Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013774.1 Kokia drynarioides strain JFW-HI SEQ_128802, 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: 72413
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:3690 original size:21 final size:20
Alignment explanation
Indices: 3636--3690 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
3626 TTTATAGCTT
3636 TTTTTATAAATTATGTTTATAA
1 TTTTTA-AAATT-TGTTTATAA
** *
3658 TTTTTATGATTTTTTTAATAA
1 TTTTTAAAATTTGTTT-ATAA
3679 TTTTTAAAATTT
1 TTTTTAAAATTT
3691 AAAAGGACTC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.15
21 17 0.63
22 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTAAAATTTGTTTATAA
Found at i:3905 original size:17 final size:17
Alignment explanation
Indices: 3883--3959 Score: 84
Period size: 17 Copynumber: 4.5 Consensus size: 17
3873 CCAACAGGAT
3883 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
3900 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
3917 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
3933 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
*
3951 TTAAGTTTA
1 TTAAATTTA
3960 AATTTATTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 4 0.08
17 41 0.84
18 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:3908 original size:23 final size:23
Alignment explanation
Indices: 3881--3968 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 23
3871 GCCCAACAGG
3881 ATTTAAATTTATTTTAAAATTAA
1 ATTTAAATTTATTTTAAAATTAA
* *
3904 ATTT-ATTTTAAGTTTAAATTTACTTAAA
1 ATTTAAATTT-ATTTTAAA---A-TT-AA
* *
3932 ATTTAAATTTATTATAAATTTAA
1 ATTTAAATTTATTTTAAAATTAA
*
3955 GTTTAAATTTATTT
1 ATTTAAATTTATTT
3969 AAATCAAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
22 4 0.08
23 25 0.50
24 2 0.04
26 1 0.02
27 2 0.04
28 12 0.24
29 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATTTATTTTAAAATTAA
Found at i:3919 original size:6 final size:6
Alignment explanation
Indices: 3881--3965 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
3871 GCCCAACAGG
* * * *
3881 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
3926 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA GTTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA ATTTA
3966 TTTAAATCAA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
4 3 0.05
5 12 0.20
6 42 0.70
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:3925 original size:34 final size:34
Alignment explanation
Indices: 3881--3959 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
3871 GCCCAACAGG
* *
3881 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
3915 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
*
3949 ATTTAAGTTTA
1 ATTTAAATTTA
3960 AATTTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 6 0.15
34 33 0.85
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:3978 original size:22 final size:23
Alignment explanation
Indices: 3933--3978 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3923 TTACTTAAAA
**
3933 TTTAAATTTATTATAAATTTAAG
1 TTTAAATTTATTATAAATCAAAG
3956 TTTAAATTTATT-TAAATCAAAG
1 TTTAAATTTATTATAAATCAAAG
3978 T
1 T
3979 CCAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTAAATTTATTATAAATCAAAG
Found at i:5730 original size:58 final size:59
Alignment explanation
Indices: 5617--6030 Score: 333
Period size: 58 Copynumber: 7.1 Consensus size: 59
5607 GCCCTGAAGG
* * * ** ** *
5617 CCCCTAAACTTCCAAAAATTTCATTATTGACCCCAAAATTTCCAAAATTTCCATTTTTGA
1 CCCCAAAACTTCCAAAAATTACATT-TTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
* * *
5677 CCTCAAAACTTCCAAAAATTATA-TTTTACCCTCGAACCTCCAAAAATTCCATTTTTGA
1 CCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
* *
5735 CCCCAAAATTTCCAAAAATTACATTTTTACCCCC-AACTTCCAAAAATTCCATTTTT-A
1 CCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
5792 CCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCCAAAAATTCCA-TTTTGA
1 CCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
*** * * * ** *
5850 CCTTGAAACTTTCAAAAATTAC-TATTTCACCCCCAAATGTCCAAAAATTTCATTTTTGA
1 CCCCAAAACTTCCAAAAATTACAT-TTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
* ** ** * * ** *
5909 -TCCTGATTTTCCTAAAAATTGC-TATTTTACCCCCGGATGTCCAAAAATTCCGTTTTTGA
1 CCCCAAAACTTCC-AAAAATTACAT-TTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
* * * * * *** * *
5968 -TCCTAATCTTTTCAAAAGTTATCA-TTTTACCCCCGAGTGTCTAAAAATTCCATTTTTAA
1 CCCCAAAAC-TTCCAAAAATTA-CATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
6027 CCCC
1 CCCC
6031 GAACTTTTTC
Statistics
Matches: 292, Mismatches: 52, Indels: 20
0.80 0.14 0.05
Matches are distributed among these distances:
57 39 0.13
58 130 0.45
59 98 0.34
60 25 0.09
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (59 bp):
CCCCAAAACTTCCAAAAATTACATTTTTACCCCCGAACCTCCAAAAATTCCATTTTTGA
Found at i:5732 original size:29 final size:29
Alignment explanation
Indices: 5617--5906 Score: 259
Period size: 29 Copynumber: 10.0 Consensus size: 29
5607 GCCCTGAAGG
* * *
5617 CCCCTAAACTTCCAAAAATTTCATTATTGA
1 CCCCAAAACTTCCAAAAATTCCATT-TTTA
* *
5647 CCCCAAAATTTCCAAAATTTCCATTTTTGA
1 CCCCAAAACTTCCAAAAATTCCATTTTT-A
*
5677 CCTCAAAACTTCCAAAAATT--ATATTTTA
1 CCCCAAAACTTCCAAAAATTCCAT-TTTTA
* *
5705 CCCTC-GAACCTCCAAAAATTCCATTTTTGA
1 CCC-CAAAACTTCCAAAAATTCCATTTTT-A
* *
5735 CCCCAAAATTTCCAAAAATTACATTTTTA
1 CCCCAAAACTTCCAAAAATTCCATTTTTA
*
5764 CCCC-CAACTTCCAAAAATTCCATTTTTA
1 CCCCAAAACTTCCAAAAATTCCATTTTTA
*
5792 CCCCAAAACTTCCAAAAATTACATTTTTA
1 CCCCAAAACTTCCAAAAATTCCATTTTTA
** * *
5821 CCCCCGAACCTCCAAAAATTCCATTTTGA
1 CCCCAAAACTTCCAAAAATTCCATTTTTA
*** * * *
5850 CCTTGAAACTTTCAAAAATTAC-TATTTCA
1 CCCCAAAACTTCCAAAAATTCCAT-TTTTA
* *
5879 CCCCCAAA-TGTCCAAAAATTTCATTTTT
1 CCCCAAAACT-TCCAAAAATTCCATTTTT
5907 GATCCTGATT
Statistics
Matches: 210, Mismatches: 39, Indels: 23
0.77 0.14 0.08
Matches are distributed among these distances:
28 45 0.21
29 100 0.48
30 65 0.31
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCCAAAACTTCCAAAAATTCCATTTTTA
Found at i:6423 original size:96 final size:96
Alignment explanation
Indices: 6313--6497 Score: 252
Period size: 96 Copynumber: 1.9 Consensus size: 96
6303 AAAACCTTAA
*
6313 AATCGAGACAATA-TTCTTTTAT-TTCGAGTT-TCGAAAATTTACGCCTTAACTTACTAGGTGCA
1 AATCGAGACAATATTTC-CTTATCTTCGA-TTCT-GAAAATTTACGCCTTAACTTACTAGGTGCA
**
6375 ATTTTTCTTCAAATCGAA-ATAATCGAATACCCTT
63 ACCTTTCTTCAAATC-AAGATAATCGAATACCCTT
* * *
6409 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAAATTTGCGGCTTAACTTACTAGGTGCAACC
1 AATCGAGACAATATTTCCTTATCTTCGATTCTGAAAATTTACGCCTTAACTTACTAGGTGCAACC
6474 TTTCTTCAAATCAAGATAATCGAA
66 TTTCTTCAAATCAAGATAATCGAA
6498 CATCCTTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
95 2 0.03
96 68 0.86
97 9 0.11
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (96 bp):
AATCGAGACAATATTTCCTTATCTTCGATTCTGAAAATTTACGCCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAGATAATCGAATACCCTT
Found at i:10170 original size:2 final size:2
Alignment explanation
Indices: 10163--10195 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10153 AATCAGCCTG
10163 TA 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 TA T
10196 CACATTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14953 original size:40 final size:40
Alignment explanation
Indices: 14863--14974 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
14853 TAGTGATCTA
* * **
14863 GCAGTGTTTACAGTGTCACTGCCAGTTTAGTTGTAATGTC
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAGTAACATC
* *
14903 GCAG-GTTTTACAGTGTCACTACCAATTCAGTAGTAACATC
1 GCAGTG-TTTACAGTGTCACTGCCAGTTCAGTAGTAACATC
*
14943 GCTGTGTTTACAGTGTCACTGCCAGTTCAGTA
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTA
14975 AGTACTCCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 1 0.02
40 59 0.97
41 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAGTAACATC
Found at i:15199 original size:21 final size:21
Alignment explanation
Indices: 15175--15218 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
15165 CGATAATACA
15175 CTACGCACGGCCAGACACACG
1 CTACGCACGGCCAGACACACG
15196 CTACGCACGGCCAGACACACG
1 CTACGCACGGCCAGACACACG
15217 CT
1 CT
15219 CGTGTGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.43, G:0.23, T:0.07
Consensus pattern (21 bp):
CTACGCACGGCCAGACACACG
Found at i:19051 original size:2 final size:2
Alignment explanation
Indices: 19044--19089 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
19034 GCCTCGTCTT
19044 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
19086 CA CA
1 CA CA
19090 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:21271 original size:20 final size:20
Alignment explanation
Indices: 21233--21283 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
21223 AAAATAGGTT
21233 AATAATATTTTATAAAAATAGA
1 AATAAT-TTTTATAAAAATA-A
*
21255 AATAATTTTTA-ATAAATAA
1 AATAATTTTTATAAAAATAA
21274 AATTAATTTT
1 AA-TAATTTT
21284 GTAAAATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.48
21 5 0.19
22 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAATTTTTATAAAAATAA
Found at i:21290 original size:19 final size:19
Alignment explanation
Indices: 21239--21289 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 19
21229 GGTTAATAAT
21239 ATTTTATAAAAATAGAAATA
1 ATTTT-TAAAAATAGAAATA
21259 ATTTTTAATAAATA-AAATTA
1 ATTTTTAA-AAATAGAAA-TA
21279 ATTTTGTAAAA
1 ATTTT-TAAAA
21290 TCTAACAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (19 bp):
ATTTTTAAAAATAGAAATA
Found at i:21649 original size:3 final size:3
Alignment explanation
Indices: 21643--21669 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21633 ACGACGAGAG
21643 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
21670 CGTAGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29136 original size:3 final size:3
Alignment explanation
Indices: 29128--29159 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29118 ATATGAGTAT
29128 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
29160 TGACAACGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:33344 original size:22 final size:20
Alignment explanation
Indices: 33319--33369 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
33309 AATTTAGTTA
33319 ATTTTAATTTTTATGTTTTTAT
1 ATTTTAA-TTTTA-GTTTTTAT
*
33341 ATTTATCGATTTTAGTTTTTAT
1 ATTT-T-AATTTTAGTTTTTAT
33363 ATTTTAA
1 ATTTTAA
33370 AATTATTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 16 0.64
23 6 0.24
24 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
ATTTTAATTTTAGTTTTTAT
Found at i:33402 original size:12 final size:12
Alignment explanation
Indices: 33385--33409 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33375 TTTGGTTAAC
33385 CTATATCATTAT
1 CTATATCATTAT
33397 CTATATCATTAT
1 CTATATCATTAT
33409 C
1 C
33410 CATGTATAAT
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:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (12 bp):
CTATATCATTAT
Found at i:34871 original size:62 final size:59
Alignment explanation
Indices: 34802--34917 Score: 151
Period size: 62 Copynumber: 1.9 Consensus size: 59
34792 AGTGATTATT
* * *
34802 TAATATTAAAGTAAATATAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAATATC
1 TAATATTAAAGTAAATATAATATTTA-TCT-T-GATAAATATTATATTAATTTAATAATATC
* * *
34864 TAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TAATATTAAAGTAAATATAATATTTATCTTGATAAATATTATATTAATTTAATA
34918 TTAAAGCGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 22 0.46
60 1 0.02
61 2 0.04
62 23 0.48
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (59 bp):
TAATATTAAAGTAAATATAATATTTATCTTGATAAATATTATATTAATTTAATAATATC
Found at i:35984 original size:43 final size:43
Alignment explanation
Indices: 35912--36066 Score: 188
Period size: 43 Copynumber: 3.7 Consensus size: 43
35902 AGGAAAAATG
*
35912 CCGCTAAAGAACATGG--TTTAGCAGCGCTTTCCTTATAAACC
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTTATAAACC
* * * * * *
35953 CCACTAAAGAACATGATCTTTAGTGGCGCTTTTCTCACAAACC
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTTATAAACC
* * *
35996 TCGCTAAAGAACATGGTCTTTAGCGGTGCTTTCCTTATAAACG
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTTATAAACC
* *
36039 CGGCTAAAGAGCATGGTCTTTAGCGGCG
1 CCGCTAAAGAACATGGTCTTTAGCGGCG
36067 TTTTTCTCAC
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
41 14 0.15
43 78 0.85
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (43 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCTTATAAACC
Found at i:36032 original size:86 final size:84
Alignment explanation
Indices: 35913--36079 Score: 235
Period size: 86 Copynumber: 2.0 Consensus size: 84
35903 GGAAAAATGC
*
35913 CGCTAAAGAACATGGTTTAGCAGCGCTTTCCTTATAAACCCCACTAAAGAACATGATCTTTAGTG
1 CGCTAAAGAACATGGTTTAGCAGCGCTTTCCTTATAAACCCCACTAAAGAACATGATCTTTAGCG
35978 GCGCTTTTCTCACAAACCT
66 GCGCTTTTCTCACAAACCT
* * * ** * *
35997 CGCTAAAGAACATGGTCTTTAGCGGTGCTTTCCTTATAAACGCGGCTAAAGAGCATGGTCTTTAG
1 CGCTAAAGAACATGG--TTTAGCAGCGCTTTCCTTATAAACCCCACTAAAGAACATGATCTTTAG
*
36062 CGGCGTTTTTCTCACAAA
64 CGGCGCTTTTCTCACAAA
36080 TACCGCTAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 15 0.21
86 57 0.79
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (84 bp):
CGCTAAAGAACATGGTTTAGCAGCGCTTTCCTTATAAACCCCACTAAAGAACATGATCTTTAGCG
GCGCTTTTCTCACAAACCT
Found at i:36088 original size:43 final size:42
Alignment explanation
Indices: 35912--36089 Score: 155
Period size: 43 Copynumber: 4.2 Consensus size: 42
35902 AGGAAAAATG
* * * * *
35912 CCGCTAAAGAACATGG--TTTAGCAGCGCTTTCCTTATAAACC
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAA-A
* * * *
35953 CCACTAAAGAACATGATCTTTAGTGGCGCTTTTCTCACAAAC
1 CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAAA
* * * *
35995 CTCGCTAAAGAACATGGTCTTTAGCGGTGCTTTCCTTA-TAAA
1 C-CGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAAA
* *
36037 CGCGGCTAAAGAGCATGGTCTTTAGCGGCGTTTTTCTCACAAATA
1 C-C-GCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAA-A
36082 CCGCTAAA
1 CCGCTAAA
36090 ATTAATAGAT
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
41 14 0.13
42 6 0.06
43 84 0.77
44 3 0.03
45 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
CCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACAAAA
Found at i:36111 original size:18 final size:18
Alignment explanation
Indices: 36088--36125 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
36078 AATACCGCTA
36088 AAATTAATAGATTTTAAC
1 AAATTAATAGATTTTAAC
36106 AAATTAATAGATTTTAAC
1 AAATTAATAGATTTTAAC
36124 AA
1 AA
36126 CTCATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATTAATAGATTTTAAC
Found at i:36461 original size:21 final size:21
Alignment explanation
Indices: 36404--36470 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
36394 CATATTTTTT
**
36404 TGTTGCCTCTGCTTCCCTCAC
1 TGTTGCCTCCACTTCCCTCAC
* * *
36425 TGCTGCCTTCGCTTCCCTCAC
1 TGTTGCCTCCACTTCCCTCAC
* *
36446 TGTTGCCTCCATTTCCCTCGC
1 TGTTGCCTCCACTTCCCTCAC
36467 TGTT
1 TGTT
36471 ACATCCGCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.04, C:0.42, G:0.15, T:0.39
Consensus pattern (21 bp):
TGTTGCCTCCACTTCCCTCAC
Found at i:41665 original size:41 final size:41
Alignment explanation
Indices: 41620--41772 Score: 139
Period size: 41 Copynumber: 3.7 Consensus size: 41
41610 ACTCTGACCT
41620 TTAGCGGCGCTTTCTCATAAACGCCGCTAAAAGTCAGAGCA
1 TTAGCGGCGCTTTCTCATAAACGCCGCTAAAAGTCAGAGCA
* *** ** * * *
41661 TTAGCGGTGCTTATGGGA-AAGTGCTGTTAAAGGTCAGAGCA
1 TTAGCGGCGCTT-TCTCATAAACGCCGCTAAAAGTCAGAGCA
*
41702 TTACCGGCGCTTTCTCATAAACGCCGCT-AAAGCTCAGAGCA
1 TTAGCGGCGCTTTCTCATAAACGCCGCTAAAAG-TCAGAGCA
* * * * *
41743 TTAGTGGCGTTTTCCCATAAGCACCGCTAA
1 TTAGCGGCGCTTTCTCATAAACGCCGCTAA
41773 TGCTCTACCT
Statistics
Matches: 83, Mismatches: 25, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
40 5 0.06
41 75 0.90
42 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (41 bp):
TTAGCGGCGCTTTCTCATAAACGCCGCTAAAAGTCAGAGCA
Found at i:43441 original size:31 final size:31
Alignment explanation
Indices: 43386--43449 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
43376 CAACGATTTG
* *
43386 ATTTTAATTAAATAAATATTAAAAATTTGTAAA
1 ATTTTAA-TAAATAAATATGAAAAAGTT-TAAA
*
43419 ATTTTAA-AAATATATATGAAAAAGTTTAAA
1 ATTTTAATAAATAAATATGAAAAAGTTTAAA
43449 A
1 A
43450 ATCGGTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 5 0.18
31 16 0.57
33 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (31 bp):
ATTTTAATAAATAAATATGAAAAAGTTTAAA
Found at i:44506 original size:18 final size:18
Alignment explanation
Indices: 44483--44537 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
44473 AGCAATTATT
44483 AATATTTTAATATTTAAA
1 AATATTTTAATATTTAAA
* *
44501 AATATTTTTATATTT-TA
1 AATATTTTAATATTTAAA
*
44518 ATTATTTTTAAT-TTTAAA
1 AATA-TTTTAATATTTAAA
44536 AA
1 AA
44538 ACTAATTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTTTAATATTTAAA
Found at i:44531 original size:16 final size:17
Alignment explanation
Indices: 44481--44534 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
44471 CTAGCAATTA
*
44481 TTAA-TATTTTAATATT
1 TTAATTATTTTTATATT
* *
44497 TAAAAATATTTTTATATT
1 T-TAATTATTTTTATATT
44515 TTAATTATTTTTA-ATT
1 TTAATTATTTTTATATT
44531 TTAA
1 TTAA
44535 AAAACTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.25
17 12 0.38
18 12 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATTATTTTTATATT
Found at i:48257 original size:25 final size:27
Alignment explanation
Indices: 48201--48261 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
48191 ACATATTTTC
48201 TCAAAATTTTACCAAAGGTAAAATCGA
1 TCAAAATTTTACCAAAGGTAAAATCGA
* * *
48228 T-AAAATTTTA-CGAAGGTAAATTTG-
1 TCAAAATTTTACCAAAGGTAAAATCGA
48252 TCAAAATTTT
1 TCAAAATTTT
48262 GTTGGGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 19 0.63
26 9 0.30
27 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (27 bp):
TCAAAATTTTACCAAAGGTAAAATCGA
Found at i:49949 original size:16 final size:18
Alignment explanation
Indices: 49920--49956 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
49910 TTATAATCCA
*
49920 TTTCATCTCAATTCT-AT
1 TTTCATATCAATTCTCAT
49937 TTTCATATC-ATTCTCAT
1 TTTCATATCAATTCTCAT
49954 TTT
1 TTT
49957 AGTTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTCATATCAATTCTCAT
Found at i:50987 original size:21 final size:21
Alignment explanation
Indices: 50958--51001 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
50948 TATTTTATAA
50958 TATTAATTAATAA-AATATTAT
1 TATTAATT-ATAATAATATTAT
* *
50979 TATTTATTATAATACTATTAT
1 TATTAATTATAATAATATTAT
51000 TA
1 TA
51002 ATGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TATTAATTATAATAATATTAT
Found at i:53023 original size:59 final size:57
Alignment explanation
Indices: 52932--53232 Score: 302
Period size: 59 Copynumber: 5.1 Consensus size: 57
52922 AAATGGTATT
* * * *
52932 TTTTTGGAGAATTCGAGGTCAAAAATGAAATTTTGGAAAGTTGAAGGGTAAAAATGTAA
1 TTTTTGGAAAATT-TAGGTTAAAAATGGAATTTTGGAAAGTTGAA-GGTAAAAATGTAA
* * *
52991 TTTTTGGAAAATTTGAGGTTAAAAATGGAATTTTGGAAAATTCAAGGTCAAAAATGTAG
1 TTTTTGGAAAATTT-AGGTTAAAAATGGAATTTTGGAAAGTTGAAGGT-AAAAATGTAA
*
53050 TTTTTGGAAAATTTAGGGTTAAAAATGGAATTTTGGAAAATTTG-AGGTTAAAAATG-AA
1 TTTTTGGAAAATTTA-GGTTAAAAATGGAATTTTGG-AAAGTTGAAGG-TAAAAATGTAA
* * * * * * *
53108 ATTTTGGAAAATTTAGGGTAAAAATGTAATTTTTGGAAATTTTAAGGTTAAAATGGAA
1 TTTTTGGAAAATTTAGGTTAAAAATGGAA-TTTTGGAAAGTTGAAGGTAAAAATGTAA
* ** * *
53166 -TTTTGGAAAATTTAGGGTAAAAAAATGGAATTTTAAAAAGTTCGGAGGTAAAAATGTTA
1 TTTTTGGAAAATTTA-GGT-TAAAAATGGAATTTTGGAAAGTT-GAAGGTAAAAATGTAA
53225 TTTTTGGA
1 TTTTTGGA
53233 CAGTTGGGGA
Statistics
Matches: 204, Mismatches: 26, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
57 39 0.19
58 41 0.20
59 111 0.54
60 13 0.06
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.35
Consensus pattern (57 bp):
TTTTTGGAAAATTTAGGTTAAAAATGGAATTTTGGAAAGTTGAAGGTAAAAATGTAA
Found at i:53040 original size:88 final size:87
Alignment explanation
Indices: 52933--53232 Score: 342
Period size: 88 Copynumber: 3.4 Consensus size: 87
52923 AATGGTATTT
* * * * *
52933 TTTTGGAGAATTCGAGGTCAAAAATG-AAATTTTGGAAAGTTGAAGGGTAAAAATGTAATTTTTG
1 TTTTGGAAAATTCAAGGTCAAAAATGTAATTTTTGGAAAATT-AAGGGTAAAAATGGAA-TTTTG
52997 GAAAATTTGAGGTTAAAAATGGAA
64 GAAAATTTGAGGTTAAAAATGGAA
* *
53021 TTTTGGAAAATTCAAGGTCAAAAATGTAGTTTTTGGAAAATTTAGGGTTAAAAATGGAATTTTGG
1 TTTTGGAAAATTCAAGGTCAAAAATGTAATTTTTGGAAAATTAAGGG-TAAAAATGGAATTTTGG
*
53086 AAAATTTGAGGTTAAAAATGAAA
65 AAAATTTGAGGTTAAAAATGGAA
* * * *
53109 TTTTGGAAAATTTAGGGT-AAAAATGTAATTTTTGGAAATTTTAA-GGTTAAAATGGAATTTTGG
1 TTTTGGAAAATTCAAGGTCAAAAATGTAATTTTTGGAAA-ATTAAGGGTAAAAATGGAATTTTGG
*
53172 AAAATTT-AGGGTAAAAAAATGGAA
65 AAAATTTGA-GGT-TAAAAATGGAA
* * *
53196 TTTT-AAAAAGTTCGGAGGT-AAAAATGTTATTTTTGGA
1 TTTTGGAAAA-TTC-AAGGTCAAAAATGTAATTTTTGGA
53233 CAGTTGGGGA
Statistics
Matches: 184, Mismatches: 21, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
85 1 0.01
86 30 0.16
87 36 0.20
88 95 0.52
89 22 0.12
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.35
Consensus pattern (87 bp):
TTTTGGAAAATTCAAGGTCAAAAATGTAATTTTTGGAAAATTAAGGGTAAAAATGGAATTTTGGA
AAATTTGAGGTTAAAAATGGAA
Found at i:53204 original size:29 final size:28
Alignment explanation
Indices: 52952--53199 Score: 271
Period size: 29 Copynumber: 8.5 Consensus size: 28
52942 ATTCGAGGTC
* * *
52952 AAAAATGAAATTTTGGAAAGTTGAAGGGT
1 AAAAATGGAATTTTGGAAAATT-TAGGGT
* *
52981 AAAAATGTAATTTTTGGAAAATTTGAGGTT
1 AAAAATGGAA-TTTTGGAAAATTT-AGGGT
* *
53011 AAAAATGGAATTTTGGAAAATTCAAGGT
1 AAAAATGGAATTTTGGAAAATTTAGGGT
* *
53039 CAAAAATGTAGTTTTTGGAAAATTTAGGGTT
1 -AAAAATGGA-ATTTTGGAAAATTTAGGG-T
*
53070 AAAAATGGAATTTTGGAAAATTTGAGGTT
1 AAAAATGGAATTTTGGAAAATTT-AGGGT
*
53099 AAAAATGAAATTTTGGAAAATTTAGGGT
1 AAAAATGGAATTTTGGAAAATTTAGGGT
* * *
53127 AAAAATGTAATTTTTGGAAATTTTAAGGT
1 AAAAATGGAA-TTTTGGAAAATTTAGGGT
*
53156 TAAAATGGAATTTTGGAAAATTTAGGGT
1 AAAAATGGAATTTTGGAAAATTTAGGGT
53184 AAAAAAATGGAATTTT
1 --AAAAATGGAATTTT
53200 AAAAAGTTCG
Statistics
Matches: 185, Mismatches: 25, Indels: 17
0.81 0.11 0.07
Matches are distributed among these distances:
28 32 0.17
29 89 0.48
30 63 0.34
31 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTGGAAAATTTAGGGT
Found at i:55054 original size:12 final size:12
Alignment explanation
Indices: 55039--55071 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
55029 GAACTAAATT
55039 TAAATTTAAAAA
1 TAAATTTAAAAA
55051 TAAATTT-AAAA
1 TAAATTTAAAAA
*
55062 TCAATTTAAA
1 TAAATTTAAA
55072 CTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:55055 original size:29 final size:28
Alignment explanation
Indices: 55023--55087 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
55013 AAACCATTTC
* *
55023 AAATTTGAACTAAATTTAAATTTAAAAA
1 AAATTTGAAATAAATTTAAACTTAAAAA
* *
55051 TAAATTTAAAATCAATTTAAACTTAAAAA
1 -AAATTTGAAATAAATTTAAACTTAAAAA
*
55080 AAGTTTGA
1 AAATTTGA
55088 TCCAAAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (28 bp):
AAATTTGAAATAAATTTAAACTTAAAAA
Found at i:55612 original size:49 final size:49
Alignment explanation
Indices: 55445--56021 Score: 333
Period size: 49 Copynumber: 11.7 Consensus size: 49
55435 TCAATCCGCA
* * ** *
55445 TGGTACTAAATTCGCCGTTGCGGCTTAAAAT-TTTCTTTTCATG-CTTCTG
1 TGGTACTAGATTCGCCATTGCGGCTT-AAATCTTTCCCTTCATGTTTTC-G
* * * * * ** *
55494 AGGT-GTAAGATTCGCTATTGCGACTTAAACCTTT-CCTTTTTGCGTCTTCG
1 TGGTACT-AGATTCGCCATTGCGGCTTAAATCTTTCCCTTCAT--GTTTTCG
* * *
55544 TGGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTTTTCG
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTTCG
* * * * *
55593 TGGTACTAGATTCACCGTTGCAGCTTAAATCTTTCCGTTCATG-TCTCTG
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTTC-G
* * * * * *
55642 AGGTA-TAAAGTTCGCCATCGTGGCTTAAACCTTTCCCTTCATGTCTTCG
1 TGGTACTAGA-TTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTTCG
* * *
55691 TGGTACTGGATTCACCATTGCGGCTTGAATCTTTCCCTTCATGCTTTT-G
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-TTTTCG
* * * * *
55740 AGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT--TGTATCTTCG
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-T-TTCG
* * * * *
55789 TGGTACTGGATTCGTCGTTGCGGCTTAAATATTTCCCTTTCATG-TCTC-
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCC-TTCATGTTTTCG
* * * * * *
55837 TGAGTTACAAGGTTAGTCATTGCGACTTAAACCTTTCCCTT--TGTATCTTCG
1 TG-G-TACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-T-TTCG
* *
55888 TGGTACTGGATTCGCCGA-TGCGGCTTAAATCTTTCCCTTTCATGTCTCTC-
1 TGGTACTAGATTCGCC-ATTGCGGCTTAAATCTTTCCC-TTCATGT-TTTCG
* * * * * *
55938 AGGTA-TAAGGTTTGCCATTGCGACTTAAACCTTTCCCTT-TTGTGTCTTCG
1 TGGTACT-AGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGT-T-TTCG
* * *
55988 TGGTACTGGATTCACCGTTGCGGCTTAAATCTTT
1 TGGTACTAGATTCGCCATTGCGGCTTAAATCTTT
56022 TCGTTTATGT
Statistics
Matches: 394, Mismatches: 101, Indels: 65
0.70 0.18 0.12
Matches are distributed among these distances:
46 1 0.00
47 5 0.01
48 21 0.05
49 227 0.58
50 119 0.30
51 15 0.04
52 6 0.02
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (49 bp):
TGGTACTAGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTTTTCG
Found at i:55876 original size:99 final size:99
Alignment explanation
Indices: 55561--56021 Score: 599
Period size: 99 Copynumber: 4.7 Consensus size: 99
55551 GGATTCGTCG
* * * *
55561 TTGCGGCTTAAATCTTTCCCTTCATGT-T-TTCGTGGTACTAGATTCACCGTTGCAGCTTAAATC
1 TTGCGACTTAAACCTTTCCCTT--TGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATC
* * *
55624 TTT-CCGTTCATGTCTCTGAGGTATAAAGTTCGCCA
64 TTTCCCTTTCATGTCTCTGAGGTACAAGGTTCGCCA
* * * ** * * *
55659 TCGTGGCTTAAACCTTTCCCTTCATGTCTTCGTGGTACTGGATTCACCATTGCGGCTTGAATCTT
1 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTT
*
55724 TCCC-TTCATG-CTTTTGAGGTACAAGGTTCGCCA
66 TCCCTTTCATGTC-TCTGAGGTACAAGGTTCGCCA
** *
55757 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCGTCGTTGCGGCTTAAATATT
1 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTT
* * *
55822 TCCCTTTCATGTCTCTGAGTTACAAGGTTAGTCA
66 TCCCTTTCATGTCTCTGAGGTACAAGGTTCGCCA
* *
55856 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCGCCGATGCGGCTTAAATCTT
1 TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTT
* * *
55921 TCCCTTTCATGTCTCTCAGGTATAAGGTTTGCCA
66 TCCCTTTCATGTCTCTGAGGTACAAGGTTCGCCA
*
55955 TTGCGACTTAAACCTTTCCCTTTTGTGTCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCT
1 TTGCGACTTAAACCTTTCCC-TTTGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCT
56020 TT
65 TT
56022 TCGTTTATGT
Statistics
Matches: 318, Mismatches: 38, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
96 1 0.00
97 2 0.01
98 135 0.42
99 136 0.43
100 44 0.14
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.39
Consensus pattern (99 bp):
TTGCGACTTAAACCTTTCCCTTTGTATCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTT
TCCCTTTCATGTCTCTGAGGTACAAGGTTCGCCA
Found at i:63206 original size:59 final size:58
Alignment explanation
Indices: 63137--63372 Score: 228
Period size: 58 Copynumber: 4.1 Consensus size: 58
63127 ACTTTCAGAC
* ** * **
63137 ATTCGGGGGTAAAATGATAATTTTTAGAATGTTTGGGGTTAAAATTGGAATTTTTGG-GT
1 ATTCGAGGGTAAAATG-TAATTTTTAGAAAATTTGAGGTTAAAATTGGAA-TTTTGGAAA
* * * *
63196 ATTCGAGGGTAAAATGGCAATTTTTAGAGAATTTGAGGTAAAAAATGGAATTTTGGAAA
1 ATTCGAGGGTAAAAT-GTAATTTTTAGAAAATTTGAGGTTAAAATTGGAATTTTGGAAA
* * ** *
63255 ATTCGGGGGTAAAATGTAATTTTT-GAAAAAGTCAAGGTCAAAA-TGGAATTTTGGAAA
1 ATTCGAGGGTAAAATGTAATTTTTAG-AAAATTTGAGGTTAAAATTGGAATTTTGGAAA
* * **
63312 ATTCGAGGGTAAATATGTAATTTTTGGAAAATTTGGGGTTAAAA-TAAAATTTTGGAAA
1 ATTCGAGGGTAAA-ATGTAATTTTTAGAAAATTTGAGGTTAAAATTGGAATTTTGGAAA
63370 ATT
1 ATT
63373 TAGGGTTAAA
Statistics
Matches: 147, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
57 27 0.18
58 64 0.44
59 55 0.37
60 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
ATTCGAGGGTAAAATGTAATTTTTAGAAAATTTGAGGTTAAAATTGGAATTTTGGAAA
Found at i:63257 original size:29 final size:29
Alignment explanation
Indices: 63176--63392 Score: 124
Period size: 29 Copynumber: 7.5 Consensus size: 29
63166 TGTTTGGGGT
* ** *
63176 TAAAATTGGAATTTTTGG-GTATTCGAGGG
1 TAAAAATGGAATTTTTGGAAAATTTGA-GG
* *
63205 T-AAAATGGCAATTTTTAGAGAATTTGAGG
1 TAAAAATGG-AATTTTTGGAAAATTTGAGG
* *
63234 TAAAAAATGGAA-TTTTGGAAAATTCGGGGG
1 T-AAAAATGGAATTTTTGGAAAATT-TGAGG
* * * **
63264 T-AAAATGTAATTTTTGAAAAAGTCAAGG
1 TAAAAATGGAATTTTTGGAAAATTTGAGG
* *
63292 TCAAAATGGAA-TTTTGGAAAATTCGAGGG
1 TAAAAATGGAATTTTTGGAAAATTTGA-GG
* * *
63321 TAAATATGTAATTTTTGGAAAATTTGGGG
1 TAAAAATGGAATTTTTGGAAAATTTGAGG
* * *
63350 TTAAAAT-AAAATTTTGGAAAATTT-AGGG
1 TAAAAATGGAATTTTTGGAAAATTTGA-GG
* *
63378 TTAAAATTGAATTTT
1 TAAAAATGGAATTTT
63393 AGATAGTTCG
Statistics
Matches: 147, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
28 53 0.36
29 62 0.42
30 25 0.17
31 7 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTGGAAAATTTGAGG
Found at i:63277 original size:28 final size:28
Alignment explanation
Indices: 63237--63425 Score: 148
Period size: 28 Copynumber: 6.6 Consensus size: 28
63227 TTTGAGGTAA
*
63237 AAAATGGAATTTTGGAAAATTCGGGGGT
1 AAAATGTAATTTTGGAAAATTCGGGGGT
* * **
63265 AAAATGTAATTTTTGAAAAAGTC-AAGGT
1 AAAATGTAA-TTTTGGAAAATTCGGGGGT
* *
63293 CAAAATGGAATTTTGGAAAATTCGAGGGT
1 -AAAATGTAATTTTGGAAAATTCGGGGGT
* *
63322 AAATATGTAATTTTTGGAAAATTTGGGGTT
1 AAA-ATGTAA-TTTTGGAAAATTCGGGGGT
** ** *
63352 AAAATAAAATTTTGGAAAATTTAGGGTT
1 AAAATGTAATTTTGGAAAATTCGGGGGT
* * *
63380 AAAAT-TGAATTTTAGATAGTTCGGGGGT
1 AAAATGT-AATTTTGGAAAATTCGGGGGT
63408 AAAAATGTAACTTTTGGA
1 -AAAATGTAA-TTTTGGA
63426 TATTTTAGGG
Statistics
Matches: 128, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
28 63 0.49
29 39 0.30
30 26 0.20
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAATTCGGGGGT
Found at i:64604 original size:3 final size:3
Alignment explanation
Indices: 64596--64628 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
64586 GGGAAAATTG
64596 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
64629 GATGATAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.