Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012922.1 Kokia drynarioides strain JFW-HI SEQ_127938, 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: 87059
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:6913 original size:18 final size:18
Alignment explanation
Indices: 6890--6926 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6880 ACAATTTATA
6890 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
6908 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
6926 T
1 T
6927 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:8733 original size:19 final size:18
Alignment explanation
Indices: 8705--8741 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
8695 GATGAAAGTT
8705 AATAACAATTTTGATTAC
1 AATAACAATTTTGATTAC
8723 AATATACAATTTTGATTAC
1 AATA-ACAATTTTGATTAC
8742 GATGAGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (18 bp):
AATAACAATTTTGATTAC
Found at i:9224 original size:22 final size:20
Alignment explanation
Indices: 9180--9235 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
9170 TGAACCAAAC
*
9180 TTAATAAATAA-TATTATA-
1 TTAATATATAAGTATTATAG
* *
9198 AT-ATATGTAAGTATTATAG
1 TTAATATATAAGTATTATAG
9217 TTAATATATAAGTATTATA
1 TTAATATATAAGTATTATA
9236 ATCGGTCAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.20
18 8 0.27
19 1 0.03
20 15 0.50
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TTAATATATAAGTATTATAG
Found at i:15725 original size:18 final size:18
Alignment explanation
Indices: 15702--15738 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15692 GATAGTTTAA
*
15702 TATTTGATTTATTCAAAT
1 TATTTGAGTTATTCAAAT
*
15720 TATTTGAGTTATTCGAAT
1 TATTTGAGTTATTCAAAT
15738 T
1 T
15739 CGAAAATTCA
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:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (18 bp):
TATTTGAGTTATTCAAAT
Found at i:16163 original size:13 final size:13
Alignment explanation
Indices: 16147--16171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16137 TTTTTTATTT
16147 TTTTAATTTAAAA
1 TTTTAATTTAAAA
16160 TTTTAATTTAAA
1 TTTTAATTTAAA
16172 TAATATCGTA
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:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAATTTAAAA
Found at i:20226 original size:18 final size:18
Alignment explanation
Indices: 20207--20256 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
20197 CTTATGATAT
20207 TTTTATTAAG-AATAATA
1 TTTTATTAAGTAATAATA
*
20224 TTTTAATAAGTAATAATA
1 TTTTATTAAGTAATAATA
*
20242 TTTTATTAATTAATA
1 TTTTATTAAGTAATA
20257 TTATAAAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TTTTATTAAGTAATAATA
Found at i:24619 original size:31 final size:31
Alignment explanation
Indices: 24583--24892 Score: 263
Period size: 31 Copynumber: 10.0 Consensus size: 31
24573 ATTTGCTCTA
24583 ATATTGAAAAGGTTATATCTGAAATGGATAT
1 ATATTGAAAAGGTTATATCTGAAATGGATAT
* * * *
24614 TTATTGAAAATGTTATAT-TCGTAATGGATGT
1 ATATTGAAAAGGTTATATCT-GAAATGGATAT
* ** *
24645 CTATCAAAAAGGTTATAT-TCAAAATGGATAT
1 ATATTGAAAAGGTTATATCT-GAAATGGATAT
* * *
24676 ATACTGAAAAGGTCATATC-CAGAATGGATAT
1 ATATTGAAAAGGTTATATCTGA-AATGGATAT
* * *
24707 CTATTGAAAATGTTATAT-TCAGAATGGATAT
1 ATATTGAAAAGGTTATATCTGA-AATGGATAT
* ***
24738 ATATTGAAAAAGGTTATATCTAAAACAAATAT
1 ATATTG-AAAAGGTTATATCTGAAATGGATAT
*
24770 CTATTGAAAAGGTTATATCTGAAATGGATAT
1 ATATTGAAAAGGTTATATCTGAAATGGATAT
* * *
24801 AAATTGAAAAGGTCATAT-TCGAAATGGATCT
1 ATATTGAAAAGGTTATATCT-GAAATGGATAT
* * *
24832 AAATTGAAAACGTCATATCTGAAATGGATAT
1 ATATTGAAAAGGTTATATCTGAAATGGATAT
* * * *
24863 CTATTGGAAAGGTTGTATCTTAAA-GGATAT
1 ATATTGAAAAGGTTATATCTGAAATGGATAT
24893 TAAACGAAAA
Statistics
Matches: 226, Mismatches: 45, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
30 9 0.04
31 192 0.85
32 23 0.10
33 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (31 bp):
ATATTGAAAAGGTTATATCTGAAATGGATAT
Found at i:27404 original size:38 final size:38
Alignment explanation
Indices: 27353--27435 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
27343 AAATGTTTCT
27353 GAGATTCATAACTTTCTGGGATTAGTAGGATACTACAA
1 GAGATTCATAACTTTCTGGGATTAGTAGGATACTACAA
27391 GAGATTCATAACTTTCTGGGATTAGTAGGATACTACAA
1 GAGATTCATAACTTTCTGGGATTAGTAGGATACTACAA
27429 GAGATTC
1 GAGATTC
27436 GTGGAAGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (38 bp):
GAGATTCATAACTTTCTGGGATTAGTAGGATACTACAA
Found at i:38571 original size:17 final size:17
Alignment explanation
Indices: 38548--38601 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
38538 CTTTCAAATG
38548 ATATTTTATTAA-TAAT
1 ATATTTTATTAAGTAAT
*
38564 ACTATTTTAATAAGTAAT
1 A-TATTTTATTAAGTAAT
*
38582 GATATTTTATTAATTAAT
1 -ATATTTTATTAAGTAAT
38600 AT
1 AT
38602 TATAAAGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.03
17 12 0.38
18 18 0.56
19 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
ATATTTTATTAAGTAAT
Found at i:38599 original size:18 final size:17
Alignment explanation
Indices: 38544--38595 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
38534 ATGGCTTTCA
38544 AATGATATTTTATTAAT
1 AATGATATTTTATTAAT
*
38561 AAT-ACTATTTTAATAAGT
1 AATGA-TATTTTATTAA-T
38579 AATGATATTTTATTAAT
1 AATGATATTTTATTAAT
38596 TAATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 14 0.47
19 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
AATGATATTTTATTAAT
Found at i:38905 original size:43 final size:43
Alignment explanation
Indices: 38844--38930 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
38834 CATTAATGGA
38844 AGCTTAGAAAGCTTAAGTGAAGTAGATATATTTTTGGATAGGG
1 AGCTTAGAAAGCTTAAGTGAAGTAGATATATTTTTGGATAGGG
38887 AGCTTAGAAAGCTTAAGTGAAGTAGATATATTTTTGGATAGGG
1 AGCTTAGAAAGCTTAAGTGAAGTAGATATATTTTTGGATAGGG
38930 A
1 A
38931 ATAATTAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
AGCTTAGAAAGCTTAAGTGAAGTAGATATATTTTTGGATAGGG
Found at i:48020 original size:63 final size:63
Alignment explanation
Indices: 47942--48068 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
47932 AAGACCTTCG
47942 ATTCAATAGCTTAAAACTTGATTTAAATGGCTAGACTATGTTTAAAAATATTAAAAATACAAA
1 ATTCAATAGCTTAAAACTTGATTTAAATGGCTAGACTATGTTTAAAAATATTAAAAATACAAA
48005 ATTCAATAGCTTAAAACTTGATTTAAATGGCTAGACTATGTTTAAAAATATTAAAAATACAAA
1 ATTCAATAGCTTAAAACTTGATTTAAATGGCTAGACTATGTTTAAAAATATTAAAAATACAAA
48068 A
1 A
48069 CCTTACTCCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (63 bp):
ATTCAATAGCTTAAAACTTGATTTAAATGGCTAGACTATGTTTAAAAATATTAAAAATACAAA
Found at i:49155 original size:17 final size:16
Alignment explanation
Indices: 49115--49147 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
49105 AGTTATCAAA
49115 ATTTAATTTTTATAAAT
1 ATTT-ATTTTTATAAAT
49132 ATTTATTTTT-TAAAT
1 ATTTATTTTTATAAAT
49147 A
1 A
49148 GGTTTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATTTTTATAAAT
Found at i:50090 original size:24 final size:24
Alignment explanation
Indices: 50062--50112 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
50052 AGAAATAATC
* * *
50062 TTTCAGTTAAATTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
50086 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
50110 TTT
1 TTT
50113 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:50121 original size:24 final size:24
Alignment explanation
Indices: 50074--50124 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
50064 TCAGTTAAAT
* *
50074 TCTGTTTATTTGTTTCAATTAAAC
1 TCTGTTTAGTTGTTTCAATCAAAC
* *
50098 TCTGTTTAGTTGTTTGAGTCAAAC
1 TCTGTTTAGTTGTTTCAATCAAAC
50122 TCT
1 TCT
50125 TATTAGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (24 bp):
TCTGTTTAGTTGTTTCAATCAAAC
Found at i:53380 original size:30 final size:26
Alignment explanation
Indices: 53309--53396 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 26
53299 GTTTGACACA
*
53309 TTTTCCTAATTTGGTATCTAAACTTT
1 TTTTCCTAATTTGGTACCTAAACTTT
*
53335 TTTTGGCCCAATTTGGTACCTAAACTTGGCAT
1 TTTT--CCTAATTTGGTACCTAAACTT----T
*
53367 TTTTCCTAATTTGGTACCTAAGCTTT
1 TTTTCCTAATTTGGTACCTAAACTTT
53393 TTTT
1 TTTT
53397 AGGTTCCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
26 9 0.17
28 19 0.37
30 19 0.37
32 5 0.10
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (26 bp):
TTTTCCTAATTTGGTACCTAAACTTT
Found at i:53872 original size:89 final size:89
Alignment explanation
Indices: 53772--53956 Score: 203
Period size: 89 Copynumber: 2.1 Consensus size: 89
53762 AATTACGTAC
* * ** * ** *
53772 CAAATTAAGAAAAAGA-GTCAAGTTTAGGTGCGAAATTGGACCCCAACAAGTTTAAGTACTGACT
1 CAAATTAAGAAAAA-ATGTCAAGTATAGGTACGAAATTGGA-CAAAAAAAGTTTAAGTACCAAAT
* *
53836 TAAGAAAAATTATCAAATTTAGGTAT
64 TAAGAAAAAGTATCAAATTTAGATAT
* * *
53862 CAAATT-AGAAAAAATTGTCAAGTATGGGTACTAAATTGGACAAAAAAAGTTTATGTACCAAATT
1 CAAATTAAGAAAAAA-TGTCAAGTATAGGTACGAAATTGGACAAAAAAAGTTTAAGTACCAAATT
*
53926 AAGAAAAAGTATCAAGTTTAGATAT
65 AAGAAAAAGTATCAAATTTAGATAT
53951 CAAATT
1 CAAATT
53957 TTATTCATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
88 1 0.01
89 52 0.66
90 26 0.33
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (89 bp):
CAAATTAAGAAAAAATGTCAAGTATAGGTACGAAATTGGACAAAAAAAGTTTAAGTACCAAATTA
AGAAAAAGTATCAAATTTAGATAT
Found at i:54292 original size:13 final size:13
Alignment explanation
Indices: 54276--54300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54266 TGGGTTATGA
54276 GTTTAAGGTTTAT
1 GTTTAAGGTTTAT
54289 GTTTAAGGTTTA
1 GTTTAAGGTTTA
54301 AGATTTTGGG
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:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
GTTTAAGGTTTAT
Found at i:55159 original size:15 final size:15
Alignment explanation
Indices: 55139--55186 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
55129 TTATCTCAGA
55139 TTATATTTTAGTTAT
1 TTATATTTTAGTTAT
*
55154 TTATATTTGAG--AT
1 TTATATTTTAGTTAT
55167 GTTATATTTTAGTTAT
1 -TTATATTTTAGTTAT
55183 TTAT
1 TTAT
55187 GTTAACGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 10 0.36
15 14 0.50
16 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.62
Consensus pattern (15 bp):
TTATATTTTAGTTAT
Found at i:60977 original size:22 final size:22
Alignment explanation
Indices: 60935--60977 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
60925 TAGGTTTTTG
*
60935 TTTAAAATATATATTTGAATTC
1 TTTAAAATATATATATGAATTC
*
60957 TTTAAACATGTATATAT-AATT
1 TTTAAA-ATATATATATGAATT
60978 TAAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTAAAATATATATATGAATTC
Found at i:64115 original size:21 final size:21
Alignment explanation
Indices: 64075--64113 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64065 GATTAAAAAA
64075 TTTTAAAAAAAGTTTTAAATT
1 TTTTAAAAAAAGTTTTAAATT
*
64096 TTTTAATAAAA-TTTTAAA
1 TTTTAAAAAAAGTTTTAAA
64114 ATACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (21 bp):
TTTTAAAAAAAGTTTTAAATT
Found at i:64713 original size:12 final size:12
Alignment explanation
Indices: 64689--64722 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
64679 TTCAACAAAA
*
64689 TTAA-AAAAATT
1 TTAATAAAATTT
64700 TTAATAAAATTT
1 TTAATAAAATTT
64712 TTAATAAAATT
1 TTAATAAAATT
64723 CCAAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATAAAATTT
Found at i:64756 original size:14 final size:15
Alignment explanation
Indices: 64725--64782 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
64715 ATAAAATTCC
*
64725 AAAATATATAAATAT
1 AAAATATAAAAATAT
* *
64740 AAATTTTAAAAAT-T
1 AAAATATAAAAATAT
*
64754 AAAATATAAAAATGAA
1 AAAATATAAAAAT-AT
64770 AAAATTATAAAAA
1 AAAA-TATAAAAA
64783 AAGAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 12 0.35
15 10 0.29
16 4 0.12
17 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAATATAAAAATAT
Found at i:65004 original size:22 final size:24
Alignment explanation
Indices: 64978--65043 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
64968 TCAGCAAATT
*
64978 TTTAAAATTTAAATATTTTTTC-C
1 TTTAAAATTTATATATTTTTTCAC
** *
65001 -TTAACTTTTATATATTATTTCAC
1 TTTAAAATTTATATATTTTTTCAC
65024 TTTAAAAATTTATATATTTT
1 TTT-AAAATTTATATATTTT
65044 ATAATTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 17 0.52
23 1 0.03
24 2 0.06
25 13 0.39
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTAAAATTTATATATTTTTTCAC
Found at i:68480 original size:15 final size:15
Alignment explanation
Indices: 68396--68482 Score: 88
Period size: 15 Copynumber: 5.9 Consensus size: 15
68386 TTTTGGTGTG
68396 AGAAAAGTAAA-TGCA
1 AGAAAA-TAAATTGCA
* *
68411 A-AAATTTAATTGCA
1 AGAAAATAAATTGCA
* * *
68425 AGAAAGTAAAGTGAA
1 AGAAAATAAATTGCA
* *
68440 AGAAAGTAAAGTGCA
1 AGAAAATAAATTGCA
68455 AGAAAATAAATTGCA
1 AGAAAATAAATTGCA
68470 AGAAAATAAATTG
1 AGAAAATAAATTG
68483 GATCCCATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
13 3 0.05
14 8 0.13
15 50 0.82
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (15 bp):
AGAAAATAAATTGCA
Found at i:69132 original size:25 final size:23
Alignment explanation
Indices: 69091--69136 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
69081 CCAATTAGGG
69091 AATTATTATTTAGATTTAATTAT
1 AATTATTATTTAGATTTAATTAT
*
69114 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
69137 TAGATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTAT
Found at i:70240 original size:12 final size:12
Alignment explanation
Indices: 70223--70247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70213 GTTGTCAAAA
70223 ATATGCTTTAAG
1 ATATGCTTTAAG
70235 ATATGCTTTAAG
1 ATATGCTTTAAG
70247 A
1 A
70248 GTCTAAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATATGCTTTAAG
Found at i:78105 original size:24 final size:25
Alignment explanation
Indices: 78078--78131 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
78068 CGACAAAAAT
*
78078 TTCTTCCTTTTCTCCTTCT-TTTC-C
1 TTCTTCCTTTT-TCCTCCTCTTTCTC
78102 TTC-TCCTTTTTCCTCCTCTTTCTC
1 TTCTTCCTTTTTCCTCCTCTTTCTC
78126 TTCTTC
1 TTCTTC
78132 TTTCTCTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.23
23 11 0.42
24 7 0.27
25 2 0.08
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (25 bp):
TTCTTCCTTTTTCCTCCTCTTTCTC
Found at i:78134 original size:24 final size:24
Alignment explanation
Indices: 78078--78143 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
78068 CGACAAAAAT
*
78078 TTCTTCCTTTTCTCCTTCTTTTCC
1 TTCTTCTTTTTCTCCTTCTTTTCC
*
78102 TTCTCCTTTTTCCTCC-TC-TTTCTC
1 TTCTTCTTTTT-CTCCTTCTTTTC-C
*
78126 TTCTTCTTTCTCTTCCTT
1 TTCTTCTTTTTC-TCCTT
78144 AGTACCCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
23 5 0.15
24 24 0.71
25 5 0.15
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (24 bp):
TTCTTCTTTTTCTCCTTCTTTTCC
Found at i:81064 original size:22 final size:22
Alignment explanation
Indices: 81032--81076 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
81022 AGCTGTCCTA
*
81032 ACACCACCAAAATGACCTCCAT
1 ACACCAACAAAATGACCTCCAT
81054 ACACCAACAAAATGACCTCCAT
1 ACACCAACAAAATGACCTCCAT
81076 A
1 A
81077 GAGAGCATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.38, G:0.04, T:0.13
Consensus pattern (22 bp):
ACACCAACAAAATGACCTCCAT
Found at i:81606 original size:17 final size:17
Alignment explanation
Indices: 81584--81617 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
81574 TACTACCAAC
81584 AACTCTTTCTCTGTGGT
1 AACTCTTTCTCTGTGGT
81601 AACTCTTTCTCTGTGGT
1 AACTCTTTCTCTGTGGT
81618 TGTATAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (17 bp):
AACTCTTTCTCTGTGGT
Done.