Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012195.1 Kokia drynarioides strain JFW-HI SEQ_127196, 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: 96429
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:199 original size:4 final size:4
Alignment explanation
Indices: 179--264 Score: 77
Period size: 4 Copynumber: 21.2 Consensus size: 4
169 AACACATTAC
* * * *
179 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT C-TT CTTT CTTT CCTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT -CTTT
* *
227 CCTT CTTC CTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
265 CCGTTTATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
3 6 0.09
4 51 0.76
5 10 0.15
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:211 original size:20 final size:20
Alignment explanation
Indices: 186--265 Score: 108
Period size: 20 Copynumber: 3.9 Consensus size: 20
176 TACCTTTCTT
186 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
206 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
*
226 TCCTTCTTCCTTTCTTT-CTT
1 TCCTTCTT-CTTTCTTTCCTC
*
246 TCTTTCCTTTCTTTCTTTCC
1 TCCTT-C-TTCTTTCTTTCC
266 CGTTTATTTG
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
20 34 0.63
21 17 0.31
22 3 0.06
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:213 original size:17 final size:17
Alignment explanation
Indices: 179--264 Score: 92
Period size: 17 Copynumber: 5.3 Consensus size: 17
169 AACACATTAC
179 CTTTCTTTCC-TT-CTT
1 CTTTCTTTCCTTTCCTT
*
194 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTTTCCTT
211 C-TTCTTT-CTTTCCTCT
1 CTTTCTTTCCTTTCCT-T
* *
227 CCTTC-TTCCTTTCTTT
1 CTTTCTTTCCTTTCCTT
*
243 CTTTCTTTCCTTTCTTT
1 CTTTCTTTCCTTTCCTT
260 CTTTC
1 CTTTC
265 CCGTTTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
15 16 0.26
16 16 0.26
17 29 0.48
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
CTTTCTTTCCTTTCCTT
Found at i:8600 original size:6 final size:6
Alignment explanation
Indices: 8589--8617 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8579 TAAAATTAGG
8589 TATATT TATATT TATATT TATATT TATAT
1 TATATT TATATT TATATT TATATT TATAT
8618 GTCAATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:8881 original size:67 final size:65
Alignment explanation
Indices: 8766--8946 Score: 253
Period size: 67 Copynumber: 2.8 Consensus size: 65
8756 ATTCAATTTC
* *
8766 ATTTTTTTATTATT-TTTATTTATTTATTTTT-TGAATATAAATATATAAATATAAAATAATATT
1 ATTTTATT-TTATTATTTATTTATTTATTTTTATGAATATAAATAAATAAATATAAAATAATATT
8829 A
65 A
* *
8830 ATTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATAT
1 ATTTTATTTTATTATTTATTTATTTATT-TT-TATGAATATAAATAAATAAATATAAAATAATAT
8895 TA
64 TA
* *
8897 ATTTTATTTTATTATTTATTTA-TTA-TTTTATCAATATAGATAAATAAATA
1 ATTTTATTTTATTATTTATTTATTTATTTTTATGAATATAAATAAATAAATA
8947 ACAAACCCAA
Statistics
Matches: 106, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
63 24 0.23
64 23 0.22
65 3 0.03
66 4 0.04
67 52 0.49
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (65 bp):
ATTTTATTTTATTATTTATTTATTTATTTTTATGAATATAAATAAATAAATATAAAATAATATTA
Found at i:8921 original size:63 final size:64
Alignment explanation
Indices: 8769--8946 Score: 238
Period size: 63 Copynumber: 2.8 Consensus size: 64
8759 CAATTTCATT
* *
8769 TTTTTATTATTTTTATTTATTTATT-TTT-TGAATATAAATATATAAATATAAAATAATATTAA
1 TTTTTATTATTATTATTTATTTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAA
* *
8831 TTTTGTTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATT
1 TTTT-TATTATTA-TTATTTATTTATTATT-TATGAATATAAATAAATAAATATAAAATAATATT
8896 AA
63 AA
* *
8898 -TTTTATT-TTATTATTTATTTATTATTTTATCAATATAGATAAATAAATA
1 TTTTTATTATTATTATTTATTTATTA-TTTATGAATATAAATAAATAAATA
8947 ACAAACCCAA
Statistics
Matches: 102, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
62 4 0.04
63 39 0.38
64 18 0.18
65 5 0.05
66 4 0.04
67 32 0.31
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (64 bp):
TTTTTATTATTATTATTTATTTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAA
Found at i:15424 original size:34 final size:34
Alignment explanation
Indices: 15375--15439 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
15365 AAAAAGTAAT
* *
15375 AGTTGAATGATTTAAATAAAAACTTTCAAATCAA
1 AGTTGAATGACTTAAATAAAAAATTTCAAATCAA
* *
15409 AGTTTAATGACTTAAATAAAAAATTTTAAAT
1 AGTTGAATGACTTAAATAAAAAATTTCAAAT
15440 AGTTTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (34 bp):
AGTTGAATGACTTAAATAAAAAATTTCAAATCAA
Found at i:17174 original size:20 final size:20
Alignment explanation
Indices: 17149--17188 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17139 TAAATAAGAA
17149 TCGTTCCTATTTTGATCACC
1 TCGTTCCTATTTTGATCACC
17169 TCGTTCCTATTTTGATCACC
1 TCGTTCCTATTTTGATCACC
17189 CCAAAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.10, T:0.45
Consensus pattern (20 bp):
TCGTTCCTATTTTGATCACC
Found at i:25039 original size:138 final size:138
Alignment explanation
Indices: 24769--25039 Score: 337
Period size: 137 Copynumber: 2.0 Consensus size: 138
24759 CTACACCTCT
** *
24769 ATATAAAAGCAAATGATCAAAGAATTTATTTACATTTTGTCTATTGAATTATACTCGTTTTCTCA
1 ATATAAAAGCAAATGATCAAAGAATTTATTTACA-TGCGTCTATTGAATTATACTCGTCTTCTCA
* * * *
24834 CTTTGACAACTAGACCATTTTTGTCTCATTTTGGTATAAGAACTATCATTTTAATCCCATTTTAC
65 CTTTGACAACCAAACCATTTTTGTCTCATTTTGGTACAAGAACAATCATTTTAATCCCATTTTAC
24899 CCCCTCAAA
130 CCCCTCAAA
* * * * * *
24908 ATATAAAAGTAGATGATCAAAGATTTTATTTACA-GCGTCTCTTGAATTATACTTGTCTTCTTAC
1 ATATAAAAGCAAATGATCAAAGAATTTATTTACATGCGTCTATTGAATTATACTCGTCTTCTCAC
* ** * * **
24972 TTTGGCGGCCAAACTATTTTTGTCTCACTTTTGGTACACGAACAATCATTTTCGTCCCATTTTAC
66 TTTGACAACCAAACCATTTTTGTCTCA-TTTTGGTACAAGAACAATCATTTTAATCCCATTTTAC
25037 CCC
130 CCC
25040 AAAATTTATT
Statistics
Matches: 111, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
137 45 0.41
138 35 0.32
139 31 0.28
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.40
Consensus pattern (138 bp):
ATATAAAAGCAAATGATCAAAGAATTTATTTACATGCGTCTATTGAATTATACTCGTCTTCTCAC
TTTGACAACCAAACCATTTTTGTCTCATTTTGGTACAAGAACAATCATTTTAATCCCATTTTACC
CCCTCAAA
Found at i:28813 original size:16 final size:16
Alignment explanation
Indices: 28794--28829 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28784 TTATAAGTTT
28794 AATTTAAGATAAATTA
1 AATTTAAGATAAATTA
* *
28810 AATTTAAGCTCAATTA
1 AATTTAAGATAAATTA
28826 AATT
1 AATT
28830 CACTTATTAA
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:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
AATTTAAGATAAATTA
Found at i:32313 original size:23 final size:24
Alignment explanation
Indices: 32277--32322 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
32267 AATGACATGA
32277 TTTATATTTTAAAA-ATTAATTTT
1 TTTATATTTTAAAATATTAATTTT
*
32300 TTTAT-TTTTCAAAATATTTATTT
1 TTTATATTTT-AAAATATTAATTT
32323 GAGCGAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 9 0.45
24 7 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTATATTTTAAAATATTAATTTT
Found at i:40620 original size:6 final size:6
Alignment explanation
Indices: 40599--40663 Score: 69
Period size: 6 Copynumber: 10.3 Consensus size: 6
40589 AAGAAGTAAT
*
40599 AGGGAG AGAGGAAG AGGGAG AGGGAG AGGGAG AGGGAG AGAGGAG -GGAGGG
1 AGGGAG AG-GG-AG AGGGAG AGGGAG AGGGAG AGGGAG AG-GGAG AGG-GAG
*
40650 AGGGAG AGAGAG AG
1 AGGGAG AGGGAG AG
40664 AGGTATAGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
5 1 0.02
6 36 0.71
7 10 0.20
8 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:40957 original size:17 final size:15
Alignment explanation
Indices: 40920--40970 Score: 65
Period size: 12 Copynumber: 3.6 Consensus size: 15
40910 TTTAGGGATT
40920 AATTAA-ATAAATTA
1 AATTAATATAAATTA
40934 AATTAA-AT--ATTA
1 AATTAATATAAATTA
40946 AATTAATATAAATTA
1 AATTAATATAAATTA
40961 TAATTAATAT
1 -AATTAATAT
40971 TTTTGGGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 8 0.24
15 4 0.12
16 9 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTAATATAAATTA
Found at i:40966 original size:21 final size:20
Alignment explanation
Indices: 40919--40967 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
40909 ATTTAGGGAT
40919 TAATTAAATAAATTAAATTA
1 TAATTAAATAAATTAAATTA
* *
40939 AATATTAAATTAATATAAATTA
1 TA-ATTAAATAAAT-TAAATTA
40961 TAATTAA
1 TAATTAA
40968 TATTTTTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATTAAATAAATTAAATTA
Found at i:40969 original size:27 final size:26
Alignment explanation
Indices: 40920--40971 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
40910 TTTAGGGATT
40920 AATTAAATAAATTAAATTAAATATTA
1 AATTAAATAAATTAAATTAAATATTA
40946 AATTAATATAAATTATAATT-AATATT
1 AATTAA-ATAAATTA-AATTAAATATT
40972 TTTGGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.25
27 14 0.58
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAATAAATTAAATTAAATATTA
Found at i:71866 original size:13 final size:14
Alignment explanation
Indices: 71842--71883 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
71832 TTTGAATCTT
*
71842 AAATCTCAAACCTC
1 AAATCACAAACCTC
71856 AAA-CACAAACC-C
1 AAATCACAAACCTC
*
71868 AAATCTCAAACCTC
1 AAATCACAAACCTC
71882 AA
1 AA
71884 CCTTGGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 14 0.58
14 6 0.25
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATCACAAACCTC
Found at i:71964 original size:6 final size:6
Alignment explanation
Indices: 71955--71979 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71945 TCGAGTTTAG
71955 GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA G
71980 ATTCAGGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTTGA
Found at i:73736 original size:31 final size:31
Alignment explanation
Indices: 73701--73793 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
73691 ATTTGAGTAC
*
73701 CAAATTGAATATTAAAACTAAATTCACATAT
1 CAAATTGAATATTAAAACTAAATTCAAATAT
* * * ** *
73732 CAAATTCAGACA-AAAAAAAAAACTCAAATAT
1 CAAATTGA-ATATTAAAACTAAATTCAAATAT
** *
73763 CAAATTGAATATTAACCCTAAATTGAAATAT
1 CAAATTGAATATTAAAACTAAATTCAAATAT
73794 ATATATATGT
Statistics
Matches: 44, Mismatches: 16, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
30 2 0.05
31 40 0.91
32 2 0.05
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (31 bp):
CAAATTGAATATTAAAACTAAATTCAAATAT
Found at i:75198 original size:14 final size:14
Alignment explanation
Indices: 75179--75205 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
75169 CCTTTCTTTA
75179 TTTTTTGCTTTTTT
1 TTTTTTGCTTTTTT
75193 TTTTTTGCTTTTT
1 TTTTTTGCTTTTT
75206 ATGATAGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (14 bp):
TTTTTTGCTTTTTT
Found at i:79840 original size:15 final size:16
Alignment explanation
Indices: 79815--79857 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
79805 AAAAATTTTA
* *
79815 AATTCTTTTAAGTTTG
1 AATTATTTTAAATTTG
*
79831 AATT-TTTTAAATTTT
1 AATTATTTTAAATTTG
79846 AATTATTTTAAA
1 AATTATTTTAAA
79858 ATTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (16 bp):
AATTATTTTAAATTTG
Found at i:79856 original size:16 final size:15
Alignment explanation
Indices: 79807--79867 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 15
79797 CAAGTTTTAA
79807 AAATTTTAAATTCTTTT
1 AAATTTT-AATT-TTTT
* *
79824 AAGTTTGAATTTTTT
1 AAATTTTAATTTTTT
79839 AAATTTTAATTATTTT
1 AAATTTTAATT-TTTT
*
79855 AAAATTTTCATTT
1 -AAATTTTAATTT
79868 AAGGTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.35
16 9 0.24
17 15 0.41
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (15 bp):
AAATTTTAATTTTTT
Found at i:84712 original size:19 final size:18
Alignment explanation
Indices: 84683--84719 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
84673 TTTAAAAAGT
84683 TAATAAAAAAATCTAAAA
1 TAATAAAAAAATCTAAAA
84701 TAATACAAAAAATCTAAAA
1 TAATA-AAAAAATCTAAAA
84720 AATTTTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (18 bp):
TAATAAAAAAATCTAAAA
Found at i:93274 original size:23 final size:23
Alignment explanation
Indices: 93248--93299 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
93238 ATTAATCTAA
*
93248 AATTTTAATAATTTTTCCTATTT
1 AATTTTAATAATTTTCCCTATTT
*
93271 AATTTCAATAATTTTCCCTATTT
1 AATTTTAATAATTTTCCCTATTT
93294 AATTTT
1 AATTTT
93300 TGAACTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.58
Consensus pattern (23 bp):
AATTTTAATAATTTTCCCTATTT
Found at i:95299 original size:96 final size:96
Alignment explanation
Indices: 95110--95301 Score: 237
Period size: 96 Copynumber: 2.0 Consensus size: 96
95100 TTTTTGGGAA
** * *
95110 AAGGATATTCAATTATCTCGATTTGAAGAAAGGTTGCAACTAGTAAGTTAAGGCGCAAATTTTTA
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCAACTAGTAAGTTAAAGCGCAAATTTTGA
*
95175 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* * * *
95206 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAAGCGCAAATTTTCG
1 AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCAACTAGTAAGTTAAAGCGCAAATTTT-G
* *
95271 A-AACTCGAA-ATAAA-AGAATATTGTCTCGATT
65 AGAA-TCGAAGATAAAGA-AACATTGCCTCGATT
95302 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
95 1 0.01
96 75 0.91
97 6 0.07
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCAATTATCTCGATTTGAAGAAAAATTGCAACTAGTAAGTTAAAGCGCAAATTTTGA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:95548 original size:29 final size:29
Alignment explanation
Indices: 95506--95577 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
95496 ATCGGAGTTG
* * *
95506 AAAATGAGACTTTTTGGATACTCGAGGGT
1 AAAATGATAATTTTTGGATACTCGAGGGC
* *
95535 AAAATGATAA-TTTTGGATTCTCGGGGGC
1 AAAATGATAATTTTTGGATACTCGAGGGC
*
95563 AAAATGGTAATTTTT
1 AAAATGATAATTTTT
95578 AGAAAGGTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGATAATTTTTGGATACTCGAGGGC
Found at i:95557 original size:28 final size:28
Alignment explanation
Indices: 95517--95576 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
95507 AAATGAGACT
*
95517 TTTTGGATACTCGAGGGTAAAATGATAA
1 TTTTGGATACTCGAGGGCAAAATGATAA
* * *
95545 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACTCGAGGGCAAAATGATAA
95573 TTTT
1 TTTT
95577 TAGAAAGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATGATAA
Found at i:95676 original size:59 final size:59
Alignment explanation
Indices: 95592--95757 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 59
95582 AGGTCAGGTT
* * * *
95592 AAAAATGGAATTTTTAGACACCCGGGGGTGAAACGGTAACTTTTAAAAAAATCGGGATC
1 AAAAATGGAATTTTTGGACATCCGGGGGTAAAACGGTAACTTTTAAAAAAATCGAGATC
* * * ** *
95651 AAAAACGGAATTTTTGGACATCCGGGGGTAAAATGGTAATTTTTAGGAAAATTGAGATC
1 AAAAATGGAATTTTTGGACATCCGGGGGTAAAACGGTAACTTTTAAAAAAATCGAGATC
* *** * * *
95710 AAAAATGAAATTTTTGGACATTTAGGGGTAAAATGATAATTTTTAAAA
1 AAAAATGGAATTTTTGGACATCCGGGGGTAAAACGGTAACTTTTAAAA
95758 GTTTTGGGGT
Statistics
Matches: 89, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 89 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGACATCCGGGGGTAAAACGGTAACTTTTAAAAAAATCGAGATC
Found at i:95742 original size:29 final size:28
Alignment explanation
Indices: 95710--95928 Score: 203
Period size: 29 Copynumber: 7.6 Consensus size: 28
95700 AATTGAGATC
95710 AAAAATGAAATTTTTGGACA-TTTAGGGGT
1 AAAAATGAAATTTTTGGA-AGTTT-GGGGT
**
95739 -AAAATGATAATTTTTAAAAGTTTTGGGGTT
1 AAAAATGA-AATTTTTGGAAG-TTTGGGG-T
* * * * *
95769 TAAAATGGAATTTTTAGAGGTTCGGGGT
1 AAAAATGAAATTTTTGGAAGTTTGGGGT
95797 CAAAAAT-ATAATTTTTGGAAGTTTGGGG-
1 -AAAAATGA-AATTTTTGGAAGTTTGGGGT
* *
95825 GAAAATGTAATTTTTGGAAGTGTTGGGGT
1 AAAAATGAAATTTTTGGAAGT-TTGGGGT
*
95854 AAAAATGGAATTTTTGGAAGTTTGGGAGT
1 AAAAATGAAATTTTTGGAAGTTTGGG-GT
*
95883 CAAAAATGAAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGAAATTTTTGGAAGTTTG-GGGT
*
95913 AAAAATGTAATTTTTG
1 AAAAATGAAATTTTTG
95929 AATAGTTTAG
Statistics
Matches: 159, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.11
28 20 0.13
29 75 0.47
30 38 0.24
31 8 0.05
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (28 bp):
AAAAATGAAATTTTTGGAAGTTTGGGGT
Found at i:95774 original size:59 final size:56
Alignment explanation
Indices: 95710--95936 Score: 206
Period size: 59 Copynumber: 3.9 Consensus size: 56
95700 AATTGAGATC
* *
95710 AAAAATGAAATTTTTGGACATTTAGGGGT-AAAATGATAATTTTTAAAAGTTTTGGGGTT
1 AAAAATGAAATTTTTGGA-AGTTCGGGGTAAAAATG-TAATTTTTAAAAG-TTTGGGG-T
* * * * * **
95769 TAAAATGGAATTTTTAGAGGTTCGGGGTCAAAAATATAATTTTTGGAAGTTTGGGG-
1 AAAAATGAAATTTTTGGAAGTTCGGGGT-AAAAATGTAATTTTTAAAAGTTTGGGGT
* * * * **
95825 GAAAATGTAATTTTTGGAAGTGTTGGGGTAAAAATGGAATTTTTGGAAGTTTGGGAGT
1 AAAAATGAAATTTTTGGAAGT-TCGGGGTAAAAATGTAATTTTTAAAAGTTTGGG-GT
*
95883 CAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAATAGTTT
1 -AAAAATGAAATTTTTGGAAGTTCG-GGGTAAAAATGTAATTTTT-AAAAGTTT
95937 AGGGACCTCC
Statistics
Matches: 137, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
56 41 0.30
57 7 0.05
58 16 0.12
59 63 0.46
60 10 0.07
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (56 bp):
AAAAATGAAATTTTTGGAAGTTCGGGGTAAAAATGTAATTTTTAAAAGTTTGGGGT
Found at i:95866 original size:115 final size:115
Alignment explanation
Indices: 95711--95928 Score: 266
Period size: 115 Copynumber: 1.9 Consensus size: 115
95701 ATTGAGATCA
* **
95711 AAAATGAAATTTTTGGACATTTAGGGGTAAAATGATAATTTTTAAAAGTTTTGGG-GTTTAAAAT
1 AAAATGAAATTTTTGGACATTTAGGGGTAAAATGAGAATTTTTAAAAG-TTTGGGAGTCAAAAAT
* *
95775 GGAATTTTTAGAGGTTCG-GGGTCAAAAATATAATTTTTGGAAGTTTGGGGG
65 GAAATTTTTAGAAGTTCGAGGGT-AAAAATATAATTTTTGGAAGTTTGGGGG
* **
95826 AAAATGTAATTTTTGGA-AGTGTT-GGGGTAAAAATG-GAATTTTTGGAAGTTTGGGAGTCAAAA
1 AAAATGAAATTTTTGGACA-T-TTAGGGGT-AAAATGAGAATTTTTAAAAGTTTGGGAGTCAAAA
* *
95888 ATGAAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTG
63 ATGAAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTTG
95929 AATAGTTTAG
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
114 7 0.08
115 69 0.78
116 12 0.14
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (115 bp):
AAAATGAAATTTTTGGACATTTAGGGGTAAAATGAGAATTTTTAAAAGTTTGGGAGTCAAAAATG
AAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTTTGGAAGTTTGGGGG
Done.