Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold440
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: 783396
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 6
Found at i:120860 original size:2 final size:2
Alignment explanation
Indices: 120853--120893 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
120843 ACATTAATTC
120853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
120894 GCTGCTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:120961 original size:21 final size:21
Alignment explanation
Indices: 120937--120977 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
120927 TCCTGGAGGG
*
120937 CCACCGGGAGGTCCAGGTGGA
1 CCACCAGGAGGTCCAGGTGGA
* *
120958 CCACCAGGCGGTCCGGGTGG
1 CCACCAGGAGGTCCAGGTGG
120978 TCCTGGTGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.32, G:0.44, T:0.10
Consensus pattern (21 bp):
CCACCAGGAGGTCCAGGTGGA
Found at i:121010 original size:33 final size:33
Alignment explanation
Indices: 120973--121052 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
120963 AGGCGGTCCG
* *
120973 GGTGGTCCTGGTGGTGGGGCAGCATAAGGAAAA
1 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
121006 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
1 GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
121039 GGTGGGCCGGGTGG
1 GGTGGGCCGGGTGG
121053 AGGTGGAGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.20, C:0.12, G:0.53, T:0.15
Consensus pattern (33 bp):
GGTGGGCCGGGTGGTGGGGCAGCATAAGGAAAA
Found at i:121099 original size:24 final size:24
Alignment explanation
Indices: 121046--121109 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
121036 AAAGGTGGGC
121046 CGGGTGGAGGTGGAGCAAGTGCGA
1 CGGGTGGAGGTGGAGCAAGTGCGA
** *
121070 TAGGTGGAGGTGGAGCAGGTGCGA
1 CGGGTGGAGGTGGAGCAAGTGCGA
* *
121094 CGGGTGGTGGAGGAGC
1 CGGGTGGAGGTGGAGC
121110 TGGAGCAGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.11, G:0.56, T:0.14
Consensus pattern (24 bp):
CGGGTGGAGGTGGAGCAAGTGCGA
Found at i:121444 original size:24 final size:22
Alignment explanation
Indices: 121412--121465 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
121402 ACTTTAGTTA
*
121412 AATTATTATTAAATTAATGAAAAAT
1 AATTTTTATTAAA-T-AT-AAAAAT
*
121437 -ATTTTTATTTAATATAAAAAT
1 AATTTTTATTAAATATAAAAAT
121458 AATTTTTA
1 AATTTTTA
121466 AATATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.23
22 9 0.35
23 1 0.04
24 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTTTTATTAAATATAAAAAT
Found at i:122304 original size:45 final size:45
Alignment explanation
Indices: 122240--122329 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
122230 GAGCTCCAGG
*
122240 TCCAGGACCGCCTGGTCCAGGAGGACCCCAACCACCAGGACCTCC
1 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
*
122285 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGTCCTCC
1 TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
122330 AGGTCCCGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.22, C:0.44, G:0.24, T:0.09
Consensus pattern (45 bp):
TCCAGGACCGCCAGGTCCAGGAGGACCCCAACCACCAGGACCTCC
Found at i:125324 original size:2 final size:2
Alignment explanation
Indices: 125317--125391 Score: 116
Period size: 2 Copynumber: 38.0 Consensus size: 2
125307 ATCTTCCTTC
125317 AT AT AT AT 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 AT AT AT AT
* * *
125359 AT AT AT AT AT AT -T CT AC CT 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
125392 GCGCTTCATT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:129383 original size:2 final size:2
Alignment explanation
Indices: 129376--129405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
129366 TATTGATCCC
129376 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
129406 ATATAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:129797 original size:56 final size:56
Alignment explanation
Indices: 129702--129837 Score: 229
Period size: 56 Copynumber: 2.4 Consensus size: 56
129692 TTCACACCCG
* *
129702 AGTCCGAGTAACTTAA-ATGCCATGTGTCATTTTTTCTGGTCAAAGAACAATTCCCA
1 AGTCTGAGTAAC-TAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
129758 AGTCTGAGTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
1 AGTCTGAGTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
*
129814 AGTTTGAGTAACTAAGATGCCATG
1 AGTCTGAGTAACTAAGATGCCATG
129838 ATGGTTAAGT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 3 0.04
56 73 0.96
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (56 bp):
AGTCTGAGTAACTAAGATGCCATGTGTCATTTTTACTGGTCAAAGAACAATTCCCA
Found at i:130204 original size:170 final size:166
Alignment explanation
Indices: 129917--130256 Score: 468
Period size: 170 Copynumber: 2.0 Consensus size: 166
129907 GAGCAGAAGA
* *
129917 CAAGCCACAAAGACATTACACACCTTTGTGCAAATCTTCAAGAGAAAACATTATTTATTAACAAG
1 CAAGCCACAAAGACATTACACACCTTTGTACAAATCTTCAAGAGAAAACATTAATTATTAACAAG
* * *
129982 GTAAAACTATATCATCAAGATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGGTCTTAG
66 GT--AACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTCTTAA
* * *
130047 AAACAAGCCCCGAACAATGTTTATTTGACCATTGAAAC
129 AAACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
*
130085 CAAGCCACAAAGACATTACACGCCATTT-TACAAATCTTCAAGAGAAAACATAACTAAAATTATT
1 CAAGCCACAAAGACATTACACACC-TTTGTACAAATCTTCAAGAGAAAACAT---T--AATTATT
** * *
130149 AATGAGGT-ACTATATCATCAAAATTTTATGAGTTTCAGTAATCCGAACTGGATAAACTATGCTC
60 AACAAGGTAACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTC
*
130213 TTAAAAACAAGCCCTAAACAATATTAATTTGACCATTGAAAC
125 TTAAAAACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
130255 CA
1 CA
130257 GACTGAAAAC
Statistics
Matches: 152, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
168 45 0.30
169 3 0.02
170 91 0.60
171 1 0.01
173 12 0.08
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (166 bp):
CAAGCCACAAAGACATTACACACCTTTGTACAAATCTTCAAGAGAAAACATTAATTATTAACAAG
GTAACTATATCATCAAAATTTTATGAGTTTCAGTAATCCAAACCGGATAAACTATGCTCTTAAAA
ACAAGCCCCAAACAATATTAATTTGACCATTGAAAC
Found at i:138761 original size:26 final size:25
Alignment explanation
Indices: 138732--138781 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
138722 TTCAAATTAA
138732 ATTATTTTAAATTTT-TATTTATTTTT
1 ATTATTTT-AATTTTATA-TTATTTTT
*
138758 ATTATTTTGATTTTATATTATTTT
1 ATTATTTTAATTTTATATTATTTT
138782 AAATTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (25 bp):
ATTATTTTAATTTTATATTATTTTT
Found at i:138778 original size:16 final size:15
Alignment explanation
Indices: 138752--138781 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
138742 ATTTTTATTT
138752 ATTTTTATTATTTTG
1 ATTTTTATTATTTTG
138767 ATTTTATATTATTTT
1 ATTTT-TATTATTTT
138782 AAATTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
ATTTTTATTATTTTG
Found at i:138865 original size:22 final size:21
Alignment explanation
Indices: 138834--138875 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
138824 TTCATATTAT
138834 TTTAAATTTGAGTCAATTAAG
1 TTTAAATTTGAGTCAATTAAG
*
138855 TTTAACATTTGAGTTAATTAA
1 TTTAA-ATTTGAGTCAATTAA
138876 TCTTGAGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTAAATTTGAGTCAATTAAG
Found at i:139327 original size:29 final size:27
Alignment explanation
Indices: 139295--139357 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
139285 ATGTATTCGT
* *
139295 ATTATATTTATATATTTTATTATATTATA
1 ATTAAATTTAAATATTTTA-TAT-TTATA
139324 ATTAAATTTAAATATTTTATATTTAT-
1 ATTAAATTTAAATATTTTATATTTATA
139350 A-TAAATTT
1 ATTAAATTT
139358 CGATACATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 4 0.12
28 3 0.09
29 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTAAATTTAAATATTTTATATTTATA
Found at i:139427 original size:20 final size:20
Alignment explanation
Indices: 139378--139427 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
139368 GTAAATCATA
* *
139378 TTATGTTATA-TTTATATAT
1 TTATATTATATTTTAAATAT
*
139397 TTATATAATATTTTAAATAT
1 TTATATTATATTTTAAATAT
139417 TT-TATTTATAT
1 TTATA-TTATAT
139428 CATATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATATTATATTTTAAATAT
Found at i:139568 original size:29 final size:31
Alignment explanation
Indices: 139516--139579 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
139506 ATATTCGATT
* * *
139516 AAATTTTATTTTTTAAATTTAAATTTAATTA
1 AAATATTATTTTTTAAATTAAAATTAAATTA
*
139547 AAATATTA-TTTTT-AATTAAAATTAAATTT
1 AAATATTATTTTTTAAATTAAAATTAAATTA
139576 AAAT
1 AAAT
139580 TTAACTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.59
30 5 0.17
31 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
AAATATTATTTTTTAAATTAAAATTAAATTA
Found at i:139583 original size:18 final size:16
Alignment explanation
Indices: 139528--139577 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
139518 ATTTTATTTT
*
139528 TTAAATTTAAATTTAA
1 TTAAAATTAAATTTAA
**
139544 TTAAAATATTATTTTTAA
1 TT-AAA-ATTAAATTTAA
139562 TTAAAATTAAATTTAA
1 TTAAAATTAAATTTAA
139578 ATTTAACTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 11 0.41
17 6 0.22
18 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAATTAAATTTAA
Found at i:145590 original size:2 final size:2
Alignment explanation
Indices: 145583--145621 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
145573 GAAAAACAAA
145583 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
145622 ATCTGTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:146681 original size:24 final size:23
Alignment explanation
Indices: 146654--146737 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 23
146644 AATATGATAC
146654 AAAAATTA-AAATATAAAGTAATAT
1 AAAAATTATAAATATAAA-TAAT-T
*
146678 AAAAA-TATAAATATAAATATTTT
1 AAAAATTATAAATATAAATA-ATT
*
146701 AAAATTTATATAATATAAATAATT
1 AAAAATTATA-AATATAAATAATT
146725 AAAATATTA-AAAT
1 AAAA-ATTATAAAT
146738 TTATTATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 12 0.24
24 26 0.51
25 13 0.25
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
AAAAATTATAAATATAAATAATT
Found at i:146764 original size:33 final size:32
Alignment explanation
Indices: 146681--146751 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
146671 GTAATATAAA
*
146681 AATATAAAT-A-TAAATATTTTAAAATTTATAT
1 AATATAAATAATTAAA-ATATTAAAATTTATAT
146712 AATATAAATAATTAAAATATTAAAATTTAT-T
1 AATATAAATAATTAAAATATTAAAATTTATAT
146743 ATATATAAA
1 A-ATATAAA
146752 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 11 0.31
32 21 0.58
33 4 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AATATAAATAATTAAAATATTAAAATTTATAT
Found at i:146916 original size:3 final size:3
Alignment explanation
Indices: 146908--146936 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
146898 AATTCATTAT
146908 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
146937 TTAGGTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:147993 original size:19 final size:20
Alignment explanation
Indices: 147966--148004 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
147956 TATTTAAATA
147966 TAATAAAAA-TATACAATTT
1 TAATAAAAATTATACAATTT
*
147985 TAATTAAAATTATACAATTT
1 TAATAAAAATTATACAATTT
148005 AAAGACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATAAAAATTATACAATTT
Found at i:149178 original size:22 final size:19
Alignment explanation
Indices: 149149--149189 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 19
149139 ATATTTTTTA
149149 AAATTTAATTATAAAATATAT
1 AAATTTAA-TATAAAA-ATAT
149170 AAATATTAATATAAAAATAT
1 AAAT-TTAATATAAAAATAT
149190 CTTTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTTAATATAAAAATAT
Found at i:152314 original size:13 final size:12
Alignment explanation
Indices: 152297--152339 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
152287 AGCTAAGATT
152297 TTTATATTTTTA
1 TTTATATTTTTA
*
152309 TTT-TATTTTAA
1 TTTATATTTTTA
*
152320 TTTAAAATTTTTA
1 TTT-ATATTTTTA
152333 TTTATAT
1 TTTATAT
152340 AATATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTATATTTTTA
Found at i:152329 original size:24 final size:23
Alignment explanation
Indices: 152302--152374 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
152292 AGATTTTTAT
* *
152302 ATTTTTATTTTATTTTAATTTAAA
1 ATTTTTATTTTA-TATAATATAAA
152326 ATTTTTA-TTTATATAATATAAA
1 ATTTTTATTTTATATAATATAAA
* *
152348 ATTATTTAATTTTA-ATTATAAAAA
1 ATT-TTT-ATTTTATATAATATAAA
152372 ATT
1 ATT
152375 AATTTTTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 12 0.29
23 7 0.17
24 19 0.45
25 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTTTATTTTATATAATATAAA
Found at i:152367 original size:22 final size:21
Alignment explanation
Indices: 152310--152370 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
152300 ATATTTTTAT
152310 TTTATTTTAATT-TAAAATT-
1 TTTATTTTAATTATAAAATTA
*
152329 TTTATTTATATAATATAAAATTA
1 TTTATTT-TA-ATTATAAAATTA
152352 TTTAATTTTAATTATAAAA
1 TTT-ATTTTAATTATAAAA
152371 AATTAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 7 0.20
20 2 0.06
21 2 0.06
22 15 0.43
23 5 0.14
24 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATTTTAATTATAAAATTA
Found at i:152375 original size:24 final size:22
Alignment explanation
Indices: 152310--152385 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 22
152300 ATATTTTTAT
152310 TTTATTTTAATT-T-AAAATT-
1 TTTATTTTAATTATAAAAATTA
*
152329 TTTA-TTTATATAATATAAAATTA
1 TTTATTTTA-ATTATA-AAAATTA
152352 TTTAATTTTAATTATAAAAAATTA
1 TTT-ATTTTAATTAT-AAAAATTA
*
152376 ATT-TTTTAAT
1 TTTATTTTAAT
152386 ATTATTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.09
19 6 0.13
20 1 0.02
22 13 0.28
23 3 0.07
24 14 0.30
25 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATTTTAATTATAAAAATTA
Found at i:152386 original size:43 final size:43
Alignment explanation
Indices: 152306--152387 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
152296 TTTTATATTT
* ** *
152306 TTATTTTATTTTAATTTAAAATTTTTATTTATATAATATAAAA
1 TTATTTAATTTTAATTTAAAAAATTAATTTATATAATATAAAA
*
152349 TTATTTAATTTTAATTATAAAAAATTAATTT-TTTAATAT
1 TTATTTAATTTTAATT-TAAAAAATTAATTTATATAATAT
152388 TATTTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 22 0.67
44 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (43 bp):
TTATTTAATTTTAATTTAAAAAATTAATTTATATAATATAAAA
Found at i:152984 original size:18 final size:15
Alignment explanation
Indices: 152953--152999 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
152943 AATATATGTG
*
152953 TTAAAATTTATATAA
1 TTAAATTTTATATAA
152968 TTAATATTATTAT-TATA
1 TTAA-ATT-TTATATA-A
152985 TTAAATTTTATATAA
1 TTAAATTTTATATAA
153000 ATATATTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 9 0.33
16 9 0.33
17 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:165282 original size:12 final size:11
Alignment explanation
Indices: 165256--165280 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
165246 ATCAAATTGG
165256 AAACAAAAAAA
1 AAACAAAAAAA
165267 AAACAAAAAAA
1 AAACAAAAAAA
165278 AAA
1 AAA
165281 ACCCATTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAACAAAAAAA
Found at i:166893 original size:24 final size:24
Alignment explanation
Indices: 166866--166927 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 24
166856 TAAAATTTAA
166866 ATATTTAATTTTTAA-TATTTAAAT
1 ATATTTAATTTTTAATTA-TTAAAT
*
166890 ATATATT--TTTATTAATTATTAACT
1 ATAT-TTAATTT-TTAATTATTAAAT
*
166914 ATATTTAATATTTA
1 ATATTTAATTTTTA
166928 TTTAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
23 5 0.16
24 20 0.65
25 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATTTAATTTTTAATTATTAAAT
Found at i:166899 original size:22 final size:22
Alignment explanation
Indices: 166824--166900 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
166814 AATTATTTTT
166824 TATAT-ATTTTTAAAAATTT-AA
1 TATATAATTTTT-AAAATTTAAA
* **
166845 TTTATAATTAATAAAATTTAAA
1 TATATAATTTTTAAAATTTAAA
* *
166867 TATTTAATTTTTAATATTTAAA
1 TATATAATTTTTAAAATTTAAA
166889 TATAT-ATTTTTA
1 TATATAATTTTTA
166901 TTAATTATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 18 0.40
22 27 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATAATTTTTAAAATTTAAA
Found at i:167164 original size:10 final size:10
Alignment explanation
Indices: 167138--167275 Score: 58
Period size: 10 Copynumber: 13.8 Consensus size: 10
167128 TATTTATTCG
167138 TATTATA-TT
1 TATTATATTT
167147 TA-TATATTT
1 TATTATATTT
167156 TATTATATTT
1 TATTATATTT
*
167166 TAATCATA-TT
1 T-ATTATATTT
**
167176 TAAAATATTT
1 TATTATATTT
167186 TA-TATAATTT
1 TATTAT-ATTT
*
167196 TAATATATTT
1 TATTATATTT
*
167206 T-TAATATTAT
1 TATTATATT-T
*
167216 TATATAAATTT
1 TAT-TATATTT
* * *
167227 T-TAAAAATT
1 TATTATATTT
167236 TA-TATATTT
1 TATTATATTT
*
167245 ATATTATTTTT
1 -TATTATATTT
167256 TAATTACT-TTT
1 T-ATTA-TATTT
167267 ATATTATAT
1 -TATTATAT
167276 AATTATATCA
Statistics
Matches: 99, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
8 4 0.04
9 27 0.27
10 33 0.33
11 29 0.29
12 6 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTATATTT
Found at i:167207 original size:11 final size:10
Alignment explanation
Indices: 167148--167212 Score: 71
Period size: 10 Copynumber: 6.4 Consensus size: 10
167138 TATTATATTT
167148 ATATATTTTA
1 ATATATTTTA
*
167158 TTATATTTTA
1 ATATATTTTA
167168 ATCATA-TTTA
1 AT-ATATTTTA
*
167178 AAATATTTT-
1 ATATATTTTA
167187 ATATAATTTTA
1 ATAT-ATTTTA
167198 ATATATTTTTA
1 ATATA-TTTTA
167209 ATAT
1 ATAT
167213 TATTATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 6 0.13
10 24 0.52
11 16 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATATTTTA
Found at i:167219 original size:30 final size:29
Alignment explanation
Indices: 167141--167254 Score: 112
Period size: 30 Copynumber: 3.9 Consensus size: 29
167131 TTATTCGTAT
167141 TATATTTAT-ATATTTTAT-TATATTTTAA
1 TATATTTATAATATTTTATATA-ATTTTAA
*
167169 TCATATTTAAAATATTTTATATAATTTTAA
1 T-ATATTTATAATATTTTATATAATTTTAA
*
167199 TATATTTTTAATATTATTATATAAATTTTTAA
1 TATATTTATAATATT-TTATAT-AA-TTTTAA
* *
167231 -AAATTTAT-ATA-TTTATATTATTTT
1 TATATTTATAATATTTTATATAATTTT
167255 TTAATTACTT
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.05
27 1 0.01
28 7 0.09
29 20 0.27
30 26 0.35
31 10 0.14
32 6 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TATATTTATAATATTTTATATAATTTTAA
Found at i:167540 original size:28 final size:25
Alignment explanation
Indices: 167497--167558 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 25
167487 ATTAAAAAGT
*
167497 TTTAAATTTTAAATTTGTTTATATTTAAA
1 TTTAAA-TTTAAATTTATTTA-ATTT--A
167526 TTTAAATTTAAATTTATTTAATTTA
1 TTTAAATTTAAATTTATTTAATTTA
167551 TTTAAATT
1 TTTAAATT
167559 ATTTATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 9 0.28
27 4 0.12
28 13 0.41
29 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAAATTTAAATTTATTTAATTTA
Found at i:167550 original size:9 final size:9
Alignment explanation
Indices: 167531--167571 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
167521 TTAAATTTAA
167531 ATTTAAATTT
1 ATTT-AATTT
167541 ATTTAATTT
1 ATTTAATTT
*
167550 ATTTAAATT
1 ATTTAATTT
167559 ATTTATATTT
1 ATTTA-ATTT
167569 ATT
1 ATT
167572 ATTTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 18 0.64
10 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
ATTTAATTT
Found at i:167555 original size:19 final size:19
Alignment explanation
Indices: 167531--167571 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
167521 TTAAATTTAA
167531 ATTTAAATTTATTTA-ATTT
1 ATTTAAA-TTATTTATATTT
167550 ATTTAAATTATTTATATTT
1 ATTTAAATTATTTATATTT
167569 ATT
1 ATT
167572 ATTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTAAATTATTTATATTT
Found at i:167573 original size:22 final size:23
Alignment explanation
Indices: 167504--167581 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 23
167494 AGTTTTAAAT
* *
167504 TTTAAATTTGTTTATATTTA-AA
1 TTTAAATTTATTTATATTTATTA
*
167526 TTTAAATTTAAATTTAT-TTAATTTA
1 TTTAAATTT--ATTTATATTTA-TTA
167551 TTTAAA-TTATTTATATTTATTA
1 TTTAAATTTATTTATATTTATTA
167573 TTTATAATT
1 TTTA-AATT
167582 AATAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
22 22 0.49
23 8 0.18
24 8 0.18
25 7 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (23 bp):
TTTAAATTTATTTATATTTATTA
Found at i:168412 original size:23 final size:23
Alignment explanation
Indices: 168338--168489 Score: 84
Period size: 23 Copynumber: 6.6 Consensus size: 23
168328 TTTTAGCATG
* * *
168338 ATATGAAAAAATAATATAATTAT
1 ATATAAAAAAATAACATAAATAT
*
168361 ACTATAAAAGATAAT-ACGA-ATATAGT
1 A-TATAAAA-A-AATAAC-ATAAATA-T
168387 ATATAAAAAAATAACATAAATAT
1 ATATAAAAAAATAACATAAATAT
* * *
168410 ATATTAAAAAACAACATAAATACG
1 ATATAAAAAAATAACATAAATA-T
* *
168434 ATA-CAAAAAATAACATGAATAT
1 ATATAAAAAAATAACATAAATAT
*
168456 A-A-AACAAAA-AACATGAACATA-
1 ATATAAAAAAATAACAT-AA-ATAT
*
168477 ATATGAAAAAATA
1 ATATAAAAAAATA
168490 TTACGACCAC
Statistics
Matches: 99, Mismatches: 17, Indels: 25
0.70 0.12 0.18
Matches are distributed among these distances:
20 5 0.05
21 8 0.08
22 5 0.05
23 46 0.46
24 17 0.17
25 12 0.12
26 6 0.06
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (23 bp):
ATATAAAAAAATAACATAAATAT
Found at i:168485 original size:26 final size:24
Alignment explanation
Indices: 168438--168485 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
168428 AATACGATAC
168438 AAAAAATAACATGAATATAAAACA
1 AAAAAATAACATGAATATAAAACA
168462 AAAAACATGAACAT-AATATGAAAA
1 AAAAA-AT-AACATGAATAT-AAAA
168486 AATATTACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAAAATAACATGAATATAAAACA
Found at i:168584 original size:27 final size:26
Alignment explanation
Indices: 168523--168592 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
168513 ATACGAATAT
168523 GACAC-AAAAAAATAACATAAACACA
1 GACACTAAAAAAATAACATAAACACA
168548 GA-ACTAAAAAAAATAACATGAAAACACA
1 GACACT-AAAAAAATAACAT--AAACACA
168576 -ACACTAAAAAAATAACA
1 GACACTAAAAAAATAACA
168593 CAACATGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 13 0.32
27 13 0.32
28 10 0.25
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.10
Consensus pattern (26 bp):
GACACTAAAAAAATAACATAAACACA
Found at i:168608 original size:23 final size:25
Alignment explanation
Indices: 168521--168633 Score: 92
Period size: 27 Copynumber: 4.6 Consensus size: 25
168511 GAATACGAAT
*
168521 ATGACAC-AAAAAAATAACATAAAC
1 ATGACACTAAAAAAATAACACAAAC
* *
168545 ACAGA-ACTAAAAAAAATAACATGAAAAC
1 A-TGACACT-AAAAAAATAACA--CAAAC
**
168573 ACAACACTAAAAAAATAACAC-AAC
1 ATGACACTAAAAAAATAACACAAAC
* *
168597 ATGACA-T-AAAAAATAATACAAAT
1 ATGACACTAAAAAAATAACACAAAC
168620 ATGACACTAAAAAA
1 ATGACACTAAAAAA
168634 TAAAATAGCT
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
22 11 0.15
23 9 0.13
24 11 0.15
25 7 0.10
26 12 0.17
27 13 0.18
28 8 0.11
ACGTcount: A:0.66, C:0.16, G:0.04, T:0.13
Consensus pattern (25 bp):
ATGACACTAAAAAAATAACACAAAC
Found at i:168610 original size:22 final size:24
Alignment explanation
Indices: 168521--168636 Score: 85
Period size: 24 Copynumber: 4.7 Consensus size: 24
168511 GAATACGAAT
* *
168521 ATGACACAAAAAAATAACATAAAC
1 ATGACACTAAAAAATAACACAAAC
* *
168545 ACAGA-ACTAAAAAAAATAACATGAAAAC
1 A-TGACACT--AAAAAATAACA--CAAAC
**
168573 ACAACACTAAAAAAATAACAC-AAC
1 ATGACACT-AAAAAATAACACAAAC
* *
168597 ATGACA-TAAAAAATAATACAAAT
1 ATGACACTAAAAAATAACACAAAC
168620 ATGACACTAAAAAATAA
1 ATGACACTAAAAAATAA
168637 AATAGCTCGC
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
22 11 0.15
23 9 0.12
24 20 0.27
25 2 0.03
26 11 0.15
27 13 0.18
28 8 0.11
ACGTcount: A:0.66, C:0.16, G:0.04, T:0.14
Consensus pattern (24 bp):
ATGACACTAAAAAATAACACAAAC
Found at i:169297 original size:13 final size:13
Alignment explanation
Indices: 169279--169327 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
169269 AAAATAATAA
169279 TATTTTAATAAAT
1 TATTTTAATAAAT
*
169292 TATTTTAAAATAATAA
1 TATTTT--AATAA-AT
169308 TATTTTAATAAAT
1 TATTTTAATAAAT
169321 TATTTTA
1 TATTTTA
169328 TAAGCAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 14 0.45
14 5 0.16
15 5 0.16
16 7 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATTTTAATAAAT
Found at i:169310 original size:29 final size:29
Alignment explanation
Indices: 169269--169327 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
169259 CATACGAATA
169269 AAAATAATAATATTTTAATAAATTATTTT
1 AAAATAATAATATTTTAATAAATTATTTT
169298 AAAATAATAATATTTTAATAAATTATTTT
1 AAAATAATAATATTTTAATAAATTATTTT
169327 A
1 A
169328 TAAGCAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAAATAATAATATTTTAATAAATTATTTT
Found at i:169363 original size:2 final size:2
Alignment explanation
Indices: 169356--169383 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
169346 TCAATCTTCA
169356 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
169384 GTGGGTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:169616 original size:21 final size:18
Alignment explanation
Indices: 169588--169637 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
169578 TATTTTATTT
169588 AAATTTAATTATAAAATATA
1 AAATTTAA-TATAAAA-ATA
169608 AAATATTAATATAAAAATA
1 AAAT-TTAATATAAAAATA
**
169627 ATTTTTAATAT
1 AAATTTAATAT
169638 TTAATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.26
19 5 0.19
20 11 0.41
21 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTAATATAAAAATA
Found at i:169811 original size:22 final size:21
Alignment explanation
Indices: 169767--169808 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
169757 AAAAATTATT
169767 TATTTAAATTTAATTATAAAA
1 TATTTAAATTTAATTATAAAA
169788 TATTTAAATATTAA-TATAAAA
1 TATTTAAAT-TTAATTATAAAA
169809 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAATTTAATTATAAAA
Found at i:170267 original size:142 final size:142
Alignment explanation
Indices: 170117--170389 Score: 440
Period size: 143 Copynumber: 1.9 Consensus size: 142
170107 AATTTTGCTT
* * *
170117 TCCCAATGTATTACGTTAACAATTTATTTATTCGT-ATTTTTTTATGTATTTTATTATTTTAATC
1 TCCCAATGTATTACGTTAACAATTTATTTATTCGTGATGTTTTTATGTATTTTATTATATCAATC
* * *
170181 ATATTTAAAATATTTTATATTTATCTCAGTTTTGATACGTCATATTGTATGAATTTTGAGAATAT
66 ATATTTAAAATATTTTATATTTATATCAGTTTTGATACATCATATTGTATGAATTTTGAAAATAT
170246 AAAAATCTGTTG
131 AAAAATCTGTTG
*
170258 TCCCAAATGTATTACGTTAGCAATTTATTTATTCGTGATGTTTTTATGTATTTTATTATATCAAT
1 TCCC-AATGTATTACGTTAACAATTTATTTATTCGTGATGTTTTTATGTATTTTATTATATCAAT
* * *
170323 CGTATTTAAAATATTTTATATTTATATCAGTTTTGATATATCATATTTTATGAATTTTGAAAATA
65 CATATTTAAAATATTTTATATTTATATCAGTTTTGATACATCATATTGTATGAATTTTGAAAATA
170388 TA
130 TA
170390 TTCATTCAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
141 4 0.03
142 30 0.25
143 86 0.72
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (142 bp):
TCCCAATGTATTACGTTAACAATTTATTTATTCGTGATGTTTTTATGTATTTTATTATATCAATC
ATATTTAAAATATTTTATATTTATATCAGTTTTGATACATCATATTGTATGAATTTTGAAAATAT
AAAAATCTGTTG
Found at i:170785 original size:9 final size:9
Alignment explanation
Indices: 170773--170800 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
170763 AAATATACCA
170773 AAAATATTT
1 AAAATATTT
170782 AAAATATTT
1 AAAATATTT
170791 AAAATATTT
1 AAAATATTT
170800 A
1 A
170801 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAAATATTT
Found at i:170999 original size:15 final size:15
Alignment explanation
Indices: 170981--171011 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
170971 TAAATATTAG
*
170981 ATATGGATATATTTA
1 ATATGAATATATTTA
170996 ATATGAATATATTTA
1 ATATGAATATATTTA
171011 A
1 A
171012 ATTTTTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (15 bp):
ATATGAATATATTTA
Found at i:173854 original size:2 final size:2
Alignment explanation
Indices: 173847--173886 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
173837 AATGTGCTTT
173847 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
173887 CTTACTATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175214 original size:6 final size:6
Alignment explanation
Indices: 175205--175234 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
175195 AATAAAAATT
*
175205 ATTTAA ATTTAA ATTCAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
175235 TACTATCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:175472 original size:19 final size:19
Alignment explanation
Indices: 175450--175490 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
175440 GATAATTTTG
175450 AATATAATATAAAAATATA
1 AATATAATATAAAAATATA
*
175469 AATATAATATAAATATATA
1 AATATAATATAAAAATATA
175488 AAT
1 AAT
175491 GTGTCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATAATATAAAAATATA
Found at i:175479 original size:11 final size:11
Alignment explanation
Indices: 175450--175485 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
175440 GATAATTTTG
175450 AATATAATAT-
1 AATATAATATA
175460 AA-A-AATATA
1 AATATAATATA
175469 AATATAATATA
1 AATATAATATA
175480 AATATA
1 AATATA
175486 TAAATGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.22
9 3 0.13
10 3 0.13
11 12 0.52
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAATATA
Found at i:176166 original size:20 final size:20
Alignment explanation
Indices: 176120--176167 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
176110 ATTATTAACG
* *
176120 TATAATAATTTATATAAATA
1 TATAATATTTTAAATAAATA
*
176140 TAAAATATTTTAAATATAAT-
1 TATAATATTTTAAATA-AATA
176160 TATAATAT
1 TATAATAT
176168 AATAAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATATTTTAAATAAATA
Found at i:176170 original size:5 final size:5
Alignment explanation
Indices: 176152--176192 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
176142 AAATATTTTA
*
176152 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AA
176193 ATATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 6 0.19
5 20 0.65
6 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:176183 original size:29 final size:28
Alignment explanation
Indices: 176131--176207 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 28
176121 ATAATAATTT
*
176131 ATATAAAT-ATAAAATATTTTAAATATA
1 ATATAAATAATAAAATATTATAAATATA
176158 ATTATAATATAATAAAATA-TATAAATATA
1 A-TATAA-ATAATAAAATATTATAAATATA
*
176187 ATATAAATATTAAAATTATTA
1 ATATAAATAATAAAA-TATTA
176208 AAAAATTCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.21
28 12 0.28
29 14 0.33
30 8 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAAATAATAAAATATTATAAATATA
Found at i:176186 original size:18 final size:18
Alignment explanation
Indices: 176131--176200 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
176121 ATAATAATTT
* *
176131 ATATAAATATAAAATATT
1 ATATAAATATTAAATATA
*
176149 TTA-AATATAATTATAATATA
1 ATATAA-AT-ATTA-AATATA
176169 ATA-AAATATATAAATATA
1 ATATAAATAT-TAAATATA
176187 ATATAAATATTAAA
1 ATATAAATATTAAA
176201 ATTATTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.05
18 19 0.44
19 13 0.30
20 9 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATTAAATATA
Found at i:176193 original size:11 final size:11
Alignment explanation
Indices: 176131--176196 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
176121 ATAATAATTT
176131 ATATAAATATAA
1 ATAT-AATATAA
* *
176143 A-ATATTTTAA
1 ATATAATATAA
176153 ATATAAT-TATA
1 ATATAATATA-A
176164 ATAT-A-ATAA
1 ATATAATATAA
176173 A-AT-ATATAA
1 ATATAATATAA
176182 ATATAATATAA
1 ATATAATATAA
176193 ATAT
1 ATAT
176197 TAAAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 3 0.07
9 7 0.16
10 13 0.29
11 21 0.47
12 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:176685 original size:17 final size:17
Alignment explanation
Indices: 176665--176698 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
176655 CTATTTATTT
*
176665 AATTTAAATTTTTAATA
1 AATTTAAATATTTAATA
176682 AATTTAAATATTTAATA
1 AATTTAAATATTTAATA
176699 GAAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAATATTTAATA
Found at i:176716 original size:30 final size:33
Alignment explanation
Indices: 176682--176752 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 33
176672 ATTTTTAATA
176682 AATTTAAATATTTA-ATAGA-AA-ATATT-ATTT
1 AATTTAAATATTTAGATA-ATAATATATTAATTT
176712 AATTT-AA-ATTTAGATAATAATATATTAATTT
1 AATTTAAATATTTAGATAATAATATATTAATTT
176743 AATTTAAATA
1 AATTTAAATA
176753 ATAAACAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
28 6 0.17
29 7 0.20
30 10 0.29
31 9 0.26
32 2 0.06
33 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (33 bp):
AATTTAAATATTTAGATAATAATATATTAATTT
Found at i:176797 original size:25 final size:24
Alignment explanation
Indices: 176700--176806 Score: 96
Period size: 25 Copynumber: 4.5 Consensus size: 24
176690 TATTTAATAG
176700 AAAATATTAT-TTAATTTAAATTT
1 AAAATATTATATTAATTTAAATTT
*
176723 AGATAATAATATATTAATTT-AATTT
1 A-A-AATATTATATTAATTTAAATTT
* * ** *
176748 -AAATAATAAACAAATTCAAATTTT
1 AAAATATTATATTAATTTAAA-TTT
176772 AAAATATTTATATTAATTTAAATTT
1 AAAATA-TTATATTAATTTAAATTT
176797 -AAATATTATA
1 AAAATATTATA
176807 AAAATATAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
22 12 0.18
23 9 0.13
24 9 0.13
25 20 0.30
26 17 0.25
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (24 bp):
AAAATATTATATTAATTTAAATTT
Found at i:177544 original size:22 final size:21
Alignment explanation
Indices: 177479--177544 Score: 55
Period size: 23 Copynumber: 3.1 Consensus size: 21
177469 TATTAAATAT
*
177479 AATATAAAA-AAATA-ATTAA
1 AATATAAAATAATTATATTAA
* *
177498 AATATAATATAATTATAATACA
1 AATATAAAATAATTATATTA-A
* *
177520 AATATAAAAATATTTCTATTAA
1 AATAT-AAAATAATTATATTAA
177542 AAT
1 AAT
177545 CAAATGGCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 8 0.22
20 4 0.11
21 3 0.08
22 10 0.28
23 11 0.31
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATAAAATAATTATATTAA
Found at i:178487 original size:15 final size:15
Alignment explanation
Indices: 178469--178497 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
178459 AAATTTTAAA
178469 TATATAAATATATTC
1 TATATAAATATATTC
178484 TATATAAATATATT
1 TATATAAATATATT
178498 TAATTTATAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATAAATATATTC
Found at i:182011 original size:159 final size:158
Alignment explanation
Indices: 181721--182114 Score: 540
Period size: 159 Copynumber: 2.5 Consensus size: 158
181711 CTCAATCCTT
* * * *
181721 TCATCACCCAGACTTTCCCTTGCTATGCTTTTATCAGCAGAATGCTTAAAATCCTCGTTCAATTT
1 TCATCACCCAGATTTTCCATTGCTATGCTTTTATCAGCAGAATGCTT-AAATCCTCATTCAATTC
* * **
181786 GGAAATTTCATCTTTTCGGCTCCCTTGCAAACGAGGGTCCTTATCTAAATCTTTGAAACCACCAT
65 GGAAATTTCATCTTTTCGGCTCCCTTGCAAACGAAGGCCCTTATCTAAATCTTCAAAACCACCAT
181851 TCTCGACCT-TCGCCTTAACCAGCATAGTC
130 TCTCGACCTCT-GCCTTAACCAGCATAGTC
* *
181880 TCATCTCCCAGATTTTCTATTGCTATGCTTTTATCAGCAGAATGCTTACAATCCTCATTCAATTC
1 TCATCACCCAGATTTTCCATTGCTATGCTTTTATCAGCAGAATGCTTA-AATCCTCATTCAATTC
* * *
181945 GGAAATTTCATCTTTTTGGCTCCCTTGCAAACTAAGGCCCTTATCTAAATCTTCAAAACCAGCAT
65 GGAAATTTCATCTTTTCGGCTCCCTTGCAAACGAAGGCCCTTATCTAAATCTTCAAAACCACCAT
* * ** *
182010 TCTCGATCTCTGGCTTAACTGGTATAGTC
130 TCTCGACCTCTGCCTTAACCAGCATAGTC
* *
182039 TCATCACCCGGATTTTCCATTACTATGCTTTTATCAGCAGAATGCTTAAATTCCTCATTCAA-TC
1 TCATCACCCAGATTTTCCATTGCTATGCTTTTATCAGCAGAATGCTTAAA-TCCTCATTCAATTC
182103 TGGAAAATTTCA
65 -GG-AAATTTCA
182115 CCAAAACATC
Statistics
Matches: 208, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
158 5 0.02
159 194 0.93
160 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (158 bp):
TCATCACCCAGATTTTCCATTGCTATGCTTTTATCAGCAGAATGCTTAAATCCTCATTCAATTCG
GAAATTTCATCTTTTCGGCTCCCTTGCAAACGAAGGCCCTTATCTAAATCTTCAAAACCACCATT
CTCGACCTCTGCCTTAACCAGCATAGTC
Found at i:182260 original size:3 final size:3
Alignment explanation
Indices: 182252--182296 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
182242 CCCCAACGAC
182252 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
182297 CCACCTTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:183409 original size:6 final size:6
Alignment explanation
Indices: 183398--183468 Score: 58
Period size: 6 Copynumber: 11.5 Consensus size: 6
183388 CAAAATTATC
* *
183398 TTATAT TTATA- TTATAT TTATA- -TATTT TTATAT ATTATAA TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT -TTATAT TTATAT
183444 TTAAAATAT TATATAT TTATAT TTA
1 TT---ATAT T-TATAT TTATAT TTA
183469 AAAAATTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
4 3 0.06
5 5 0.09
6 29 0.55
7 10 0.19
9 5 0.09
10 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
TTATAT
Found at i:183458 original size:22 final size:22
Alignment explanation
Indices: 183433--183499 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
183423 TTTTATATAT
183433 TATAATTATATTTAAAATATTA
1 TATAATTATATTTAAAATATTA
* *
183455 TATATTTATATTTAAAAAATTA
1 TATAATTATATTTAAAATATTA
183477 -ATAATTTATATTTATATAATATT
1 TATAA-TTATATTTA-A-AATATT
183500 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.08
22 29 0.76
23 1 0.03
24 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATTATATTTAAAATATTA
Found at i:183458 original size:29 final size:28
Alignment explanation
Indices: 183399--183514 Score: 82
Period size: 28 Copynumber: 4.2 Consensus size: 28
183389 AAAATTATCT
* *
183399 TATATTTAT-ATTATATTTATATATTTT
1 TATATTTATAATTATATTTAAATATTTA
183426 TATATATTATAATTATATTTAAA-ATATTA
1 TATAT-TTATAATTATATTTAAATAT-TTA
* * * *
183455 TATATTTATATTTAAAAAATT-AATAATT-
1 TATATTTATAATT--ATATTTAAATATTTA
* *
183483 TATATTTAT-ATAATATTTAAAT-TTTT
1 TATATTTATAATTATATTTAAATATTTA
183509 TATATT
1 TATATT
183515 ATATGGTGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
25 6 0.09
26 9 0.13
27 6 0.09
28 22 0.31
29 22 0.31
30 5 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATTTATAATTATATTTAAATATTTA
Found at i:184413 original size:9 final size:8
Alignment explanation
Indices: 184395--184428 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
184385 CCAATGCAAC
184395 TTATATTA
1 TTATATTA
184403 TTATGATTA
1 TTAT-ATTA
184412 TTATTATTA
1 TTA-TATTA
184421 TTATATTA
1 TTATATTA
184429 AAAAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 9 0.38
9 14 0.58
10 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
TTATATTA
Found at i:185618 original size:21 final size:20
Alignment explanation
Indices: 185587--185645 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
185577 TAAATAATTT
* *
185587 AATTTAATTAATTTAAATTA
1 AATTTATTTAATTTAAAATA
**
185607 ATATTTATTTAATAAAAAATA
1 A-ATTTATTTAATTTAAAATA
185628 AATTTTATTTAAATTTAA
1 AA-TTTATTT-AATTTAA
185646 TTATTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 23 0.77
22 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTATTTAATTTAAAATA
Found at i:193884 original size:14 final size:16
Alignment explanation
Indices: 193865--193897 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
193855 GATTCATAGG
193865 GTTT-AATCA-TTTAA
1 GTTTAAATCATTTTAA
193879 GTTTAAATCATTTTAA
1 GTTTAAATCATTTTAA
193895 GTT
1 GTT
193898 AATTATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 5 0.29
16 8 0.47
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (16 bp):
GTTTAAATCATTTTAA
Found at i:194067 original size:20 final size:20
Alignment explanation
Indices: 194044--194087 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
194034 CTAATTTGTG
*
194044 TATAAT-TTTATTTAAATTAT
1 TATAATATTTATATAAATT-T
194064 TAT-ATATTTATATAAATTT
1 TATAATATTTATATAAATTT
194083 TATAA
1 TATAA
194088 ATCAGTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATAATATTTATATAAATTT
Found at i:194500 original size:13 final size:13
Alignment explanation
Indices: 194468--194506 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
194458 TATATTATTT
194468 ATTTTATATAA-A
1 ATTTTATATAATA
*
194480 A-TTAATATAATA
1 ATTTTATATAATA
194492 ATTTTATATAATA
1 ATTTTATATAATA
194505 AT
1 AT
194507 AAAAATTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.35
12 3 0.13
13 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTTATATAATA
Found at i:195036 original size:17 final size:15
Alignment explanation
Indices: 194993--195027 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
194983 ATTTTAAAAA
194993 ATATTAAAATTTATT
1 ATATTAAAATTTATT
195008 ATATTAAAAATTTA-T
1 ATATT-AAAATTTATT
195023 ATATT
1 ATATT
195028 TTAATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTAAAATTTATT
Found at i:195830 original size:6 final size:7
Alignment explanation
Indices: 195813--195978 Score: 50
Period size: 7 Copynumber: 24.4 Consensus size: 7
195803 TCATATATTT
195813 TTATATA
1 TTATATA
195820 TTATA-A
1 TTATATA
195826 TTATAT-
1 TTATATA
*
195832 TTAAAATA
1 TT-ATATA
195840 TTATATA
1 TTATATA
195847 TT-TATA
1 TTATATA
* * *
195853 TAATTTT
1 TTATATA
195860 TTATATA
1 TTATATA
*
195867 ATA-ATAA
1 TTATAT-A
* *
195874 TAATTTA
1 TTATATA
*
195881 TTTTATA
1 TTATATA
*
195888 -TAAATA
1 TTATATA
*
195894 TTA-ACTCG
1 TTATA-T-A
195902 TT-TATA
1 TTATATA
*
195908 TTTTAATA
1 TTAT-ATA
*
195916 TCATAT-
1 TTATATA
195922 TTATATA
1 TTATATA
195929 TT-TATA
1 TTATATA
195935 TTATAT-
1 TTATATA
*
195941 TATATTTAA
1 T-TATAT-A
195950 TTATAT-
1 TTATATA
*
195956 TTTTATA
1 TTATATA
*
195963 TTTTA-A
1 TTATATA
195969 TTATATA
1 TTATATA
195976 TTA
1 TTA
195979 CATTCAAAAT
Statistics
Matches: 114, Mismatches: 26, Indels: 38
0.64 0.15 0.21
Matches are distributed among these distances:
6 44 0.39
7 54 0.47
8 15 0.13
9 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:195963 original size:34 final size:37
Alignment explanation
Indices: 195903--195974 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 37
195893 ATTAACTCGT
195903 TTATATTTTAATATCATATTTATATA-TTTATATTATA
1 TTATATTTTAATATCATATTTATATATTTTA-ATTATA
*
195940 TTATA-TTTAAT-T-ATATTTTTATATTTTAATTATA
1 TTATATTTTAATATCATATTTATATATTTTAATTATA
195974 T
1 T
195975 ATTACATTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 17 0.52
35 5 0.15
36 6 0.18
37 5 0.15
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (37 bp):
TTATATTTTAATATCATATTTATATATTTTAATTATA
Found at i:196619 original size:16 final size:16
Alignment explanation
Indices: 196569--196620 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
196559 AAATTAATTG
*
196569 AATTTTAATTGTTTAT
1 AATTTTAATTTTTTAT
** * *
196585 -ATTTTAAAATCTTAA
1 AATTTTAATTTTTTAT
196600 AATTTTAATTTTTTAT
1 AATTTTAATTTTTTAT
196616 AATTT
1 AATTT
196621 AAATAAATAT
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTTAT
Found at i:200258 original size:25 final size:25
Alignment explanation
Indices: 200196--200265 Score: 99
Period size: 24 Copynumber: 2.8 Consensus size: 25
200186 AATAAAAATT
*
200196 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
200220 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
*
200245 AGCCTCC-ATATTTGACAAATA
1 AGCCACCAAT-TTTGACAAATA
200266 CAAAGGAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
24 21 0.50
25 21 0.50
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:200311 original size:27 final size:27
Alignment explanation
Indices: 200250--200320 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
200240 AAACAAGCCT
* *
200250 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
200278 TCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
200305 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
200321 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:202795 original size:216 final size:216
Alignment explanation
Indices: 202418--202859 Score: 651
Period size: 216 Copynumber: 2.0 Consensus size: 216
202408 ACCCTAAAGT
*
202418 TAGCTATTGAAGTACGAGAGCCTAAATCTATATATACCATAAGAAAACACTTTCTATTTCAATGT
1 TAGCTATTGAAGTACGAGAGCCTAAATCTATATATACCACAAGAAAACACTTTCTATTTCAATGT
* * * * *
202483 TGGAGAACCACACCCTAAAACTTTTTCTTTTTCTCTTGTTAGGCGTAGGTCATCACTCCGCATGC
66 TGGAGAACCACACCCCAAAACTTTTTCTTTTTCTCATGCTAGGCATAGGTCACCACTCCGCATGC
* * *
202548 CACCACTTCGAGTGTTGAGCATTGTAAGATGAAGCTAGCTTTGATATCAATTGATACAAACCTTT
131 CACCACTTCGAATATTGAGCATTGCAAGATGAAGCTAGCTTTGATATCAATTGATACAAACCTTT
202613 GGAGAA-CTACA-CTCCAAAAAC
196 GGAGAATC-ACATC-CCAAAAAC
** * *
202634 TAGCTATTGAAGTGGGAGAGCCTAAGT-TCATATATACCACAAGAAAACTCTTTCTATTTCAATG
1 TAGCTATTGAAGTACGAGAGCCTAAATCT-ATATATACCACAAGAAAACACTTTCTATTTCAATG
202698 TTGGAGAACCACACCCCAAAACCTTTTT-TTTTTCTCATGCTAGGCATAGGTCACCACTCCGCAT
65 TTGGAGAACCACACCCCAAAA-CTTTTTCTTTTTCTCATGCTAGGCATAGGTCACCACTCCGCAT
* * * *
202762 GCCATCACTAT-GAATATTGAGGATTGCAAGATGAAGCTAGTTTTGATATCAATTGATACAGACC
129 GCCACCACT-TCGAATATTGAGCATTGCAAGATGAAGCTAGCTTTGATATCAATTGATACAAACC
202826 TTTGGAGAATCACATCCCAAAAAC
193 TTTGGAGAATCACATCCCAAAAAC
202850 TAGCTATTGA
1 TAGCTATTGA
202860 GATCAGAAAG
Statistics
Matches: 204, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
215 1 0.00
216 194 0.95
217 9 0.04
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (216 bp):
TAGCTATTGAAGTACGAGAGCCTAAATCTATATATACCACAAGAAAACACTTTCTATTTCAATGT
TGGAGAACCACACCCCAAAACTTTTTCTTTTTCTCATGCTAGGCATAGGTCACCACTCCGCATGC
CACCACTTCGAATATTGAGCATTGCAAGATGAAGCTAGCTTTGATATCAATTGATACAAACCTTT
GGAGAATCACATCCCAAAAAC
Found at i:206288 original size:13 final size:14
Alignment explanation
Indices: 206256--206293 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
206246 AAGTCACATC
* *
206256 AATATTTATTTAAT
1 AATATTAATGTAAT
206270 AATATTAATGTAA-
1 AATATTAATGTAAT
206283 AATATTAATGT
1 AATATTAATGT
206294 GTTCGATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (14 bp):
AATATTAATGTAAT
Found at i:206631 original size:19 final size:20
Alignment explanation
Indices: 206592--206633 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
206582 ATATTATTTT
* *
206592 AATATTAATATTTATGTATA
1 AATATTAATATGTAAGTATA
206612 AATATTAA-ATGTAAGTATA
1 AATATTAATATGTAAGTATA
206631 AAT
1 AAT
206634 TTGATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (20 bp):
AATATTAATATGTAAGTATA
Found at i:214466 original size:3 final size:3
Alignment explanation
Indices: 214458--214486 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
214448 TTTCAACGAA
214458 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
214487 ATGTAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:214726 original size:18 final size:19
Alignment explanation
Indices: 214700--214745 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
214690 TTTATTATAA
*
214700 AAAAT-TAAAATTTAATT-
1 AAAATATAAAATTAAATTG
214717 AAAATATAAAATTAAATTG
1 AAAATATAAAATTAAATTG
214736 AAAA-ATAAAA
1 AAAATATAAAA
214746 AATAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 17 0.65
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATAAAATTAAATTG
Found at i:214765 original size:22 final size:22
Alignment explanation
Indices: 214718--214785 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
214708 AATTTAATTA
* *
214718 AAATATAAAATTAAATTGAAAAAT
1 AAATA-AAAATTAAATT-ATATAT
214742 AAA-AAATAATT-AATTATTATAT
1 AAATAAA-AATTAAATTA-TATAT
214764 AAATAAAAATTAAATTATATAT
1 AAATAAAAATTAAATTATATAT
214786 TATTTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 1 0.03
22 21 0.55
23 13 0.34
24 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (22 bp):
AAATAAAAATTAAATTATATAT
Found at i:214779 original size:27 final size:26
Alignment explanation
Indices: 214738--214788 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
214728 TTAAATTGAA
214738 AAATAAAAAATAATTA-ATTATTATAT
1 AAATAAAAAATAATTATA-TATTATAT
*
214764 AAATAAAAATTAAATTATATATTAT
1 AAATAAAAAAT-AATTATATATTAT
214789 TTATATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 11 0.50
28 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
AAATAAAAAATAATTATATATTATAT
Found at i:214815 original size:15 final size:16
Alignment explanation
Indices: 214777--214831 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
214767 TAAAAATTAA
*
214777 ATTATATATTATTTAT
1 ATTATATTTTATTTAT
214793 ATTATATTTTATTT-T
1 ATTATATTTTATTTAT
* * *
214808 ATTTTATTTTTAATGAT
1 ATTATA-TTTTATTTAT
214825 ATTATAT
1 ATTATAT
214832 AAATATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 6 0.19
16 20 0.62
17 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTATATTTTATTTAT
Found at i:214853 original size:8 final size:7
Alignment explanation
Indices: 214844--214961 Score: 55
Period size: 7 Copynumber: 16.1 Consensus size: 7
214834 ATATATATTA
214844 ATTAAAT
1 ATTAAAT
214851 AATTATAAT
1 -ATTA-AAT
*
214860 CTTATAAT
1 ATTA-AAT
*
214868 ATAAAAT
1 ATTAAAT
*
214875 AATAAAT
1 ATTAAAT
214882 ATTAAAT
1 ATTAAAT
214889 -TTAAATTT
1 ATTAAA--T
214897 ATTAAA-
1 ATTAAAT
*
214903 ATTATAT
1 ATTAAAT
*
214910 AATATAAT
1 ATTA-AAT
214918 -TTATTAAT
1 ATTA--AAT
*
214926 ATTAAAA
1 ATTAAAT
*
214933 ATTATAT
1 ATTAAAT
214940 ATATAAAT
1 AT-TAAAT
*
214948 A-TATAT
1 ATTAAAT
214954 ATTAAAT
1 ATTAAAT
214961 A
1 A
214962 CTATAATTAT
Statistics
Matches: 84, Mismatches: 16, Indels: 21
0.69 0.13 0.17
Matches are distributed among these distances:
6 15 0.18
7 33 0.39
8 25 0.30
9 11 0.13
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAAAT
Found at i:214920 original size:29 final size:28
Alignment explanation
Indices: 214843--214959 Score: 82
Period size: 29 Copynumber: 4.0 Consensus size: 28
214833 AATATATATT
* *
214843 AATTAAATAATTATAATCTTATAATA-TAA
1 AATTATATAA-TATAAT-TTATTATATTAA
*
214872 AATAATA-AATATTAAATTTAAATT-TATTAA
1 AATTATATAATA-T-AATTT--ATTATATTAA
214902 AATTATATAATATAATTTATTAATATTAAA
1 AATTATATAATATAATTTATT-ATATT-AA
*
214932 AATTATAT-ATATAA-ATATATATATTAA
1 AATTATATAATATAATTTAT-TATATTAA
214959 A
1 A
214960 TACTATAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
27 8 0.11
28 13 0.18
29 26 0.36
30 22 0.30
31 4 0.05
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTATATAATATAATTTATTATATTAA
Found at i:214938 original size:23 final size:23
Alignment explanation
Indices: 214879--214938 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
214869 TAAAATAATA
*
214879 AATATT-AAATTTA-AATTTATT
1 AATATTAAAAATTATAATTTATT
* *
214900 AAAATTATATAA-TATAATTTATT
1 AATATTA-AAAATTATAATTTATT
214923 AATATTAAAAATTATA
1 AATATTAAAAATTATA
214939 TATATAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 5 0.17
22 5 0.17
23 20 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATTAAAAATTATAATTTATT
Found at i:214952 original size:14 final size:13
Alignment explanation
Indices: 214924--214970 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
214914 TAATTTATTA
*
214924 ATATTAAAAATTAT
1 ATATTAAATA-TAT
214938 ATATATAAATATAT
1 ATAT-TAAATATAT
214952 ATATTAAATACTAT
1 ATATTAAATA-TAT
214966 A-ATTA
1 ATATTA
214971 TTATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.33
14 15 0.50
15 5 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:215152 original size:9 final size:9
Alignment explanation
Indices: 215125--215173 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
215115 TGATAATTCG
215125 TATA-TTTA
1 TATATTTTA
215133 TATAATATTTA
1 TAT-AT-TTTA
215144 TATATTTTA
1 TATATTTTA
* *
215153 TCTATTATA
1 TATATTTTA
215162 TATATTTTA
1 TATATTTTA
215171 TAT
1 TAT
215174 TTATATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 3 0.09
9 22 0.65
10 2 0.06
11 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (9 bp):
TATATTTTA
Found at i:215165 original size:18 final size:17
Alignment explanation
Indices: 215138--215179 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
215128 ATTTATATAA
215138 TATTTATATATTTTATC
1 TATTTATATATTTTATC
215155 TATTATATATATTTTA--
1 TATT-TATATATTTTATC
215171 TATTTATAT
1 TATTTATAT
215180 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.21
16 4 0.17
17 4 0.17
18 11 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTATATATTTTATC
Found at i:215859 original size:16 final size:16
Alignment explanation
Indices: 215825--215865 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
215815 AGTAACTTTA
**
215825 ATTTTAAATTTAAGTT
1 ATTTTAAATTTAAAAT
215841 ATTTTAAATTTAAAAT
1 ATTTTAAATTTAAAAT
*
215857 ATTTCAAAT
1 ATTTTAAAT
215866 CAGAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAAATTTAAAAT
Found at i:215930 original size:25 final size:26
Alignment explanation
Indices: 215900--215968 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 26
215890 ATTTATTTTT
*
215900 GAATTAAAATAATATTATAAAAA-TA
1 GAATTAATATAATATTATAAAAATTA
* * *
215925 GAATTATTATATTATTTTAAAAATTA
1 GAATTAATATAATATTATAAAAATTA
215951 -AATTAATATAA-A-TATAAA
1 GAATTAATATAATATTATAAA
215969 TTTTTTATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 5 0.14
24 1 0.03
25 28 0.78
26 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
GAATTAATATAATATTATAAAAATTA
Found at i:216007 original size:24 final size:25
Alignment explanation
Indices: 215980--216040 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
215970 TTTTTATAAA
215980 ATAATAATAAATAATT-TTT-AATTT
1 ATAATAAT-AATAATTATTTAAATTT
*
216004 ATAATAATAATTATTATTTAAATTT
1 ATAATAATAATAATTATTTAAATTT
*
216029 ACAATAA-AATAA
1 ATAATAATAATAA
216041 AAAATATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 6 0.19
24 15 0.47
25 11 0.34
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAATAATAATAATTATTTAAATTT
Found at i:216107 original size:13 final size:14
Alignment explanation
Indices: 216084--216112 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
216074 AGTAATTTTT
216084 TTATTTAATTATTA
1 TTATTTAATTATTA
216098 TTATTT-ATTATTA
1 TTATTTAATTATTA
216111 TT
1 TT
216113 TCTCGGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTAATTATTA
Found at i:216883 original size:37 final size:37
Alignment explanation
Indices: 216841--217030 Score: 106
Period size: 37 Copynumber: 5.1 Consensus size: 37
216831 ATTTATATAT
*
216841 TTAATAAGTAAATAGTTTAAAAATTTTTCAATAAAAA
1 TTAATAAGTAAATAGTTTAAAAATTTTTAAATAAAAA
* * *
216878 TTAATAA-TGAAA-ATTTTTAAAATAATTTAAATAAAAA
1 TTAATAAGT-AAATAGTTTAAAAAT-TTTTAAATAAAAA
* * ** * * *
216915 TTAATTAA-TTAATA---T-ATAATTTTATTTATTATAT
1 TTAA-TAAGTAAATAGTTTAAAAATTTT-TAAATAAAAA
* * * *
216949 TTAATAAGTAAATAGTTTAAAATTTTTTCATTTAAAA
1 TTAATAAGTAAATAGTTTAAAAATTTTTAAATAAAAA
* * *
216986 TTAATAATGAAAAAAGTTTAAAAATAATTTAAATAAAAAA
1 TTAATAA-GTAAATAGTTTAAAAAT-TTTTAAAT-AAAAA
217026 TTAAT
1 TTAAT
217031 TAATAAAAAA
Statistics
Matches: 113, Mismatches: 27, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
33 5 0.04
34 18 0.16
35 1 0.01
36 10 0.09
37 40 0.35
38 25 0.22
39 5 0.04
40 9 0.08
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (37 bp):
TTAATAAGTAAATAGTTTAAAAATTTTTAAATAAAAA
Found at i:216957 original size:108 final size:111
Alignment explanation
Indices: 216804--217034 Score: 362
Period size: 108 Copynumber: 2.1 Consensus size: 111
216794 TTTTAAAATT
216804 AATTAATTAATTAATTATTATAAATTTATTTATATATTTAATAAGTAAATAGTTTAAAAATTTTT
1 AATTAATTAATTAATTATTATAAATTTATTTATATATTTAATAAGTAAATAGTTTAAAAATTTTT
* *
216869 CAATAAAAATTAATAATG-AAAATTTTTAAAATAATTTAAAT-AAA
66 CAATAAAAATTAATAATGAAAAAGTTTAAAAATAATTTAAATAAAA
* *
216913 AATTAATTAATTAA-TA-TATAATTTTATTTATTATATTTAATAAGTAAATAGTTTAAAATTTTT
1 AATTAATTAATTAATTATTATAAATTTATTTA-TATATTTAATAAGTAAATAGTTTAAAAATTTT
* *
216976 TCATTTAAAATTAATAATGAAAAAAGTTTAAAAATAATTTAAATAAAA
65 TCAATAAAAATTAATAATG-AAAAAGTTTAAAAATAATTTAAATAAAA
217024 AATTAATTAAT
1 AATTAATTAAT
217035 AAAAAATAAA
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
107 13 0.12
108 50 0.45
109 14 0.12
110 21 0.19
111 14 0.12
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (111 bp):
AATTAATTAATTAATTATTATAAATTTATTTATATATTTAATAAGTAAATAGTTTAAAAATTTTT
CAATAAAAATTAATAATGAAAAAGTTTAAAAATAATTTAAATAAAA
Found at i:217026 original size:16 final size:14
Alignment explanation
Indices: 217005--217043 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
216995 AAAAAAGTTT
217005 AAAAATAATTTAAATA
1 AAAAATAA-TT-AATA
217021 AAAAATTAATTAATA
1 AAAAA-TAATTAATA
217036 AAAAATAA
1 AAAAATAA
217044 AGAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 9 0.41
16 7 0.32
17 3 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATAATTAATA
Found at i:217265 original size:37 final size:37
Alignment explanation
Indices: 217191--217264 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
217181 AAATTTTAAG
* *
217191 TTTAAATTAAAATTTATTATTTAAAATATTAAAAAAA
1 TTTAAATTAAAATTTATTAATTAAAATAATAAAAAAA
*
217228 TTTAAATTAATATTTA-TAATTAAAATTAAATAAAAAA
1 TTTAAATTAAAATTTATTAATTAAAA-T-AATAAAAAA
217265 TATTATTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 8 0.25
37 16 0.50
38 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (37 bp):
TTTAAATTAAAATTTATTAATTAAAATAATAAAAAAA
Found at i:217764 original size:11 final size:12
Alignment explanation
Indices: 217741--217770 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
217731 TTTTGAAATG
217741 AAATAATAATAT
1 AAATAATAATAT
217753 AAATAA-AATAT
1 AAATAATAATAT
217764 AAATAAT
1 AAATAAT
217771 TGATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:217915 original size:21 final size:21
Alignment explanation
Indices: 217870--217915 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
217860 ATTTTTATTT
* **
217870 TAATTTTATTATTATAATATT
1 TAATCTTATTATTATAATAAC
*
217891 TAATCTTATTATTATAGTAAC
1 TAATCTTATTATTATAATAAC
217912 TAAT
1 TAAT
217916 TTCAACTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATCTTATTATTATAATAAC
Found at i:218110 original size:17 final size:16
Alignment explanation
Indices: 218057--218111 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
218047 ATTATATTTT
218057 TAAAA-TTTATATAATA
1 TAAAATTTTATA-AATA
218073 T-AAATTTT-TAACATA
1 TAAAATTTTATAA-ATA
218088 TTAAAATTGTTATAAATA
1 -TAAAATT-TTATAAATA
218106 TAAAAT
1 TAAAAT
218112 ACATTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
14 1 0.03
15 8 0.24
16 5 0.15
17 11 0.33
18 5 0.15
19 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAAATTTTATAAATA
Found at i:218197 original size:9 final size:9
Alignment explanation
Indices: 218177--218233 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
218167 AAAATTGATA
218177 TAAATATA-
1 TAAATATAT
218185 -AAATATAT
1 TAAATATAT
*
218193 TAAATATAA
1 TAAATATAT
218202 TAAA-ATAT
1 TAAATATAT
218210 ATAAATATAAT
1 -TAAATAT-AT
218221 ATAAATATAT
1 -TAAATATAT
218231 TAA
1 TAA
218234 TTATCAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.17
8 3 0.07
9 18 0.43
10 4 0.10
11 10 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAATATAT
Found at i:218206 original size:19 final size:19
Alignment explanation
Indices: 218182--218233 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
218172 TGATATAAAT
218182 ATAAAATATATTAAATATA
1 ATAAAATATATTAAATATA
218201 ATAAAATATA-TAAATATA
1 ATAAAATATATTAAATATA
218219 ATATAAATATATTAA
1 ATA-AAATATATTAA
218234 TTATCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.35
19 17 0.55
20 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAAAATATATTAAATATA
Found at i:218217 original size:34 final size:34
Alignment explanation
Indices: 218117--218219 Score: 106
Period size: 34 Copynumber: 3.0 Consensus size: 34
218107 AAAATACATT
* *
218117 AAATATTATTTAATATAATATAATATATAAATAT-
1 AAATA-TATTAAATATAATAAAATATATAAATATA
* *
218151 AAAT-TTTTAACGTAT--TAAAATTGATATAAATATA
1 AAATATATTAA-ATATAATAAAA-T-ATATAAATATA
218185 AAATATATTAAATATAATAAAATATATAAATATA
1 AAATATATTAAATATAATAAAATATATAAATATA
218219 A
1 A
218220 TATAAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
31 4 0.07
32 5 0.09
33 13 0.23
34 23 0.41
35 6 0.11
36 5 0.09
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (34 bp):
AAATATATTAAATATAATAAAATATATAAATATA
Found at i:220344 original size:29 final size:29
Alignment explanation
Indices: 220280--220334 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
220270 TGCTTTAAGA
*
220280 GAGTCC-TTAGTCAACAATGGTACCAAAT
1 GAGTCCTTTAGCCAACAATGGTACCAAAT
220308 GAGTCCTTTAGCCAACAATGGTACCAA
1 GAGTCCTTTAGCCAACAATGGTACCAA
220335 TAGGTACCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (29 bp):
GAGTCCTTTAGCCAACAATGGTACCAAAT
Found at i:228090 original size:33 final size:32
Alignment explanation
Indices: 228034--228119 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 32
228024 TGAATACGAA
228034 TTATATATAAAATAATAAAATATTTTTAAAAT
1 TTATATATAAAATAATAAAATATTTTTAAAAT
*
228066 TTATATAATATAAATTAT-AAATATTTTT-AAA-
1 TTATAT-ATA-AAATAATAAAATATTTTTAAAAT
*
228097 TTA-ACAT-AAAT-ATAAAATATTTT
1 TTATATATAAAATAATAAAATATTTT
228120 AAATATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
26 2 0.04
27 13 0.27
29 2 0.04
30 1 0.02
31 3 0.06
32 9 0.18
33 13 0.27
34 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (32 bp):
TTATATATAAAATAATAAAATATTTTTAAAAT
Found at i:228094 original size:26 final size:26
Alignment explanation
Indices: 228065--228133 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
228055 ATTTTTAAAA
228065 TTTATATAATATAAAT-TATAAATATT
1 TTTATATAATATAAATATA-AAATATT
* *
228091 TTTAAATTAACATAAATATAAAATATT
1 TTTATA-TAATATAAATATAAAATATT
*
228118 TTAAATATAATTATAA
1 TT-TATATAA-TATAA
228134 CTTTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.15
27 21 0.62
28 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTATATAATATAAATATAAAATATT
Found at i:228178 original size:16 final size:16
Alignment explanation
Indices: 228142--228172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
228132 AACTTTAAAA
*
228142 AAAAAAATTTAAACTC
1 AAAATAATTTAAACTC
228158 AAAATAATTTAAACT
1 AAAATAATTTAAACT
228173 TGAAATGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATTTAAACTC
Found at i:228330 original size:22 final size:22
Alignment explanation
Indices: 228305--228347 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
228295 TTAAAATTAC
*
228305 TTAAATTTAATTAATTTAAATA
1 TTAAATTTAATTAACTTAAATA
*
228327 TTAAATTTAATTGACTTAAAT
1 TTAAATTTAATTAACTTAAAT
228348 CTAATTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAAATTTAATTAACTTAAATA
Found at i:228378 original size:16 final size:16
Alignment explanation
Indices: 228359--228441 Score: 86
Period size: 16 Copynumber: 5.5 Consensus size: 16
228349 TAATTATGAT
*
228359 TAATTTAAAACTAAAA
1 TAATTTAAAATTAAAA
*
228375 TAATTTAAATTTAAAA
1 TAATTTAAAATTAAAA
*
228391 T-ATTT-TAA-TAAAA
1 TAATTTAAAATTAAAA
228404 -AATTTAAAATTAAAA
1 TAATTTAAAATTAAAA
* *
228419 TAATTAAAAATTTAAA
1 TAATTTAAAATTAAAA
228435 -AATTTAA
1 TAATTTAA
228442 TTTAATTCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
13 9 0.16
14 3 0.05
15 15 0.27
16 28 0.51
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATTTAAAATTAAAA
Found at i:228388 original size:22 final size:21
Alignment explanation
Indices: 228360--228435 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
228350 AATTATGATT
*
228360 AATTTAAAACTAAAATAATTTA
1 AATTTAAAA-TAAAATAATTAA
*** *
228382 AATTTAAAATATTTTAATAAAA
1 AATTTAAAATAAAATAAT-TAA
228404 AATTTAAAATTAAAATAATTAAA
1 AATTTAAAA-TAAAATAATT-AA
228427 AATTTAAAA
1 AATTTAAAA
228436 ATTTAATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
21 6 0.14
22 19 0.45
23 17 0.40
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTAAAATAAAATAATTAA
Found at i:228412 original size:8 final size:8
Alignment explanation
Indices: 228401--228441 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
228391 TATTTTAATA
228401 AAAAATTT
1 AAAAATTT
228409 -AAAA-TT
1 AAAAATTT
*
228415 AAAATAATT
1 AAAA-ATTT
228424 AAAAATTT
1 AAAAATTT
228432 AAAAATTT
1 AAAAATTT
228440 AA
1 AA
228442 TTTAATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
6 2 0.07
7 7 0.24
8 14 0.48
9 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAAATTT
Found at i:228920 original size:3 final size:3
Alignment explanation
Indices: 228912--228940 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
228902 GGGCTTTTTC
228912 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
228941 GGGGTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:230200 original size:266 final size:261
Alignment explanation
Indices: 229718--230485 Score: 949
Period size: 261 Copynumber: 2.9 Consensus size: 261
229708 GTAGATTGAC
* ** **
229718 TGCTTTTGATGAAAGGGACAACTCAGTCTTTAAGTCTCAAACTTTATCCAATTATTCAATGAAAG
1 TGCTTTTGATGAAAGGGGCAACTCA-TCTTTAAGTCTCAAACTTTATCCGGTTATTTGAT-AAAG
* * * * *
229783 GACTAGCAACTTATAGGTTCAATCAAGAATCTCAGCTTTA-CGACACTGCTTTAAACAAATTCTT
64 GACTAGTAACTTTTAGGTTCAATCAAGGATATCAGCTTTAGTGACACTGCTTTAAACAAATTCTT
* * * ** *
229847 AGTGCTAACTCATTTGCTGTTCGTACTGGTTG-AT-TGTTTCGTTCTTATTTTTCATTATTTTAC
129 AATGCTAACTCATTCGCAGTTCGTACCAGTAGTATAT-TTT-GTTCTTATTTTTCATTATTTTAC
* * *
229910 TTGATTTTATATTGGAGTTTTCATAAGTGTGTGAGTATAAAGCCATGGCTGTTCTTGAATTAGTG
192 TTGA-TTTATAGTGGAGGTTTCATAA-TG-GTGAGTAT-AAGCCATGGCTGTTCTTGAATTAGTA
229975 TACTTTACT
253 TACTTTACT
*
229984 TGCTTTTGATGAAAGGGGCAACTCCATCTTTAAGTCTCGAACTTTATCCGGTTATTTGATAAAGG
1 TGCTTTTGATGAAAGGGGCAACT-CATCTTTAAGTCTCAAACTTTATCCGGTTATTTGATAAAGG
* ** *
230049 ACTAGTAACTTTTAGGTTCAATCAAGGATTTCAGCTTTAGTGACTTTGCTTTAAAGAAATTCTTA
65 ACTAGTAACTTTTAGGTTCAATCAAGGATATCAGCTTTAGTGACACTGCTTTAAACAAATTCTTA
*
230114 ATGCTAACTCATTCGCAGTTTGTACCAGTAGTATATTTTGTTCTTATTTTTCATTATTTTACTTG
130 ATGCTAACTCATTCGCAGTTCGTACCAGTAGTATATTTTGTTCTTATTTTTCATTATTTTACTTG
* * *
230179 ATTTAGTAGTGGAGGTTTCATAATGGTTGAGTATATGGCCATGGCTGATCTTGAATTAGTATATT
195 ATTTA-TAGTGGAGGTTTCATAATGG-TGAGTATA-AGCCATGGCTGTTCTTGAATTAGTATACT
230244 TTACT
257 TTACT
* * * *
230249 TGCTTTGGATGAAAGAGGCAACTTCGTCTTTAAGTCTCAAACTCTATCCGGTTATTTG---AA-G
1 TGCTTTTGATGAAAGGGGCAAC-TCATCTTTAAGTCTCAAACTTTATCCGGTTATTTGATAAAGG
* * * **
230310 ACTAGTAACTTTTATGTTCAATCAAGGATATCAACATTAGTGACACTGCTTTAAACAAATTCTGG
65 ACTAGTAACTTTTAGGTTCAATCAAGGATATCAGCTTTAGTGACACTGCTTTAAACAAATTCTTA
* ** * *
230375 ATGCTAACTCATTCGCAGTTCGTACCAGTAGTATATATCATTCTTATTTTTCACTATTTTATTTG
130 ATGCTAACTCATTCGCAGTTCGTACCAGTAGTATATTTTGTTCTTATTTTTCATTATTTTACTTG
* *
230440 ATTTCATCGAGGAGGTTTCATAATGGTCGAGTAT-AGCCATGGCTGT
195 ATTT-ATAGTGGAGGTTTCATAATGGT-GAGTATAAGCCATGGCTGT
230486 GCCTGGATTT
Statistics
Matches: 441, Mismatches: 51, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
259 10 0.02
260 1 0.00
261 144 0.33
262 3 0.01
264 2 0.00
265 134 0.30
266 139 0.32
267 7 0.02
268 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (261 bp):
TGCTTTTGATGAAAGGGGCAACTCATCTTTAAGTCTCAAACTTTATCCGGTTATTTGATAAAGGA
CTAGTAACTTTTAGGTTCAATCAAGGATATCAGCTTTAGTGACACTGCTTTAAACAAATTCTTAA
TGCTAACTCATTCGCAGTTCGTACCAGTAGTATATTTTGTTCTTATTTTTCATTATTTTACTTGA
TTTATAGTGGAGGTTTCATAATGGTGAGTATAAGCCATGGCTGTTCTTGAATTAGTATACTTTAC
T
Done.