Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016217.1 Corchorus capsularis cultivar CVL-1 contig16238, 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: 142413
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:3964 original size:33 final size:33
Alignment explanation
Indices: 3924--3990 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3914 TGGCATGGGG
3924 CAACCGGCCACAACCGGCCATCGCATGGAGCAT
1 CAACCGGCCACAACCGGCCATCGCATGGAGCAT
* *
3957 CAACCGGCCACAACCGGCTATCGCATGGGGCAT
1 CAACCGGCCACAACCGGCCATCGCATGGAGCAT
3990 C
1 C
3991 CGCGCACAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.39, G:0.25, T:0.10
Consensus pattern (33 bp):
CAACCGGCCACAACCGGCCATCGCATGGAGCAT
Found at i:4001 original size:30 final size:31
Alignment explanation
Indices: 3916--4006 Score: 107
Period size: 33 Copynumber: 2.9 Consensus size: 31
3906 ATGCTCAATG
*
3916 GCATGGGGCAACCG-GCCACAACCGGCCATC
1 GCATGGGGCATCCGCGCCACAACCGGCCATC
* *
3946 GCATGGAGCATCAAC-CGGCCACAACCGGCTATC
1 GCATGGGGCATC--CGC-GCCACAACCGGCCATC
3979 GCATGGGGCATCCGCG-CACAACCGGCCA
1 GCATGGGGCATCCGCGCCACAACCGGCCA
4007 ATGGATCCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
30 21 0.41
31 2 0.04
32 2 0.04
33 26 0.51
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (31 bp):
GCATGGGGCATCCGCGCCACAACCGGCCATC
Found at i:5388 original size:21 final size:21
Alignment explanation
Indices: 5358--5429 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
5348 AGGCTAACCT
*
5358 AGGCGCGGGTCACCCTTACCC
1 AGGCGCGGGTCACCCTTGCCC
*
5379 AGGCGTGGGTCACCCTTGCCC
1 AGGCGCGGGTCACCCTTGCCC
*
5400 AGGTGCGGGTCACCCTTGCCC
1 AGGCGCGGGTCACCCTTGCCC
5421 AGGCGCGGG
1 AGGCGCGGG
5430 CTACACCAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.11, C:0.38, G:0.36, T:0.15
Consensus pattern (21 bp):
AGGCGCGGGTCACCCTTGCCC
Found at i:5503 original size:21 final size:21
Alignment explanation
Indices: 5464--5505 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5454 TATTCCGGAA
*
5464 CCTTGCCCAGGCGCGGGTTAC
1 CCTTGCCCAGGCGCAGGTTAC
*
5485 CCTTGCCCAGGCGTAGGTTAC
1 CCTTGCCCAGGCGCAGGTTAC
5506 ACCAGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.36, G:0.31, T:0.21
Consensus pattern (21 bp):
CCTTGCCCAGGCGCAGGTTAC
Found at i:11835 original size:32 final size:32
Alignment explanation
Indices: 11799--12247 Score: 457
Period size: 32 Copynumber: 13.5 Consensus size: 32
11789 GCCTGACGCT
*
11799 AAGGCCAAGTGTCATCGGCAAGTGCCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* * *
11831 AAGGCCAAGTGCCATCAGCAGGTGCCGATGCT
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* * * *
11863 AAGGCCAAGTGTCATCAGTAGGTGTCGATCCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* *
11895 AAGGCCAAGTGTCATCAGCAGGTGCCGGTGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* *
11927 AACGCCATGTGTCATCGCCAAGGCCAAGTGCCGATGCCC
1 AAGGCCAAGTGTCAT---C-A-G-CAAGTGCCGATG-CC
* * * *
11966 AAGGCCAAGTGCCGACGCCAAGGGTGTCCAAGTCCCGACGCC
1 AAGGCCAAGTGTC-A--TC-A----G--CAAGTGCCGATGCC
* *
12008 AAGGCCAAGTGTCATCAGCAGGTGTCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* * *
12040 AGGGCCAAGTGTCATCAACAGGTGCCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
*
12072 AAGGCCAAGTGTCATCAGCAAGTGTCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
*
12104 AAGGCCAAATGTCATCAGCAAGTGCCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* * * *
12136 AGGGCCAAGTTTCATCAGCAATTACCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* *
12168 AGGGCCAAGTGTCATCAGCAAGTGTCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
* *
12200 AAGGCCAAGTGCCATCAGCAAGTGTCGATGCC
1 AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
*
12232 AAGGCCAAGTGCCATC
1 AAGGCCAAGTGTCATC
12248 GGAGAATGCC
Statistics
Matches: 353, Mismatches: 50, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
32 294 0.83
34 1 0.00
35 1 0.00
36 1 0.00
37 1 0.00
38 11 0.03
39 16 0.05
40 1 0.00
41 1 0.00
42 15 0.04
43 11 0.03
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (32 bp):
AAGGCCAAGTGTCATCAGCAAGTGCCGATGCC
Found at i:12210 original size:19 final size:19
Alignment explanation
Indices: 12186--12242 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
12176 GTGTCATCAG
12186 CAAGTGTCGATGCCAAGGC
1 CAAGTGTCGATGCCAAGGC
*
12205 CAAGTG-CCAT--C-A-G-
1 CAAGTGTCGATGCCAAGGC
12218 CAAGTGTCGATGCCAAGGC
1 CAAGTGTCGATGCCAAGGC
12237 CAAGTG
1 CAAGTG
12243 CCATCGGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
13 6 0.20
14 4 0.13
15 1 0.03
16 2 0.07
17 1 0.03
18 4 0.13
19 12 0.40
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (19 bp):
CAAGTGTCGATGCCAAGGC
Found at i:12545 original size:48 final size:48
Alignment explanation
Indices: 12507--12721 Score: 173
Period size: 48 Copynumber: 4.7 Consensus size: 48
12497 GGTGTTCCCT
* *
12507 CATGATCTTCGGGGGCAAAAAATGGCCGAAATGCCATAGATTAACCAG
1 CATGAGCTTCGGGGGCAAAAAATGGCCAAAATGCCATAGATTAACCAG
*
12555 CATGAGCTTCGGGGGCAAAAATTGGCCAAAATGCCAT--A-T------
1 CATGAGCTTCGGGGGCAAAAAATGGCCAAAATGCCATAGATTAACCAG
*** * * * *
12594 CATGAG-TTCCGGACCCAAAAATTGGCCGAAATGCCATAGGTTAACCAT
1 CATGAGCTT-CGGGGGCAAAAAATGGCCAAAATGCCATAGATTAACCAG
* * * *
12642 CATGAGCTTTGGGGGCAAAAATTGGCCAAAATGCCATAGGTTAACCAT
1 CATGAGCTTCGGGGGCAAAAAATGGCCAAAATGCCATAGATTAACCAG
* ***
12690 CATGAG-TTCCCGACCCAAAAAATGGCCAAAAT
1 CATGAGCTT-CGGGGGCAAAAAATGGCCAAAAT
12722 TAGAAATCCA
Statistics
Matches: 136, Mismatches: 19, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
38 2 0.01
39 30 0.22
42 1 0.01
45 1 0.01
46 1 0.01
47 2 0.01
48 97 0.71
49 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (48 bp):
CATGAGCTTCGGGGGCAAAAAATGGCCAAAATGCCATAGATTAACCAG
Found at i:18673 original size:24 final size:24
Alignment explanation
Indices: 18644--18705 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 24
18634 AGTCTCTAGG
*
18644 AAGAGGAAAAAGAAGAAAGTGAGA
1 AAGAGGAAAAAGAAGAAAGTGAAA
*
18668 ACGAGGAAAAAG--G-AAGTGAAA
1 AAGAGGAAAAAGAAGAAAGTGAAA
*
18689 AAGAGGAAGAAGAAGAA
1 AAGAGGAAAAAGAAGAA
18706 CCTGCTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 17 0.55
22 1 0.03
23 1 0.03
24 12 0.39
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.03
Consensus pattern (24 bp):
AAGAGGAAAAAGAAGAAAGTGAAA
Found at i:24228 original size:133 final size:133
Alignment explanation
Indices: 23958--24198 Score: 432
Period size: 133 Copynumber: 1.8 Consensus size: 133
23948 GCTTGTACTG
*
23958 TTGAATCCACTTGTACTGTTGTTCGAACAATTTCAATATAAGTGAGAAGTAATCAAGCTGCAGAA
1 TTGAATCCACTTGTACTGTTGTTCGAACAATTTCAATATAAATGAGAAGTAATCAAGCTGCAGAA
*
24023 ACTAAGCTTGAGTTCTATCATCTCTCTATTCTTCATTTTTATCTTATCTTTTAATCATATCACAA
66 ACTAAGCTTGAGTTCTATCATCTCTCTATTCTTCATTTTTATCTTAACTTTTAATCATATCACAA
24088 CTT
131 CTT
24091 TTGAATCCACTTGTACTGTTGTTCGAACAATTTCAATATAAATGAGAAGTAATCAAGCTGCAGAA
1 TTGAATCCACTTGTACTGTTGTTCGAACAATTTCAATATAAATGAGAAGTAATCAAGCTGCAGAA
* *
24156 ATTAAGCTTGAGTTCTATCATCTCTGT-TT-TTCATTTTTATCTT
66 ACTAAGCTTGAGTTCTATCATCTCTCTATTCTTCATTTTTATCTT
24199 TTAAACTTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
131 14 0.13
132 2 0.02
133 89 0.85
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (133 bp):
TTGAATCCACTTGTACTGTTGTTCGAACAATTTCAATATAAATGAGAAGTAATCAAGCTGCAGAA
ACTAAGCTTGAGTTCTATCATCTCTCTATTCTTCATTTTTATCTTAACTTTTAATCATATCACAA
CTT
Found at i:31253 original size:21 final size:21
Alignment explanation
Indices: 31227--31267 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31217 AGAGCATGGA
*
31227 GATGGAACAGTGACTGAAAGG
1 GATGGAACAATGACTGAAAGG
31248 GATGGAACAATGACTGAAAG
1 GATGGAACAATGACTGAAAG
31268 AGCATGTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.34, T:0.15
Consensus pattern (21 bp):
GATGGAACAATGACTGAAAGG
Found at i:34815 original size:21 final size:20
Alignment explanation
Indices: 34791--34963 Score: 126
Period size: 21 Copynumber: 8.4 Consensus size: 20
34781 ACTCTTTGAA
* *
34791 TTACTGATCACCTTTTACTTT
1 TTACTGATTACCTTTTAC-TC
*
34812 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
* *
34833 TTACTAATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
34854 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
34875 TTACTGATTACC---T--T-
1 TTACTGATTACCTTTTACTC
34889 TTACTGATTA-CTATTTAACTC
1 TTACTGATTACCT-TTT-ACTC
*
34910 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
*
34932 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
34955 TTACTGATT
1 TTACTGATT
34964 TCTATTTTTA
Statistics
Matches: 123, Mismatches: 13, Indels: 31
0.74 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 10 0.08
15 1 0.01
17 2 0.02
20 1 0.01
21 58 0.47
22 45 0.37
23 4 0.03
24 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:34858 original size:42 final size:41
Alignment explanation
Indices: 34812--34943 Score: 159
Period size: 42 Copynumber: 3.3 Consensus size: 41
34802 CTTTTACTTT
*
34812 TTACTGATTACTATTTTACTCTTACTAATTACCATTTTGCTC
1 TTACTGATTACTATTTTACTCTTACTGATTACCATTTT-CTC
34854 TTACTGATTACTATTTTACTCTTACTGATTACC----T-T-
1 TTACTGATTACTATTTTACTCTTACTGATTACCATTTTCTC
* *
34889 TTACTGATTACTATTTAACTCTTTACTGATTACTATTTTACTC
1 TTACTGATTACTATTTTACTC-TTACTGATTACCATTTT-CTC
34932 TTTACTGATTAC
1 -TTACTGATTAC
34944 CTTCTTACTT
Statistics
Matches: 78, Mismatches: 3, Indels: 16
0.80 0.03 0.16
Matches are distributed among these distances:
35 20 0.26
36 12 0.15
38 1 0.01
40 1 0.01
42 33 0.42
44 11 0.14
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (41 bp):
TTACTGATTACTATTTTACTCTTACTGATTACCATTTTCTC
Found at i:34893 original size:35 final size:37
Alignment explanation
Indices: 34854--34930 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
34844 CATTTTGCTC
* *
34854 TTACTGATTACTATTTTACTC-TTACTGATTAC-CTT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
34889 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
34926 TTACT
1 TTACT
34931 CTTTACTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 20 0.53
36 11 0.29
37 7 0.18
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (37 bp):
TTACTGATTACTATTTAACTCTTTACTGATTACTATT
Found at i:34914 original size:22 final size:22
Alignment explanation
Indices: 34888--34979 Score: 123
Period size: 22 Copynumber: 4.1 Consensus size: 22
34878 CTGATTACCT
*
34888 TTTACTGATTACTATTTAACTC
1 TTTACTGATTACTATTTTACTC
34910 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
34932 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
34954 TTTACTGATTTCTATTTTTACTC
1 TTTACTGATTACTA-TTTTACTC
34977 TTT
1 TTT
34980 TTTACTTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.03
22 48 0.79
23 11 0.18
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:35008 original size:27 final size:26
Alignment explanation
Indices: 34951--35159 Score: 185
Period size: 27 Copynumber: 7.8 Consensus size: 26
34941 TACCTTCTTA
* * *
34951 CTTTTTACTGATTTCTA-TTTTTACT
1 CTTTTTACTGAATACCATTTTTTACT
* *
34976 CTTTTTTACTTATTACCATTTTCTTACT
1 C-TTTTTACTGAATACCATTTT-TTACT
*
35004 CTTTTTACTGATTATCC-TTTTCTTACT
1 CTTTTTACTGAATA-CCATTTT-TTACT
35031 -TTTTTACTGAATACCATTTTTTACT
1 CTTTTTACTGAATACCATTTTTTACT
*
35056 CTTTTTTACTGAATACCA-TTTTTATT
1 C-TTTTTACTGAATACCATTTTTTACT
*
35082 CTTTTTACCACTGAATACCA-TTTTAACT
1 CTTTTT---ACTGAATACCATTTTTTACT
*
35110 CCTTTTTTACTGAATACCATTTTTTATT
1 -C-TTTTTACTGAATACCATTTTTTACT
* *
35138 CTTTTCTACTTATTACCATTTT
1 CTTTT-TACTGAATACCATTTT
35160 CACTTTACTA
Statistics
Matches: 158, Mismatches: 12, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
25 13 0.08
26 41 0.26
27 67 0.42
28 31 0.20
29 1 0.01
30 5 0.03
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.57
Consensus pattern (26 bp):
CTTTTTACTGAATACCATTTTTTACT
Found at i:35010 original size:53 final size:54
Alignment explanation
Indices: 34910--35160 Score: 194
Period size: 53 Copynumber: 4.8 Consensus size: 54
34900 TATTTAACTC
34910 TTTACTGATTACTA-TTTTACTC---TTTACTGATTACC---TTCTTA--C-TT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTTT
* *
34954 TTTACTGATTTCTATTTTTACTCTTTTTTACTTATTACCATTTTCTTACTC-TT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTTT
*
35007 TTTACTGATTATCCT-TTTCTTA--CTTTTTTACTGAATACCATTTT-TTACTCTTT
1 TTTACTGATTA--CTATTT-TTACTCTTTTTTACTGATTACCATTTTCTTACTCTTT
* * * * * *
35060 TTTACTGAATACCATTTTTATTCTTTTTACCACTGAATACCA-TTT-TAACTCCTTT
1 TTTACTGATTACTATTTTTACTCTTTTT--TACTGATTACCATTTTCTTACT-CTTT
* * * * *
35115 TTTACTGAATACCATTTTTTATTCTTTTCTACTTATTACCATTTTC
1 TTTACTGATTACTA-TTTTTACTCTTTTTTACTGATTACCATTTTC
35161 ACTTTACTAA
Statistics
Matches: 172, Mismatches: 13, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
44 13 0.08
45 8 0.05
48 12 0.07
51 10 0.06
52 9 0.05
53 51 0.30
54 19 0.11
55 37 0.22
56 13 0.08
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.56
Consensus pattern (54 bp):
TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTTT
Found at i:35116 original size:55 final size:56
Alignment explanation
Indices: 35036--35142 Score: 182
Period size: 55 Copynumber: 1.9 Consensus size: 56
35026 TTACTTTTTT
*
35036 ACTGAATACCATTTTTTACTCTTTTTTACTGAATACCA-TTTTTATTCTTTTTACC
1 ACTGAATACCATTTTTAACTCTTTTTTACTGAATACCATTTTTTATTCTTTTTACC
35091 ACTGAATACCA-TTTTAACTCCTTTTTTACTGAATACCATTTTTTATTCTTTT
1 ACTGAATACCATTTTTAACT-CTTTTTTACTGAATACCATTTTTTATTCTTTT
35143 CTACTTATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
54 7 0.14
55 29 0.59
56 13 0.27
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.52
Consensus pattern (56 bp):
ACTGAATACCATTTTTAACTCTTTTTTACTGAATACCATTTTTTATTCTTTTTACC
Found at i:35168 original size:21 final size:21
Alignment explanation
Indices: 35144--35188 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35134 TATTCTTTTC
* *
35144 TACTTATTACCATTTTCACTT
1 TACTAATTACCATTTACACTT
* *
35165 TACTAATTACTATTTACTCTT
1 TACTAATTACCATTTACACTT
35186 TAC
1 TAC
35189 CATTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (21 bp):
TACTAATTACCATTTACACTT
Found at i:35210 original size:36 final size:36
Alignment explanation
Indices: 35144--35416 Score: 381
Period size: 36 Copynumber: 7.6 Consensus size: 36
35134 TATTCTTTTC
* * * *
35144 TACTTATTACCATTTT-CACTTTACTAATTACTATT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
35179 TACTCTTTACCATTTTACTTTTTACTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
35215 TACTTTTTACCATTTTACCCTTTACTGATTATTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
35251 TACTTTTTACCATTTTACCCTTTCCTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
*
35287 TACTTTTTACCATTTTACTCTTTACTGATTACTATT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
*
35323 TACTTTTTACCATTATACTCTTTACTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
35359 TACTCTTTACCATTTTACTCTTTACTGATT-TTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
*
35394 T-GTTCTTTACCATTTTACTCTTT
1 TACTT-TTTACCATTTTACTCTTT
35417 TTAACTTGAT
Statistics
Matches: 214, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
34 1 0.00
35 37 0.17
36 176 0.82
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (36 bp):
TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
Found at i:35484 original size:40 final size:40
Alignment explanation
Indices: 35440--35528 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
35430 TAAATACCAT
**
35440 CTTTTGAC-CTTAATTACTGATATACTGACT-ACTTCTTTTA
1 CTTTT-ACTCTTAATTACCAATATACTG-CTCACTTCTTTTA
* *
35480 CTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTA
1 CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
35520 CTTTTACTC
1 CTTTTACTC
35529 CATTCTACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.49
Consensus pattern (40 bp):
CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
Found at i:35550 original size:32 final size:32
Alignment explanation
Indices: 35511--35783 Score: 221
Period size: 32 Copynumber: 8.1 Consensus size: 32
35501 TTACTGCTCC
*
35511 CTTCTTTTACTTTTACTCCATTCTACT-AATA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
*
35542 TCTTCTTTTACCTTGATTCTTAATTACCCATT-TACTGATTA
1 -CTTCTTTTA-C----TT-TT-ACT--CCATTCTACTGATTA
* *
35583 CTTCTTTTACTCTTACTCCATTCTGCTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
* * *
35615 CCTT-TTTTACTTTTACTCAATTCTATTGATTG
1 -CTTCTTTTACTTTTACTCCATTCTACTGATTA
*
35647 CTTATTTTACTTTTACTTACTCCATTCTACTGATTA
1 CTTCTTTTAC--TT--TTACTCCATTCTACTGATTA
* *
35683 TTTCTTTTACTTTTACTCCATTTTACTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
* *
35715 CTTCCTCTTACCTTTACTCCATT-TACTGATTA
1 CTT-CTTTTACTTTTACTCCATTCTACTGATTA
* * **
35747 CTTCCTCTTACTTTCACTCCATTCTACCAATTA
1 CTT-CTTTTACTTTTACTCCATTCTACTGATTA
35780 CTTC
1 CTTC
35784 CTCTTTTACT
Statistics
Matches: 199, Mismatches: 23, Indels: 38
0.77 0.09 0.15
Matches are distributed among these distances:
31 8 0.04
32 98 0.49
33 33 0.17
34 6 0.03
35 1 0.01
36 25 0.13
37 2 0.01
38 2 0.01
39 3 0.02
40 13 0.07
41 8 0.04
ACGTcount: A:0.20, C:0.26, G:0.03, T:0.51
Consensus pattern (32 bp):
CTTCTTTTACTTTTACTCCATTCTACTGATTA
Found at i:35563 original size:72 final size:72
Alignment explanation
Indices: 35471--35606 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
35461 ATACTGACTA
* * * * *
35471 CTTCTTTTACTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTACTCCATTCTA
1 CTTCTTTTACCTTGACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCTA
35536 CTAATAT
66 CTAATAT
* * *
35543 CTTCTTTTACCTTGATTCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTACTCCATTCT
1 CTTCTTTTACCTTGACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCT
35607 GCTGATTACC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.20, C:0.26, G:0.02, T:0.51
Consensus pattern (72 bp):
CTTCTTTTACCTTGACTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCTA
CTAATAT
Found at i:35623 original size:72 final size:72
Alignment explanation
Indices: 35471--35624 Score: 193
Period size: 72 Copynumber: 2.1 Consensus size: 72
35461 ATACTGACTA
* * * * * *
35471 CTTCTTTTACTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTACTCCATTCTA
1 CTTCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCTA
*
35536 CTAATAT
66 CTAATAC
* * *
35543 CTTCTTTTACCTTGATTCTTAATTACCCATTTACTGATTACTTCTTTTACTCTTACTCCATTCTG
1 CTTCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCTA
*
35608 CTGATTAC
66 CT-AATAC
35616 CTT-TTTTAC
1 CTTCTTTTAC
35625 TTTTACTCAA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
72 64 0.91
73 6 0.09
ACGTcount: A:0.19, C:0.26, G:0.03, T:0.51
Consensus pattern (72 bp):
CTTCTTTTACCTTGATTCTTAATTACCAATTTACTGATCACTTCTTTTACTCTTACTCCATTCTA
CTAATAC
Found at i:35674 original size:36 final size:36
Alignment explanation
Indices: 35627--35699 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
35617 TTTTTTACTT
* *
35627 TTACTCAATTCTATTGATTGCTTATTTTACTTTTAC
1 TTACTCAATTCTACTGATTACTTATTTTACTTTTAC
* * *
35663 TTACTCCATTCTACTGATTATTTCTTTTACTTTTAC
1 TTACTCAATTCTACTGATTACTTATTTTACTTTTAC
35699 T
1 T
35700 CCATTTTACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.04, T:0.56
Consensus pattern (36 bp):
TTACTCAATTCTACTGATTACTTATTTTACTTTTAC
Found at i:35725 original size:17 final size:17
Alignment explanation
Indices: 35705--35758 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
35695 TTACTCCATT
35705 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
35722 TTACCT--TTAC-TCCAT-
1 TTA-CTGATTACTTCC-TC
35737 TTACTGATTACTTCCTC
1 TTACTGATTACTTCCTC
35754 TTACT
1 TTACT
35759 TTCACTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.06
15 6 0.19
16 10 0.32
17 11 0.35
18 2 0.06
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.48
Consensus pattern (17 bp):
TTACTGATTACTTCCTC
Found at i:35766 original size:65 final size:65
Alignment explanation
Indices: 35663--35788 Score: 182
Period size: 65 Copynumber: 1.9 Consensus size: 65
35653 TTACTTTTAC
* * * * **
35663 TTACTCCATTCTACTGATTATTTCTTTTACTTTTACTCCATTTTACTGATTACTTCCTCTTACCT
1 TTACTCCATTCTACTGATTATTCCTCTTACTTTCACTCCATTCTACCAATTACTTCCTCTTACCT
35728 TTACTCCATT-TACTGATTACTTCCTCTTACTTTCACTCCATTCTACCAATTACTTCCTCTT
1 TTACTCCATTCTACTGATTA-TTCCTCTTACTTTCACTCCATTCTACCAATTACTTCCTCTT
35789 TTACTTCTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 9 0.17
65 45 0.83
ACGTcount: A:0.19, C:0.29, G:0.02, T:0.49
Consensus pattern (65 bp):
TTACTCCATTCTACTGATTATTCCTCTTACTTTCACTCCATTCTACCAATTACTTCCTCTTACCT
Found at i:39278 original size:25 final size:24
Alignment explanation
Indices: 39228--39298 Score: 106
Period size: 25 Copynumber: 2.9 Consensus size: 24
39218 TAATGAACTA
* * *
39228 AAAATGACTAAAGTGCCCCTAGTC
1 AAAATGACCAAAATGCCCCTGGTC
39252 AAAATGACCAAAATGCCCCTGGTTC
1 AAAATGACCAAAATGCCCCTGG-TC
39277 AAAATGACCAAAATGCCCCTGG
1 AAAATGACCAAAATGCCCCTGG
39299 GTGACTTCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 19 0.44
25 24 0.56
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.18
Consensus pattern (24 bp):
AAAATGACCAAAATGCCCCTGGTC
Found at i:39759 original size:66 final size:64
Alignment explanation
Indices: 39650--39785 Score: 209
Period size: 66 Copynumber: 2.1 Consensus size: 64
39640 TGATTCTTCG
* *
39650 ACTAGTCTAACAAAGTAGTCTCGAGGCCTTGAGATACCCAAAAAAGCAAGGGTGAGGATCCTCTC
1 ACTAGTCTAACAAAGTAGTCTCGAGGCCTTGAGATA-CCAAAAAACCAA-GATGAGGATCCTCTC
39715 C
64 C
* * *
39716 GCTAGTCTAACAAAGTAGTCTTGAGGCCTTGAGATACCAAAAAACCAAGATGAGGATCCTTTCC
1 ACTAGTCTAACAAAGTAGTCTCGAGGCCTTGAGATACCAAAAAACCAAGATGAGGATCCTCTCC
39780 ACTAGT
1 ACTAGT
39786 AGACCTGTCC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 19 0.30
65 11 0.17
66 34 0.53
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (64 bp):
ACTAGTCTAACAAAGTAGTCTCGAGGCCTTGAGATACCAAAAAACCAAGATGAGGATCCTCTCC
Found at i:42969 original size:69 final size:67
Alignment explanation
Indices: 42883--43053 Score: 229
Period size: 69 Copynumber: 2.5 Consensus size: 67
42873 AATCCTTTGA
* *
42883 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAGTCTAAGACTTTGTTCCATCC-AAGTAAC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTCTAAGACTTGGTTCCATCCAAAGT---
42947 AAGGG
63 AAGGG
* * * *
42952 CTTTTCTC-TAAGCCAAACTCGTTTCCGTACAAGTCAGTTTAAGCCTTGGTTCCATCCAAAGTAA
1 CTTTTC-CATAAGCCAAACTCGTTTCCATACGAGTCAGTCTAAGACTTGGTTCCATCCAAAGTAA
43016 GGG
65 GGG
*
43019 CTTTTCCATTAGCCAAACTCGTTTCCATACGAGTC
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTC
43054 TGCAATTTGG
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
66 1 0.01
67 35 0.39
69 49 0.54
70 5 0.06
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (67 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTCTAAGACTTGGTTCCATCCAAAGTAAG
GG
Found at i:43149 original size:29 final size:29
Alignment explanation
Indices: 43108--43167 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
43098 GTTTGAAATC
*
43108 TCTTCGACTCAAGCTGCTTTTTCCTCACT
1 TCTTCGACTCAAGCTGCTCTTTCCTCACT
* * *
43137 TCTTCGAAC-CAAGTTGGTCTTTCCTCGCT
1 TCTTCG-ACTCAAGCTGCTCTTTCCTCACT
43166 TC
1 TC
43168 AATGTGAGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.40
Consensus pattern (29 bp):
TCTTCGACTCAAGCTGCTCTTTCCTCACT
Found at i:49594 original size:2 final size:2
Alignment explanation
Indices: 49587--49616 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49577 TTGCTCACAA
49587 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
49617 ACACCTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:51386 original size:18 final size:18
Alignment explanation
Indices: 51363--51400 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
51353 TCTCCTTTAA
*
51363 GCTTGTCTATGCTTCCTT
1 GCTTGTCCATGCTTCCTT
51381 GCTTGTCCATGCTTCCTT
1 GCTTGTCCATGCTTCCTT
51399 GC
1 GC
51401 AATCCTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.32, G:0.18, T:0.45
Consensus pattern (18 bp):
GCTTGTCCATGCTTCCTT
Found at i:54046 original size:6 final size:6
Alignment explanation
Indices: 54035--54066 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54025 ATTAATCTGC
54035 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
54067 GCTTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:54813 original size:62 final size:62
Alignment explanation
Indices: 54578--54819 Score: 268
Period size: 62 Copynumber: 3.9 Consensus size: 62
54568 TAGGACAAAC
* * * ** *
54578 CTTTCTTAGTTTGTAAAGTCGACCATGGATTGGTCTTCTTCAAATTCAAACCTCAGACATGT
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGACAAGT
* * * *
54640 CTTTCTTAGTTTTTAAAGTCGACCACAGACTAGTCTTCTTCAGCTTCAGACCTCAGACAAGT
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGACAAGT
* * * * * * * *
54702 CTTTTCTTAGTTTTTTAAAGTTGACCACCGACTGGCCTACTTCATTTTCAAACCTTAGAGAGGT
1 C-TTTCTTAG-TTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGACAAGT
* * * *
54766 CTTTCTTAGTTTTTAAAATTGACCACGGATTGGTCTTCTTCAGTTTCAGACCTC
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTC
54820 GGATTGGTCT
Statistics
Matches: 150, Mismatches: 28, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
62 91 0.61
63 16 0.11
64 43 0.29
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (62 bp):
CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGACAAGT
Found at i:54829 original size:62 final size:62
Alignment explanation
Indices: 54578--54874 Score: 260
Period size: 62 Copynumber: 4.8 Consensus size: 62
54568 TAGGACAAAC
* * * ** * *
54578 CTTTCTTAGTTTGTAAAGTCGACCATGGATTGGTCTTCTTCAAATTCAAACCTCAGACATGT
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGAAAGGT
* * * *
54640 CTTTCTTAGTTTTTAAAGTCGACCACAGACTAGTCTTCTTCAGCTTCAGACCTCAGACAA-GT
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGA-AAGGT
* * * * * * *
54702 CTTTTCTTAGTTTTTTAAAGTTGACCACCGACTGGCCTACTTCATTTTCAAACCTTAGAGAGGT
1 C-TTTCTTAG-TTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGAAAGGT
* * * * * **
54766 CTTTCTTAGTTTTTAAAATTGACCACGGATTGGTCTTCTTCAGTTTCAGACCTCGGATTGGT
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGAAAGGT
* * * * *
54828 CTTCCTCA-ATTTTACA-TCGACCACAGACTGGTC-TCATTCAGTTTCAA
1 CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTC-TTCAGTTTCAA
54875 CATCAGCAAT
Statistics
Matches: 192, Mismatches: 38, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
59 2 0.01
60 24 0.12
61 6 0.03
62 100 0.52
63 18 0.09
64 42 0.22
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (62 bp):
CTTTCTTAGTTTTTAAAGTCGACCACGGACTGGTCTTCTTCAGTTTCAAACCTCAGAAAGGT
Found at i:66510 original size:342 final size:342
Alignment explanation
Indices: 65885--66518 Score: 1223
Period size: 342 Copynumber: 1.9 Consensus size: 342
65875 TGCTCTTGAA
* *
65885 GAGGAAATTGATAGTCTGACCATTGATGACACTGGCTCAGAATCTGATGAAGAGACTGAAATTCA
1 GAGGAAATTGATAGTCTAACCATTGATGACACTGGCTCAAAATCTGATGAAGAGACTGAAATTCA
65950 AAGAAGAAGAAGAAACAAGAGGAATTTCAAGAAGGATAAATTCAAAGCAGAAGTCAGCAAACAAA
66 AAGAAGAAGAAGAAACAAGAGGAATTTCAAGAAGGATAAATTCAAAGCAGAAGTCAGCAAACAAA
* *
66015 ACCAGCTGATTTTCTATGAATGTAGAAAGCCTTGTCACACCAAGAATGACTGTCCACTGAACAGT
131 ACCAACTGATTTTCTATGAATGTAGAAAGCCTTGTCACACCAAGAATGACTATCCACTGAACAGT
66080 GCTAAGAATCAAAAGAAAACCAGAAAGAAAAAGAAGGCAATGATGTCTTCAACATGGTCTAACAT
196 GCTAAGAATCAAAAGAAAACCAGAAAGAAAAAGAAGGCAATGATGTCTTCAACATGGTCTAACAT
66145 TGACACTTCTTTAGCTGAAGCAAGTGATGAAGAGGAAGACATCAAAGCCAACCTGTTCCTCACGA
261 TGACACTTCTTTAGCTGAAGCAAGTGATGAAGAGGAAGACATCAAAGCCAACCTGTTCCTCACGA
66210 CAAAGGAAGATGAACCT
326 CAAAGGAAGATGAACCT
66227 GAGGAAATTGATAGTCTAACCATTGATGACACTGGCTCAAAATCTGATGAAGAGACTGAAATTCA
1 GAGGAAATTGATAGTCTAACCATTGATGACACTGGCTCAAAATCTGATGAAGAGACTGAAATTCA
66292 AAGAAGAAGAAGAAACAAGAGGAATTTCAAGAAGGATAAATTCAAAGCAGAAGTCAGCAAACAAA
66 AAGAAGAAGAAGAAACAAGAGGAATTTCAAGAAGGATAAATTCAAAGCAGAAGTCAGCAAACAAA
66357 ACCAACTGATTTTCTATGAATGTAGAAAGCCTTGTCACACCAAGAATGACTATCCACTGAACAGT
131 ACCAACTGATTTTCTATGAATGTAGAAAGCCTTGTCACACCAAGAATGACTATCCACTGAACAGT
*
66422 GCTAAGAATCAAAAGAAAAGCAGAAAGAAAAAGAAGGCAATGATGTCTTCAACATGGTCTAACAT
196 GCTAAGAATCAAAAGAAAACCAGAAAGAAAAAGAAGGCAATGATGTCTTCAACATGGTCTAACAT
66487 TGACACTTCTTTAGCTGAAGCAAGTGATGAAG
261 TGACACTTCTTTAGCTGAAGCAAGTGATGAAG
66519 GATAGCTTGA
Statistics
Matches: 287, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
342 287 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.20
Consensus pattern (342 bp):
GAGGAAATTGATAGTCTAACCATTGATGACACTGGCTCAAAATCTGATGAAGAGACTGAAATTCA
AAGAAGAAGAAGAAACAAGAGGAATTTCAAGAAGGATAAATTCAAAGCAGAAGTCAGCAAACAAA
ACCAACTGATTTTCTATGAATGTAGAAAGCCTTGTCACACCAAGAATGACTATCCACTGAACAGT
GCTAAGAATCAAAAGAAAACCAGAAAGAAAAAGAAGGCAATGATGTCTTCAACATGGTCTAACAT
TGACACTTCTTTAGCTGAAGCAAGTGATGAAGAGGAAGACATCAAAGCCAACCTGTTCCTCACGA
CAAAGGAAGATGAACCT
Found at i:70019 original size:15 final size:15
Alignment explanation
Indices: 69999--70030 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
69989 CCATGGACGA
69999 GACAGATACAGAAAT
1 GACAGATACAGAAAT
*
70014 GACAGATTCAGAAAT
1 GACAGATACAGAAAT
70029 GA
1 GA
70031 AGAAGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (15 bp):
GACAGATACAGAAAT
Found at i:79236 original size:31 final size:31
Alignment explanation
Indices: 79198--79300 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
79188 GGTTAAATAC
79198 TCAATTCAGGATATAACGTTTA-C-CTTGAAAT-
1 TCAATTCAGGATATAACGTTTACCACTTG---TG
* *
79229 TCAATTCAGGATACACCG-TTACCACTTGTG
1 TCAATTCAGGATATAACGTTTACCACTTGTG
***
79259 TCAATTCAGGATATAACG-TTATCGTTTTGTG
1 TCAATTCAGGATATAACGTTTA-CCACTTGTG
79290 TCAATTCAGGA
1 TCAATTCAGGA
79301 CATGAGGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
29 1 0.02
30 22 0.36
31 34 0.56
32 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (31 bp):
TCAATTCAGGATATAACGTTTACCACTTGTG
Found at i:79263 original size:30 final size:31
Alignment explanation
Indices: 79229--79300 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
79219 ACCTTGAAAT
*
79229 TCAATTCAGGATACACCGTTA-CCACTTGTG
1 TCAATTCAGGATACAACGTTATCCACTTGTG
* ***
79259 TCAATTCAGGATATAACGTTATCGTTTTGTG
1 TCAATTCAGGATACAACGTTATCCACTTGTG
79290 TCAATTCAGGA
1 TCAATTCAGGA
79301 CATGAGGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (31 bp):
TCAATTCAGGATACAACGTTATCCACTTGTG
Found at i:79639 original size:21 final size:21
Alignment explanation
Indices: 79615--79657 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
79605 AAATGAACTT
*
79615 CACCTGGAAAATAAGAACAAC
1 CACCTGAAAAATAAGAACAAC
*
79636 CACCTGAAAAATAAGAATAAC
1 CACCTGAAAAATAAGAACAAC
79657 C
1 C
79658 CACACTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.12
Consensus pattern (21 bp):
CACCTGAAAAATAAGAACAAC
Found at i:80640 original size:30 final size:31
Alignment explanation
Indices: 80588--80653 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
80578 TTTTATCCTG
80588 AATTGACACAAAACGATAACGTTATATACTA
1 AATTGACACAAAACGATAACGTTATATACTA
* * * *
80619 AATTGACACAAGA-GGTAACGTTATATCCTG
1 AATTGACACAAAACGATAACGTTATATACTA
80649 AATTG
1 AATTG
80654 CATTTTGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (31 bp):
AATTGACACAAAACGATAACGTTATATACTA
Found at i:83598 original size:19 final size:19
Alignment explanation
Indices: 83576--83615 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
83566 AAAAGAAACC
83576 AAATCTCTAAGTAAAGACT
1 AAATCTCTAAGTAAAGACT
* * *
83595 AAATTTTTAAGTAAATACT
1 AAATCTCTAAGTAAAGACT
83614 AA
1 AA
83616 TCCAGATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (19 bp):
AAATCTCTAAGTAAAGACT
Found at i:83637 original size:18 final size:18
Alignment explanation
Indices: 83614--83648 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
83604 AGTAAATACT
*
83614 AATCCAGATTAATTCATC
1 AATCCAGATTAAGTCATC
83632 AATCCAGATTAAGTCAT
1 AATCCAGATTAAGTCAT
83649 TTCCAATTTA
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:0.20, G:0.09, T:0.31
Consensus pattern (18 bp):
AATCCAGATTAAGTCATC
Found at i:86767 original size:58 final size:58
Alignment explanation
Indices: 86704--87359 Score: 959
Period size: 58 Copynumber: 11.4 Consensus size: 58
86694 TAAACGCTTT
* * * * * * *
86704 CAGGAACTGTCTTCAGATCCATCCACGAGCAGTCTTCATACTCTTTCTTAAAATTTTT
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
* * * *
86762 TAGGAACTGTCTTTAGAACCATCTATGAGCACTCTTCGTACTCATTCTTAAAGTCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
*
86820 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTTGTACTCATTCTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
* *
86878 CAGGAACTGTCTTCAAAACAATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
* *
86936 TAGGAACTGTCTTCAGAACCATCTATGAGCAATCTTCGTACTCATTCTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
*
86994 CAGGAATTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTC---CTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
* * * *
87049 CAGCAACTGTATTCAAAACCATCTATGAGCAGTCTTCGTACTAATTCTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
*
87107 TAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTT-AAATACTT-
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAAT-CTTC
87164 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTT-AAATACTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAAT-CTTC
* *
87222 CAAGAACTGTCTTTAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAATAAT-TT-
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTT-AA-AATCTTC
* * *
87280 CAGGAATTGTCTTCAGATCCCTCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
1 CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
* *
87338 CAAGAACTGTCTTCAGATCCAT
1 CAGGAACTGTCTTCAGAACCAT
87360 TCTTAAATAT
Statistics
Matches: 541, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
55 50 0.09
56 3 0.01
57 64 0.12
58 418 0.77
59 2 0.00
60 1 0.00
61 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (58 bp):
CAGGAACTGTCTTCAGAACCATCTATGAGCAGTCTTCGTACTCATTCTTAAAATCTTC
Found at i:87381 original size:36 final size:35
Alignment explanation
Indices: 87322--87403 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 35
87312 TCTTCGTACT
87322 CATTCTTAAAATCTTCCAAGAACTGTCTTCAGATC
1 CATTCTTAAAATCTTCCAAGAACTGTCTTCAGATC
*
87357 CATTCTTAAATATCTT-TAAGGAACTGTCTTCAGATC
1 CATTCTTAAA-ATCTTCCAA-GAACTGTCTTCAGATC
87393 CATTCTTAAAA
1 CATTCTTAAAA
87404 GGAAAGTCTC
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
35 13 0.30
36 31 0.70
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (35 bp):
CATTCTTAAAATCTTCCAAGAACTGTCTTCAGATC
Found at i:89441 original size:64 final size:64
Alignment explanation
Indices: 89309--89441 Score: 162
Period size: 64 Copynumber: 2.1 Consensus size: 64
89299 TTTGTTTCTC
* * * *
89309 TTTCTTTTTGCGACCTCTTCCTGTTTTAGGCCCAGTTTATTTATTTTTTTTATTTATATATTTT
1 TTTCTTTTTGCGACCTCTTCCTGTTTTAGGCCCAGTTTATTTATTTTTTATATTTACATATGTA
* * * *
89373 TTTCTTTTTGCGACGTCTTTCTTTTTTAGGCCCAGTTTTTTTATTTTTTAT-TTTAGGCATA-GT
1 TTTCTTTTTGCGACCTCTTCCTGTTTTAGGCCCAGTTTATTTATTTTTTATATTTA--CATATGT
89436 A
64 A
89437 TTTCT
1 TTTCT
89442 GGACTGGATC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 4 0.07
64 52 0.88
65 3 0.05
ACGTcount: A:0.14, C:0.15, G:0.11, T:0.60
Consensus pattern (64 bp):
TTTCTTTTTGCGACCTCTTCCTGTTTTAGGCCCAGTTTATTTATTTTTTATATTTACATATGTA
Found at i:91923 original size:22 final size:22
Alignment explanation
Indices: 91898--91939 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
91888 GTGATATTCG
*
91898 AATAGGATATGAAGA-AAGAATC
1 AATAGAATATG-AGACAAGAATC
91920 AATAGAATATGAGACAAGAA
1 AATAGAATATGAGACAAGAA
91940 AAGAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.17
Consensus pattern (22 bp):
AATAGAATATGAGACAAGAATC
Found at i:98573 original size:21 final size:20
Alignment explanation
Indices: 98549--98721 Score: 135
Period size: 21 Copynumber: 8.4 Consensus size: 20
98539 ACTCTTTGAA
*
98549 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
*
98569 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
* *
98591 TTACTAATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
98612 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
98633 TTACTGATTACC---T--T-
1 TTACTGATTACCTTTTACTC
98647 TTACTGATTA-CTATTTAACTC
1 TTACTGATTACCT-TTT-ACTC
*
98668 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
*
98690 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
98713 TTACTGATT
1 TTACTGATT
98722 TCTATTTTTA
Statistics
Matches: 124, Mismatches: 12, Indels: 31
0.74 0.07 0.19
Matches are distributed among these distances:
13 1 0.01
14 10 0.08
15 1 0.01
17 2 0.02
20 1 0.01
21 57 0.46
22 47 0.38
23 4 0.03
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:98616 original size:42 final size:43
Alignment explanation
Indices: 98549--98737 Score: 184
Period size: 42 Copynumber: 4.6 Consensus size: 43
98539 ACTCTTTGAA
*
98549 TTACTGATCACC-TTTTACTCTTTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
* *
98591 TTACTAATTACCATTTTGCTC-TTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
*
98633 TTACTGATTA-C------CT-TTTACTGATTACTATTTAACTC
1 TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
* * *
98668 TTTACTGATTACTATTTTACTCTTTACTGATTACCT-TCTTACTTT
1 -TTACTGATTACCATTTTACTCTTTACTGATTA-CTATTTTAC-TC
* *
98713 TTACTGATTTCTATTTTTACTCTTT
1 TTACTGATTACCA-TTTTACTCTTT
98738 TTTACTTATT
Statistics
Matches: 123, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
35 22 0.18
36 10 0.08
41 1 0.01
42 40 0.33
43 9 0.07
44 27 0.22
45 14 0.11
ACGTcount: A:0.22, C:0.21, G:0.05, T:0.53
Consensus pattern (43 bp):
TTACTGATTACCATTTTACTCTTTACTGATTACTATTTTACTC
Found at i:98651 original size:35 final size:37
Alignment explanation
Indices: 98612--98688 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
98602 CATTTTGCTC
* *
98612 TTACTGATTACTATTTTACTC-TTACTGATTAC-CTT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
98647 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
1 TTACTGATTACTATTTAACTCTTTACTGATTACTATT
98684 TTACT
1 TTACT
98689 CTTTACTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 20 0.53
36 11 0.29
37 7 0.18
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (37 bp):
TTACTGATTACTATTTAACTCTTTACTGATTACTATT
Found at i:98672 original size:22 final size:22
Alignment explanation
Indices: 98646--98737 Score: 123
Period size: 22 Copynumber: 4.1 Consensus size: 22
98636 CTGATTACCT
*
98646 TTTACTGATTACTATTTAACTC
1 TTTACTGATTACTATTTTACTC
98668 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
98690 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
98712 TTTACTGATTTCTATTTTTACTC
1 TTTACTGATTACTA-TTTTACTC
98735 TTT
1 TTT
98738 TTTACTTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.03
22 48 0.79
23 11 0.18
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:98768 original size:53 final size:53
Alignment explanation
Indices: 98668--98845 Score: 175
Period size: 53 Copynumber: 3.5 Consensus size: 53
98658 TATTTAACTC
98668 TTTACTGATTACTA-TTTTACTC---TTTACTGATTACC---TTCTTA--CTT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
* *
98712 TTTACTGATTTCTATTTTTACTCTTTTTTACTTATTACCATTTTCTTACTCTT
1 TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
*
98765 TTTACTGATTATCCT-TTTCTTA--CTTTTTTACTGAATACCATTTT-TTACTCTTT
1 TTTACTGATTA--CTATTT-TTACTCTTTTTTACTGATTACCATTTTCTTACTC-TT
* * *
98818 TTTACTGAATACCATTTTTATTCTTTTT
1 TTTACTGATTACTATTTTTACTCTTTTT
98846 ACCACTGAAT
Statistics
Matches: 111, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
44 13 0.12
45 8 0.07
48 12 0.11
51 10 0.09
52 9 0.08
53 51 0.46
54 3 0.03
55 5 0.05
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.59
Consensus pattern (53 bp):
TTTACTGATTACTATTTTTACTCTTTTTTACTGATTACCATTTTCTTACTCTT
Found at i:98820 original size:28 final size:27
Alignment explanation
Indices: 98726--98919 Score: 175
Period size: 28 Copynumber: 7.1 Consensus size: 27
98716 CTGATTTCTA
* *
98726 TTTTTACTCTTTTTTACTTATTACCAT
1 TTTTTACTCTTTTTTACTGAATACCAT
*
98753 TTTCTTACTC-TTTTTACTGATTATCC-T
1 TTT-TTACTCTTTTTTACTGAATA-CCAT
98780 TTTCTTA--CTTTTTTACTGAATACCAT
1 TTT-TTACTCTTTTTTACTGAATACCAT
98806 TTTTTACTCTTTTTTACTGAATACCA-
1 TTTTTACTCTTTTTTACTGAATACCAT
* * *
98832 TTTTTATTCTTTTTACCACTGAATATCA-
1 TTTTTACTCTTTTT--TACTGAATACCAT
*
98860 TTTTAACTCCTTTTTTTACTGAATACCATT
1 TTTTTACT-C-TTTTTTACTGAATACCA-T
* * * *
98890 TTTTTATTCTTTTCTACTTATTACCAT
1 TTTTTACTCTTTTTTACTGAATACCAT
98917 TTT
1 TTT
98920 CACTTTACTA
Statistics
Matches: 141, Mismatches: 14, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.04
26 29 0.21
27 45 0.32
28 48 0.34
29 2 0.01
30 11 0.08
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTTTACTCTTTTTTACTGAATACCAT
Found at i:98928 original size:21 final size:21
Alignment explanation
Indices: 98904--98948 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
98894 TATTCTTTTC
* *
98904 TACTTATTACCATTTTCACTT
1 TACTAATTACCATTTACACTT
* *
98925 TACTAATTACTATTTACTCTT
1 TACTAATTACCATTTACACTT
98946 TAC
1 TAC
98949 CATTTTACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (21 bp):
TACTAATTACCATTTACACTT
Found at i:98970 original size:36 final size:36
Alignment explanation
Indices: 98904--99176 Score: 363
Period size: 36 Copynumber: 7.6 Consensus size: 36
98894 TATTCTTTTC
* * * *
98904 TACTTATTACCATTTT-CACTTTACTAATTACTATT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
98939 TACTCTTTACCATTTTACTTTTTACTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
98975 TACTTTTTACCATTTTACCCTTTACTGATTATTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
99011 TACTTTTTACCATTTTACCCTTTCCTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
99047 TAATTTTTACCATTTTACTCTTTACTGATTACTATT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
*
99083 TACTTTTTACCATTATACTCTTTACTGATTACTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
99119 TACTCTTTACCATTTTACTCTTTACTGATT-TTCTT
1 TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
* *
99154 T-GTTCTTTACCCTTTTACTCTTT
1 TACTT-TTTACCATTTTACTCTTT
99177 TTAACTTGAT
Statistics
Matches: 211, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
34 1 0.00
35 36 0.17
36 174 0.82
ACGTcount: A:0.20, C:0.22, G:0.03, T:0.55
Consensus pattern (36 bp):
TACTTTTTACCATTTTACTCTTTACTGATTACTCTT
Found at i:99266 original size:40 final size:40
Alignment explanation
Indices: 99200--99288 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
99190 TAAATACCAT
** *
99200 CTTTTGAC-CTTAATTACTGATATACTGACT-AGTTCTTTTA
1 CTTTT-ACTCTTAATTACCAATATACTG-CTCACTTCTTTTA
* *
99240 CTTTTACTCTTAATTACCAATTTACTGCTCCCTTCTTTTA
1 CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
99280 CTTTTACTC
1 CTTTTACTC
99289 CATTCTACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.10
40 38 0.90
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.49
Consensus pattern (40 bp):
CTTTTACTCTTAATTACCAATATACTGCTCACTTCTTTTA
Found at i:99310 original size:32 final size:32
Alignment explanation
Indices: 99271--99543 Score: 248
Period size: 32 Copynumber: 8.2 Consensus size: 32
99261 TTACTGCTCC
*
99271 CTTCTTTTACTTTTACTCCATTCTACT-AATA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
*
99302 TCTTCTTTTACCTTGATTCTTAATTAACCATT-TACTGATTA
1 -CTTCTTTTA-C----TT-TT-ACT--CCATTCTACTGATTA
* *
99343 CTTCTTTTACTCTTACTCCTATTCTTGCTGATTA
1 CTTCTTTTACTTTTACTCC-ATTC-TACTGATTA
* * *
99377 CCTT-TTTTACTTTTACTCAATTCTATTGATTG
1 -CTTCTTTTACTTTTACTCCATTCTACTGATTA
*
99409 CTTATTTTACTTTTACTCCATTCTACTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
* *
99441 TTTCTTTTACTTTTACTCCATTTTACTGATTA
1 CTTCTTTTACTTTTACTCCATTCTACTGATTA
* *
99473 CTACCTCTTACTTTTACTCCATT-TACTGATTA
1 CT-TCTTTTACTTTTACTCCATTCTACTGATTA
* * *
99505 CTTCCTCTTACTTTCACTCCATTCTACGGATTA
1 CTT-CTTTTACTTTTACTCCATTCTACTGATTA
99538 CTTCTT
1 CTTCTT
99544 CTTTTACTTC
Statistics
Matches: 200, Mismatches: 23, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
31 5 0.03
32 104 0.52
33 36 0.18
34 23 0.12
35 4 0.02
37 2 0.01
38 2 0.01
39 3 0.01
40 13 0.06
41 8 0.04
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.52
Consensus pattern (32 bp):
CTTCTTTTACTTTTACTCCATTCTACTGATTA
Found at i:99325 original size:72 final size:73
Alignment explanation
Indices: 99232--99367 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 73
99222 TACTGACTAG
* * * * *
99232 TTCTTTTACTTTTACTCTTAATT-ACCAATTTACTGCTCCCTTCTTTTACTTTTACTCC-ATTCT
1 TTCTTTTACCTTGACTCTTAATTAACC-ATTTACTGATCACTTCTTTTACTCTTACTCCTATTCT
99295 ACTAATATC
65 ACTAATATC
* *
99304 TTCTTTTACCTTGATTCTTAATTAACCATTTACTGATTACTTCTTTTACTCTTACTCCTATTCT
1 TTCTTTTACCTTGACTCTTAATTAACCATTTACTGATCACTTCTTTTACTCTTACTCCTATTCT
99368 TGCTGATTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
72 47 0.85
73 8 0.15
ACGTcount: A:0.21, C:0.25, G:0.02, T:0.52
Consensus pattern (73 bp):
TTCTTTTACCTTGACTCTTAATTAACCATTTACTGATCACTTCTTTTACTCTTACTCCTATTCTA
CTAATATC
Found at i:99471 original size:64 final size:65
Alignment explanation
Indices: 99329--99540 Score: 236
Period size: 65 Copynumber: 3.3 Consensus size: 65
99319 TCTTAATTAA
* * * *
99329 CCATT-TACTGATTACTTCTTTTACTCTTACTCCTATTCTTGCTGATTACCTT-TTTTACTTTTA
1 CCATTCTACTGATTACTTATTTTACTTTTACTCC-ATTC-TACTGATTACTTTCTTTTACTTTTA
99392 CT
64 CT
* * *
99394 CAATTCTATTGATTGCTTATTTTACTTTTACTCCATTCTACTGATTA-TTTCTTTTACTTTTACT
1 CCATTCTACTGATTACTTATTTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTTTTACT
* * * * *
99458 CCATTTTACTGATTAC-TACCTCTTACTTTTACTCCATT-TACTGATTACTTCCTCTTACTTTCA
1 CCATTCTACTGATTACTTA--TTTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTTTTA
99521 CT
64 CT
*
99523 CCATTCTACGGATTACTT
1 CCATTCTACTGATTACTT
99541 CTTCTTTTAC
Statistics
Matches: 124, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
63 4 0.03
64 42 0.34
65 53 0.43
66 25 0.20
ACGTcount: A:0.19, C:0.25, G:0.05, T:0.51
Consensus pattern (65 bp):
CCATTCTACTGATTACTTATTTTACTTTTACTCCATTCTACTGATTACTTTCTTTTACTTTTACT
Found at i:99483 original size:17 final size:16
Alignment explanation
Indices: 99453--99516 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 16
99443 TCTTTTACTT
*
99453 TTACTCCATTTTACTGA
1 TTACTCC-TCTTACTGA
*
99470 TTACTACCTCTTACT-T
1 TTACT-CCTCTTACTGA
99486 TTACTCCAT-TTACTGA
1 TTACTCC-TCTTACTGA
99502 TTACTTCCTCTTACT
1 TTAC-TCCTCTTACT
99517 TTCACTCCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
15 7 0.18
16 11 0.28
17 19 0.49
18 2 0.05
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.48
Consensus pattern (16 bp):
TTACTCCTCTTACTGA
Found at i:99524 original size:97 final size:98
Alignment explanation
Indices: 99329--99552 Score: 251
Period size: 97 Copynumber: 2.3 Consensus size: 98
99319 TCTTAATTAA
* * * * *
99329 CCATT-TACTGATTACTTCTTTTACTCTTACTCCTATTCTTGCTGATTACCTTTTTTACTTTTAC
1 CCATTCTACTGATTATTTCTTTTACTTTTACTCCTATTCTTACTGATTACCTCTCTTACTTTTAC
* * * *
99393 TCAATTCTATTGATTGCTTATTTTACTTTTACT
66 TCAATTCTACTGATTACTTATCTTACTTTCACT
99426 CCATTCTACTGATTATTTCTTTTACTTTTACTCC-ATT-TTACTGATTA-CTACCTCTTACTTTT
1 CCATTCTACTGATTATTTCTTTTACTTTTACTCCTATTCTTACTGATTACCT--CTCTTACTTTT
* *
99488 ACTCCATT-TACTGATTACTTCCTCTTACTTTCACT
64 ACTCAATTCTACTGATTACTT-ATCTTACTTTCACT
*
99523 CCATTCTACGGATTACTTCTTCTTTTACTT
1 CCATTCTACTGATTA--T-TTCTTTTACTT
99553 CTTTAGCTTA
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
95 2 0.02
96 19 0.18
97 49 0.45
98 26 0.24
99 1 0.01
100 11 0.10
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (98 bp):
CCATTCTACTGATTATTTCTTTTACTTTTACTCCTATTCTTACTGATTACCTCTCTTACTTTTAC
TCAATTCTACTGATTACTTATCTTACTTTCACT
Found at i:103061 original size:25 final size:25
Alignment explanation
Indices: 103011--103083 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
103001 TAATGAACTA
* * *
103011 AAAATGACTAAAGTGTCCCCTAGTTC
1 AAAATGACCAAAATG-CCCCTGGTTC
103037 AAAATGACCAAAATGCCCCTGGTTC
1 AAAATGACCAAAATGCCCCTGGTTC
103062 AAAATGACCAAAATGCCCCTGG
1 AAAATGACCAAAATGCCCCTGG
103084 GTGACTTCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
25 31 0.70
26 13 0.30
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (25 bp):
AAAATGACCAAAATGCCCCTGGTTC
Found at i:103990 original size:39 final size:38
Alignment explanation
Indices: 103936--104048 Score: 131
Period size: 39 Copynumber: 2.9 Consensus size: 38
103926 TAGAGAAGAA
* * *
103936 AATTGTCCTTGTGTTATATGTGTTTAGGGACTTT-AGTAT
1 AATTGCCCCTGTGTTATATGTGTTT-GGGACTTTGAG-AG
*
103975 AGA-TGCCTCTGTGTTATATGTGTTTGAGGACTTTGAGAG
1 A-ATTGCCCCTGTGTTATATGTGTTTG-GGACTTTGAGAG
104014 AATTGCCCCTGTGTTATATGTGTTTGGGGACTTTG
1 AATTGCCCCTGTGTTATATGTGTTT-GGGACTTTG
104049 GGGAGAGATA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
38 2 0.03
39 58 0.91
40 4 0.06
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (38 bp):
AATTGCCCCTGTGTTATATGTGTTTGGGACTTTGAGAG
Found at i:105788 original size:20 final size:20
Alignment explanation
Indices: 105763--105802 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
105753 TGCCATGCTT
*
105763 TTGTCTCTGCCGCAACTATG
1 TTGTCTCTACCGCAACTATG
*
105783 TTGTCTCTACCGCAGCTATG
1 TTGTCTCTACCGCAACTATG
105803 ATACTTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGTCTCTACCGCAACTATG
Found at i:106853 original size:23 final size:23
Alignment explanation
Indices: 106795--106853 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
106785 TTAGCTAATT
*
106795 AAGAAAACTAAAGCAAAATATAA
1 AAGAAAACTAAATCAAAATATAA
* * *
106818 AGGAAATCTAAATCAATATATAA
1 AAGAAAACTAAATCAAAATATAA
*
106841 AAGAAACCTAAAT
1 AAGAAAACTAAAT
106854 ATATGAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.19
Consensus pattern (23 bp):
AAGAAAACTAAATCAAAATATAA
Found at i:106856 original size:19 final size:19
Alignment explanation
Indices: 106832--106868 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
106822 AATCTAAATC
106832 AATATATAAAAGAAACCTA
1 AATATATAAAAGAAACCTA
*
106851 AATATATGAAAGAAACCT
1 AATATATAAAAGAAACCT
106869 CCAACATAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (19 bp):
AATATATAAAAGAAACCTA
Found at i:109543 original size:12 final size:12
Alignment explanation
Indices: 109526--109561 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
109516 GCAAAAATTT
*
109526 CAAAATTAGGTA
1 CAAAATTAAGTA
109538 CAAAATTAAGTA
1 CAAAATTAAGTA
*
109550 CAATATTAAGTA
1 CAAAATTAAGTA
109562 ATCACCATTC
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:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (12 bp):
CAAAATTAAGTA
Found at i:112884 original size:14 final size:14
Alignment explanation
Indices: 112861--112894 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
112851 GGCAACCCAA
* *
112861 TTTTAATTTTTAGT
1 TTTTATTTTTTAGG
112875 TTTTATTTTTTAGG
1 TTTTATTTTTTAGG
112889 TTTTAT
1 TTTTAT
112895 GAATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (14 bp):
TTTTATTTTTTAGG
Found at i:116307 original size:19 final size:18
Alignment explanation
Indices: 116283--116319 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
116273 TTGAAGATTT
116283 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
116302 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
116320 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:122032 original size:24 final size:24
Alignment explanation
Indices: 122005--122061 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
121995 AGGAGTTTGA
122005 ACTTGTTGATTTT-GACCATCCTTT
1 ACTTGTTGATTTTAG-CCATCCTTT
122029 ACTTGTTGATTTTAGCCATCCTTT
1 ACTTGTTGATTTTAGCCATCCTTT
122053 ACTTGTTGA
1 ACTTGTTGA
122062 ATATCATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (24 bp):
ACTTGTTGATTTTAGCCATCCTTT
Found at i:122228 original size:2 final size:2
Alignment explanation
Indices: 122221--122246 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
122211 TTCCTCACAA
122221 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
122247 ATACCTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:128517 original size:32 final size:32
Alignment explanation
Indices: 128471--128544 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
128461 CGGGTTTAAG
*
128471 TCGGGTTCGAGTTGAATTTGGATCAGGTCAAT
1 TCGGGTTCGGGTTGAATTTGGATCAGGTCAAT
* *
128503 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGATCAGGTCAAT
128535 TCGGGTTCGG
1 TCGGGTTCGG
128545 TTTCAGTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.16, C:0.12, G:0.36, T:0.35
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGATCAGGTCAAT
Found at i:128723 original size:16 final size:16
Alignment explanation
Indices: 128702--128779 Score: 95
Period size: 16 Copynumber: 4.9 Consensus size: 16
128692 AACTTTTGCA
128702 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
128718 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * *
128734 TTCAGGTTTGAGCTTTT
1 TTCGGGTTCG-GGTTTT
128751 TT-GGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
128766 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
128780 CAGGCGAGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
15 7 0.14
16 37 0.73
17 7 0.14
ACGTcount: A:0.04, C:0.12, G:0.33, T:0.51
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:130372 original size:16 final size:16
Alignment explanation
Indices: 130351--130386 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
130341 CCATTTGCTC
130351 TGCCTTGCTGCATTAT
1 TGCCTTGCTGCATTAT
* *
130367 TGCCTTGTTGCATTGT
1 TGCCTTGCTGCATTAT
130383 TGCC
1 TGCC
130387 CTGAGATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.44
Consensus pattern (16 bp):
TGCCTTGCTGCATTAT
Found at i:138706 original size:16 final size:16
Alignment explanation
Indices: 138681--138712 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
138671 AGGAATAGAC
138681 AATCAATCAAAGCAAT
1 AATCAATCAAAGCAAT
*
138697 AATCACTCAAAGCAAT
1 AATCAATCAAAGCAAT
138713 GCAAGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.22, G:0.06, T:0.19
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:138880 original size:28 final size:25
Alignment explanation
Indices: 138800--138872 Score: 103
Period size: 25 Copynumber: 2.9 Consensus size: 25
138790 CGGCTCGGAT
* *
138800 GTGACTGGTGATGGC-TCGGTGATAG
1 GTGACAGGTGGTGGCAT-GGTGATAG
138825 GTGACAGGTGGTGGCATGGTGATAG
1 GTGACAGGTGGTGGCATGGTGATAG
*
138850 GTGACCGGTGGTGGCATGGTGAT
1 GTGACAGGTGGTGGCATGGTGAT
138873 GACCGGTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 43 0.98
26 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.47, T:0.26
Consensus pattern (25 bp):
GTGACAGGTGGTGGCATGGTGATAG
Found at i:141552 original size:21 final size:21
Alignment explanation
Indices: 141506--141552 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
141496 GTGACTCGGC
*
141506 ATGGCGCGGCATAGGCTCGTG
1 ATGGCGCGGCATAGGCGCGTG
*
141527 GTGGCGCGGCATAGTGCGCG-G
1 ATGGCGCGGCATAG-GCGCGTG
141548 ATGGC
1 ATGGC
141553 TTGGCATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (21 bp):
ATGGCGCGGCATAGGCGCGTG
Found at i:142086 original size:28 final size:27
Alignment explanation
Indices: 142021--142099 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
142011 ATTAGGGACG
*
142021 CCCAGGGGTATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
*
142048 CCCAGTGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
** * *
142075 CTTAGGGGGCATTTTAGTCGTTTTT
1 CCCA-GGGGCATTTTGGTCATTTTT
142100 TAGTTCACCT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 27 0.61
28 17 0.39
ACGTcount: A:0.14, C:0.18, G:0.25, T:0.43
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Done.