Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003682.1 Hibiscus syriacus cultivar Beakdansim tig00007863_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: 73365
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1344 original size:2 final size:2
Alignment explanation
Indices: 1337--1372 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1327 GATAAGTATT
* *
1337 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1373 AAATGTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3180 original size:43 final size:44
Alignment explanation
Indices: 3084--3182 Score: 123
Period size: 43 Copynumber: 2.3 Consensus size: 44
3074 ATAAAAATCA
* * *
3084 ATTCATGTTTC-TTTCTTATTCAGACACATTTCAGAACTTTCAC
1 ATTCATTTTTCATTTCCTATTCAGACACATTTCAAAACTTTCAC
* *
3127 ATTTCA-TTTTCATTTCCT-TTCAGATACTTTTCAAAACTTTCAC
1 A-TTCATTTTTCATTTCCTATTCAGACACATTTCAAAACTTTCAC
3170 ATTCATTTTTCAT
1 ATTCATTTTTCAT
3183 ATCTACTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
42 4 0.08
43 35 0.73
44 9 0.19
ACGTcount: A:0.25, C:0.22, G:0.04, T:0.48
Consensus pattern (44 bp):
ATTCATTTTTCATTTCCTATTCAGACACATTTCAAAACTTTCAC
Found at i:17822 original size:81 final size:81
Alignment explanation
Indices: 17697--17998 Score: 392
Period size: 81 Copynumber: 3.7 Consensus size: 81
17687 CCCAAATGCA
* * * * *
17697 TTTAACCTTTCATCTAACTTGCATGATTGACA-CTTGTCTGCCAAATCCACAGCTAGGCCATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTT-TCTACCAAATGCACAGCTAGGCCATTTA
*
17761 TCTTTTACTCAACGGCC
65 TCTTTTACTCAACGGTC
* * *
17778 TTTAACCGTTCATCTAACCGGGATAATTGACACCTTTCTACCAAATGCACAACTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTAT
*
17843 ATTTTACTCAACGGTC
66 CTTTTACTCAACGGTC
* *
17859 TTTAACCGTTCATCTAACTGGCATAATTGACATCTTTC-AGCCAAATGCAAAGCTAGGCCATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTA-CCAAATGCACAGCTAGGCCATTTA
*
17923 TCTTTTACTCAACGATC
65 TCTTTTACTCAACGGTC
** * * * * *
17940 TTTAACTATTCATTTAATTGACATAATTGACACCTTTCTACCAAATGCATAGTTAGGCC
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCC
17999 TGAAAGGCAC
Statistics
Matches: 193, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
80 1 0.01
81 188 0.97
82 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (81 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTTAT
CTTTTACTCAACGGTC
Found at i:17925 original size:162 final size:162
Alignment explanation
Indices: 17697--17988 Score: 433
Period size: 162 Copynumber: 1.8 Consensus size: 162
17687 CCCAAATGCA
* * * * *
17697 TTTAACCTTTCATCTAACTTGCATGATTGACACTTGTCTGCCAAATCCACAGCTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACTTGTCAGCCAAATCCAAAGCTAGGCCATTTAT
* * **
17762 CTTTTACTCAACGGCCTTTAACCGTTCATCTAACCGGGATAATTGACACCTTTCTACCAAATGCA
66 CTTTTACTCAACGACCTTTAACCATTCATCTAACCGACATAATTGACACCTTTCTACCAAATGCA
17827 CAACTAGGCCATTTATATTTTACTCAACGGTC
131 CAACTAGGCCATTTATATTTTACTCAACGGTC
*
17859 TTTAACCGTTCATCTAACTGGCATAATTGACATCTT-TCAGCCAAATGCAAAGCTAGGCCATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACA-CTTGTCAGCCAAATCCAAAGCTAGGCCATTTA
* * * **
17923 TCTTTTACTCAACGATCTTTAACTATTCATTTAATTGACATAATTGACACCTTTCTACCAAATGC
65 TCTTTTACTCAACGACCTTTAACCATTCATCTAACCGACATAATTGACACCTTTCTACCAAATGC
17988 A
130 A
17989 TAGTTAGGCC
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
162 111 0.97
163 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (162 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACTTGTCAGCCAAATCCAAAGCTAGGCCATTTAT
CTTTTACTCAACGACCTTTAACCATTCATCTAACCGACATAATTGACACCTTTCTACCAAATGCA
CAACTAGGCCATTTATATTTTACTCAACGGTC
Found at i:18062 original size:68 final size:68
Alignment explanation
Indices: 17961--18333 Score: 516
Period size: 68 Copynumber: 5.5 Consensus size: 68
17951 ATTTAATTGA
** * * *
17961 CATAATTGACACCTTTCTACCAAATGCATAGTTAGGCCTGAAAGGCACTTAGACTTTCATCTAAC
1 CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
18026 TGG
66 TGG
*
18029 CATAATTGACACC-TTCTTGTCAAATGTACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAA
1 CATAATTGACACCTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAA
18093 CTGG
65 CTGG
* * * * * *
18097 CATAATTGGCACATTTCTTTTAAATGCACAGTCAGGCCTCAAAGGCACTTAGCCTTTCATTTAAC
1 CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
18162 TGG
66 TGG
* * * *
18165 CATAATTGACA-CTTTCTATCAAATGCACATTTAGGCCTCAAAGGCGCTTATCCTTTCATCTAAC
1 CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
18229 TGG
66 TGG
* * * * *
18232 CATAATTGATACCTTTCTGTCAAATGCACAATTAGGCCTCAAATGAACTTGGCCTTTCATCTAAC
1 CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
18297 TGG
66 TGG
* *
18300 TATAATTGACACCTTTATGTCAAATGCACAGTTA
1 CATAATTGACACCTTTCTGTCAAATGCACAGTTA
18334 ACCATATTAA
Statistics
Matches: 268, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
67 61 0.23
68 204 0.76
69 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (68 bp):
CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
TGG
Found at i:18257 original size:135 final size:135
Alignment explanation
Indices: 17961--18333 Score: 512
Period size: 135 Copynumber: 2.7 Consensus size: 135
17951 ATTTAATTGA
* * * *
17961 CATAATTGACACCTTTCTACCAAATGCATAGTTAGGCCTGAAAGGCACTTAGACTTTCATCTAAC
1 CATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
* *
18026 TGGCATAATTGACACCTTCTTGTCAAATGTACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCT
66 TGGCATAATTGACACTTTC-TGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCT
18091 AACTGG
130 AACTGG
* * * * * *
18097 CATAATTGGCACATTTCTTTTAAATGCACAGTCAGGCCTCAAAGGCACTTAGCCTTTCATTTAAC
1 CATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
* * * *
18162 TGGCATAATTGACACTTTCTATCAAATGCACATTTAGGCCTCAAAGGCGCTTATCCTTTCATCTA
66 TGGCATAATTGACACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTA
18227 ACTGG
131 ACTGG
* * * * * *
18232 CATAATTGATACCTTTCTGTCAAATGCACAATTAGGCCTCAAATGAACTTGGCCTTTCATCTAAC
1 CATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
* *
18297 TGGTATAATTGACACCTTTATGTCAAATGCACAGTTA
66 TGGCATAATTGACA-CTTTCTGTCAAATGCACAGTTA
18334 ACCATATTAA
Statistics
Matches: 205, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
135 113 0.55
136 92 0.45
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (135 bp):
CATAATTGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAAC
TGGCATAATTGACACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTA
ACTGG
Found at i:18298 original size:203 final size:204
Alignment explanation
Indices: 17948--18331 Score: 556
Period size: 203 Copynumber: 1.9 Consensus size: 204
17938 TCTTTAACTA
* * *
17948 TTCATTTAATTGACATAATTGACACCTTTCTACCAAATGCATAGTTAGGCCTGAAAGGCACTTAG
1 TTCATTTAACTGACATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* * *
18013 ACTTTCATCTAACTGGCATAATTGACACCTTCTTGTCAAATGTACAGTTAGGCCTCAAAGGCACT
66 ACTTTCATCTAACTGGCATAATTGACACCTTCTTGTCAAATGCACAATTAGGCCTCAAAGGAACT
* * * *
18078 TAGCCTTTCATCTAACTGGCATAATTGGCACATTTCTTTTAAATGCACAGTCAGGCCTCAAAGGC
131 TAGCCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTCAGGCCTCAAAGGC
18143 ACTTAGCCT
196 ACTTAGCCT
* * * * *
18152 TTCATTTAACTGGCATAATTGACA-CTTTCTATCAAATGCACATTTAGGCCTCAAAGGCGCTTAT
1 TTCATTTAACTGACATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* * *
18216 CCTTTCATCTAACTGGCATAATTGATACCTT-TCTGTCAAATGCACAATTAGGCCTCAAATGAAC
66 ACTTTCATCTAACTGGCATAATTGACACCTTCT-TGTCAAATGCACAATTAGGCCTCAAAGGAAC
* * *
18280 TTGGCCTTTCATCTAACTGGTATAATTGACACCTTTATGTCAAATGCACAGT
130 TTAGCCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGT
18332 TAACCATATT
Statistics
Matches: 158, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
202 1 0.01
203 135 0.85
204 22 0.14
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (204 bp):
TTCATTTAACTGACATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
ACTTTCATCTAACTGGCATAATTGACACCTTCTTGTCAAATGCACAATTAGGCCTCAAAGGAACT
TAGCCTTTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTCAGGCCTCAAAGGC
ACTTAGCCT
Found at i:18606 original size:54 final size:55
Alignment explanation
Indices: 18548--18748 Score: 242
Period size: 55 Copynumber: 3.7 Consensus size: 55
18538 ACATATATTT
* * *
18548 CCATACAAAAATTAATACTCTTAGTATGGATTTCTTAG-TTTGCACACATAGTGC
1 CCATACAAAAATTCATACACTTAGTATGAATTTCTTAGATTTGCACACATAGTGC
* * * *
18602 CCATACATAAATTCATACAATTTGTATGAATTTCTTAGTTTTGCACACATAGTGC
1 CCATACAAAAATTCATACACTTAGTATGAATTTCTTAGATTTGCACACATAGTGC
** ** * * *
18657 CTGTACGGAAATTTATACACTTAGTATGAATTTCTTAGATTTGTACACAAAGTGC
1 CCATACAAAAATTCATACACTTAGTATGAATTTCTTAGATTTGCACACATAGTGC
* * *
18712 CCATACCAAAATTCATACACTTGGTATGGATTTCTTA
1 CCATACAAAAATTCATACACTTAGTATGAATTTCTTA
18749 AGTTTTTGCG
Statistics
Matches: 123, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
54 32 0.26
55 91 0.74
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (55 bp):
CCATACAAAAATTCATACACTTAGTATGAATTTCTTAGATTTGCACACATAGTGC
Found at i:18684 original size:109 final size:111
Alignment explanation
Indices: 18556--18754 Score: 296
Period size: 110 Copynumber: 1.8 Consensus size: 111
18546 TTCCATACAA
* * *
18556 AAATTAATACTCTTAGTATGGATTTCTTAG-TTTGCACACATAGTGCCCATA-CATAAATTCATA
1 AAATTAATACACTTAGTATGAATTTCTTAGATTTGCACACAAAGTGCCCATACCA-AAATTCATA
*
18619 CAATTTGTATGAATTTCTT-AGTTTTGCACACATAGTGCCTGTACGG
65 CAATTGGTATGAATTTCTTAAGTTTTGCACACATAGTGCCTGTACGG
* *
18665 AAATTTATACACTTAGTATGAATTTCTTAGATTTGTACACAAAGTGCCCATACCAAAATTCATAC
1 AAATTAATACACTTAGTATGAATTTCTTAGATTTGCACACAAAGTGCCCATACCAAAATTCATAC
* *
18730 ACTTGGTATGGATTTCTTAAGTTTT
66 AATTGGTATGAATTTCTTAAGTTTT
18755 TGCGCGCTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 27 0.34
110 44 0.56
111 8 0.10
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (111 bp):
AAATTAATACACTTAGTATGAATTTCTTAGATTTGCACACAAAGTGCCCATACCAAAATTCATAC
AATTGGTATGAATTTCTTAAGTTTTGCACACATAGTGCCTGTACGG
Found at i:19103 original size:19 final size:21
Alignment explanation
Indices: 19059--19109 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
19049 TCCCCATCAT
*
19059 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
19081 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
19100 GGTACCGATA
1 GGTATCGATA
19110 TGGTGTCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
21 4 0.15
22 12 0.44
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:22537 original size:42 final size:41
Alignment explanation
Indices: 22444--22533 Score: 123
Period size: 40 Copynumber: 2.2 Consensus size: 41
22434 TCATGCCGGG
22444 TATATAT-ATTTAAATTAAATATATAAATATTATATATATA
1 TATATATAATTTAAATTAAATATATAAATATTATATATATA
* * *
22484 TATATTTTAATTTAAATTAAATTTAT-TA-ATTATATATATA
1 TATA-TATAATTTAAATTAAATATATAAATATTATATATATA
22524 TATATATAAT
1 TATATATAAT
22534 AATTATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
39 5 0.11
40 20 0.45
41 3 0.07
42 16 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (41 bp):
TATATATAATTTAAATTAAATATATAAATATTATATATATA
Found at i:22585 original size:12 final size:12
Alignment explanation
Indices: 22550--22585 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
22540 TTTTAATATT
*
22550 TATCGGGTCAGG
1 TATCGGGTCGGG
22562 TATCGGGTCGGG
1 TATCGGGTCGGG
*
22574 TATCGGGGCGGG
1 TATCGGGTCGGG
22586 GATTACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.17, G:0.50, T:0.22
Consensus pattern (12 bp):
TATCGGGTCGGG
Found at i:23826 original size:81 final size:81
Alignment explanation
Indices: 23699--24073 Score: 403
Period size: 81 Copynumber: 4.6 Consensus size: 81
23689 CCCAAAGGCA
* * * * * * * *
23699 TTTAACCTTTCATCTAACTTGTATGACTGACA-CTTGATTGCCAAATGCACAGCTAGACCATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTA-TGACAAATGCACAGCTAGGCCATTTA
23763 TCTTTTACTCAACAATC
65 TCTTTTACTCAACAATC
* * * *
23780 TTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGAAAAATGCAAAGCTAGGCCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGACAAATGCACAGCTAGGCCATTTAT
* * *
23845 CTTTTATTCAACGATA
66 CTTTTACTCAACAATC
* * * * * *
23861 TTTAACCGTTCTTCTAACTGGCATAATTGACACTTTTCT-ACCAAATGTACGGCTAGGCAATTTA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGA-CAAATGCACAGCTAGGCCATTTA
*
23925 TCTTTTACTCAACAGTC
65 TCTTTTACTCAACAATC
* * * * *
23942 TTTAATCGTTCATCTAACTGGCATAATTGACATCTTTATGCCAAATGCACATCTAGGTCATTTAT
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGACAAATGCACAGCTAGGCCATTTAT
***
24007 CTTTTACTCAATGGTC
66 CTTTTACTCAACAATC
** * * *
24023 TTTAATTGTTCATCTAACTGACATAATTGACATCTTTATGCCAAATGCACA
1 TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGACAAATGCACA
24074 TTAGGCCTCA
Statistics
Matches: 250, Mismatches: 41, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
80 1 0.00
81 246 0.98
82 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (81 bp):
TTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGACAAATGCACAGCTAGGCCATTTAT
CTTTTACTCAACAATC
Found at i:24074 original size:81 final size:81
Alignment explanation
Indices: 23737--24073 Score: 408
Period size: 81 Copynumber: 4.2 Consensus size: 81
23727 GACACTTGAT
*
23737 TGCCAAATGCACAGCTAGACCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACT-AG
1 TGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGA-
* *
23801 CATAATTGACACCTTTC
65 CATAATTGACATCTTTA
** * * * * * *
23818 TGAAAAATGCAAAGCTAGGCCATTTATCTTTTATTCAACGATATTTAACCGTTCTTCTAACTGGC
1 TGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGAC
*
23883 ATAATTGACA-CTTTTC
66 ATAATTGACATC-TTTA
* * * * * * *
23899 TACCAAATGTACGGCTAGGCAATTTATCTTTTACTCAACAGTCTTTAATCGTTCATCTAACTGGC
1 TGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGAC
23964 ATAATTGACATCTTTA
66 ATAATTGACATCTTTA
* * *** **
23980 TGCCAAATGCACATCTAGGTCATTTATCTTTTACTCAATGGTCTTTAATTGTTCATCTAACTGAC
1 TGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGAC
24045 ATAATTGACATCTTTA
66 ATAATTGACATCTTTA
24061 TGCCAAATGCACA
1 TGCCAAATGCACA
24074 TTAGGCCTCA
Statistics
Matches: 220, Mismatches: 33, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 1 0.00
81 218 0.99
82 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
TGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACAATCTTTAACCGTTCATCTAACTGAC
ATAATTGACATCTTTA
Found at i:24169 original size:68 final size:68
Alignment explanation
Indices: 24031--24489 Score: 609
Period size: 68 Copynumber: 6.8 Consensus size: 68
24021 TCTTTAATTG
* * * * *
24031 TTCATCTAACT-GACATAATTGACATCTTTATGCCAAATGCACA-TTAGGCCTCAAAGGTATTTA
1 TTCATCTAACTAG-CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
24094 GCCT
65 GCCT
* * ** * * *
24098 TTCATCTGACTAGTATAATTGACACCTTTCTACCAAATGTACAGTTAGGCCTCAAAGACGCTTAG
1 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
24163 CCT
66 CCT
* * * *
24166 TTCATCTAACTGGCATAATTGGCACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
24231 CCT
66 CCT
* * *
24234 TTCATCTAAC-AGTCATAATTGACACCTTTCTGTCAAATACACACTTATGCCTCAAAGGCACTTA
1 TTCATCTAACTAG-CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
24298 GCCT
65 GCCT
* *
24302 TTCATCTAACTAACATAATTGACACTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
24367 CCT
66 CCT
** * * ** *
24370 TTCATCTATTTGGAATAATTGACATATTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
24435 CAT
66 CCT
*
24438 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
1 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
24490 ATTAATATTT
Statistics
Matches: 342, Mismatches: 46, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
67 36 0.11
68 305 0.89
69 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:24814 original size:55 final size:55
Alignment explanation
Indices: 24700--24907 Score: 303
Period size: 55 Copynumber: 3.8 Consensus size: 55
24690 ACATATATTT
* * *
24700 CCCATACAAAAATTAATACACTTAGTATGGATTTCTTAG-TTTGCACACATAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
*
24754 CCCATACGAAAATTCATATACTTCA-TATGAATTTCTTAGTTTTGCACACATAGTG
1 CCCATACGAAAATTCATACACTT-AGTATGAATTTCTTAGTTTTGCACACATAGTG
* *
24809 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
* * *
24864 CCCATACCAAAATTCATACACTTGGTATGGATTTCTTAAGTTTT
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTT-AGTTTT
24908 TGCATGTTTA
Statistics
Matches: 139, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
54 34 0.24
55 99 0.71
56 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (55 bp):
CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
Found at i:25306 original size:19 final size:21
Alignment explanation
Indices: 25263--25315 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
25253 TACCCCCATC
*
25263 ATGGTATCAATACTACTATACT
1 ATGGTATCGATACTACTATA-T
25285 ATGGTATCGATACT-CTAT-T
1 ATGGTATCGATACTACTATAT
*
25304 ATGGTACCGATA
1 ATGGTATCGATA
25316 TCATTTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.41
21 4 0.14
22 13 0.45
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:28911 original size:12 final size:12
Alignment explanation
Indices: 28894--28918 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28884 GTACTGTAGA
28894 TTATTGCACTTG
1 TTATTGCACTTG
28906 TTATTGCACTTG
1 TTATTGCACTTG
28918 T
1 T
28919 ATGGATGCAT
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:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATTGCACTTG
Found at i:30517 original size:2 final size:2
Alignment explanation
Indices: 30506--30582 Score: 50
Period size: 2 Copynumber: 38.0 Consensus size: 2
30496 TACACTTATG
* * * * *
30506 TA TA -A TA TA TA TA TA TA TA TA TA TA CA CA CA CA TGA GTA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA
* *
30549 TA TA TA -A GTA TA TA AA TA TA TA TA AA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
30583 AACATTTTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
1 2 0.03
2 56 0.90
3 3 0.05
4 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (2 bp):
TA
Found at i:30583 original size:10 final size:10
Alignment explanation
Indices: 30557--30584 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
30547 TATATATAAG
30557 TATATAAATA
1 TATATAAATA
30567 TATATAAATA
1 TATATAAATA
30577 TATATAAA
1 TATATAAA
30585 CATTTTCCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATATAAATA
Found at i:31154 original size:2 final size:2
Alignment explanation
Indices: 31147--31174 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31137 ATTTTTAAGA
31147 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
31175 TACTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33362 original size:8 final size:8
Alignment explanation
Indices: 33349--33406 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
33339 AACCCGACCC
33349 GACCCGTT
1 GACCCGTT
33357 GACCC---
1 GACCCGTT
33362 GACCCGTT
1 GACCCGTT
**
33370 GACCCGACCC
1 GACCCG--TT
33380 GACCCGTT
1 GACCCGTT
33388 GACCCGTT
1 GACCCGTT
33396 GA-CCGTT
1 GACCCGTT
33403 GACC
1 GACC
33407 GGAGTTGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
5 5 0.12
7 7 0.17
8 22 0.55
10 6 0.15
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.17
Consensus pattern (8 bp):
GACCCGTT
Found at i:33363 original size:18 final size:18
Alignment explanation
Indices: 33357--33393 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
33347 CCGACCCGTT
33357 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
33375 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
33393 G
1 G
33394 TTGACCGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:33393 original size:13 final size:13
Alignment explanation
Indices: 33344--33380 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
33334 GTCACAACCC
33344 GACCCGACCCGTT
1 GACCCGACCCGTT
33357 GACCCGACCCGTT
1 GACCCGACCCGTT
33370 GACCCGACCCG
1 GACCCGACCCG
33381 ACCCGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:36329 original size:47 final size:48
Alignment explanation
Indices: 36269--36359 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
36259 TCCGACTTGA
* * *
36269 ATTCTGTTATGATACTTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
36316 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
36360 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:36376 original size:24 final size:24
Alignment explanation
Indices: 36269--36359 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
36259 TCCGACTTGA
*
36269 ATTCTGTTATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
36293 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
36316 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
36340 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
36360 TTGAATTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.37
24 37 0.63
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:38573 original size:13 final size:13
Alignment explanation
Indices: 38555--38622 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
38545 GTCACAACCC
38555 GACCCGACCCGTT
1 GACCCGACCCGTT
38568 GACCCGACCC---
1 GACCCGACCCGTT
38578 GACCCGTTGACCC---
1 GACCC---GACCCGTT
38591 GACCCGACCCGTT
1 GACCCGACCCGTT
38604 GACCCGACCCGTT
1 GACCCGACCCGTT
38617 GACCCG
1 GACCCG
38623 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.20
13 39 0.80
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:38574 original size:18 final size:18
Alignment explanation
Indices: 38551--38628 Score: 129
Period size: 18 Copynumber: 4.2 Consensus size: 18
38541 ACCGGTCACA
38551 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
38569 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
38587 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
38605 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
38626 ACC
1 ACC
38629 GTTGACCCGT
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
18 45 0.79
21 12 0.21
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:38607 original size:8 final size:8
Alignment explanation
Indices: 38596--38657 Score: 82
Period size: 8 Copynumber: 8.5 Consensus size: 8
38586 GACCCGACCC
38596 GACCCGTT
1 GACCCGTT
38604 GACCC---
1 GACCCGTT
38609 GACCCGTT
1 GACCCGTT
38617 GACCCGTT
1 GACCCGTT
38625 GA-CCGTT
1 GACCCGTT
38632 GACCCGTT
1 GACCCGTT
38640 GA-CCGTT
1 GACCCGTT
38647 GA-CCGTT
1 GACCCGTT
38654 GACC
1 GACC
38658 GGAGTTGACC
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.10
7 21 0.43
8 23 0.47
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:38632 original size:7 final size:7
Alignment explanation
Indices: 38612--38658 Score: 76
Period size: 7 Copynumber: 6.4 Consensus size: 7
38602 TTGACCCGAC
38612 CCGTTGA
1 CCGTTGA
38619 CCCGTTGA
1 -CCGTTGA
38627 CCGTTGA
1 CCGTTGA
38634 CCCGTTGA
1 -CCGTTGA
38642 CCGTTGA
1 CCGTTGA
38649 CCGTTGA
1 CCGTTGA
38656 CCG
1 CCG
38659 GAGTTGACCA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 24 0.63
8 14 0.37
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:38632 original size:15 final size:15
Alignment explanation
Indices: 38612--38658 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
38602 TTGACCCGAC
38612 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
38627 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
38642 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
38656 CCG
1 CCG
38659 GAGTTGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.13, C:0.34, G:0.28, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:41174 original size:23 final size:24
Alignment explanation
Indices: 41136--41217 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
41126 AATTCTATTA
*
41136 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
41160 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
41183 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
41207 TGATACTTGAC
1 TGATACTTGAC
41218 TTGAATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.41
24 30 0.59
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:43430 original size:18 final size:18
Alignment explanation
Indices: 43407--43478 Score: 91
Period size: 18 Copynumber: 4.3 Consensus size: 18
43397 ACCGGTCACA
43407 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
43425 ACCCGACCTGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
43442 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
43456 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
43474 ACCCG
1 ACCCG
43479 TTGACCGGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.24
18 34 0.76
ACGTcount: A:0.17, C:0.49, G:0.21, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:43450 original size:31 final size:31
Alignment explanation
Indices: 43411--43478 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
43401 GTCACAACCC
*
43411 GACCCGACCCGTTGACCCGACCTGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
43442 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
43473 GACCCG
1 GACCCG
43479 TTGACCGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:43478 original size:13 final size:13
Alignment explanation
Indices: 43429--43465 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
43419 CCGTTGACCC
*
43429 GACCTGACCCGTT
1 GACCCGACCCGTT
*
43442 TACCCGACCCGTT
1 GACCCGACCCGTT
43455 GACCCGACCCG
1 GACCCGACCCG
43466 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:43494 original size:26 final size:28
Alignment explanation
Indices: 43447--43504 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
43437 CCGTTTACCC
43447 GACCCGTTGACCCGACCCGACC-C-GTT
1 GACCCGTTGACCCGACCCGACCACTGTT
* ***
43473 GACCCGTTGACCGGAGTTGACCACTGTT
1 GACCCGTTGACCCGACCCGACCACTGTT
43501 GACC
1 GACC
43505 AAAACTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 18 0.69
27 1 0.04
28 7 0.27
ACGTcount: A:0.17, C:0.38, G:0.26, T:0.19
Consensus pattern (28 bp):
GACCCGTTGACCCGACCCGACCACTGTT
Found at i:45983 original size:24 final size:24
Alignment explanation
Indices: 45956--46046 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
45946 TCCGACTTGA
* *
45956 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* * *
45980 ATTCTGATCTGATA-TTTACATGG
1 ATTCTGATATGATACTTGACCTGG
* *
46003 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACCTGG
46027 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
46047 TTGAATTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:54476 original size:21 final size:21
Alignment explanation
Indices: 54450--54489 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54440 CAGAACCCTA
*
54450 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
54471 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
54490 TCAAAGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:54524 original size:20 final size:21
Alignment explanation
Indices: 54471--54532 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
54461 ATTCCCCTGT
54471 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
54495 GGTGGAATCGGTTCCCTC-AA
1 GGGGGGATCGGTTCCCTCAAA
*
54515 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
54533 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 3 0.09
23 7 0.21
24 4 0.12
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:64537 original size:22 final size:22
Alignment explanation
Indices: 64505--64555 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
64495 ACCTTAGCAT
*
64505 GCTTGCTCCTATAGGAGGTATA
1 GCTTGCCCCTATAGGAGGTATA
*
64527 GCTTGCCCCTATAGGAGGTCTA
1 GCTTGCCCCTATAGGAGGTATA
64549 GCTTGCC
1 GCTTGCC
64556 ACTACCTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.29
Consensus pattern (22 bp):
GCTTGCCCCTATAGGAGGTATA
Found at i:68931 original size:22 final size:21
Alignment explanation
Indices: 68882--68952 Score: 85
Period size: 19 Copynumber: 3.5 Consensus size: 21
68872 AGCAAAAATG
*
68882 GTATCGATACCATAGGAAGGA
1 GTATCGATACCATAGTAAGGA
*
68903 --ATCGATACCATAGTATGGTA
1 GTATCGATACCATAGTAAGG-A
*
68923 GTATCGATACCATGGTAAGG-
1 GTATCGATACCATAGTAAGGA
68943 GTATCGATAC
1 GTATCGATAC
68953 TAGGTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 16 0.37
20 11 0.26
22 16 0.37
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (21 bp):
GTATCGATACCATAGTAAGGA
Found at i:68986 original size:95 final size:94
Alignment explanation
Indices: 68875--69047 Score: 244
Period size: 95 Copynumber: 1.8 Consensus size: 94
68865 AACATAAAGC
*
68875 AAAAATGGTATCGATACC-ATAGGAAGGAATC-G-ATACCATAGTATGGTAGTATCGATACCATG
1 AAAAATGGTATCGATACCGA-AGG-AGGAATCAGTATA--ATAGTATAGTAGTATCGATACCATG
68937 GTAAGGGTATCGATACTAGGTAATATCGAATCT
62 GTAAGGGTATCGATACTAGGTAATATCGAATCT
* * *
68970 AAAATTGGTATCGATACCGGAAGGGGGTATCAGTATAATAGTATAGTAGTATCGATACCATGGTA
1 AAAAATGGTATCGATACC-GAAGGAGGAATCAGTATAATAGTATAGTAGTATCGATACCATGGTA
69035 AGGGTATCGATAC
65 AGGGTATCGATAC
69048 CATGGAGCCA
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
95 62 0.89
96 4 0.06
97 4 0.06
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (94 bp):
AAAAATGGTATCGATACCGAAGGAGGAATCAGTATAATAGTATAGTAGTATCGATACCATGGTAA
GGGTATCGATACTAGGTAATATCGAATCT
Found at i:69443 original size:54 final size:54
Alignment explanation
Indices: 69377--69796 Score: 491
Period size: 54 Copynumber: 7.8 Consensus size: 54
69367 AACAGTCACT
* * *
69377 AAGTGTTCATTTCTCGGAATTCATCGTATGTGGATGAATAACCGTTTCGGCACA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* ** * * * * * *
69431 AAGTGTGTATTTCACATAATTTATCCTATGGGGATGAATAAACGTTTTGGTACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * *
69485 AAGTGTGTATTTCACAGAATTCATCCTATGTGGATGGAA-AACCGTTTCGGTACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGAT-GAATAACCGTTTCGGCACA
* * * * * * *
69539 AAGTGTACGTTTCACGGAATTCATCTTAAGTGGATGAATAATCATTTCGGCATA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * * *
69593 AATTGTGCATTTCACAGAATTCATCCTATGAGGATGAATAATCGTTTCGGCACC
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * * * *
69647 AAGTGTGCATTTCATGGAATTTATCCTATGTGGATGAATAACCATTTCGACACT
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
*
69701 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATA
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
* * *
69755 AAGTGTACATTTCACGGAATTCATCATATGGGGATGAATAAC
1 AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAAC
69797 ACTAAGTACG
Statistics
Matches: 308, Mismatches: 56, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 3 0.01
54 302 0.98
55 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (54 bp):
AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACA
Found at i:69653 original size:162 final size:162
Alignment explanation
Indices: 69373--69795 Score: 569
Period size: 162 Copynumber: 2.6 Consensus size: 162
69363 ACCAAACAGT
* * * *
69373 CACTAAGTGTTCATTTCTCGGAATTCATCGTATGTGGATGAATAACCGTTTCGGCACAAAGTGTG
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* * * * * * *
69438 TATTTCACATAATTTATCCTATGGGGATGAATAAACGTTTTGGTACTAAGTGTGTATTTCACAGA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
* *
69503 ATTCATCCTATGTGGATGGAA-AACCGTTTCGG
131 ATTCATCCTATGTGGAT-GAATAACCATTTCGA
* * * * * * *
69535 TACTAAGTGTACGTTTCACGGAATTCATCTTAAGTGGATGAATAATCATTTCGGCATAAATTGTG
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* * **
69600 CATTTCACAGAATTCATCCTATGAGGATGAATAATCGTTTCGGCACCAAGTGTGCATTTCATGGA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
*
69665 ATTTATCCTATGTGGATGAATAACCATTTCGA
131 ATTCATCCTATGTGGATGAATAACCATTTCGA
* *
69697 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTA
1 CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
* *
69762 CATTTCACGGAATTCATCATATGGGGATGAATAA
66 CATTTCACAGAATTCATCCTATGGGGATGAATAA
69796 CACTAAGTAC
Statistics
Matches: 224, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
161 3 0.01
162 221 0.99
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (162 bp):
CACTAAGTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATAAAGTGTG
CATTTCACAGAATTCATCCTATGGGGATGAATAAACGTTTCGGCACCAAGTGTGCATTTCACAGA
ATTCATCCTATGTGGATGAATAACCATTTCGA
Done.