Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011574.1 Kokia drynarioides strain JFW-HI SEQ_126563, 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: 50588
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 109 characters in sequence are not A, C, G, or T
Found at i:29 original size:21 final size:21
Alignment explanation
Indices: 3--62 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1 TG
3 CACTTCCCACCACCACTC-GTC
1 CACTTCCCACCACCAC-CAGTC
* * *
24 CACTTCCTACCCCCACCAGTG
1 CACTTCCCACCACCACCAGTC
45 CAC-TCACCACCACCACCA
1 CACTTC-CCACCACCACCA
63 CCTATCCACT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.09
21 29 0.91
ACGTcount: A:0.23, C:0.57, G:0.05, T:0.15
Consensus pattern (21 bp):
CACTTCCCACCACCACCAGTC
Found at i:60 original size:42 final size:42
Alignment explanation
Indices: 1--231 Score: 170
Period size: 42 Copynumber: 5.4 Consensus size: 42
1 TGCACTTC-CCACCACCACTCGTCCACTTCCTACCCCCACCAG
1 TGCAC-TCACCACCACCACTCGTCCACTTCCTACCCCCACCAG
* * * * *
43 TGCACTCACCACCACCACCACCTATCCACTCTCC-ACCTCTACTAG
1 TGCACTCACCACCACCA-C-TC-GTCCACT-TCCTACCCCCACCAG
* * *
88 TGCACTCACCATCGCCA-TCCGTCCAC-TCTCTACCCCCACTAG
1 TGCACTCACCACCACCACT-CGTCCACTTC-CTACCCCCACCAG
* * * *
130 TGCACTCACCATCACCA-TCCGTCCACTCCCTACCTCCACCAA
1 TGCACTCACCACCACCACT-CGTCCACTTCCTACCCCCACCAG
* * * * *
172 TGCACTCAACTCCACTACTCGTGCACTCTCCATA--CCCACCAA
1 TGCACTCACCACCACCACTCGTCCACT-TCC-TACCCCCACCAG
214 TGCACTCACCACCACCAC
1 TGCACTCACCACCACCAC
232 CTGTCCATTT
Statistics
Matches: 151, Mismatches: 26, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
40 2 0.01
41 3 0.02
42 105 0.70
43 6 0.04
44 3 0.02
45 29 0.19
46 3 0.02
ACGTcount: A:0.23, C:0.51, G:0.06, T:0.19
Consensus pattern (42 bp):
TGCACTCACCACCACCACTCGTCCACTTCCTACCCCCACCAG
Found at i:231 original size:21 final size:21
Alignment explanation
Indices: 36--232 Score: 80
Period size: 21 Copynumber: 9.2 Consensus size: 21
26 CTTCCTACCC
36 CCACCAGTGCACTCACCACCA
1 CCACCAGTGCACTCACCACCA
* * * *
57 CCACCACCTATCCACTCTCCACCT
1 CCACCA---GTGCACTCACCACCA
* * * *
81 CTACTAGTGCACTCACCATCG
1 CCACCAGTGCACTCACCACCA
* * * *
102 CCATCC-GTCCACTCTCTACCC
1 CCA-CCAGTGCACTCACCACCA
* *
123 CCACTAGTGCACTCACCATCA
1 CCACCAGTGCACTCACCACCA
* *
144 CCATCC-GTCCACTC-CCTACCT
1 CCA-CCAGTGCACTCACC-ACCA
* * *
165 CCACCAATGCACTCAACTCCA
1 CCACCAGTGCACTCACCACCA
* * *
186 CTACTC-GTGCACTCTCCA-TA
1 CCAC-CAGTGCACTCACCACCA
*
206 CCCACCAATGCACTCACCACCA
1 -CCACCAGTGCACTCACCACCA
228 CCACC
1 CCACC
233 TGTCCATTTA
Statistics
Matches: 120, Mismatches: 43, Indels: 26
0.63 0.23 0.14
Matches are distributed among these distances:
20 7 0.06
21 93 0.77
22 5 0.04
24 15 0.12
ACGTcount: A:0.24, C:0.51, G:0.07, T:0.19
Consensus pattern (21 bp):
CCACCAGTGCACTCACCACCA
Found at i:345 original size:81 final size:81
Alignment explanation
Indices: 230--388 Score: 246
Period size: 81 Copynumber: 2.0 Consensus size: 81
220 CACCACCACC
* * * * *
230 ACCTGTCCATTTACCACCTTCACTCATCAAGTCTCTACCACCACCAATACAATCCCGACCTCCAC
1 ACCTGTCCATTCACCAACTCCACCCATCAAGTCTCTACCACCACCAATACAATCCCGACCTCCAA
295 CAACTCTATCACCAGA
66 CAACTCTATCACCAGA
* * *
311 ACCTGTCCATTCATCAACTCCACCCATCAAGTCTCTACCACCACCAATACAATCTCGACCTTCAA
1 ACCTGTCCATTCACCAACTCCACCCATCAAGTCTCTACCACCACCAATACAATCCCGACCTCCAA
376 CAACTCTATCACC
66 CAACTCTATCACC
389 TCCACCCGTC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.30, C:0.43, G:0.04, T:0.23
Consensus pattern (81 bp):
ACCTGTCCATTCACCAACTCCACCCATCAAGTCTCTACCACCACCAATACAATCCCGACCTCCAA
CAACTCTATCACCAGA
Found at i:496 original size:60 final size:60
Alignment explanation
Indices: 428--613 Score: 275
Period size: 60 Copynumber: 3.1 Consensus size: 60
418 AACAATCCCA
* * *
428 ACCTCCACCTGTCAGGTCTCTACCACCACCAATTCAATCTCGACATCCACCAACTCTATC
1 ACCTCCACCCGTCAGGTCTCTACCACCACCAGTACAATCTCGACATCCACCAACTCTATC
* *
488 ACCTCCACCCGTCAGGTCTCTACCACCACCAGTAC-ATACCCGACATCCACCAACTCTGTC
1 ACCTCCACCCGTCAGGTCTCTACCACCACCAGTACAAT-CTCGACATCCACCAACTCTATC
* * * *
548 ACCTCCACCCGTCAGGTCTCTATCACCACCAGTACAATCTCGACCTTCATCAACTCTATC
1 ACCTCCACCCGTCAGGTCTCTACCACCACCAGTACAATCTCGACATCCACCAACTCTATC
608 ACCTCC
1 ACCTCC
614 TCATGTTTTG
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 2 0.02
60 109 0.96
61 2 0.02
ACGTcount: A:0.25, C:0.45, G:0.08, T:0.22
Consensus pattern (60 bp):
ACCTCCACCCGTCAGGTCTCTACCACCACCAGTACAATCTCGACATCCACCAACTCTATC
Found at i:537 original size:102 final size:102
Alignment explanation
Indices: 341--538 Score: 281
Period size: 102 Copynumber: 1.9 Consensus size: 102
331 CACCCATCAA
* * *
341 GTCTCTACCACCACCAATACAATCTCGACCTTCAACAACTCTATCACCTCCACCCGTCAAGTCTT
1 GTCTCTACCACCACCAATACAATCTCGACATCCAACAACTCTATCACCTCCACCCGTCAAGTCTC
* * *
406 TACCTCTACCAGAACAATCCCAACCTCCACCTGTCAG
66 TACCACCACCAGAACAATCCCAACATCCACCTGTCAG
* * *
443 GTCTCTACCACCACCAATTCAATCTCGACATCCACCAACTCTATCACCTCCACCCGTCAGGTCTC
1 GTCTCTACCACCACCAATACAATCTCGACATCCAACAACTCTATCACCTCCACCCGTCAAGTCTC
* *
508 TACCACCACCAGTAC-ATACCCGACATCCACC
66 TACCACCACCAGAACAAT-CCCAACATCCACC
539 AACTCTGTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 2 0.02
102 82 0.98
ACGTcount: A:0.28, C:0.44, G:0.07, T:0.21
Consensus pattern (102 bp):
GTCTCTACCACCACCAATACAATCTCGACATCCAACAACTCTATCACCTCCACCCGTCAAGTCTC
TACCACCACCAGAACAATCCCAACATCCACCTGTCAG
Found at i:2049 original size:235 final size:234
Alignment explanation
Indices: 1566--2178 Score: 763
Period size: 235 Copynumber: 2.6 Consensus size: 234
1556 ATTTATTATT
* **
1566 AATATATTATATGATATGATATAGCATTATATAATATAGTAGG-ATGACTAACGGTCAAATGTAC
1 AATATAATATATGATATGATATAGCATTATATAATATAGTAGGAATGACTAACTTTCAAATGTAC
* ** * *
1630 AAAAATGCATGGGGACTTAGAGCATATTTCAACTAGTATAACAATAAACAATAATAGTAT-TATT
66 AAAAA-GTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATA-TATATAAT
1694 AAGTAAT-ATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAGATAT
129 AAGTAATAATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAGATAT
*
1758 AGTATTACATGATAATATAATGTTTAATTATACATAACCTATT
194 AGTATTACATGATAATATAATGTTTAATTATA-ATAA-CTATA
* *
1801 AATATATTATATGATATGATATAGCATTATATAATATAATAGGAATG-CTAACTTTCAAATGTAC
1 AATATAATATATGATATGATATAGCATTATATAATATAGTAGGAATGACTAACTTTCAAATGTAC
**
1865 GGAAAGTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATATAATAATA
66 AAAAAGTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATAT-ATAATA
* * *
1930 AGTAATAAT-TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAAGAT
130 AGTAATAATATAATGTACTACTATTATAGA--T-AATTATTATAATATAAATTATAATAAAAGAT
* *
1994 ATAGTATTACATGGTATTATAATGTTTAATTAT-AT-A-TATA
192 ATAGTATTACATGATAATATAATGTTTAATTATAATAACTATA
* * * * *
2034 AACTATTAATATATGATAT-A-AT---ATTATATAGTACAGGA-GAAGGACTAACTTTCAAATAT
1 AA-TA-TAATATATGATATGATATAGCATTATATAATATAGTAGGAATGACTAACTTTCAAATGT
* * *
2093 ATAAAAAGTATAAGAACTTAAAGCATATTTCAACTAGTATAATAATAAACAATAATATATTATAA
64 ACAAAAAGTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATA-TATAA
*
2158 TAATTAAT-ATAT-ATGCTACTA
128 TAAGTAATAATATAATG-TACTA
2179 GTATAGTATG
Statistics
Matches: 336, Mismatches: 29, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
229 9 0.03
230 97 0.29
231 1 0.00
233 10 0.03
234 49 0.15
235 102 0.30
236 7 0.02
237 1 0.00
238 60 0.18
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (234 bp):
AATATAATATATGATATGATATAGCATTATATAATATAGTAGGAATGACTAACTTTCAAATGTAC
AAAAAGTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATATATAATAA
GTAATAATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAGATATAG
TATTACATGATAATATAATGTTTAATTATAATAACTATA
Found at i:2131 original size:230 final size:233
Alignment explanation
Indices: 1562--2178 Score: 731
Period size: 230 Copynumber: 2.7 Consensus size: 233
1552 AAAAATTTAT
* * * * **
1562 TATTAATATATTATATGATATGATATAGCATTATATAATA-TAGTAGGATGACTAACGGTCAAAT
1 TATTAATATATTATATGATATGATATAACATTATATAATACAAG-AGGAAGGCTAACTTTCAAAT
* * ** * *
1626 GTACAAAAATGCATGGGGACTTAGAGCATATTTCAACTAGTATAACAATAAACAATAATAGTAT-
65 ATACAAAAA-GTATAAGAACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATA-TATA
*
1690 TATTAAGTAAT-ATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAG
128 TAATAAGTAATAATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAG
1754 ATATAGTATTACATGATAATATAATGTTTAATTATACATAACC
193 ATATAGTATTACATGATAATATAATGTTTAATTATA-ATAA-C
* * * * *
1797 TATTAATATATTATATGATATGATATAGCATTATATAATATAATAGGAATGCTAACTTTCAAATG
1 TATTAATATATTATATGATATGATATAACATTATATAATACAAGAGGAAGGCTAACTTTCAAATA
** *
1862 TACGGAAAGTATAAGGACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATATAATA
66 TACAAAAAGTATAAGAACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATAT-ATA
* * *
1927 ATAAGTAATAAT-TAATGTACTACTATTATATATGTCTATTATTATAATATAGATTATAATAAAA
130 ATAAGTAATAATATAATGTACTACTATTATAGA--T-AATTATTATAATATAAATTATAATAAAA
* *
1991 GATATAGTATTACATGGTATTATAATGTTTAATTAT-AT-A-
192 GATATAGTATTACATGATAATATAATGTTTAATTATAATAAC
* * *
2030 TA-TAA-ACTATTA-AT-ATATGATATAATATTATATAGTACAGGA-GAAGGACTAACTTTCAAA
1 TATTAATA-TATTATATGATATGATATAACATTATATAATACAAGAGGAAGG-CTAACTTTCAAA
* *
2090 TATATAAAAAGTATAAGAACTTAAAGCATATTTCAACTAGTATAATAATAAACAATAATATATTA
64 TATACAAAAAGTATAAGAACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATA-TA
*
2155 TAATAATTAAT-ATAT-ATGCTACTA
128 TAATAAGTAATAATATAATG-TACTA
2179 GTATAGTATG
Statistics
Matches: 337, Mismatches: 33, Indels: 29
0.84 0.08 0.07
Matches are distributed among these distances:
229 9 0.03
230 107 0.32
231 4 0.01
232 8 0.02
233 5 0.01
234 46 0.14
235 92 0.27
236 5 0.01
237 1 0.00
238 60 0.18
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.36
Consensus pattern (233 bp):
TATTAATATATTATATGATATGATATAACATTATATAATACAAGAGGAAGGCTAACTTTCAAATA
TACAAAAAGTATAAGAACTTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATATATAA
TAAGTAATAATATAATGTACTACTATTATAGATAATTATTATAATATAAATTATAATAAAAGATA
TAGTATTACATGATAATATAATGTTTAATTATAATAAC
Found at i:9027 original size:18 final size:19
Alignment explanation
Indices: 8984--9029 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
8974 TATCATTAAT
*
8984 AATTCAATATTAATATAAA
1 AATTTAATATTAATATAAA
* *
9003 TATTTAATATTATTA-AAA
1 AATTTAATATTAATATAAA
9021 AATTTAATA
1 AATTTAATA
9030 ATATAAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTAATATTAATATAAA
Found at i:18259 original size:21 final size:20
Alignment explanation
Indices: 18233--18277 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18223 TATTCAAAAA
*
18233 AAAATTAAGATAATTATAAAT
1 AAAATTAAG-TAATAATAAAT
* *
18254 AAAATTATGTTATAATAAAT
1 AAAATTAAGTAATAATAAAT
18274 AAAA
1 AAAA
18278 ATATATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAATTAAGTAATAATAAAT
Found at i:18303 original size:30 final size:33
Alignment explanation
Indices: 18234--18317 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 33
18224 ATTCAAAAAA
* *
18234 AAATTAAGATAATTATAAATAAAATTATGTTATAAT
1 AAATTAA-ATAA--ATATATAAAATTATATTATAAT
*
18270 AAA-T-AA-AAATATATAAAATTACTATT-TATT
1 AAATTAAATAAATATATAAAATTA-TATTATAAT
18300 AAATTAAATAAATATATA
1 AAATTAAATAAATATATA
18318 TATTTTTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
30 18 0.44
31 4 0.10
32 4 0.10
33 10 0.24
34 1 0.02
35 1 0.02
36 3 0.07
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (33 bp):
AAATTAAATAAATATATAAAATTATATTATAAT
Found at i:26174 original size:266 final size:266
Alignment explanation
Indices: 25693--26224 Score: 764
Period size: 266 Copynumber: 2.0 Consensus size: 266
25683 CTTTATATCA
* *
25693 TAAAAAAAGGAAATAAAAACATAATTTTCTTTTTATCTTATATTACAATATCTAATATTATCGTC
1 TAAAAAAAGGAAATAAAAACATAATATTCTTTTTATCTTATATTACAATATCTAATATCATCGTC
* * *
25758 ACCATTATTTTTACACTAATCGCGGATAAACGCACTGCTCATCCAAAAATAGAATGAGTTGACTT
66 ACCATTACTTTTACACTAATCACGGATAAACGCACCGCTCATCCAAAAATAGAATGAGTTGACTT
* *
25823 GAGAGATAGAAAAAAATGAGAACAGAAGAATAACACCGTCGTTCCATAAAAAGCCAATTCAAATA
131 GAGAGATAGAAAAAAATGAGAACAGAAGAACAACACCGTCGCTCCATAAAAAGCCAATTCAAATA
*
25888 TATTCTTTTTTCACGAATATAATAT-GAAAGTATTGAGACTAAATTTTCAGACATACAGCTTTAC
196 TATTCTTTTTTCAAGAATATAATATGGAAA-TATTGAGACTAAATTTTCAGACATACAGCTTTAC
25952 AGATACC
260 AGATACC
* * * *
25959 TAAAAAAAGGGAATAAAAACATAATATTCTTTTTATCTTATATTACAGTATCTAATCTCATTGTC
1 TAAAAAAAGGAAATAAAAACATAATATTCTTTTTATCTTATATTACAATATCTAATATCATCGTC
* * * * * * * * *
26024 ATCTTTGCTTTTACACTAATCACGGATAAATGTACCGCTCATTCGAAGATAGAATGAGTTGGCTT
66 ACCATTACTTTTACACTAATCACGGATAAACGCACCGCTCATCCAAAAATAGAATGAGTTGACTT
* * * *
26089 GGGAGATAGAAAGAAAA-GAGAATAGAAGAACAGCACCGTCGCTGCATAAAAAGCCAATTCAAAT
131 GAGAGATAGAAA-AAAATGAGAACAGAAGAACAACACCGTCGCTCCATAAAAAGCCAATTCAAAT
* *
26153 ATATT-TCTTTTTCAAGAATATAATATGGAAATGTTGGGACTAAATTTTCAGACATACAGCTTTA
195 ATATTCT-TTTTTCAAGAATATAATATGGAAATATTGAGACTAAATTTTCAGACATACAGCTTTA
*
26217 CATATACC
259 CAGATACC
26225 AATTTTCTTT
Statistics
Matches: 235, Mismatches: 28, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
265 1 0.00
266 226 0.96
267 8 0.03
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (266 bp):
TAAAAAAAGGAAATAAAAACATAATATTCTTTTTATCTTATATTACAATATCTAATATCATCGTC
ACCATTACTTTTACACTAATCACGGATAAACGCACCGCTCATCCAAAAATAGAATGAGTTGACTT
GAGAGATAGAAAAAAATGAGAACAGAAGAACAACACCGTCGCTCCATAAAAAGCCAATTCAAATA
TATTCTTTTTTCAAGAATATAATATGGAAATATTGAGACTAAATTTTCAGACATACAGCTTTACA
GATACC
Found at i:29652 original size:2 final size:2
Alignment explanation
Indices: 29645--29695 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
29635 GTATAATACA
29645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
29686 AT AT AT AT AT
1 AT AT AT AT AT
29696 GTAAAACATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40904 original size:44 final size:45
Alignment explanation
Indices: 40842--40934 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 45
40832 AAGGAAAATA
* * *
40842 TTTGGTTGTTAGTAGAG-TTAGACTTCATGAGTAGGATTAAGGAG
1 TTTGGTTGTCAGTAGAGTTTAGACTTCACGAGTAGGATTAACGAG
*
40886 TTTGGTTGTCAGTGGAGTTTTTAGACTTCACGAGTAGGATTAACGAG
1 TTTGGTTGTCAGTAGAG--TTTAGACTTCACGAGTAGGATTAACGAG
40933 TT
1 TT
40935 GACAAGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 15 0.36
47 27 0.64
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.38
Consensus pattern (45 bp):
TTTGGTTGTCAGTAGAGTTTAGACTTCACGAGTAGGATTAACGAG
Found at i:47891 original size:17 final size:19
Alignment explanation
Indices: 47865--47907 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
47855 TCCTTCTTTC
*
47865 CTCTTCTCTTTT-ATT-CT
1 CTCTTTTCTTTTCATTCCT
*
47882 CTCTTTTCTTTTCTTTCCT
1 CTCTTTTCTTTTCATTCCT
47901 CTCTTTT
1 CTCTTTT
47908 ACACCGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 11 0.50
18 2 0.09
19 9 0.41
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (19 bp):
CTCTTTTCTTTTCATTCCT
Found at i:49983 original size:16 final size:16
Alignment explanation
Indices: 49962--49992 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49952 ATTTTCGAAT
49962 TATTTAAAACTATTTA
1 TATTTAAAACTATTTA
*
49978 TATTTATAACTATTT
1 TATTTAAAACTATTT
49993 TTTCTAAAAA
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:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTAAAACTATTTA
Found at i:50233 original size:6 final size:6
Alignment explanation
Indices: 50221--50255 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
50211 CATTTCATAG
* *
50221 GTATAT ATATAT ATATAT GTATAT GTATAT GTATA
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATA
50256 GGTGAATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (6 bp):
GTATAT
Done.