Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005895.1 Hibiscus syriacus cultivar Beakdansim tig00013838_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: 128328
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16689 original size:3 final size:3
Alignment explanation
Indices: 16683--16731 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
16673 GATGAGGAGG
* * * * *
16683 AGA AGA AGA AGA ATA AGA AGA AGA CGA GGA GGA GGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
16731 A
1 A
16732 TAAGGGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.59, C:0.02, G:0.37, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:17500 original size:17 final size:17
Alignment explanation
Indices: 17475--17509 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17465 ACGAAGGATA
17475 ATAACAGAAAAACGAAG
1 ATAACAGAAAAACGAAG
*
17492 ATAAGAGAAAAACGAAG
1 ATAACAGAAAAACGAAG
17509 A
1 A
17510 AAATTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.09, G:0.20, T:0.06
Consensus pattern (17 bp):
ATAACAGAAAAACGAAG
Found at i:17695 original size:23 final size:23
Alignment explanation
Indices: 17665--17711 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
17655 TTGGTTACAC
17665 AGTCGTTTTATCACGAACAACAT
1 AGTCGTTTTATCACGAACAACAT
17688 AGTCGTTTTATCACGAACAACAT
1 AGTCGTTTTATCACGAACAACAT
17711 A
1 A
17712 ATAAATGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (23 bp):
AGTCGTTTTATCACGAACAACAT
Found at i:27978 original size:19 final size:19
Alignment explanation
Indices: 27937--27979 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
27927 ATTAAATCAG
* *
27937 CCTTTGGCTAAAGCTTATG
1 CCTTGGGCTAAAGCTTATA
*
27956 CCTTGGGCTAAAGCTTCTA
1 CCTTGGGCTAAAGCTTATA
27975 CCTTG
1 CCTTG
27980 ATTCAAATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (19 bp):
CCTTGGGCTAAAGCTTATA
Found at i:28708 original size:124 final size:118
Alignment explanation
Indices: 28474--28714 Score: 340
Period size: 124 Copynumber: 1.9 Consensus size: 118
28464 AGCCTTCGGC
*
28474 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAGCATTTAAAAAAAAAAAAAAAACTAG
1 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTAAAAAAAAAAAAAAAACTAG
28539 AAAAGAAAATAAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAGA
66 AAAAGAAAATAAAAAAGGAAAACTTTATTAAACT-----A-AAGAAACAAGAGTTGAGA
28598 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTTAAAAATAAAATAAAATAAA
1 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACA-TTT--AAA-AAAA-AAAA-AAA
*
28663 AACTAGAAAAGAAAATAAAAAAAGGAAAACTTTATTAAACT-AAGAAAGAAGA
60 AACTAGAAAAGAAAAT-AAAAAAGGAAAACTTTATTAAACTAAAGAAACAAGA
28715 AACAAGAGTT
Statistics
Matches: 108, Mismatches: 2, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
124 51 0.47
125 3 0.03
127 3 0.03
128 4 0.04
129 4 0.04
130 19 0.18
131 24 0.22
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.20
Consensus pattern (118 bp):
TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTAAAAAAAAAAAAAAAACTAG
AAAAGAAAATAAAAAAGGAAAACTTTATTAAACTAAAGAAACAAGAGTTGAGA
Found at i:28724 original size:131 final size:124
Alignment explanation
Indices: 28474--28728 Score: 438
Period size: 131 Copynumber: 2.0 Consensus size: 124
28464 AGCCTTCGGC
*
28474 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAGCATTTAAAAAAAAAAAAAAAACTAG
1 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTAAAAAAAAAAAAAAAACTAG
28539 AAAAGAAAATAAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAGA
66 AAAAGAAAATAAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAGA
28598 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTTAAAAATAAAATAAAATAAA
1 TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACA-TTT--AAA-AAAA-AAAA-AAA
28663 AACTAGAAAAGAAAATAAAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAG
60 AACTAGAAAAGAAAAT-AAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAG
28728 A
124 A
28729 AACGAATTCT
Statistics
Matches: 123, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
124 41 0.33
125 3 0.02
127 3 0.02
128 4 0.03
129 4 0.03
130 19 0.15
131 49 0.40
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.20
Consensus pattern (124 bp):
TATGAAAAACTTAGCTAAGCATGGTAGAGACCATACTTAACATTTAAAAAAAAAAAAAAAACTAG
AAAAGAAAATAAAAAAGGAAAACTTTATTAAACTAAGAAAGAAGAAACAAGAGTTGAGA
Found at i:33054 original size:183 final size:184
Alignment explanation
Indices: 32761--33147 Score: 647
Period size: 183 Copynumber: 2.1 Consensus size: 184
32751 ATTAAATTTT
*
32761 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
32826 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* * *
32890 TTATTTTATAATTATATATTGTTTAAATTATTTGTAAACTGTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
*
32944 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAGCCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
33008 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
33073 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
33128 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
33148 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
182 2 0.01
183 125 0.65
184 65 0.34
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:33294 original size:15 final size:15
Alignment explanation
Indices: 33274--33302 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
33264 AAAAAAAGTT
33274 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
33289 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
33303 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:34124 original size:49 final size:49
Alignment explanation
Indices: 34063--34156 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 49
34053 TAACTAATTT
* *
34063 TTAATTACAGTTGACCAAGTCATTGAATTATTTTAAAATAACATTAATA
1 TTAATTAAAGTTGACCAAGTCAATGAATTATTTTAAAATAACATTAATA
34112 TTAATTAAAGTTGACCAAGTCAATGAATTATTTTAAAATAACATT
1 TTAATTAAAGTTGACCAAGTCAATGAATTATTTTAAAATAACATT
34157 TGAGCACGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (49 bp):
TTAATTAAAGTTGACCAAGTCAATGAATTATTTTAAAATAACATTAATA
Found at i:54891 original size:34 final size:34
Alignment explanation
Indices: 54853--54944 Score: 175
Period size: 34 Copynumber: 2.7 Consensus size: 34
54843 TAGTGATTGT
*
54853 GAGGACACCAAAGGCCTCCATCGTCTTGTCTCAA
1 GAGGACACCAAAGGCCTCCATCGTCTCGTCTCAA
54887 GAGGACACCAAAGGCCTCCATCGTCTCGTCTCAA
1 GAGGACACCAAAGGCCTCCATCGTCTCGTCTCAA
54921 GAGGACACCAAAGGCCTCCATCGT
1 GAGGACACCAAAGGCCTCCATCGT
54945 TCCATTCCAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (34 bp):
GAGGACACCAAAGGCCTCCATCGTCTCGTCTCAA
Found at i:56050 original size:44 final size:44
Alignment explanation
Indices: 55959--56513 Score: 255
Period size: 43 Copynumber: 12.7 Consensus size: 44
55949 ATTTTATGAA
* * * * *
55959 ATTGAAAAAAA-TAGAGGCTTTAATCATAAAGGTAGAAATTAAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
* *
56002 ATTGAAAAAAGATTAGGGGCATCAATTATAAAGGT-GTAATTGAT
1 ATTGAAAAAA-ATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
* * *
56046 ATTG-AAAAATTTAGGGGCCTCAATAATAAAGGTAGAAATTGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
* * * * *
56089 ATTGAAAAAACTTATGGGCCTCAATTGTAAAGGTA-AAGAGTGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAA-ATTGAG
*
56133 ATTGAAAAAAACTTAGGAG-ACTCAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAAAA-TTAGGGGCA-TCAATTATAAAGGTAGAAATTGAG
* * *
56178 ATTGAAAAAACTTATGGG---C-----TAAAGGTA-AAGAGTGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAA-ATTGAG
* * * * *
56214 ATTGAAAAAAACTTAGGAG-ACTCAATTATAAAGTTAAAAAAGTGGG
1 ATTGAAAAAAA-TTAGGGGCA-TCAATTATAAAGGT-AGAAATTGAG
* * * * *
56260 ATT--AACAAGTTAGGGGCCTCAATTATAAAGATGGAAATTGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
* *
56302 ATT-ACAAAAATTTA-GGGCCTCAATTGTAAAAGTAGAAAAGGTAGAAA-TGAG
1 ATTGA-AAAAAATTAGGGGCATCAA-T-T---A-T---AAAGGTAGAAATTGAG
* * * ** *
56353 ATTGAAAAAACTTAAGGGCCTCAATTATAAATTTA-AAA-CGTAGG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTG-A-G
* * ** * **
56397 ATT-AAAAAAATTAGGGACCTCAATTATAATTGTAAAAAAAGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
* * * * *
56440 ATTG-AAAAAATTAGAGACTTCAATTATACAA-ATA-AAAGGTGAG
1 ATTGAAAAAAATTAGGGGCATCAATTATA-AAGGTAGAAA-TTGAG
* * *
56483 ATTGAATAAAATTA-AGACATCAATTATAAAG
1 ATTGAAAAAAATTAGGGGCATCAATTATAAAG
56514 ATAAAAAAAT
Statistics
Matches: 406, Mismatches: 63, Indels: 86
0.73 0.11 0.15
Matches are distributed among these distances:
35 2 0.00
36 23 0.06
37 5 0.01
40 1 0.00
41 1 0.00
42 39 0.10
43 136 0.33
44 86 0.21
45 60 0.15
46 12 0.03
47 3 0.01
48 1 0.00
49 1 0.00
50 1 0.00
51 16 0.04
52 19 0.05
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (44 bp):
ATTGAAAAAAATTAGGGGCATCAATTATAAAGGTAGAAATTGAG
Found at i:56534 original size:12 final size:13
Alignment explanation
Indices: 56511--56536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56501 ATCAATTATA
56511 AAGATAAAAAAAT
1 AAGATAAAAAAAT
56524 AAGATAAAAAAAT
1 AAGATAAAAAAAT
56537 TAAAGGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAGATAAAAAAAT
Found at i:63050 original size:41 final size:41
Alignment explanation
Indices: 62956--63256 Score: 223
Period size: 41 Copynumber: 7.3 Consensus size: 41
62946 GGTTCATCTA
* * *
62956 TAGTGGCGTTTTT-TAACAAACGTCG-TAACAGAGTAGTACTT
1 TAGTGGCGTTTTTAT-ACAAACGCCGCTAA-AGACTCGTACTT
*** *
62997 TAGCAACATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
63038 TAGTGGCGTTTTTTATACAAACGCCACTATAGACTTGTACTT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * * * *
63080 TAGTTGCATTTTTATAAAAACGCCGCTATACAATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
63121 TAGTGGCGTTTGTGTTTATAAACGCCGCTAAAGACTCGCACAT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * * * *
63164 TAGCGGCGTTTATATACAACCGCCGCTATACACTTGTA-TGT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACT-T
* * * * *
63205 TAGCGACATTTTTATACGAACGCCACTATAA-ACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTA-AAGACTCGTACTT
63246 TAGTGGCGTTT
1 TAGTGGCGTTT
63257 GAGTTTGCAA
Statistics
Matches: 201, Mismatches: 51, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
41 127 0.63
42 43 0.21
43 31 0.15
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:63081 original size:83 final size:83
Alignment explanation
Indices: 62956--63248 Score: 263
Period size: 83 Copynumber: 3.5 Consensus size: 83
62946 GGTTCATCTA
* * * * * *
62956 TAGTGGCGTTTTTTA-ACAAACGTC-GTAACAGAGTAGTACTTTAGCAACATTTTTATACAAACG
1 TAGTGGCGTTTTTTATACAAACGCCACT-ATAGACTCGTACTTTAGCAGCATTTTTATACAAACG
* * *
63019 CCGCTAAAGACTCGTACTT
65 CCGCTATACACTTGTACTT
* ** *
63038 TAGTGGCGTTTTTTATACAAACGCCACTATAGACTTGTACTTTAGTTGCATTTTTATAAAAACGC
1 TAGTGGCGTTTTTTATACAAACGCCACTATAGACTCGTACTTTAGCAGCATTTTTATACAAACGC
*
63103 CGCTATACAATTGTACTT
66 CGCTATACACTTGTACTT
* * * * * * * * *
63121 TAGTGGCGTTTGTGTT-TATAAACGCCGCTAAAGACTCGCACATTAGCGGCGTTTATATACAACC
1 TAGTGGCGTTT-T-TTATACAAACGCCACTATAGACTCGTACTTTAGCAGCATTTTTATACAAAC
63185 GCCGCTATACACTTGTA-TGT
64 GCCGCTATACACTTGTACT-T
* * * * *
63205 TAGCGAC-ATTTTTATACGAACGCCACTATAAACTCGTACTTTAG
1 TAGTGGCGTTTTTTATACAAACGCCACTATAGACTCGTACTTTAG
63249 TGGCGTTTGA
Statistics
Matches: 169, Mismatches: 36, Indels: 12
0.78 0.17 0.06
Matches are distributed among these distances:
81 2 0.01
82 39 0.23
83 66 0.39
84 60 0.36
85 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (83 bp):
TAGTGGCGTTTTTTATACAAACGCCACTATAGACTCGTACTTTAGCAGCATTTTTATACAAACGC
CGCTATACACTTGTACTT
Found at i:63190 original size:84 final size:83
Alignment explanation
Indices: 63003--63240 Score: 223
Period size: 84 Copynumber: 2.9 Consensus size: 83
62993 ACTTTAGCAA
* * * * *
63003 CATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCACTAT
1 CATTTATATACAAACGCCGCTATACACTTGTACTTTAGTGGCGTTTTTTATACAAACGCCACTAA
* * * **
63068 AGACTTGTACTTTAGTTG
66 AGACTCGCACATTAGCGG
* * * * *
63086 CATTTTTATAAAAACGCCGCTATACAATTGTACTTTAGTGGCGTTTGTGTT-TATAAACGCCGCT
1 CATTTATATACAAACGCCGCTATACACTTGTACTTTAGTGGCGTTT-T-TTATACAAACGCCACT
63150 AAAGACTCGCACATTAGCGG
64 AAAGACTCGCACATTAGCGG
* * * * * *
63170 CGTTTATATACAACCGCCGCTATACACTTGTA-TGTTAGCGAC-ATTTTTATACGAACGCCACTA
1 CATTTATATACAAACGCCGCTATACACTTGTACT-TTAGTGGCGTTTTTTATACAAACGCCACTA
63233 TAA-ACTCG
65 -AAGACTCG
63241 TACTTTAGTG
Statistics
Matches: 126, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
81 2 0.02
82 17 0.13
83 46 0.37
84 59 0.47
85 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (83 bp):
CATTTATATACAAACGCCGCTATACACTTGTACTTTAGTGGCGTTTTTTATACAAACGCCACTAA
AGACTCGCACATTAGCGG
Found at i:63217 original size:125 final size:126
Alignment explanation
Indices: 63011--63273 Score: 336
Period size: 125 Copynumber: 2.1 Consensus size: 126
63001 AACATTTTTA
* * * * *
63011 TACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTTATACAAACGCCACTATAGACTTGT
1 TACAAACGCCGCTAAAGACTCGCACATTAGCGGCGTTTTATATACAAACGCCACTATACACTTGT
* * * *
63076 ACTTTAGTTGCATTTTTATAAAAACGCCGCTATACAA-TTGTACTTTAGTGGCGTTTGTGTT
66 ACTTTAGTCGCATTTTTATAAAAACGCCACTATA-AACTCGTACTTTAGTGGCGTTTGAGTT
* * *
63137 TATAAACGCCGCTAAAGACTCGCACATTAGCGGCG-TTTATATACAACCGCCGCTATACACTTGT
1 TACAAACGCCGCTAAAGACTCGCACATTAGCGGCGTTTTATATACAAACGCCACTATACACTTGT
**
63201 A-TGTTAG-CGACATTTTTATACGAACGCCACTATAAACTCGTACTTTAGTGGCGTTTGAGTT
66 ACT-TTAGTCG-CATTTTTATAAAAACGCCACTATAAACTCGTACTTTAGTGGCGTTTGAGTT
*
63262 TGCAAACGCCGC
1 TACAAACGCCGC
63274 AATTTTATAA
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
124 4 0.03
125 83 0.70
126 31 0.26
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (126 bp):
TACAAACGCCGCTAAAGACTCGCACATTAGCGGCGTTTTATATACAAACGCCACTATACACTTGT
ACTTTAGTCGCATTTTTATAAAAACGCCACTATAAACTCGTACTTTAGTGGCGTTTGAGTT
Found at i:63346 original size:21 final size:21
Alignment explanation
Indices: 63322--63362 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
63312 CGTCGTTTAC
*
63322 CCAAACCCATCTGCTTCACTA
1 CCAAACCCATATGCTTCACTA
63343 CCAAACCCATATGCTTCACT
1 CCAAACCCATATGCTTCACT
63363 GCCATTTTTA
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:0.29, C:0.41, G:0.05, T:0.24
Consensus pattern (21 bp):
CCAAACCCATATGCTTCACTA
Found at i:66480 original size:43 final size:43
Alignment explanation
Indices: 66410--66675 Score: 358
Period size: 43 Copynumber: 6.2 Consensus size: 43
66400 ATGGTAATTA
* *
66410 GCGGCGTTTGTATCCAAAAATGTCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
66453 GCGGCGTTTGTAT-CAAAACACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAA-ACGCCGCTATAGATCTGACCTTTT
* * *
66496 ACGGCGTTTGTATCCAAAAACGCCTCTATAGATCTGTCCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* ** *
66539 GCGGCGTTTGT-TACAAAAATACCGCTATAGATCTGACATTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
66581 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGATCTCATCCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA-CCTTTT
* * * *
66624 GCAGTGTTTGTATCCAGAAACGCCGCAATAGATCTGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
66667 GCGGCGTTT
1 GCGGCGTTT
66676 TTATTTTACA
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
42 61 0.32
43 106 0.55
44 26 0.13
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:66655 original size:128 final size:129
Alignment explanation
Indices: 66410--66675 Score: 392
Period size: 128 Copynumber: 2.1 Consensus size: 129
66400 ATGGTAATTA
* ** * *
66410 GCGGCGTTTGTATCCAAAAATGTCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCAAAACACG
1 GCGGCGTTTGTATACAAAAATACCGCTATAGATCTGACATTTTGCGGCGTTTGTATCAAAAAACG
* * * * *
66475 CCGCTATAGATCTGACCTTTTACGGCGTTTGTATCCAAAAACGCCTCTATAGATCTGTCCTTTT
66 CCGCTATAGATCTCACCTTTTACAGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
66539 GCGGCGTTTGT-TACAAAAATACCGCTATAGATCTGACATTTTGCGGCGTTTGT-TCAAAAAACG
1 GCGGCGTTTGTATACAAAAATACCGCTATAGATCTGACATTTTGCGGCGTTTGTATCAAAAAACG
* * *
66602 CCGCTATAGATCTCATCCTTTTGCAGTGTTTGTATCCAGAAACGCCGCAATAGATCTGACCTTTT
66 CCGCTATAGATCTCA-CCTTTTACAGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
66667 GCGGCGTTT
1 GCGGCGTTT
66676 TTATTTTACA
Statistics
Matches: 123, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
127 23 0.19
128 89 0.72
129 11 0.09
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (129 bp):
GCGGCGTTTGTATACAAAAATACCGCTATAGATCTGACATTTTGCGGCGTTTGTATCAAAAAACG
CCGCTATAGATCTCACCTTTTACAGCGTTTGTATCCAAAAACGCCGCAATAGATCTGACCTTTT
Found at i:66901 original size:14 final size:14
Alignment explanation
Indices: 66882--66908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66872 ATCAAGTTGC
66882 TTCCCTTAGTAGAA
1 TTCCCTTAGTAGAA
66896 TTCCCTTAGTAGA
1 TTCCCTTAGTAGA
66909 TTTTCTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (14 bp):
TTCCCTTAGTAGAA
Found at i:73813 original size:2 final size:2
Alignment explanation
Indices: 73806--73840 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73796 GAATCATTAC
73806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73841 ATGTTACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76932 original size:25 final size:24
Alignment explanation
Indices: 76884--76955 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 24
76874 GAAAAAAATG
*
76884 AAATATTTTTAAATTAAGTTAATAGTA
1 AAATATATTT-AA-TAAGTTAATA-TA
76911 AAATATATTTAATAAGTTAATATA
1 AAATATATTTAATAAGTTAATATA
76935 AAA-ATATTT--TAAGTTAATATA
1 AAATATATTTAATAAGTTAATATA
76956 TATAAAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 12 0.27
23 6 0.14
24 5 0.11
25 10 0.23
26 2 0.05
27 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (24 bp):
AAATATATTTAATAAGTTAATATA
Found at i:76962 original size:24 final size:23
Alignment explanation
Indices: 76897--76970 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
76887 TATTTTTAAA
*
76897 TTAAGTTAATAGTA-AAATATATT
1 TTAAGTTAATA-TATAAAAATATT
76920 TAATAAGTT-A-ATATAAAAATATT
1 T--TAAGTTAATATATAAAAATATT
76943 TTAAGTTAATATATATAAAATTATT
1 TTAAGTTAATATATA-AAAA-TATT
76968 TTA
1 TTA
76971 TATATAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 16 0.37
24 5 0.12
25 13 0.30
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTAAGTTAATATATAAAAATATT
Found at i:77750 original size:31 final size:32
Alignment explanation
Indices: 77707--77779 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
77697 GTTAACTCGG
* *
77707 GTGACCACATCTTAATTAAAT-AAAAACGAAA
1 GTGACCATATCTTAATTAAATAAAAAACAAAA
*
77738 GTGACCATATCTTACTTAAATAAAAAACAAAA
1 GTGACCATATCTTAATTAAATAAAAAACAAAA
*
77770 GTGATCATAT
1 GTGACCATAT
77780 ATTATGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 19 0.51
32 18 0.49
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (32 bp):
GTGACCATATCTTAATTAAATAAAAAACAAAA
Found at i:84425 original size:20 final size:20
Alignment explanation
Indices: 84402--84448 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
84392 GTTTTCAAAT
84402 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
84422 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATATGTAAA
84442 TCGCAAC
1 TCGCAAC
84449 ACAGAAGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:84462 original size:20 final size:20
Alignment explanation
Indices: 84439--84487 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
84429 GCGAATTTGT
84439 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
84459 AATTCGTAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
84479 AATTCGCAA
1 AATTCGCAA
84488 AGCGCGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:84531 original size:21 final size:21
Alignment explanation
Indices: 84507--84644 Score: 122
Period size: 21 Copynumber: 6.7 Consensus size: 21
84497 ATTTTCATAA
84507 CGCGTTGCGAATTTGGAGAAT
1 CGCGTTGCGAATTTGGAGAAT
* * *
84528 CGCGTTACGATTTTGGAGAAC
1 CGCGTTGCGAATTTGGAGAAT
*
84549 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGAATTTGGAGAAT
* *
84570 CGCGTTGCGAATTT-GAAAAC
1 CGCGTTGCGAATTTGGAGAAT
* *
84590 CACGTTGCGATTTTGGA-AA-
1 CGCGTTGCGAATTTGGAGAAT
* ** *
84609 CTGTGTTGCGAAACTGGAG-TT
1 C-GCGTTGCGAATTTGGAGAAT
*
84630 CGCGTTGCAAATTTG
1 CGCGTTGCGAATTTG
84645 TTGGTTATTT
Statistics
Matches: 93, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
19 1 0.01
20 39 0.42
21 53 0.57
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
CGCGTTGCGAATTTGGAGAAT
Found at i:84554 original size:42 final size:41
Alignment explanation
Indices: 84507--84606 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 41
84497 ATTTTCATAA
* * *
84507 CGCGTTGCGAATTTGGAGAATCGCGTTACGATTTTGGAGAAC
1 CGCGTTGCGATTTTGGAGAATCGCGTTACGAATTT-GAAAAC
*
84549 CGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAC
1 CGCGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAAC
*
84590 CACGTTGCGATTTTGGA
1 CGCGTTGCGATTTTGGA
84607 AACTGTGTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (41 bp):
CGCGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAAC
Found at i:84597 original size:20 final size:20
Alignment explanation
Indices: 84572--84609 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
84562 TGGAGAATCG
84572 CGTTGCGAATTTGAAAACCA
1 CGTTGCGAATTTGAAAACCA
* *
84592 CGTTGCGATTTTGGAAAC
1 CGTTGCGAATTTGAAAAC
84610 TGTGTTGCGA
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:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
CGTTGCGAATTTGAAAACCA
Found at i:84616 original size:20 final size:21
Alignment explanation
Indices: 84507--84619 Score: 131
Period size: 21 Copynumber: 5.5 Consensus size: 21
84497 ATTTTCATAA
* *
84507 CGCGTTGCGAATTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAC
*
84528 CGCGTTACGATTTTGGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
84549 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAC
* *
84570 CGCGTTGCGAATTT-GAAAAC
1 CGCGTTGCGATTTTGGAGAAC
*
84590 CACGTTGCGATTTTGGA-AAC
1 CGCGTTGCGATTTTGGAGAAC
* *
84610 TGTGTTGCGA
1 CGCGTTGCGA
84620 AACTGGAGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 26 0.33
21 52 0.67
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
CGCGTTGCGATTTTGGAGAAC
Found at i:93278 original size:2 final size:2
Alignment explanation
Indices: 93271--93297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93261 AAATATTATG
93271 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
93298 AACACTAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101681 original size:5 final size:5
Alignment explanation
Indices: 101671--101696 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
101661 TATTATTATT
101671 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
101697 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:103407 original size:23 final size:23
Alignment explanation
Indices: 103342--103410 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
103332 CATTTATTTG
* * * *
103342 TTGTGTTCGAATAAGTTTGTTTT
1 TTGTGTTCGTATATGTTCGTTTA
* *
103365 TTGTGTTTGTGT-TGTTCGTTTA
1 TTGTGTTCGTATATGTTCGTTTA
*
103387 TTGTGTTCGTTTATGTTCGTTTA
1 TTGTGTTCGTATATGTTCGTTTA
103410 T
1 T
103411 AGTCATTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
22 17 0.46
23 20 0.54
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.61
Consensus pattern (23 bp):
TTGTGTTCGTATATGTTCGTTTA
Found at i:106883 original size:2 final size:2
Alignment explanation
Indices: 106876--106915 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
106866 ATTATGTCAA
106876 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
106916 TAAAATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118997 original size:43 final size:43
Alignment explanation
Indices: 118934--119035 Score: 177
Period size: 43 Copynumber: 2.4 Consensus size: 43
118924 CTTAACGATT
* * *
118934 GAAAAGAAAAAGAAGCAATCTTGATGAACAAGTTACTGCAGTG
1 GAAAAGAAAAATAAGAAATCTTGATGAACAAGTTACTGCAATG
118977 GAAAAGAAAAATAAGAAATCTTGATGAACAAGTTACTGCAATG
1 GAAAAGAAAAATAAGAAATCTTGATGAACAAGTTACTGCAATG
119020 GAAAAGAAAAATAAGA
1 GAAAAGAAAAATAAGA
119036 CTTAACAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (43 bp):
GAAAAGAAAAATAAGAAATCTTGATGAACAAGTTACTGCAATG
Found at i:119323 original size:42 final size:42
Alignment explanation
Indices: 119264--119376 Score: 190
Period size: 42 Copynumber: 2.7 Consensus size: 42
119254 CGCCCTAACA
* *
119264 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
119306 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
119348 TTCCGAAAAACGAATTACTTGAAATAAAC
1 TTCCGAAAAACGAATTACGTGAAACAAAC
119377 CCGAGAATTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:120022 original size:13 final size:14
Alignment explanation
Indices: 119998--120028 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
119988 TTTGGGAAAT
119998 AAATTTTAATAAAA
1 AAATTTTAATAAAA
120012 AAATTTT-ATAAAA
1 AAATTTTAATAAAA
120025 AAAT
1 AAAT
120029 ATTTTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTTTAATAAAA
Found at i:120417 original size:2 final size:2
Alignment explanation
Indices: 120410--120450 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
120400 ATGATCATAG
120410 AT AT AT AT AT AT AT AT AT AT AT -T 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
120451 TCAAATTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:120437 original size:19 final size:19
Alignment explanation
Indices: 120413--120451 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
120403 ATCATAGATA
120413 TATATATATATATATATAT
1 TATATATATATATATATAT
120432 TATATATATATATATATAT
1 TATATATATATATATATAT
120451 T
1 T
120452 CAAATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:120556 original size:27 final size:26
Alignment explanation
Indices: 120509--120567 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
120499 CGTTTAAAAT
*
120509 GGTTTTTAAATTTTATGATGTTGTTA
1 GGTTTTTAAATTTTATGATGTTATTA
* * *
120535 GGTTTTTATATTTTGTTTATGTTATTA
1 GGTTTTTAAATTTT-ATGATGTTATTA
120562 GAGTTT
1 G-GTTT
120568 AGTCCCTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 13 0.48
27 10 0.37
28 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.19, T:0.61
Consensus pattern (26 bp):
GGTTTTTAAATTTTATGATGTTATTA
Found at i:122655 original size:45 final size:44
Alignment explanation
Indices: 122586--122704 Score: 165
Period size: 42 Copynumber: 2.8 Consensus size: 44
122576 CTTACGATTG
* *
122586 AAAGAAAAAGAA-AATCTTGATGAACAAGTTACTACTGCGATGGA
1 AAAG-AAAAGAAGAATCCTGATGAACAAGTTACTACTGCAATGGA
122630 AAAGAAAAGAAGAAGTCCTGATGAACAAG-T--TACTGCAATGGA
1 AAAGAAAAGAAGAA-TCCTGATGAACAAGTTACTACTGCAATGGA
*
122672 AAAGAAAAGAAGAATTCTGATGAACAAGTTACT
1 AAAGAAAAGAAGAATCCTGATGAACAAGTTACT
122705 GCAATGGAGC
Statistics
Matches: 67, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
41 13 0.19
42 26 0.39
43 7 0.10
44 8 0.12
45 13 0.19
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (44 bp):
AAAGAAAAGAAGAATCCTGATGAACAAGTTACTACTGCAATGGA
Found at i:122676 original size:42 final size:41
Alignment explanation
Indices: 122586--122712 Score: 175
Period size: 41 Copynumber: 3.0 Consensus size: 41
122576 CTTACGATTG
* *
122586 AAAGAAAAAGAA-AATCTTGATGAACAAGTTACTACTGCGATGGA
1 AAAG-AAAAGAAGAATCCTGATGAACAAG-T--TACTGCAATGGA
122630 AAAGAAAAGAAGAAGTCCTGATGAACAAGTTACTGCAATGGA
1 AAAGAAAAGAAGAA-TCCTGATGAACAAGTTACTGCAATGGA
*
122672 AAAGAAAAGAAGAATTCTGATGAACAAGTTACTGCAATGGA
1 AAAGAAAAGAAGAATCCTGATGAACAAGTTACTGCAATGGA
122713 GCTCGGTTGA
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
41 26 0.33
42 25 0.32
43 7 0.09
44 7 0.09
45 13 0.17
ACGTcount: A:0.48, C:0.11, G:0.22, T:0.19
Consensus pattern (41 bp):
AAAGAAAAGAAGAATCCTGATGAACAAGTTACTGCAATGGA
Found at i:125101 original size:58 final size:58
Alignment explanation
Indices: 125011--125126 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
125001 CATTACTATT
*
125011 CTATTAGGAATGGGTATGAGATCCGAATCAAATAGTTTTAACCCGATTTAATTCGATC
1 CTATTAGGAATAGGTATGAGATCCGAATCAAATAGTTTTAACCCGATTTAATTCGATC
*
125069 CTATTAGGAATAGGTATGAGATTCGAATCAAATAGTTTTAACCCGATTTAATTCGATC
1 CTATTAGGAATAGGTATGAGATCCGAATCAAATAGTTTTAACCCGATTTAATTCGATC
125127 GCATCATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (58 bp):
CTATTAGGAATAGGTATGAGATCCGAATCAAATAGTTTTAACCCGATTTAATTCGATC
Done.