Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013035.1 Kokia drynarioides strain JFW-HI SEQ_128053, 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: 98742
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:440 original size:20 final size:21
Alignment explanation
Indices: 391--443 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
381 TCACAAATTG
391 TTATTTAAATTATACATTATT
1 TTATTTAAATTATACATTATT
*
412 TT-TTGAAATTATA-ATT-TT
1 TTATTTAAATTATACATTATT
430 TTATCTTAAATTAT
1 TTAT-TTAAATTAT
444 TTTTTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 4 0.14
20 18 0.64
21 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTTAAATTATACATTATT
Found at i:2569 original size:3 final size:3
Alignment explanation
Indices: 2563--2587 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2553 AATAAAAAAA
2563 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2588 GAAATTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6171 original size:27 final size:26
Alignment explanation
Indices: 6141--6198 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
6131 TATATAAAAA
* * *
6141 TAAAAAATCTTTTAATATAATTATTAT
1 TAAAAAATATTTAAAAATAATT-TTAT
**
6168 TAAATTATATTTAAAAATAATTTTAT
1 TAAAAAATATTTAAAAATAATTTTAT
6194 TAAAA
1 TAAAA
6199 TTTAATAACA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAAAAATATTTAAAAATAATTTTAT
Found at i:6283 original size:58 final size:58
Alignment explanation
Indices: 6208--6348 Score: 176
Period size: 58 Copynumber: 2.4 Consensus size: 58
6198 ATTTAATAAC
* * * * *
6208 AATAATAATCATTTTAAAAATGTTATTGAATTATATATTA-TTTTATTAAATTTTATTT
1 AATAATAATCATGTT-AAAATATAATTAAATTATATATTATTTTTATTAAATTATATTT
* *
6266 AATAATAATTATGTTAAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTT
1 AATAATAATCATGTTAAAATATAATTAAATTATATATTATTTTTATTAAATTATATTT
* * *
6324 AATAATAATCTTATTAAAATTTAAT
1 AATAATAATCATGTTAAAATATAAT
6349 AACAATAATC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 20 0.28
58 51 0.72
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (58 bp):
AATAATAATCATGTTAAAATATAATTAAATTATATATTATTTTTATTAAATTATATTT
Found at i:20505 original size:20 final size:21
Alignment explanation
Indices: 20466--20505 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20456 TGGTTAATGA
*
20466 TTTTTTTTTGTTGTTTTTTAT
1 TTTTTTTTTGTTGTTATTTAT
20487 TTTTTTTTTGTT-TTATTTA
1 TTTTTTTTTGTTGTTATTTA
20506 AAAGAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (21 bp):
TTTTTTTTTGTTGTTATTTAT
Found at i:25013 original size:22 final size:21
Alignment explanation
Indices: 24985--25029 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
24975 AACTATTTAA
*
24985 ATCTTTTAAACTGCACATGTAC
1 ATCTTTTAAACTACACAT-TAC
*
25007 ATCTTTTAGACTACACATTAC
1 ATCTTTTAAACTACACATTAC
25028 AT
1 AT
25030 ATGTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (21 bp):
ATCTTTTAAACTACACATTAC
Found at i:26221 original size:5 final size:5
Alignment explanation
Indices: 26213--26241 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
26203 ATGAATTGAA
26213 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
26242 ATGTATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:26724 original size:22 final size:22
Alignment explanation
Indices: 26699--26742 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
26689 TTTATTTTTT
* **
26699 TTAAAATTATTTTTTATATATA
1 TTAAAATCATTTTAAATATATA
*
26721 TTAACATCATTTTAAATATATA
1 TTAAAATCATTTTAAATATATA
26743 AATATAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAAATCATTTTAAATATATA
Found at i:26929 original size:2 final size:2
Alignment explanation
Indices: 26922--26952 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26912 TTAAAGTATG
26922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26953 TCTTAGAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28120 original size:41 final size:40
Alignment explanation
Indices: 28075--28166 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
28065 GTGGTATTTT
**
28075 TAACGGCGTTTGGACAAAAAACGTTGCAAAAAGTAAAGCAA
1 TAACGGCGTTTGGAC-AAAAACGCCGCAAAAAGTAAAGCAA
* *** * *
28116 TAACGACGTTTTTTCATAAACGCCGCAAAAAGTAAATCAA
1 TAACGGCGTTTGGACAAAAACGCCGCAAAAAGTAAAGCAA
28156 TAACGGCGTTT
1 TAACGGCGTTT
28167 ACGAGAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 31 0.74
41 11 0.26
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (40 bp):
TAACGGCGTTTGGACAAAAACGCCGCAAAAAGTAAAGCAA
Found at i:28358 original size:26 final size:26
Alignment explanation
Indices: 28329--28382 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
28319 TAACCATTAT
* *
28329 TTTAAAACGTATGTAAACTTAAAAAA
1 TTTAAAACGTATATAAACTAAAAAAA
*
28355 TTTAAAACTTATATAAACTAAAAAAA
1 TTTAAAACGTATATAAACTAAAAAAA
28381 TT
1 TT
28383 AAATTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (26 bp):
TTTAAAACGTATATAAACTAAAAAAA
Found at i:28598 original size:13 final size:13
Alignment explanation
Indices: 28571--28601 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
28561 ACTGTAATCA
28571 TTTTCTTTTCTTT
1 TTTTCTTTTCTTT
28584 TTTTCCTTTTCTTT
1 TTTT-CTTTTCTTT
28598 TTTT
1 TTTT
28602 TTACTATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTCTTT
Found at i:30067 original size:23 final size:22
Alignment explanation
Indices: 29932--30104 Score: 138
Period size: 23 Copynumber: 7.5 Consensus size: 22
29922 CGAAGTACTT
29932 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAAGCACACAAGTGC----GA
29958 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
29980 ATCCAGTAAGCACACACAGTGC-A
1 A-ACAGTAAGCACACA-AGTGCGA
* * *
30003 ATCAGTAGGCACACATAGCGC-A
1 AACAGTAAGCACACA-AGTGCGA
*
30025 AATCAAG-AGGCACACAAAGTGCGA
1 AA-C-AGTAAGCACAC-AAGTGCGA
*
30049 AACAGTAAGCACACGAAGTACGA
1 AACAGTAAGCACAC-AAGTGCGA
*
30072 AACAGTAAGCACATAAAGTGCGA
1 AACAGTAAGCACA-CAAGTGCGA
30095 AACAGTAAGC
1 AACAGTAAGC
30105 GCGCTAGCAT
Statistics
Matches: 127, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
22 22 0.17
23 79 0.62
24 6 0.05
26 15 0.12
27 5 0.04
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCGA
Found at i:30578 original size:26 final size:26
Alignment explanation
Indices: 30547--30596 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
30537 ATAAATTTCA
30547 GACCCTTAACTCTTTATATATAATAC
1 GACCCTTAACTCTTTATATATAATAC
30573 GACCCTTAACTCTTTATATATAAT
1 GACCCTTAACTCTTTATATATAAT
30597 TTTTAGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (26 bp):
GACCCTTAACTCTTTATATATAATAC
Found at i:33839 original size:43 final size:43
Alignment explanation
Indices: 33786--33925 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
33776 TTTGTTAATA
* * *
33786 TTAGTAGCGTTTGTAGGAAAAATCCCGCTAAAGACCATGTTCT
1 TTAGCAGCGTTTGTAGGAAAAAGCCCGCTAAAGACCATGATCT
* * **
33829 TTAGCAGCGTTTGCAGG-AAAAGCGCAATAAAGACCATGATCT
1 TTAGCAGCGTTTGTAGGAAAAAGCCCGCTAAAGACCATGATCT
*
33871 TTAGC-GACGTTTGT-GGAAAAAGCGCCGCTAAAGACCATGGTCT
1 TTAGCAG-CGTTTGTAGGAAAAAGC-CCGCTAAAGACCATGATCT
* *
33914 ATAGCGGCGTTT
1 TTAGCAGCGTTT
33926 TTCCTCATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 3 0.04
42 37 0.46
43 39 0.49
44 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (43 bp):
TTAGCAGCGTTTGTAGGAAAAAGCCCGCTAAAGACCATGATCT
Found at i:33872 original size:42 final size:42
Alignment explanation
Indices: 33792--33925 Score: 121
Period size: 42 Copynumber: 3.1 Consensus size: 42
33782 AATATTAGTA
* ** *
33792 GCGTTTGTAGGAAAAATC-CCGCTAAAGACCATGTTCTTTAGC
1 GCGTTTG-AGGAAAAAGCGCCAATAAAGACCATGATCTTTAGC
33834 AGCGTTTGCAGG-AAAAGCG-CAATAAAGACCATGATCTTTAGC
1 -GCGTTTG-AGGAAAAAGCGCCAATAAAGACCATGATCTTTAGC
* ** * *
33876 GACGTTTGTGGAAAAAGCGCCGCTAAAGACCATGGTCTATAGC
1 G-CGTTTGAGGAAAAAGCGCCAATAAAGACCATGATCTTTAGC
33919 GGCGTTT
1 -GCGTTT
33926 TTCCTCATAA
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
41 3 0.04
42 38 0.50
43 34 0.45
44 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (42 bp):
GCGTTTGAGGAAAAAGCGCCAATAAAGACCATGATCTTTAGC
Found at i:35442 original size:82 final size:82
Alignment explanation
Indices: 35305--35469 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
35295 TCCCTTTGCC
*
35305 CTCCCATTGGCCAACCAAGCTCTCACGTTAGTTCAAAGTGCTTGAACTTGATTAAATATGTTAAT
1 CTCCCATTGGCCAACCAAGCTCTCACGTTAGTTCAAAGTACTTGAACTTGATTAAATATGTTAAT
35370 TTGACTGCTCCCATTTA
66 TTGACTGCTCCCATTTA
35387 CTCCCATTGGCCAACCAAGCTCTCACGTTAGTTCAAAGTACTTGAACTTGATTAAATATGTTAAT
1 CTCCCATTGGCCAACCAAGCTCTCACGTTAGTTCAAAGTACTTGAACTTGATTAAATATGTTAAT
35452 TTGACTGCTCCCATTTA
66 TTGACTGCTCCCATTTA
35469 C
1 C
35470 ATCAGTACTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (82 bp):
CTCCCATTGGCCAACCAAGCTCTCACGTTAGTTCAAAGTACTTGAACTTGATTAAATATGTTAAT
TTGACTGCTCCCATTTA
Found at i:37793 original size:78 final size:76
Alignment explanation
Indices: 37656--37807 Score: 180
Period size: 78 Copynumber: 2.0 Consensus size: 76
37646 TTCAGCTCAG
* * *
37656 TGCATCCTCCTCCATAATGCCATCACCAACCTCATTCCATGCATCTCCTACACCAGCAGTTCCAT
1 TGCATCCTCCTCCATAATGCCATCACCAACCTCATTACATGCATCTCC-ACACAAGCAGTTCCAC
37721 CAAAACAGAAAA
65 CAAAACAGAAAA
* ** * *
37733 TGCATCCTCCTCCAATAGTGCCATCGTCGACCTCATTACATGCATCTCC-CGAGAAGGCAGTTCC
1 TGCATCCTCCTCC-ATAATGCCATCACCAACCTCATTACATGCATCTCCAC-ACAA-GCAGTTCC
*
37797 ACCAATACAGA
63 ACCAAAACAGA
37808 GCTCAGTGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.02
77 15 0.24
78 47 0.75
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.22
Consensus pattern (76 bp):
TGCATCCTCCTCCATAATGCCATCACCAACCTCATTACATGCATCTCCACACAAGCAGTTCCACC
AAAACAGAAAA
Found at i:38754 original size:29 final size:29
Alignment explanation
Indices: 38722--38784 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
38712 TGAAAAGTAA
38722 AAAAATTAAATTCTTAAAAATAAAAATA-T
1 AAAAATTAAATT-TTAAAAATAAAAATAGT
* *
38751 AAAAATTAAATTTTAAATATATAAATAGT
1 AAAAATTAAATTTTAAAAATAAAAATAGT
38780 AAAAA
1 AAAAA
38785 ATTTAGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 13 0.42
29 18 0.58
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAATTAAATTTTAAAAATAAAAATAGT
Found at i:39493 original size:60 final size:60
Alignment explanation
Indices: 39400--39518 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
39390 TGCCACATAA
*
39400 GATTACCGTTAGAGAGATAACGGAACTTAACGGCACGGTGATCACTTCTTAACAAAATAG
1 GATTACCGTTAGAGAGATAACGGAACTTAACGGCACGGTGATCACTTCATAACAAAATAG
*
39460 GATTACCGTTAGGGAGATAACGGAACTTAACGGCACGGTGATCACTTCATAACAAAATA
1 GATTACCGTTAGAGAGATAACGGAACTTAACGGCACGGTGATCACTTCATAACAAAATA
39519 CTAACACAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (60 bp):
GATTACCGTTAGAGAGATAACGGAACTTAACGGCACGGTGATCACTTCATAACAAAATAG
Found at i:39590 original size:31 final size:29
Alignment explanation
Indices: 39521--39591 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
39511 ACAAAATACT
* ***
39521 AACACAAGTGACTAAAATGTAACATTTCA
1 AACAAAAGTGACTAAAATGTAACAAGGCA
*
39550 AACATAAGTGACTAAAATGTAACCTAAGGCA
1 AACAAAAGTGACTAAAATGTAA-C-AAGGCA
39581 AACAAAAGTGA
1 AACAAAAGTGA
39592 TTATTTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.60
30 1 0.03
31 13 0.37
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (29 bp):
AACAAAAGTGACTAAAATGTAACAAGGCA
Found at i:44651 original size:21 final size:22
Alignment explanation
Indices: 44597--44651 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
44587 AAAAAAATCT
* *
44597 ATTTT-TTTTTATTTTGCTACA
1 ATTTTATTATTATGTTGCTACA
*
44618 ATTTCATTATTATGTTGCTAC-
1 ATTTTATTATTATGTTGCTACA
*
44639 ATTTTATTGTTAT
1 ATTTTATTATTAT
44652 TGTTTGGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (22 bp):
ATTTTATTATTATGTTGCTACA
Found at i:44655 original size:22 final size:23
Alignment explanation
Indices: 44597--44655 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
44587 AAAAAAATCT
*
44597 ATTTT-TTTTTATT-TTGCTACA
1 ATTTTATTATTATTGTTGCTACA
*
44618 ATTTCATTATTA-TGTTGCTAC-
1 ATTTTATTATTATTGTTGCTACA
*
44639 ATTTTATTGTTATTGTT
1 ATTTTATTATTATTGTT
44656 TGGATATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.63
Consensus pattern (23 bp):
ATTTTATTATTATTGTTGCTACA
Found at i:46549 original size:6 final size:6
Alignment explanation
Indices: 46503--46539 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
46493 TCTTCTTTTG
*
46503 TTCC-C TTCCTC TTCCTC TTCCTC TTCCTC TTCATC TT
1 TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TTCCTC TT
46540 TCTTCTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (6 bp):
TTCCTC
Found at i:48787 original size:33 final size:33
Alignment explanation
Indices: 48750--48816 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
48740 CTTTCTTTAT
48750 TCATATTATATACATATTACTCCACAGGGAGAA
1 TCATATTATATACATATTACTCCACAGGGAGAA
48783 TCATATTATATACATATTACTCCACAGGGAGAA
1 TCATATTATATACATATTACTCCACAGGGAGAA
48816 T
1 T
48817 TGAAGGTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (33 bp):
TCATATTATATACATATTACTCCACAGGGAGAA
Found at i:54394 original size:20 final size:20
Alignment explanation
Indices: 54353--54394 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
54343 TTAGACCGTG
* *
54353 ATTTTTTAGTTTAAAGTGTA
1 ATTTTTTAGCTTAAAGTATA
54373 ATTTTTTAGACTTAAA-TATA
1 ATTTTTTAG-CTTAAAGTATA
54393 AT
1 AT
54395 ATGTATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTTTTAGCTTAAAGTATA
Found at i:57115 original size:4 final size:4
Alignment explanation
Indices: 57108--57133 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
57098 TACATGTATG
57108 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
57134 GATAATTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:59130 original size:2 final size:2
Alignment explanation
Indices: 59123--59148 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59113 GAGATTGAAG
59123 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59149 GAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61529 original size:16 final size:17
Alignment explanation
Indices: 61510--61541 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
61500 ATTTAATCTA
61510 AATATTTATTA-AAAAT
1 AATATTTATTATAAAAT
61526 AATATTTATTATAAAA
1 AATATTTATTATAAAA
61542 ATTAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTTATTATAAAAT
Found at i:80411 original size:6 final size:6
Alignment explanation
Indices: 80400--80429 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
80390 GCAATGAGCG
*
80400 CTGCAA CTGCAA CTGCAA CTGCAA CAGCAA
1 CTGCAA CTGCAA CTGCAA CTGCAA CTGCAA
80430 TAAGCCCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.17, T:0.13
Consensus pattern (6 bp):
CTGCAA
Done.