Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015005.1 Kokia drynarioides strain JFW-HI SEQ_130049, 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: 495468
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 326 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:356282 original size:20 final size:20
Alignment explanation
Indices: 356239--356282 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
356229 AATTTTATCT
**
356239 TAAATTATAAATTTTTTATT
1 TAAATTATAAATTTTTTAAA
356259 TAAATT-TAAATTTTTTCAAA
1 TAAATTATAAATTTTTT-AAA
356279 TAAA
1 TAAA
356283 AATACTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATTATAAATTTTTTAAA
Found at i:359146 original size:28 final size:27
Alignment explanation
Indices: 359092--359163 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
359082 TTAATTAACT
* *
359092 TTTTAAAATTTAAAAAATTCAAAAAA-TA
1 TTTTAAAA--TAATAAATTAAAAAAATTA
359120 TTATTAGAAATAATAAATTAAAAAAATTA
1 TT-TTA-AAATAATAAATTAAAAAAATTA
*
359149 TTTTAAAATTATAAA
1 TTTTAAAATAATAAA
359164 AATTATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 9 0.24
28 19 0.50
29 7 0.18
30 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
TTTTAAAATAATAAATTAAAAAAATTA
Found at i:359159 original size:20 final size:20
Alignment explanation
Indices: 359134--359171 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
359124 TAGAAATAAT
359134 AAATTAAAAAAATTATTTTA
1 AAATTAAAAAAATTATTTTA
*
359154 AAATTATAAAAATTATTT
1 AAATTAAAAAAATTATTT
359172 AATATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTAAAAAAATTATTTTA
Found at i:359191 original size:28 final size:28
Alignment explanation
Indices: 359149--359202 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
359139 AAAAAAATTA
* *
359149 TTTTAAAATTATAAAAATTATTTAATAT
1 TTTTAAAATTATAAAAAATAATTAATAT
* *
359177 TTTTAATATTTTAAAAAATAATTAAT
1 TTTTAAAATTATAAAAAATAATTAAT
359203 TGTTAACATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTTTAAAATTATAAAAAATAATTAATAT
Found at i:362381 original size:51 final size:51
Alignment explanation
Indices: 362321--362424 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
362311 AAAACGAATA
362321 TAATACAATCTGGAGATAATATAAATTATTCCATTGATGAAACCATATTAC
1 TAATACAATCTGGAGATAATATAAATTATTCCATTGATGAAACCATATTAC
362372 TAATACAATCTGGAGATAATATAAATTATTCCATTGATGAAACCATATTAC
1 TAATACAATCTGGAGATAATATAAATTATTCCATTGATGAAACCATATTAC
362423 TA
1 TA
362425 TACCCAAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (51 bp):
TAATACAATCTGGAGATAATATAAATTATTCCATTGATGAAACCATATTAC
Found at i:362419 original size:26 final size:26
Alignment explanation
Indices: 362339--362419 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
362329 TCTGGAGATA
362339 ATATAAATTATTCCATTGATGAAACC
1 ATATAAATTATTCCATTGATGAAACC
* * * * * *
362365 ATATTACTAATACAATCTGGA-GATA--
1 ATATAAATTATTCCAT-T-GATGAAACC
362390 ATATAAATTATTCCATTGATGAAACC
1 ATATAAATTATTCCATTGATGAAACC
362416 ATAT
1 ATAT
362420 TACTATACCC
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 2 0.05
24 4 0.11
25 11 0.29
26 15 0.39
27 4 0.11
28 2 0.05
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (26 bp):
ATATAAATTATTCCATTGATGAAACC
Found at i:370144 original size:16 final size:16
Alignment explanation
Indices: 370123--370154 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
370113 TTTACTCTTA
370123 CTTGCATTTTCTTCGT
1 CTTGCATTTTCTTCGT
370139 CTTGCATTTTCTTCGT
1 CTTGCATTTTCTTCGT
370155 ATTTTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.12, T:0.56
Consensus pattern (16 bp):
CTTGCATTTTCTTCGT
Found at i:377844 original size:4 final size:4
Alignment explanation
Indices: 377837--377865 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
377827 AAAAAAAAAA
377837 AAAG AAAG AAAG AAAG AAAG -AAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
377866 TGAGAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:377875 original size:19 final size:18
Alignment explanation
Indices: 377831--377875 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
377821 NNNNNAAAAA
*
377831 AAAAAAAAAGAAAGAAAG
1 AAAAAAGAAGAAAGAAAG
*
377849 AAAGAAAGAAGAAAGAATG
1 AAA-AAAGAAGAAAGAAAG
377868 AGAAAAAG
1 A-AAAAAG
377876 GAAAAGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 18 0.78
20 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAGAAAGAAAG
Found at i:378049 original size:18 final size:18
Alignment explanation
Indices: 378026--378060 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
378016 GGAAGAAATG
378026 TAAGTTTGACTAATTTTT
1 TAAGTTTGACTAATTTTT
*
378044 TAAGTTTGATTAATTTT
1 TAAGTTTGACTAATTTT
378061 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (18 bp):
TAAGTTTGACTAATTTTT
Found at i:379044 original size:14 final size:15
Alignment explanation
Indices: 379025--379070 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
379015 AATCTAGCTA
379025 ATTAATTACCAAAAT
1 ATTAATTACCAAAAT
*
379040 A-TAATATA-AAAAAT
1 ATTAAT-TACCAAAAT
379054 AATTAATTACCAAAAT
1 -ATTAATTACCAAAAT
379070 A
1 A
379071 ATATCCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.36
15 7 0.28
16 9 0.36
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATTACCAAAAT
Found at i:379068 original size:16 final size:16
Alignment explanation
Indices: 379023--379072 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
379013 TAAATCTAGC
379023 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
*
379039 T-A-TAATATA-AAAAA
1 TAATTAAT-TACCAAAA
379053 TAATTAATTACCAAAA
1 TAATTAATTACCAAAA
379069 TAAT
1 TAAT
379073 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATTAATTACCAAAA
Found at i:380848 original size:45 final size:45
Alignment explanation
Indices: 380780--380916 Score: 197
Period size: 45 Copynumber: 3.0 Consensus size: 45
380770 CCCTAGATCA
*
380780 TCAAGCCAATGATATC-AGCCTCAGTTTGACGAGCCACAGCAATAC
1 TCAAGCCAAGGATATCAAG-CTCAGTTTGACGAGCCACAGCAATAC
*
380825 TCAAGCCAAGGATATCAAGCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAAGCTCAGTTTGACGAGCCACAGCAATAC
* * *
380870 TCAAGCCAAGGATATCAGGCTTAGTTTGACAAGCCACCA-CAATAC
1 TCAAGCCAAGGATATCAAGCTCAGTTTGACGAGCCA-CAGCAATAC
380915 TC
1 TC
380917 TATTCCTCCC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
45 81 0.96
46 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAAGCTCAGTTTGACGAGCCACAGCAATAC
Found at i:384314 original size:4 final size:4
Alignment explanation
Indices: 384292--384372 Score: 67
Period size: 4 Copynumber: 20.2 Consensus size: 4
384282 AACATATTAC
* * * * * *
384292 CTTT CTCT CCTT C-TT CTTT CTTT CCTCT CCTT C-TT CCTT CTTC CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
*
384339 CTTT CTTT CTTT CTTT CTTTT CTTT TTTT CTTT C
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT C
384373 CCGTTTATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
3 6 0.10
4 49 0.79
5 7 0.11
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:384321 original size:20 final size:20
Alignment explanation
Indices: 384292--384355 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
384282 AACATATTAC
384292 CTTT-CTCTCCTTCTTCTTT
1 CTTTCCTCTCCTTCTTCTTT
*
384311 CTTTCCTCTCCTTCTTCCTT
1 CTTTCCTCTCCTTCTTCTTT
* *
384331 C-TTCCTTTCTTTCTTTCTTT
1 CTTTCCTCTCCTTC-TTCTTT
384351 CTTTC
1 CTTTC
384356 TTTTCTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 14 0.37
20 21 0.55
21 3 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTCCTCTCCTTCTTCTTT
Found at i:385587 original size:8 final size:9
Alignment explanation
Indices: 385566--385592 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
385556 AATTCAAATT
385566 TTTTTTCGA
1 TTTTTTCGA
385575 TTTTTTCGA
1 TTTTTTCGA
385584 TTTTTTCGA
1 TTTTTTCGA
385593 ATAGAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (9 bp):
TTTTTTCGA
Found at i:386289 original size:168 final size:166
Alignment explanation
Indices: 385913--386317 Score: 460
Period size: 167 Copynumber: 2.4 Consensus size: 166
385903 GATACTGATC
*
385913 TTTTTTATATACAATAAAAAATGAGATTAAGTAAACCTCAAATATAAAATATTACCCAATTATAT
1 TTTTTT-TATACAATAAAAAATGAGATTAAGTAAACCTCAAATATGAAATATTACCCAATTATAT
*
385978 AAAATTGTATTGATTTACCGATTTTTTGGTGTATCGTTTTGCATATATCGTTATTTAAAAAAAAA
65 AAAATTGTATTGATTTACCGATTTTTTGGTGTATCGTTTTGAATATATCGTTATTTAAAAAAAAA
** * *
386043 TTTGATATAGGTATACAAAATATATTTGAAAATATAAA
130 TTTGA-ATAGGTATACAAAATATATTCAAAAAAAGAAA
***** * *
386081 AAAAATTATACAATAAAAAATGAGATTAGGTAAACCTCAAATATGAAATATT-GCCAATTATATA
1 TTTTTTTATACAATAAAAAATGAGATTAAGTAAACCTCAAATATGAAATATTACCCAATTATATA
* ** * ** * * **
386145 AATTTGTATTAGTACTTTTTC-TTTTTTTTTTGGTATTGTTTTGAATATATCGTCATTTTTTTAA
66 AAATTGTATT-G-A-TTTACCGATTTTTTGGT-GTATCGTTTTGAATATATCGT--TATTTAAAA
* *
386209 AAAAA-TTG-ATAGGTATATAAAATATA-TCAAAAAAAGAGA
125 AAAAATTTGAATAGGTATACAAAATATATTCAAAAAAAGAAA
*
386248 TTTTTTTATACAATAAAAAAAAGAGATTAAGTAAACCTCAAATATGAAATATTACCCAATTATAT
1 TTTTTTTATACAAT-AAAAAATGAGATTAAGTAAACCTCAAATATGAAATATTACCCAATTATAT
386313 AAAAT
65 AAAAT
386318 ATTTTTCCAA
Statistics
Matches: 195, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
166 20 0.10
167 62 0.32
168 62 0.32
169 37 0.19
170 3 0.02
171 11 0.06
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (166 bp):
TTTTTTTATACAATAAAAAATGAGATTAAGTAAACCTCAAATATGAAATATTACCCAATTATATA
AAATTGTATTGATTTACCGATTTTTTGGTGTATCGTTTTGAATATATCGTTATTTAAAAAAAAAT
TTGAATAGGTATACAAAATATATTCAAAAAAAGAAA
Found at i:389879 original size:35 final size:35
Alignment explanation
Indices: 389833--389899 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
389823 TGCTATTTAA
389833 AATGTAATACCCTCATATCCGACCCAATCATCGAG
1 AATGTAATACCCTCATATCCGACCCAATCATCGAG
389868 AATGTAATACCCTCATATCCGACCCAATCATC
1 AATGTAATACCCTCATATCCGACCCAATCATC
389900 AGGTCAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.33, G:0.09, T:0.24
Consensus pattern (35 bp):
AATGTAATACCCTCATATCCGACCCAATCATCGAG
Found at i:390415 original size:2 final size:2
Alignment explanation
Indices: 390408--390452 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
390398 CCTTTATGTG
390408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
390450 TA T
1 TA T
390453 TAGAATCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:392894 original size:7 final size:7
Alignment explanation
Indices: 392884--392910 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
392874 TAGAATATTG
392884 TATATAA
1 TATATAA
392891 TATATAA
1 TATATAA
392898 TATATAA
1 TATATAA
392905 TATATA
1 TATATA
392911 TTCTCTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:395413 original size:41 final size:41
Alignment explanation
Indices: 395356--395442 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
395346 TGTAAATGAA
395356 TATGGTGAATGGAACTGGGGGGCTCCCGATCGCTGGTTTTC
1 TATGGTGAATGGAACTGGGGGGCTCCCGATCGCTGGTTTTC
395397 TATGGTGAATGGAACTGGGGGGCTCCCGATCGCTGGTTTTC
1 TATGGTGAATGGAACTGGGGGGCTCCCGATCGCTGGTTTTC
395438 TATGG
1 TATGG
395443 AGATATTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.15, C:0.18, G:0.37, T:0.30
Consensus pattern (41 bp):
TATGGTGAATGGAACTGGGGGGCTCCCGATCGCTGGTTTTC
Found at i:395901 original size:153 final size:153
Alignment explanation
Indices: 395695--395987 Score: 586
Period size: 153 Copynumber: 1.9 Consensus size: 153
395685 TGCCAGAAGG
395695 GGTATGATTGACGATTCGAGCTGTGTTGTGTGTGGAGCTGCGCAAGAGACGATCTTGCATACACG
1 GGTATGATTGACGATTCGAGCTGTGTTGTGTGTGGAGCTGCGCAAGAGACGATCTTGCATACACG
395760 CGAGTTTGCAAAGTTGCCTCGGATTATTGAATGAAGTTGCTGCCTTCAGATGCTGTCACTATGTT
66 CGAGTTTGCAAAGTTGCCTCGGATTATTGAATGAAGTTGCTGCCTTCAGATGCTGTCACTATGTT
395825 TTTTTTTTTTCTGCAGGTCTCGA
131 TTTTTTTTTTCTGCAGGTCTCGA
395848 GGTATGATTGACGATTCGAGCTGTGTTGTGTGTGGAGCTGCGCAAGAGACGATCTTGCATACACG
1 GGTATGATTGACGATTCGAGCTGTGTTGTGTGTGGAGCTGCGCAAGAGACGATCTTGCATACACG
395913 CGAGTTTGCAAAGTTGCCTCGGATTATTGAATGAAGTTGCTGCCTTCAGATGCTGTCACTATGTT
66 CGAGTTTGCAAAGTTGCCTCGGATTATTGAATGAAGTTGCTGCCTTCAGATGCTGTCACTATGTT
395978 TTTTTTTTTT
131 TTTTTTTTTT
395988 NNNNNNNNNN
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 140 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (153 bp):
GGTATGATTGACGATTCGAGCTGTGTTGTGTGTGGAGCTGCGCAAGAGACGATCTTGCATACACG
CGAGTTTGCAAAGTTGCCTCGGATTATTGAATGAAGTTGCTGCCTTCAGATGCTGTCACTATGTT
TTTTTTTTTTCTGCAGGTCTCGA
Found at i:399256 original size:50 final size:52
Alignment explanation
Indices: 399202--399323 Score: 137
Period size: 49 Copynumber: 2.4 Consensus size: 52
399192 TCAAATCTTG
* * *
399202 TTTATTTAATTTGTTTTTTTCAAATCTA-G-TATTTTGCATAAATATAAATA-
1 TTTATTTAATTTGTTTTATTCAAAT-TATGATATTTTACATAAACATAAATAT
* *
399252 TTTATTTAACTTG-TTTGTTC-AATTATGATATTTTACATAAACATAAATAT
1 TTTATTTAATTTGTTTTATTCAAATTATGATATTTTACATAAACATAAATAT
* *
399302 TTTATTTATTTTATTTTATTCA
1 TTTATTTAATTTGTTTTATTCA
399324 TAACTTTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
47 2 0.03
48 4 0.07
49 25 0.42
50 22 0.37
51 6 0.10
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (52 bp):
TTTATTTAATTTGTTTTATTCAAATTATGATATTTTACATAAACATAAATAT
Found at i:400859 original size:21 final size:22
Alignment explanation
Indices: 400815--400865 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
400805 ATGAATTTGT
* *
400815 AAAACATTA-TTAAAATTTATA
1 AAAACATTAGATAAAATTCATA
*
400836 AAAATATTAGATAAAATTCA-A
1 AAAACATTAGATAAAATTCATA
400857 AAAACATTA
1 AAAACATTA
400866 AAGCTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAACATTAGATAAAATTCATA
Found at i:401883 original size:32 final size:32
Alignment explanation
Indices: 401847--401911 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
401837 TAAATACAAT
401847 TCACTCTAACCATGTATATACACTATTAATTA
1 TCACTCTAACCATGTATATACACTATTAATTA
401879 TCACTCTAACCATGTATATACACTATTAATTA
1 TCACTCTAACCATGTATATACACTATTAATTA
401911 T
1 T
401912 ATTACTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (32 bp):
TCACTCTAACCATGTATATACACTATTAATTA
Found at i:404051 original size:18 final size:18
Alignment explanation
Indices: 404024--404061 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
404014 GGCAAACATA
404024 TTTTTCATTTTATTCAAT
1 TTTTTCATTTTATTCAAT
*
404042 TTTTTTATTTTATTCAAT
1 TTTTTCATTTTATTCAAT
404060 TT
1 TT
404062 AATCCCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTCATTTTATTCAAT
Found at i:406259 original size:62 final size:62
Alignment explanation
Indices: 406151--406317 Score: 221
Period size: 62 Copynumber: 2.6 Consensus size: 62
406141 ATTTTTTTAA
* * *
406151 GAATTTTAGGATTTAGGTTTTAAAATTTTAGGGATTTTCGAGATTTTTAGGGTTGTTGGGTTTGG
1 GAATTTT-GG-TTTAGG-TTTAAAATTTTGGGGATTTTCGGGATTTTTAGGGTTCTTGGGTTT-G
406216 G
62 G
* *
406217 GAA-TTTGGTTTAGGTTTAAGAAATTTGGGGA-TTTCGGGATTTTTGGGGTTCTTGGGTTTGG
1 GAATTTTGGTTTAGGTTTAA-AATTTTGGGGATTTTCGGGATTTTTAGGGTTCTTGGGTTTGG
*
406278 GAATTTTGGTTTAAGTTTAAAATTTTGGGGATTTTCGGGA
1 GAATTTTGGTTTAGGTTTAAAATTTTGGGGATTTTCGGGA
406318 CTTAGGTTTC
Statistics
Matches: 91, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
61 15 0.16
62 53 0.58
63 15 0.16
64 2 0.02
65 3 0.03
66 3 0.03
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (62 bp):
GAATTTTGGTTTAGGTTTAAAATTTTGGGGATTTTCGGGATTTTTAGGGTTCTTGGGTTTGG
Found at i:408867 original size:52 final size:51
Alignment explanation
Indices: 408790--408971 Score: 195
Period size: 52 Copynumber: 3.5 Consensus size: 51
408780 AAATAGGTTT
*
408790 GATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTAAGAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTT-ACGGATTAAGAGGTCC
* * * *
408842 GATGGCTATGTGTCATTGTGAGTATACGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCC-TTACGGATTAAGAGGTCC
* * ** * * **
408894 GAAGACTATATGTCATAATGAGTATGTGATTAACAATACGGATTAA-AGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGA--ATCCTTACGGATTAAGAGGTCC
*
408946 GATGACTCTGTGTCATCGTGAGTATA
1 GATGACTATGTGTCATCGTGAGTATA
408972 AAAAAAGCAT
Statistics
Matches: 105, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
52 92 0.88
53 11 0.10
54 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (51 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTACGGATTAAGAGGTCC
Found at i:418660 original size:52 final size:52
Alignment explanation
Indices: 418582--418821 Score: 268
Period size: 52 Copynumber: 4.6 Consensus size: 52
418572 TGAATGAAAT
* * * *
418582 AGGTCTGATAACTATGTGTCATCATGAGTATATGAATCCTTCATGGATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTAAG
** * * * * **
418634 AGGTCTAATGACTATGTTTCATCATGATTATATGAATCCTTTACAAATTAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTAAG
* *
418686 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTAAG
* * * *
418738 AGGTCCGATGACTGTGCGTCATCGTGAGTATATGATTCTCAAT-ACGGATTAA-
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-C-TTCACGGATTAAG
* *
418790 AGGTCCAATGACTCTGTGTCATCGTGAGTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATA
418822 AAAAATGCAT
Statistics
Matches: 162, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
52 152 0.94
53 9 0.06
54 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATTAAG
Found at i:419511 original size:21 final size:21
Alignment explanation
Indices: 419487--419535 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
419477 TTTTAGTATT
* *
419487 GGTAGAGGTGAAACTTATATC
1 GGTAGAAGAGAAACTTATATC
**
419508 GGTAGAAGAGTCACTTATATC
1 GGTAGAAGAGAAACTTATATC
419529 GGTAGAA
1 GGTAGAA
419536 CTATCACTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.27
Consensus pattern (21 bp):
GGTAGAAGAGAAACTTATATC
Found at i:422624 original size:17 final size:17
Alignment explanation
Indices: 422582--422625 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
422572 ATATAAGAAT
*
422582 ATGGAACGTATAAATTA
1 ATGGAATGTATAAATTA
422599 ATGGAATGTATAAATTA
1 ATGGAATGTATAAATTA
*
422616 ATGGTATGTA
1 ATGGAATGTA
422626 AGTAGATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.34
Consensus pattern (17 bp):
ATGGAATGTATAAATTA
Found at i:428617 original size:30 final size:30
Alignment explanation
Indices: 428577--428642 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
428567 ACAGTTTATC
*
428577 TATGACATATGGTAAAGTAATTGATTGTAG
1 TATGATATATGGTAAAGTAATTGATTGTAG
*
428607 TATGATATATGGTAAAGTTATTGATTGTAG
1 TATGATATATGGTAAAGTAATTGATTGTAG
428637 TATGAT
1 TATGAT
428643 TACTTATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.41
Consensus pattern (30 bp):
TATGATATATGGTAAAGTAATTGATTGTAG
Found at i:433692 original size:33 final size:34
Alignment explanation
Indices: 433650--433714 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
433640 GATTAGGTAG
433650 TATTTTTCTTAATGA-AAAAATCATACACAAAAT
1 TATTTTTCTTAATGAGAAAAATCATACACAAAAT
433683 TATTTTTCTTAATGAGAAAAATCATACACAAA
1 TATTTTTCTTAATGAGAAAAATCATACACAAA
433715 CATGGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 15 0.48
34 16 0.52
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (34 bp):
TATTTTTCTTAATGAGAAAAATCATACACAAAAT
Found at i:442042 original size:24 final size:23
Alignment explanation
Indices: 442015--442066 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
442005 GTAATTTAAA
*
442015 ACAAAACATTATGGCAGGAGAGTT
1 ACAAAACATAATGGC-GGAGAGTT
442039 AC-AAACATAATGGCGGAGAGTT
1 ACAAAACATAATGGCGGAGAGTT
442061 ACAAAA
1 ACAAAA
442067 TAATAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
23 14 0.54
24 2 0.08
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.17
Consensus pattern (23 bp):
ACAAAACATAATGGCGGAGAGTT
Found at i:442059 original size:22 final size:23
Alignment explanation
Indices: 442018--442070 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
442008 ATTTAAAACA
*
442018 AAACATTATGGCAGGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
442041 AAACATAATGGC-GGAGAGTTAC
1 AAACATAATGGCAGGAGAGTTAC
442063 AAA-ATAAT
1 AAACATAAT
442071 AATAACTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 5 0.17
22 13 0.45
23 11 0.38
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (23 bp):
AAACATAATGGCAGGAGAGTTAC
Found at i:448942 original size:35 final size:35
Alignment explanation
Indices: 448896--448967 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 35
448886 AAAAGTTGAT
448896 AAAATTAT-AAAAAAAAAAAAAAAATTAGGGTTAA
1 AAAATTATAAAAAAAAAAAAAAAAATTAGGGTTAA
448930 NAAAATTATAAAAAAAAAAAAAAAAAATTAGGGTTAA
1 -AAAATTAT-AAAAAAAAAAAAAAAAATTAGGGTTAA
448967 A
1 A
448968 GGAGAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 8 0.23
36 1 0.03
37 26 0.74
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.19
Consensus pattern (35 bp):
AAAATTATAAAAAAAAAAAAAAAAATTAGGGTTAA
Found at i:450231 original size:54 final size:54
Alignment explanation
Indices: 450164--450293 Score: 163
Period size: 54 Copynumber: 2.4 Consensus size: 54
450154 TAATCAAGTT
* * * * * * *
450164 GATATCTAGTTAATTTATTATATCAATTCAATCAAAGGTTTTATTAATAATATA
1 GATATCCAATTAATTTATGACACCAAATCAATCAAAGATTTTATTAATAATATA
*
450218 GATA-CACAATTAATCTATGACACCAAATCAATCAAAGATTTTATTAATAATATA
1 GATATC-CAATTAATTTATGACACCAAATCAATCAAAGATTTTATTAATAATATA
*
450272 GATATCCAATTAACTTATGACA
1 GATATCCAATTAATTTATGACA
450294 TTAACTCAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.02
54 62 0.97
55 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (54 bp):
GATATCCAATTAATTTATGACACCAAATCAATCAAAGATTTTATTAATAATATA
Found at i:450304 original size:54 final size:54
Alignment explanation
Indices: 450191--450293 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
450181 TTATATCAAT
*
450191 TCAATCAAAGGTTTTATTAATAATATAGATACACAATTAATCTATGACACCAAA
1 TCAATCAAAGATTTTATTAATAATATAGATACACAATTAATCTATGACACCAAA
450245 TCAATCAAAGATTTTATTAATAATATAGATATC-CAATTAA-CTTATGACA
1 TCAATCAAAGATTTTATTAATAATATAGATA-CACAATTAATC-TATGACA
450294 TTAACTCAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
53 1 0.02
54 44 0.96
55 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (54 bp):
TCAATCAAAGATTTTATTAATAATATAGATACACAATTAATCTATGACACCAAA
Found at i:456929 original size:18 final size:17
Alignment explanation
Indices: 456896--456929 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
456886 AAATTAATTT
456896 AATATAATTATAAATAA
1 AATATAATTATAAATAA
*
456913 AATATATATTTTAAATA
1 AATATA-ATTATAAATA
456930 CTTTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATATAATTATAAATAA
Found at i:460139 original size:22 final size:22
Alignment explanation
Indices: 460095--460140 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
460085 TAGAATCTTG
* *
460095 AAAACTTAAATTTATTAACATT
1 AAAAATTAAATTTATCAACATT
460117 AAAAATTAAATTTCATCAA-ATT
1 AAAAATTAAATTT-ATCAACATT
460139 AA
1 AA
460141 TCTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATTAAATTTATCAACATT
Found at i:460769 original size:29 final size:30
Alignment explanation
Indices: 460717--460777 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
460707 AAAATAAAAG
*
460717 TATAAAAATTGAATTTCAAATTTTAATAAA
1 TATAAAAATTGAATTACAAATTTTAATAAA
* * *
460747 TATAAAAATT-TATTACATATTTTAATGAA
1 TATAAAAATTGAATTACAAATTTTAATAAA
460776 TA
1 TA
460778 ACAATAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
TATAAAAATTGAATTACAAATTTTAATAAA
Found at i:465926 original size:56 final size:56
Alignment explanation
Indices: 465837--465952 Score: 223
Period size: 56 Copynumber: 2.1 Consensus size: 56
465827 TCACTTTAAT
465837 AATTAATCTTTCGATTGACGAGTTGACAATAATTGGAGATACTAATATTAACATGA
1 AATTAATCTTTCGATTGACGAGTTGACAATAATTGGAGATACTAATATTAACATGA
*
465893 AATTAATCTTTCGATTGACGAGTTGACAGTAATTGGAGATACTAATATTAACATGA
1 AATTAATCTTTCGATTGACGAGTTGACAATAATTGGAGATACTAATATTAACATGA
465949 AATT
1 AATT
465953 GTTATCATTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (56 bp):
AATTAATCTTTCGATTGACGAGTTGACAATAATTGGAGATACTAATATTAACATGA
Found at i:467147 original size:16 final size:16
Alignment explanation
Indices: 467118--467153 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
467108 TTATTATAAC
467118 TTTATTTTGCTTTTAA
1 TTTATTTTGCTTTTAA
467134 TTTATGTTTG-TTTTAA
1 TTTAT-TTTGCTTTTAA
467150 TTTA
1 TTTA
467154 CATGATACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.69
Consensus pattern (16 bp):
TTTATTTTGCTTTTAA
Found at i:467531 original size:18 final size:18
Alignment explanation
Indices: 467508--467562 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
467498 ATTTGTTTTT
467508 TTATTAATTTATAATTTA
1 TTATTAATTTATAATTTA
* *
467526 TTATTAAATTA-AAATTA
1 TTATTAATTTATAATTTA
**
467543 AAATTATATTTAT-ATTTA
1 TTATTA-ATTTATAATTTA
467561 TT
1 TT
467563 TTATACTGCC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTAATTTATAATTTA
Found at i:474332 original size:18 final size:18
Alignment explanation
Indices: 474311--474345 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
474301 CAGAATTCAG
*
474311 CTCTTTTTCATTCTTTTT
1 CTCTCTTTCATTCTTTTT
*
474329 CTCTCTTTCCTTCTTTT
1 CTCTCTTTCATTCTTTT
474346 AAAAAGACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
CTCTCTTTCATTCTTTTT
Found at i:475606 original size:29 final size:29
Alignment explanation
Indices: 475543--475623 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 29
475533 TAAAAATTAT
* * *
475543 ACATAAATTTTGATTTAATGTGTAATTTGAT
1 ACATAAATTTTAATTT--GGTGTAATTTGAC
475574 ACATAAATTTTAATTTGGTGTAATTAT-AC
1 ACATAAATTTTAATTTGGTGTAATT-TGAC
*
475603 ACATGAAACTTTAATTGTGGT
1 ACAT-AAATTTTAATT-TGGT
475624 TCAAATGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 13 0.30
30 11 0.26
31 19 0.44
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (29 bp):
ACATAAATTTTAATTTGGTGTAATTTGAC
Found at i:475618 original size:30 final size:30
Alignment explanation
Indices: 475574--475650 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
475564 GTAATTTGAT
* *
475574 ACAT-AAATTTTAATTTGGTGT-AATTATAC
1 ACATGAAACTTTAATTTGGT-TCAAATATAC
* *
475603 ACATGAAACTTTAATTGTGGTTCAAATGTAT
1 ACATGAAACTTTAATT-TGGTTCAAATATAC
*
475634 ATATGAAACTTTAATTT
1 ACATGAAACTTTAATTT
475651 TGATCTAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.10
30 12 0.30
31 24 0.60
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.43
Consensus pattern (30 bp):
ACATGAAACTTTAATTTGGTTCAAATATAC
Found at i:476412 original size:16 final size:17
Alignment explanation
Indices: 476381--476413 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
476371 TACGAATGAA
*
476381 ATTTTTTATAATATTTT
1 ATTTTTTATAACATTTT
476398 ATTTTTTA-AACATTTT
1 ATTTTTTATAACATTTT
476414 TATAATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTATAACATTTT
Found at i:476726 original size:8 final size:7
Alignment explanation
Indices: 476693--476723 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
476683 ATTCATACTT
476693 AAACAAA
1 AAACAAA
476700 AAACAAA
1 AAACAAA
476707 AAACAAA
1 AAACAAA
476714 AAACAAA
1 AAACAAA
476721 AAA
1 AAA
476724 ACATCCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACAAA
Found at i:480066 original size:177 final size:177
Alignment explanation
Indices: 479748--480102 Score: 516
Period size: 177 Copynumber: 2.0 Consensus size: 177
479738 AATAAAATAT
* *
479748 TATTTAAATACGTGGAACAATGACACGAGTCATGTAGGTATACTGGACGAGCTTGAAGATATCAA
1 TATTTAAATACGTGAAACAATGACACGAGTCATGTAGGTATACTGAACGAGCTTGAAGATATCAA
* * * *
479813 ACTATTGTTAGATTAACGATCAGAAGCTGAGGTTAGTTTTTGAAATTTTCAATTATACAATATTT
66 ACTATTGTTAGATCAACGATCAGAAGCCGAGATTAGTTTTTGAAATTTTCAATGATACAATATTT
* * *
479878 ACATAAGGATTTGAAATTTAATA-TAGGGTACGTAATAGAATTTATAA
131 ACATAAGGATTTGAAATTTAATATTA-GGTACATAATAAAACTTATAA
* * * * *
479925 TATTTGAATAGGTGAAACAATGACGTC-AGTCATGTGGGTATACTGAATGAGCTTGAAGATATCA
1 TATTTAAATACGTGAAACAATGAC-ACGAGTCATGTAGGTATACTGAACGAGCTTGAAGATATCA
* * *
479989 AGCTATTGTTAGATCAATGATCAGAAGCCGAGATTAGTTTTTGAAATTTTCAATGATATAATATT
65 AACTATTGTTAGATCAACGATCAGAAGCCGAGATTAGTTTTTGAAATTTTCAATGATACAATATT
*
480054 TACATGAGGATTTGAAATTTAATATTAGGTACATAATAAAACTTATAA
130 TACATAAGGATTTGAAATTTAATATTAGGTACATAATAAAACTTATAA
480102 T
1 T
480103 TTCATACTGT
Statistics
Matches: 158, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
177 155 0.98
178 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (177 bp):
TATTTAAATACGTGAAACAATGACACGAGTCATGTAGGTATACTGAACGAGCTTGAAGATATCAA
ACTATTGTTAGATCAACGATCAGAAGCCGAGATTAGTTTTTGAAATTTTCAATGATACAATATTT
ACATAAGGATTTGAAATTTAATATTAGGTACATAATAAAACTTATAA
Found at i:481053 original size:10 final size:10
Alignment explanation
Indices: 481038--481062 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
481028 TCAAGATGAA
481038 GGTGGCGTGG
1 GGTGGCGTGG
481048 GGTGGCGTGG
1 GGTGGCGTGG
481058 GGTGG
1 GGTGG
481063 AGGTGAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.72, T:0.20
Consensus pattern (10 bp):
GGTGGCGTGG
Found at i:486169 original size:17 final size:17
Alignment explanation
Indices: 486147--486181 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
486137 CCATATCTAC
486147 TTTGAAAGGCTCTTCAA
1 TTTGAAAGGCTCTTCAA
*
486164 TTTGAAAGGTTCTTCAA
1 TTTGAAAGGCTCTTCAA
486181 T
1 T
486182 CCCAAGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (17 bp):
TTTGAAAGGCTCTTCAA
Found at i:494233 original size:2 final size:2
Alignment explanation
Indices: 494226--494259 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
494216 AAGAAATACG
494226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494260 TTCTTAGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.