Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002093.1 Hibiscus syriacus cultivar Beakdansim tig00004274_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: 128441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1041 original size:18 final size:19
Alignment explanation
Indices: 1000--1041 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
990 TATTTTATTC
* *
1000 TATTATTTTTAATAATTTG
1 TATTAATTTTAAAAATTTG
1019 T-TTAATTTTAAAAATTT-
1 TATTAATTTTAAAAATTTG
1036 TATTAA
1 TATTAA
1042 CATCATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTAATTTTAAAAATTTG
Found at i:7568 original size:63 final size:62
Alignment explanation
Indices: 7457--7576 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 62
7447 TCAAAAACTA
* *
7457 TCCATAAGTCCAGAAAAACCTAGGTAAATTGTCCATATATTCCTTAGAAGATAGGTATATTG
1 TCCATAAGTCCAGAAAAACATAGGTAAATTGTCCATATATTCCATAGAAGATAGGTATATTG
* * * * * *
7519 TCCATATGTCCCGAAAGACATAGGTAATTATGTCCATATGTTCCATAGAATATAGGTA
1 TCCATAAGTCCAGAAAAACATAGGTAAAT-TGTCCATATATTCCATAGAAGATAGGTA
7577 AACCCTCGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
62 24 0.49
63 25 0.51
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (62 bp):
TCCATAAGTCCAGAAAAACATAGGTAAATTGTCCATATATTCCATAGAAGATAGGTATATTG
Found at i:7574 original size:32 final size:31
Alignment explanation
Indices: 7477--7577 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 31
7467 CAGAAAAACC
* * *
7477 TAGGTAA-ATTGTCCATATATTCCTTAGAAGA
1 TAGGTAATA-TGTCCATATGTTCCATAGAACA
* *
7508 TAGGT-ATATTGTCCATATGTCCCGAAAG-ACA
1 TAGGTAATA-TGTCCATATGTTCC-ATAGAACA
*
7539 TAGGTAATTATGTCCATATGTTCCATAGAATA
1 TAGGTAA-TATGTCCATATGTTCCATAGAACA
7571 TAGGTAA
1 TAGGTAA
7578 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
30 1 0.02
31 29 0.51
32 25 0.44
33 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (31 bp):
TAGGTAATATGTCCATATGTTCCATAGAACA
Found at i:11518 original size:26 final size:26
Alignment explanation
Indices: 11479--11528 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11469 ATCAAAATGA
*
11479 TAGTTTATGAACTAAACGCGTTAAGT
1 TAGTTTATGAACTAAACACGTTAAGT
*
11505 TAGTTTATGTACTAAACACGTTAA
1 TAGTTTATGAACTAAACACGTTAA
11529 ATTTTTAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (26 bp):
TAGTTTATGAACTAAACACGTTAAGT
Found at i:16298 original size:40 final size:40
Alignment explanation
Indices: 16222--16299 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
16212 ATCTCTTAAT
**
16222 TTGAGAAAGAAAATGGTTGTGTTCTTAGTGGGACTGAAGA
1 TTGAGAAAGAAAATGGTTGTGTTCTTAGTGAAACTGAAGA
16262 TTGAGAAAGAAAATGGTTGTGTTCTTAGTGAAACTGAA
1 TTGAGAAAGAAAATGGTTGTGTTCTTAGTGAAACTGAA
16300 AATTTAGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (40 bp):
TTGAGAAAGAAAATGGTTGTGTTCTTAGTGAAACTGAAGA
Found at i:20951 original size:32 final size:31
Alignment explanation
Indices: 20889--20951 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
20879 AAAATCTATC
* * *
20889 TGATCATCTATTTATTATTTAATTTTTATTT
1 TGATCATCTAATTATTATTTAAATTATATTT
* *
20920 TGATCATTTAATTATTTTTTTAAATTATATTT
1 TGATCATCTAATTA-TTATTTAAATTATATTT
20952 AATATTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (31 bp):
TGATCATCTAATTATTATTTAAATTATATTT
Found at i:22153 original size:2 final size:2
Alignment explanation
Indices: 22146--22170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22136 TCTCGTTGTT
22146 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22171 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23438 original size:2 final size:2
Alignment explanation
Indices: 23431--23457 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23421 GATGATTAAA
23431 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23458 GATAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24316 original size:129 final size:129
Alignment explanation
Indices: 24174--24420 Score: 431
Period size: 129 Copynumber: 1.9 Consensus size: 129
24164 TATTTATATA
*
24174 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* *
24239 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTTACCACCTAATTATTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTATATATGCT
24303 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
* * * *
24368 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
24421 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 111 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (129 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTATATATGCT
Found at i:24781 original size:28 final size:27
Alignment explanation
Indices: 24750--24812 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
24740 AGTTGATACA
*
24750 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
24778 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
24806 ATATTTT
1 ATATTTT
24813 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:24913 original size:16 final size:18
Alignment explanation
Indices: 24892--24925 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
24882 ATTTCTTATT
24892 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
24908 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
24926 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:25072 original size:21 final size:21
Alignment explanation
Indices: 25048--25090 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25038 TATTACCTTA
25048 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
25069 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
25090 A
1 A
25091 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:25108 original size:35 final size:35
Alignment explanation
Indices: 25059--25144 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
25049 ATTGAAGTAT
** * *
25059 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
25094 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
25129 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
25145 TGATTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:26770 original size:2 final size:2
Alignment explanation
Indices: 26763--26796 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
26753 GGTAAAATGA
* *
26763 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26797 GTAAATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28175 original size:12 final size:12
Alignment explanation
Indices: 28149--28193 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
28139 AAGAAAAATG
28149 TAATA-AATATA
1 TAATATAATATA
*
28160 TAATATAATTTA
1 TAATATAATATA
28172 TAATATAAATATA
1 TAATAT-AATATA
28185 TATATATAA
1 TA-ATATAA
28194 GGACGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:28428 original size:20 final size:20
Alignment explanation
Indices: 28405--28446 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28395 GAATCCTTCG
28405 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
28425 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
28445 TC
1 TC
28447 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:28701 original size:105 final size:105
Alignment explanation
Indices: 28504--29137 Score: 1187
Period size: 105 Copynumber: 6.0 Consensus size: 105
28494 CGTTGTGAAG
* * *
28504 CTGAAATTGGGTAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAG-AAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
28569 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
28610 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
28675 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
28715 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
28780 CTGGAGTACAATATCCTTCGTTGTGAAGTTGCAACTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
28820 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
28885 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
28925 CTGAAATTGAGAAACGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
28990 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
29030 CTGAAATTGAGAAATGTTCGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
29095 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
29135 CTG
1 CTG
29138 GGTAAAACCT
Statistics
Matches: 516, Mismatches: 12, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
105 506 0.98
106 10 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:39395 original size:10 final size:10
Alignment explanation
Indices: 39370--39403 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
39360 AACGTTAGTA
*
39370 AAATAGAAAT
1 AAATAAAAAT
*
39380 AGATAAAAAT
1 AAATAAAAAT
39390 AAATAAAAAT
1 AAATAAAAAT
39400 AAAT
1 AAAT
39404 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:40894 original size:2 final size:2
Alignment explanation
Indices: 40887--40920 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40877 GGTAAAATGA
* *
40887 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40921 GTAAATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42302 original size:12 final size:12
Alignment explanation
Indices: 42276--42320 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
42266 AAGAAAAATG
42276 TAATA-AATATA
1 TAATATAATATA
*
42287 TAATATAATTTA
1 TAATATAATATA
42299 TAATATAAATATA
1 TAATAT-AATATA
42312 TATATATAA
1 TA-ATATAA
42321 GGACGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 9 0.31
14 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:42676 original size:38 final size:36
Alignment explanation
Indices: 42600--42677 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 36
42590 TTTTTATATT
* *
42600 TTTAATTTTGTAAAAAATATATATATATATTATGAA
1 TTTAATTTTGTAAAAAATATATAAATATATTATCAA
* *
42636 TTTAATTTTTTAAAGAAAATATATAAA-ATATTTTACAA
1 TTTAATTTTGT-AA-AAAATATATAAATATATTAT-CAA
42674 TTTA
1 TTTA
42678 TAATATTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
36 10 0.29
37 8 0.23
38 17 0.49
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAATATATAAATATATTATCAA
Found at i:42684 original size:17 final size:18
Alignment explanation
Indices: 42656--42700 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
42646 TAAAGAAAAT
* *
42656 ATATAAAATATTTTAC-A
1 ATATATAATATTATACAA
*
42673 ATTTATAATATTATACAA
1 ATATATAATATTATACAA
42691 ATATATAATA
1 ATATATAATA
42701 AGGACAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATATAATATTATACAA
Found at i:47720 original size:15 final size:15
Alignment explanation
Indices: 47702--47767 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
47692 TTCCGGAAAA
47702 TGAATTACTGGAATT
1 TGAATTACTGGAATT
47717 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* * **
47732 TGAATTTCTGAAAAA
1 TGAATTACTGGAATT
47747 TGAATTACTGGAATT
1 TGAATTACTGGAATT
47762 TGAATT
1 TGAATT
47768 CTGAAAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:47736 original size:30 final size:30
Alignment explanation
Indices: 47702--47783 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
47692 TTCCGGAAAA
* **
47702 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGAAAAATGAATTACTGGAATT
*
47732 TGAATTTCTGAAAAATGAATTACTGGAATT
1 TGAATTACTGAAAAATGAATTACTGGAATT
47762 TGAATT-CTGAAAAATGAATTAC
1 TGAATTACTGAAAAATGAATTAC
47784 ATTTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (30 bp):
TGAATTACTGAAAAATGAATTACTGGAATT
Found at i:47779 original size:29 final size:30
Alignment explanation
Indices: 47717--47783 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
47707 TACTGGAATT
47717 TGAATTACTGGAATTTGAATTTCTGAAAAA
1 TGAATTACTGGAATTTGAATTTCTGAAAAA
47747 TGAATTACTGGAATTTGAA-TTCTGAAAAA
1 TGAATTACTGGAATTTGAATTTCTGAAAAA
47776 TGAATTAC
1 TGAATTAC
47784 ATTTCTGGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (30 bp):
TGAATTACTGGAATTTGAATTTCTGAAAAA
Found at i:47781 original size:14 final size:14
Alignment explanation
Indices: 47732--47781 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
47722 TACTGGAATT
47732 TGAATTTCTGAAAAA
1 TGAA-TTCTGAAAAA
* **
47747 TGAATTACTGGAATT
1 TGAATT-CTGAAAAA
47762 TGAATTCTGAAAAA
1 TGAATTCTGAAAAA
47776 TGAATT
1 TGAATT
47782 ACATTTCTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (14 bp):
TGAATTCTGAAAAA
Found at i:47789 original size:20 final size:20
Alignment explanation
Indices: 47766--47815 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
47756 GGAATTTGAA
47766 TTCTGAAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
*
47786 TTCTGGAAAATGAATTACAT
1 TTCTGAAAAATGAATTACAT
47806 TTCTGGAAAA
1 TTCT-GAAAA
47816 CATCTGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (20 bp):
TTCTGAAAAATGAATTACAT
Found at i:47969 original size:22 final size:22
Alignment explanation
Indices: 47914--48004 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 22
47904 AAATATTAAA
47914 TATAATAAA-TAATATTATTTAT
1 TATAA-AAATTAATATTATTTAT
*
47936 TATAAAACTTAATATTA-TTAT
1 TATAAAAATTAATATTATTTAT
* * *
47957 TTTAAAATATTAAAATAATTTAT
1 TATAAAA-ATTAATATTATTTAT
**
47980 T-T-ATTATTAAATATTATTT-T
1 TATAAAAATT-AATATTATTTAT
48000 TATAA
1 TATAA
48005 TTTTATTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
20 5 0.09
21 22 0.41
22 22 0.41
23 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAAAAATTAATATTATTTAT
Found at i:48020 original size:48 final size:47
Alignment explanation
Indices: 47909--48021 Score: 113
Period size: 49 Copynumber: 2.3 Consensus size: 47
47899 ATTACAAATA
*
47909 TTAAATATAATAAATAATATTATTTATTATAAAACTTAATATTATTATT
1 TTAAA-ATAA-AAATAATATTATTTATTATAAAACTTAATATTATAATT
* *
47958 TTAAAATATTAAAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATT
1 TTAAAATA--AAAATAATATTATTTATTA-TAAA-ACTTAATATTATAATT
*
48007 TTATTAATAAAAATA
1 TTA-AAATAAAAATA
48022 TTAGTATTGA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
48 19 0.35
49 30 0.55
50 6 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (47 bp):
TTAAAATAAAAATAATATTATTTATTATAAAACTTAATATTATAATT
Found at i:48197 original size:30 final size:28
Alignment explanation
Indices: 48140--48317 Score: 106
Period size: 30 Copynumber: 6.4 Consensus size: 28
48130 CTTTACTAAA
*
48140 ATATTATTGAAATATATAAATAATATTAT
1 ATATTATT-AAATATATAAAAAATATTAT
48169 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAAAAA--TATTAT
*
48199 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAA-A-AATAT-TAT
* ** *
48228 ATATTATTATAATATAATTAATTATTTTAT
1 ATATTATTA-AATAT-ATAAAAAATATTAT
* *
48258 ATAATATTAAA-A-AT--ATAATATTAT
1 ATATTATTAAATATATAAAAAATATTAT
* *
48282 ATTATTA-TAAATAT-TAATAAATATTAA
1 A-TATTATTAAATATATAAAAAATATTAT
48309 ATATT-TTAA
1 ATATTATTAA
48318 TAATTAATAT
Statistics
Matches: 118, Mismatches: 14, Indels: 37
0.70 0.08 0.22
Matches are distributed among these distances:
24 13 0.11
25 6 0.05
26 9 0.08
27 8 0.07
28 15 0.13
29 28 0.24
30 31 0.26
31 5 0.04
32 3 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATATTATTAAATATATAAAAAATATTAT
Found at i:48212 original size:59 final size:59
Alignment explanation
Indices: 48140--48289 Score: 157
Period size: 59 Copynumber: 2.6 Consensus size: 59
48130 CTTTACTAAA
*
48140 ATATTATTGAAATATATAA-ATAATATTATTCATTATTAAATATATAAAAAATT-TATTAT
1 ATATTATTAAAATATATAATATAATATTATT-ATTATTAAA-ATATAAAAAATTATATTAT
* * ** *
48199 ATATTATTAAAATA-AAAATATAATATCT-TATATTATTATAATATAATTAATTATTTTAT
1 ATATTATTAAAATATATAATATAATAT-TAT-TATTATTAAAATATAAAAAATTATATTAT
* *
48258 ATAATATTAAAA-ATATAATATTATATTATTAT
1 ATATTATTAAAATATATAATATAATATTATTAT
48290 AAATATTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
58 18 0.24
59 56 0.74
60 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (59 bp):
ATATTATTAAAATATATAATATAATATTATTATTATTAAAATATAAAAAATTATATTAT
Found at i:48251 original size:18 final size:19
Alignment explanation
Indices: 48217--48262 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
48207 AAAATAAAAA
*
48217 TATAATAT-CTTATATTAT
1 TATAATATAATTATATTAT
48235 TATAATATAATTA-ATTAT
1 TATAATATAATTATATTAT
*
48253 T-TTATATAAT
1 TATAATATAAT
48263 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 14 0.56
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATATAATTATATTAT
Found at i:48274 original size:31 final size:31
Alignment explanation
Indices: 48238--48321 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
48228 ATATTATTAT
48238 AATATAATTAATTATTTTATATAATATTAAA
1 AATATAATTAATTATTTTATATAATATTAAA
* *
48269 AATATAA-T-ATTATATTATTATAAATATTAAT
1 AATATAATTAATTATTTTA-TAT-AATATTAAA
*
48300 AA-AT-ATTAAATATTTTA-ATAAT
1 AATATAATTAATTATTTTATATAAT
48322 TAATATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
28 3 0.07
29 11 0.24
30 7 0.16
31 24 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATATAATTAATTATTTTATATAATATTAAA
Found at i:48282 original size:22 final size:23
Alignment explanation
Indices: 48257--48300 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
48247 AATTATTTTA
48257 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
48279 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
48301 AATATTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:48300 original size:59 final size:59
Alignment explanation
Indices: 48159--48326 Score: 151
Period size: 54 Copynumber: 2.9 Consensus size: 59
48149 AAATATATAA
* *
48159 ATAATATTAT-TCATTATTAAATATATAA-AAAATTTATTATATATTAT-TAA-AATAAAAAT
1 ATAATATTATATTATTA-TAAATAT-TAATAAAATTAATTAT-T-TTATATAATAATAAAAAT
* *
48218 ATAATATCT-TA-TATTAT---TA-TAATATAATTAATTATTTTATATAATATTAAAAAT
1 ATAATAT-TATATTATTATAAATATTAATAAAATTAATTATTTTATATAATAATAAAAAT
*
48272 ATAATATTATATTATTATAAATATTAATAAATATTAAATATTTTA-ATAATTAATA
1 ATAATATTATATTATTATAAATATTAATAAA-ATTAATTATTTTATATAA-TAATA
48327 TTTTGATGAA
Statistics
Matches: 89, Mismatches: 7, Indels: 25
0.74 0.06 0.21
Matches are distributed among these distances:
52 4 0.04
53 8 0.09
54 27 0.30
55 8 0.09
58 3 0.03
59 22 0.25
60 17 0.19
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (59 bp):
ATAATATTATATTATTATAAATATTAATAAAATTAATTATTTTATATAATAATAAAAAT
Found at i:48305 original size:22 final size:22
Alignment explanation
Indices: 48262--48307 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48252 TTTTATATAA
*
48262 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
48284 TATTATAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
48306 TA
1 TA
48308 AATATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:48309 original size:17 final size:16
Alignment explanation
Indices: 48255--48313 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
48245 TTAATTATTT
48255 TATATAATATTAA-AAA
1 TATA-AATATTAATAAA
* *
48271 TAT-AATATTATATTAT
1 TATAAATATTA-ATAAA
48287 TATAAATATTAATAAA
1 TATAAATATTAATAAA
48303 TATTAAATATT
1 TA-TAAATATT
48314 TTAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 7 0.20
15 1 0.03
16 12 0.34
17 15 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAATATTAATAAA
Found at i:48313 original size:26 final size:28
Alignment explanation
Indices: 48269--48327 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
48259 TAATATTAAA
*
48269 AATATAATATTATATTATTATAAAT-ATT
1 AATATAATATTATAATATT-TAAATAATT
*
48297 AATA-AATATTA-AATATTTTAATAATT
1 AATATAATATTATAATATTTAAATAATT
48323 AATAT
1 AATAT
48328 TTTGATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 4 0.15
26 12 0.44
27 7 0.26
28 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATAATATTATAATATTTAAATAATT
Found at i:48561 original size:42 final size:42
Alignment explanation
Indices: 48502--48616 Score: 187
Period size: 42 Copynumber: 2.7 Consensus size: 42
48492 ATGAATTACA
* *
48502 TTCCGGAAAACGAATTACGTGAAATAAACAC-GAGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACTG-GAAAACATT
*
48544 TTCCGGAAAACAAATTACGTGAAACAAACACTGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACTGGAAAACATT
48586 TTCCGGAAAACGAATTACGTGAAACAAACAC
1 TTCCGGAAAACGAATTACGTGAAACAAACAC
48617 AAAAATTCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 67 0.99
43 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACTGGAAAACATT
Found at i:50019 original size:52 final size:53
Alignment explanation
Indices: 49927--50028 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 53
49917 GGGATCCTAA
* *
49927 GAAACAATACTTTGATCATAAAACTTACACGTCTCGTAATTCATAATTAACTG
1 GAAACAATACTTTGATCATAAAACTTACACGCCTCATAATTCATAATTAACTG
* * * *
49980 GAAA-AATACTTTGTTCGTTAAACTTACACGCCTCATAATTCATACTTAA
1 GAAACAATACTTTGATCATAAAACTTACACGCCTCATAATTCATAATTAA
50029 ATTACTAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (53 bp):
GAAACAATACTTTGATCATAAAACTTACACGCCTCATAATTCATAATTAACTG
Found at i:51963 original size:19 final size:19
Alignment explanation
Indices: 51939--51975 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
51929 TTGAATTTGA
51939 CAAAAAAAAGTCAT-TTTTT
1 CAAAAAAAA-TCATATTTTT
51958 CAAAAAAAATCATATTTT
1 CAAAAAAAATCATATTTT
51976 ATGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (19 bp):
CAAAAAAAATCATATTTTT
Found at i:53237 original size:619 final size:619
Alignment explanation
Indices: 52058--53292 Score: 2290
Period size: 619 Copynumber: 2.0 Consensus size: 619
52048 TTCATATTTA
*
52058 GATTCACTTTTGATTTTTCGATTAAGTTCCGTTTATGACGTAATTTCTTTCACTATAACTAAGAG
1 GATTCACTTTTGATTTTTCGATTAAGTTCCGTTTATGACGTAATTTCTATCACTATAACTAAGAG
* *
52123 GTATTGTGGGACGTTGAATTGAAGGTCAAGGGCGATCAAATGGATATTAAATGATCGATTGGTGT
66 GTATTGTGGGACGTTGAATTAAAGGTCAAGGGCGATCAAATGGAGATTAAATGATCGATTGGTGT
52188 AGCTAAAAAACTAAGGTAATACACTACTACATGTTGTATGCTTTTCGAAACTCATTAATAATTAG
131 AGCTAAAAAACTAAGGTAATACACTACTACATGTTGTATGCTTTTCGAAACTCATTAATAATTAG
52253 TAAATGCATGAATGGAAATGATTGGTCAATTAGATGCATTTAATTATTGTTGGACTCGAACTGAA
196 TAAATGCATGAATGGAAATGATTGGTCAATTAGATGCATTTAATTATTGTTGGACTCGAACTGAA
52318 TTTGGTATAAAAGCATAACACTTTATAAGACCCAGATGGCTCGTATAAAAATTAAAAGACTGATC
261 TTTGGTATAAAAGCATAACACTTTATAAGACCCAGATGGCTCGTATAAAAATTAAAAGACTGATC
*
52383 AAAAACCATTCTAAGTTCAGTAATTAATAAGTAAATAAATTGACCTTAGGATCTGTAAATTTTTG
326 AAAAACCATTCTAAGTTCAGTAATTAATAAGTAAATAAATTGACCTTAAGATCTGTAAATTTTTG
*
52448 ATTAAATTATTTAAAGGTTAAATGTCTGGAATACTTGGATAAGAAATTACAAAAATAGTTCTATG
391 ATTAAATTATTTAAAGGTTAAATGTCTGGAATACTTGGATAAGAAATTACAAAAATAGTCCTATG
52513 GAGAAAAATTAAGAAAATGCCATTGTACTGTGAGAAGACCAAGATTGCCCCTGAAAGTGAAAAAT
456 GAGAAAAATTAAGAAAATGCCATTGTACTGTGAGAAGACCAAGATTGCCCCTGAAAGTGAAAAAT
52578 AACCTTGAAATAACATACCTTACCAAATTACCATAAAATGTACATGTGTTTAGGTTGAACAGAAT
521 AACCTTGAAATAACATACCTTACCAAATTACCATAAAATGTACATGTGTTTAGGTTGAACAGAAT
52643 TACCAAAATGTCCCAGAGCTACAAAATAACTTTT
586 TACCAAAATGTCCCAGAGCTACAAAATAACTTTT
* * *
52677 GATTCACTTTTGATTTTTCGATTAAGTTTCGTTTATGACGTAATTTCTATCGCTATAACTACGAG
1 GATTCACTTTTGATTTTTCGATTAAGTTCCGTTTATGACGTAATTTCTATCACTATAACTAAGAG
*
52742 GTATTGTGGGACGTTGAATTAAAGGTCAAGGGCGATCAAATGGAGATTAAATGATCTATTGGTGT
66 GTATTGTGGGACGTTGAATTAAAGGTCAAGGGCGATCAAATGGAGATTAAATGATCGATTGGTGT
*
52807 AGCTAAAAAACTAAGGTAATACACTACTACCTGTTGTATGCTTTTCGAAACTCATTAATAATTAG
131 AGCTAAAAAACTAAGGTAATACACTACTACATGTTGTATGCTTTTCGAAACTCATTAATAATTAG
*
52872 TAAATGCATGAATGTAAATGATTGGTCAATTAGATGCATTTAATTATTGTTGGACTCGAACTGAA
196 TAAATGCATGAATGGAAATGATTGGTCAATTAGATGCATTTAATTATTGTTGGACTCGAACTGAA
52937 TTTGGTATAAAAGCATAACACTTTATAAGACCCAGATGGCTCGTATAAAAATTAAAAGACTGATC
261 TTTGGTATAAAAGCATAACACTTTATAAGACCCAGATGGCTCGTATAAAAATTAAAAGACTGATC
* * * *
53002 AGAAACCATTCTAAGTTTAGTAATTAATTAGTAAATAAATTGACCTTAAGATCTGTAAATTTTTT
326 AAAAACCATTCTAAGTTCAGTAATTAATAAGTAAATAAATTGACCTTAAGATCTGTAAATTTTTG
*
53067 ATTAAATTCTTTAAAGGTTAAATGTCTGGAATACTTGGATAAGAAATTACAAAAATAGTCCTATG
391 ATTAAATTATTTAAAGGTTAAATGTCTGGAATACTTGGATAAGAAATTACAAAAATAGTCCTATG
*
53132 GAGAAAAATTAAGAAAATGCCATTGTACTGTGAGAAGACCAAGATTTCCCCTGAAAGTGAAAAAT
456 GAGAAAAATTAAGAAAATGCCATTGTACTGTGAGAAGACCAAGATTGCCCCTGAAAGTGAAAAAT
*
53197 AACCTTGAAATAACATACCTTACCAAATTACCATAAAATGTACATGTGTTTAGGTTGAATAGAAT
521 AACCTTGAAATAACATACCTTACCAAATTACCATAAAATGTACATGTGTTTAGGTTGAACAGAAT
**
53262 TACCAAAATGTCTTAGAGCTACAAAATAACT
586 TACCAAAATGTCCCAGAGCTACAAAATAACT
53293 AAAATAACCT
Statistics
Matches: 596, Mismatches: 20, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
619 596 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (619 bp):
GATTCACTTTTGATTTTTCGATTAAGTTCCGTTTATGACGTAATTTCTATCACTATAACTAAGAG
GTATTGTGGGACGTTGAATTAAAGGTCAAGGGCGATCAAATGGAGATTAAATGATCGATTGGTGT
AGCTAAAAAACTAAGGTAATACACTACTACATGTTGTATGCTTTTCGAAACTCATTAATAATTAG
TAAATGCATGAATGGAAATGATTGGTCAATTAGATGCATTTAATTATTGTTGGACTCGAACTGAA
TTTGGTATAAAAGCATAACACTTTATAAGACCCAGATGGCTCGTATAAAAATTAAAAGACTGATC
AAAAACCATTCTAAGTTCAGTAATTAATAAGTAAATAAATTGACCTTAAGATCTGTAAATTTTTG
ATTAAATTATTTAAAGGTTAAATGTCTGGAATACTTGGATAAGAAATTACAAAAATAGTCCTATG
GAGAAAAATTAAGAAAATGCCATTGTACTGTGAGAAGACCAAGATTGCCCCTGAAAGTGAAAAAT
AACCTTGAAATAACATACCTTACCAAATTACCATAAAATGTACATGTGTTTAGGTTGAACAGAAT
TACCAAAATGTCCCAGAGCTACAAAATAACTTTT
Found at i:54342 original size:21 final size:21
Alignment explanation
Indices: 54300--54342 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54290 TTTCTGGGCT
* * *
54300 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
54321 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
54342 A
1 A
54343 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:59346 original size:21 final size:18
Alignment explanation
Indices: 59320--59370 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
59310 TGCTAGAGTT
59320 TTTTTTTTGGTGTTATTGATA
1 TTTTTTTTGGT-TT-TTG-TA
*
59341 TTTTTTTTGGTTTTTGTT
1 TTTTTTTTGGTTTTTGTA
59359 TTTTTTTTGGTT
1 TTTTTTTTGGTT
59371 AGGGGTGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.45
19 3 0.10
20 2 0.07
21 11 0.38
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (18 bp):
TTTTTTTTGGTTTTTGTA
Found at i:59818 original size:12 final size:12
Alignment explanation
Indices: 59740--59824 Score: 91
Period size: 12 Copynumber: 6.8 Consensus size: 12
59730 ATGATGGAAG
*
59740 TGATGGTGA-TT
1 TGATGATGAGTT
59751 TCGATGATGAGTT
1 T-GATGATGAGTT
*
59764 TGACGATGAGTT
1 TGATGATGAGTT
* *
59776 CGATGATGAATT
1 TGATGATGAGTT
59788 TGATGATGAGTT
1 TGATGATGAGTT
59800 CGATGATGATGAGTT
1 ---TGATGATGAGTT
59815 TGATGATGAG
1 TGATGATGAG
59825 GAATTTGGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
11 1 0.02
12 46 0.74
13 3 0.05
15 12 0.19
ACGTcount: A:0.26, C:0.05, G:0.33, T:0.36
Consensus pattern (12 bp):
TGATGATGAGTT
Found at i:59831 original size:15 final size:15
Alignment explanation
Indices: 59777--59831 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
59767 CGATGAGTTC
59777 GATGATGAATTTGAT
1 GATGATGAATTTGAT
*
59792 GATGA-G--TTCGAT
1 GATGATGAATTTGAT
*
59804 GATGATGAGTTTGAT
1 GATGATGAATTTGAT
*
59819 GATGAGGAATTTG
1 GATGATGAATTTG
59832 GTCACGGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 10 0.30
13 1 0.03
14 1 0.03
15 21 0.64
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (15 bp):
GATGATGAATTTGAT
Found at i:66623 original size:20 final size:20
Alignment explanation
Indices: 66594--66683 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
66584 ACAGGTTCCA
* *
66594 AAATCACAACGCGAATATGT
1 AAATCGCAACGAGAATATGT
*
66614 AAATCGCAACGATAATATGT
1 AAATCGCAACGAGAATATGT
* *
66634 AAATCGCAACGATAATATTT
1 AAATCGCAACGAGAATATGT
* *
66654 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGAGAATATGT
66674 AAATCGCAAC
1 AAATCGCAAC
66684 ACAGAAGTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGAGAATATGT
Found at i:66700 original size:20 final size:20
Alignment explanation
Indices: 66677--66722 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
66667 AATTTGTAAA
66677 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
66697 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
66717 TCGCAA
1 TCGCAA
66723 AAAGCGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:67107 original size:20 final size:20
Alignment explanation
Indices: 67059--67134 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
67049 TCATATTTAA
* *
67059 ATTCGAGTTGCGATTTACAT
1 ATTCGCGTTGCGATTTACCT
** * *
67079 ATTATCGTTACGATTTATCT
1 ATTCGCGTTGCGATTTACCT
*
67099 ATTCGCGTTGCAATTTACCT
1 ATTCGCGTTGCGATTTACCT
67119 ATTCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
67135 TGGAAAATCG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACCT
Found at i:67133 original size:40 final size:40
Alignment explanation
Indices: 67059--67134 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
67049 TCATATTTAA
* *
67059 ATTCGAGTTGCGATTTACATATTATCGTTACGATTTATCT
1 ATTCGAGTTGCAATTTACATATTAGCGTTACGATTTATCT
* * * *
67099 ATTCGCGTTGCAATTTACCTATTCGCGTTGCGATTT
1 ATTCGAGTTGCAATTTACATATTAGCGTTACGATTT
67135 TGGAAAATCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (40 bp):
ATTCGAGTTGCAATTTACATATTAGCGTTACGATTTATCT
Found at i:67147 original size:21 final size:21
Alignment explanation
Indices: 67121--67160 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
67111 ATTTACCTAT
67121 TCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGGAAAA
*
67142 TCGCGTTGTGATTTTGGAA
1 TCGCGTTGCGATTTTGGAA
67161 CTTGTATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTGGAAAA
Found at i:74107 original size:21 final size:21
Alignment explanation
Indices: 74074--74113 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
74064 ACAAGAGGCC
* *
74074 AATTTGGGGTTAAGTGGGTTG
1 AATTCGGGGTTAAATGGGTTG
*
74095 AATTCGGGTTTAAATGGGT
1 AATTCGGGGTTAAATGGGT
74114 CGGGTTTGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (21 bp):
AATTCGGGGTTAAATGGGTTG
Found at i:79530 original size:2 final size:2
Alignment explanation
Indices: 79523--79549 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79513 AGAAAGCACA
79523 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
79550 TGGGATTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:84134 original size:14 final size:14
Alignment explanation
Indices: 84115--84152 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
84105 GTAAAATACG
*
84115 GTATGAACAGTATC
1 GTATGAACAATATC
84129 GTATGAACAATATC
1 GTATGAACAATATC
84143 G--TGAACAATA
1 GTATGAACAATA
84153 CCCGAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 9 0.39
14 14 0.61
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (14 bp):
GTATGAACAATATC
Found at i:85016 original size:23 final size:23
Alignment explanation
Indices: 84989--85032 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
84979 CAAAAGACCG
84989 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
85012 CGTAGAATTGCACCGTAGTGC
1 CGTAGAAATGCACCGAAGTGC
85033 TATATAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:86573 original size:17 final size:17
Alignment explanation
Indices: 86551--86592 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
86541 CGGGGAGGAG
*
86551 GAAGAAGAAATGAAGAA
1 GAAGAAGAAAGGAAGAA
*
86568 GAAGAAGAAAGGAATAA
1 GAAGAAGAAAGGAAGAA
86585 GAAGAAGA
1 GAAGAAGA
86593 TAAAATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (17 bp):
GAAGAAGAAAGGAAGAA
Found at i:87727 original size:31 final size:31
Alignment explanation
Indices: 87689--87750 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
87679 TCTACATTAC
*
87689 ACTTTTAGGTGTCTA-CTGTTATATTTTTTAA
1 ACTTTTAGGTGTCTATC-CTTATATTTTTTAA
87720 ACTTTTAGGTGTCTATCCTTATATTTTTTAA
1 ACTTTTAGGTGTCTATCCTTATATTTTTTAA
87751 TTCTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (31 bp):
ACTTTTAGGTGTCTATCCTTATATTTTTTAA
Found at i:96197 original size:90 final size:90
Alignment explanation
Indices: 96044--96233 Score: 353
Period size: 90 Copynumber: 2.1 Consensus size: 90
96034 TATTAGTCCC
*
96044 TAAATTTGGATTTTTGTTCATTTTGATGTCTTGGTACTCTAAGATTGTGTCATGTGATATAATCT
1 TAAATGTGGATTTTTGTTCATTTTGATGTCTTGGTACTCTAAGATTGTGTCATGTGATATAATCT
*
96109 TATAGTCTTACATCACTAAAGAGGT
66 TATACTCTTACATCACTAAAGAGGT
96134 TAAATGTGGATTTTTGTTCATTTTGATGTCTTGGTACTCTAAGATTGTGTCATGTGATATAATCT
1 TAAATGTGGATTTTTGTTCATTTTGATGTCTTGGTACTCTAAGATTGTGTCATGTGATATAATCT
*
96199 TATACTCTTACATCACTAAATAGGT
66 TATACTCTTACATCACTAAAGAGGT
96224 TAAATGTGGA
1 TAAATGTGGA
96234 AAATAAATAT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 97 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (90 bp):
TAAATGTGGATTTTTGTTCATTTTGATGTCTTGGTACTCTAAGATTGTGTCATGTGATATAATCT
TATACTCTTACATCACTAAAGAGGT
Found at i:97856 original size:20 final size:20
Alignment explanation
Indices: 97820--97858 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
97810 AATATTTTAG
**
97820 AAATTCATATTTTTTTTCTA
1 AAATTCATATTCATTTTCTA
97840 AAATTCATATTCATTTTCT
1 AAATTCATATTCATTTTCT
97859 TATTTTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTCATATTCATTTTCTA
Found at i:112530 original size:20 final size:20
Alignment explanation
Indices: 112502--112541 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
112492 TATATTTCTT
*
112502 TTTTTCCTTTACTTTCTTCC
1 TTTTCCCTTTACTTTCTTCC
**
112522 TTTTCCCTTTTTTTTCTTCC
1 TTTTCCCTTTACTTTCTTCC
112542 CCCTCATCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCCCTTTACTTTCTTCC
Found at i:123059 original size:225 final size:229
Alignment explanation
Indices: 122649--123118 Score: 713
Period size: 226 Copynumber: 2.1 Consensus size: 229
122639 TTTATTTTGG
* * *
122649 TCGGGTCAGGTCGGTTTCTTATGTGTGATATTCAGGTCGGTCGAGTTCGGGTTTAGGGTGAAAAA
1 TCGGGTCGGGTCGGTTTCTTAAGTGTGACATTCAGGTC-GTCGAGTTCGGGTTTAGGGTGAAAAA
*
122714 TACCCGACCCGACCCTAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
65 TACCCGACCCGACCCTAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATA
122779 TCCCTCTATATATAATTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAA-TTTTTTTA
130 TCCCTCTATATATAA-TTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTTA
* *
122843 TTATTTTGGGTCGGGTCGGGTTTCTAATTCATATAT
194 TTATTTCGGGTCGGGTCGGATTTCTAATTCATATAT
* *
122879 TCGGGTCGGGTCGGTTTTTTTAAGTGTGACATTCGGGTC-T-G-GTTCGGGTTTAGGGTG-AAAA
1 TCGGGTCGGGTCGG-TTTCTTAAGTGTGACATTCAGGTCGTCGAGTTCGGGTTTAGGGTGAAAAA
* *
122940 TACCTGACCCGACCC-AAAAAATATATAATTTTACCTTATATATATATATGAATAATTACAATAA
65 TACCCGACCCGACCCTAAAAAATATATAATTTTACCTTATATAT-T-TAGGAATAATTACAATAA
* *
123004 TA-CTCCTCTATATATAA-TTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTT
128 TATC-CCTCTATATATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTT
*
123067 TTTTATTTCGGGTCGGGTCGGATTTCTAATTCATATAT
192 TATTATTTCGGGTCGGGTCGGATTTCTAATTCATATAT
123105 TCGGGTCGGGTCGG
1 TCGGGTCGGGTCGG
123119 GTGAAACTTT
Statistics
Matches: 222, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
225 64 0.29
226 75 0.34
227 48 0.22
228 1 0.00
229 1 0.00
230 13 0.06
231 20 0.09
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (229 bp):
TCGGGTCGGGTCGGTTTCTTAAGTGTGACATTCAGGTCGTCGAGTTCGGGTTTAGGGTGAAAAAT
ACCCGACCCGACCCTAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAT
CCCTCTATATATAATTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAATTTTTTTTATT
ATTTCGGGTCGGGTCGGATTTCTAATTCATATAT
Done.