Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012539.1 Kokia drynarioides strain JFW-HI SEQ_127548, 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: 101769
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12876 original size:17 final size:17
Alignment explanation
Indices: 12846--12913 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
12836 TAGTTGTAGT
*
12846 TTAATTGTCCTTGCATTA
1 TTAA-TGTCATTGCATTA
*
12864 TTAATGTCATTGCATTT
1 TTAATGTCATTGCATTA
* *
12881 TTATTGTCACTGCATCTA
1 TTAATGTCATTGCAT-TA
*
12899 -TATTGTCATTGCATT
1 TTAATGTCATTGCATT
12914 TCCATAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 1 0.02
17 37 0.86
18 5 0.12
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (17 bp):
TTAATGTCATTGCATTA
Found at i:12887 original size:34 final size:34
Alignment explanation
Indices: 12849--12914 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
12839 TTGTAGTTTA
12849 ATTGTC-CTTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCAC-TGCATCTA-TAATGTCATTGCATTTTT
*
12883 ATTGTCACTGCATCTATATTGTCATTGCATTT
1 ATTGTCACTGCATCTATAATGTCATTGCATTT
12915 CCATAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (34 bp):
ATTGTCACTGCATCTATAATGTCATTGCATTTTT
Found at i:16989 original size:24 final size:23
Alignment explanation
Indices: 16961--17017 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
16951 AAATACAACT
* *
16961 TAAAATAATAAAATACACAAAAAA
1 TAAAATAA-AAAAAAAACAAAAAA
**
16985 TAAAATTAAAAAAAAAACAAAATT
1 TAAAA-TAAAAAAAAAACAAAAAA
17009 TAAAATAAA
1 TAAAATAAA
17018 GGTTATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.14
24 21 0.75
25 3 0.11
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.19
Consensus pattern (23 bp):
TAAAATAAAAAAAAAACAAAAAA
Found at i:16999 original size:17 final size:18
Alignment explanation
Indices: 16979--17013 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16969 TAAAATACAC
*
16979 AAAAAATAAAA-TTAAAA
1 AAAAAACAAAATTTAAAA
16996 AAAAAACAAAATTTAAAA
1 AAAAAACAAAATTTAAAA
17014 TAAAGGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAAACAAAATTTAAAA
Found at i:25389 original size:20 final size:20
Alignment explanation
Indices: 25364--25413 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
25354 ATCTATCAAC
25364 TATGCTTGCATTGACGTGTG
1 TATGCTTGCATTGACGTGTG
25384 TATGCTTGCATTGACGTGTG
1 TATGCTTGCATTGACGTGTG
25404 TATGCTTGCA
1 TATGCTTGCA
25414 CAATCATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (20 bp):
TATGCTTGCATTGACGTGTG
Found at i:29062 original size:17 final size:17
Alignment explanation
Indices: 29031--29088 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
29021 TAATTGTCCA
* *
29031 TGCATTATTAATGTCAT
1 TGCATTTTTATTGTCAT
**
29048 TGCATTTTTATTGTCGC
1 TGCATTTTTATTGTCAT
* **
29065 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
29082 TGCATTT
1 TGCATTT
29089 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:29069 original size:34 final size:34
Alignment explanation
Indices: 29023--29088 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
29013 TTGTAGTATA
*
29023 ATTGTCCATGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCCATGCATCTA-CAATGTCATTGCATTTTT
*
29057 ATTGTCGC-TGCATCTACATTGTCATTGCATTT
1 ATTGTC-CATGCATCTACAATGTCATTGCATTT
29089 CCATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 25 0.89
35 3 0.11
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.47
Consensus pattern (34 bp):
ATTGTCCATGCATCTACAATGTCATTGCATTTTT
Found at i:42415 original size:45 final size:44
Alignment explanation
Indices: 42365--42458 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42355 TCTAGACCCT
* *
42365 GAAAGGGTACTTTTGAGTTCA-GCGGAGGCACCATCTCCGGAAGTC
1 GAAAGGGTACTTTTGAGTTCATG-GGAGGAACCATCTCCAGAA-TC
*
42410 GAAAGGGTACTTTTGAGTTCATGGGAGGAAGCATCTCCAGAATC
1 GAAAGGGTACTTTTGAGTTCATGGGAGGAACCATCTCCAGAATC
42454 GAAAG
1 GAAAG
42459 AAAAAGCTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 7 0.16
45 37 0.82
46 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (44 bp):
GAAAGGGTACTTTTGAGTTCATGGGAGGAACCATCTCCAGAATC
Found at i:57677 original size:15 final size:15
Alignment explanation
Indices: 57657--57686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
57647 GATGAAGGAG
*
57657 AAGGAAGAGAAAGAA
1 AAGGAAGAAAAAGAA
57672 AAGGAAGAAAAAGAA
1 AAGGAAGAAAAAGAA
57687 GAAGAGAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGGAAGAAAAAGAA
Found at i:59772 original size:14 final size:14
Alignment explanation
Indices: 59753--59780 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59743 AGCAGCAACT
59753 CTTGATGCTGAGTG
1 CTTGATGCTGAGTG
59767 CTTGATGCTGAGTG
1 CTTGATGCTGAGTG
59781 AGAGAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (14 bp):
CTTGATGCTGAGTG
Found at i:63077 original size:109 final size:109
Alignment explanation
Indices: 62881--63100 Score: 368
Period size: 109 Copynumber: 2.0 Consensus size: 109
62871 TAGGAATACT
* *
62881 TTATCTTGGGACATAAACTAGGTGTTTAGACAACCTAAGCCCCCCTTTAAATCAGTGATTTGTGC
1 TTATATTGGGACATAAACTAGGTGTTTAGACAACCTAAGCCCCCCTTTAAATCAGTGATTTGGGC
62946 ATTAATCAAAGCACACCAGACCACTCACCTTGATCAAGCTTCGC
66 ATTAATCAAAGCACACCAGACCACTCACCTTGATCAAGCTTCGC
* ** *
62990 TTATATTGGGACATAAATTAGGTGTTTAGACCTCCTAAGCCCCTCTTTAAATCAGTGATTTGGGC
1 TTATATTGGGACATAAACTAGGTGTTTAGACAACCTAAGCCCCCCTTTAAATCAGTGATTTGGGC
* *
63055 ATTAATCAAAGCACACTAGACCACTCACCTTGATCAAGCTTTGC
66 ATTAATCAAAGCACACCAGACCACTCACCTTGATCAAGCTTCGC
63099 TT
1 TT
63101 TAATGGCAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (109 bp):
TTATATTGGGACATAAACTAGGTGTTTAGACAACCTAAGCCCCCCTTTAAATCAGTGATTTGGGC
ATTAATCAAAGCACACCAGACCACTCACCTTGATCAAGCTTCGC
Found at i:64297 original size:17 final size:17
Alignment explanation
Indices: 64275--64313 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
64265 CTCCACCTTG
* *
64275 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
64292 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
64309 ACAAG
1 ACAAG
64314 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:71578 original size:45 final size:44
Alignment explanation
Indices: 71513--71610 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 44
71503 TTGATGGCGT
* * *
71513 ACCATCTCCGGAAGCCGAAAGGGTACTTTTGAGTTTAGTGGAGGC
1 ACCATCTCCGGAAGCCGAAAGGATACTTTTGAGTTCAGGGGA-GC
*
71558 ACCATCTCCGGAAGCTGAAAGGATACTTTTGAGTTCAGGGGAGC
1 ACCATCTCCGGAAGCCGAAAGGATACTTTTGAGTTCAGGGGAGC
*
71602 AGCATCTCC
1 ACCATCTCC
71611 AGAATCGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 10 0.21
45 38 0.79
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (44 bp):
ACCATCTCCGGAAGCCGAAAGGATACTTTTGAGTTCAGGGGAGC
Found at i:73787 original size:41 final size:41
Alignment explanation
Indices: 73726--73939 Score: 227
Period size: 41 Copynumber: 5.1 Consensus size: 41
73716 GCCATAAGTT
* *
73726 TTCCTTTAACCATATTCTCATTCTCATCTCGAGACATGAGTC
1 TTCC-TTAATCATAATCTCATTCTCATCTCGAGACATGAGTC
73768 TTCCTTAATCATAATCTCATTCTCAT-TCCGAGACATGAGTC
1 TTCCTTAATCATAATCTCATTCTCATCT-CGAGACATGAGTC
* * *
73809 TTCCTTATTCATAATCTCATTTTGAT-TCTGAGACATGAGTC
1 TTCCTTAATCATAATCTCATTCTCATCTC-GAGACATGAGTC
* *
73850 TTCCTTATTCATAAACTCATTCTCATCTCGAGACATGAGTC
1 TTCCTTAATCATAATCTCATTCTCATCTCGAGACATGAGTC
* * * * * * *
73891 GTCCATTTATACA-ATTTCACATGCTCAACCCGAGACATGAGTC
1 TTCC-TTAAT-CATA-ATCTCATTCTCATCTCGAGACATGAGTC
73934 TTCCTT
1 TTCCTT
73940 TTTATACACC
Statistics
Matches: 148, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.01
41 107 0.72
42 12 0.08
43 27 0.18
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (41 bp):
TTCCTTAATCATAATCTCATTCTCATCTCGAGACATGAGTC
Found at i:74784 original size:22 final size:21
Alignment explanation
Indices: 74737--74784 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
74727 AACTTACATA
*
74737 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* *
74758 TTTAACCTTAATTAATCCTATT
1 ATTAA-CTTAATTAATCATATT
74780 ATTAA
1 ATTAA
74785 TCAATACTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:77782 original size:195 final size:190
Alignment explanation
Indices: 77430--77799 Score: 454
Period size: 195 Copynumber: 1.9 Consensus size: 190
77420 CTGTCTATAC
* *
77430 TATAAATTGTTCCCTAACAATGCTGCTCACACGAGCTGTCAAGAGTATGCATAAAGCATAGTCCC
1 TATAAATTGTTCCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCATAAAGCATAATCCC
* * *
77495 AACCATCATAGGGCCTAAAATCCCTTTAGGATTCATATCTCATTCTCGAGTCACAATGCTGCTCA
66 AACCATCATAGGGCCTAAAATCCATTTAGGATTCATATCTCATTCTCGACTCACAATGCTACTCA
* * * * *
77560 CACGAGCTGTCGAGGAGTCGTAACATATGCGGTACCTCAGCCATCGATAAGATATCTGTG
131 CACGAGCTGTCGAGGACTCGCAACATATGCGATACCCCAACCATCGATAAGATATCTGTG
* * * * * *
77620 TATATAATTGTTCCCTAACGATGTTGCTCACACGAGCTGTCGAGAATGTGCACTTATGCATAAAT
1 TATA-AATTGTTCCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCA-TAAAGCAT-AAT
* * ** * * *
77685 CTCAGCCATCATAGGGCCTGTAATCCATTCTTGGATTCTTTTCTCATT-TCCTGACTCACAATGC
63 CCCAACCATCATAGGGCCTAAAATCCATT-TAGGATTCATATCTCATTCT-C-GACTCACAATGC
* *
77749 TACTCACACGAGCTGTTGAGGACTTGCAACATATGCGATACCCCAACCATC
125 TACTCACACGAGCTGTCGAGGACTCGCAACATATGCGATACCCCAACCATC
77800 TCGTAAGTTT
Statistics
Matches: 149, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
190 4 0.03
191 42 0.28
192 6 0.04
193 27 0.18
194 16 0.11
195 54 0.36
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (190 bp):
TATAAATTGTTCCCTAACAATGCTGCTCACACGAGCTGTCAAGAATATGCATAAAGCATAATCCC
AACCATCATAGGGCCTAAAATCCATTTAGGATTCATATCTCATTCTCGACTCACAATGCTACTCA
CACGAGCTGTCGAGGACTCGCAACATATGCGATACCCCAACCATCGATAAGATATCTGTG
Found at i:83742 original size:15 final size:16
Alignment explanation
Indices: 83722--83751 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
83712 CTCACCGTTG
83722 ATTATTT-TCACATAA
1 ATTATTTCTCACATAA
83737 ATTATTTCTCACATA
1 ATTATTTCTCACATA
83752 TAGTCTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTTCTCACATAA
Found at i:86941 original size:195 final size:194
Alignment explanation
Indices: 86513--86951 Score: 481
Period size: 195 Copynumber: 2.3 Consensus size: 194
86503 CTCGATACTG
* * * * * * *
86513 CTCACATGAGCTATCGAGGACTAGCAGCGTATGCGATACC-CTAGCCATTGGTACGACGCATGTT
1 CTCACATGAGCTATCGAGGACTAGCAACATATGCGGTACCTC-AGCCATCGATACGAC-CATCTA
* * * * * *
86577 TGCATTATAAATTGTTCCCTAATGATGCTGCTCACATGAGCTGTCGAGAGTGTGTATAAAGCATA
64 TGCATTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATA
* * * *
86642 GTCCCAACCATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCGAGTCACGATGCT
129 ATCCCAACCATCGTAGGACCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCACGATGCT
*
86707 G
194 A
* * * * *
86708 CTCACACGAGCTGTCGAGGACTCGCATCATATGCGGTACCTCAGCCATCGATACGA-TATCTATG
1 CTCACATGAGCTATCGAGGACTAGCAACATATGCGGTACCTCAGCCATCGATACGACCATCTATG
* * * *
86772 CA-TAT-AACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCTATAATATGCACTTATGCATAA
66 CATTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCA-TAAAGCAT-A
* * * * * *
86835 ATCTCAACCATCGTAGGACCTGTAATCCATTCTTGGATTCTTTTCTCATTTCCCAACTCACGATG
129 ATCCCAACCATCGTAGGACCTATAATCCATT-TAGGATCCATATCTC-TTTCCCAACTCACGATG
86900 CTA
192 CTA
* *
86903 CTCACATGAGCTATCGAGGACTTGCAACATATGCGGTACCTTAGCCATC
1 CTCACATGAGCTATCGAGGACTAGCAACATATGCGGTACCTCAGCCATC
86952 ATGTCGGTTT
Statistics
Matches: 202, Mismatches: 37, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
191 39 0.19
192 9 0.04
193 35 0.17
194 11 0.05
195 107 0.53
196 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (194 bp):
CTCACATGAGCTATCGAGGACTAGCAACATATGCGGTACCTCAGCCATCGATACGACCATCTATG
CATTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAAT
CCCAACCATCGTAGGACCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCACGATGCTA
Found at i:91501 original size:45 final size:45
Alignment explanation
Indices: 91435--91542 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
91425 TTGATGGCGT
*
91435 ACCATCTCCGGAAG-CTAAAAGGGTACTTTTGAGTTC-AGCGAAGGC
1 ACCATCTCCGGAAGTC-GAAAGGGTACTTTTGAGTTCAAG-GAAGGC
*
91480 ACCATCTCCGGAAGTCGAAAGGGTACTTTTGAGTTCAAGGGAGGC
1 ACCATCTCCGGAAGTCGAAAGGGTACTTTTGAGTTCAAGGAAGGC
* *
91525 AGCATCTCCAGAA-TCGAA
1 ACCATCTCCGGAAGTCGAA
91543 TGTAGAAGCT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
44 5 0.09
45 49 0.86
46 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (45 bp):
ACCATCTCCGGAAGTCGAAAGGGTACTTTTGAGTTCAAGGAAGGC
Found at i:93235 original size:11 final size:11
Alignment explanation
Indices: 93219--93251 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
93209 AGTTCACAAA
93219 ATTATTTTTCC
1 ATTATTTTTCC
*
93230 ATTATTTTTCA
1 ATTATTTTTCC
93241 ATTATTTTTCC
1 ATTATTTTTCC
93252 CTCAATACTA
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:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTTCC
Found at i:96339 original size:22 final size:22
Alignment explanation
Indices: 96313--96372 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
96303 TCGACTTCCT
96313 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
96335 TATTTTCTTTTATTTTTAATTA
1 TATTTTCTTTTACTTTTAATTA
* *
96357 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTACTTTT
96373 CCTTAGATCG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:96362 original size:21 final size:22
Alignment explanation
Indices: 96326--96372 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
96316 TTTCTATTTC
*
96326 TTTTAATTATATTTTCTTTTAT
1 TTTTAATTATAGTTTCTTTTAT
96348 TTTTAATTAT-GTTTCTTTTAT
1 TTTTAATTATAGTTTCTTTTAT
96369 TTTT
1 TTTT
96373 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTATAGTTTCTTTTAT
Found at i:99135 original size:18 final size:18
Alignment explanation
Indices: 99112--99167 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
99102 GGCAACCCAA
99112 TTATTTTTTTTTTATTTT
1 TTATTTTTTTTTTATTTT
*
99130 TTATTTTTCTATCTTA--TT
1 TTATTTTT-T-TTTTATTTT
*
99148 TTATTTATTTATTTATTTT
1 TTATTT-TTTTTTTATTTT
99167 T
1 T
99168 GTCCAGGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 3 0.10
18 17 0.57
19 6 0.20
20 4 0.13
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
TTATTTTTTTTTTATTTT
Found at i:99156 original size:4 final size:4
Alignment explanation
Indices: 99112--99165 Score: 51
Period size: 4 Copynumber: 13.5 Consensus size: 4
99102 GGCAACCCAA
*
99112 TTAT TT-T TTTT TTAT TT-T TTAT TT-T TCTAT CTTATT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T-TAT -TTA-T TTAT TTAT TTAT
99160 TTAT TT
1 TTAT TT
99166 TTGTCCAGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
3 8 0.19
4 27 0.63
5 6 0.14
6 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.80
Consensus pattern (4 bp):
TTAT
Found at i:99563 original size:32 final size:32
Alignment explanation
Indices: 99525--99587 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
99515 AATTTTGATT
99525 TTGCTATGATTAAATTTGTCTCCACTGTTTTA
1 TTGCTATGATTAAATTTGTCTCCACTGTTTTA
99557 TTGCTATGATTAAATTTGTCTCCACTGTTTT
1 TTGCTATGATTAAATTTGTCTCCACTGTTTT
99588 GCTAAAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.51
Consensus pattern (32 bp):
TTGCTATGATTAAATTTGTCTCCACTGTTTTA
Found at i:100856 original size:22 final size:22
Alignment explanation
Indices: 100830--100872 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
100820 TCGACTTCCT
100830 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
*
100852 TATTTTCTTTTATTTTTAATT
1 TATTTTCTTTTACTTTTAATT
100873 TTGTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Done.