Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003473.1 Kokia drynarioides strain JFW-HI SEQ_116275, 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: 45746
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5571 original size:17 final size:17
Alignment explanation
Indices: 5530--5572 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 17
5520 AAATTTTATT
5530 TATTTATTA-AT-AATA
1 TATTTATTATATAAATA
5545 -ATTT-TT-TATAAATA
1 TATTTATTATATAAATA
5559 TATTTATTATATAA
1 TATTTATTATATAA
5573 TTTTTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
13 4 0.17
14 8 0.35
15 4 0.17
16 2 0.09
17 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATTATATAAATA
Found at i:6724 original size:16 final size:18
Alignment explanation
Indices: 6703--6735 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
6693 AAATTTAAGT
6703 ATTAAA-AAAA-TAAAAA
1 ATTAAATAAAAGTAAAAA
6719 ATTAAATAAAAGTAAAA
1 ATTAAATAAAAGTAAAA
6736 TGAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
ATTAAATAAAAGTAAAAA
Found at i:11072 original size:38 final size:40
Alignment explanation
Indices: 10992--11077 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 40
10982 TAAAAAGTAT
* *
10992 TTATATTTAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATA-TTAAAAACACTACAATAAATACAATAAATATTTTA
*
11033 TTATATTAAAAACAC-A-AATAAATACAATAAATTTTTTA
1 TTATATTAAAAACACTACAATAAATACAATAAATATTTTA
*
11071 TTGTATT
1 TTATATT
11078 CAATATAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
38 25 0.61
39 1 0.02
40 10 0.24
41 5 0.12
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATACAATAAATATTTTA
Found at i:12893 original size:21 final size:21
Alignment explanation
Indices: 12864--12903 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12854 TCATTAATAT
*
12864 TTTAATAATTTATTTATTAAA
1 TTTAATAATATATTTATTAAA
*
12885 TTTATTAATATATTTATTA
1 TTTAATAATATATTTATTA
12904 TGCATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATAATATATTTATTAAA
Found at i:12901 original size:12 final size:12
Alignment explanation
Indices: 12856--12903 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
12846 TTTTTATATC
12856 ATTAATAT-TTT
1 ATTAATATATTT
* *
12867 AATAATTTATTT
1 ATTAATATATTT
12879 ATT-A-A-ATTT
1 ATTAATATATTT
12888 ATTAATATATTT
1 ATTAATATATTT
12900 ATTA
1 ATTA
12904 TGCATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
9 7 0.24
10 1 0.03
11 8 0.28
12 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTAATATATTT
Found at i:15084 original size:2 final size:2
Alignment explanation
Indices: 15077--15109 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15067 AAATAATTAT
15077 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
15110 TGCGAGGGAA
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:16860 original size:70 final size:70
Alignment explanation
Indices: 16747--16890 Score: 245
Period size: 70 Copynumber: 2.1 Consensus size: 70
16737 TACAAGTATA
*
16747 ATACTAAAAACTCCAGAGAGTTATAATTCTTACCCTGCAACTTCTACCGATACAAGTCATGC-AA
1 ATACTAAAAACTCCAGAGAGTTATAATTCTTACCCTGCAACTTCTACCGATACAAGT-ATACAAA
16811 CTACCG
65 CTACCG
* *
16817 ATACTAAAAACTCTAGAGAGTTATAATTCTTACCCTGCAACTTCTACTGATACAAGTATACAAAC
1 ATACTAAAAACTCCAGAGAGTTATAATTCTTACCCTGCAACTTCTACCGATACAAGTATACAAAC
16882 TACCG
66 TACCG
16887 ATAC
1 ATAC
16891 ATCAATACAC
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 3 0.04
70 67 0.96
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (70 bp):
ATACTAAAAACTCCAGAGAGTTATAATTCTTACCCTGCAACTTCTACCGATACAAGTATACAAAC
TACCG
Found at i:19104 original size:29 final size:30
Alignment explanation
Indices: 19058--19495 Score: 180
Period size: 29 Copynumber: 14.9 Consensus size: 30
19048 GCTTAGAAGG
19058 TCCCTAAAC-TTCCAAAAATTACATTTTGA
1 TCCCTAAACTTTCCAAAAATTACATTTTGA
*
19087 TCCCTAAACTTTCCAAAAA-TATATTTTGA
1 TCCCTAAACTTTCCAAAAATTACATTTTGA
* *
19116 TTCCTAAACTTTCCAAAAATTACATTCT-A
1 TCCCTAAACTTTCCAAAAATTACATTTTGA
* * * *
19145 ACCCAAAACTTTTCAAAAATCACATTTTTG-
1 TCCCTAAACTTTCCAAAAATTACA-TTTTGA
* * * *
19175 CCCCTGAACTTTTCAAAAA--ACATATTT-T
1 TCCCTAAACTTTCCAAAAATTACAT-TTTGA
*
19203 TGCCCTTGAAC-TTCCAAAAATT-CTATTTTTG-
1 T-CCC-TAAACTTTCCAAAAATTAC-A-TTTTGA
* ** * * *
19234 CCCCCGAAC-TTCTAAAAATCACATTTTTGC
1 TCCCTAAACTTTCCAAAAATTACA-TTTTGA
* *
19264 T-CC-AAAC-TTACAAAAATTATATTTTTGA
1 TCCCTAAACTTTCCAAAAATTACA-TTTTGA
* * *
19292 -CCTTGAACTTTCCTAAAATTACCATTTT-A
1 TCCCTAAACTTTCCAAAAATTA-CATTTTGA
* * *
19321 CCCCCAAAC-ATCCAAAAATTACCATTTT-A
1 TCCCTAAACTTTCCAAAAATTA-CATTTTGA
* * *
19350 -CCCTTGAA-TGTCCAAAAATTAAATTTTTGA
1 TCCC-TAAACTTTCCAAAAATTACA-TTTTGA
*
19380 --CCTCAAACTTTTCAAAAATTACCATTTT-A
1 TCCCT-AAACTTTCCAAAAATTA-CATTTTGA
*
19409 -CCC-ACGAAC-ATCCAAAAATTACCATTTT-A
1 TCCCTA--AACTTTCCAAAAATTA-CATTTTGA
* *
19438 -CCCTCGAAC-GTCCAAAAATTACCATTTTGA
1 TCCCT-AAACTTTCCAAAAATTA-CATTTTGA
*
19468 -CCCCAAACTTTCCAAAAATTACCATTTT
1 TCCCTAAACTTTCCAAAAATTA-CATTTT
19496 ACCCTCGAGC
Statistics
Matches: 324, Mismatches: 51, Indels: 67
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.00
28 32 0.10
29 178 0.55
30 106 0.33
31 6 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
TCCCTAAACTTTCCAAAAATTACATTTTGA
Found at i:19185 original size:59 final size:59
Alignment explanation
Indices: 19059--19193 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
19049 CTTAGAAGGT
* * * * *
19059 CCCTAAAC-TTCCAAAAATTACATTTTGATCCCTAAACTTTCCAAAAATATATTTTGAT
1 CCCTAAACTTTCCAAAAATTACATTCTGAACCCAAAACTTTCCAAAAATACATTTTGAC
* *
19117 TCCTAAACTTTCCAAAAATTACATTCT-AACCCAAAACTTTTCAAAAATCACATTTTTG-C
1 CCCTAAACTTTCCAAAAATTACATTCTGAACCCAAAACTTTCCAAAAAT-ACA-TTTTGAC
* *
19176 CCCTGAACTTTTCAAAAA
1 CCCTAAACTTTCCAAAAA
19194 ACATATTTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 25 0.39
59 34 0.53
60 5 0.08
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (59 bp):
CCCTAAACTTTCCAAAAATTACATTCTGAACCCAAAACTTTCCAAAAATACATTTTGAC
Found at i:19300 original size:57 final size:58
Alignment explanation
Indices: 19158--19301 Score: 157
Period size: 57 Copynumber: 2.5 Consensus size: 58
19148 CAAAACTTTT
* * * * * *
19158 CAAAAATCACATTTTTGCCCCTGAACTTTTCAAAAAACATATTTTTGCCCTTGAACTTC
1 CAAAAATTATATTTTTGCCCCTGAACTTCTCAAAAAACACATTTTTGCCC-TAAACTTA
* * *
19217 CAAAAATTCTATTTTTGCCCCCGAACTTCT-AAAAATCACATTTTTGCTCC-AAACTTA
1 CAAAAATTATATTTTTGCCCCTGAACTTCTCAAAAAACACATTTTTGC-CCTAAACTTA
* *
19274 CAAAAATTATATTTTTGACCTTGAACTT
1 CAAAAATTATATTTTTGCCCCTGAACTT
19302 TCCTAAAATT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
57 29 0.41
58 15 0.21
59 27 0.38
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (58 bp):
CAAAAATTATATTTTTGCCCCTGAACTTCTCAAAAAACACATTTTTGCCCTAAACTTA
Found at i:19337 original size:59 final size:59
Alignment explanation
Indices: 19296--19531 Score: 257
Period size: 59 Copynumber: 4.0 Consensus size: 59
19286 TTTTGACCTT
* * *
19296 GAACTTTCCTAAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTTTACCCTT
1 GAACTTTCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCTC
* * * * *
19355 GAA-TGTCCAAAAATTA-AATTTTTGA-CCTCAAACTTTTCAAAAATTACCATTTTACCCAC
1 GAACTTTCCAAAAATTACCA-TTTT-ACCCTCAAAC-ATCCAAAAATTACCATTTTACCCTC
* * *
19414 GAAC-ATCCAAAAATTACCATTTTACCCTCGAACGTCCAAAAATTACCATTTTGACCC-C
1 GAACTTTCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTACCATTTT-ACCCTC
* * * * *
19472 AAACTTTCCAAAAATTACCATTTTACCCTCGAGCATCAAAAAATTACCATTTTGCCCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCTC
19531 G
1 G
19532 GCATCCAAAA
Statistics
Matches: 148, Mismatches: 20, Indels: 18
0.80 0.11 0.10
Matches are distributed among these distances:
57 1 0.01
58 47 0.32
59 99 0.67
60 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (59 bp):
GAACTTTCCAAAAATTACCATTTTACCCTCAAACATCCAAAAATTACCATTTTACCCTC
Found at i:19347 original size:88 final size:87
Alignment explanation
Indices: 19063--19528 Score: 358
Period size: 88 Copynumber: 5.3 Consensus size: 87
19053 GAAGGTCCCT
* * *
19063 AAACTTCCAAAAATTACATTTTGATCCCTAAACTTTCCAAAAA-TATA-TTTTGATTCC-TAAAC
1 AAACATCCAAAAATTACATTTTG-CCCCTGAAC-TTCCAAAAATTATATTTTTGA--CCTTAAAC
* * *
19125 TTTCCAAAAATTA-CATTCTAACCCA
62 TTTCCAAAAATTACCATTTTACCCCC
* * * * ** * *
19150 AAACTTTTCAAAAATCACATTTTTGCCCCTGAACTTTTCAAAAAACATATTTTTGCCCTTGAAC-
1 AAAC-ATCCAAAAATTACA-TTTTGCCCCTGAAC-TTCCAAAAATTATATTTTTGACCTTAAACT
* *
19214 TTCCAAAAATT-CTATTTTTGCCCCC
63 TTCCAAAAATTACCA-TTTTACCCCC
* * * * * * * *
19239 GAACTTCTAAAAATCACATTTTTGCTCC-AAACTTACAAAAATTATATTTTTGACCTTGAACTTT
1 AAACATCCAAAAATTACA-TTTTGCCCCTGAACTTCCAAAAATTATATTTTTGACCTTAAACTTT
*
19303 CCTAAAATTACCATTTTACCCCC
65 CCAAAAATTACCATTTTACCCCC
* * * *
19326 AAACATCCAAAAATTACCATTTTACCCTTGAA-TGTCCAAAAATTAAATTTTTGACCTCAAACTT
1 AAACATCCAAAAATTA-CATTTTGCCCCTGAACT-TCCAAAAATTATATTTTTGACCTTAAACTT
* *
19390 TTCAAAAATTACCATTTTACCCAC
64 TCCAAAAATTACCATTTTACCCCC
* * * * **
19414 GAACATCCAAAAATTACCATTTT-ACCCTCGAACGTCCAAAAATTACCA-TTTTGACCCCAAACT
1 AAACATCCAAAAATTA-CATTTTGCCCCT-GAACTTCCAAAAATTA-TATTTTTGACCTTAAACT
*
19477 TTCCAAAAATTACCATTTTACCCTC
63 TTCCAAAAATTACCATTTTACCCCC
* * *
19502 GAGCATCAAAAAATTACCATTTTGCCC
1 AAACATCCAAAAATTA-CATTTTGCCC
19529 TCGGCATCCA
Statistics
Matches: 312, Mismatches: 51, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
86 25 0.08
87 48 0.15
88 210 0.67
89 24 0.08
90 5 0.02
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (87 bp):
AAACATCCAAAAATTACATTTTGCCCCTGAACTTCCAAAAATTATATTTTTGACCTTAAACTTTC
CAAAAATTACCATTTTACCCCC
Found at i:19513 original size:29 final size:29
Alignment explanation
Indices: 19306--19543 Score: 250
Period size: 29 Copynumber: 8.2 Consensus size: 29
19296 GAACTTTCCT
* *
19306 AAAATTACCATTTTACCCCCAAACATCCA
1 AAAATTACCATTTTACCCTCGAACATCCA
* **
19335 AAAATTACCATTTTACCCTTGAATGTCCA
1 AAAATTACCATTTTACCCTCGAACATCCA
* * * *
19364 AAAATTA-AATTTTTGA-CCTCAAACTTTTCA
1 AAAATTACCA-TTTT-ACCCTCGAAC-ATCCA
*
19394 AAAATTACCATTTTACCCACGAACATCCA
1 AAAATTACCATTTTACCCTCGAACATCCA
*
19423 AAAATTACCATTTTACCCTCGAACGTCCA
1 AAAATTACCATTTTACCCTCGAACATCCA
* *
19452 AAAATTACCATTTTGACCC-CAAACTTTCCA
1 AAAATTACCATTTT-ACCCTCGAAC-ATCCA
* *
19482 AAAATTACCATTTTACCCTCGAGCATCAA
1 AAAATTACCATTTTACCCTCGAACATCCA
* *
19511 AAAATTACCATTTTGCCCTCG-GCATCCA
1 AAAATTACCATTTTACCCTCGAACATCCA
19539 AAAAT
1 AAAAT
19544 CGTATTTTTA
Statistics
Matches: 175, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
28 12 0.07
29 116 0.66
30 46 0.26
31 1 0.01
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAACATCCA
Found at i:25961 original size:49 final size:49
Alignment explanation
Indices: 25887--26456 Score: 344
Period size: 49 Copynumber: 11.7 Consensus size: 49
25877 CCATGAAGAT
*
25887 ATGAAGGGAAAGGTTTAAGTCGCAACGGGGAACCTTGTACCTCAGAAAA
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
* * ** ** * * *
25936 ATGAAGGGAAAGATTTAAGTTGCAACAACGAATCC-AATACCAC-GAGGAT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGA-AAA
* * * * *
25985 ATGGAGGGAATGGTTTAAGTCGCAACGGTGAACCTTATACCTCAAAAAA
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
* * * * * * *
26034 ATGAAGGGAAAGATTTAAGCCACAACGGCGAATCC-AGTACCAC-GAGGAC
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGA-AAA
* * * *
26083 ATGGAGGGAATGGTCTAAGTCACAACGGCGAACCTTGTACCTCAGAAAA
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
* * * * ** * *
26132 ATTAAGCGAAA-GTTTAAGCCGTAACGAAGAATCC-AGTA-C-CATGAAGAC
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAA-AA
* * *
26180 ATGGAGGGAATGGTTTAAGTCACAACGGCGAACCTTGTACCTCA-AAAA
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
* * * *
26228 CATGAAGGG-AAGGATTTAAGCCGCAACGGTGAATCC-AGTA-C-CATGAAGAT
1 -ATGAAGGGAAAGG-TTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAA-AA
* **
26278 ATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGC
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
* * ** * * *
26327 ATGAAAGGAAAGATTTAAGTCGCAACGGCGAATCC-AATACCACA-AGGAT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGA-AAA
* * * * * *
26376 ATAAAAGGAAAGGTTTAAGTCGCAACGCCAAACCTTGTACTTC-GAAAGC
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAA-A
* * * *
26425 ATGAAGGAAAAGATTTAAGCCGTAACGGCGAA
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA
26457 TCCAGTACCA
Statistics
Matches: 385, Mismatches: 106, Indels: 60
0.70 0.19 0.11
Matches are distributed among these distances:
46 2 0.01
47 6 0.02
48 45 0.12
49 307 0.80
50 21 0.05
51 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (49 bp):
ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAA
Found at i:26066 original size:98 final size:98
Alignment explanation
Indices: 25876--26513 Score: 742
Period size: 98 Copynumber: 6.5 Consensus size: 98
25866 AAGTTTCAGA
* * * *
25876 ACCATGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGGGAACCTTGTACCTCAGAAAAATGAA
1 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
** ** *
25941 GGGAAAGATTTAAGTTGCAACAACGAATCCAAT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
* * * *
25974 ACCACGAGGATATGGAGGGAATGGTTTAAGTCGCAACGGTGAACCTTATACCTCAAAAAAATGAA
1 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
*
26039 GGGAAAGATTTAAGCCACAACGGCGAATCCAGT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
* * * * * * *
26072 ACCACGAGGACATGGAGGGAATGGTCTAAGTCACAACGGCGAACCTTGTACCTCAGAAAAATTAA
1 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
* * **
26137 GCGAAAG-TTTAAGCCGTAACGAAGAATCCAGT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
* * * * *
26169 ACCATGAAGACATGGAGGGAATGGTTTAAGTCACAACGGCGAACCTTGTACCTCAAAAACATGAA
1 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
* *
26234 GGGAAGGATTTAAGCCGCAACGGTGAATCCAGT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
* * **
26267 ACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAA
1 ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
* * *
26332 AGGAAAGATTTAAGTCGCAACGGCGAATCCAAT
66 GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
** * * * * * **
26365 ACCAC-AAGGATATAAAAGGAAAGGTTTAAGTCGCAACGCCAAACCTTGTACTTCGAAAGCATGA
1 ACCACGAA-GATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGA
* *
26429 AGGAAAAGATTTAAGCCGTAACGGCGAATCCAGT
65 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
** * * *
26463 ACCATAAAGATATGGAGGGAAAGG-TTACAATTGCAACGACGAACCTTGTAC
1 ACCACGAAGATATGGAGGGAAAGGTTTA-AGTCGCAACGGCGAACCTTGTAC
26514 TTTAGAAAAT
Statistics
Matches: 468, Mismatches: 68, Indels: 8
0.86 0.12 0.01
Matches are distributed among these distances:
97 90 0.19
98 376 0.80
99 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (98 bp):
ACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAAAAAAATGAA
GGGAAAGATTTAAGCCGCAACGGCGAATCCAGT
Found at i:26412 original size:293 final size:294
Alignment explanation
Indices: 25876--26488 Score: 811
Period size: 293 Copynumber: 2.1 Consensus size: 294
25866 AAGTTTCAGA
* * *
25876 ACCATGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGGGAACCTTGTACCTCAGAAAAATGAA
1 ACCATGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAAAATGAA
** * *
25941 GGGAAAGATTTAAGTTGCAACAACGAATCCAATACCACGAGGATATGGAGGGAATGGTTTAAGTC
66 GGGAAAGATTTAAGCCGCAACAACGAATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAGTC
* * *
26006 GCAACGGTGAACCTTATACCTCAAAAAAATGAAGGGAAAGATTTAAGCCACAACGGCGAATCCAG
131 GCAACGGCGAACCTTATACCTCAAAAAAATGAAAGGAAAGATTTAAGCCACAACGGCGAATCCAA
* ** * * * * *
26071 TACCACGAGGACATGGAGGGAATGGTCTAAGTCACAACGGCGAACCTTGTACCTCAGAAA-AATT
196 TACCACAAGGACATAAAAGGAAAGGTCTAAGTCACAACGCCAAACCTTGTACCTC-GAAAGAATG
26135 AAGCG-AAAG-TTTAAGCCGTAACGAAGAATCCAGT
260 AAG-GAAAAGATTTAAGCCGTAACGAAGAATCCAGT
* *
26169 ACCATGAAGACATGGAGGGAATGGTTTAAGTCACAACGGCGAACCTTGTACCTCA-AAAACATGA
1 ACCATGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAAA-ATGA
* *** * *
26233 AGGGAAGGATTTAAGCCGCAACGGTGAATCCAGTACCATGAAGATATGGAGGGAAAGGTTTAAGT
65 AGGGAAAGATTTAAGCCGCAACAACGAATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAGT
* * ** * *
26298 CGCAACGGCGAACCTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGTCGCAACGGCGAATCCA
130 CGCAACGGCGAACCTTATACCTCAAAAAAATGAAAGGAAAGATTTAAGCCACAACGGCGAATCCA
* * * * *
26363 ATACCACAAGGATATAAAAGGAAAGGTTTAAGTCGCAACGCCAAACCTTGTACTTCGAAAGCATG
195 ATACCACAAGGACATAAAAGGAAAGGTCTAAGTCACAACGCCAAACCTTGTACCTCGAAAGAATG
**
26428 AAGGAAAAGATTTAAGCCGTAACGGCGAATCCAGT
260 AAGGAAAAGATTTAAGCCGTAACGAAGAATCCAGT
*
26463 ACCATAAAGATATGGAGGGAAAGGTT
1 ACCATGAAGATATGGAGGGAAAGGTT
26489 ACAATTGCAA
Statistics
Matches: 274, Mismatches: 42, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
292 9 0.03
293 219 0.80
294 46 0.17
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (294 bp):
ACCATGAAGATATGGAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAAAATGAA
GGGAAAGATTTAAGCCGCAACAACGAATCCAATACCACGAAGATATGGAGGGAAAGGTTTAAGTC
GCAACGGCGAACCTTATACCTCAAAAAAATGAAAGGAAAGATTTAAGCCACAACGGCGAATCCAA
TACCACAAGGACATAAAAGGAAAGGTCTAAGTCACAACGCCAAACCTTGTACCTCGAAAGAATGA
AGGAAAAGATTTAAGCCGTAACGAAGAATCCAGT
Found at i:26878 original size:78 final size:78
Alignment explanation
Indices: 26749--26897 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
26739 GTGAAGTTAC
* * * * *
26749 ATCACCATCAACCAATCTCTTACCCTGAGTCTGGGGCAGATTATAGCCATTCGATCTCTTACCCC
1 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCATTCGATCTCTTACCCC
26814 AAGCCTAGGATAG
66 AAGCCTAGGATAG
* * *
26827 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCGATCTTTTACCCC
1 ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCATTCGATCTCTTACCCC
*
26892 GAGCCT
66 AAGCCT
26898 GGGGCAGATT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (78 bp):
ATCACCATCAACCAATCTCTTACCCCGAGCCTAGGACAGATTACAGCCATTCGATCTCTTACCCC
AAGCCTAGGATAG
Found at i:26889 original size:39 final size:39
Alignment explanation
Indices: 26763--27101 Score: 176
Period size: 39 Copynumber: 8.7 Consensus size: 39
26753 CCATCAACCA
* * * * ** *
26763 ATCTCTTACCCTGAGTCTGGGGCAGATTATAGCCATTCG
1 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
* * ** ** *
26802 ATCTCTTACCCCAAGCCTAGGATAGATCACCA-TCAACCA
1 ATCTCTTACCCCGAGCCTAGGACAGAT-TGCAGTCATTCG
26841 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
1 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
* * * * *
26880 ATCTTTTACCCCGAGCCTGGGGCAGATTGCAGCCGTTCG
1 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
* **
26919 ATCTCTTACCTCGAGCCT-GTGGTAGA-T-CA-TCA-TCAG
1 ATCTCTTACCCCGAGCCTAG-GACAGATTGCAGTCATTC-G
* **
26955 CAAATCTCTTACCTCGAGCCTGAGG-CAGATTGCAACCATTCG
1 ---ATCTCTTACCCCGAGCCT-AGGACAGATTGCAGTCATTCG
* * * * ** ** *
26997 ATCTCTTACCTCAAACCTGAAGA-AGATCACTA-TCAGCCA
1 ATCTCTTACCCCGAGCCT-AGGACAGATTGC-AGTCATTCG
* * *
27036 ATCTCTTACCCCGAGCATGGGGCAGATTGCAGTCATTCG
1 ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
*
27075 ATCTCTTACCTCGAGCCTGAGG-CAGAT
1 ATCTCTTACCCCGAGCCT-AGGACAGAT
27102 CATCATCAGC
Statistics
Matches: 226, Mismatches: 56, Indels: 36
0.71 0.18 0.11
Matches are distributed among these distances:
35 2 0.01
36 2 0.01
37 2 0.01
38 6 0.03
39 200 0.88
40 6 0.03
41 3 0.01
42 3 0.01
43 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAGGACAGATTGCAGTCATTCG
Found at i:26923 original size:78 final size:76
Alignment explanation
Indices: 26841--27139 Score: 261
Period size: 78 Copynumber: 3.8 Consensus size: 76
26831 CCATCAACCA
* *
26841 ATCTCTTACCCCGAGCCT-AGGACAGATTGCAGTCATTCGATCTTTTACCCCGAGCCTGGGGCAG
1 ATCTCTTACCTCGAGCCTGAGGACAGATT-CA-TCA-TCGATCTCTTACCCCGAGCCTGGGGCAG
*
26905 ATTGCAGCCGTTCG
63 ATTGCAGCCATTCG
* * * *
26919 ATCTCTTACCTCGAGCCTGTGG-TAGA-TCATCATCAGCAAATCTCTTACCTCGAGCCTGAGGCA
1 ATCTCTTACCTCGAGCCTGAGGACAGATTCATCATC-G---ATCTCTTACCCCGAGCCTGGGGCA
*
26982 GATTGCAACCATTCG
62 GATTGCAGCCATTCG
* * * * * * *
26997 ATCTCTTACCTCAAACCTGAAGA-AGATCACTATCAGCCAATCTCTTACCCCGAGCATGGGGCAG
1 ATCTCTTACCTCGAGCCTGAGGACAGAT-TC-ATCA-TCGATCTCTTACCCCGAGCCTGGGGCAG
*
27061 ATTGCAGTCATTCG
63 ATTGCAGCCATTCG
* *
27075 ATCTCTTACCTCGAGCCTGAGG-CAGA-TCATCATCAGCCAATCTCTTA-CCCGATCATGGGGCA
1 ATCTCTTACCTCGAGCCTGAGGACAGATTCATCATC-G---ATCTCTTACCCCGAGCCTGGGGCA
27137 GAT
62 GAT
27140 GGCTATCATT
Statistics
Matches: 179, Mismatches: 27, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
74 3 0.02
75 8 0.04
76 3 0.02
77 18 0.10
78 139 0.78
79 2 0.01
80 1 0.01
81 4 0.02
82 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (76 bp):
ATCTCTTACCTCGAGCCTGAGGACAGATTCATCATCGATCTCTTACCCCGAGCCTGGGGCAGATT
GCAGCCATTCG
Found at i:26974 original size:117 final size:117
Alignment explanation
Indices: 26763--27006 Score: 321
Period size: 117 Copynumber: 2.1 Consensus size: 117
26753 CCATCAACCA
* * *
26763 ATCTCTTACCCTGAGTCTGGGGCAGATTATAGCCATTCGATCTCTTACCCCAAGCCTAGGATAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTCGATCTCTTACCCCAAGCCTAGGATAGA
* **
26828 TCACCATCAACCAATCTCTTACCCCGAGCCT-AGGACAGATTGCAGTCATTCG
66 TCACCATCAACAAATCTCTTACCCCGAGCCTGAGG-CAGATTGCAACCATTCG
* * * * * *
26880 ATCTTTTACCCCGAGCCTGGGGCAGATTGCAGCCGTTCGATCTCTTACCTCGAGCCT-GTGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTCGATCTCTTACCCCAAGCCTAG-GATAG
* * *
26944 ATCATCATCAGCAAATCTCTTACCTCGAGCCTGAGGCAGATTGCAACCATTCG
65 ATCACCATCAACAAATCTCTTACCCCGAGCCTGAGGCAGATTGCAACCATTCG
26997 ATCTCTTACC
1 ATCTCTTACC
27007 TCAAACCTGA
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
116 1 0.01
117 105 0.96
118 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (117 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATTACAGCCATTCGATCTCTTACCCCAAGCCTAGGATAGA
TCACCATCAACAAATCTCTTACCCCGAGCCTGAGGCAGATTGCAACCATTCG
Found at i:27118 original size:39 final size:39
Alignment explanation
Indices: 26919--27123 Score: 177
Period size: 39 Copynumber: 5.3 Consensus size: 39
26909 CAGCCGTTCG
* * *
26919 ATCTCTTACCTCGAGCCTGTGGTAGATCATCATCAGCAA
1 ATCTCTTACCTCGAGCCTGAGGCAGATCATCATCAGCCA
* ** *
26958 ATCTCTTACCTCGAGCCTGAGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCTCGAGCCTGAGGCAGATCAT-C-ATCAGCCA
* * * *
26997 ATCTCTTACCTCAAACCTGAAGAAGATCA-CTATCAGCCA
1 ATCTCTTACCTCGAGCCTGAGGCAGATCATC-ATCAGCCA
* * * ** *
27036 ATCTCTTACCCCGAGCATGGGGCAGAT--TGCAGTCATTCG
1 ATCTCTTACCTCGAGCCTGAGGCAGATCAT-CA-TCAGCCA
27075 ATCTCTTACCTCGAGCCTGAGGCAGATCATCATCAGCCA
1 ATCTCTTACCTCGAGCCTGAGGCAGATCATCATCAGCCA
27114 ATCTCTTACC
1 ATCTCTTACC
27124 CGATCATGGG
Statistics
Matches: 125, Mismatches: 32, Indels: 18
0.71 0.18 0.10
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 119 0.95
40 2 0.02
41 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCTCGAGCCTGAGGCAGATCATCATCAGCCA
Found at i:28396 original size:30 final size:30
Alignment explanation
Indices: 28362--28705 Score: 216
Period size: 29 Copynumber: 11.7 Consensus size: 30
28352 TAAACTATTC
**
28362 AAAATTACATTTTGATTCTCAAACTTTCCA
1 AAAATTACATTTTGACCCTCAAACTTTCCA
* *
28392 AAAATTACATTTTAAACCC-CAAACTTTTCA
1 AAAATTACATTTT-GACCCTCAAACTTTCCA
* * *
28422 AAAATCACATTTTTG-CCCTCGAAC-TTCTA
1 AAAATTACA-TTTTGACCCTCAAACTTTCCA
* * *
28451 AAAATCACTTTTTTACCC-CTAAAC-TTCCA
1 AAAATTACATTTTGACCCTC-AAACTTTCCA
**
28480 AAAATTACATTTTAGA-CCTTGAACTTTCCA
1 AAAATTACATTTT-GACCCTCAAACTTTCCA
* * *
28510 AAAATTACCATTTT-ACCCTCGAAC-ATCAA
1 AAAATTA-CATTTTGACCCTCAAACTTTCCA
* * *
28539 AAAATTACCATTTT-ACTCTCGAA-TGTCCA
1 AAAATTA-CATTTTGACCCTCAAACTTTCCA
* * * *
28568 AAAAATACATTTTTAACCTTAAACTTTCCA
1 AAAATTACATTTTGACCCTCAAACTTTCCA
* * * * *
28598 AAAATTTCCATATT-ACCCCCGAAC-ATCCA
1 AAAA-TTACATTTTGACCCTCAAACTTTCCA
* * *
28627 AAATTTACCATTTT-ACCCTCGAA-TGTCCA
1 AAAATTA-CATTTTGACCCTCAAACTTTCCA
28656 AAAATTACCATTTTGACCC-CAAACTTTCCA
1 AAAATTA-CATTTTGACCCTCAAACTTTCCA
28686 AAAATTACCATTTT-ACCCTC
1 AAAATTA-CATTTTGACCCTC
28706 GGGTGTCTGA
Statistics
Matches: 249, Mismatches: 46, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
28 13 0.05
29 124 0.50
30 94 0.38
31 18 0.07
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAACTTTCCA
Found at i:28526 original size:59 final size:58
Alignment explanation
Indices: 28349--28703 Score: 239
Period size: 59 Copynumber: 6.0 Consensus size: 58
28339 CCGAGAACGT
* * *
28349 CCCTAAACTATTC-AAAATTACATTTTGATTCTCAAACTTTCCAAAAATTA-CATTTTAAAC
1 CCCTAAACT-TCCAAAAATTACATTTTGA-CCTCGAACTTTCCAAAAATTACCATTTT--AC
* * * * * **
28409 CCC-AAACTTTTCAAAAATCACATTTTTGCCCTCGAAC-TTCTAAAAATCACTTTTTTAC
1 CCCTAAAC-TTCCAAAAATTACA-TTTTGACCTCGAACTTTCCAAAAATTACCATTTTAC
*
28467 CCCTAAACTTCCAAAAATTACATTTTAGACCTTGAACTTTCCAAAAATTACCATTTTA-
1 CCCTAAACTTCCAAAAATTACATTTT-GACCTCGAACTTTCCAAAAATTACCATTTTAC
* * * * * *
28525 CCCTCGAACATCAAAAAATTACCATTTT-ACTCTCGAA-TGTCCAAAAAATA-CATTTTTAA
1 CCCT-AAACTTCCAAAAATTA-CATTTTGAC-CTCGAACTTTCCAAAAATTACCA-TTTTAC
* * * * * *
28584 CCTTAAACTTTCCAAAAATTTCCATATT-ACCCCCGAAC-ATCCAAAATTTACCATTTTA-
1 CCCTAAAC-TTCCAAAAA-TTACATTTTGA-CCTCGAACTTTCCAAAAATTACCATTTTAC
* * *
28642 CCCTCGAA-TGTCCAAAAATTACCATTTTGACCCCAAACTTTCCAAAAATTACCATTTTAC
1 CCCT-AAACT-TCCAAAAATTA-CATTTTGACCTCGAACTTTCCAAAAATTACCATTTTAC
28702 CC
1 CC
28704 TCGGGTGTCT
Statistics
Matches: 233, Mismatches: 39, Indels: 46
0.73 0.12 0.14
Matches are distributed among these distances:
57 9 0.04
58 73 0.31
59 111 0.48
60 35 0.15
61 5 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTACATTTTGACCTCGAACTTTCCAAAAATTACCATTTTAC
Found at i:28704 original size:59 final size:58
Alignment explanation
Indices: 28476--28757 Score: 234
Period size: 59 Copynumber: 4.8 Consensus size: 58
28466 CCCCTAAACT
** * **
28476 TCCAAAAATTA-CATTTTAGACCTTGAACTTTCCAAAAATTACCATTTTACCCTCGAACA
1 TCCAAAAATTACCATTTT--ACCCCGAACTATCCAAAAATTACCATTTTACCCTCGAATG
* * * * * ** *
28535 TCAAAAAATTACCATTTTACTCTCGAA-TGTCCAAAAAATA-CATTTTTAACCTTAAACTT
1 TCCAAAAATTACCATTTTAC-CCCGAACTATCCAAAAATTACCA-TTTTACCCTCGAA-TG
* * *
28594 TCCAAAAATTTCCATATTACCCCCGAAC-ATCCAAAATTTACCATTTTACCCTCGAATG
1 TCCAAAAATTACCATTTTA-CCCCGAACTATCCAAAAATTACCATTTTACCCTCGAATG
* * **
28652 TCCAAAAATTACCATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGGGTG
1 TCCAAAAATTACCATTTT-ACCCCGAACTATCCAAAAATTACCATTTTACCCTCGAATG
** *
28711 TCTGAAAATTACCGTTTTACCTCC-AAGC-ATCCAAAAATTACCATTTT
1 TCCAAAAATTACCATTTTACC-CCGAA-CTATCCAAAAATTACCATTTT
28758 GCCCCCGACA
Statistics
Matches: 181, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
57 2 0.01
58 70 0.39
59 100 0.55
60 9 0.05
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCCGAACTATCCAAAAATTACCATTTTACCCTCGAATG
Found at i:28731 original size:88 final size:86
Alignment explanation
Indices: 28388--28706 Score: 338
Period size: 88 Copynumber: 3.6 Consensus size: 86
28378 TCTCAAACTT
* * * * *
28388 TCCAAAAATTACATTTTAAACCCCAAACTTTTCAAAAATCA-CATTTTTGCCCTCGAACTTCTAA
1 TCCAAAAATTACATTTT-GACCCCAAACTTTCCAAAAATTACCA-TTTTACCCTCGAACATC-AA
* ** *
28452 AAATCACTTTTTTACCC-CTAAACT-
63 AAATTACCATTTTACCCTC-GAA-TG
***
28476 TCCAAAAATTACATTTTAGACCTTGAACTTTCCAAAAATTACCATTTTACCCTCGAACATCAAAA
1 TCCAAAAATTACATTTT-GACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATC-AAA
*
28541 AATTACCATTTTACTCTCGAATG
64 AATTACCATTTTACCCTCGAATG
* * ** * * *
28564 TCCAAAAAATACATTTTTAACCTTAAACTTTCCAAAAATTTCCATATTACCCCCGAACATCCAAA
1 TCCAAAAATTACA-TTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACAT-CAAA
*
28629 ATTTACCATTTTACCCTCGAATG
64 AATTACCATTTTACCCTCGAATG
28652 TCCAAAAATTACCATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCG
1 TCCAAAAATTA-CATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCG
28707 GGTGTCTGAA
Statistics
Matches: 196, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 185 0.94
89 10 0.05
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (86 bp):
TCCAAAAATTACATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCAAAAA
TTACCATTTTACCCTCGAATG
Found at i:28744 original size:88 final size:86
Alignment explanation
Indices: 28388--28763 Score: 337
Period size: 88 Copynumber: 4.3 Consensus size: 86
28378 TCTCAAACTT
* * * * *
28388 TCCAAAAATTACATTTTAAACCCCAAACTTTTCAAAAATCA-CATTTTTGCCCTCGAACTTCTAA
1 TCCAAAAATTACATTTT-GACCCCAAACTTTCCAAAAATTACCA-TTTTACCCTCGAACATCTAA
* **
28452 AAATCACTTTTTTACC-CCTAAACT-
64 AAATTACCATTTTACCTCC--AA-TG
*** *
28476 TCCAAAAATTACATTTTAGACCTTGAACTTTCCAAAAATTACCATTTTACCCTCGAACATCAAAA
1 TCCAAAAATTACATTTT-GACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAA
*
28541 AATTACCATTTTACTCTCGAATG
65 AATTACCATTTTAC-CTCCAATG
* * ** * * * *
28564 TCCAAAAAATACATTTTTAACCTTAAACTTTCCAAAAATTTCCATATTACCCCCGAACATCCAAA
1 TCCAAAAATTACA-TTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAA
* *
28629 ATTTACCATTTTACCCTCGAATG
65 AATTACCATTTTA-CCTCCAATG
**** *
28652 TCCAAAAATTACCATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGGGTGTCTGAA
1 TCCAAAAATTA-CATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAA
*
28717 AATTACCGTTTTACCTCCAA-G
65 AATTACCATTTTACCTCCAATG
*
28738 CATCCAAAAATTACCATTTTGCCCCC
1 --TCCAAAAATTA-CATTTTGACCCC
28764 GACATCCAAA
Statistics
Matches: 241, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
86 1 0.00
87 7 0.03
88 222 0.92
89 10 0.04
90 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (86 bp):
TCCAAAAATTACATTTTGACCCCAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCTAAAA
ATTACCATTTTACCTCCAATG
Found at i:28747 original size:29 final size:29
Alignment explanation
Indices: 28506--28776 Score: 141
Period size: 29 Copynumber: 9.3 Consensus size: 29
28496 CCTTGAACTT
*
28506 TCCAAAAATTACCATTTTACCCTCGAA-CA
1 TCCAAAAATTACCATTTTA-CCTCCAAGCA
* *
28535 TCAAAAAATTACCATTTTACTCTCGAATG--
1 TCCAAAAATTACCATTTTAC-CTCCAA-GCA
* * * *
28564 TCCAAAAAATA-CATTTTTAACCT-TAAACTT
1 TCCAAAAATTACCA-TTTT-ACCTCCAAGC-A
* * *
28594 TCCAAAAATTTCCATATTACCCCCGAA-CA
1 TCCAAAAATTACCATTTTACCTCC-AAGCA
* *
28623 TCCAAAATTTACCATTTTACCCTCGAATG--
1 TCCAAAAATTACCATTTTA-CCTCCAA-GCA
* *
28652 TCCAAAAATTACCATTTTGACC-CCAAACTT
1 TCCAAAAATTACCATTTT-ACCTCCAAGC-A
** **
28682 TCCAAAAATTACCATTTTACC-CTCGGGTG
1 TCCAAAAATTACCATTTTACCTC-CAAGCA
** *
28711 TCTGAAAATTACCGTTTTACCTCCAAGCA
1 TCCAAAAATTACCATTTTACCTCCAAGCA
* * *
28740 TCCAAAAATTACCATTTTGCCCCCGA-CA
1 TCCAAAAATTACCATTTTACCTCCAAGCA
28768 TCCAAAAAT
1 TCCAAAAAT
28777 CGTATTTTTA
Statistics
Matches: 185, Mismatches: 37, Indels: 41
0.70 0.14 0.16
Matches are distributed among these distances:
28 19 0.10
29 123 0.66
30 39 0.21
31 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCTCCAAGCA
Found at i:29777 original size:18 final size:18
Alignment explanation
Indices: 29750--29785 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29740 GTGACTCCCT
* *
29750 TTTTATAATTTTTTTCGA
1 TTTTAAAATTTTGTTCGA
29768 TTTTAAAATTTTGTTCGA
1 TTTTAAAATTTTGTTCGA
29786 GACTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTTAAAATTTTGTTCGA
Found at i:39133 original size:30 final size:30
Alignment explanation
Indices: 39067--39133 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
39057 GTTTAAAAAA
*
39067 AGTGACGTAAATAAAAACTTTCAAATAATT
1 AGTGACGTAAATAAAAACTTTCAAACAATT
* * *
39097 ATGTGACTTAAAT-GAAACTTTCAAACAGTT
1 A-GTGACGTAAATAAAAACTTTCAAACAATT
39127 CAGTGAC
1 -AGTGAC
39134 CGTTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (30 bp):
AGTGACGTAAATAAAAACTTTCAAACAATT
Found at i:40760 original size:38 final size:38
Alignment explanation
Indices: 40718--40792 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
40708 TAGGCTCGCG
* * *
40718 CTAACTATTTTGGAGGTTGTTGTGTTGAACTTGCAAGT
1 CTAACTATTTTGAAGATTGTGGTGTTGAACTTGCAAGT
40756 CTAACTATTTTGAAGATTGTGGTGTTGAACTTGCAAG
1 CTAACTATTTTGAAGATTGTGGTGTTGAACTTGCAAG
40793 CCTGAGATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (38 bp):
CTAACTATTTTGAAGATTGTGGTGTTGAACTTGCAAGT
Found at i:41435 original size:35 final size:35
Alignment explanation
Indices: 41389--41456 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
41379 AATATAATAT
*
41389 ATTTTGTTTAACTTGATTTGCAAGCAATCTCTTCG
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTCG
*
41424 ATTTTGTTTAACTTGACTTGCAAGTAATCTCTT
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTT
41457 ATTTGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTCG
Found at i:43418 original size:35 final size:35
Alignment explanation
Indices: 43372--43440 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
43362 AAGATAATAT
43372 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
*
43407 ATTTTGTTTAACTTGACTTGCAAGTAATCTCTTA
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTA
43441 TTTGACTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
Found at i:43616 original size:71 final size:71
Alignment explanation
Indices: 43492--43679 Score: 191
Period size: 71 Copynumber: 2.6 Consensus size: 71
43482 GTTGGGAGTT
* * * * * * * *
43492 TGTTAGAGGTTGCGGTTTGTAACATGCGAGCCTTAATATATTAGATGGGAGTTTATA-AATTTTG
1 TGTTGGAGGCTGCGGTTTGTAACCTGCGAGCCTTAATATGTCAGTTAGGAGTTTATAGAA-TTCG
43556 CTAACTA
65 CTAACTA
* * * * * *
43563 TGTTGGATGTTGCGGTTT-TGATCCTGCGAGCCTTAATGTGTCAGTTAGGAGTTTGTAGCATTCG
1 TGTTGGAGGCTGCGGTTTGT-AACCTGCGAGCCTTAATATGTCAGTTAGGAGTTTATAGAATTCG
*
43627 CTAACTG
65 CTAACTA
* *
43634 TGTTGGAGGCTGTGGTTTGTAACCTGCGAGCCTTAATATGACAGTT
1 TGTTGGAGGCTGCGGTTTGTAACCTGCGAGCCTTAATATGTCAGTT
43680 GGAAGGTTTT
Statistics
Matches: 95, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
70 1 0.01
71 92 0.97
72 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (71 bp):
TGTTGGAGGCTGCGGTTTGTAACCTGCGAGCCTTAATATGTCAGTTAGGAGTTTATAGAATTCGC
TAACTA
Found at i:43708 original size:71 final size:71
Alignment explanation
Indices: 43576--43773 Score: 174
Period size: 71 Copynumber: 2.8 Consensus size: 71
43566 TGGATGTTGC
* * * * * * *
43576 GGTTTTGATCCTGC-GAGCCTTAATGTGTCAGTTAGG-AGTTTGTAGCAT-TCGCTAACTGTGTT
1 GGTTTTGAACCT-CTGAGCCCTAATATGACAGTT-GGAAGTTTGTAAC-TCTCTCTAACCGTGTT
* *
43638 GGAGGCTGT
63 AGAGGCTAT
* *
43647 GG-TTTGTAACCTGC-GAGCCTTAATATGACAGTTGGAAGGTTT-TAACTCTCTGTAACCGTGTT
1 GGTTTTG-AACCT-CTGAGCCCTAATATGACAGTTGGAA-GTTTGTAACTCTCTCTAACCGTGTT
43709 AGAGGCTAT
63 AGAGGCTAT
* * *
43718 GGTTTTGATCCTCTGAGCCCTAATGTGACAGTTGGGAGTTTGTAACTCTCTCTAAC
1 GGTTTTGAACCTCTGAGCCCTAATATGACAGTTGGAAGTTTGTAACTCTCTCTAAC
43774 TATTTGAACA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
70 12 0.11
71 86 0.81
72 8 0.08
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (71 bp):
GGTTTTGAACCTCTGAGCCCTAATATGACAGTTGGAAGTTTGTAACTCTCTCTAACCGTGTTAGA
GGCTAT
Done.