Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012210.1 Kokia drynarioides strain JFW-HI SEQ_127211, 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: 66538
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:157 original size:16 final size:16
Alignment explanation
Indices: 136--198 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
126 TTTGACTGAC
*
136 CAAAAATAAAACAAAT
1 CAAAAAAAAAACAAAT
*
152 CAAAAACCAAAA-AAAT
1 CAAAAA-AAAAACAAAT
*
168 AAAATAAAAAAACAAAAT
1 CAAA-AAAAAAAC-AAAT
186 -AAAAAAAAAACAA
1 CAAAAAAAAAACAA
199 CATTAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 2 0.05
16 25 0.62
17 9 0.22
18 4 0.10
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (16 bp):
CAAAAAAAAAACAAAT
Found at i:178 original size:13 final size:13
Alignment explanation
Indices: 160--192 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
150 ATCAAAAACC
*
160 AAAAAAATAAAAT
1 AAAAAAACAAAAT
173 AAAAAAACAAAAT
1 AAAAAAACAAAAT
186 AAAAAAA
1 AAAAAAA
193 AAACAACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAAACAAAAT
Found at i:1793 original size:27 final size:27
Alignment explanation
Indices: 1741--1857 Score: 96
Period size: 27 Copynumber: 4.3 Consensus size: 27
1731 AATTTTTAAA
* *
1741 AAAATTAAATCCTTT-TGTTCCATTTTCT
1 AAAATT-AATCCTTTAT-TTCTATTTTTT
*
1769 -AAATTAATCCTTTATTTGTATTTTTT
1 AAAATTAATCCTTTATTTCTATTTTTT
* * *
1795 AAAATCAAACCCTTTTATTCCT-TTTTTT
1 AAAAT-TAATCC-TTTATTTCTATTTTTT
** *
1823 TTAATTAATCCTTTATTTTTATTTTTT
1 AAAATTAATCCTTTATTTCTATTTTTT
1850 AAAATTAA
1 AAAATTAA
1858 ACCCCTTTTT
Statistics
Matches: 69, Mismatches: 15, Indels: 11
0.73 0.16 0.12
Matches are distributed among these distances:
26 23 0.33
27 26 0.38
28 13 0.19
29 7 0.10
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.56
Consensus pattern (27 bp):
AAAATTAATCCTTTATTTCTATTTTTT
Found at i:1809 original size:28 final size:27
Alignment explanation
Indices: 1777--1878 Score: 73
Period size: 28 Copynumber: 3.7 Consensus size: 27
1767 CTAAATTAAT
*
1777 CCTTTATTTGTATTTTTTAAAATCAAAC
1 CCTTTATTTATATTTTTTAAAAT-AAAC
** ** * *
1805 CCTTTTATTCCT-TTTTTTTTAATTAAT
1 CC-TTTATTTATATTTTTTAAAATAAAC
*
1832 CCTTTATTTTTATTTTTTAAAATTAAACC
1 CCTTTATTTATATTTTTTAAAA-TAAA-C
1861 CCTTT-TTTATATTCTTTT
1 CCTTTATTTATATT-TTTT
1879 TAATTAAATC
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
26 7 0.12
27 12 0.21
28 21 0.38
29 16 0.29
ACGTcount: A:0.25, C:0.15, G:0.01, T:0.60
Consensus pattern (27 bp):
CCTTTATTTATATTTTTTAAAATAAAC
Found at i:1879 original size:55 final size:55
Alignment explanation
Indices: 1770--1885 Score: 164
Period size: 55 Copynumber: 2.1 Consensus size: 55
1760 CCATTTTCTA
* *
1770 AATTAATCCTTTATTTGTATTTTTTAAAATCAAACCCTTTTATTCCTTTTTTTTT
1 AATTAATCCTTTATTTGTATTTTTTAAAATCAAACCCTTTTATTCATTTCTTTTT
* *
1825 AATTAATCCTTTATTTTTATTTTTTAAAATTAAACCCCTTTT-TT-ATATTCTTTTT
1 AATTAATCCTTTATTTGTATTTTTTAAAATCAAA-CCCTTTTATTCAT-TTCTTTTT
1880 AATTAA
1 AATTAA
1886 ATCATCTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
54 1 0.02
55 47 0.85
56 7 0.13
ACGTcount: A:0.28, C:0.13, G:0.01, T:0.58
Consensus pattern (55 bp):
AATTAATCCTTTATTTGTATTTTTTAAAATCAAACCCTTTTATTCATTTCTTTTT
Found at i:6507 original size:7 final size:7
Alignment explanation
Indices: 6495--6539 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
6485 AGAAGAAAGG
6495 AAAAGAA
1 AAAAGAA
6502 AAAAGAA
1 AAAAGAA
6509 AAAAGGAA
1 AAAA-GAA
6517 AAAAGAA
1 AAAAGAA
* *
6524 GAAA-TA
1 AAAAGAA
6530 AAAAGAA
1 AAAAGAA
6537 AAA
1 AAA
6540 TGAGAGGTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 4 0.12
7 21 0.66
8 7 0.22
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:6508 original size:20 final size:21
Alignment explanation
Indices: 6479--6518 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
6469 ATTTCACCCA
*
6479 AAAAAGAGAAGAAAGGAAAAG
1 AAAAAGAGAAAAAAGGAAAAG
6500 AAAAA-AGAAAAAAGGAAAA
1 AAAAAGAGAAAAAAGGAAAA
6519 AAGAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAAAAAGGAAAAG
Found at i:6517 original size:15 final size:14
Alignment explanation
Indices: 6495--6539 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
6485 AGAAGAAAGG
6495 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
6509 AAAAGGAAAAAAGAA
1 AAAA-GAAAAAAGAA
* *
6524 GAAA-TAAAAAGAA
1 AAAAGAAAAAAGAA
6537 AAA
1 AAA
6540 TGAGAGGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 10 0.37
14 4 0.15
15 13 0.48
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:6521 original size:28 final size:29
Alignment explanation
Indices: 6478--6544 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 29
6468 TATTTCACCC
*
6478 AAAAAAGAGAAGAAAGGAA-AAGA-AAAAAG
1 AAAAAAGAGAA-AAAAGAAGAA-ATAAAAAG
6507 AAAAAAG-GAAAAAAGAAGAAATAAAAAG
1 AAAAAAGAGAAAAAAGAAGAAATAAAAAG
*
6535 AAAAATGAGA
1 AAAAAAGAGA
6545 GGTCGAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 7 0.21
28 17 0.52
29 9 0.27
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (29 bp):
AAAAAAGAGAAAAAAGAAGAAATAAAAAG
Found at i:7782 original size:42 final size:42
Alignment explanation
Indices: 7711--8195 Score: 544
Period size: 42 Copynumber: 11.8 Consensus size: 42
7701 CAAAACCATT
*
7711 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGGCATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * * *
7753 CAATTTTTTACCTCGATCATGGGGTAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* *
7795 CAATCTCTTA-CCCGATCATAGGGTAGATT---GACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* *
7833 CAATCTCTTACCCCAACCATGGGGCAGATTGAAG-CTATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC-ATCATC
* *
7875 CAATCTCTTACCCCAATCATGGAGCAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * * *
7917 TAATCTCTTATCCCGACCACGGGGCAGATTGAAG---TCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * ***
7956 TAATCTTTTACCCCGATCATAAAGCAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * *
7998 CAATCTCTTACCCCGATTATGAGGCAAATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * *
8040 CAATATCTTACCCCGATCATGGGGCAGATTAAAGACATTATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
** * * *
8082 CAATCTCTTACCCAAACCATGTGGAAGATTGAAG-C--CATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* *
8121 CAATCTCTTACCCCGATAATGGGGTAGATTGAAGACATCATC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
* * *
8163 TAATCT-TTGACCTCGACCATGGGGCAGATTGAA
1 CAATCTCTT-ACCCCGATCATGGGGCAGATTGAA
8196 TCACTGATGG
Statistics
Matches: 371, Mismatches: 59, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
38 19 0.05
39 78 0.21
40 1 0.00
41 21 0.06
42 251 0.68
43 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATC
Found at i:7999 original size:123 final size:121
Alignment explanation
Indices: 7711--8195 Score: 530
Period size: 123 Copynumber: 4.0 Consensus size: 121
7701 CAAAACCATT
* * * * * *
7711 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGGCATCATCCAATTTTTTACCTCGATCATGGG
1 CAATCTCTTACCCCAACCATGGGGCAGATTGAA-GCATCATCCAATCTCTTACCCCGATCATGGA
* * * *
7776 GTAGATTGAAGACATCATCCAATCTCTTACCCGATCATAGGGTAGATTGACA-TCATC
65 GCAGATTGAAGACATCATCCAATCTCTTACCCGACCATGGGGCAGATTGA-AGTCATC
*
7833 CAATCTCTTACCCCAACCATGGGGCAGATTGAAGCTATCATCCAATCTCTTACCCCAATCATGGA
1 CAATCTCTTACCCCAACCATGGGGCAGATTGAAGC-ATCATCCAATCTCTTACCCCGATCATGGA
* *
7898 GCAGATTGAAGACATCATCTAATCTCTTATCCCGACCACGGGGCAGATTGAAGTCATC
65 GCAGATTGAAGACATCATCCAATCTCTTA-CCCGACCATGGGGCAGATTGAAGTCATC
* * * * *** *
7956 TAATCTTTTACCCCGATCATAAAGCAGATTGAAGACATCATCCAATCTCTTACCCCGATTAT-GA
1 CAATCTCTTACCCCAACCATGGGGCAGATTGAAG-CATCATCCAATCTCTTACCCCGATCATGGA
* * * * *
8020 GGCAAATTGAAGACATCATCCAATATCTTACCCCGATCATGGGGCAGATTAAAGACATTATC
65 -GCAGATTGAAGACATCATCCAATCTCTTA-CCCGACCATGGGGCAGATTGAAG---TCATC
* * * * *
8082 CAATCTCTTACCCAAACCATGTGGAAGATTGAAGC--CATCCAATCTCTTACCCCGATAATGGGG
1 CAATCTCTTACCCCAACCATGGGGCAGATTGAAGCATCATCCAATCTCTTACCCCGATCATGGAG
* *
8145 TAGATTGAAGACATCATCTAATCT-TTGACCTCGACCATGGGGCAGATTGAA
66 CAGATTGAAGACATCATCCAATCTCTT-ACC-CGACCATGGGGCAGATTGAA
8196 TCACTGATGG
Statistics
Matches: 305, Mismatches: 47, Indels: 21
0.82 0.13 0.06
Matches are distributed among these distances:
121 2 0.01
122 89 0.29
123 182 0.60
124 2 0.01
125 1 0.00
126 29 0.10
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (121 bp):
CAATCTCTTACCCCAACCATGGGGCAGATTGAAGCATCATCCAATCTCTTACCCCGATCATGGAG
CAGATTGAAGACATCATCCAATCTCTTACCCGACCATGGGGCAGATTGAAGTCATC
Found at i:8052 original size:165 final size:164
Alignment explanation
Indices: 7711--8195 Score: 559
Period size: 165 Copynumber: 2.9 Consensus size: 164
7701 CAAAACCATT
* * * *
7711 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGGCATCATCCAATTTTTTACCTCGATCATGGG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACC-CGACCATGGG
*
7776 GTAGATTGAAGACATCATCCAATCTCTTA-CCCGATCATAGGGTAGATT---GACATCATCCAAT
65 GAAGATTGAAG---TCATCCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACATCATCCAAT
* *
7837 CTCTTACCCCAACCATGGGGCAGATTGAAGCTATCATC
127 CTCTTACCCCAACCATGAGGCAAATTGAAGCTATCATC
* * * *
7875 CAATCTCTTACCCCAATCATGGAGCAGATTGAAGACATCATCTAATCTCTTATCCCGACCACGGG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTA-CCCGACCATGGG
* * * ** *
7940 GCAGATTGAAGTCATCTAATCTTTTACCCCGATCATAAAGCAGATTGAAGACATCATCCAATCTC
65 GAAGATTGAAGTCATCCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACATCATCCAATCTC
* **
8005 TTACCCCGATTATGAGGCAAATTGAAGAC-ATCATC
130 TTACCCCAACCATGAGGCAAATTGAAG-CTATCATC
* * * * *
8040 CAATATCTTACCCCGATCATGGGGCAGATTAAAGACATTATCCAATCTCTTACCCAAACCATGTG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCC-GACCATGGG
* * * *
8105 GAAGATTGAAGCCATCCAATCTCTTACCCCGATAATGGGGTAGATTGAAGACATCATCTAATCT-
65 GAAGATTGAAGTCATCCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACATCATCCAATCTC
* * * *
8169 TTGACCTCGACCATGGGGCAGATTGAA
130 TT-ACCCCAACCATGAGGCAAATTGAA
8196 TCACTGATGG
Statistics
Matches: 270, Mismatches: 43, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
161 13 0.05
162 16 0.06
164 69 0.26
165 171 0.63
166 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (164 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCGACCATGGGG
AAGATTGAAGTCATCCAATCTCTTACCCCGATCATAGGGTAGATTGAAGACATCATCCAATCTCT
TACCCCAACCATGAGGCAAATTGAAGCTATCATC
Found at i:9524 original size:21 final size:21
Alignment explanation
Indices: 9498--9540 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9488 ATCTGACATA
*
9498 AATGCATTGACATCAGTACTC
1 AATGCATTGACATCAATACTC
9519 AATGCATTGACATCAATACTC
1 AATGCATTGACATCAATACTC
9540 A
1 A
9541 CATTACACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (21 bp):
AATGCATTGACATCAATACTC
Found at i:19747 original size:42 final size:42
Alignment explanation
Indices: 19667--19888 Score: 213
Period size: 42 Copynumber: 5.4 Consensus size: 42
19657 ACCTATCAAG
* * *
19667 CACCATTCAATCTCTTAT-CCCGATCATGGGGCAGATTGAAGA
1 CACCATCCAATCTCTT-TCCCCGATCATAGGGCAAATTGAAGA
* * *
19709 CATCATCCAATCTCTTTCCCCGACCATAAGGCAAATTGAAG-
1 CACCATCCAATCTCTTTCCCCGATCATAGGGCAAATTGAAGA
* *
19750 CACCATCCAATCTCTTACCCCAATCATAGGGCAAATTGAAGA
1 CACCATCCAATCTCTTTCCCCGATCATAGGGCAAATTGAAGA
* * * * * * *
19792 TATCATCCAATCTCTTACCTCGACCATTGGGCAGATTGAAG-
1 CACCATCCAATCTCTTTCCCCGATCATAGGGCAAATTGAAGA
* * *
19833 CA--ATCCAATATCTTAT-CTCGATCATGGGGCAAATTGAAGA
1 CACCATCCAATCTCTT-TCCCCGATCATAGGGCAAATTGAAGA
*
19873 TACCATCCAATCTCTT
1 CACCATCCAATCTCTT
19889 ACCCAATCAT
Statistics
Matches: 148, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
39 31 0.21
40 1 0.01
41 38 0.26
42 78 0.53
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (42 bp):
CACCATCCAATCTCTTTCCCCGATCATAGGGCAAATTGAAGA
Found at i:19803 original size:83 final size:83
Alignment explanation
Indices: 19664--19892 Score: 318
Period size: 83 Copynumber: 2.8 Consensus size: 83
19654 AACACCTATC
* * * *
19664 AAGCACCATTCAATCTCTTATCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTTCCC
1 AAGCACCATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
19729 CGACCATAAGGCAAATTG
66 CGACCATAAGGCAAATTG
* * * *
19747 AAGCACCATCCAATCTCTTACCCCAATCATAGGGCAAATTGAAGATATCATCCAATCTCTTACCT
1 AAGCACCATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
** *
19812 CGACCATTGGGCAGATTG
66 CGACCATAAGGCAAATTG
* * *
19830 AAGCA--ATCCAATATCTTATCTCGATCATGGGGCAAATTGAAGATACCATCCAATCTCTTACCC
1 AAGCACCATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
19893 AATCATGAGG
Statistics
Matches: 128, Mismatches: 18, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
81 51 0.40
83 77 0.60
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (83 bp):
AAGCACCATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
CGACCATAAGGCAAATTG
Found at i:19874 original size:81 final size:82
Alignment explanation
Indices: 19664--19930 Score: 308
Period size: 83 Copynumber: 3.3 Consensus size: 82
19654 AACACCTATC
* * * *
19664 AAGCACCATTCAATCTCTTATCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTTCCC
1 AAGCA-CATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
19729 CGACCATAAGGCAAATTG
65 CGACCATAAGGCAAATTG
* * * *
19747 AAGCACCATCCAATCTCTTACCCCAATCATAGGGCAAATTGAAGATATCATCCAATCTCTTACCT
1 AAGCA-CATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCC
** *
19812 CGACCATTGGGCAGATTG
65 CGACCATAAGGCAAATTG
* * *
19830 AAGCA-ATCCAATATCTTATCTCGATCATGGGGCAAATTGAAGATACCATCCAATCTCTTA-CCC
1 AAGCACATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCCC
* * *
19893 AATCATGAGG-AAGATTG
66 GACCATAAGGCAA-ATTG
* *
19910 AAGC-CATCCTATCTTTTATCC
1 AAGCACATCCAATCTCTTATCC
19931 TAATCAGAGG
Statistics
Matches: 155, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
79 1 0.01
80 28 0.18
81 49 0.32
83 77 0.50
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (82 bp):
AAGCACATCCAATCTCTTATCCCGATCATGGGGCAAATTGAAGATATCATCCAATCTCTTACCCC
GACCATAAGGCAAATTG
Found at i:20099 original size:91 final size:91
Alignment explanation
Indices: 19952--20139 Score: 256
Period size: 91 Copynumber: 2.1 Consensus size: 91
19942 AAGATTGCAG
* * *
19952 ACCATCCAATCTTTTACCTCTAATCAAGAGGGACAGATTGAAGCCGTCGACCAATCTTTTACCCC
1 ACCATCCAATCTTTTACCTCTAATCAAAAGGGACAAATTGAAGCCATCGACCAATCTTTTACCCC
*
20017 T-AATCAAGAGGGGCAGATTAAAGCC
66 TAAATCAAGAGGGGCAAATTAAAGCC
* *
20042 ACCATCCAATCTTTTACC-CTTAAGTCAAAAGGGACAAATTGAAGTCATC-ATCTAATCTTTTAC
1 ACCATCCAATCTTTTACCTC-TAA-TCAAAAGGGACAAATTGAAGCCATCGA-CCAATCTTTTAC
* *
20105 CCCTAAATCAAGAGGGGCAAATTGAAGCT
63 CCCTAAATCAAGAGGGGCAAATTAAAGCC
20134 ACCATC
1 ACCATC
20140 TCACAGAAGC
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
89 1 0.01
90 22 0.26
91 36 0.42
92 27 0.31
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (91 bp):
ACCATCCAATCTTTTACCTCTAATCAAAAGGGACAAATTGAAGCCATCGACCAATCTTTTACCCC
TAAATCAAGAGGGGCAAATTAAAGCC
Found at i:20126 original size:46 final size:45
Alignment explanation
Indices: 19862--20132 Score: 217
Period size: 45 Copynumber: 6.2 Consensus size: 45
19852 GATCATGGGG
** * * *
19862 CAAATTGAAGATACCATCCAATCTCTTA-CCC-AATCATGA-GGA
1 CAAATTGAAGCCATCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19904 -AGATTGAAG-C--CATCCTATCTTTTA-TCCTAATC-AGAGGGA
1 CAAATTGAAGCCATCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * * *
19943 -AGATTGCAG--ACCATCCAATCTTTTACCTCTAATCAAGAGGGA
1 CAAATTGAAGCCATCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19985 CAGATTGAAGCCGTCGA-CCAATCTTTTACCCCTAATCAAGAGGGG
1 CAAATTGAAGCCATC-ATCCAATCTTTTACCCCTAATCAAGAGGGA
* * * * *
20030 CAGATTAAAGCCACCATCCAATCTTTTACCCTTAAGTCAAAAGGGA
1 CAAATTGAAGCCATCATCCAATCTTTTACCCCTAA-TCAAGAGGGA
* * *
20076 CAAATTGAAGTCATCATCTAATCTTTTACCCCTAAATCAAGAGGGG
1 CAAATTGAAGCCATCATCCAATCTTTTACCCCT-AATCAAGAGGGA
20122 CAAATTGAAGC
1 CAAATTGAAGC
20133 TACCATCTCA
Statistics
Matches: 186, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
38 16 0.09
39 15 0.08
40 13 0.07
41 14 0.08
42 7 0.04
43 8 0.04
44 1 0.01
45 56 0.30
46 54 0.29
47 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
CAAATTGAAGCCATCATCCAATCTTTTACCCCTAATCAAGAGGGA
Found at i:20140 original size:46 final size:45
Alignment explanation
Indices: 19740--20139 Score: 226
Period size: 46 Copynumber: 9.4 Consensus size: 45
19730 GACCATAAGG
* *
19740 CAAATTGAAGC-ACCATCCAATCTCTTACCCC-AATC-ATAGGG-
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * * * * * **
19781 CAAATTGAAGATATCATCCAATCTCTTACCTC-GA-CCATTGGG-
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * * * * * *
19823 CAGATTGAAGC-A--ATCCAATATCTTATCTC-GATCATG-GGG-
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19862 CAAATTGAAGATACCATCCAATCTCTTA-CCC-AATCATGA-GGA
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19904 -AGATTGAAG---CCATCCTATCTTTTA-TCCTAATC-AGAGGGA
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19943 -AGATTGCAG--ACCATCCAATCTTTTACCTCTAATCAAGAGGGA
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * *
19985 CAGATTGAAGCCGT-CGA-CCAATCTTTTACCCCTAATCAAGAGGGG
1 CAAATTGAAG-C-TACCATCCAATCTTTTACCCCTAATCAAGAGGGA
* * * * *
20030 CAGATTAAAGCCACCATCCAATCTTTTACCCTTAAGTCAAAAGGGA
1 CAAATTGAAGCTACCATCCAATCTTTTACCCCTAA-TCAAGAGGGA
* * *
20076 CAAATTGAAG-TCATCATCTAATCTTTTACCCCTAAATCAAGAGGGG
1 CAAATTGAAGCT-ACCATCCAATCTTTTACCCCT-AATCAAGAGGGA
20122 CAAATTGAAGCTACCATC
1 CAAATTGAAGCTACCATC
20140 TCACAGAAGC
Statistics
Matches: 290, Mismatches: 45, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
38 17 0.06
39 44 0.15
40 16 0.06
41 36 0.12
42 52 0.18
43 8 0.03
44 3 0.01
45 52 0.18
46 59 0.20
47 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (45 bp):
CAAATTGAAGCTACCATCCAATCTTTTACCCCTAATCAAGAGGGA
Found at i:20738 original size:21 final size:21
Alignment explanation
Indices: 20712--20753 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20702 CAAGCCCAAT
20712 ACTAAGGGAGGCAAAACCTAA
1 ACTAAGGGAGGCAAAACCTAA
*
20733 ACTAAGGGAGGCAAACCCTAA
1 ACTAAGGGAGGCAAAACCTAA
20754 TCTGCTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (21 bp):
ACTAAGGGAGGCAAAACCTAA
Found at i:21287 original size:16 final size:16
Alignment explanation
Indices: 21266--21301 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21256 TTTACATTCG
* *
21266 AAAATATACATATATA
1 AAAATATAAATAAATA
21282 AAAATATAAATAAATA
1 AAAATATAAATAAATA
21298 AAAA
1 AAAA
21302 GTGAGAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATATAAATAAATA
Found at i:22299 original size:28 final size:27
Alignment explanation
Indices: 22213--22299 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 27
22203 CCTTTATTTC
22213 TATTTTTTTAAAAATTAAACCCTTTTAT
1 TATTTTTTT-AAAATTAAACCCTTTTAT
*** * * *
22241 TCCCTTTTTAAAATTAATCCTTTATTTT
1 TATTTTTTTAAAATTAAACCCTT-TTAT
22269 TATTTTTTTAAAATTAAACCCCTTTTAT
1 TATTTTTTTAAAATTAAA-CCCTTTTAT
22297 TAT
1 TAT
22300 ATTCTTTTTA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
27 12 0.27
28 29 0.64
29 4 0.09
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTTTTTTAAAATTAAACCCTTTTAT
Found at i:22851 original size:109 final size:112
Alignment explanation
Indices: 22727--22946 Score: 250
Period size: 113 Copynumber: 2.0 Consensus size: 112
22717 AAAATCAAGG
* * * * * *
22727 CAATGTTCTTTTATTTTAGGGAAATCGAGAAAT-TGTACCCTAATGTGTTGGGTA-CAG-TTTTT
1 CAATGTTATGTTATTTTAGGGAAATCAAAAAATATGTACCCTAACGTGTTGGATATCAGTTTTTT
** *
22789 CTTTGAATC-TAAATAATTGATTATCCTATTTAAAGTCGATAAATGCT
66 CTTTGAA-CATAAATAATTGAACATCCTATTTAAAATCGATAAATGCT
* * * *
22836 CAATGTTATGTTATTTTAGGGGATTCAAAAAATATGTGCCCTAACGTGTTGGATATGAGTTTTTT
1 CAATGTTATGTTATTTTAGGGAAATCAAAAAATATGTACCCTAACGTGTTGGATATCAG-TTTTT
* * *
22901 TCTTTGAACATAAGTAATTGAACATCTTATTTAAAATTGATAAATG
65 TCTTTGAACATAAATAATTGAACATCCTATTTAAAATCGATAAATG
22947 TTCTTTATTT
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
109 27 0.30
110 18 0.20
111 2 0.02
112 1 0.01
113 42 0.47
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (112 bp):
CAATGTTATGTTATTTTAGGGAAATCAAAAAATATGTACCCTAACGTGTTGGATATCAGTTTTTT
CTTTGAACATAAATAATTGAACATCCTATTTAAAATCGATAAATGCT
Found at i:24783 original size:31 final size:30
Alignment explanation
Indices: 24722--24785 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
24712 AAAAAATCAT
* * *
24722 TTTGACTCTTTTAAAATATTGATGGTCAAA
1 TTTGACTCTTTTAAAAGATTGAGGGCCAAA
*
24752 TTTGACTCATTTTAAAAGATTTAGGGCCAAA
1 TTTGACTC-TTTTAAAAGATTGAGGGCCAAA
24783 TTT
1 TTT
24786 AACTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTGACTCTTTTAAAAGATTGAGGGCCAAA
Found at i:26799 original size:35 final size:35
Alignment explanation
Indices: 26760--26838 Score: 149
Period size: 35 Copynumber: 2.3 Consensus size: 35
26750 AGTGGTTCAC
*
26760 TTTGAGCATCAATTTCTCATTCATCACTCATCCAT
1 TTTGAGCATCAATTTCTCATTCATCACTCACCCAT
26795 TTTGAGCATCAATTTCTCATTCATCACTCACCCAT
1 TTTGAGCATCAATTTCTCATTCATCACTCACCCAT
26830 TTTGAGCAT
1 TTTGAGCAT
26839 TTGATATATT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (35 bp):
TTTGAGCATCAATTTCTCATTCATCACTCACCCAT
Found at i:27279 original size:25 final size:25
Alignment explanation
Indices: 27251--27307 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
27241 CTTCTTCCTG
27251 TTAAACTCTGTATTAAGTTTCCCAC
1 TTAAACTCTGTATTAAGTTTCCCAC
27276 TTAAACTCTGTATTAAGTTTCCCAC
1 TTAAACTCTGTATTAAGTTTCCCAC
27301 TTAAACT
1 TTAAACT
27308 TCGATTAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (25 bp):
TTAAACTCTGTATTAAGTTTCCCAC
Found at i:39305 original size:15 final size:15
Alignment explanation
Indices: 39285--39325 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
39275 CAAAACCCCA
39285 AAATTCTTTATATCG
1 AAATTCTTTATATCG
39300 AAATTCTTTATATCG
1 AAATTCTTTATATCG
*
39315 TAATTCTTTAT
1 AAATTCTTTAT
39326 GTCATATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (15 bp):
AAATTCTTTATATCG
Found at i:41946 original size:46 final size:46
Alignment explanation
Indices: 41879--41971 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
41869 CAAGGAATGA
41879 AATAAAAAGTTCTCTTGTTTATCTTTCTTTTGTACTACCTCTTTGT
1 AATAAAAAGTTCTCTTGTTTATCTTTCTTTTGTACTACCTCTTTGT
41925 AATAAAAAGTTCTCTTGTTTATCTTTCTTTTGTACTACCTCTTTGT
1 AATAAAAAGTTCTCTTGTTTATCTTTCTTTTGTACTACCTCTTTGT
41971 A
1 A
41972 TTGATATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.52
Consensus pattern (46 bp):
AATAAAAAGTTCTCTTGTTTATCTTTCTTTTGTACTACCTCTTTGT
Found at i:44289 original size:88 final size:88
Alignment explanation
Indices: 44140--44317 Score: 329
Period size: 88 Copynumber: 2.0 Consensus size: 88
44130 TGACCAGTTA
*
44140 AACCATCTTGGATTATATATGATGCGAAATTTAATTGAGAATTCATATAAGCATTTATTAAAGAA
1 AACCATCCTGGATTATATATGATGCGAAATTTAATTGAGAATTCATATAAGCATTTATTAAAGAA
44205 CCAGAGGATTCTTTAATTTAAAG
66 CCAGAGGATTCTTTAATTTAAAG
* *
44228 AACCATCCTGGATTATATATGATGCGAAATTTAATTGAGAATTCATATAGGTATTTATTAAAGAA
1 AACCATCCTGGATTATATATGATGCGAAATTTAATTGAGAATTCATATAAGCATTTATTAAAGAA
44293 CCAGAGGATTCTTTAATTTAAAG
66 CCAGAGGATTCTTTAATTTAAAG
44316 AA
1 AA
44318 TTCTCATGTG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (88 bp):
AACCATCCTGGATTATATATGATGCGAAATTTAATTGAGAATTCATATAAGCATTTATTAAAGAA
CCAGAGGATTCTTTAATTTAAAG
Found at i:47414 original size:16 final size:16
Alignment explanation
Indices: 47390--47428 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
47380 TAGCATTGTT
47390 GACGAGTCTTCCAATG
1 GACGAGTCTTCCAATG
*
47406 GATGAGTCTTCCAATG
1 GACGAGTCTTCCAATG
47422 GACGAGT
1 GACGAGT
47429 GTCCTAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (16 bp):
GACGAGTCTTCCAATG
Found at i:47577 original size:24 final size:24
Alignment explanation
Indices: 47545--47592 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
47535 TTAGACTAGT
47545 TGTAAAGGTGGTTTGAGCATCTGC
1 TGTAAAGGTGGTTTGAGCATCTGC
47569 TGTAAAGGTGGTTTGAGCATCTGC
1 TGTAAAGGTGGTTTGAGCATCTGC
47593 CATAGAAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.33
Consensus pattern (24 bp):
TGTAAAGGTGGTTTGAGCATCTGC
Found at i:50045 original size:108 final size:108
Alignment explanation
Indices: 49807--50070 Score: 289
Period size: 108 Copynumber: 2.5 Consensus size: 108
49797 GTGGAAATGA
* * * * * * *
49807 ATCACTATTTAATTCGTCAG-TTGTCCGACTAGTGCTGAGCACATATTTGTCAATTTATCCGAGT
1 ATCACTATTTAATACATCAGTTTATCTGACTAGTGCTGGGCACAAATTCGTCAATTTATCCGAGT
* * * *
49871 AGAGCTGGATGTAATATTGTTGGTTAATCCAATTAGAGCTGAG
66 AGAGCTGGATGCAATATCGTTGCTTAATCCAACTAGAGCTGAG
* * * * * *
49914 CTCACTATTTAATTCATCAGTTTATTTGACTAGTGTTGGGCACACATTCGTCGATTTATCCGAGT
1 ATCACTATTTAATACATCAGTTTATCTGACTAGTGCTGGGCACAAATTCGTCAATTTATCCGAGT
* * *
49979 AGTGCTGGGTGCAATATCGTTGCTTAATCCAACTAGAGCTGGG
66 AGAGCTGGATGCAATATCGTTGCTTAATCCAACTAGAGCTGAG
* * * *
50022 ATCACT-TTTAATACTGTCGGTTTATCTAACTAGCGCTGGGCACAAATTC
1 ATCACTATTTAATAC-ATCAGTTTATCTGACTAGTGCTGGGCACAAATTC
50071 TATGTAGTCT
Statistics
Matches: 129, Mismatches: 26, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
107 25 0.19
108 104 0.81
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (108 bp):
ATCACTATTTAATACATCAGTTTATCTGACTAGTGCTGGGCACAAATTCGTCAATTTATCCGAGT
AGAGCTGGATGCAATATCGTTGCTTAATCCAACTAGAGCTGAG
Found at i:54444 original size:23 final size:23
Alignment explanation
Indices: 54417--54872 Score: 543
Period size: 23 Copynumber: 19.8 Consensus size: 23
54407 ATATTACATC
* * *
54417 TTAATAATTGAGCACAAATCATA
1 TTAATATTTAAGCACAAATCACA
*
54440 TTAATATTTAAGCATAAATCACA
1 TTAATATTTAAGCACAAATCACA
* *
54463 TTAATATTTAAGCATAAATCATA
1 TTAATATTTAAGCACAAATCACA
* *
54486 TTAATATTTGAGCACAAATCATA
1 TTAATATTTAAGCACAAATCACA
* *
54509 TTAATATTTTAGCATAAATCACA
1 TTAATATTTAAGCACAAATCACA
* * *
54532 TAAATATTTAAGCATAAATCAGA
1 TTAATATTTAAGCACAAATCACA
* * * * *
54555 TTAATTTTTGAGAACAAATTATA
1 TTAATATTTAAGCACAAATCACA
54578 TTAATATTTAAGCACAAATCACA
1 TTAATATTTAAGCACAAATCACA
54601 TTAATATTTAAGCACAAATCACA
1 TTAATATTTAAGCACAAATCACA
* * *
54624 TTAATATATGAGCACAAATCATA
1 TTAATATTTAAGCACAAATCACA
54647 TTAATATTTAAGCACAAATCACA
1 TTAATATTTAAGCACAAATCACA
* * *
54670 TTAATATTTAAGAATAAATCATA
1 TTAATATTTAAGCACAAATCACA
* *
54693 TTAATATTTAGGAACAAATCACA
1 TTAATATTTAAGCACAAATCACA
54716 TTAATATTTAAGCACAAATCACA
1 TTAATATTTAAGCACAAATCACA
* *
54739 TTAATATTTAAGCATAAATCATA
1 TTAATATTTAAGCACAAATCACA
* * *
54762 TTAACATTTAAGCATAAATGACA
1 TTAATATTTAAGCACAAATCACA
* * *
54785 ATAATATTTAAGCATAAATCAAA
1 TTAATATTTAAGCACAAATCACA
* *
54808 TTAATATTTAAGCATAAATCATA
1 TTAATATTTAAGCACAAATCACA
* * *
54831 TTAACATATAAGCATAAATCACA
1 TTAATATTTAAGCACAAATCACA
* *
54854 ATAATATTTAAGCATAAAT
1 TTAATATTTAAGCACAAAT
54873 ACAAGAATAC
Statistics
Matches: 377, Mismatches: 56, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 377 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (23 bp):
TTAATATTTAAGCACAAATCACA
Found at i:54528 original size:69 final size:69
Alignment explanation
Indices: 54417--54872 Score: 635
Period size: 69 Copynumber: 6.6 Consensus size: 69
54407 ATATTACATC
*
54417 TTAATAATTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
54482 CATA
66 CATA
* *
54486 TTAATATTTGAGCACAAATCATATTAATATTTTAGCATAAATCACATAAATATTTAAGCATAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
*
54551 CAGA
66 CATA
* * * * *
54555 TTAATTTTTGAGAACAAATTATATTAATATTTAAGCACAAATCACATTAATATTTAAGCACAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
*
54620 CACA
66 CATA
* * *
54624 TTAATATATGAGCACAAATCATATTAATATTTAAGCACAAATCACATTAATATTTAAGAATAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
54689 CATA
66 CATA
* * *
54693 TTAATATTT-AGGAACAAATCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAA
1 TTAATATTTGA-GCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAA
54757 TCATA
65 TCATA
* * * * * * *
54762 TTAACATTTAAGCATAAATGACAATAATATTTAAGCATAAATCAAATTAATATTTAAGCATAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
54827 CATA
66 CATA
* * * * * *
54831 TTAACATATAAGCATAAATCACAATAATATTTAAGCATAAAT
1 TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAAT
54873 ACAAGAATAC
Statistics
Matches: 353, Mismatches: 32, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
68 1 0.00
69 351 0.99
70 1 0.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (69 bp):
TTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATATTTAAGCATAAAT
CATA
Found at i:57002 original size:20 final size:19
Alignment explanation
Indices: 56973--57037 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
56963 ATTTTAAAAT
*
56973 CAAGTTAAAATGATTTCAA
1 CAAGTCAAAATGATTTCAA
* *
56992 CCAAGTCAAAATCATTTTAA
1 -CAAGTCAAAATGATTTCAA
57012 CACA-TCAAAATGATTTTCAAA
1 CA-AGTCAAAATGA-TTTC-AA
57033 CAAGT
1 CAAGT
57038 AAGAATTGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.28
20 21 0.58
21 5 0.14
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (19 bp):
CAAGTCAAAATGATTTCAA
Found at i:60515 original size:11 final size:11
Alignment explanation
Indices: 60499--60531 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
60489 TCTAAAAAGA
60499 TAAATATAAAT
1 TAAATATAAAT
*
60510 TAAATACAAAT
1 TAAATATAAAT
60521 TAAATATAAAT
1 TAAATATAAAT
60532 AATATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:61347 original size:118 final size:118
Alignment explanation
Indices: 61106--61353 Score: 293
Period size: 118 Copynumber: 2.1 Consensus size: 118
61096 TATTTTGTTG
* * ***
61106 ATTTTCTCTTTTTTTTTCTTTAAGAATATATTGGACCTTTTGACGCGAAATGAAATGACTCCCAA
1 ATTTTCTTTTTTTTTTTCTTTAAGAATATATTAGACCTTTTGACGCGAAATGAAATGACAAACAA
* * * ** * *
61171 GCACTCCATCCCGGTTGCTCAGCCCAATATGCTCCAAATCATTTTTTTTTCTT
66 GCACTCCATCCCGGTTACTCAACCCAACACACTCCAAATCATTTATTTATCTT
* * * *
61224 ATTTTCCTTTTTTTTTTTGTTT-AGAATATGTTAGCCCTTTTGACGCGAAGTGAAATGACAAACA
1 ATTTT-CTTTTTTTTTTTCTTTAAGAATATATTAGACCTTTTGACGCGAAATGAAATGACAAACA
* *
61288 AGCACTCCATCCCGGTTACTCAACCTAACACACTCCAAATTTATTTATTTAT-TT
65 AGCACTCCATCCCGGTTACTCAACCCAACACACTCCAAA-TCATTTATTTATCTT
*
61342 CTTTTCTTTTTT
1 ATTTTCTTTTTT
61354 CGGTTAGCGA
Statistics
Matches: 109, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
117 7 0.06
118 79 0.72
119 23 0.21
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (118 bp):
ATTTTCTTTTTTTTTTTCTTTAAGAATATATTAGACCTTTTGACGCGAAATGAAATGACAAACAA
GCACTCCATCCCGGTTACTCAACCCAACACACTCCAAATCATTTATTTATCTT
Found at i:62023 original size:23 final size:23
Alignment explanation
Indices: 61997--62043 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
61987 TTTCCTGGAC
*
61997 ATATAATAAATAAATA-AAAATAA
1 ATATAA-AAATAAAAAGAAAATAA
*
62020 ATATAAAAGTAAAAAGAAAATAA
1 ATATAAAAATAAAAAGAAAATAA
62043 A
1 A
62044 AAATTGGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (23 bp):
ATATAAAAATAAAAAGAAAATAA
Found at i:62032 original size:18 final size:17
Alignment explanation
Indices: 62011--62044 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62001 AATAAATAAA
*
62011 TAAAAATAAATATAAAAG
1 TAAAAAGAAA-ATAAAAG
62029 TAAAAAGAAAATAAAA
1 TAAAAAGAAAATAAAA
62045 AATTGGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAAAGAAAATAAAAG
Found at i:65381 original size:19 final size:19
Alignment explanation
Indices: 65357--65395 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
65347 CTAATTCAAC
65357 CAGGATTCTTCTATCTGTT
1 CAGGATTCTTCTATCTGTT
65376 CAGGATTCTTCTATCTGTT
1 CAGGATTCTTCTATCTGTT
65395 C
1 C
65396 CTATAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (19 bp):
CAGGATTCTTCTATCTGTT
Done.