Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013404.1 Kokia drynarioides strain JFW-HI SEQ_128429, 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: 18630
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.33
Warning! 671 characters in sequence are not A, C, G, or T
Found at i:1292 original size:16 final size:17
Alignment explanation
Indices: 1253--1294 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1243 TGAACCCCTT
1253 TTTAAATTTATTATACA
1 TTTAAATTTATTATACA
* *
1270 TTT-AATTTTTTTTA-A
1 TTTAAATTTATTATACA
1285 TTTAAATTTA
1 TTTAAATTTA
1295 AATTAAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTATTATACA
Found at i:1339 original size:16 final size:18
Alignment explanation
Indices: 1303--1342 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
1293 TAAATTAAGT
*
1303 TTAAATTTACTTTTAAAA
1 TTAAAATTACTTTTAAAA
1321 TTAAAATTA-TTTT-AAA
1 TTAAAATTACTTTTAAAA
1337 TTAAAA
1 TTAAAA
1343 AAAATCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 4 0.19
18 8 0.38
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATTACTTTTAAAA
Found at i:4668 original size:15 final size:17
Alignment explanation
Indices: 4643--4679 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
4633 ATGTGAAGAA
4643 TATTATTTAAAATT-AT
1 TATTATTTAAAATTGAT
4659 TATT-TTTAAAATTGAT
1 TATTATTTAAAATTGAT
4675 TATTA
1 TATTA
4680 AGATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATTTAAAATTGAT
Found at i:4703 original size:18 final size:18
Alignment explanation
Indices: 4665--4703 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4655 TTATTATTTT
*
4665 TAAAATTGATTATTAAGA
1 TAAAATTGAATATTAAGA
4683 TAAAATTGAAATATTAA-A
1 TAAAATTG-AATATTAAGA
4701 TAA
1 TAA
4704 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (18 bp):
TAAAATTGAATATTAAGA
Found at i:4804 original size:22 final size:22
Alignment explanation
Indices: 4779--4822 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4769 AGGTTTAATA
4779 ATATTGAAAATTATA-ATATTTT
1 ATATT-AAAATTATACATATTTT
* *
4801 ATATTAATATTTTACATATTTT
1 ATATTAAAATTATACATATTTT
4823 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTAAAATTATACATATTTT
Found at i:5377 original size:17 final size:17
Alignment explanation
Indices: 5355--5399 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
5345 TGGAAATTGG
* *
5355 ATTTAAGTTTATTTTAA
1 ATTTAAATTTATTATAA
5372 ATTTAAATTTATTATAA
1 ATTTAAATTTATTATAA
*
5389 AATTAAATTTA
1 ATTTAAATTTA
5400 AAAAGTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:6166 original size:3 final size:3
Alignment explanation
Indices: 6158--6215 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
6148 AAATTTTTAT
** * * *
6158 TAA TAA TAA TTT TAA AAA TAA TAA TAA TAA TAA TAT TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6206 TGAA TAA TAA
1 T-AA TAA TAA
6216 ATAAAAAAGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:7273 original size:30 final size:28
Alignment explanation
Indices: 7247--7501 Score: 182
Period size: 29 Copynumber: 8.7 Consensus size: 28
7237 TAAACTTTCT
*
7247 AAAAATTACCATTTTACCTCCAAACTTCC
1 AAAAATTACCATTTTACC-CCGAACTTCC
* *
7276 AAAAA-TCCCATCTTTGACCCCGAACCTTCT
1 AAAAATTACCAT-TTT-ACCCCGAA-CTTCC
7306 AAAAATTACCATTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTACCC-CGAACTTCC
* * *
7335 AAGAA-T-CTCATTTTTGACCCCGAGCCTTTC
1 AAAAATTAC-CA-TTTT-ACCCCGA-ACTTCC
7365 AAAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTA-CCCCGAACTTCC
* * *
7394 AAAAA-TCCCATTTTTGACCTCGAACCTTCT
1 AAAAATTACCA-TTTT-ACCCCGAA-CTTCC
*
7424 AAAAATTACTATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTA-CCCCGAACTTCC
* *
7453 AAAAA-T-CTCATTTTTGACTCCGAACCCTCC
1 AAAAATTAC-CA-TTTT-ACCCCGAA-CTTCC
*
7483 AAAAA-TACCATTTTGCCCC
1 AAAAATTACCATTTTACCCC
7502 CGTGCATCCG
Statistics
Matches: 181, Mismatches: 23, Indels: 45
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.01
28 17 0.09
29 75 0.41
30 74 0.41
31 12 0.07
32 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCCGAACTTCC
Found at i:7315 original size:59 final size:59
Alignment explanation
Indices: 7243--7503 Score: 373
Period size: 59 Copynumber: 4.4 Consensus size: 59
7233 TCCCTAAACT
* * *
7243 TTCTAAAAATTACCATTTTACCTCCAAACTTCCAAAAATCCCATCTTTGACCCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
7302 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAGAATCTCATTTTTGACCCCGAGCC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
7361 TT-TCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
7420 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
7479 CTCCAAAAA-TACCATTTTGCCCCCG
1 TTCTAAAAATTACCATTTTACCCCCG
7504 TGCATCCGAA
Statistics
Matches: 180, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
58 15 0.08
59 164 0.91
60 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.06, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:10860 original size:59 final size:59
Alignment explanation
Indices: 10768--11205 Score: 569
Period size: 59 Copynumber: 7.4 Consensus size: 59
10758 TCCCTAAACT
* * *
10768 TTCTAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATCTTTGACTCCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
** * *
10827 TTCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATATTTGACCCCGAGCC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
10886 TTCTAAAAAATACCATTTTACCCCATC-AACTTCCAAAAATCTCATTTTTGACCCCGAATC
1 TTCTAAAAATTACCATTTTACCCC--CGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * **
10946 TTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATCTTTGACCCTAAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
11005 TTCTAAAAATAACCATTTTACCCCCGAACTACCAAAAATCTCATTTTTGACCCCTAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * *
11064 TT-TCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAACCTCGAACC
1 TTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* **
11123 TTTTAAAAATTACCATTTTACCCCC-AACTTCCAAAAATCCCATTTTTGACTTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* * * *
11181 CTC-CAAAACTACCATTTTGCCCCCG
1 TTCTAAAAATTACCATTTTACCCCCG
11206 TGCATCCGAA
Statistics
Matches: 332, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
57 18 0.05
58 33 0.10
59 228 0.69
60 53 0.16
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
Found at i:10894 original size:30 final size:29
Alignment explanation
Indices: 10789--11205 Score: 264
Period size: 30 Copynumber: 14.2 Consensus size: 29
10779 ACTATTTTAC
10789 CCCCGAA-CTTCCAAAAATCCCATCTTTGA
1 CCCCGAACCTTCCAAAAATCCCAT-TTTGA
* * *
10818 CTCCGAACCTTCTAAAAATTACCATTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTGA
*
10847 CCCTTGAA-CTTCCAAAAATCCCATATTTGA
1 CCC-CGAACCTTCCAAAAATCCCAT-TTTGA
* * *
10877 CCCCGAGCCTTCTAAAAAATACCATTTT-A
1 CCCCGAACCTTC-CAAAAATCCCATTTTGA
* *
10906 CCCC-ATCAACTTCCAAAAATCTCATTTTTGA
1 CCCCGA--ACCTTCCAAAAATCCCA-TTTTGA
* * *
10937 CCCCGAATCTTCTAAAAATTACCATTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTGA
* *
10966 CCCCCAAACTTCCAAAAATCCCATCTTTGA
1 CCCCGAACCTTCCAAAAATCCCAT-TTTGA
** * *
10996 CCCTAAACCTTCTAAAAATAACCATTTT-A
1 CCCCGAACCTTCCAAAAAT-CCCATTTTGA
* *
11025 CCCCCGAA-CTACCAAAAATCTCATTTTTGA
1 -CCCCGAACCTTCCAAAAATCCCA-TTTTGA
* * *
11055 CCCCTAACCTTTCAAAAATTACCATTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTGA
* *
11084 CCCCCGAA-CTTCCAAAAATTCCATTTTTAA
1 -CCCCGAACCTTCCAAAAATCCCA-TTTTGA
* ** *
11114 CCTCGAACCTTTTAAAAATTACCATTTT-A
1 CCCCGAACCTTCCAAAAA-TCCCATTTTGA
*
11143 CCCCCAA-CTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCCCA-TTTTGA
** * * * *
11172 CTTCGAACCCTCCAAAACTACCATTTTGC
1 CCCCGAACCTTCCAAAAATCCCATTTTGA
11201 CCCCG
1 CCCCG
11206 TGCATCCGAA
Statistics
Matches: 298, Mismatches: 61, Indels: 58
0.71 0.15 0.14
Matches are distributed among these distances:
27 4 0.01
28 29 0.10
29 114 0.38
30 116 0.39
31 34 0.11
32 1 0.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (29 bp):
CCCCGAACCTTCCAAAAATCCCATTTTGA
Found at i:15794 original size:109 final size:108
Alignment explanation
Indices: 15674--15949 Score: 313
Period size: 108 Copynumber: 2.5 Consensus size: 108
15664 AAAAAACAAT
* *
15674 ATATTTTTAAATCTGGAAAAGGTGATGTTAG-CTATTGGGTGCTAAACACCAAAAAAAATTTTAT
1 ATATTTTTAAATCTGGAAAAGGTGATG-TAGACCATTGGATGCTAAACACCAAAAAAAA-TTTA-
* *
15738 TTGTATTTTTTGAGTTTCGGCCATTGCTTGCCAAACA-CTCAAAAA
63 TTCTATTTTTTGAGTGTCGGCCATTGCTTGCCAAACACCTCAAAAA
* * * * *
15783 ATATTTTTAAATCTGAAAAAAGTGGTGTCGACCATTGGATGCTAAACACCCAAAAAAATTTATTC
1 ATATTTTTAAATCTGGAAAAGGTGATGTAGACCATTGGATGCTAAACACCAAAAAAAATTTATTC
* * * * *
15848 TCTTTTTTGGGTGTCGGTCATTGCTTGTCAAACACCTTAAAAA
66 TATTTTTTGAGTGTCGGCCATTGCTTGCCAAACACCTCAAAAA
* * * * *** *
15891 ATATTTTTAAATCTAGAAAAGATGGTGTAGGCCATTACTTGCCAAACACCAAAAAAAAT
1 ATATTTTTAAATCTGGAAAAGGTGATGTAGACCATTGGATGCTAAACACCAAAAAAAAT
15950 ATTTTTAAAT
Statistics
Matches: 140, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
107 31 0.22
108 61 0.44
109 48 0.34
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (108 bp):
ATATTTTTAAATCTGGAAAAGGTGATGTAGACCATTGGATGCTAAACACCAAAAAAAATTTATTC
TATTTTTTGAGTGTCGGCCATTGCTTGCCAAACACCTCAAAAA
Found at i:15937 original size:57 final size:56
Alignment explanation
Indices: 15857--16067 Score: 189
Period size: 57 Copynumber: 3.8 Consensus size: 56
15847 CTCTTTTTTG
* * * * *
15857 GGTGTCGGTCATTGCTTGTCAAACACCTTAAAAAATATTTTTAAATCTAGAAAAGAT
1 GGTGTAGGCCATTACTTGCCAAACACC-AAAAAAATATTTTTAAATCTAGAAAAGAT
* *
15914 GGTGTAGGCCATTACTTGCCAAACACCAAAAAAAATATTTTTAAATCTAAAAAAAAT
1 GGTGTAGGCCATTACTTGCCAAACACC-AAAAAAATATTTTTAAATCTAGAAAAGAT
** * *** * * * *
15971 AATGTAGGTCATTGGATGGCAATCA-CAAAAAAA-AATTTT-AATCTGGGAAAAG-T
1 GGTGTAGGCCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCT-AGAAAAGAT
* *
16024 GGTGTAGACCATTAC-TGCCAAACAACAAAAAAATATTTTTAAAT
1 GGTGTAGGCCATTACTTGCCAAACACCAAAAAAATATTTTTAAAT
16068 TTGAAAAAGG
Statistics
Matches: 121, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
52 7 0.06
53 23 0.19
54 14 0.12
55 10 0.08
56 1 0.01
57 66 0.55
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (56 bp):
GGTGTAGGCCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCTAGAAAAGAT
Found at i:15943 original size:107 final size:108
Alignment explanation
Indices: 15717--15947 Score: 279
Period size: 107 Copynumber: 2.1 Consensus size: 108
15707 ATTGGGTGCT
* *
15717 AAACACCAAAAAAAATTTTATTTGTATTTTTTGAGTTTCGGCCATTGCTTGCCAAACACTCAAAA
1 AAACACC-AAAAAAATTTTATTTCTATTTTTTGAGTGTCGGCCATTGCTTGCCAAACACTCAAAA
* ** *
15782 AATATTTTTAAATCTGAAAAAAGTGGTGTCGACCATTGGATGCT
65 AATATTTTTAAATCTGAAAAAAGTGGTGTAGACCATTACATGCC
* * * * *
15826 AAACACCCAAAAAAA-TTTA-TTCTCTTTTTTGGGTGTCGGTCATTGCTTGTCAAACACCTTAAA
1 AAACA-CCAAAAAAATTTTATTTCTATTTTTTGAGTGTCGGCCATTGCTTGCCAAACA-CTCAAA
* * *
15889 AAATATTTTTAAATCT-AGAAAAGATGGTGTAGGCCATTACTTGCC
64 AAATATTTTTAAATCTGAAAAAAG-TGGTGTAGACCATTACATGCC
15934 AAACACCAAAAAAA
1 AAACACCAAAAAAA
15948 ATATTTTTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
107 46 0.44
108 45 0.43
109 12 0.11
110 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (108 bp):
AAACACCAAAAAAATTTTATTTCTATTTTTTGAGTGTCGGCCATTGCTTGCCAAACACTCAAAAA
ATATTTTTAAATCTGAAAAAAGTGGTGTAGACCATTACATGCC
Found at i:16218 original size:61 final size:58
Alignment explanation
Indices: 16114--16275 Score: 166
Period size: 56 Copynumber: 2.8 Consensus size: 58
16104 CTCAATTTTT
* * ** *
16114 TTTTTAAATATGAGAAAAGTGATGTAGGTCATTGCTTGTTAAACAAAAAAAAAAAAAAACA
1 TTTTTAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGTAAAC--AAAAAAAAAAAAA-A
* * * ***
16175 TTTTTAAATTTGAAAAAAGTGGTGCAAGTCATTGGGTGGTAAAC-ACCCAAAAAAAAA
1 TTTTTAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGTAAACAAAAAAAAAAAAAA
* *
16232 -TTTAAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGCAAACA
1 TTTTTAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGTAAACA
16276 CCCAAAAATT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
56 38 0.45
57 1 0.01
58 9 0.11
61 36 0.43
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (58 bp):
TTTTTAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGTAAACAAAAAAAAAAAAAA
Found at i:16260 original size:56 final size:58
Alignment explanation
Indices: 16165--16283 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 58
16155 AACAAAAAAA
* * *
16165 AAAAAAAACATTTTTAAATTTGAAAAAAGTGGTGCAAGTCATTGGGTGGTAAACACCC
1 AAAAAAAACATTTTAAAATTTGAAAAAAGTGATGCAAGTCATTGGGTGGCAAACACCC
* *
16223 AAAAAAAA-A-TTTAAAATTTGAGAAAAGTGATGTAAGTCATTGGGTGGCAAACACCC
1 AAAAAAAACATTTTAAAATTTGAAAAAAGTGATGCAAGTCATTGGGTGGCAAACACCC
16279 AAAAA
1 AAAAA
16284 TTATTTTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 47 0.84
57 1 0.02
58 8 0.14
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (58 bp):
AAAAAAAACATTTTAAAATTTGAAAAAAGTGATGCAAGTCATTGGGTGGCAAACACCC
Found at i:18260 original size:57 final size:56
Alignment explanation
Indices: 18146--18385 Score: 200
Period size: 57 Copynumber: 4.3 Consensus size: 56
18136 AGGGAAAAAT
* *** * * *
18146 AAAGATAGTGTAGGTCATTGGATGGCAATCAC-AAAAAAATATTTTTAAATCTAAA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
*
18201 AAAGATGGCGTAGGTCATTACTTGCCAAACATCAAAAAAAATATTTTTAAATCTGAA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACA-CAAAAAAAATATTTTTAAATCTGAA
* *** * * ** **
18258 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAAA-A-AATT-AATCTGGG
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
*** * * *
18311 AAAGATGGTGTACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATTTGGA
1 AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
* * *
18367 AAAGGTGATGTAGATCATT
1 AAAGATGGTGTAGGTCATT
18386 GAGTGGCAAA
Statistics
Matches: 143, Mismatches: 37, Indels: 9
0.76 0.20 0.05
Matches are distributed among these distances:
53 36 0.25
54 3 0.02
55 27 0.19
56 31 0.22
57 46 0.32
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (56 bp):
AAAGATGGTGTAGGTCATTACTTGCCAAACACAAAAAAAATATTTTTAAATCTGAA
Found at i:18350 original size:112 final size:111
Alignment explanation
Indices: 18146--18370 Score: 310
Period size: 112 Copynumber: 2.0 Consensus size: 111
18136 AGGGAAAAAT
***
18146 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATATTTTTAAATCTAAAAAAGATGGCG
1 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
*** *
18211 TAGGTCATTACTTGCCAAACATCAAAAAAAATATTTTTAAATCTGAA
66 TACACCATTACTTGCCAAACA-CCAAAAAAATATTTTTAAATCTGAA
*** *
18258 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAA-AAAATT-AATCTGGGAAAGATGGTG
1 AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
* *
18321 TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATTTGGA
66 TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCTGAA
18367 AAAG
1 AAAG
18371 GTGATGTAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
109 26 0.26
110 32 0.32
111 3 0.03
112 39 0.39
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (111 bp):
AAAGATAGTGTAGGTCATTGGATGGCAATCACAAAAAAATAAAATTAAATCTAAAAAAGATGGCG
TACACCATTACTTGCCAAACACCAAAAAAATATTTTTAAATCTGAA
Found at i:18504 original size:53 final size:53
Alignment explanation
Indices: 18447--18561 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 53
18437 CATTGCTTGT
18447 CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
1 CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
* *** * * * *
18500 CAAACACCCAAAAAAATTTTTTAATTTGATAAAAGTGGTGTAAGTCATTGGGTGG
1 CAAACA--TAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
18555 CAAACAT
1 CAAACAT
18562 CCAAAAATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
53 6 0.12
55 45 0.88
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.26
Consensus pattern (53 bp):
CAAACATAAAAAAAAAATTAAATTTGAAAAAAATGGTGCAAGTCATTGGGTGG
Found at i:18539 original size:55 final size:56
Alignment explanation
Indices: 18467--18577 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
18457 AAAAAAATTA
18467 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAA-AATTTTTT
1 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
* * * * *
18522 AATTTGATAAAAGTGGTGTAAGTCATTGGGTGGCAAACATCCAAAAATTATTTTTT
1 AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
18578 TTTATTCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 43 0.86
56 7 0.14
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (56 bp):
AATTTGAAAAAAATGGTGCAAGTCATTGGGTGGCAAACACCCAAAAATAATTTTTT
Done.