43418 AGACTCTTCACAAAGACATG
1 AGACCCTTCACAAAGACATG
43438 AAGATCACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.17
Consensus pattern (21 bp):
AGACCCTTCACAAAGACATGC
Found at i:45077 original size:16 final size:16
Alignment explanation
Indices: 45058--45095 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
45048 GAATGACGCT
45058 GAGCTAGAAGCCGTTA
1 GAGCTAGAAGCCGTTA
45074 GAGCTAGAAGCCGTTA
1 GAGCTAGAAGCCGTTA
45090 GAGCTA
1 GAGCTA
45096 AGAACAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (16 bp):
GAGCTAGAAGCCGTTA
Found at i:46448 original size:23 final size:22
Alignment explanation
Indices: 46422--46489 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
46412 GCTCGTATAA
46422 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
46445 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46467 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
46489 T
1 T
46490 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:46748 original size:30 final size:30
Alignment explanation
Indices: 46703--46761 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
46693 ATCGCGTAGT
* *
46703 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
46733 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
46762 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:47164 original size:19 final size:20
Alignment explanation
Indices: 47127--47164 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47117 TTTTTTCTCA
*
47127 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
47147 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
47165 TCAAGCCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:47263 original size:67 final size:68
Alignment explanation
Indices: 47128--47278 Score: 227
Period size: 68 Copynumber: 2.2 Consensus size: 68
47118 TTTTTCTCAT
* *
47128 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
47192 TGA
66 TGA
* *
47195 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAG-CATTCTGGAATTTCAT-TTCG
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCA-TCTGGAATTTCATATACG
*
47258 TTGA
65 ATGA
47262 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
47279 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
67 37 0.48
68 40 0.52
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
TGA
Found at i:47290 original size:67 final size:67
Alignment explanation
Indices: 47128--47300 Score: 226
Period size: 67 Copynumber: 2.6 Consensus size: 67
47118 TTTTTCTCAT
* *
47128 GGGGGAATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCCATCTGGAATTTCATATACGAT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGAT
47193 GA
66 GA
* *
47195 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAG-CATTCTGGAATTTCAT-TTCG
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCCA-TCTGGAATTTCATATACG
*
47258 TTGA
64 ATGA
* *
47262 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
47301 AGCCCAGAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
65 6 0.06
67 49 0.52
68 40 0.42
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGAT
GA
Found at i:52353 original size:22 final size:22
Alignment explanation
Indices: 52312--52379 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
52302 CTCGTATAAA
52312 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
52335 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
52357 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
52379 T
1 T
52380 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:52638 original size:30 final size:30
Alignment explanation
Indices: 52593--52651 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
52583 ATCGCGTAGT
* *
52593 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
52623 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
52652 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:53053 original size:19 final size:20
Alignment explanation
Indices: 53016--53053 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53006 TTTTTTCTCA
*
53016 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
53036 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
53054 TCAAGCCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:53152 original size:67 final size:68
Alignment explanation
Indices: 53017--53167 Score: 227
Period size: 68 Copynumber: 2.2 Consensus size: 68
53007 TTTTTCTCAT
* *
53017 GGGGGAATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
53081 TGA
66 TGA
* *
53084 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAG-CATTCTGGAATTTCAT-TTCG
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCA-TCTGGAATTTCATATACG
*
53147 TTGA
65 ATGA
53151 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
53168 TTGAATGGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
67 37 0.48
68 40 0.52
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCCATCTGGAATTTCATATACGA
TGA
Found at i:55365 original size:34 final size:32
Alignment explanation
Indices: 55312--55381 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
55302 ACCTTACAAC
*
55312 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
55344 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
55378 TCCC
1 TCCC
55382 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:55866 original size:13 final size:13
Alignment explanation
Indices: 55850--55910 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
55840 CAGATGCATA
55850 GATGCACTGCAGG
1 GATGCACTGCAGG
55863 GATGCA-T----G
1 GATGCACTGCAGG
55871 GATGCACTGCAGG
1 GATGCACTGCAGG
55884 GATGCA-T----G
1 GATGCACTGCAGG
55892 GATGCACTGCAGG
1 GATGCACTGCAGG
55905 GATGCA
1 GATGCA
55911 TGGATGCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
8 14 0.37
9 2 0.05
12 2 0.05
13 20 0.53
ACGTcount: A:0.25, C:0.20, G:0.38, T:0.18
Consensus pattern (13 bp):
GATGCACTGCAGG
Found at i:55868 original size:21 final size:21
Alignment explanation
Indices: 55842--55920 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
55832 CATTAGTGCA
*
55842 GATGCATAGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
55863 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
55884 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
55905 GATGCATGGATGCACT
1 GATGCATGGATGCACT
55921 TTGACACCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:56026 original size:30 final size:30
Alignment explanation
Indices: 55992--56051 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
55982 ACCTTTGAAT
55992 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
56022 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
56052 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:57371 original size:19 final size:20
Alignment explanation
Indices: 57328--57375 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
57318 TCTAAATCCT
*
57328 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
57348 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
57367 TTTTCAAAA
1 TTTTCAAAA
57376 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:58943 original size:30 final size:30
Alignment explanation
Indices: 58886--58945 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
58876 AACTTTGAAT
58886 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
58916 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
58946 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:61915 original size:23 final size:23
Alignment explanation
Indices: 61897--61972 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
61887 AATGCACCAA
*
61897 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
61920 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
*
61943 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGT
61966 AGTGCCA
1 AGTGCCA
61973 TATAATAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGT
Found at i:62162 original size:103 final size:103
Alignment explanation
Indices: 61994--62205 Score: 325
Period size: 103 Copynumber: 2.1 Consensus size: 103
61984 CCATAAGGAT
* * * *
61994 CACATATCATTCCTTAATAATCATATACATATACTAGGGATCAAGTATATATCTCACCAGGCTTC
1 CACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTC
* *
62059 ACATATGTTCCAAAGAATACATATATGTCCCGAAAGAC
66 ACACATATTCCAAAGAATACATATATGTCCCGAAAGAC
* * * *
62097 CGCATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTC
1 CACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTC
*
62162 ACACATATTCCAAAGAATACATATATGTCCCGAAGGAC
66 ACACATATTCCAAAGAATACATATATGTCCCGAAAGAC
62200 CACATA
1 CACATA
62206 GACCCTCGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
CACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATATCTCACCAGACTTC
ACACATATTCCAAAGAATACATATATGTCCCGAAAGAC
Found at i:65291 original size:42 final size:42
Alignment explanation
Indices: 65230--65326 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
65220 ACAATTTAAG
* * *
65230 TCCTTCGGGCCATCAGTAAGTCT-TTCGAGCATGATGATGAAA
1 TCCTTCAGGCCATCAGTAAG-CTGTTAGAGCAAGATGATGAAA
* * *
65272 TCCTTCAGGTCATCTGTAAGCTGTTAGAGCAAGATGAT-AAG
1 TCCTTCAGGCCATCAGTAAGCTGTTAGAGCAAGATGATGAAA
* *
65313 TCATTCGGGCCATC
1 TCCTTCAGGCCATC
65327 CATAAGACCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
41 15 0.33
42 30 0.67
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (42 bp):
TCCTTCAGGCCATCAGTAAGCTGTTAGAGCAAGATGATGAAA
Found at i:65513 original size:42 final size:42
Alignment explanation
Indices: 65446--65580 Score: 162
Period size: 42 Copynumber: 3.2 Consensus size: 42
65436 ACTTAGTAAG
* * * * *
65446 TCCTTCAGACCATCAATAAGCCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
* * * *
65488 TCCTTCGGGCCATCAGTAAGTCTTTCGTGAATGATGATGAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
* *
65530 TCTTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
*
65572 TCATTCGGG
1 TCCTTCGGG
65581 AAATTTATAA
Statistics
Matches: 76, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
Found at i:65685 original size:42 final size:42
Alignment explanation
Indices: 65621--65700 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
65611 AAACAAACCT
* * *
65621 ATCATTAAGTCTTTCAAGCATGATTATGAAGTCCTTCGAGCC
1 ATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGAGCC
* *
65663 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG
1 ATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCG
65701 GGTAATTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGAGCC
Found at i:65727 original size:122 final size:122
Alignment explanation
Indices: 65497--65785 Score: 411
Period size: 122 Copynumber: 2.4 Consensus size: 122
65487 ATCCTTCGGG
* * *
65497 CCATCAGTAAGTCTTTCGTGAATGATGATGAAGTCTTTTGGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
**
65562 GATGATTAAATCATTCGGGAAATTTATAAGCCTTCACGGAAGAGTAGTGAAACAAA-
66 GATGATTAAATCATTCGGGAAATTTATAAGCCTTCACCAAAGAGTAGTGAAACAAAT
* * * * *
65618 CCTATCATTAAGTCTTTCAAGCATGATTATGAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCA
1 CC-ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCA
* * * * *
65683 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTTACCAAAGAGTAGTGAAGCAAAT
65 TGATGATTAAATCATTCGGGAAATTTATAAGCCTTCACCAAAGAGTAGTGAAACAAAT
*
65741 CCATCAGTAAGTCTTTCGAGCAAGATGAT-AAGTCTTTCGGGCCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCAT
65786 TTTAAGCCTT
Statistics
Matches: 145, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
121 16 0.11
122 127 0.88
123 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (122 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCATTCGGGAAATTTATAAGCCTTCACCAAAGAGTAGTGAAACAAAT
Found at i:66212 original size:53 final size:53
Alignment explanation
Indices: 66036--66399 Score: 447
Period size: 53 Copynumber: 6.9 Consensus size: 53
66026 AGAATCACAC
*
66036 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-CTGTAGG
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* **
66086 CAGAAGATTCTTCGAGTTTTACTCCCTGAAGCAAGAGGGAG-G-A-TTGTAGG
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
66136 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
66189 CAGAAGATTGTTCGAGTTTTACTCTCTGAAGCAAGAGGAAGCGAACCCGTTGG
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
66242 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * **
66295 CAGAAGATTATTCGAGTTCTACTCCTTGAAGCAATAGGGAGCGAACCC-TATTTT
1 CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTA--GG
* * * *
66349 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGATGGAGAGAACCCGT
1 CAGAAGATTGTTCGAGTT--TTACTCCCTGAAGCAAGAGGGAGCGAACCCGT
66400 CATTTGAAGA
Statistics
Matches: 278, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
50 87 0.31
51 1 0.00
52 3 0.01
53 147 0.53
54 16 0.06
55 14 0.05
56 10 0.04
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:71898 original size:3 final size:3
Alignment explanation
Indices: 71890--71926 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
71880 ATGAAAAAGT
71890 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
71927 ATCGGGCCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71970 original size:24 final size:24
Alignment explanation
Indices: 71937--71991 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 24
71927 ATCGGGCCTG
71937 CAAAGCTGTAGTTTGCCAGAATTTT
1 CAAA-CTGTAGTTTGCCAGAATTTT
71962 CAAACTGTAGTTTGCCAGAATTTT
1 CAAACTGTAGTTTGCCAGAATTTT
71986 CAAACT
1 CAAACT
71992 TCGTTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (24 bp):
CAAACTGTAGTTTGCCAGAATTTT
Found at i:72413 original size:31 final size:31
Alignment explanation
Indices: 72375--72473 Score: 155
Period size: 31 Copynumber: 3.2 Consensus size: 31
72365 TTGCAATACA
72375 GTCCCTCAACATTTAGTTCGTTTGTAATATG
1 GTCCCTCAACATTTAGTTCGTTTGTAATATG
* *
72406 GTCCCTCAACATTTAGCAT-GTTTGCAATATG
1 GTCCCTCAACATTTAG-TTCGTTTGTAATATG
*
72437 GTCCCTCAACATTTAGTCCGTTTGTAATATG
1 GTCCCTCAACATTTAGTTCGTTTGTAATATG
72468 GTCCCT
1 GTCCCT
72474 GACGTAACTG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
31 60 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
GTCCCTCAACATTTAGTTCGTTTGTAATATG
Found at i:76396 original size:23 final size:22
Alignment explanation
Indices: 76331--76389 Score: 93
Period size: 23 Copynumber: 2.7 Consensus size: 22
76321 GGGGTATCAA
*
76331 TTCCCCTAC-AGGGGGAATCGG
1 TTCCCCTTCAAGGGGGAATCGG
76352 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AAGGGGGAATCGG
76375 TTCCCCTTCAAGGGG
1 TTCCCCTTCAAGGGG
76390 AGTATCGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 8 0.23
22 6 0.17
23 21 0.60
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.22
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCGG
Found at i:76401 original size:23 final size:22
Alignment explanation
Indices: 76319--76402 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 22
76309 CATAACCTCC
* * *
76319 AGGGGGTATCAATTCCCCTAC-
1 AGGGGGAATCGATTCCCCTTCA
*
76340 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCCTTC-A
*
76363 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGATTCCCCTTCA
*
76385 AGGGGAGTATCGATTCCC
1 AGGGG-GAATCGATTCCC
76403 TCTGCACCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.31
22 6 0.11
23 31 0.57
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
AGGGGGAATCGATTCCCCTTCA
Found at i:96094 original size:58 final size:58
Alignment explanation
Indices: 96004--96119 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
95994 TATAAGAGTA
96004 GTGTTAGCCTTTATTTGTTTTGGGTACTTCAAATAGGATTTGATTGTTGTATCTTTCT
1 GTGTTAGCCTTTATTTGTTTTGGGTACTTCAAATAGGATTTGATTGTTGTATCTTTCT
96062 GTGTTAGCCTTTATTTGTTTTGGGTACTTCAAATAGGATTTGATTGTTGTATCTTTCT
1 GTGTTAGCCTTTATTTGTTTTGGGTACTTCAAATAGGATTTGATTGTTGTATCTTTCT
96120 ATTGATTTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.17, C:0.10, G:0.21, T:0.52
Consensus pattern (58 bp):
GTGTTAGCCTTTATTTGTTTTGGGTACTTCAAATAGGATTTGATTGTTGTATCTTTCT
Found at i:106530 original size:15 final size:15
Alignment explanation
Indices: 106512--106550 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
106502 AGCGTGAGGA
106512 AGAGAGTAGATGGG-G
1 AGAGAGTAGA-GGGTG
106527 AGAGAGTAGAGGGTG
1 AGAGAGTAGAGGGTG
106542 AGAGGAGTA
1 AGA-GAGTA
106551 TGATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 5 0.23
ACGTcount: A:0.36, C:0.00, G:0.51, T:0.13
Consensus pattern (15 bp):
AGAGAGTAGAGGGTG
Found at i:111834 original size:18 final size:19
Alignment explanation
Indices: 111811--111853 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
111801 CAGTAATCCT
111811 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
111829 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
111849 ATTCC
1 ATTCC
111854 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:121156 original size:22 final size:22
Alignment explanation
Indices: 121121--121175 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
121111 TTCAGAGGGA
121121 ACCGATT-CCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
121142 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
121164 ACCGATTCCCCC
1 ACCGATTCCCCC
121176 TGAATGGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:126189 original size:10 final size:10
Alignment explanation
Indices: 126174--126198 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
126164 CTCGAAACTC
126174 TATTAGTGAT
1 TATTAGTGAT
126184 TATTAGTGAT
1 TATTAGTGAT
126194 TATTA
1 TATTA
126199 TGCTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (10 bp):
TATTAGTGAT
Found at i:133702 original size:45 final size:46
Alignment explanation
Indices: 133614--133704 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 46
133604 ATGGCGACGT
* *
133614 TGATGGTGAAGGTGATCTTTTAAGAGAGAAAATAATTGAAAAAACTA
1 TGATGGTGAAAGTGATATTTTAAGAGAG-AAATAATTGAAAAAACTA
133661 TGATGGTGAAAGTGATATTTTAAGAGAG-AATAATTGAAAAAACT
1 TGATGGTGAAAGTGATATTTTAAGAGAGAAATAATTGAAAAAACT
133705 GGACGTGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 16 0.38
47 26 0.62
ACGTcount: A:0.45, C:0.03, G:0.23, T:0.29
Consensus pattern (46 bp):
TGATGGTGAAAGTGATATTTTAAGAGAGAAATAATTGAAAAAACTA
Found at i:143436 original size:128 final size:128
Alignment explanation
Indices: 143208--143463 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
143198 GTCGACAAGC
143208 TTCTTCACTTCATTTAGCACCCGTGAACTTAGATCAGAGCCCCAAAATATGGTTGCAAGCTTAGC
1 TTCTTCACTTCATTTAGCACCCGTGAACTTAGATCAGAGCCCCAAAATATGGTTGCAAGCTTAGC
143273 ACTTAACAATGCATCTAGGAGTACATCTCAAAGCATATGCTTACTTAGCTGTTCGTCAAAGAT
66 ACTTAACAATGCATCTAGGAGTACATCTCAAAGCATATGCTTACTTAGCTGTTCGTCAAAGAT
143336 TTCTTCACTTCATTTAGCACCCGTGAACTTAGATCAGAGCCCCAAAATATGGTTGCAAGCTTAGC
1 TTCTTCACTTCATTTAGCACCCGTGAACTTAGATCAGAGCCCCAAAATATGGTTGCAAGCTTAGC
143401 ACTTAACAATGCATCTAGGAGTACATCTCAAAGCATATGCTTACTTAGCTGTTCGTCAAAGAT
66 ACTTAACAATGCATCTAGGAGTACATCTCAAAGCATATGCTTACTTAGCTGTTCGTCAAAGAT
143464 AAGCAAGGGT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (128 bp):
TTCTTCACTTCATTTAGCACCCGTGAACTTAGATCAGAGCCCCAAAATATGGTTGCAAGCTTAGC
ACTTAACAATGCATCTAGGAGTACATCTCAAAGCATATGCTTACTTAGCTGTTCGTCAAAGAT
Found at i:144670 original size:138 final size:138
Alignment explanation
Indices: 144422--144697 Score: 507
Period size: 138 Copynumber: 2.0 Consensus size: 138
144412 GGGAAATAAC
*
144422 ATGATAAGCCAAGTAAACAACAGAGGAAAAAAGTTATAGTTCAAAATTCAAAGCAATGATCACTC
1 ATGATAAGCCAAGTAAACAACAGAGGAAAAAAATTATAGTTCAAAATTCAAAGCAATGATCACTC
* *
144487 GTAACAAACAATATCCATTGAGTACAAACACAGATCCATCTTACTTGGGCAGTAAGTGACTTGAT
66 GTAACAAACAATATCCATCGAGTACAAACACAAATCCATCTTACTTGGGCAGTAAGTGACTTGAT
144552 AACTTCCT
131 AACTTCCT
* *
144560 ATGATAAGCTAAGTAAACAACAGAGGAAAAAAATTATAGTTCAAAATTCAAAGCAATTATCACTC
1 ATGATAAGCCAAGTAAACAACAGAGGAAAAAAATTATAGTTCAAAATTCAAAGCAATGATCACTC
144625 GTAACAAACAATATCCATCGAGTACAAACACAAATCCATCTTACTTGGGCAGTAAGTGACTTGAT
66 GTAACAAACAATATCCATCGAGTACAAACACAAATCCATCTTACTTGGGCAGTAAGTGACTTGAT
144690 AACTTCCT
131 AACTTCCT
144698 TTGCTGCTTT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 133 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (138 bp):
ATGATAAGCCAAGTAAACAACAGAGGAAAAAAATTATAGTTCAAAATTCAAAGCAATGATCACTC
GTAACAAACAATATCCATCGAGTACAAACACAAATCCATCTTACTTGGGCAGTAAGTGACTTGAT
AACTTCCT
Found at i:152827 original size:18 final size:18
Alignment explanation
Indices: 152804--152891 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
152794 GGAATGTTTT
*
152804 TGAAGGAATTATAATCTG
1 TGAAGGAATTAGAATCTG
152822 TGAAGGAATTAGAATCTG
1 TGAAGGAATTAGAATCTG
* *
152840 TGAAAGAATTAGAATATG
1 TGAAGGAATTAGAATCTG
*
152858 TGAAGGAATTGGAATCTG
1 TGAAGGAATTAGAATCTG
* *
152876 T-CAGGAATTGGAATCT
1 TGAAGGAATTAGAATCT
152892 AATTCCATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
17 14 0.22
18 49 0.78
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (18 bp):
TGAAGGAATTAGAATCTG
Found at i:153738 original size:256 final size:254
Alignment explanation
Indices: 153244--153860 Score: 815
Period size: 261 Copynumber: 2.4 Consensus size: 254
153234 CTCCATTCGA
* * *
153244 GACCCGACCCGACCAAAATAAAGTTTCACACGACCCGACCCGAATATATAAATTAGAAACCCAAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
* * *
153309 TCGACCCGAAATAATAAAAAATTTATTTTTATTCAATAAAAACAATTACTTAATTGAAAAAATAT
66 CCGACCCGAAATAATAAAAAA--TATTTTTATTCAATAAAAACAATAACTTAATTGAAAAAAAAT
153374 ATATAGAGAGAGGGTAATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATTTTTTT
129 ATATAGAGAGAGGGTAATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATA----TTT
**
153439 GGTTCGGGTCGAGTATTTTTCACCCTAAACTTGAA-CCCGACCCGAATATCACACTTAAAAAAAC
190 -GTTCGGGTCGAGTATTTTTCACCCTAAACCCGAACCCCGACCCGAATATCACACTTAAAAAAAC
153503 C
254 C
* *
153504 TGACCCGATCCGAACAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCAA
1 -GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA--C--
* **
153569 CCGACCCGACCCGAAATAATAAACAAATATTTTTATTCAATTAAAACGGTAACTTAATTGAAAAA
61 CCGACCCGACCCGAAATAATAAA-AAATATTTTTATTCAATAAAAACAATAACTTAATTG-AAAA
* * *
153634 AAAATTATATATAGA-TGGGT-ATTATTGT-ATTATTCCTAAATATATAAGGTAAAATTATATA-
124 AAAA-TATATAGAGAGAGGGTAATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATAT
153695 TT-TTCGGGTCGAGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAA
188 TTGTTCGGGTCGAGTATTTTTCACCCTAAACCCGAA--C--CCCGACCCGAATATCACACTTAAA
153759 AAAACC
249 AAAACC
* *
153765 GTCCCGACCCGACCAAAATAAAGTTTCACCCGACCC-A----AATATATGAATTAGAAACTCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
153825 CCGACCCAAAATAATAAAAAATATTTTTATTCAATA
66 CCGACCCGAAATAATAAAAAATATTTTTATTCAATA
153861 TATAAATAAA
Statistics
Matches: 322, Mismatches: 22, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
250 17 0.05
251 21 0.07
253 1 0.00
255 17 0.05
256 31 0.10
258 2 0.01
259 1 0.00
260 33 0.10
261 85 0.26
263 33 0.10
264 37 0.11
265 32 0.10
266 12 0.04
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.27
Consensus pattern (254 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
CCGACCCGAAATAATAAAAAATATTTTTATTCAATAAAAACAATAACTTAATTGAAAAAAAATAT
ATAGAGAGAGGGTAATTATTGTAATTATTCATAAATATATAAGGTAAAATTATATATTTGTTCGG
GTCGAGTATTTTTCACCCTAAACCCGAACCCCGACCCGAATATCACACTTAAAAAAACC
Found at i:154521 original size:18 final size:20
Alignment explanation
Indices: 154485--154521 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
154475 GTACATTGAA
*
154485 TTTTAAAATACTAATAATTT
1 TTTTAAAATACTAAAAATTT
154505 TTTTAAAA-A-TAAAAATT
1 TTTTAAAATACTAAAAATT
154522 AATATTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 1 0.06
20 8 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAATACTAAAAATTT
Found at i:159432 original size:2 final size:2
Alignment explanation
Indices: 159425--159475 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
159415 CTTATTAACG
159425 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
159467 TA TA TA TA T
1 TA TA TA TA T
159476 TTTTTCATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:170371 original size:18 final size:19
Alignment explanation
Indices: 170350--170385 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
170340 ATATTTCAAT
170350 TTAT-TAAAATACAATTTA
1 TTATGTAAAATACAATTTA
170368 TTATGTAAAATACAATTT
1 TTATGTAAAATACAATTT
170386 TGATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
TTATGTAAAATACAATTTA
Found at i:174688 original size:30 final size:30
Alignment explanation
Indices: 174654--174726 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
174644 CCCGAAGGAC
174654 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
174684 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
174714 CTGTCCATAGGTC
1 CTATCCAGAGGTC
174727 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:174743 original size:30 final size:30
Alignment explanation
Indices: 174700--174784 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
174690 AGAGGTCATA
* *
174700 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATAGGTCCCG
* * *
174730 AAGAACCTAGGTAAACTGTCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATAGGTCCCG
* *
174761 TAGAACATAGGTATACTGTCCATA
1 AAGAACCTAGGTA-ACTGTCCATA
174785 TGTCTTGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.24
31 35 0.76
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATAGGTCCCG
Found at i:174750 original size:31 final size:31
Alignment explanation
Indices: 174712--174839 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
174702 GATCCTCGGT
* *
174712 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
174743 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
174774 TACTGTCCATATGTCTTGAA-AGACATAAGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
174806 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
174837 AAC
1 AAC
174840 CCTCGACTCT
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.67
32 23 0.30
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:176330 original size:21 final size:21
Alignment explanation
Indices: 176306--176350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
176296 TTTTGTTCGT
* *
176306 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
176327 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
176348 TTG
1 TTG
176351 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:182411 original size:37 final size:36
Alignment explanation
Indices: 182341--182411 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
182331 ATATTTTAAA
*
182341 TTTTGTAAAAAAATTATATAAATATTATGAATTTAT
1 TTTTGTAAAAAAATTATATAAATATTATCAATTTAT
* *
182377 TTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 TTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
182412 GTAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTTGTAAAAAAATTATATAAATATTATCAATTTAT
Found at i:182593 original size:20 final size:20
Alignment explanation
Indices: 182557--182594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
182547 ATCATATTCC
**
182557 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
182577 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
182595 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:183547 original size:22 final size:23
Alignment explanation
Indices: 183500--183547 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
183490 GGTTACATAG
*
183500 TTTTTTTATAATTAAAAAAATGA
1 TTTTTTTATAATTAAAAAAATAA
* *
183523 TTTTTTTA-AATTAATAATATAA
1 TTTTTTTATAATTAAAAAAATAA
183545 TTT
1 TTT
183548 AAGTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTTTTATAATTAAAAAAATAA
Found at i:191209 original size:21 final size:21
Alignment explanation
Indices: 191185--191252 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
191175 ATGGAGTACA
191185 AAATGCTTATGCACAAACACG
1 AAATGCTTATGCACAAACACG
* * *
191206 AAATGATGTA-GGACAAAATCACT
1 AAATGCT-TATGCAC-AAA-CACG
* *
191229 AAGTGCTTATGCACGAACACG
1 AAATGCTTATGCACAAACACG
191250 AAA
1 AAA
191253 AGAGATGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
21 14 0.41
22 9 0.26
23 11 0.32
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (21 bp):
AAATGCTTATGCACAAACACG
Found at i:198899 original size:27 final size:27
Alignment explanation
Indices: 198836--198892 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
198826 ATCATTTTAT
198836 TAATGAAATTTAATTATCATTATTAAA
1 TAATGAAATTTAATTATCATTATTAAA
198863 TAATGAAATTTAATTATCATTATTAAA
1 TAATGAAATTTAATTATCATTATTAAA
198890 TAA
1 TAA
198893 ATAAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
TAATGAAATTTAATTATCATTATTAAA
Found at i:198900 original size:22 final size:26
Alignment explanation
Indices: 198826--198907 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 26
198816 AATTCACTCC
* *
198826 ATCATT-TTATTAATGAAATTTAATT
1 ATCATTATTAATAATGAAATTAAATT
*
198851 ATCATTATTAAATAATGAAATTTAATT
1 ATCATTATT-AATAATGAAATTAAATT
198878 ATCATTATT-A-AAT-AAA-TAAATT
1 ATCATTATTAATAATGAAATTAAATT
*
198900 ATTATTAT
1 ATCATTAT
198908 ATTGAATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
22 12 0.23
23 3 0.06
24 3 0.06
25 7 0.13
26 2 0.04
27 25 0.48
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
ATCATTATTAATAATGAAATTAAATT
Found at i:203358 original size:31 final size:29
Alignment explanation
Indices: 203307--203366 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
203297 ACCTATTTTT
** *
203307 TAAAAAATAATTTAGTTACTTATTTTGAA
1 TAAAAAATAATTTAAATACTTACTTTGAA
203336 TAAAAAGATAAATTTAAATACTTACTTTGAA
1 TAAAAA-AT-AATTTAAATACTTACTTTGAA
203367 AAATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.23
30 2 0.08
31 18 0.69
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (29 bp):
TAAAAAATAATTTAAATACTTACTTTGAA
Found at i:206075 original size:105 final size:104
Alignment explanation
Indices: 205776--206798 Score: 1515
Period size: 105 Copynumber: 9.9 Consensus size: 104
205766 CATTGTTCCA
* * ** * *
205776 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-ATTGGGAAATTG-TTGTTGACAAG
* * * *
205841 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
205882 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
205943 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
205982 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAATTGTTGTTGACAAGC
*
206047 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
206087 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
206148 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
206187 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
*
206248 GCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
206287 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
206351 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
206392 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
206453 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
206492 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAA-TTGTTGTTGACAAG
*
206556 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
206597 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTGTTGTTGACAAGC
206662 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
206702 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGG-AAATTG-TTGTTGACAA
* *
206767 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTG
63 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
206799 ACTCTAAAGC
Statistics
Matches: 851, Mismatches: 47, Indels: 37
0.91 0.05 0.04
Matches are distributed among these distances:
100 355 0.42
101 7 0.01
102 19 0.02
103 14 0.02
104 10 0.01
105 364 0.43
106 42 0.05
107 40 0.05
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:206129 original size:205 final size:206
Alignment explanation
Indices: 205776--206798 Score: 1557
Period size: 205 Copynumber: 5.0 Consensus size: 206
205766 CATTGTTCCA
* * * *
205776 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAA-TGGGAAA-T-TTTGTTGACAAC
* * * *
205841 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
**
205906 TTGAAATTGAATCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
128 TTGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
205968 CTTGCGTTGTCTGG
193 CTTGCATTGTCTGG
* * * *
205982 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGAATGGGAAATT-TTGTTGACAACC
* *
206047 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
206112 TGAAATTGGCTCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
129 TGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
206174 TTGCGTTGTCTGG
194 TTGCATTGTCTGG
*
206187 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATTTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
*
206249 CGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
206314 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
206379 TTGCATTGTCTGG
194 TTGCATTGTCTGG
* *
206392 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATTTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
206454 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
206519 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
206584 TTGCATTGTCTGG
194 TTGCATTGTCTGG
* *
206597 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GAATGGGAAATT-TTGTTGACAACC
*
206662 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
64 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
206727 TGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 TGAAATTGGCTCT-GAATT-GG-AAAGT-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
*
206792 AAACTTG
190 GAACTTG
206799 ACTCTAAAGC
Statistics
Matches: 765, Mismatches: 36, Indels: 26
0.93 0.04 0.03
Matches are distributed among these distances:
200 88 0.12
201 6 0.01
202 1 0.00
203 7 0.01
204 3 0.00
205 471 0.62
206 40 0.05
207 6 0.01
209 5 0.01
210 91 0.12
211 3 0.00
212 43 0.06
213 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATGGGAAATTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCATTGTCTGG
Found at i:206322 original size:305 final size:309
Alignment explanation
Indices: 205776--206798 Score: 1659
Period size: 305 Copynumber: 3.3 Consensus size: 309
205766 CATTGTTCCA
* * *
205776 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTAGAA-C-TGAAATTGTTTATTGACAA
* * * *
205840 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
205905 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
128 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
* *
205970 TGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTG
193 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG
206035 TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
258 TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
206087 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTATTGACAACCA
206148 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
*
206213 GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCATGAAGTTGAACTTGC
131 GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
*
206278 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTG
196 GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG
*
206343 TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 TTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
206392 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-TGAAA-T-TTTGTTGACAAGCA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTATTGACAACCA
206453 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
206518 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
206583 CTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
191 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGT
* * *
206648 TATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
256 TGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
206702 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACT--G-AAATTGTTTATTGACAA
*
206767 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTG
63 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
206799 ACTCTAAAGC
Statistics
Matches: 674, Mismatches: 25, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
305 385 0.57
306 2 0.00
307 5 0.01
308 4 0.01
309 2 0.00
310 192 0.28
311 37 0.05
312 2 0.00
314 1 0.00
315 3 0.00
316 1 0.00
317 40 0.06
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (309 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAGAACTGAAATTGTTTATTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
GTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTG
TTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:207471 original size:22 final size:22
Alignment explanation
Indices: 207394--207464 Score: 124
Period size: 22 Copynumber: 3.2 Consensus size: 22
207384 TTGTGTTTGG
*
207394 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
207416 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
207438 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
207460 TCAAA
1 TCAAA
207465 AGATTGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:208150 original size:15 final size:16
Alignment explanation
Indices: 208105--208151 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
208095 TTTTGTCCCT
208105 TTTTC-TTTTTGATT-
1 TTTTCTTTTTTGATTC
* *
208119 TTTGCTTTTTTGCTTC
1 TTTTCTTTTTTGATTC
208135 TTTTCTTTTTTG-TTC
1 TTTTCTTTTTTGATTC
208150 TT
1 TT
208152 GATTGGATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 13 0.46
16 11 0.39
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTTTGATTC
Found at i:212470 original size:18 final size:17
Alignment explanation
Indices: 212447--212489 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
212437 ATATATACAT
*
212447 ATAATAATAATAACTTGA
1 ATAATAATAATAA-ATGA
*
212465 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
212482 ATAA-AATA
1 ATAATAATA
212490 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:212922 original size:37 final size:36
Alignment explanation
Indices: 212879--212980 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
212869 ATAGTAGAAC
212879 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
212916 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
212950 TCTATCCTATTTTTAGGAGTTTCAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
212981 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:216247 original size:2 final size:2
Alignment explanation
Indices: 216242--216266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
216232 TAAAAAATCA
216242 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
216267 CATACATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:216472 original size:55 final size:55
Alignment explanation
Indices: 216325--216523 Score: 245
Period size: 56 Copynumber: 3.6 Consensus size: 55
216315 AGGGCCCCCA
* * * * *
216325 AAAAATAGGGGCTCCGAAATCGAATATATCTATCAGTTGTTGTCACTCATAAGCAT
1 AAAAATAGGGTC-CCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAGCAT
* * *
216381 AAAAATAAGGGTCTCGAAATCGAGTATATATATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAAT-AGGGTCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAGCAT
* *
216437 AAAAATAGGGTCCCGAAATTGAATATATCTATCAGTTGTTACCATTAAGAAGCAT
1 AAAAATAGGGTCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAGCAT
** * *
216492 AAAAATAGGAACCCTGGAATTGAATATATCTA
1 AAAAATAGGGTCCC-GAAATCGAATATATCTA
216524 GAAAATAGGG
Statistics
Matches: 125, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
55 56 0.45
56 64 0.51
57 5 0.04
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (55 bp):
AAAAATAGGGTCCCGAAATCGAATATATCTATCAGTTGTTGCCATTAAGAAGCAT
Found at i:216595 original size:2 final size:2
Alignment explanation
Indices: 216588--216641 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
216578 GGCCCTGTAC
216588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
216630 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
216642 ACAAAAAGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218685 original size:15 final size:15
Alignment explanation
Indices: 218661--218696 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
218651 GAATTATTAA
*
218661 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
218676 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
218691 ATTAAA
1 ATTAAA
218697 CGTATAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:218696 original size:23 final size:23
Alignment explanation
Indices: 218670--218761 Score: 64
Period size: 23 Copynumber: 3.9 Consensus size: 23
218660 AATTAATTTA
218670 TAAAATATTAAATTATAAAAT-AT
1 TAAAATA-TAAATTATAAAATAAT
* *
218693 TAAACGTAT-AATTATAAATTAAT
1 TAAA-ATATAAATTATAAAATAAT
* **
218716 TAAAATTTTAAA-TATAATTTAAT
1 TAAAA-TATAAATTATAAAATAAT
*
218739 TAAAATACAATATTTATAAAATA
1 TAAAATATAA-A-TTATAAAATA
218762 TTAGTTTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
22 13 0.25
23 29 0.55
24 4 0.08
25 7 0.13
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (23 bp):
TAAAATATAAATTATAAAATAAT
Found at i:218731 original size:29 final size:28
Alignment explanation
Indices: 218677--218741 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
218667 TTATAAAATA
218677 TTAAATT-ATAAAATATTAAACGTATAAT
1 TTAAATTAATAAAATATTAAAC-TATAAT
*
218705 TATAAATTAATTAAAATTTTAAA-TATAAT
1 T-TAAATTAA-TAAAATATTAAACTATAAT
218734 TT-AATTAA
1 TTAAATTAA
218742 AATACAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 2 0.06
29 13 0.39
30 1 0.03
31 11 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TTAAATTAATAAAATATTAAACTATAAT
Found at i:218739 original size:17 final size:17
Alignment explanation
Indices: 218699--218744 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
218689 ATATTAAACG
218699 TATAATTATAAATTAAT
1 TATAATTATAAATTAAT
* *
218716 TAAAATTTTAAATATAAT
1 TATAATTATAAAT-TAAT
218734 T-TAATTA-AAAT
1 TATAATTATAAAT
218745 ACAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TATAATTATAAATTAAT
Found at i:221140 original size:29 final size:30
Alignment explanation
Indices: 221108--221171 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
221098 TAAGAGTTTA
*
221108 GAAAA-TTTGGGGACC-ATTCTATAATATTT
1 GAAAAGTTGGGGGACCAATTC-ATAATATTT
*
221137 GAAAAGTTGGGGGACCAATTCATAATTTTT
1 GAAAAGTTGGGGGACCAATTCATAATATTT
221167 GAAAA
1 GAAAA
221172 AGTTTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.16
30 22 0.71
31 4 0.13
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (30 bp):
GAAAAGTTGGGGGACCAATTCATAATATTT
Found at i:223024 original size:23 final size:23
Alignment explanation
Indices: 222956--223024 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
222946 AAATCTTATA
* *
222956 TGGCACTACGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* *
222979 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
223002 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
223025 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:226599 original size:7 final size:7
Alignment explanation
Indices: 226583--226622 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
226573 CAAAAAAGGA
226583 GAAAGAAG
1 GAAA-AAG
*
226591 GAAAGAG
1 GAAAAAG
226598 GAAAAAG
1 GAAAAAG
226605 GAAAAAG
1 GAAAAAG
226612 GAAAAA-
1 GAAAAAG
226618 GAAAA
1 GAAAA
226623 CAGAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.17
7 21 0.70
8 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
GAAAAAG
Found at i:227316 original size:5 final size:5
Alignment explanation
Indices: 227306--227344 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
227296 TAATGGGAAG
227306 GAGAT GAGAT GAGAT GAGAT GAGAT GAGAT GAGAT GAGA
1 GAGAT GAGAT GAGAT GAGAT GAGAT GAGAT GAGAT GAGA
227345 GCAAGAGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.18
Consensus pattern (5 bp):
GAGAT
Found at i:232408 original size:23 final size:23
Alignment explanation
Indices: 232382--232456 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
232372 ATACACTGAC
232382 GTGCCACGTAGAAATGCACCGTA
1 GTGCCACGTAGAAATGCACCGTA
* *
232405 GTGCCACGTAGAATTGCACCGAA
1 GTGCCACGTAGAAATGCACCGTA
*
232428 GTGCCGCGTAGAAATGCACCGTA
1 GTGCCACGTAGAAATGCACCGTA
232451 GTGCCA
1 GTGCCA
232457 TATAATGTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (23 bp):
GTGCCACGTAGAAATGCACCGTA
Found at i:234467 original size:17 final size:17
Alignment explanation
Indices: 234445--234477 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
234435 TTCACTTATT
234445 AACTCATTTCCTTTAAA
1 AACTCATTTCCTTTAAA
*
234462 AACTCATTTTCTTTAA
1 AACTCATTTCCTTTAA
234478 TCTTTCATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (17 bp):
AACTCATTTCCTTTAAA
Found at i:237323 original size:23 final size:23
Alignment explanation
Indices: 237296--237354 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
237286 TCGCGTTTTT
* *
237296 ATGCATCGTAGTGCCACGTAGAA
1 ATGCACCGTAGTGCCACATAGAA
* * *
237319 TTGCACCGAAGTGCCGCATAGAA
1 ATGCACCGTAGTGCCACATAGAA
237342 ATGCACCGTAGTG
1 ATGCACCGTAGTG
237355 TCATATAATG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (23 bp):
ATGCACCGTAGTGCCACATAGAA
Found at i:244710 original size:20 final size:20
Alignment explanation
Indices: 244687--244872 Score: 150
Period size: 20 Copynumber: 9.2 Consensus size: 20
244677 TTTTAATTTT
244687 GCAACACAGAAGTCAAATTC
1 GCAACACAGAAGTCAAATTC
* *
244707 GCAACGCA-ATAGTGAAATTC
1 GCAACACAGA-AGTCAAATTC
*
244727 GCAACACAAAAGTCAAATTC
1 GCAACACAGAAGTCAAATTC
* *
244747 GCAACGC-GATAGTCAAATTT
1 GCAACACAGA-AGTCAAATTC
*
244767 GCAACA-TGAATTTGT-AAA-TC
1 GCAACACAGAA---GTCAAATTC
*
244787 GCAACACATAAGTCAAATTC
1 GCAACACAGAAGTCAAATTC
*
244807 GCAACGC-GATAGTCAAATTC
1 GCAACACAGA-AGTCAAATTC
* * *
244827 TCAACACAAAAGTCAAATTT
1 GCAACACAGAAGTCAAATTC
* *
244847 GCAACGCAGAATTTCAAATTC
1 GCAACACAGAA-GTCAAATTC
244868 GCAAC
1 GCAAC
244873 TGAATTTCAA
Statistics
Matches: 131, Mismatches: 22, Indels: 25
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.02
19 7 0.05
20 101 0.77
21 19 0.15
22 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
GCAACACAGAAGTCAAATTC
Found at i:244751 original size:60 final size:60
Alignment explanation
Indices: 244697--244872 Score: 196
Period size: 60 Copynumber: 2.9 Consensus size: 60
244687 GCAACACAGA
244697 AGTCAAATTCGCAACGCAATAGTGAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCAATAGTGAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * *
244757 AGTCAAATTTGCAACATG-AAT-TTGTAAA-TCGCAACACATAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAAC--GCAATAGTG-AAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
* * * * * * **
244817 AGTCAAATTCTCAACACAAAAGTCAAATTTGCAACGCAGAATTTCAAATTCGCAAC
1 AGTCAAATTCGCAACGCAATAGTGAAATTCGCAACACA-AAAGTCAAATTCGCAAC
244873 TGAATTTCAA
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
59 5 0.05
60 69 0.73
61 20 0.21
62 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCAATAGTGAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
Found at i:244900 original size:38 final size:40
Alignment explanation
Indices: 244855--244949 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 40
244845 TTGCAACGCA
*
244855 GAATTTCAAATTCGCAACT-GAATTTCAAATTCACAAC-T
1 GAATTTCAAATTCGCAACTAGAATTTCAAATTCACAACAC
* * *
244893 GAATTTCAAATTCGCAACTAGATTTTCGAATTCGCAACAC
1 GAATTTCAAATTCGCAACTAGAATTTCAAATTCACAACAC
*
244933 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
244950 AGGTTTTAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 19 0.38
39 25 0.50
40 6 0.12
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (40 bp):
GAATTTCAAATTCGCAACTAGAATTTCAAATTCACAACAC
Found at i:244924 original size:20 final size:19
Alignment explanation
Indices: 244855--244949 Score: 120
Period size: 19 Copynumber: 4.9 Consensus size: 19
244845 TTGCAACGCA
244855 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
244874 GAATTTCAAATTCACAACT
1 GAATTTCAAATTCGCAACT
244893 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
* * *
244912 AGATTTTCGAATTCGCAACAC
1 -GAATTTCAAATTCGCAAC-T
*
244933 GAATTT-AATTTCGCAAC
1 GAATTTCAAATTCGCAAC
244950 AGGTTTTAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 45 0.68
20 21 0.32
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:244950 original size:19 final size:19
Alignment explanation
Indices: 244923--244969 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
244913 GATTTTCGAA
244923 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
244942 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
244960 TTCGCAACAC
1 TTCGCAACAC
244970 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:245125 original size:14 final size:15
Alignment explanation
Indices: 245106--245144 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
245096 TTCCCATCTC
245106 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
245120 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
245136 TAATTTTTT
1 TAATTTTTT
245145 AATGGTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:245938 original size:24 final size:24
Alignment explanation
Indices: 245880--245926 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
245870 AGTCAGTATT
*
245880 CGAAATTTGATCTTGGTCAATACA
1 CGAACTTTGATCTTGGTCAATACA
245904 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
245927 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACA
Found at i:248540 original size:20 final size:20
Alignment explanation
Indices: 248525--248633 Score: 166
Period size: 20 Copynumber: 5.5 Consensus size: 20
248515 AATTCGCAAC
248525 GCGAGTTTGACTTTCGCGTT
1 GCGAGTTTGACTTTCGCGTT
*
248545 GCAAGTTTGACTTTCGCGTT
1 GCGAGTTTGACTTTCGCGTT
248565 GCGAGTTTGACTTTCGCGTT
1 GCGAGTTTGACTTTCGCGTT
248585 GCGAGTTTGACTTTCGCGTT
1 GCGAGTTTGACTTTCGCGTT
* *
248605 GCGAATTT-ACCTTTCTCGTT
1 GCGAGTTTGA-CTTTCGCGTT
*
248625 GCGAATTTG
1 GCGAGTTTG
248634 TACCTTCAAC
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
19 1 0.01
20 82 0.99
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (20 bp):
GCGAGTTTGACTTTCGCGTT
Found at i:250098 original size:21 final size:21
Alignment explanation
Indices: 250074--250193 Score: 109
Period size: 21 Copynumber: 5.7 Consensus size: 21
250064 GCGGGCGAGA
* *
250074 CCTCTTGAATGATGACAGTGG
1 CCTCTTGAATGATGAGAGGGG
* * * *
250095 CCTCTTGAACGGTGGGAGAGG
1 CCTCTTGAATGATGAGAGGGG
*
250116 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
250137 CCTTTTGAACGAT-AGGAGGGG
1 CCTCTTGAATGATGA-GAGGGG
* *
250158 CCTCTTGAATGATAAGAGGTG
1 CCTCTTGAATGATGAGAGGGG
250179 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
250194 TAGGTGCATT
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
20 2 0.03
21 74 0.95
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:250128 original size:42 final size:42
Alignment explanation
Indices: 250054--250187 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 42
250044 GTGAATCATG
* *
250054 CTCTTGAACGGCGGGCGAGACCTCTTGAATGATGACAGTGGC
1 CTCTTGAACGGCGGGAGAGACCTCTTGAATGATGACAGGGGC
* * * *
250096 CTCTTGAACGGTGGGAGAGGCTTCTTCG-ATGATGAGAGGGGC
1 CTCTTGAACGGCGGGAGAGACCTCTT-GAATGATGACAGGGGC
* *** * * * * *
250138 CTTTTGAACGATAGGAGGGGCCTCTTGAATGATAAGAGGTGC
1 CTCTTGAACGGCGGGAGAGACCTCTTGAATGATGACAGGGGC
250180 CTCTTGAA
1 CTCTTGAA
250188 TGATGATAGG
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 74 0.97
43 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (42 bp):
CTCTTGAACGGCGGGAGAGACCTCTTGAATGATGACAGGGGC
Found at i:250620 original size:63 final size:63
Alignment explanation
Indices: 250526--250647 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
250516 ACCACGTAGC
* **
250526 GCACCATTATCATCGCGTAAAAAATCCACCTCACCACGTAAAG-ACCGAACCTCATCACGCCAT
1 GCACCATTATCATCACGTAAAAAATCCACCTCACCACACAAAGCACCG-ACCTCATCACGCCAT
* ** **
250589 GCACCATTATCTTCACGTAAAGTA-CCAACCTCATGACACAAAGCACCGACCTCATCACG
1 GCACCATTATCATCACGTAAAAAATCC-ACCTCACCACACAAAGCACCGACCTCATCACG
250648 TAACTCCCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
62 2 0.04
63 43 0.88
64 4 0.08
ACGTcount: A:0.34, C:0.36, G:0.11, T:0.18
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAAAATCCACCTCACCACACAAAGCACCGACCTCATCACGCCAT
Found at i:252400 original size:19 final size:20
Alignment explanation
Indices: 252365--252402 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
252355 TAAATTTGCA
252365 ACGCGAAAATAAAAATCGCG
1 ACGCGAAAATAAAAATCGCG
*
252385 ACGCGAAACT-AAAATCGC
1 ACGCGAAAATAAAAATCGC
252403 TTTGCGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (20 bp):
ACGCGAAAATAAAAATCGCG
Found at i:252454 original size:20 final size:20
Alignment explanation
Indices: 252416--252454 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
252406 GCGATTTTGC
* * *
252416 TGTTGCGATTTTCATTTTCG
1 TGTTGCGAATTTAAGTTTCG
252436 TGTTGCGAATTTAAGTTTC
1 TGTTGCGAATTTAAGTTTC
252455 AAAAACTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
TGTTGCGAATTTAAGTTTCG
Found at i:252953 original size:20 final size:20
Alignment explanation
Indices: 252928--253146 Score: 164
Period size: 20 Copynumber: 10.9 Consensus size: 20
252918 TAATATTGTG
252928 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
252948 TTTCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
252968 TATCGCATTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * *
252988 TTTTGTGTTGCGAATTTGCC
1 TTTCGCGTTGCGAATTTGAC
*
253008 TATCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
253028 -TTCTGTGTTGTG-ATTT-AC
1 TTTC-GCGTTGCGAATTTGAC
*
253046 AAATTCGCGTTGCGAATTTTGAC
1 --TTTCGCGTTGCGAA-TTTGAC
* * *
253069 TTTTGTGTTGCGATTTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
253089 -TTCTGTGTTGCG-ATTT-AC
1 TTTC-GCGTTGCGAATTTGAC
* *
253107 ATATTCGAGTTGCGAAATTGGA-
1 -T-TTCGCGTTGCG-AATTTGAC
*
253129 GTTCGCGTTGCGAATTTG
1 TTTCGCGTTGCGAATTTG
253147 TTCGTCATTT
Statistics
Matches: 158, Mismatches: 27, Indels: 29
0.74 0.13 0.14
Matches are distributed among these distances:
18 4 0.03
19 16 0.10
20 112 0.71
21 17 0.11
22 6 0.04
23 3 0.02
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:253035 original size:40 final size:40
Alignment explanation
Indices: 252930--253086 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
252920 ATATTGTGTT
* ** *
252930 TCGCGTTGCGAATTTGACTTTCGCATTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGCCTA
*
252970 TCGCATTGCGAATTTGACTTTTGTGTTGCGAATTTGCCTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGCCTA
* * * **
253010 TCGCGTTGCGAATTTGACTTCTGTGTTGTG-ATTTACAAA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGCCTA
*
253049 TTCGCGTTGCGAATTTTGACTTTTGTGTTGCGATTTTG
1 -TCGCGTTGCGAA-TTTGACTTTTGTGTTGCGAATTTG
253087 ACTTCTGTGT
Statistics
Matches: 99, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 6 0.06
40 74 0.75
41 16 0.16
42 3 0.03
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.43
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGCCTA
Found at i:253058 original size:60 final size:59
Alignment explanation
Indices: 252929--253146 Score: 217
Period size: 60 Copynumber: 3.6 Consensus size: 59
252919 AATATTGTGT
* ** *
252929 TTCGCGTTGCGAATTTGACTTTCGCATTGCGAATTTGACTATC-GCATTGCGAATTTGAC-T
1 TTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAA
* * * * *
252989 TTTGTGTTGCGAATTTGCCTATCGCGTTGCGAATTTGACTTCTGTGTTGTGATTTACAAA
1 TTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTAC-AA
* * *
253049 TTCGCGTTGCGAATTTTGACTTTTGTGTTGCGATTTTGACTTCTGTGTTGCGATTTACATA
1 TTCGCGTTGCGAA-TTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACA-A
* * *
253110 TTCGAGTTGCGAAATTGGA-GTTCGCGTTGCGAATTTG
1 TTCGCGTTGCG-AATTTGACTTTCGCGTTGCGAATTTG
253147 TTCGTCATTT
Statistics
Matches: 129, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
58 2 0.02
59 6 0.05
60 66 0.51
61 53 0.41
62 2 0.02
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (59 bp):
TTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAA
Found at i:261172 original size:42 final size:42
Alignment explanation
Indices: 261111--261259 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 42
261101 AAGGAAATTA
*
261111 GCGGCGTTTGTATCC-AAAAACGCTGTTATAGATCTGACCTTT
1 GCGGCGTTTGT-TCCTAAAAACGCCGTTATAGATCTGACCTTT
* *
261153 GCGGCTTTTGTTCCTAAAAACGCCGTTAT-GCATCTGATCTTTT
1 GCGGCGTTTGTTCCTAAAAACGCCGTTATAG-ATCTGA-CCTTT
* * * *
261196 GCGACGTTTGTT-CTAAAAAATGCCGCTATAGATATGACCTATT
1 GCGGCGTTTGTTCCT-AAAAACGCCGTTATAGATCTGACCT-TT
*
261239 GCGGCGTTTGTTCCAAAAAAC
1 GCGGCGTTTGTTCCTAAAAAC
261260 ATCGCTATAG
Statistics
Matches: 88, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
41 4 0.05
42 33 0.38
43 49 0.56
44 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCTAAAAACGCCGTTATAGATCTGACCTTT
Found at i:261294 original size:21 final size:21
Alignment explanation
Indices: 261265--261326 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
261255 AAAACATCGC
* *
261265 TATAGATATCATCCTTTTGCA
1 TATAAATATCAACCTTTTGCA
261286 TATAAATATCAACCTTTTGCA
1 TATAAATATCAACCTTTTGCA
261307 TATAAATATCAACCTTTTGC
1 TATAAATATCAACCTTTTGC
261327 GGCGTTTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (21 bp):
TATAAATATCAACCTTTTGCA
Found at i:261366 original size:42 final size:43
Alignment explanation
Indices: 261315--261414 Score: 139
Period size: 42 Copynumber: 2.3 Consensus size: 43
261305 CATATAAATA
*
261315 TCAACCTTTTGCGGCGTTTGTTCCAAAAACGCTACTATAGATC
1 TCAACCTTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATC
* *
261358 TCAA-CTTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATC
1 TCAACCTTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATC
** *
261400 TTGACCTATTGCGGC
1 TCAACCTTTTGCGGC
261415 ATTTTTGGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.76
43 12 0.24
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (43 bp):
TCAACCTTTTGCGGCGTTTGTTCCAAAAACGCCACTATAGATC
Found at i:262141 original size:60 final size:61
Alignment explanation
Indices: 262076--262189 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 61
262066 TATAGGATAA
* *
262076 TGTTTTATTGAG-CCTCTCGACTATT-AAAAGTTACAAAATAGTCCTTCGACTATAGTGAGT
1 TGTTTTATTGAGTCC-CTCGACTATTAAAAAATTACAAAATAGTCCTTCAACTATAGTGAGT
* * * * *
262136 TGTTTTGTTGTGTCCCTCTACTATTAAAAAATTACAAAATGGTCGTTCAACTAT
1 TGTTTTATTGAGTCCCTCGACTATTAAAAAATTACAAAATAGTCCTTCAACTAT
262190 TCATTATGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
60 19 0.42
61 26 0.58
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (61 bp):
TGTTTTATTGAGTCCCTCGACTATTAAAAAATTACAAAATAGTCCTTCAACTATAGTGAGT
Found at i:265881 original size:46 final size:46
Alignment explanation
Indices: 265812--265919 Score: 137
Period size: 46 Copynumber: 2.3 Consensus size: 46
265802 TTAAATGTTT
* * * *
265812 ATCTTAAATTTTGACTTTTTTATTATTTATTTTATTGATT-TGTTCA
1 ATCTAAAATTTT-ATTTTTTTATTATCTATTTTATTGATTGTGTCCA
* *
265858 TTTTAAAATTTGTATTTTTTTATTATCTATTTTATTGATTGTGTCCA
1 ATCTAAAATTT-TATTTTTTTATTATCTATTTTATTGATTGTGTCCA
265905 ATCTAAAATTTTATT
1 ATCTAAAATTTTATT
265920 GTTACACATC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
46 37 0.71
47 15 0.29
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (46 bp):
ATCTAAAATTTTATTTTTTTATTATCTATTTTATTGATTGTGTCCA
Found at i:271622 original size:2 final size:2
Alignment explanation
Indices: 271615--271645 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
271605 ATGATATCTA
*
271615 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
271646 AAACCGAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:273236 original size:17 final size:19
Alignment explanation
Indices: 273214--273248 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
273204 GCTTTTGTTC
273214 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
273231 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
273249 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:300459 original size:39 final size:39
Alignment explanation
Indices: 300386--300460 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
300376 TCATGTGTTA
* ***
300386 GTTAATTGATGCGGAGCTTTAAATTTATTTTTTATTATC
1 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATTATC
300425 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATT
1 GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATT
300461 TTTATTATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (39 bp):
GTTAATTGAGGCGGAGCTTTAAATTTAAAATTTATTATC
Found at i:300496 original size:28 final size:28
Alignment explanation
Indices: 300443--300496 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
300433 AGGCGGAGCT
* *
300443 TTAAATTTAAAATTTATTTTTATTATCG
1 TTAAACTTAAAATTTAATTTTATTATCG
300471 TTAAACTTAAAATTTAAATTTT-TTAT
1 TTAAACTTAAAATTT-AATTTTATTAT
300497 TAACTCATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (28 bp):
TTAAACTTAAAATTTAATTTTATTATCG
Found at i:304953 original size:41 final size:41
Alignment explanation
Indices: 304897--304979 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
304887 GATTAGACAT
304897 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
1 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
*
304938 ATATGAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
1 ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
304979 A
1 A
304980 CTCTTGGGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.24
Consensus pattern (41 bp):
ATATAAACACACAGTGAATAAAGCAGCAGTATCAATTCTTC
Found at i:313461 original size:26 final size:29
Alignment explanation
Indices: 313408--313467 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
313398 GTCCTCTGAA
*
313408 ATTTTTAAATTTTCTTATATTTTAAATTT
1 ATTTTTAAATTTTCTTATATTATAAATTT
* *
313437 TTTTTTATATTTTC-TAT-TTAT-AATTT
1 ATTTTTAAATTTTCTTATATTATAAATTT
313463 ATTTT
1 ATTTT
313468 CATTTCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 9 0.33
27 3 0.11
28 3 0.11
29 12 0.44
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (29 bp):
ATTTTTAAATTTTCTTATATTATAAATTT
Found at i:314557 original size:32 final size:32
Alignment explanation
Indices: 314438--314562 Score: 132
Period size: 31 Copynumber: 4.0 Consensus size: 32
314428 AACATCGGCA
* * * *
314438 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
314469 AATGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
314500 ACTGTCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
314532 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
314563 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.06
31 43 0.56
32 25 0.32
33 4 0.05
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:314702 original size:30 final size:31
Alignment explanation
Indices: 314666--314723 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
314656 TATCACATGT
* *
314666 CATATAAGCTCATAGTTTC-TTTCATATATA
1 CATATAAGCACATAGCTTCTTTTCATATATA
*
314696 CATATAATCACATAGCTTCTTTTCATAT
1 CATATAAGCACATAGCTTCTTTTCATAT
314724 TCTCATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (31 bp):
CATATAAGCACATAGCTTCTTTTCATATATA
Found at i:315112 original size:2 final size:2
Alignment explanation
Indices: 315107--315136 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
315097 TATCTTATTC
315107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315137 CCGCAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:318743 original size:31 final size:32
Alignment explanation
Indices: 318705--318797 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 32
318695 GAACCTCGAC
* *
318705 AACTGTCCATAGGTCTCGAAAAACCTAGGTA-
1 AACTGTCCATATGTCTCGAAAAACATAGGTAT
* ** *
318736 AACTGTCCATATGTTTCTTAGAACATAGGTAT
1 AACTGTCCATATGTCTCGAAAAACATAGGTAT
* *
318768 AA-TGTCCATATGTCTCGAAAGATATAGGTA
1 AACTGTCCATATGTCTCGAAAAACATAGGTA
318798 ATTCTATCCA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
31 47 0.96
32 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (32 bp):
AACTGTCCATATGTCTCGAAAAACATAGGTAT
Found at i:321802 original size:5 final size:5
Alignment explanation
Indices: 321792--321819 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
321782 AGGGATTTTT
321792 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
321820 GAGAACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:332612 original size:20 final size:20
Alignment explanation
Indices: 332580--332626 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
332570 CTATATACCA
332580 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
332600 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
332620 GGTAAAA
1 GGTAAAA
332627 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:332806 original size:17 final size:19
Alignment explanation
Indices: 332767--332809 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
332757 CAGGTAAAAT
332767 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
332787 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
332804 ATGATA
1 ATGATA
332810 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:332828 original size:178 final size:180
Alignment explanation
Indices: 332366--332837 Score: 671
Period size: 182 Copynumber: 2.6 Consensus size: 180
332356 TCGATCCAAA
* *
332366 TTAAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATG
1 TTAAAAATGTATCGATCCAAAACGATATAACAGGTAAAA-TATGATAAAACCGGTATCA-AAATG
* * * * * * * *
332430 ATAAAATCGGTCAAGCGCTACTGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAC
64 ATAAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAC
* *
332495 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTT
129 TTCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTT
* * *
332547 TTAAAAAATGTATCGATCCAAAACTATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATG
1 TT-AAAAATGTATCGATCCAAAACGATATAACAGGT-AAAATATGATAAAACCGGTATCAAAATG
*
332612 ATAAAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACAC
64 ATAAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAC
* ** *
332676 TTTGTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATAC-T
129 TTCGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTT
* *
332727 TTAAAAATATATCGATCCACAACGATATAACAGGTAAAATATGATAAAACCGGTATCAAAATGAT
1 TTAAAAATGTATCGATCCAAAACGATATAACAGGTAAAATATGATAAAACCGGTATCAAAATGAT
* *
332792 AAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
332838 CGTAAGTACG
Statistics
Matches: 261, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
178 72 0.28
179 29 0.11
180 3 0.01
181 62 0.24
182 90 0.34
183 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
TTAAAAATGTATCGATCCAAAACGATATAACAGGTAAAATATGATAAAACCGGTATCAAAATGAT
AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTT
Found at i:335057 original size:21 final size:21
Alignment explanation
Indices: 335010--335073 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
335000 AAAGACAATC
*
335010 AGAGTCGAAGAGAAACT-GAT
1 AGAGTCGAAGAGAAACTCGAG
* *
335030 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
335051 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
335072 AG
1 AG
335074 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.39, C:0.16, G:0.31, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:337808 original size:342 final size:345
Alignment explanation
Indices: 337133--337820 Score: 1101
Period size: 342 Copynumber: 2.0 Consensus size: 345
337123 TACCGGTTTT
* *
337133 ATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCCA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCA
* *
337198 AAATGAATGGAAAACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCTATCCAAAA
65 AAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCAAAA
337263 TCATCGAACCCAAAAATATAATGTATATGTAATTTTCAATCTAACCGGTACAATTATACCGATTT
130 TCATCGAACCCAAAAATATAATGTATATGTAATTTTCAATCTAACCGGTACAATTATACCGATTT
*
337328 TATGAGAGAATATGTATAAAATAATGTCGACACTAATAGTTTTGTGTCGATATTTTTTCCCAGAA
195 TATGAGAGAATATGTATAAAATAATGTCGACACTAATAGTTTTATGTCGATATTTTTTCCCAGAA
* *
337393 TGAATGGAAAACAGGGTGCACCGATAAAGTGTCGATCCATATATAAAAAGTGTCGATTTCCAAAA
260 TGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATTCCCAAAA
337458 TCATCGAACCC-AAAGTATAA
325 TCATCGAACCCAAAAGTATAA
*
337478 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAG-TT-TGTCGATA-TTTTTTCCCAG
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAA
*
337540 AATGAATGGAAAACAGGGTGCACCGATAAAGTGTCGATCCATATA-AAAAGTGTCGATTCCAAAA
66 AATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGA-TCCAAAA
* *
337604 TCATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
130 TCATCGAACCCAAAAATATAATGT-ATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGAT
* *
337668 TTTATGAGAGAATATGTCTAAAA-ATGTGTCGACACTAATA-TAGTTTATGTCGATATTTTTTTT
193 TTTATGAGAGAATATGTATAAAATA-ATGTCGACACTAATAGT--TTTATGTCGATA--TTTTTT
337731 CCCAGAATGAATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGA-T
253 CCCAGAATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATT
337793 CCCAAAATCATCGAACCCAAAAGTATAA
318 CCCAAAATCATCGAACCCAAAAGTATAA
337821 TGTAATATGT
Statistics
Matches: 321, Mismatches: 13, Indels: 20
0.91 0.04 0.06
Matches are distributed among these distances:
340 21 0.07
341 80 0.25
342 84 0.26
343 39 0.12
344 31 0.10
345 66 0.21
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (345 bp):
ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAA
AATGAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCAAAAT
CATCGAACCCAAAAATATAATGTATATGTAATTTTCAATCTAACCGGTACAATTATACCGATTTT
ATGAGAGAATATGTATAAAATAATGTCGACACTAATAGTTTTATGTCGATATTTTTTCCCAGAAT
GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATTCCCAAAAT
CATCGAACCCAAAAGTATAA
Found at i:338024 original size:191 final size:197
Alignment explanation
Indices: 337478--338206 Score: 1206
Period size: 197 Copynumber: 3.8 Consensus size: 197
337468 CAAAGTATAA
337478 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAG-TT-TGTCGATATTTTTTCCCAGA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGA
* *
337541 ATGAATGGAAAACAGGGTGCACCGATAAAGTGTCGATCC--ATATAAAAAGTGTCGATTCCAAAA
66 ATGAATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
337604 TCATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
130 TCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
337668 TTT
195 TTT
* *
337671 ATGAGAGAATATGTCTAAA-AATGTGTCGACACTAATATAGTTTATGTCGATATTTTTTTTCCCA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTCCCA
337735 GAATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAA
64 GAATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAA
337799 ATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
129 ATCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG
337864 TTTT
194 TTTT
*
337868 ATGAGAGAATATGTATAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATA-TTTTCCCCAGA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGA
337930 ATGAATGG-AAACA-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAT
66 ATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
337992 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT-ACCGGTACAATTATACCGGTT
131 CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
338056 TT
196 TT
*
338058 ATGAGAG--TATGTATAAATAATGTATCGACACTAATATAGTTTGTG-CGATATTTTTTTTCCCA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTCCCA
* *
338120 GAATTAATGG-AAACAGGGTGCACCGATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
64 GAATGAATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
338184 AATCATCGAACCCAAAAGTATAA
128 AATCATCGAACCCAAAAGTATAA
338207 GTGTCGATCC
Statistics
Matches: 509, Mismatches: 10, Indels: 32
0.92 0.02 0.06
Matches are distributed among these distances:
188 24 0.05
189 6 0.01
190 40 0.08
191 76 0.15
192 63 0.12
193 38 0.07
194 52 0.10
195 47 0.09
196 70 0.14
197 79 0.16
198 14 0.03
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (197 bp):
ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGA
ATGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAT
CATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTT
TT
Found at i:338195 original size:386 final size:387
Alignment explanation
Indices: 337478--338206 Score: 1224
Period size: 386 Copynumber: 1.9 Consensus size: 387
337468 CAAAGTATAA
*
337478 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTCGATATTTTTTCCCAGAAT
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATA-TTTGTCGATATTTTTCCCCAGAAT
*
337543 GAATGGAAAACAGGGTGCACCGATAAAGTGTCGATCCATATAAAAAGTGTCGATTCCAAAATCAT
65 GAATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATTCCAAAATCAT
337608 CGAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
129 CGAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
* *
337673 GAGAGAATATGTCTAAAAATGTGTCGACACTAATATAGTTTATGTCGATATTTTTTTTCCCAGAA
194 GAGAG-ATATGTATAAAAATGTATCGACACTAATATAGTTTATGTCGATATTTTTTTTCCCAGAA
337738 TGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCA
258 TGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCA
337803 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
323 TCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
337868 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATAGT-TTGTGTCGATA-TTTTCCCCAGAA
1 ATGAGAGAATATGTATAAATAATGTGTCGACACTAATA-TATT-TGTCGATATTTTTCCCCAGAA
*
337931 TGAATGG-AAACA-GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGA-TCCCAAATC
64 TGAATGGAAAACAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATTCCAAAATC
337993 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCT-ACCGGTACAATTATACCGGTTT
127 ATCGAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
338057 TATGAGAG-TATGTATAAATAATGTATCGACACTAATATAGTTTGTG-CGATATTTTTTTTCCCA
191 TATGAGAGATATGTATAAA-AATGTATCGACACTAATATAGTTTATGTCGATATTTTTTTTCCCA
* *
338120 GAATTAATGG-AAACAGGGTGCACCGATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAA
255 GAATGAATGGAAAACA-GGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAA
338184 AATCATCGAACCCAAAAGTATAA
318 AATCATCGAACCCAAAAGTATAA
338207 GTGTCGATCC
Statistics
Matches: 323, Mismatches: 8, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
384 5 0.02
385 64 0.20
386 87 0.27
387 47 0.15
388 53 0.16
389 20 0.06
390 46 0.14
391 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (387 bp):
ATGAGAGAATATGTATAAATAATGTGTCGACACTAATATATTTGTCGATATTTTTCCCCAGAATG
AATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATTCCAAAATCATCG
AACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGATATGTATAAAAATGTATCGACACTAATATAGTTTATGTCGATATTTTTTTTCCCAGAATGA
ATGGAAAACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTT
Found at i:338226 original size:34 final size:36
Alignment explanation
Indices: 338169--338240 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 36
338159 CATATATAAA
338169 AAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
1 AAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
338205 AAGTGTCGAT-CC-AAATCATCGAACCCAAAAGTAT
1 AAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
338239 AA
1 AA
338241 TGTAATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 24 0.67
35 2 0.06
36 10 0.28
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (36 bp):
AAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
Found at i:339788 original size:18 final size:18
Alignment explanation
Indices: 339767--339826 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
339757 AGCGGTCGCA
339767 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* * *
339785 GAAGATGACGATGATGAT
1 GAAGATGAAGCTGACGAT
* *
339803 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
339821 GAAGAT
1 GAAGAT
339827 TATGACGATG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.37, C:0.10, G:0.35, T:0.18
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:339791 original size:6 final size:6
Alignment explanation
Indices: 339767--339858 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
339757 AGCGGTCGCA
* * * * * *
339767 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * * *
339815 GGCGAT GAAGAT TATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
339859 TGATCCAAAC
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.37, C:0.08, G:0.34, T:0.22
Consensus pattern (6 bp):
GAAGAT
Found at i:339802 original size:3 final size:3
Alignment explanation
Indices: 339782--339862 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
339772 TGAAGCTGAC
* * * * * ** * *
339782 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT TAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
339830 GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
339863 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:339821 original size:36 final size:37
Alignment explanation
Indices: 339770--339849 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 37
339760 GGTCGCAGAA
339770 GATGAAGCTGACGATGAAG-ATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGTATGACGATGATGATGAC
* *
339806 GATGAAGCTGGCGATGAAGATTATGACGATGATGATGAT
1 GATGAAGCTGACGATGAAG--TATGACGATGATGATGAC
339845 GATGA
1 GATGA
339850 TGAAGATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
36 18 0.46
39 21 0.54
ACGTcount: A:0.35, C:0.09, G:0.34, T:0.23
Consensus pattern (37 bp):
GATGAAGCTGACGATGAAGTATGACGATGATGATGAC
Done.