Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001433.1 Hibiscus syriacus cultivar Beakdansim tig00002781_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: 131977
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:135 original size:25 final size:25
Alignment explanation
Indices: 106--204 Score: 166
Period size: 25 Copynumber: 4.0 Consensus size: 25
96 GAACCAACCC
106 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
131 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
156 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
181 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
205 TCCCCTAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.12
25 63 0.88
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:3472 original size:15 final size:17
Alignment explanation
Indices: 3431--3472 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
3421 GCATGTGAAA
*
3431 TAGAATTTAGGTGCAGT
1 TAGAATTTAAGTGCAGT
3448 TAGAATTTAAGTGC-GT
1 TAGAATTTAAGTGCAGT
3464 TAG-ATTTAA
1 TAGAATTTAA
3473 TTAATTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 5 0.21
17 13 0.54
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (17 bp):
TAGAATTTAAGTGCAGT
Found at i:13475 original size:8 final size:8
Alignment explanation
Indices: 13464--13520 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
13454 TAAAAGAAGA
13464 AAAAAAAG
1 AAAAAAAG
*
13472 AAAAAAGG
1 AAAAAAAG
13480 AAAAAAAG
1 AAAAAAAG
*
13488 AGAAAGAAAT
1 A-AAA-AAAG
13498 AAGAAAAATG
1 AA-AAAAA-G
13508 AAAAAGAAG
1 AAAAA-AAG
13517 AAAA
1 AAAA
13521 TAAATAAAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 15 0.38
9 15 0.38
10 10 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (8 bp):
AAAAAAAG
Found at i:13506 original size:9 final size:9
Alignment explanation
Indices: 13455--13505 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
13445 TATTACACTT
*
13455 AAAAGAAGA
1 AAAAAAAGA
13464 AAAAAAAG-
1 AAAAAAAGA
*
13472 AAAAAAGGA
1 AAAAAAAGA
13481 AAAAAAGAGA
1 AAAAAA-AGA
13491 AAGAAATAAGA
1 AA-AAA-AAGA
13502 AAAA
1 AAAA
13506 TGAAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
8 7 0.20
9 13 0.37
10 6 0.17
11 8 0.23
12 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:13518 original size:27 final size:26
Alignment explanation
Indices: 13455--13520 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 26
13445 TATTACACTT
13455 AAAAGAAGAAAAAAAAGAAAAAAGGA
1 AAAAGAAGAAAAAAAAGAAAAAAGGA
* *
13481 AAAAAAGAGAAAGAAATAAG-AAAAATGA
1 AAAAGA-AGAAA-AAA-AAGAAAAAAGGA
13509 AAAAGAAGAAAA
1 AAAAGAAGAAAA
13521 TAAATAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 6 0.18
27 10 0.29
28 15 0.44
29 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (26 bp):
AAAAGAAGAAAAAAAAGAAAAAAGGA
Found at i:14781 original size:130 final size:129
Alignment explanation
Indices: 14467--14774 Score: 413
Period size: 130 Copynumber: 2.3 Consensus size: 129
14457 TCAACATCAA
*
14467 CTGACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCA
1 CTGACCAGATC-TCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAACCAGCCGTCCTCATCA
* * * * *
14531 CGTAGGAACGAGTTATCACCCTTCCTAAAGGTGGCCAGAGTTTTTCATCATGTATGAACCGTGTC
64 CGTAGGAACGAGTTATCA--C--CCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGTC
14596 ATCCC
125 ATCCC
* * * *
14601 CAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACG
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
* *
14666 TAGGAACCGTGTTATCA-CCTAAAGATGGCCAAGAATTCTTCATCATGTAGGAGCAGTGTCATCC
66 TAGGAA-CGAGTTATCACCCTAAAGATGGCC-AGAATTCTTCATCATGTAGGAACAGTGTCATCC
14730 C
129 C
*
14731 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGA
1 CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGA
14775 CGACCAGACC
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
129 12 0.08
130 68 0.44
133 29 0.19
134 44 0.29
135 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (129 bp):
CTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATAACCAGCCGTCCTCATCACG
TAGGAACGAGTTATCACCCTAAAGATGGCCAGAATTCTTCATCATGTAGGAACAGTGTCATCCC
Found at i:14981 original size:9 final size:10
Alignment explanation
Indices: 14963--15020 Score: 68
Period size: 9 Copynumber: 5.8 Consensus size: 10
14953 GGTCTTTTTA
14963 TATTATTTAAT
1 TATTA-TTAAT
14974 T-TTATTAAT
1 TATTATTAAT
14983 TATTATT-AT
1 TATTATTAAT
14992 TATTATT-AT
1 TATTATTAAT
15001 TATTATTAAAT
1 TATTATT-AAT
15012 TATATATTA
1 TAT-TATTA
15021 CAAATTTTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
9 24 0.56
10 8 0.19
11 7 0.16
12 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTATTAAT
Found at i:14987 original size:3 final size:3
Alignment explanation
Indices: 14963--15008 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
14953 GGTCTTTTTA
*
14963 TAT TAT T-T AAT T-T TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
15007 TA
1 TA
15009 AATTATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 32 0.84
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:15166 original size:25 final size:25
Alignment explanation
Indices: 15137--15235 Score: 166
Period size: 25 Copynumber: 4.0 Consensus size: 25
15127 GAACCAACCC
15137 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
15162 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
15187 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
15212 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
15236 TCCCCTAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 9 0.12
25 63 0.88
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:16892 original size:11 final size:11
Alignment explanation
Indices: 16863--16894 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16853 AGAAATTATT
*
16863 TTTTATTGTTA
1 TTTTATTTTTA
16874 TTTTATTTTTA
1 TTTTATTTTTA
16885 TTTTATTTTT
1 TTTTATTTTT
16895 GTTAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:16903 original size:25 final size:24
Alignment explanation
Indices: 16858--16906 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
16848 CTTATAGAAA
*
16858 TTATTTTTTATTGTTATTTTATTT
1 TTATTTTTTATTGTTAATTTATTT
*
16882 TTATTTTATTTTTGTTAATTTATTT
1 TTATTTT-TTATTGTTAATTTATTT
16907 GATGTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (24 bp):
TTATTTTTTATTGTTAATTTATTT
Found at i:18488 original size:60 final size:60
Alignment explanation
Indices: 18415--18588 Score: 192
Period size: 60 Copynumber: 2.9 Consensus size: 60
18405 TATTATTTTT
*
18415 ATTTTAAATTAGTCCCTAAATTTTTAAATA-TTCTAATTACATCCTTAAACTATGA-ATATC
1 ATTTTAAATTAGTCCCTAAATTTTTAAATATTTC-AATTACATCCTCAAACTATGACAT-TC
* * * * *
18475 ATTTTAAACTAGTCCTTAAACTTTTGAATATTTCAATTTCATCCTCAAACTATGACATTC
1 ATTTTAAATTAGTCCCTAAATTTTTAAATATTTCAATTACATCCTCAAACTATGACATTC
* * ** * *
18535 ATTTTAAATTGGTCCCTAAACTTTTTGAGCATTCCAATTTCAT-CTCAAACTATG
1 ATTTTAAATTAGTCCCTAAA-TTTTTAAATATTTCAATTACATCCTCAAACTATG
18589 TGTATTTACT
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
60 75 0.77
61 23 0.23
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (60 bp):
ATTTTAAATTAGTCCCTAAATTTTTAAATATTTCAATTACATCCTCAAACTATGACATTC
Found at i:24779 original size:11 final size:11
Alignment explanation
Indices: 24763--24787 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
24753 GTTATAAGGT
24763 ATTTTTTTATA
1 ATTTTTTTATA
24774 ATTTTTTTATA
1 ATTTTTTTATA
24785 ATT
1 ATT
24788 ATATATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:24947 original size:22 final size:22
Alignment explanation
Indices: 24920--24972 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
24910 TATATTTTTT
24920 AAATTATTTACGTTTATATGTA
1 AAATTATTTACGTTTATATGTA
*
24942 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATATGTA
24964 AAATT-TTTA
1 AAATTATTTA
24973 TTGTGTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (22 bp):
AAATTATTTACGTTTATATGTA
Found at i:28226 original size:13 final size:13
Alignment explanation
Indices: 28208--28256 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
28198 TAATAATCAA
28208 AATTAACAAAATT
1 AATTAACAAAATT
28221 AATTAACAAAA--
1 AATTAACAAAATT
* *
28232 AGTCCAACAAAATT
1 AAT-TAACAAAATT
28246 AATTAACAAAA
1 AATTAACAAAA
28257 AGTCCAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
11 2 0.07
12 7 0.24
13 18 0.62
14 2 0.07
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.22
Consensus pattern (13 bp):
AATTAACAAAATT
Found at i:28245 original size:25 final size:25
Alignment explanation
Indices: 28212--28272 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
28202 AATCAAAATT
28212 AACAAAATTAATTAACAAAAAGTCC
1 AACAAAATTAATTAACAAAAAGTCC
28237 AACAAAATTAATTAACAAAAAGTCC
1 AACAAAATTAATTAACAAAAAGTCC
28262 AACAAAATTAA
1 AACAAAATTAA
28273 CAAAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.62, C:0.15, G:0.03, T:0.20
Consensus pattern (25 bp):
AACAAAATTAATTAACAAAAAGTCC
Found at i:30576 original size:12 final size:12
Alignment explanation
Indices: 30553--30624 Score: 74
Period size: 12 Copynumber: 5.6 Consensus size: 12
30543 ACTGCAAAAA
30553 AAAATAATTAAAT
1 AAAAT-ATTAAAT
30566 AAAATATTAAAAT
1 AAAATATT-AAAT
30579 AATTAAATAATTAAAT
1 -A--AAAT-ATTAAAT
*
30595 AAAATACT-AAT
1 AAAATATTAAAT
30606 AAAATATTAAAT
1 AAAATATTAAAT
30618 AAAATAT
1 AAAATAT
30625 ACCTTAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.20
12 15 0.29
13 13 0.25
14 1 0.02
15 1 0.02
16 8 0.16
17 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATATTAAAT
Found at i:30577 original size:21 final size:21
Alignment explanation
Indices: 30553--30616 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
30543 ACTGCAAAAA
30553 AAAATAATTAAATAAAATATT
1 AAAATAATTAAATAAAATATT
30574 AAAATAATTAAATAATTAA-A-T
1 AAAATAATTAAATAA--AATATT
*
30595 AAAAT-ACT-AATAAAATATT
1 AAAATAATTAAATAAAATATT
30614 AAA
1 AAA
30617 TAAAATATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 2 0.05
18 1 0.03
19 9 0.24
20 2 0.05
21 21 0.55
22 1 0.03
23 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATTAAATAAAATATT
Found at i:30587 original size:29 final size:30
Alignment explanation
Indices: 30554--30619 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
30544 CTGCAAAAAA
30554 AAATAATTAAATAAAATA-T-TAAAATAATT
1 AAATAATTAAATAAAATACTATAAAAT-ATT
30583 AAATAATTAAATAAAATACTAATAAAATATT
1 AAATAATTAAATAAAATACT-ATAAAATATT
30614 AAATAA
1 AAATAA
30620 AATATACCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 18 0.53
30 1 0.03
31 9 0.26
32 6 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (30 bp):
AAATAATTAAATAAAATACTATAAAATATT
Found at i:30608 original size:11 final size:12
Alignment explanation
Indices: 30590--30623 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
30580 ATTAAATAAT
30590 TAAATAAAATAC
1 TAAATAAAATAC
*
30602 T-AATAAAATAT
1 TAAATAAAATAC
30613 TAAATAAAATA
1 TAAATAAAATA
30624 TACCTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATAAAATAC
Found at i:30646 original size:10 final size:10
Alignment explanation
Indices: 30631--30675 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
30621 ATATACCTTA
30631 ATTTGAGAGG
1 ATTTGAGAGG
*
30641 ATTTGAGAGA
1 ATTTGAGAGG
* *
30651 AGTTAAGAGG
1 ATTTGAGAGG
*
30661 ATTTAAGAGG
1 ATTTGAGAGG
30671 ATTTG
1 ATTTG
30676 GTGTGATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (10 bp):
ATTTGAGAGG
Found at i:31352 original size:2 final size:2
Alignment explanation
Indices: 31277--31342 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
31267 GATTATTGCA
31277 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
31319 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
31343 GACGTATATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31934 original size:15 final size:16
Alignment explanation
Indices: 31911--31950 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31901 TATAAGGTAA
*
31911 TTTTGTTATA-ATATT
1 TTTTATTATACATATT
*
31926 TTTTATTATACTTATT
1 TTTTATTATACATATT
31942 TTTTATTAT
1 TTTTATTAT
31951 GATTATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTATTATACATATT
Found at i:36082 original size:22 final size:24
Alignment explanation
Indices: 36057--36103 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
36047 ATAAAAAATT
*
36057 ATATTA-AAAAT-TTAGGGGTGCG
1 ATATTATAAAATCTTAGAGGTGCG
36079 ATATTATAAAATCTTAGAGGTGCG
1 ATATTATAAAATCTTAGAGGTGCG
36103 A
1 A
36104 AGTCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (24 bp):
ATATTATAAAATCTTAGAGGTGCG
Found at i:42668 original size:33 final size:33
Alignment explanation
Indices: 42601--42677 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
42591 CTTGGGACTT
* * *
42601 GGGCTGCTCCAATTCTTTCTGGACCAGGTGCAC
1 GGGCTGCTCCAATTCTTCCTGAACCAGGTACAC
* * *
42634 GGGCTGCTCTAATTGTTCCTGAACCGGGTACAC
1 GGGCTGCTCCAATTCTTCCTGAACCAGGTACAC
*
42667 GGGTTGCTCCA
1 GGGCTGCTCCA
42678 CTTCAGATGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (33 bp):
GGGCTGCTCCAATTCTTCCTGAACCAGGTACAC
Found at i:46155 original size:21 final size:21
Alignment explanation
Indices: 46131--46255 Score: 148
Period size: 21 Copynumber: 6.0 Consensus size: 21
46121 CTAGTCGTTG
*
46131 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
** *
46152 CAG-CAGGATACATCGATGCA
1 CAGCCTTGATGCATCGATGCA
46172 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
46193 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
*
46214 CAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
* **
46235 TAG-AATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
46255 C
1 C
46256 TAATTGCATT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.01
20 29 0.33
21 59 0.66
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.22
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:46176 original size:41 final size:41
Alignment explanation
Indices: 46131--46255 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 41
46121 CTAGTCGTTG
* * *
46131 CAGCCTTCG-TGCATGGATGCACAGCAGGATACATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGCATGATGCATCGATGCA
*
46172 CAGCCTTGATGCATCGATGCACAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAG-CATGATGCATCGATGCA
* * *
46214 CAACCTTGATGCATCGATGCATAGAATGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGCATGATGCATCGATGCA
46255 C
1 C
46256 TAATTGCATT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.01
41 37 0.50
42 36 0.49
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.22
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGCATGATGCATCGATGCA
Found at i:46322 original size:22 final size:23
Alignment explanation
Indices: 46290--46332 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
46280 ATGGATGCAA
46290 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
46313 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
46333 GCAGGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:46464 original size:28 final size:31
Alignment explanation
Indices: 46433--46491 Score: 97
Period size: 28 Copynumber: 2.0 Consensus size: 31
46423 AAACTTTGAA
46433 TAAATTCAATT-AAGTCC-AAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
46461 TAAATTCAATTCAAGTCCAAAAATCATTTTG
1 TAAATTCAATTCAAGTCCAAAAATCATTTTG
46492 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 11 0.39
29 6 0.21
30 4 0.14
31 7 0.25
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAATCATTTTG
Found at i:49392 original size:34 final size:29
Alignment explanation
Indices: 49324--49383 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
49314 AAACTTTGAA
49324 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
49353 TAAATTCAATTCAAG-CCTAAAAACCATTTTG
1 TAAATTCAATT-AAGTCC-AAAAA-CATTTTG
49384 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.46
30 8 0.29
31 7 0.25
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:52837 original size:20 final size:20
Alignment explanation
Indices: 52812--52861 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
52802 GGGAAAATCA
52812 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
52832 CAATGCGATACTGACTATCG
1 CAATGCGATACTGACTATCG
52852 CAATGCGATA
1 CAATGCGATA
52862 ATACAAAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
CAATGCGATACTGACTATCG
Found at i:52870 original size:61 final size:62
Alignment explanation
Indices: 52805--52922 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
52795 GCAAATTGGG
* * * * *
52805 AAAATCACAATGCGATACTGACTATCGCAATGCGATACTGAC-T-ATCGCAATGCGATAATAC
1 AAAATCACAACGAGATACTAACTATCGCAACGCGATAAT-ACATAATCGCAATGCGATAATAC
* *
52866 AAAATCGCAACGAGATACTAACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCACAACGAGATACTAACTATCGCAACGCGATAATACATAATCGCAATGCGAT
52923 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 2 0.04
61 33 0.69
62 13 0.27
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (62 bp):
AAAATCACAACGAGATACTAACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:52873 original size:41 final size:41
Alignment explanation
Indices: 52828--52922 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
52818 GATACTGACT
* *
52828 ATCGCAATGCGATACTGACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAACTATCGCAACGCGATAATACAAA
* * * *
52869 ATCGCAACGAGATACTAACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTAACTATCGCAACGCGATAATACAAA
52910 ATCGCAATGCGAT
1 ATCGCAATGCGAT
52923 TTTCAAAGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
ATCGCAATGCGATACTAACTATCGCAACGCGATAATACAAA
Found at i:52874 original size:21 final size:21
Alignment explanation
Indices: 52848--52922 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
52838 GATACTGACT
*
52848 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
52869 ATCGCAACGAGATACTA-ACT
1 ATCGCAACGCGATAATACAAA
* *
52889 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACAAA
*
52910 ATCGCAATGCGAT
1 ATCGCAACGCGAT
52923 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:53118 original size:22 final size:22
Alignment explanation
Indices: 53090--53133 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
53080 CACTCTCTCA
53090 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
53112 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
53134 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:53375 original size:20 final size:20
Alignment explanation
Indices: 53350--53387 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53340 ATCGCAACGC
53350 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
53370 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
53388 AGAAGCTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:54728 original size:18 final size:18
Alignment explanation
Indices: 54707--54751 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
54697 TCCACTTCGG
* *
54707 GAGCCATCACCTCGCCCA
1 GAGCCATCAACTCACCCA
* *
54725 GAGCTATCAACTCACTCA
1 GAGCCATCAACTCACCCA
54743 GAGCCATCA
1 GAGCCATCA
54752 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.40, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCAACTCACCCA
Found at i:55287 original size:19 final size:20
Alignment explanation
Indices: 55233--55299 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
55223 TAGTTTACTT
* *
55233 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
55253 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
55273 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
55292 TCGCAACG
1 TCGCAACG
55300 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:55307 original size:14 final size:14
Alignment explanation
Indices: 55288--55345 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55278 ATGCGAAATG
55288 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55302 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
55318 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
55334 AAAATCGCAACG
1 AAAATCGCAACG
55346 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55330 original size:32 final size:33
Alignment explanation
Indices: 55272--55362 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
55262 GGAAATGGCT
55272 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
55305 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
55337 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
55363 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:55379 original size:19 final size:18
Alignment explanation
Indices: 55374--55471 Score: 79
Period size: 18 Copynumber: 5.8 Consensus size: 18
55364 GCGATTTGTG
*
55374 TTTCGCGTTGCGATTTCA
1 TTTCGCATTGCGATTTCA
55392 TTTCGCATTGCGATTT--
1 TTTCGCATTGCGATTTCA
*
55408 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGA-TTTCA
55425 TTTCGCATTGCGATTGT-A
1 TTTCGCATTGCGATT-TCA
*
55443 --TCG--TTGCGATTTTTA
1 TTTCGCATTGCGA-TTTCA
55458 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
55472 AGCCATTTCC
Statistics
Matches: 65, Mismatches: 3, Indels: 24
0.71 0.03 0.26
Matches are distributed among these distances:
14 13 0.20
15 6 0.09
16 7 0.11
17 7 0.11
18 19 0.29
19 13 0.20
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.47
Consensus pattern (18 bp):
TTTCGCATTGCGATTTCA
Found at i:55429 original size:33 final size:33
Alignment explanation
Indices: 55379--55471 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
55369 TTGTGTTTCG
* *
55379 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTGTAT
55411 CGTTGCGATTTTCATTTCGCATTGCGATTGTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTGTAT
*
55444 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
55472 AGCCATTTCC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 8 0.14
33 49 0.86
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTGTAT
Found at i:55479 original size:19 final size:20
Alignment explanation
Indices: 55457--55499 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
55447 TGCGATTTTT
55457 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
55476 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
55496 ATTT
1 ATTT
55500 TTGCGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:55490 original size:20 final size:20
Alignment explanation
Indices: 55465--55511 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
55455 TTATTTCGCA
55465 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* **
55485 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGCCATTTCCGCG
55505 TTGCGAT
1 TTGCGAT
55512 TTTATGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:55971 original size:40 final size:40
Alignment explanation
Indices: 55876--55962 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
55866 GACTCACCTG
* *
55876 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCACTA
* *
55918 TCCTCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
55958 TCATC
1 TCATC
55963 GTTGAAGAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 20 0.50
41 2 0.05
42 18 0.45
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.21
Consensus pattern (40 bp):
TCATCCCTCAAGAGTCCCCCCACCGTTCAAGAGGCCACTA
Found at i:57397 original size:14 final size:14
Alignment explanation
Indices: 57378--57413 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
57368 ATTGTTTAAT
57378 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
57392 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
57406 TGATTTGT
1 TGATTTGT
57414 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:57558 original size:14 final size:16
Alignment explanation
Indices: 57539--57611 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 16
57529 CGAAACTGAC
57539 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
57553 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATGAAA
57572 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG-AATGAAA
*
57591 ATCACAACG-A-GAAA
1 ATCGCAACGAATGAAA
57605 ATCGCAA
1 ATCGCAA
57612 TGCGATTTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
14 17 0.34
15 1 0.02
16 2 0.04
17 3 0.06
18 2 0.04
19 23 0.46
20 1 0.02
21 1 0.02
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (16 bp):
ATCGCAACGAATGAAA
Found at i:57571 original size:19 final size:19
Alignment explanation
Indices: 57549--57616 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
57539 ATCGCAACGA
57549 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
57568 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATGCGAAAT
*
57587 GAAAATCACAA--CG--A-
1 GAAAATCGCAATGCGAAAT
57601 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
57617 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.50, C:0.18, G:0.19, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:57680 original size:20 final size:20
Alignment explanation
Indices: 57657--57701 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
57647 CGATTTTTCA
*
57657 TTTCGAATTGCGATAGCCAT
1 TTTCGAATTGCGATAGACAT
**
57677 TTTCGCGTTGCGATAGACAT
1 TTTCGAATTGCGATAGACAT
57697 TTTCG
1 TTTCG
57702 CGTTGCGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
TTTCGAATTGCGATAGACAT
Found at i:57702 original size:20 final size:20
Alignment explanation
Indices: 57664--57710 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
57654 TCATTTCGAA
*
57664 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGACATTTTCGCG
57684 TTGCGATAGACATTTTCGCG
1 TTGCGATAGACATTTTCGCG
57704 TTGCGAT
1 TTGCGAT
57711 TTCCCCGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGACATTTTCGCG
Found at i:57949 original size:20 final size:20
Alignment explanation
Indices: 57924--58015 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
57914 TTGAAGATGA
57924 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
57944 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
57964 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
57985 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
58005 TTGCGATTTTC
1 TTGCGATTTTC
58016 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:58044 original size:20 final size:21
Alignment explanation
Indices: 58000--58051 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
57990 ATAGTCAGTA
*
58000 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
58021 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
58041 TCGCATTGCGA
1 TCGCATTGCGA
58052 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:58267 original size:12 final size:12
Alignment explanation
Indices: 58248--58281 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58238 CTCTCCGACG
58248 ACATCCGTTCCT
1 ACATCCGTTCCT
*
58260 ATATCCGTTCCT
1 ACATCCGTTCCT
58272 ACATCC-TTCC
1 ACATCCGTTCC
58282 CCATCAGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:58864 original size:24 final size:24
Alignment explanation
Indices: 58837--58890 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58827 GTATTCGAAA
*
58837 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
58861 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
58885 TTTGAT
1 TTTGAT
58891 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:59082 original size:12 final size:12
Alignment explanation
Indices: 59065--59091 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59055 ATATAATCCT
59065 GAAGAAGAAAAA
1 GAAGAAGAAAAA
59077 GAAGAAGAAAAA
1 GAAGAAGAAAAA
59089 GAA
1 GAA
59092 AAAGTCCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:61405 original size:19 final size:19
Alignment explanation
Indices: 61363--61465 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
61353 CTTAATGTCT
* **
61363 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
61383 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
61402 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
61421 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
61435 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
61454 ATCGCAACGCGA
1 ATCGCAACGCGA
61466 TTTTCATTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 45 0.65
20 9 0.13
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:61477 original size:19 final size:19
Alignment explanation
Indices: 61455--61497 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
61445 GAAATGAAAA
61455 TCGCAACGCGATTTTCATT
1 TCGCAACGCGATTTTCATT
***
61474 TCGCGTTGCGATTTTCATT
1 TCGCAACGCGATTTTCATT
61493 TCGCA
1 TCGCA
61498 TAGCGATAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.40
Consensus pattern (19 bp):
TCGCAACGCGATTTTCATT
Found at i:61503 original size:19 final size:19
Alignment explanation
Indices: 61462--61504 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
61452 AAATCGCAAC
* *
61462 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCATA
61481 GCGATTTTCATTTCGCATA
1 GCGATTTTCATTTCGCATA
61500 GCGAT
1 GCGAT
61505 AGTACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (19 bp):
GCGATTTTCATTTCGCATA
Found at i:61630 original size:14 final size:14
Alignment explanation
Indices: 61611--61647 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61601 CATCAATTAA
61611 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
61625 ACAAATCACCTTTT
1 ACAAATCAACTTTT
61639 ACAAATCAA
1 ACAAATCAA
61648 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:63064 original size:42 final size:41
Alignment explanation
Indices: 63005--63210 Score: 166
Period size: 42 Copynumber: 4.9 Consensus size: 41
62995 GTGAATCGGG
* *
63005 CTCTTGAATGGTAGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTAGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
63047 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAAG-GGC
1 CTCTTGAACGGTAGGA-GGGACTCTTCAAGG-ATGA-CAGTGGC
* * * *
63089 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTAGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
63131 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTAGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * *
63173 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTAGGAG-GGACTCTTCAAGGATGACAG
63211 GCGAGTCGAG
Statistics
Matches: 127, Mismatches: 27, Indels: 20
0.73 0.16 0.11
Matches are distributed among these distances:
41 11 0.09
42 103 0.81
43 13 0.10
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:63146 original size:84 final size:84
Alignment explanation
Indices: 63035--63210 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
63025 CCTCTTCAAC
63035 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
63100 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
63119 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
63184 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
63203 GATGACAG
1 GATGACAG
63211 GCGAGTCGAG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:63607 original size:91 final size:90
Alignment explanation
Indices: 63429--63613 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
63419 ATTTCAAACT
*
63429 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
63494 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
**
63522 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGTT
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
63586 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
63613 T
1 T
63614 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 40 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:65261 original size:20 final size:20
Alignment explanation
Indices: 65216--65275 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
65206 TCTTTTGGTT
*
65216 GAAATGAAAATCGCAACG-A
1 GAAATGAAAATCGCAACGCG
*
65235 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACGCG
**
65256 GAAATGACTATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
65276 CAAAACACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:65816 original size:20 final size:20
Alignment explanation
Indices: 65747--65880 Score: 162
Period size: 20 Copynumber: 6.7 Consensus size: 20
65737 CGCTATGTAA
* *
65747 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
65767 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
* *
65788 ATCGTATTGCGATAGTCGGT
1 ATCGCATTGCGATAGTCAGT
*
65808 ATCGCATTGCGATGGTCAGT
1 ATCGCATTGCGATAGTCAGT
65828 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
65848 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
65868 ATCGCATTGCGAT
1 ATCGCATTGCGAT
65881 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 3 0.03
20 81 0.84
21 11 0.11
22 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:68398 original size:30 final size:31
Alignment explanation
Indices: 68341--68398 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
68331 TATGTTTGAT
* *
68341 CACTTATATTATTGATTTATTAAATTTTAGC
1 CACTTACATTATCGATTTATTAAATTTTAGC
*
68372 CACTTACATTATCGA-TTATTATATTTT
1 CACTTACATTATCGATTTATTAAATTTT
68399 TGGTCACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (31 bp):
CACTTACATTATCGATTTATTAAATTTTAGC
Found at i:68407 original size:31 final size:31
Alignment explanation
Indices: 68335--68408 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
68325 GAAAATTATG
* * *
68335 TTTGATCACTTATATTATTGATTTATTAAAT
1 TTTGGTCACTTACATTATCGATTTATTAAAT
* * *
68366 TTTAGCCACTTACATTATCGA-TTATTATATT
1 TTTGGTCACTTACATTATCGATTTATTA-AAT
68397 TTTGGTCACTTA
1 TTTGGTCACTTA
68409 GTCGTTAACT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.51
Consensus pattern (31 bp):
TTTGGTCACTTACATTATCGATTTATTAAAT
Found at i:74918 original size:25 final size:25
Alignment explanation
Indices: 74875--74924 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
74865 AGATGGTGAA
*
74875 TTTGACTAAGCCTAAATAGATCAAT
1 TTTGACTAAGCCGAAATAGATCAAT
* * *
74900 TTTGACTCAGCCGAGATAGGTCAAT
1 TTTGACTAAGCCGAAATAGATCAAT
74925 GATACTTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (25 bp):
TTTGACTAAGCCGAAATAGATCAAT
Found at i:77719 original size:20 final size:20
Alignment explanation
Indices: 77680--77719 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
77670 CACCCGCAAC
*
77680 ATCCATCCACCCATTAATAT
1 ATCCATCCACCCATCAATAT
* *
77700 ATCCATCCATCCATCCATAT
1 ATCCATCCACCCATCAATAT
77720 GTATATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.30
Consensus pattern (20 bp):
ATCCATCCACCCATCAATAT
Found at i:78091 original size:17 final size:17
Alignment explanation
Indices: 78046--78095 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
78036 TTGTTCATGT
78046 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
78063 TTTGAG----TATGAATG
1 TTTG-GTTTCTATGAATG
78077 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
78094 TT
1 TT
78096 AGAAGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.04
14 12 0.43
17 14 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:88037 original size:103 final size:103
Alignment explanation
Indices: 87812--88029 Score: 364
Period size: 103 Copynumber: 2.1 Consensus size: 103
87802 GTCGAGGGTC
87812 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
87877 TTGATCCTTGGCATATGTATATAATTCTTAATAAATTA
66 TTGATCCCTAGCATATGTATATAATTCTTAAGAAATGA
*
87915 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
87980 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATAATTCTTAAGAAATGA
88018 TATGTGGTCCTT
1 TATGTGGTCCTT
88030 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATAATTCTTAAGAAATGA
Found at i:88079 original size:23 final size:23
Alignment explanation
Indices: 88046--88111 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
88036 ATTATTATAT
*
88046 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
88069 GGCACTCCGGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
* *
88092 GGTACTTCGGTGCAATTATA
1 GGCACTACGGTGCAATTATA
88112 TGAGCTGTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:93204 original size:18 final size:19
Alignment explanation
Indices: 93181--93224 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
93171 CCAGTAATTC
*
93181 TATTCC-CTGGTAATCTTA
1 TATTCCACTAGTAATCTTA
93199 TATTCCCACTAGTAATCTTA
1 TATT-CCACTAGTAATCTTA
*
93219 CATTCC
1 TATTCC
93225 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.25, C:0.27, G:0.07, T:0.41
Consensus pattern (19 bp):
TATTCCACTAGTAATCTTA
Found at i:93762 original size:44 final size:44
Alignment explanation
Indices: 93699--93785 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
93689 ACTGCTGCTC
*
93699 AACAATAATCGATTTAAATATAATTTCATACATTATTTATAAAA
1 AACAATAATCGATTTAAATATAAATTCATACATTATTTATAAAA
*
93743 AACAATAATCGATTTAAATATAAATTCATAGATTATTTATAAA
1 AACAATAATCGATTTAAATATAAATTCATACATTATTTATAAA
93786 TTTCAACATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (44 bp):
AACAATAATCGATTTAAATATAAATTCATACATTATTTATAAAA
Found at i:95420 original size:3 final size:3
Alignment explanation
Indices: 95412--95502 Score: 137
Period size: 3 Copynumber: 30.0 Consensus size: 3
95402 TTTTTTCATT
**
95412 TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
95460 TATA TTA TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
95503 AATAAATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:96812 original size:11 final size:11
Alignment explanation
Indices: 96784--96817 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
96774 ATATGTTTAA
*
96784 ATTATTACTTTA
1 ATTATTA-TTTT
96796 ATTATTATTTT
1 ATTATTATTTT
96807 ATTATTATTTT
1 ATTATTATTTT
96818 CATACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:105667 original size:22 final size:22
Alignment explanation
Indices: 105637--105713 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
105627 ACATCTACAT
*
105637 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
* *
105659 TCTTTAAAGATAATAAATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
105681 TCTTCAAAGATTATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
105703 TTTTCAAAGAT
1 TCTTCAAAGAT
105714 TAAAGCTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TCTTCAAAGATAATAGATTCTC
Found at i:106538 original size:45 final size:45
Alignment explanation
Indices: 106474--106667 Score: 280
Period size: 45 Copynumber: 4.3 Consensus size: 45
106464 GAGAGTTTTT
* * * *
106474 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTAGAATGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
* *
106519 TGATGTTTTTAAAACCTTCGGGTCATCTATAATACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
* * *
106564 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTATAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
* *
106609 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
*
106654 GGATGTTTTCAAAA
1 TGATGTTTTCAAAA
106668 AGCCTTCAGG
Statistics
Matches: 132, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 132 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
Found at i:106754 original size:45 final size:45
Alignment explanation
Indices: 106685--106798 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
106675 AGGAGCTTTT
* *
106685 TGATATTTTCAAAACCTTGGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
106730 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
*
106775 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
106799 AGCTTTTTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 52 0.81
46 4 0.06
47 8 0.12
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:106783 original size:121 final size:121
Alignment explanation
Indices: 106564--106864 Score: 494
Period size: 121 Copynumber: 2.5 Consensus size: 121
106554 CTACAGTGCA
* * *
106564 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGACCTATAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
106629 GGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
66 GGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
*
106685 TGATATTTTCAAAACCTTGGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
* ** *
106750 GGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
66 GGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
* * * *
106806 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAGGATATTTTCAAAA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAA
106865 AGCCTTTGGG
Statistics
Matches: 167, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 167 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (121 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAACCTTCG
GGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTT
Found at i:106861 original size:76 final size:76
Alignment explanation
Indices: 106730--106946 Score: 357
Period size: 76 Copynumber: 2.9 Consensus size: 76
106720 CTACAGTGCA
* *
106730 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTT
106795 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
106806 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAGGATATTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTT
*
106871 TGGGAGCTTTT
66 CGGGAGCTTTT
* *
106882 TGATATTTTCAAAACCTTCGGGACATCTGTAAGACCTACAATGCATGATGTTTTC--AAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTT
106945 CG
66 CG
106947 AGTCATCTGT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
74 9 0.07
76 122 0.93
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (76 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAATGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:106954 original size:197 final size:197
Alignment explanation
Indices: 106609--106964 Score: 586
Period size: 197 Copynumber: 1.8 Consensus size: 197
106599 CTATAGTGCA
* * *
106609 TGATGTTTTCAAAACCTTCGGGCCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAATGCAGGATATTTTCAAAAAGCCTT
* * *
106674 CAGGAGCTTTTTGATATTTTCAAAACCTTGGGGTCATCTGTAAGACCTACAGTGCATGATGTTTT
66 CAGGAGCTTTTTGATATTTTCAAAACCTTCGGGACATCTGTAAGACCTACAATGCATGATGTTTT
*
106739 CAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTT
131 CAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTT
106804 TT
196 TT
* * **
106806 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCAGGATATTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAATGCAGGATATTTTCAAAAAGCCTT
**
106871 TGGGAGCTTTTTGATATTTTCAAAACCTTCGGGACATCTGTAAGACCTACAATGCATGATGTTTT
66 CAGGAGCTTTTTGATATTTTCAAAACCTTCGGGACATCTGTAAGACCTACAATGCATGATGTTTT
*
106936 CAAAGCCTTCGAGTCATCTGTAAGACCTA
131 CAAAACCTTCGAGTCATCTGTAAGACCTA
106965 TAATTCAAGA
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
197 145 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (197 bp):
TGATATTTTCAAAACCTTCGGGCCATCCATAAGACCTACAATGCAGGATATTTTCAAAAAGCCTT
CAGGAGCTTTTTGATATTTTCAAAACCTTCGGGACATCTGTAAGACCTACAATGCATGATGTTTT
CAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTT
TT
Found at i:107322 original size:21 final size:18
Alignment explanation
Indices: 107283--107317 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
107273 CATTTTATTT
*
107283 TTATTTTTATTATTAAAA
1 TTATTATTATTATTAAAA
107301 TTATTATTATTATTAAA
1 TTATTATTATTATTAAA
107318 TAAATAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTATTATTATTAAAA
Found at i:108618 original size:11 final size:11
Alignment explanation
Indices: 108589--108622 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
108579 GATATGTTTA
108589 AATTATTACTTT
1 AATTATTA-TTT
108601 AATTATTATTT
1 AATTATTATTT
*
108612 TATTATTATTT
1 AATTATTATTT
108623 CATACTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
AATTATTATTT
Found at i:108654 original size:2 final size:2
Alignment explanation
Indices: 108633--108672 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
108623 CATACTAGTC
* * *
108633 AT AT AA AT AA AT AA 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
108673 TTGTTTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:111338 original size:239 final size:233
Alignment explanation
Indices: 110899--111341 Score: 685
Period size: 239 Copynumber: 1.9 Consensus size: 233
110889 CTTTATTTTA
110899 GTCGGGTCGATTTTTTTAAGTGTCATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA
1 GTCGGGTCGATTTTTTTAAGTGTCATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA
* * *
110964 CTCGACCCGAAAATATATATAATTTTATCTTATATATTTAGGAATAATTACAATAATACCCCTCT
66 CCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
* *
111029 ATATATAATTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAATATAATTTTTTTATTATTTC
131 ATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
111094 GGGTCGGGTAGGGTCAGATTTCTAATTCATATATTCGG
196 GGGTCGGGTAGGGTCAGATTTCTAATTCATATATTCGG
* * * *
111132 GTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTC-TGTTTAGGGTGAAAAATA
1 GTCGGGTCGATTTTTTTAAGTGTCATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAT-
111196 CCCGACCCGACCCGACCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAA
65 ----ACCCGACCCG----AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAA
* *
111261 TACCCCTCTCTATAT-A-TTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTT
122 TACCCCTCTATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTT
111324 TATTATTTCGGGTCGGGT
187 TATTATTTCGGGTCGGGT
111342 CGAGTTTCTA
Statistics
Matches: 190, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
232 16 0.08
233 43 0.23
237 9 0.05
239 62 0.33
240 1 0.01
241 59 0.31
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (233 bp):
GTCGGGTCGATTTTTTTAAGTGTCATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATA
CCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCT
ATATATAATTTTTTTCCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTC
GGGTCGGGTAGGGTCAGATTTCTAATTCATATATTCGG
Found at i:123183 original size:12 final size:12
Alignment explanation
Indices: 123166--123190 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
123156 CGTATGTTTT
123166 ATCTGATTTACA
1 ATCTGATTTACA
123178 ATCTGATTTACA
1 ATCTGATTTACA
123190 A
1 A
123191 AGATTTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTGATTTACA
Found at i:124456 original size:13 final size:13
Alignment explanation
Indices: 124438--124463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
124428 ATCTTCCCCT
124438 ACCCTTGGTATAG
1 ACCCTTGGTATAG
124451 ACCCTTGGTATAG
1 ACCCTTGGTATAG
124464 GTTTGAGTTA
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:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
ACCCTTGGTATAG
Found at i:126760 original size:21 final size:21
Alignment explanation
Indices: 126726--126782 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
126716 GAGGGATTAT
* *
126726 GAGGTTCTT-GGGACATATAC
1 GAGGTCCTTCGGGACATACAC
*
126746 GAGGTCCTTCGGGACATACAT
1 GAGGTCCTTCGGGACATACAC
*
126767 GAGGTCATTCGGGACA
1 GAGGTCCTTCGGGACA
126783 AATTTCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
GAGGTCCTTCGGGACATACAC
Done.