Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003750.1 Kokia drynarioides strain JFW-HI SEQ_116713, 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: 167350
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:5124 original size:17 final size:17
Alignment explanation
Indices: 5104--5160 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
5094 TATTTGTCCC
*
5104 TGCATTATTAATGTCAT
1 TGCATTATTATTGTCAT
* *
5121 TGCATTTTTATTGTCAC
1 TGCATTATTATTGTCAT
*
5138 TGCATCTA-CATTGTCAT
1 TGCAT-TATTATTGTCAT
5155 TGCATT
1 TGCATT
5161 TCCATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
TGCATTATTATTGTCAT
Found at i:15387 original size:20 final size:21
Alignment explanation
Indices: 15362--15400 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15352 GCAAGTAATT
15362 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
15382 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
15401 TAAAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:27066 original size:13 final size:13
Alignment explanation
Indices: 27048--27072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27038 TATAGGGATC
27048 AATTGTAGAATTA
1 AATTGTAGAATTA
27061 AATTGTAGAATT
1 AATTGTAGAATT
27073 TAATGTGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
AATTGTAGAATTA
Found at i:40668 original size:26 final size:26
Alignment explanation
Indices: 40632--40713 Score: 114
Period size: 26 Copynumber: 3.1 Consensus size: 26
40622 ATTTCACCAA
40632 AAAAAAAAAAAGAAAAGAAAAGAAAG
1 AAAAAAAAAAAGAAAAGAAAAGAAAG
40658 AAAAAAAAAAAGAAAA-AGAAAGAAAG
1 AAAAAAAAAAAGAAAAGA-AAAGAAAG
40684 AAAGGAAAATAAAAGAAAAGAAAA-AAAG
1 AAA--AAAA-AAAAGAAAAGAAAAGAAAG
40712 AA
1 AA
40714 GAAGGAGAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
25 1 0.02
26 27 0.53
28 10 0.20
29 12 0.24
30 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAAGAAAAGAAAAGAAAG
Found at i:41165 original size:112 final size:112
Alignment explanation
Indices: 41022--41236 Score: 304
Period size: 112 Copynumber: 1.9 Consensus size: 112
41012 AATATGGGTC
* * * * **
41022 ATTTTTAATATTTTCATTCATGAGAGTTTTGCCTCCAATAAAATTCAATTTTGTTCATCTTATGA
1 ATTTTTAATATTTTCATTCATGAGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
*
41087 CCCTGTTCAAGCATTTTTGCATCGAAATAACGATTAGTAGACCAATG
66 CCATGTTCAAGCATTTTTGCATCGAAATAACGATTAGTAGACCAATG
* * **
41134 ATTTTTAATCTTTTCATTCTTTCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
1 ATTTTTAATATTTTCATTCATGAGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
* * *
41199 TCATGTTCAAGCATTTTTGCATTGAAATAACGGTTAGT
66 CCATGTTCAAGCATTTTTGCATCGAAATAACGATTAGT
41237 GGTCTAACGA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
112 89 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (112 bp):
ATTTTTAATATTTTCATTCATGAGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAA
CCATGTTCAAGCATTTTTGCATCGAAATAACGATTAGTAGACCAATG
Found at i:41960 original size:147 final size:147
Alignment explanation
Indices: 41687--42056 Score: 395
Period size: 147 Copynumber: 2.5 Consensus size: 147
41677 GGAAAGATTA
* * * * * * *
41687 AAGCCACAATGGCGAATCTTGTATCATAAAGATGTGGAGGGAAAGATT-AAATTCGTAATGACGA
1 AAGCCACAATGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTGAAGTT-GCAACGACAA
* * * * * *
41751 ATTTTGTACCCTGGAAATGTGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCCTAGAA
65 ATTTTATACCCTAGAAATATGAAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAA
41816 ATGTGGAGGGAAAAAATG
130 ATGTGGAGGGAAAAAATG
* * * *
41834 AAGCCACAATTGTGAATCTTGTACCCTAGTGATGTGGAGGGAAAGATTGAAGTTGCAACGGCAAA
1 AAGCCACAATGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTGAAGTTGCAACGACAAA
* * * * * *
41899 TCTTATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCGCAACGATGAA-CTTTATATCCTAGAG
66 TTTTATACCCTAGAAATATGAAGGGAAAGATTGAAGCCGCAACGACGAATC-TTATACCCTAGAA
*** *
41963 ATGTGGAGGGAAAGGTTT
130 ATGTGGAGGGAAAAAATG
* * * * * *
41981 AAGCCGCAATGGCGAACCTTATACCCTAGAGATGT-GAGGGGAAAAATTGAAGTCGCAACGTCAA
1 AAGCCACAATGGCGAATCTTGTACCCTAGAGATGTGGA-GGGAAAGATTGAAGTTGCAACGACAA
42045 ATTTTATACCCT
65 ATTTTATACCCT
42057 GAAGATGAGA
Statistics
Matches: 183, Mismatches: 37, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
146 3 0.02
147 176 0.96
148 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (147 bp):
AAGCCACAATGGCGAATCTTGTACCCTAGAGATGTGGAGGGAAAGATTGAAGTTGCAACGACAAA
TTTTATACCCTAGAAATATGAAGGGAAAGATTGAAGCCGCAACGACGAATCTTATACCCTAGAAA
TGTGGAGGGAAAAAATG
Found at i:42009 original size:49 final size:49
Alignment explanation
Indices: 41657--42056 Score: 327
Period size: 49 Copynumber: 8.1 Consensus size: 49
41647 GTTAAATCAA
** * * *
41657 ATACCCTAGAAGACATGAAGGGAAAGATTAAAGCCACAATGGCGAATCTT
1 ATACCCTAG-AGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * * * * ** * * *
41707 GTATCATAAAGATGTGGAGGGAAAGATTAAATTCGTAATGACGAATTTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * * *
41756 GTACCCTGGAAATGTGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * * * * * *
41805 GTACCCTAGAAATGTGGAGGGAAAAAATGAAGCCACAATTGTGAATCTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * ** * *
41854 GTACCCTAGTGATGTGGAGGGAAAGATTGAAGTTGCAACGGCAAATCTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * * * **
41903 ATACCCTAGAGATATGAAGGGAAAGGTTGAAGCCGCAACGATGAA-CTTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATC-TT
* * * *
41952 ATATCCTAGAGATGTGGAGGGAAAGGTTTAAGCCGCAATGGCGAACCTT
1 ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
* * * * * *
42001 ATACCCTAGAGATGT-GAGGGGAAAAATTGAAGTCGCAACGTCAAATTTT
1 ATACCCTAGAGATGTGGA-GGGAAAGATTGAAGCCGCAATGGCGAATCTT
42050 ATACCCT
1 ATACCCT
42057 GAAGATGAGA
Statistics
Matches: 277, Mismatches: 70, Indels: 7
0.78 0.20 0.02
Matches are distributed among these distances:
48 3 0.01
49 268 0.97
50 6 0.02
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (49 bp):
ATACCCTAGAGATGTGGAGGGAAAGATTGAAGCCGCAATGGCGAATCTT
Found at i:42353 original size:50 final size:50
Alignment explanation
Indices: 42289--42408 Score: 186
Period size: 50 Copynumber: 2.4 Consensus size: 50
42279 ATGGACCTCA
*
42289 ATCTCCCTGAAGTTGCAGTGGAATGAAGAGAAGTTACCACACCAAATCCT
1 ATCTTCCTGAAGTTGCAGTGGAATGAAGAGAAGTTACCACACCAAATCCT
* * **
42339 ATCTTCTTGAAGTTGCAGTCGAATGAATTGAAGTTACCACACCAAATCCT
1 ATCTTCCTGAAGTTGCAGTGGAATGAAGAGAAGTTACCACACCAAATCCT
*
42389 ATCTTCCTGAAGTTGTAGTG
1 ATCTTCCTGAAGTTGCAGTG
42409 AAGTGGATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (50 bp):
ATCTTCCTGAAGTTGCAGTGGAATGAAGAGAAGTTACCACACCAAATCCT
Found at i:42842 original size:40 final size:40
Alignment explanation
Indices: 42480--42856 Score: 361
Period size: 40 Copynumber: 9.3 Consensus size: 40
42470 AAGTTACATC
* *
42480 AGACCATCCAATCTCTTACCCTAACCATG-GGACAGATTGA
1 AGACCATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGA
* **
42520 AG-CCATCCAATCTTTTACCCTAACCAAAGGGTTGATTGA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
* * *
42559 AG-TCATCCAATCTTTTACCCTAACTAAAGGGCAGATTGA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
* * * *
42598 AGACACCATCCAATCTCTTA-CCTCAACCCTG-TGGCAAATTGA
1 AG--ACCATCCAATCTTTTACCCT-AA-CCAGAGGGCAGATTGA
* * * *
42640 AG-CCATCCAATCTTGTACCCTAACCAAACGGTAGATTGA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
* * * *
42679 AAATCATCCAATCTTTTACCCTAACAAGAGGGCAGATTAA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
* * * * *
42719 AGACATCATCCAATCTTTGACCTTAACCAAAAGGCATATTGA
1 AGAC--CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
*
42761 AGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
* * * *
42801 AGATCATCCAATCTTTTACCCCAACTAGAGGGCAAATTGA
1 AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
42841 AGCCACCATCCAATCT
1 AG--ACCATCCAATCT
42857 CATATCCCAA
Statistics
Matches: 274, Mismatches: 50, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.01
39 92 0.34
40 106 0.39
41 3 0.01
42 70 0.26
43 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (40 bp):
AGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
Found at i:42849 original size:82 final size:80
Alignment explanation
Indices: 42484--42892 Score: 375
Period size: 82 Copynumber: 5.0 Consensus size: 80
42474 TACATCAGAC
* * *
42484 CATCCAATCTCTTACCCTAACC-ATGGGACAGATTGAAG--CCATCCAATCTTTTACCCTAACCA
1 CATCCAATCTTTTACCCTAACCAAAGGG-CAGATTGAAGCACCATCCAATCTTTTACCCTAACTA
* **
42546 AAGGGTTGATTGAAGT
65 GAGGGCAGATTGAAGT
* *
42562 CATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACACCATCCAATCTCTTA-CCTCAACC
1 CATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG-CACCATCCAATCTTTTACCCT-AA--
* * *
42626 CT-G-TGGCAAATTGAAGC
62 CTAGAGGGCAGATTGAAGT
* * * * * *
42643 CATCCAATCTTGTACCCTAACCAAACGGTAGATTGAA-AATCATCCAATCTTTTACCCTAACAAG
1 CATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGCACCATCCAATCTTTTACCCTAACTAG
*
42707 AGGGCAGATTAAAGACAT
66 AGGGCAGATTGAAG---T
* * * *
42725 CATCCAATCTTTGACCTTAACCAAAAGGCATATTGAAG-ACCATCCAATCTTTTACCCTAACTAG
1 CATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGCACCATCCAATCTTTTACCCTAACTAG
42789 AGGGCAGATTGAAGAT
66 AGGGCAGATTGAAG-T
* * * * ** *
42805 CATCCAATCTTTTACCCCAACTAGAGGGCAAATTGAAGCCACCATCCAATCTCATATCCCAAATC
1 CATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAG-CACCATCCAATCTTTTA-CCCTAA-C
*
42870 TAGAGGGATAGATTGAAGT
63 TAGAGGG-CAGATTGAAGT
42889 CATC
1 CATC
42893 ACATCTAATC
Statistics
Matches: 269, Mismatches: 43, Indels: 32
0.78 0.12 0.09
Matches are distributed among these distances:
77 1 0.00
78 31 0.12
79 30 0.11
80 39 0.14
81 58 0.22
82 82 0.30
83 6 0.02
84 13 0.05
85 9 0.03
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (80 bp):
CATCCAATCTTTTACCCTAACCAAAGGGCAGATTGAAGCACCATCCAATCTTTTACCCTAACTAG
AGGGCAGATTGAAGT
Found at i:42866 original size:42 final size:40
Alignment explanation
Indices: 42480--42934 Score: 258
Period size: 40 Copynumber: 11.1 Consensus size: 40
42470 AAGTTACATC
* * * * *
42480 AGACCATCCAATCTCTTACCCTAACCATG-GGACAGATTGA
1 AGACCATCCAATCTTTTACCCAAACTA-GAGGGCAAATTGA
* * * ***
42520 AG-CCATCCAATCTTTTACCCTAACCAAAGGGTTGATTGA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* * * *
42559 AG-TCATCCAATCTTTTACCCTAACTAAAGGGCAGATTGA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* * *
42598 AGACACCATCCAATCTCTTACCTCAACCCT-G-TGGCAAATTGA
1 AG--ACCATCCAATCTTTTACC-CAA-ACTAGAGGGCAAATTGA
* * * * * * *
42640 AG-CCATCCAATCTTGTACCCTAACCAAACGGTAGATTGA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* * * * * *
42679 AAATCATCCAATCTTTTACCCTAACAAGAGGGCAGATTAA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* ** * * * *
42719 AGACATCATCCAATCTTTGACCTTAACCAAAAGGCATATTGA
1 AGAC--CATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* *
42761 AGACCATCCAATCTTTTACCCTAACTAGAGGGCAGATTGA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
* *
42801 AGATCATCCAATCTTTTACCCCAACTAGAGGGCAAATTGA
1 AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
**
42841 AGCCACCATCCAATCTCATATCCCAAATCTAGAGGG-ATAGATTGA
1 AG--ACCATCCAATCTTTTA-CCCAAA-CTAGAGGGCA-A-ATTGA
* * *
42886 AGTCATCACATCTAATCTTATACCTCAAATCTAGATGGGCAGATTGA
1 AG--A-C-CATCCAATCTTTTACC-CAAA-CTAGA-GGGCAAATTGA
42933 AG
1 AG
42935 CTATCAGAGG
Statistics
Matches: 334, Mismatches: 59, Indels: 37
0.78 0.14 0.09
Matches are distributed among these distances:
37 1 0.00
38 2 0.01
39 92 0.28
40 103 0.31
42 72 0.22
43 8 0.02
44 11 0.03
45 9 0.03
46 3 0.01
47 29 0.09
48 3 0.01
49 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
AGACCATCCAATCTTTTACCCAAACTAGAGGGCAAATTGA
Found at i:42982 original size:69 final size:69
Alignment explanation
Indices: 42871--43009 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
42861 TCCCAAATCT
*
42871 AGAGGGATAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGATGGGCAGATTGAAGC
1 AGAGGGATAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGAGGGGCAGATTGAAGC
42936 TATC
66 TATC
*
42940 AGAGGGGTAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGAGGGGCAGATTGAAGC
1 AGAGGGATAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGAGGGGCAGATTGAAGC
43005 TATC
66 TATC
43009 A
1 A
43010 AATCAAATCG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (69 bp):
AGAGGGATAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGAGGGGCAGATTGAAGC
TATC
Found at i:42999 original size:47 final size:47
Alignment explanation
Indices: 42940--43032 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
42930 TGAAGCTATC
* * * * *
42940 AGAGGGGTAGATTGAAG-TCATCACATCTAATCTTATACCTCAAATCT
1 AGAGGGGCAGATTGAAGCT-ATCAAATCAAATCGTATACCCCAAATCT
42987 AGAGGGGCAGATTGAAGCTATCAAATCAAATCGTATACCCCAAATC
1 AGAGGGGCAGATTGAAGCTATCAAATCAAATCGTATACCCCAAATC
43033 CAAAAGGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 39 0.98
48 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (47 bp):
AGAGGGGCAGATTGAAGCTATCAAATCAAATCGTATACCCCAAATCT
Found at i:43047 original size:47 final size:46
Alignment explanation
Indices: 42944--43053 Score: 114
Period size: 47 Copynumber: 2.3 Consensus size: 46
42934 GCTATCAGAG
* * * * * * *
42944 GGGTAGATTGAAGTCATCACATCTAATCTTATACCTCAAATCTAGA
1 GGGTCGATTGAAGTCATCAAATCAAATCGTATACCCCAAATCAAAA
*
42990 GGGGCAGATTGAAG-CTATCAAATCAAATCGTATACCCCAAATCCAAAA
1 GGGTC-GATTGAAGTC-ATCAAATCAAATCGTATACCCCAAAT-CAAAA
43038 GGGTCGATTGAAGTCA
1 GGGTCGATTGAAGTCA
43054 CGACACTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
46 4 0.08
47 39 0.76
48 8 0.16
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (46 bp):
GGGTCGATTGAAGTCATCAAATCAAATCGTATACCCCAAATCAAAA
Found at i:43323 original size:18 final size:18
Alignment explanation
Indices: 43300--43335 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43290 AAAATAAAGT
43300 TCATTTTAATATACAAAA
1 TCATTTTAATATACAAAA
*
43318 TCATTTTAATTTACAAAA
1 TCATTTTAATATACAAAA
43336 CAAAATCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
TCATTTTAATATACAAAA
Found at i:45913 original size:18 final size:18
Alignment explanation
Indices: 45879--45915 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
45869 TTGTAAATGG
*
45879 AATTTTATTTTGGATTTT
1 AATTTTATTTTAGATTTT
*
45897 AATTTTATTTTATATTTT
1 AATTTTATTTTAGATTTT
45915 A
1 A
45916 TTTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
AATTTTATTTTAGATTTT
Found at i:45969 original size:20 final size:20
Alignment explanation
Indices: 45932--45969 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45922 TATTTATATT
*
45932 ATAAAATAGTAAATAAATAA
1 ATAAAATAGTAAAAAAATAA
45952 ATAAAATA-TAAAGAAAAT
1 ATAAAATAGTAAA-AAAAT
45970 TGGGTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
ATAAAATAGTAAAAAAATAA
Found at i:46434 original size:41 final size:42
Alignment explanation
Indices: 46348--46471 Score: 162
Period size: 41 Copynumber: 3.0 Consensus size: 42
46338 GTTATGTGTG
* * * * * *
46348 TGGCTTCGATCTGCCCTTCTAGTTTAGGGGTAAAAGATCGAA
1 TGGCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGA
46390 TGGC-TCTAATCTACCCCTCTAGATTA-GGGTAAAAGATTGGA
1 TGGCTTC-AATCTACCCCTCTAGATTAGGGGTAAAAGATTGGA
*
46431 TGGCTTCAATCTACCCCTCTAGGTTAGGGGTAAAAGATTGG
1 TGGCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGG
46472 GTGGTAATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 37 0.51
42 35 0.49
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
TGGCTTCAATCTACCCCTCTAGATTAGGGGTAAAAGATTGGA
Found at i:46933 original size:49 final size:49
Alignment explanation
Indices: 46880--47220 Score: 247
Period size: 49 Copynumber: 7.0 Consensus size: 49
46870 GCTTCTCCTT
* * *
46880 ATCTCCAGGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCTCTTCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
* * * * * *
46929 ATCTCTAAGGTATAAGGTTCACCGTTACGGCTTCAACCTTTCCCTCCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
* * * * * * * * *
46978 ATCTCTAGGTTATAAGGTTTGTCATTACGACTTCAACCTTTCCCTCCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
* *** ** *
47027 ATCTCAAGGGTATAAGATTTATCGTTGCTACTTCAGTCTTTCCC-TCAAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTC-AC
* * * * * *
47076 ATTTCTAGAGTACAATATTCGCCATTGTGGCTTCAATCTTTCCCTTCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
* * ** * * *
47125 ATCTCTAAGGCACGAGATTCACCGTT--GGCTTCAAACTTTCTCTTCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
* ** * * * *
47172 ATCTCTAGGGCACGAGATTCGTCGTCGCAGCTTCAATCTTTCTCTTCAC
1 ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
47221 GTCCTTAGGA
Statistics
Matches: 233, Mismatches: 55, Indels: 8
0.79 0.19 0.03
Matches are distributed among these distances:
47 41 0.18
48 1 0.00
49 189 0.81
50 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.35
Consensus pattern (49 bp):
ATCTCTAGGGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTTCAC
Found at i:46982 original size:98 final size:97
Alignment explanation
Indices: 46880--47220 Score: 308
Period size: 98 Copynumber: 3.5 Consensus size: 97
46870 GCTTCTCCTT
* * *
46880 ATCTCCAGGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCTCTTCACATCTCTAAGGTATAAG
1 ATCTCTAGGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAG
* *
46945 GTTCACCGTTACGGCTTCAACCTTTCCCTCCAC
66 ATTCACCGTT-CGGCTTCAAACTTTCCCTCCAC
* * * * * * * * *
46978 ATCTCTAGGTTATAAGGTTTGTCATTACGACTTCAACCTTTCCCTCCACATCTC-AAGGGTATAA
1 ATCTCTAGGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAA-GGTATAA
* * ** ** *
47042 GATTTATCGTTGCTACTTCAGTCTTTCCCTCAAC
65 GATTCACCGTT-CGGCTTCAAACTTTCCCTCCAC
* * * * * **
47076 ATTTCTAGAGTACAATATTCGCCATTGTGGCTTCAATCTTTCCCTTCACATCTCTAAGGCACGAG
1 ATCTCTAGGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAG
* *
47141 ATTCACCGTT-GGCTTCAAACTTTCTCTTCAC
66 ATTCACCGTTCGGCTTCAAACTTTCCCTCCAC
* * * * * * *
47172 ATCTCTAGGGCACGAGATTCGTCGTCGCAGCTTCAATCTTTCTCTTCAC
1 ATCTCTAGGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCAC
47221 GTCCTTAGGA
Statistics
Matches: 186, Mismatches: 55, Indels: 6
0.75 0.22 0.02
Matches are distributed among these distances:
96 52 0.28
97 2 0.01
98 130 0.70
99 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.35
Consensus pattern (97 bp):
ATCTCTAGGGTACAAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTCTAAGGTATAAG
ATTCACCGTTCGGCTTCAAACTTTCCCTCCAC
Found at i:47815 original size:112 final size:112
Alignment explanation
Indices: 47669--47883 Score: 342
Period size: 112 Copynumber: 1.9 Consensus size: 112
47659 TATCGTTAGA
* * *
47669 CCACTAACCGCTATTTCAATTCAAAAATGCTTGAACAAGATTGTAAGG-TGGATAAAATTGAATT
1 CCACTAACCGCTATTTCAATGCAAAAATACTTGAACAAGATTGCAAGGCT-GATAAAATTGAATT
*
47733 TTATTGGAGGCAAAGCTCGTATGAATGAAAAGATTAAAAATCATTGGT
65 TTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTGGT
* * * *
47781 CCACTAACCGTTATTTCGATGCAAAAATACTTGAACAGGGTTGCAAGGCTGATAAAATTGAATTT
1 CCACTAACCGCTATTTCAATGCAAAAATACTTGAACAAGATTGCAAGGCTGATAAAATTGAATTT
47846 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAA
66 TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAA
47884 CTGACCCATA
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
112 93 0.99
113 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (112 bp):
CCACTAACCGCTATTTCAATGCAAAAATACTTGAACAAGATTGCAAGGCTGATAAAATTGAATTT
TATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAATCATTGGT
Found at i:48426 original size:21 final size:21
Alignment explanation
Indices: 48401--48476 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
48391 TCAAGTCAGT
48401 AAACTTCTACCGATACAAGTG
1 AAACTTCTACCGATACAAGTG
48422 AAACTTCTA-C--T---AGTG
1 AAACTTCTACCGATACAAGTG
*
48437 CAGACTTCTACCGATACAAGTG
1 -AAACTTCTACCGATACAAGTG
*
48459 AAACTTCTACCGAAACAA
1 AAACTTCTACCGATACAA
48477 ATCATGCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 4 0.09
16 8 0.18
17 1 0.02
18 1 0.02
19 1 0.02
20 1 0.02
21 25 0.56
22 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.24
Consensus pattern (21 bp):
AAACTTCTACCGATACAAGTG
Found at i:49160 original size:28 final size:28
Alignment explanation
Indices: 49120--49173 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
49110 GATATCCGAT
49120 TTACTCCTTATTGACCCAAAGGTCATGC
1 TTACTCCTTATTGACCCAAAGGTCATGC
49148 TTACTCCTTATTGACCCAAAGGTCAT
1 TTACTCCTTATTGACCCAAAGGTCAT
49174 TATGCTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (28 bp):
TTACTCCTTATTGACCCAAAGGTCATGC
Found at i:51401 original size:26 final size:25
Alignment explanation
Indices: 51372--51460 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 25
51362 ACCACTCCTT
51372 TTTCTTTTTCTCTTTTTTCTTTCTTC
1 TTTCTTTTTCTCTTTTTTCTTT-TTC
51398 TTTCTTTTTTTCTCTTTTTTTCCTTTTTTC
1 TTTC--TTTTTCTC-TTTTTT-C-TTTTTC
51428 TTT-TTTCTT-TCTTTTTTCTTTTTC
1 TTTCTTT-TTCTCTTTTTTCTTTTTC
51452 TTTCTTTTT
1 TTTCTTTTT
51461 TTAGGTGAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
24 11 0.20
25 4 0.07
26 10 0.18
27 5 0.09
28 10 0.18
29 6 0.11
30 7 0.12
31 3 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTCTTTTTCTCTTTTTTCTTTTTC
Found at i:51430 original size:44 final size:44
Alignment explanation
Indices: 51370--51462 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
51360 TGACCACTCC
51370 TTTTTCTTTTTCTCTTTTTTCTTTCTTCTTTCTTTTT-TTCTCTT
1 TTTTTCTTTTTCTCTTTTTTCTTTCTTCTTTCTTTTTCTT-TCTT
*
51414 TTTTTCCTTTTT-TCTTTTTTCTTTCTTTTTTCTTTTTCTTTCTT
1 TTTTT-CTTTTTCTCTTTTTTCTTTCTTCTTTCTTTTTCTTTCTT
51458 TTTTT
1 TTTTT
51463 AGGTGAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 38 0.83
45 8 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (44 bp):
TTTTTCTTTTTCTCTTTTTTCTTTCTTCTTTCTTTTTCTTTCTT
Found at i:51462 original size:18 final size:17
Alignment explanation
Indices: 51370--51461 Score: 118
Period size: 18 Copynumber: 5.3 Consensus size: 17
51360 TGACCACTCC
51370 TTTTTCTTTTTC--TCT
1 TTTTTCTTTTTCTTTCT
51385 TTTTTCTTTCTTCTTTCTT
1 TTTTTCTTT-TTCTTTC-T
51404 TTTTTCTCTTTT-TTTCCT
1 TTTTTCT-TTTTCTTT-CT
51422 TTTTTCTTTTTTCTTTCT
1 TTTTTC-TTTTTCTTTCT
51440 TTTTTCTTTTTCTTTCT
1 TTTTTCTTTTTCTTTCT
51457 TTTTT
1 TTTTT
51462 TAGGTGAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 14
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.13
16 3 0.04
17 16 0.23
18 24 0.35
19 15 0.22
20 2 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTCT
Found at i:57168 original size:31 final size:31
Alignment explanation
Indices: 57106--57169 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
57096 CGGTAACATC
* * **
57106 CCTAATGGAGTTTTGTATGTTGTCCGTAATG
1 CCTAATGGAGTTTTATACGTTGTCCACAATG
57137 CCTAATGGAGTTTTATACGTTGTCCACAATG
1 CCTAATGGAGTTTTATACGTTGTCCACAATG
57168 CC
1 CC
57170 CATAAAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
CCTAATGGAGTTTTATACGTTGTCCACAATG
Found at i:59928 original size:17 final size:17
Alignment explanation
Indices: 59889--59936 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
59879 ATATATATGG
59889 AAATGCAATGACAATGA
1 AAATGCAATGACAATGA
* *
59906 AGATGCAGTGACAA-GAA
1 AAATGCAATGACAATG-A
59923 AAATGCAATGACAA
1 AAATGCAATGACAA
59937 ACGAAATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (17 bp):
AAATGCAATGACAATGA
Found at i:59943 original size:17 final size:16
Alignment explanation
Indices: 59888--59944 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
59878 AATATATATG
*
59888 GAAATGCAATGACAAT
1 GAAATGCAATGACAAA
*
59904 GAAGATGCAGTGACAAGA
1 GAA-ATGCAATGACAA-A
*
59922 AAAATGCAATGACAAA
1 GAAATGCAATGACAAA
59938 CGAAATG
1 -GAAATG
59945 TGATGACAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 4 0.12
17 27 0.82
18 2 0.06
ACGTcount: A:0.51, C:0.12, G:0.23, T:0.14
Consensus pattern (16 bp):
GAAATGCAATGACAAA
Found at i:66687 original size:19 final size:19
Alignment explanation
Indices: 66643--66680 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
66633 CTTCCTCAAG
66643 GCTGTTGATTTCGAGCAGA
1 GCTGTTGATTTCGAGCAGA
66662 GCTGTTGATTTCGAGCAGA
1 GCTGTTGATTTCGAGCAGA
66681 TTTGTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (19 bp):
GCTGTTGATTTCGAGCAGA
Found at i:78055 original size:16 final size:17
Alignment explanation
Indices: 78036--78071 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
78026 TAAAAAAAAG
78036 AAGGA-TTAAATTTTAA
1 AAGGATTTAAATTTTAA
*
78052 AAGGATTTAATTTTTAA
1 AAGGATTTAAATTTTAA
78069 AAG
1 AAG
78072 AATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (17 bp):
AAGGATTTAAATTTTAA
Found at i:79501 original size:29 final size:28
Alignment explanation
Indices: 79463--79567 Score: 111
Period size: 29 Copynumber: 3.5 Consensus size: 28
79453 AGTTTTTCCT
79463 AATTTGGTACCTAAACTTTTTTTGGATCC
1 AATTTGGTACCTAAACTTTTTTT-GATCC
* ** *
79492 AATTTAGTACCTAAACTTGGCACTTTGTTCC
1 AATTTGGTACCTAAACTT---TTTTTGATCC
*
79523 TAATTTGGTACCTAAACTTTTTTTAGATTC
1 -AATTTGGTACCTAAACTTTTTTT-GATCC
79553 AATTTGGTACCTAAA
1 AATTTGGTACCTAAA
79568 TTTATTAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
29 35 0.56
30 3 0.05
31 4 0.06
32 20 0.32
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (28 bp):
AATTTGGTACCTAAACTTTTTTTGATCC
Found at i:79534 original size:32 final size:31
Alignment explanation
Indices: 79445--79541 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 31
79435 TTGATACTTG
*
79445 AACTTGACAGTTT-TTCCTAATTTGGTACCTA
1 AACTTG-CACTTTGTTCCTAATTTGGTACCTA
** * *
79476 AACTT--TTTTTGGATCC-AATTTAGTACCTA
1 AACTTGCACTTT-GTTCCTAATTTGGTACCTA
79505 AACTTGGCACTTTGTTCCTAATTTGGTACCTA
1 AACTT-GCACTTTGTTCCTAATTTGGTACCTA
79537 AACTT
1 AACTT
79542 TTTTTAGATT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
28 3 0.06
29 17 0.33
30 3 0.06
31 9 0.17
32 20 0.38
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (31 bp):
AACTTGCACTTTGTTCCTAATTTGGTACCTA
Found at i:79544 original size:61 final size:60
Alignment explanation
Indices: 79445--79567 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 60
79435 TTGATACTTG
* *
79445 AACTTGACAGTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGATCCAATTTAGTACCTA
1 AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTAGTACCTA
* * *
79505 AACTTGGCACTTTGTTCCTAATTTGGTACCTAAACTTTTTTTAGATTCAATTTGGTACCTA
1 AACTTGACACTTT-TTCCTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTAGTACCTA
79566 AA
1 AA
79568 TTTATTAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 11 0.19
61 46 0.81
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (60 bp):
AACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTAGATCCAATTTAGTACCTA
Found at i:84211 original size:121 final size:121
Alignment explanation
Indices: 83997--84239 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
83987 AATCTTTTCT
83997 TCTAGAAGAGATTGAGTTTGAGTTAGATACTCAACCGTAATAATCGAAATACCCGAATTATTAGG
1 TCTAGAAGAGATTGAGTTTGAGTTAGATACTCAACCGTAATAATCGAAATACCCGAATTATTAGG
84062 AGCTACTTCCCAATCCAGATTAATTACCCCCTGATCCCAGATTTTACGCCCAGGAA
66 AGCTACTTCCCAATCCAGATTAATTACCCCCTGATCCCAGATTTTACGCCCAGGAA
84118 TCTAGAAGAGATTGAGTTTGAGTTAGATACTCAACCGTAATAATCGAAATACCCGAATTATTAGG
1 TCTAGAAGAGATTGAGTTTGAGTTAGATACTCAACCGTAATAATCGAAATACCCGAATTATTAGG
84183 AGCTACTTCCCAATCCAGATTAATTACCCCCTGATCCCAGATTTTACGCCCAGGAA
66 AGCTACTTCCCAATCCAGATTAATTACCCCCTGATCCCAGATTTTACGCCCAGGAA
84239 T
1 T
84240 TAGGCATAGA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (121 bp):
TCTAGAAGAGATTGAGTTTGAGTTAGATACTCAACCGTAATAATCGAAATACCCGAATTATTAGG
AGCTACTTCCCAATCCAGATTAATTACCCCCTGATCCCAGATTTTACGCCCAGGAA
Found at i:88111 original size:2 final size:2
Alignment explanation
Indices: 88104--88146 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
88094 TCACAATTTC
88104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88146 A
1 A
88147 AACATATGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:90598 original size:52 final size:52
Alignment explanation
Indices: 90541--90644 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
90531 TCTTAAGTAA
*
90541 GACTATTTTCGAACTACATTAATAAATTTAGTGTGCTTATTTCTTATTTACT
1 GACTATTTTCGAACTACATTAATAAACTTAGTGTGCTTATTTCTTATTTACT
*
90593 GACTATTTTCGAACTACATTAATAAACTTCGTGTGCTTATTTCTTATTTACT
1 GACTATTTTCGAACTACATTAATAAACTTAGTGTGCTTATTTCTTATTTACT
90645 CTCTTTACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (52 bp):
GACTATTTTCGAACTACATTAATAAACTTAGTGTGCTTATTTCTTATTTACT
Found at i:90773 original size:2 final size:2
Alignment explanation
Indices: 90766--90794 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
90756 AATCGTTGTA
90766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
90795 CTAGTAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:91973 original size:18 final size:18
Alignment explanation
Indices: 91950--91992 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
91940 GAATAGGTTT
91950 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
91968 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
91986 TTAATTA
1 TTAATTA
91993 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:97665 original size:28 final size:28
Alignment explanation
Indices: 97611--97666 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
97601 AATTTAATTT
** *
97611 AAATTGATTTATAAATTTTTTTGAAATA
1 AAATTGATTTATAAATTAATATGAAATA
97639 AAATTGATTTATAAATTAAATAT-AAATA
1 AAATTGATTTATAAATT-AATATGAAATA
97667 TAACATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
AAATTGATTTATAAATTAATATGAAATA
Found at i:101665 original size:21 final size:22
Alignment explanation
Indices: 101621--101666 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
101611 CGGGATATAC
* *
101621 TTTAAAATTTAATTCAAGAGTA
1 TTTAAAATTAAATTCAAAAGTA
*
101643 TTTAAAA-TAAATTCAAAATTA
1 TTTAAAATTAAATTCAAAAGTA
101664 TTT
1 TTT
101667 TTTTTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTAAAATTAAATTCAAAAGTA
Found at i:112731 original size:3 final size:3
Alignment explanation
Indices: 112723--112765 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
112713 AATAAACTTA
112723 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
112766 TCATTTCTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:113686 original size:15 final size:16
Alignment explanation
Indices: 113655--113685 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
113645 GGTATCAAAT
*
113655 TATATCAAAATTAAAA
1 TATATAAAAATTAAAA
113671 TATATAAAAATTAAA
1 TATATAAAAATTAAA
113686 TCTCAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
TATATAAAAATTAAAA
Found at i:114161 original size:16 final size:15
Alignment explanation
Indices: 114130--114160 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
114120 CATTTTAATA
114130 TATTTTTTAAAATTT
1 TATTTTTTAAAATTT
114145 TATTTTTTAAAATTT
1 TATTTTTTAAAATTT
114160 T
1 T
114161 TTAAATTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTAAAATTT
Found at i:114616 original size:3 final size:3
Alignment explanation
Indices: 114608--114645 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
114598 TTTTAATTAT
114608 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
114646 ATCTTGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:115984 original size:15 final size:16
Alignment explanation
Indices: 115956--115989 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
115946 TTTGTTTTCG
*
115956 AAAAATTTTGTTTGAA
1 AAAAATGTTGTTTGAA
115972 AAAAATGTT-TTTGAA
1 AAAAATGTTGTTTGAA
115987 AAA
1 AAA
115990 TATTGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
AAAAATGTTGTTTGAA
Found at i:119430 original size:16 final size:16
Alignment explanation
Indices: 119409--119440 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
119399 ATTAAATATT
119409 TATTAATTTTAAGTGC
1 TATTAATTTTAAGTGC
119425 TATTAATTTTAAGTGC
1 TATTAATTTTAAGTGC
119441 AATAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TATTAATTTTAAGTGC
Found at i:120538 original size:28 final size:28
Alignment explanation
Indices: 120506--120562 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
120496 ACAAAGAAAG
*
120506 GTGCGAGCTATCACAGTAAAGCTGTGAA
1 GTGCGAGCTATCACAGTAAAGCTGCGAA
* *
120534 GTGCGAGCTGTCACAGTGAAGCTGCGAA
1 GTGCGAGCTATCACAGTAAAGCTGCGAA
120562 G
1 G
120563 CAACCGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.19
Consensus pattern (28 bp):
GTGCGAGCTATCACAGTAAAGCTGCGAA
Found at i:121216 original size:30 final size:30
Alignment explanation
Indices: 121181--121246 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
121171 AAAATACCAA
*
121181 ACATAAAAAAATATAATACATTAGTTTTAC
1 ACATAAAAAAACATAATACATTAGTTTTAC
* * *
121211 ACATAAAAAAGCATCATATATTAGTTTTAC
1 ACATAAAAAAACATAATACATTAGTTTTAC
*
121241 ATATAA
1 ACATAA
121247 CAAAGTAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.33
Consensus pattern (30 bp):
ACATAAAAAAACATAATACATTAGTTTTAC
Found at i:121892 original size:39 final size:39
Alignment explanation
Indices: 121840--121929 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
121830 AGCACCGTCG
* * * *
121840 TCGTTCACCAGTCATGCAG-TAGCCATCGATCCACCATCA
1 TCGTTCACTAGTCAAGCAGTTA-CCACCGATCAACCATCA
* *
121879 TTGTTCACTAGTCAAGTAGTTACCACCGATCAACCATCA
1 TCGTTCACTAGTCAAGCAGTTACCACCGATCAACCATCA
*
121918 TCGTTCAATAGT
1 TCGTTCACTAGT
121930 TATGGCTAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 40 0.95
40 2 0.05
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (39 bp):
TCGTTCACTAGTCAAGCAGTTACCACCGATCAACCATCA
Found at i:123245 original size:24 final size:24
Alignment explanation
Indices: 123225--123315 Score: 164
Period size: 24 Copynumber: 3.8 Consensus size: 24
123215 TCTTTCAGTT
123225 AAACTCTGTTTATTTGTTTCAATG
1 AAACTCTGTTTATTTGTTTCAATG
123249 AAACTCTGTTTATTTGTTTCAATG
1 AAACTCTGTTTATTTGTTTCAATG
*
123273 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATG
*
123297 AAACTCTGTTTAGTTGTTT
1 AAACTCTGTTTATTTGTTT
123316 GAGTCAAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATG
Found at i:125553 original size:26 final size:25
Alignment explanation
Indices: 125524--125602 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
125514 GCTTGCAAAA
*
125524 AGAGCTCACGAGCATAGCTCGTAAGG
1 AGAGCTCGC-AGCATAGCTCGTAAGG
* * * *
125550 AGAGATCGCAAACATTGTTCGTAAGG
1 AGAGCTCGC-AGCATAGCTCGTAAGG
*
125576 AGAGCTCGCAGACATAGCTCGCAAGG
1 AGAGCTCGCAG-CATAGCTCGTAAGG
125602 A
1 A
125603 TGGCGCGTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (25 bp):
AGAGCTCGCAGCATAGCTCGTAAGG
Found at i:127272 original size:25 final size:26
Alignment explanation
Indices: 127239--127306 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 26
127229 GGTCTCGCAA
127239 ACACAACTCACAAGGAGAGCT-AGCAG
1 ACACAACTCACAAGGAGAGCTCA-CAG
*
127265 A-ACAACTCACAAGGAGGGCTCACAG
1 ACACAACTCACAAGGAGAGCTCACAG
* *
127290 ACACAGCTCGCAAGGAG
1 ACACAACTCACAAGGAG
127307 GGATCGCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 22 0.59
26 15 0.41
ACGTcount: A:0.40, C:0.28, G:0.25, T:0.07
Consensus pattern (26 bp):
ACACAACTCACAAGGAGAGCTCACAG
Found at i:127308 original size:26 final size:26
Alignment explanation
Indices: 127223--127308 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
127213 ACAAAGCTCG
* * *
127223 CAAGGAGGTCTCGCAAACACAACTCA
1 CAAGGAGGGCTCACAGACACAACTCA
*
127249 CAAGGAGAGCT-AGCAGA-ACAACTCA
1 CAAGGAGGGCTCA-CAGACACAACTCA
* *
127274 CAAGGAGGGCTCACAGACACAGCTCG
1 CAAGGAGGGCTCACAGACACAACTCA
127300 CAAGGAGGG
1 CAAGGAGGG
127309 ATCGCAAGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
25 22 0.44
26 28 0.56
ACGTcount: A:0.37, C:0.27, G:0.28, T:0.08
Consensus pattern (26 bp):
CAAGGAGGGCTCACAGACACAACTCA
Found at i:129689 original size:18 final size:18
Alignment explanation
Indices: 129668--129702 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
129658 GAGAAAGTAG
129668 AAATACATTTAGAGAAAA
1 AAATACATTTAGAGAAAA
129686 AAATACATTTAGAGAAA
1 AAATACATTTAGAGAAA
129703 TGAAACAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (18 bp):
AAATACATTTAGAGAAAA
Found at i:131723 original size:40 final size:40
Alignment explanation
Indices: 131679--131763 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
131669 CTAGTACAAC
* * * *
131679 AATAATGTGGCAATGTTTACAGTGTCACTGTCAGTTTAGT
1 AATAATATCGCAATGTTTACAGTGTCACTGCCAGTTCAGT
*
131719 AATAATATCGCAGTGTTTACAGTGTCACTGCCAGTTCAGT
1 AATAATATCGCAATGTTTACAGTGTCACTGCCAGTTCAGT
*
131759 GATAA
1 AATAA
131764 CACACTCAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (40 bp):
AATAATATCGCAATGTTTACAGTGTCACTGCCAGTTCAGT
Found at i:134650 original size:17 final size:18
Alignment explanation
Indices: 134628--134661 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
134618 GAAGGGAATG
*
134628 GAATGAACAA-AAAAATA
1 GAATGAAAAAGAAAAATA
134645 GAATGAAAAAGAAAAAT
1 GAATGAAAAAGAAAAAT
134662 GATTTCTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (18 bp):
GAATGAAAAAGAAAAATA
Found at i:135744 original size:187 final size:187
Alignment explanation
Indices: 135429--135804 Score: 734
Period size: 187 Copynumber: 2.0 Consensus size: 187
135419 TTTCATTAAA
*
135429 CTTTTAAATTTTTGAAAATTTTAATTAAGTCCCTTAAAATTTAGTTGCAGGATCCACCAGTAACA
1 CTTTTAAATTTTTGAAAATTTTAATTAAGTCCCTTAAAATTTAGTTGCAGGATCCACCACTAACA
*
135494 AAAACATTAGTTTTGGAAAAAAGTGTTCATATACTCTAAGCCTTAAATCTTAAATCCTAAGCAGA
66 AAAACATTAGTTTTGGAAAAAAGTGTTCATATACTCTAAGCCTTAAACCTTAAATCCTAAGCAGA
135559 GGTTTCAAGATTAATCAATTTTTCCCAATAATTGGATGGATTTCCAATCCTCTATGT
131 GGTTTCAAGATTAATCAATTTTTCCCAATAATTGGATGGATTTCCAATCCTCTATGT
135616 CTTTTAAATTTTTGAAAATTTTAATTAAGTCCCTTAAAATTTAGTTGCAGGATCCACCACTAACA
1 CTTTTAAATTTTTGAAAATTTTAATTAAGTCCCTTAAAATTTAGTTGCAGGATCCACCACTAACA
135681 AAAACATTAGTTTTGGAAAAAAGTGTTCATATACTCTAAGCCTTAAACCTTAAATCCTAAGCAGA
66 AAAACATTAGTTTTGGAAAAAAGTGTTCATATACTCTAAGCCTTAAACCTTAAATCCTAAGCAGA
135746 GGTTTCAAGATTAATCAATTTTTCCCAATAATTGGATGGATTTCCAATCCTCTATGT
131 GGTTTCAAGATTAATCAATTTTTCCCAATAATTGGATGGATTTCCAATCCTCTATGT
135803 CT
1 CT
135805 CTTCTCTGTT
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (187 bp):
CTTTTAAATTTTTGAAAATTTTAATTAAGTCCCTTAAAATTTAGTTGCAGGATCCACCACTAACA
AAAACATTAGTTTTGGAAAAAAGTGTTCATATACTCTAAGCCTTAAACCTTAAATCCTAAGCAGA
GGTTTCAAGATTAATCAATTTTTCCCAATAATTGGATGGATTTCCAATCCTCTATGT
Found at i:140819 original size:42 final size:42
Alignment explanation
Indices: 140702--140906 Score: 270
Period size: 42 Copynumber: 4.9 Consensus size: 42
140692 AGGCGGAGCT
*
140702 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTG-A-AG
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAACAC
* * *
140742 ATCATTCAATCTTTTACCCTAACCAGAGGGTAGATTGAACAC
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAACAC
* ** *
140784 ACCATCTAATCTTTTACCCTAGTCAGAAGGCAGATTGAACAC
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAACAC
* * *
140826 ACCATCCAATCTTTTACCCCAACCAGAGGGCAGATTAAAGAC
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAACAC
* **
140868 ACCATCCAATCTTTTACCCCATTCAGAGGGCAGATTGAA
1 ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAA
140907 GCTGGGTTAT
Statistics
Matches: 142, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 34 0.24
41 1 0.01
42 107 0.75
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (42 bp):
ACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAACAC
Found at i:142757 original size:31 final size:28
Alignment explanation
Indices: 142702--142760 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
142692 TTTATTTTCC
142702 TTAAACCTTAATCTTTATATTTTATTTA
1 TTAAACCTTAATCTTTATATTTTATTTA
142730 TTAAATCCTTAAATCATTTAT-TATTTATTTA
1 TTAAA-CCTT-AATC-TTTATAT-TTTATTTA
142761 GGATTGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.19
29 4 0.15
30 5 0.19
31 13 0.48
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAAACCTTAATCTTTATATTTTATTTA
Found at i:143538 original size:6 final size:6
Alignment explanation
Indices: 143517--143581 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
143507 GTCCAACAAG
* * *
143517 ATTTAA ATTT-A TTTTAA GTTTAA ATTT-- ACTTAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
143560 ATTATAA ATTTAA TATTTAA AT
1 ATT-TAA ATTTAA -ATTTAA AT
143582 CTATTTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
4 6 0.13
5 5 0.11
6 27 0.57
7 9 0.19
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:143540 original size:17 final size:17
Alignment explanation
Indices: 143517--143578 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
143507 GTCCAACAAG
143517 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
143534 GTTTAAATTTA-CTTAA
1 ATTTAAATTTATTTTAA
*
143550 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
143567 ATTTAATATTTA
1 ATTTAA-ATTTA
143579 AATCTATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 14 0.37
17 19 0.50
18 5 0.13
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:143581 original size:24 final size:22
Alignment explanation
Indices: 143546--143591 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
143536 TTAAATTTAC
*
143546 TTAAATTTAAATTTATTATAAAT
1 TTAAATTTAAATCTATT-TAAAT
143569 TTAATATTTAAATCTATTTAAAT
1 TTAA-ATTTAAATCTATTTAAAT
143592 CAAGTCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATTTAAATCTATTTAAAT
Found at i:145504 original size:30 final size:30
Alignment explanation
Indices: 145463--145709 Score: 214
Period size: 30 Copynumber: 8.4 Consensus size: 30
145453 TAAAAATCTT
145463 ATTTTTAACCCCAAAACTT-C-AAAAATTCC
1 ATTTTT-ACCCCAAAACTTCCAAAAAATTCC
*
145492 ATTTTTTCACCCC-AAACTT-CTAAAAATTCC
1 A-TTTTT-ACCCCAAAACTTCCAAAAAATTCC
* **
145522 ATTTTTTTACCACTGAACTT-CAAAAAATTCC
1 A--TTTTTACCCCAAAACTTCCAAAAAATTCC
145553 ATTTTTGACCCCAAAACTTCCAAAAAATT-C
1 ATTTTT-ACCCCAAAACTTCCAAAAAATTCC
**
145583 A-TTTTACCCCCGAACTTCC-AAAAATTCC
1 ATTTTTACCCCAAAACTTCCAAAAAATTCC
* * *
145611 ATTTTGACCTCGAAACTTCC-AAAAATT-C
1 ATTTTTACCCCAAAACTTCCAAAAAATTCC
* * *
145639 AATTTTACCCCCAAACTTCAAAAAAAATT-C
1 ATTTTTACCCCAAAACTTC-CAAAAAATTCC
145669 ATTTTTAACCCCAAAACTTCC-AAAAATTACC
1 ATTTTT-ACCCCAAAACTTCCAAAAAATT-CC
145700 A-TTTTACCCC
1 ATTTTTACCCC
145710 CTGAATGTCC
Statistics
Matches: 184, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.04
28 30 0.16
29 50 0.27
30 52 0.28
31 45 0.24
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (30 bp):
ATTTTTACCCCAAAACTTCCAAAAAATTCC
Found at i:145600 original size:28 final size:28
Alignment explanation
Indices: 145526--145733 Score: 149
Period size: 29 Copynumber: 7.1 Consensus size: 28
145516 AATTCCATTT
* *
145526 TTTTACCACTGAACTT-CAAAAAATTCCA
1 TTTTACCCCCGAACTTCCAAAAAATT-CA
**
145554 TTTTTGACCCCAAAACTTCCAAAAAATTCA
1 -TTTT-ACCCCCGAACTTCCAAAAAATTCA
145584 TTTTACCCCCGAACTTCC-AAAAATTCCA
1 TTTTACCCCCGAACTTCCAAAAAATT-CA
*
145612 TTTTGA-CCTCGAAACTTCC-AAAAATTCAA
1 TTTT-ACCCCCG-AACTTCCAAAAAATTC-A
* *
145641 TTTTACCCCCAAACTTCAAAAAAAATTCA
1 TTTTACCCCCGAACTTC-CAAAAAATTCA
**
145670 TTTTTAACCCCAAAACTTCC-AAAAATTACCA
1 -TTTT-ACCCCCGAACTTCCAAAAAATT--CA
* *
145701 TTTTACCCCCTGAA-TGTCCAAAAACTCCA
1 TTTTACCCCC-GAACT-TCCAAAAAATTCA
145730 TTTT
1 TTTT
145734 CGACGTCAAA
Statistics
Matches: 148, Mismatches: 15, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.05
28 30 0.20
29 51 0.34
30 32 0.22
31 28 0.19
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (28 bp):
TTTTACCCCCGAACTTCCAAAAAATTCA
Found at i:148375 original size:192 final size:192
Alignment explanation
Indices: 148036--148446 Score: 544
Period size: 192 Copynumber: 2.1 Consensus size: 192
148026 AACGCTAGGA
* * *
148036 ACAAAAGTAGCAATAGTGGTACAGAA-AATTTATCAACACAAATAGATTTTAGAAAACAAGATAA
1 ACAAAAGAAGCAACAGCGGTACA-AAGAATTTATCAACACAAATAGATTTTAGAAAACAAGATAA
148100 AAAAAACAACGAAGCCCATTAAAAAATAGAAAGACATTAGGGATTTAGAAGACACCTAAATTGTT
65 AAAAAACAACGAAGCCCATTAAAAAATAGAAAGACATTAGGGATTTAGAAGACACCTAAATTGTT
* ** * * * **
148165 AGAGATTAGCTGACGGCACGGCAGGACAG-AAATGATTAGTG-TGGAGAAGGTGACAAGCTGGAG
130 AGAGATTAGCTAACGGCACAACAGGA-AGAAAAAGACTAGAGCT-GAGAAGGTGACAAGCCAGAG
* * * *
148228 ACAAAAGAAGCAACAGCGGTACAAAGGATTTATCAACACAAATAGGTTTTAGCAAACAAGTTAAA
1 ACAAAAGAAGCAACAGCGGTACAAAGAATTTATCAACACAAATAGATTTTAGAAAACAAGATAAA
* *
148293 AAAAACAATGAAGCCCATTAGAAAATAGAAAG-CATTAGGGATTTAGAAGACACCTGAAATTGTT
66 AAAAACAACGAAGCCCATTAAAAAATAGAAAGACATTAGGGATTTAGAAGACACCT-AAATTGTT
* * * *
148357 AGAGATT-GATCAACGGCACAACAGGATGAAAAAGACTGGAGCTGAGAAGGTGACAAGCCATAG
130 AGAGATTAGCT-AACGGCACAACAGGAAGAAAAAGACTAGAGCTGAGAAGGTGACAAGCCAGAG
*
148420 ACAAAAGAAGCAGCAGCGGTACAAAGA
1 ACAAAAGAAGCAACAGCGGTACAAAGA
148447 TTAACTATTG
Statistics
Matches: 191, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
191 28 0.15
192 162 0.85
193 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (192 bp):
ACAAAAGAAGCAACAGCGGTACAAAGAATTTATCAACACAAATAGATTTTAGAAAACAAGATAAA
AAAAACAACGAAGCCCATTAAAAAATAGAAAGACATTAGGGATTTAGAAGACACCTAAATTGTTA
GAGATTAGCTAACGGCACAACAGGAAGAAAAAGACTAGAGCTGAGAAGGTGACAAGCCAGAG
Found at i:152200 original size:2 final size:2
Alignment explanation
Indices: 152195--152224 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
152185 CTTCTCACAC
*
152195 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
152225 CACCACATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153738 original size:26 final size:25
Alignment explanation
Indices: 153709--153764 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
153699 AACCTATAAT
* * *
153709 AGAAAAATATTTTAGGTGTCAAATTG
1 AGAAAAA-AATTTAGGTATCAAAGTG
153735 AGAAAAAAATTTAGGTATCAAAGTG
1 AGAAAAAAATTTAGGTATCAAAGTG
153760 -GAAAA
1 AGAAAA
153765 TTAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.27
Consensus pattern (25 bp):
AGAAAAAAATTTAGGTATCAAAGTG
Found at i:154709 original size:16 final size:17
Alignment explanation
Indices: 154688--154725 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
154678 TATATAAAAA
*
154688 ATATT-ATATTAATTAT
1 ATATTAATAATAATTAT
154704 ATATTAAATAATAATTAT
1 ATATT-AATAATAATTAT
154722 ATAT
1 ATAT
154726 ATTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAATAATAATTAT
Found at i:154745 original size:27 final size:27
Alignment explanation
Indices: 154670--154738 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
154660 TTGACCCAAA
154670 TATATT-ATTATATA--AAA-AAT-AT
1 TATATTAATTATATATTAAATAATAAT
154692 TATATTAATTATATATTAAATAATAAT
1 TATATTAATTATATATTAAATAATAAT
154719 TATA-TATATT-TATATTAAAT
1 TATATTA-ATTATATATTAAAT
154739 CACTAATCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.15
23 8 0.20
25 3 0.07
26 15 0.37
27 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATATTAATTATATATTAAATAATAAT
Found at i:156224 original size:2 final size:2
Alignment explanation
Indices: 156217--156260 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
156207 AATACACAAA
156217 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
156259 CT
1 CT
156261 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:156265 original size:2 final size:2
Alignment explanation
Indices: 156260--156292 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
156250 TCTCTCTCTC
156260 TA TA TA TA 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 TA TA TA TA T
156293 TCAACTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:161259 original size:11 final size:11
Alignment explanation
Indices: 161243--161269 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
161233 AGATAATATT
161243 TTCATATCATG
1 TTCATATCATG
161254 TTCATATCATG
1 TTCATATCATG
161265 TTCAT
1 TTCAT
161270 GAATGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (11 bp):
TTCATATCATG
Found at i:163717 original size:43 final size:42
Alignment explanation
Indices: 163649--163829 Score: 157
Period size: 43 Copynumber: 4.2 Consensus size: 42
163639 ACGCCGCTAA
163649 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAACAAACC
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCC-ACAAACC
* * * * *
163692 CCGTTAGAGAACATGGTTTTTAGCGGCGCTTTTTCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACAAACC
* * * * *
163735 CTGCTAAAAAATATGGTCTTTAGCGGCACTTTCCCCACAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCACAAACC
* * * * * *
163778 CCACTATAGCTA-ATGTTCTTTAGCGGCGTTTTTCCCACAAACG
1 CCGCTAAAG-AACATGGTCTTTAGCGGCG-CTTTCCCACAAACC
*
163821 TCGCTAAAG
1 CCGCTAAAG
163830 TTAACAGATT
Statistics
Matches: 110, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.03
43 98 0.89
44 9 0.08
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (42 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACAAACC
Found at i:163800 original size:86 final size:86
Alignment explanation
Indices: 163650--163828 Score: 213
Period size: 86 Copynumber: 2.1 Consensus size: 86
163640 CGCCGCTAAC
* * **
163650 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAACAAACCCCGTTAGAGAACATGGTTTTTAG
1 CGCTAAAAAACATGGTCTTTAGCGGCACTTTCCCAACAAACCCCACTAGAGAACATGGTTTTTAG
163715 CGGCGCTTTTT-CCACAAACG-
66 CGGCG-TTTTTCCCACAAACGT
* * * * *
163735 CTGCTAAAAAATATGGTCTTTAGCGGCACTTTCCCCACAAACGCCACTATAGCTA-AT-GTTCTT
1 C-GCTAAAAAACATGGTCTTTAGCGGCACTTTCCCAACAAACCCCACTAGAG-AACATGGTT-TT
163798 TAGCGGCGTTTTTCCCACAAACGT
63 TAGCGGCGTTTTTCCCACAAACGT
163822 CGCTAAA
1 CGCTAAA
163829 GTTAACAGAT
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
85 9 0.11
86 69 0.86
87 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (86 bp):
CGCTAAAAAACATGGTCTTTAGCGGCACTTTCCCAACAAACCCCACTAGAGAACATGGTTTTTAG
CGGCGTTTTTCCCACAAACGT
Found at i:166964 original size:21 final size:22
Alignment explanation
Indices: 166938--166988 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
166928 AAGATAAGAT
*
166938 TGAAGAAGA-GAATGGCGTGCA
1 TGAAGAAGAGGAAGGGCGTGCA
*
166959 TGAAGAA-AGGAAGGGCGTGCG
1 TGAAGAAGAGGAAGGGCGTGCA
166980 TGAAGAAGA
1 TGAAGAAGA
166989 AGGTAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.41, T:0.12
Consensus pattern (22 bp):
TGAAGAAGAGGAAGGGCGTGCA
Done.