Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_30 ID=scaffold_30-JGI_221_v2.0
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: 71456
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.23
Warning! 23280 characters in sequence are not A, C, G, or T
Found at i:6192 original size:15 final size:15
Alignment explanation
Indices: 6172--6200 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6162 TTAATAGAGA
6172 GTACTTCTATTAGAT
1 GTACTTCTATTAGAT
6187 GTACTTCTATTAGA
1 GTACTTCTATTAGA
6201 ATAGTACGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
GTACTTCTATTAGAT
Found at i:12031 original size:19 final size:19
Alignment explanation
Indices: 12007--12138 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
11997 AATTTTTGAG
12007 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
12026 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
12045 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12064 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
12085 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
12104 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12123 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
12139 ATAATATGAT
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
19 86 0.82
21 19 0.18
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12074 original size:59 final size:57
Alignment explanation
Indices: 12007--12146 Score: 219
Period size: 59 Copynumber: 2.4 Consensus size: 57
11997 AATTTTTGAG
*
12007 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* *
12064 GATATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
*
12123 GATATGCAATCTTAGA-ATAATATG
1 GATATGCAATCTTAGATATGATATG
12147 ATTTTGTAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
56 7 0.09
57 16 0.21
59 54 0.70
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Found at i:12912 original size:25 final size:24
Alignment explanation
Indices: 12878--12935 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
12868 TACTTATTTT
*
12878 TTATTATTTTATATATGTATGTATAA
1 TTATT-TTTTATATATGTAT-AATAA
* *
12904 TTATTTTTTATGTATGTATAATTA
1 TTATTTTTTATATATGTATAATAA
12928 TTATTTTT
1 TTATTTTT
12936 CTTTATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 11 0.38
25 13 0.45
26 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (24 bp):
TTATTTTTTATATATGTATAATAA
Found at i:12917 original size:21 final size:21
Alignment explanation
Indices: 12880--12934 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 21
12870 CTTATTTTTT
12880 ATTATTTTATATATGTATGTATA
1 ATTATTTT-T-TATGTATGTATA
12903 ATTATTTTTTATGTATGTATA
1 ATTATTTTTTATGTATGTATA
12924 ATTATTATTTT
1 ATTATT-TTTT
12935 TCTTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.58
22 5 0.16
23 8 0.26
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
ATTATTTTTTATGTATGTATA
Found at i:13635 original size:98 final size:98
Alignment explanation
Indices: 13521--13717 Score: 367
Period size: 98 Copynumber: 2.0 Consensus size: 98
13511 TTTAAAATAA
* *
13521 TAAATGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAATGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
13586 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
13619 TAAATGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAATGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
13684 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
13717 T
1 T
13718 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAATGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:17258 original size:7 final size:7
Alignment explanation
Indices: 17242--17284 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
17232 GTTCAGATTC
17242 AAAA-AA
1 AAAACAA
17248 AAAACAA
1 AAAACAA
17255 AAAACAA
1 AAAACAA
17262 AAAAC-A
1 AAAACAA
17268 AAAAC-A
1 AAAACAA
17274 AAAACAA
1 AAAACAA
17281 AAAA
1 AAAA
17285 TGAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 16 0.46
7 19 0.54
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:17270 original size:19 final size:18
Alignment explanation
Indices: 17242--17284 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
17232 GTTCAGATTC
17242 AAAAAAAAAACAAAAAACA
1 AAAAAAAAAAC-AAAAACA
17261 AAAAACAAAAACAAAAACA
1 AAAAA-AAAAACAAAAACA
17280 AAAAA
1 AAAAA
17285 TGAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAAAACA
Found at i:17290 original size:13 final size:11
Alignment explanation
Indices: 17241--17284 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
17231 AGTTCAGATT
17241 CAAAAAAAAAA
1 CAAAAAAAAAA
17252 CAAAAAACAAAAAA
1 C--AAAA-AAAAAA
17266 CAAAAACAAAAA
1 CAAAAA-AAAAA
17278 CAAAAAA
1 CAAAAAA
17285 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.10
12 15 0.52
13 4 0.14
14 7 0.24
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:17295 original size:13 final size:13
Alignment explanation
Indices: 17242--17284 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
17232 GTTCAGATTC
17242 AAAAA-AAAAACA
1 AAAAACAAAAACA
17254 AAAAACAAAAA-A
1 AAAAACAAAAACA
17266 CAAAAACAAAAACA
1 -AAAAACAAAAACA
17280 AAAAA
1 AAAAA
17285 TGAAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.21
13 21 0.75
14 1 0.04
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAACAAAAACA
Found at i:18639 original size:45 final size:45
Alignment explanation
Indices: 18508--18646 Score: 126
Period size: 45 Copynumber: 3.2 Consensus size: 45
18498 TCAGTGAAAG
* *
18508 AGCAGATCTTGTCTTCCTGCATCGACAGCGAAGCAGATCGAAA-A-
1 AGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATC-AAAGAT
* * * * * * * *
18552 CGAAG-CCTTGCCTTCCT-CATTTG-TAGTGGAGCAGGTTAAAGAT
1 AGCAGATCTTGCCTTCCTGCA-TTGACAGCGAAGCAGATCAAAGAT
18595 AGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGAT
1 AGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGAT
*
18640 GGCAGAT
1 AGCAGAT
18647 TTTACCTCCC
Statistics
Matches: 70, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
41 3 0.04
42 12 0.17
43 15 0.21
44 17 0.24
45 23 0.33
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (45 bp):
AGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAGAT
Found at i:18956 original size:132 final size:132
Alignment explanation
Indices: 18626--19142 Score: 637
Period size: 132 Copynumber: 3.9 Consensus size: 132
18616 TTGACAGCGA
* * *
18626 AGCAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * ** * * *
18691 TCTACTTCCCTGGGCAGTAGTGGAATAGATTAAAGATAACAGATCTTGTCTTCCT--GCATTGAC
66 TCTACTTCCCTGGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCA--G-T
* *
18754 AGCGA
128 AGTGG
* *
18759 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
18824 TTTACTTCCCTGGGCAACAGTGGAATAGATTGAATATTTCAGATCTTTTCTCCCTAAGCAGTAGT
66 TCTACTTCCCTGGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
18889 GG
131 GG
* ** * *
18891 AGCAGATTGAAGATTACGGATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
18956 TCTACTTCCCTAGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGT
66 TCTACTTCCCTGGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
19021 GG
131 GG
* * * *
19023 AGTATATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * ** * *
19088 CCTA-TCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT
66 TCTACT-TCCCTGGGCAATAGTGGAATAGATTGAAGATT-TCAGATCTTATCTCCCT
19143 GCAGTTGCAG
Statistics
Matches: 335, Mismatches: 45, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
131 1 0.00
132 219 0.65
133 112 0.33
135 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (132 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAATAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:19022 original size:44 final size:44
Alignment explanation
Indices: 18842--19023 Score: 106
Period size: 44 Copynumber: 4.1 Consensus size: 44
18832 CCTGGGCAAC
* *
18842 AGTGGAATAGATTGAATATTTCAGATCTTTTCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
** * * * * * **
18886 AGTGGAGCAGATTGAAGATTACGGATTTTACCT-CC-ATGTGGTT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAG-T
* * * * * *
18929 ACAGTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCCTAGGCAAT
1 --AGTGGAATAGATTGAAGAT-TTCAGATCT-TATC-TCCCTAAGCAGT
*
18974 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGT
1 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
19018 AGTGGA
1 AGTGGA
19024 GTATATCGAA
Statistics
Matches: 98, Mismatches: 28, Indels: 24
0.65 0.19 0.16
Matches are distributed among these distances:
42 4 0.04
43 22 0.22
44 49 0.50
45 21 0.21
46 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
Found at i:19165 original size:265 final size:264
Alignment explanation
Indices: 18644--19167 Score: 662
Period size: 265 Copynumber: 2.0 Consensus size: 264
18634 AAAGATGGCA
* * * *
18644 GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGT
1 GATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAAT
* * * *
18709 AGTGGAATAGATTAAAGATAACAGATCTTGTCTTCCTGCATTGACAGCGAAGCAGATCGAAGATG
66 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTGAATAGACAGCGAAGCAGATCGAAGATG
* **
18774 GCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAATAATTTTACTTCCCTGGGC
131 GCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTACTTCCCTGGGC
* * * *
18839 AACAGTGGAATAGATTGAATATTTCAGATCTTTTCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
196 AACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCT-AGCAGTAGTGGAACAGATTGAAGA
18904 TTACG
260 TTACG
*
18909 GATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTCCCTAGGCAAT
1 GATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAAT
* ** * * * * *
18974 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCT-AAGTAG-TAGTGGAGTATATCGAAGAT
66 AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTGAA-TAGACAGCGAAGCAGATCGAAGAT
* * * *
19037 GGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGTCAGTAATCCTA-TCTCCTTGG
130 GGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTACT-TCCCTGG
* * * *
19101 TCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCTTATCTCCCT-GCAGTTGCAGTGGAATAGATT
194 GCAACAGTGGAATAGATTGAAGATT-TAAGATCTTATCTCCCTAGCAG-T--AGTGGAACAGATT
19164 GAAG
255 GAAG
19168 CACTAGCTCC
Statistics
Matches: 221, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
262 4 0.02
263 2 0.01
264 103 0.47
265 112 0.51
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (264 bp):
GATTTTACCTCCATGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTAGGCAAT
AGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTGAATAGACAGCGAAGCAGATCGAAGATG
GCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAATAATCCTACTTCCCTGGGC
AACAGTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAGCAGTAGTGGAACAGATTGAAGAT
TACG
Found at i:19395 original size:19 final size:19
Alignment explanation
Indices: 19371--19502 Score: 210
Period size: 19 Copynumber: 6.8 Consensus size: 19
19361 AATTTTTGAG
19371 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
19390 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
19409 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19428 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
19449 GATATGCAATCTTAGTTAT
1 GATATGCAATCTTAGATAT
**
19468 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19487 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
19503 ATATATGATT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 84 0.82
21 19 0.18
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:19438 original size:59 final size:57
Alignment explanation
Indices: 19371--19509 Score: 210
Period size: 59 Copynumber: 2.4 Consensus size: 57
19361 AATTTTTGAG
*
19371 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
* * *
19428 GATATATGCAATCTTAGATATGATATGCAATCTTAGTTATGATATATAATCTTAGATAT
1 G--ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
19487 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
19510 ATTTTGTAAT
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
55 5 0.07
56 2 0.03
57 16 0.21
59 53 0.70
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (57 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATACAATCTTAGATAT
Found at i:19665 original size:19 final size:17
Alignment explanation
Indices: 19629--19662 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19619 TCCCTTCATT
19629 GAAAAAGAAAAAAAGGA
1 GAAAAAGAAAAAAAGGA
*
19646 GAAAAAG-AGAAAAGGA
1 GAAAAAGAAAAAAAGGA
19662 G
1 G
19663 GAGGAGAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAAAAGGA
Found at i:20962 original size:98 final size:98
Alignment explanation
Indices: 20829--21025 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
20819 TTTAAAATAA
* * *
20829 TAAAGGAAATATTCCGAATTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAACGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
20894 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
20927 TAAACGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAACGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
20992 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
21025 T
1 T
21026 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAACGAAATATTCCGAATTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:45592 original size:10 final size:10
Alignment explanation
Indices: 45575--45605 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
45565 CAAATTATTA
45575 TATTTTTTTC
1 TATTTTTTTC
*
45585 TTTTTTTTTC
1 TATTTTTTTC
45595 TATTTTTTTC
1 TATTTTTTTC
45605 T
1 T
45606 GCTTTAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (10 bp):
TATTTTTTTC
Found at i:46645 original size:9 final size:10
Alignment explanation
Indices: 46631--46673 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
46621 ATTAATATCC
46631 AAAT-AAGTA
1 AAATAAAGTA
*
46640 AAATAAAATA
1 AAATAAAGTA
46650 AAATAAAGTAA
1 AAATAAAGT-A
46661 TAAATAAAGTA
1 -AAATAAAGTA
46672 AA
1 AA
46674 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 4 0.14
10 14 0.48
11 2 0.07
12 9 0.31
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (10 bp):
AAATAAAGTA
Found at i:46662 original size:27 final size:28
Alignment explanation
Indices: 46632--46684 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
46622 TTAATATCCA
* *
46632 AATAAGTAAAATAAA-ATAAAATAAAGT
1 AATAAATAAAATAAAGAAAAAATAAAGT
*
46659 AATAAATAAAGTAAAGAAAAAATAAA
1 AATAAATAAAATAAAGAAAAAATAAA
46685 AAATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.19
Consensus pattern (28 bp):
AATAAATAAAATAAAGAAAAAATAAAGT
Found at i:46664 original size:13 final size:12
Alignment explanation
Indices: 46631--46699 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 12
46621 ATTAATATCC
46631 AAATAAGTAAAAT
1 AAATAA-TAAAAT
46644 -AA-AATAAAAT
1 AAATAATAAAAT
46654 AAAGTAAT-AAAT
1 AAA-TAATAAAAT
46666 AAAGTAA-AGAAA-
1 AAA-TAATA-AAAT
46678 AAATAA-AAAAT
1 AAATAATAAAAT
46689 AAA-AATAAAAT
1 AAATAATAAAAT
46700 TGGGTTGCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
10 11 0.22
11 16 0.33
12 16 0.33
13 6 0.12
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (12 bp):
AAATAATAAAAT
Found at i:46667 original size:17 final size:16
Alignment explanation
Indices: 46644--46685 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
46634 TAAGTAAAAT
46644 AAAATAAAATAAAGTAA
1 AAAATAAAATAAAG-AA
* *
46661 TAAATAAAGTAAAGAA
1 AAAATAAAATAAAGAA
46677 AAAATAAAA
1 AAAATAAAA
46686 AATAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAGAA
Found at i:46689 original size:27 final size:27
Alignment explanation
Indices: 46631--46691 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
46621 ATTAATATCC
* *
46631 AAATAAGTAAAATAAAATAAAATAAAG
1 AAATAAATAAAATAAAAAAAAATAAAG
* *
46658 TAATAAATAAAGTAAAGAAAAAATAAA-
1 AAATAAATAAAATAAA-AAAAAATAAAG
46685 AAATAAA
1 AAATAAA
46692 AATAAAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (27 bp):
AAATAAATAAAATAAAAAAAAATAAAG
Found at i:46698 original size:12 final size:11
Alignment explanation
Indices: 46639--46698 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
46629 CCAAATAAGT
46639 AAAATAAAAT-
1 AAAATAAAATA
*
46649 AAAATAAAGTA
1 AAAATAAAATA
*
46660 ATAAATAAAGTA
1 A-AAATAAAATA
46672 AAGAA-AAAATAA
1 AA-AATAAAAT-A
46684 AAAATAAAAATA
1 AAAAT-AAAATA
46696 AAA
1 AAA
46699 TTGGGTTGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
10 9 0.21
11 8 0.19
12 20 0.48
13 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (11 bp):
AAAATAAAATA
Done.