Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008744.1 Hibiscus syriacus cultivar Beakdansim tig00111833_pilon, 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: 364351
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:182492 original size:20 final size:22
Alignment explanation
Indices: 182467--182506 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
182457 TGTTGTATAT
182467 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
182487 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
182507 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:182838 original size:29 final size:30
Alignment explanation
Indices: 182806--182874 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
182796 GAAACATTTT
182806 AAAACTTTTAATAAATTCAATT-AAGTCCA
1 AAAACTTTTAATAAATTCAATTCAAGTCCA
**
182835 AAAA-TATTTTGTAAATTCAATTCAAGTCCA
1 AAAACT-TTTAATAAATTCAATTCAAGTCCA
182865 AAAACATTTT
1 AAAAC-TTTT
182875 GCCTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 1 0.03
29 18 0.53
30 11 0.32
31 3 0.09
32 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAACTTTTAATAAATTCAATTCAAGTCCA
Found at i:182864 original size:30 final size:29
Alignment explanation
Indices: 182817--182875 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
182807 AAACTTTTAA
*
182817 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
182846 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
182876 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:184178 original size:19 final size:20
Alignment explanation
Indices: 184135--184182 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
184125 TCTAAATCAT
*
184135 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
184155 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
184174 TTTTCAAAA
1 TTTTCAAAA
184183 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:185591 original size:21 final size:21
Alignment explanation
Indices: 185565--185620 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
185555 TTAGTGCAGG
185565 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
185586 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
185607 TGCATGGATGCACT
1 TGCATGGATGCACT
185621 TTGACACCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:185721 original size:29 final size:29
Alignment explanation
Indices: 185689--185751 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
185679 GAAAGCTTTT
185689 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
* *
185719 AAATATTTTGTAAATTTAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
185749 AAA
1 AAA
185752 CATCTTGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
30 14 0.48
31 5 0.17
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:187305 original size:38 final size:38
Alignment explanation
Indices: 187247--187328 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
187237 GGCGTTACAC
* ** *
187247 GACCCAAAAATTATTTACCCTCCACCTGACCCAAA-CT
1 GACCCGAAAATTATGCACCCTCCACCCGACCCAAATCT
**
187284 AGACCCGAAAATTATGCACCCTTTACCCGACCCAAATCT
1 -GACCCGAAAATTATGCACCCTCCACCCGACCCAAATCT
187323 GACCCG
1 GACCCG
187329 CCATTTTGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 35 0.95
39 2 0.05
ACGTcount: A:0.33, C:0.38, G:0.10, T:0.20
Consensus pattern (38 bp):
GACCCGAAAATTATGCACCCTCCACCCGACCCAAATCT
Found at i:192789 original size:17 final size:17
Alignment explanation
Indices: 192767--192801 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
192757 TTTTACCGGA
192767 TTAAAAACCAATTTTTT
1 TTAAAAACCAATTTTTT
**
192784 TTAAAAACTGATTTTTT
1 TTAAAAACCAATTTTTT
192801 T
1 T
192802 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (17 bp):
TTAAAAACCAATTTTTT
Found at i:193146 original size:23 final size:24
Alignment explanation
Indices: 193116--193163 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
193106 TTTATTTTAT
193116 AATA-TTTTAAAATTAAGATAAAA
1 AATATTTTTAAAATTAAGATAAAA
* *
193139 AATATTTTTATAGTTAAGATAAAA
1 AATATTTTTAAAATTAAGATAAAA
193163 A
1 A
193164 TAAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (24 bp):
AATATTTTTAAAATTAAGATAAAA
Found at i:193168 original size:30 final size:30
Alignment explanation
Indices: 193129--193263 Score: 143
Period size: 30 Copynumber: 4.6 Consensus size: 30
193119 ATTTTAAAAT
*
193129 TAAG-ATAAAAAATATTTTTATAGTTAAGA
1 TAAGAATAAAATATATTTTTATAGTTAAGA
* * *
193158 TAAAAATAAAATATATTTCTTA-AATTAAAA
1 TAAGAATAAAATATATTT-TTATAGTTAAGA
*
193188 TAAGAATAAAATGTA-TTTTATAAGTTAAGA
1 TAAGAATAAAATATATTTTTAT-AGTTAAGA
* * **
193218 TAAGATTAAAATGTACCTTT-TAGTTAAGA
1 TAAGAATAAAATATATTTTTATAGTTAAGA
193247 TAAGAATAAAATATATT
1 TAAGAATAAAATATATT
193264 CGATAAATTA
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.03
29 26 0.30
30 52 0.60
31 6 0.07
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (30 bp):
TAAGAATAAAATATATTTTTATAGTTAAGA
Found at i:193296 original size:89 final size:88
Alignment explanation
Indices: 193149--193312 Score: 208
Period size: 89 Copynumber: 1.9 Consensus size: 88
193139 AATATTTTTA
* *
193149 TAGTTAAGATAAAAATAAAATATATTTCTTAAATTAAAATAAGAATAAAATGTATTTTATAAGTT
1 TAGTTAAGATAAAAATAAAATATATTTCATAAATTAAAATAAGAATAAAATATATTTTA-AAGTT
193214 AAGATAAGATTAAAATGTACCTTT
65 AAGATAAGATTAAAATGTACCTTT
* * * *
193238 TAGTTAAGATAAGAATAAAATATA-TTCGATAAATTAAGAA-AA-AATATATATATTTTTTAATG
1 TAGTTAAGATAAAAATAAAATATATTTC-ATAAATTAA-AATAAGAATA-AAATATATTTTAAAG
*
193300 TTAAGATATGATT
63 TTAAGATAAGATT
193313 TTAAATCAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
88 21 0.32
89 42 0.65
90 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (88 bp):
TAGTTAAGATAAAAATAAAATATATTTCATAAATTAAAATAAGAATAAAATATATTTTAAAGTTA
AGATAAGATTAAAATGTACCTTT
Found at i:194267 original size:20 final size:21
Alignment explanation
Indices: 194234--194272 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
194224 TTAGGGTTTA
194234 TATTTCTTAATTG-ATTTAGG
1 TATTTCTTAATTGAATTTAGG
* *
194254 TATTTTTTATTTGAATTTA
1 TATTTCTTAATTGAATTTA
194273 AAATTAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (21 bp):
TATTTCTTAATTGAATTTAGG
Found at i:200366 original size:20 final size:20
Alignment explanation
Indices: 200343--200395 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
200333 CCCTACTAGA
*
200343 AGTATTGATACTCTACCCTC
1 AGTATCGATACTCTACCCTC
*
200363 AGTATCGATATTCTACCCTC
1 AGTATCGATACTCTACCCTC
200383 AGTATCGATACTC
1 AGTATCGATACTC
200396 CCTTAAGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTCTACCCTC
Found at i:201943 original size:23 final size:23
Alignment explanation
Indices: 201917--201961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
201907 TATAAATGAA
* *
201917 GTTCGTGAACATTAAACAAACAT
1 GTTCATGAACAATAAACAAACAT
*
201940 GTTCATGAACAATAAATAAACA
1 GTTCATGAACAATAAACAAACA
201962 AACATGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (23 bp):
GTTCATGAACAATAAACAAACAT
Found at i:202863 original size:31 final size:29
Alignment explanation
Indices: 202805--202863 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
202795 ACTTTTTTTA
*
202805 GTGGCCAAAATAAAAATGTTAAAAGTTTG
1 GTGGCCAAAATAAAAATGTGAAAAGTTTG
202834 GTGGCCAAAATACAAAGAT-TGGAAAAGTTT
1 GTGGCCAAAATA-AAA-ATGT-GAAAAGTTT
202864 ATAGACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.46
30 4 0.15
31 10 0.38
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (29 bp):
GTGGCCAAAATAAAAATGTGAAAAGTTTG
Found at i:202891 original size:31 final size:31
Alignment explanation
Indices: 202856--202916 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
202846 CAAAGATTGG
*
202856 AAAAGTTTATAGACCAAAAAG-GTAATTTTCC
1 AAAAGTTTAGAGA-CAAAAAGTGTAATTTTCC
*
202887 AAAAGTTTAGAGACTAAAAGTGTAATTTTC
1 AAAAGTTTAGAGACAAAAAGTGTAATTTTC
202917 AAAGGTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (31 bp):
AAAAGTTTAGAGACAAAAAGTGTAATTTTCC
Found at i:204125 original size:19 final size:20
Alignment explanation
Indices: 204082--204126 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
204072 TACTATGCTG
*
204082 GAAATTTATGTTAGAGTGTT
1 GAAATTTATGTTAGAATGTT
204102 GAAATTTATGTTAGAATG-T
1 GAAATTTATGTTAGAATGTT
204121 GAAATT
1 GAAATT
204127 GGTTTGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (20 bp):
GAAATTTATGTTAGAATGTT
Found at i:207760 original size:16 final size:17
Alignment explanation
Indices: 207739--207781 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
207729 ATGTAAAAAT
207739 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
207755 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
207772 AAATATTTAA
1 AAATATTTAA
207782 TCAAGTAGAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:212718 original size:68 final size:66
Alignment explanation
Indices: 212617--212742 Score: 189
Period size: 68 Copynumber: 1.9 Consensus size: 66
212607 TTTAAATTAT
* * * *
212617 AATTTTTAGACTATTTTTTTATTTTACATATTAAGTTGTATTTGAGTAGTTTGGTAAGGTAATAG
1 AATTATTAGACTATTTTTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGGTAATAG
212682 A
66 A
*
212683 AATTATTAGACTATTTATTTTCATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAG
1 AATTATTAGACTATTT-TTTT-ATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAG
212743 TTTTATTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 15 0.28
67 4 0.08
68 34 0.64
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (66 bp):
AATTATTAGACTATTTTTTTATTTTACAGATTAAATCGTATTTGAGTAGTTTGGTAAGGTAATAG
A
Found at i:212828 original size:18 final size:19
Alignment explanation
Indices: 212794--212829 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
212784 ATTAATTAGA
212794 ATATTTATTTTGATTTAAC
1 ATATTTATTTTGATTTAAC
*
212813 ATATTTTTTTTG-TTTAA
1 ATATTTATTTTGATTTAA
212830 ATTTTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (19 bp):
ATATTTATTTTGATTTAAC
Found at i:214971 original size:22 final size:23
Alignment explanation
Indices: 214938--214980 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
214928 ATATTAAATA
214938 AAATATTGATATTATCCACATAG
1 AAATATTGATATTATCCACATAG
*
214961 AAATA-TGATATTATTCACAT
1 AAATATTGATATTATCCACAT
214981 TCATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (23 bp):
AAATATTGATATTATCCACATAG
Found at i:215034 original size:27 final size:27
Alignment explanation
Indices: 215004--215055 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
214994 ACATCAACAA
*
215004 ATATCCATCACATTCATTCAAATATTG
1 ATATCAATCACATTCATTCAAATATTG
* *
215031 ATATTAATCATATTCATTCAAATAT
1 ATATCAATCACATTCATTCAAATAT
215056 AACATCAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATCAATCACATTCATTCAAATATTG
Found at i:217955 original size:19 final size:18
Alignment explanation
Indices: 217923--217970 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
217913 GGTAAAAATT
* *
217923 AAAATTATACTTATGACGA
1 AAAATTAAATTTATGA-GA
**
217942 AAAATTAAATTTATGATT
1 AAAATTAAATTTATGAGA
217960 AAAATTAAATT
1 AAAATTAAATT
217971 AATTAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAATTAAATTTATGAGA
Found at i:217993 original size:27 final size:24
Alignment explanation
Indices: 217963--218017 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
217953 TATGATTAAA
*
217963 ATTAAATTAATTAATTACTAAAATATT
1 ATTAAATTAATT-A-TAAT-AAATATT
*
217990 ATTAATTTAATTATAATAAATATT
1 ATTAAATTAATTATAATAAATATT
218014 ATTA
1 ATTA
218018 GAGTTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
25 3 0.12
26 1 0.04
27 11 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAAATTAATTATAATAAATATT
Found at i:218118 original size:47 final size:47
Alignment explanation
Indices: 218051--218145 Score: 154
Period size: 47 Copynumber: 2.0 Consensus size: 47
218041 TTAAAAATAT
* *
218051 TTTTAACATTTTTACTAGAAATACTAAATCAAATGTTGATCTAATTA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
* *
218098 TTTTAACATTTTTACTAGAAATATTAAATCAAATATTTATCAAATTA
1 TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
218145 T
1 T
218146 ACTAATGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (47 bp):
TTTTAACATTTTTACTAGAAATACTAAATCAAATATTGATCAAATTA
Found at i:218237 original size:24 final size:24
Alignment explanation
Indices: 218191--218237 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
218181 CTAATGACGA
* * *
218191 AAAATTAAATTTATGATTTAAATT
1 AAAATTAAATTAATGACTAAAATT
*
218215 AAAATTAAATTAATTACTAAAAT
1 AAAATTAAATTAATGACTAAAAT
218238 ATTATTAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AAAATTAAATTAATGACTAAAATT
Found at i:218457 original size:22 final size:24
Alignment explanation
Indices: 218402--218458 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
218392 CTATTGAGGT
218402 TATTATTTTTCGTCATTATAATAAA
1 TATT-TTTTTCGTCATTATAATAAA
* *
218427 TATTATTTTTTGTCATTATAAT-TA
1 TATT-TTTTTCGTCATTATAATAAA
218451 TATTTTTT
1 TATTTTTT
218459 AACATTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.13
24 5 0.17
25 21 0.70
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (24 bp):
TATTTTTTTCGTCATTATAATAAA
Found at i:221128 original size:23 final size:23
Alignment explanation
Indices: 221098--221156 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
221088 CTGAATGATT
221098 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
*
221121 CAGTGCTGACTGATTCAGTAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
221144 TAGTGATGACTGA
1 CAGTGCTGACTGA
221157 GCACAGAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:221798 original size:2 final size:2
Alignment explanation
Indices: 221793--221819 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
221783 AAAATCATAC
221793 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
221820 TACCCCTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:224464 original size:2 final size:2
Alignment explanation
Indices: 224457--224481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
224447 CAACCAAATA
224457 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 A
224482 GATACTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:227409 original size:25 final size:25
Alignment explanation
Indices: 227369--227418 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
227359 AGTTTTAGTA
* *
227369 AACACGTCTTCTTTCAAATCGATGG
1 AACACGTCTCCATTCAAATCGATGG
227394 AACACGTCTCCATTCAAATCGATGG
1 AACACGTCTCCATTCAAATCGATGG
227419 GGGAAACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (25 bp):
AACACGTCTCCATTCAAATCGATGG
Found at i:227845 original size:2 final size:2
Alignment explanation
Indices: 227838--227898 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
227828 GGTAAACATT
227838 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
227880 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
227899 TAACTGATGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:241237 original size:28 final size:28
Alignment explanation
Indices: 241197--241252 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
241187 TTATTATGGT
241197 AAGTTATATCAATATGTATAATTGTGGC
1 AAGTTATATCAATATGTATAATTGTGGC
241225 AAGTTATATCAATATGTATAATTGTGGC
1 AAGTTATATCAATATGTATAATTGTGGC
241253 CTTTAGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (28 bp):
AAGTTATATCAATATGTATAATTGTGGC
Found at i:244199 original size:30 final size:30
Alignment explanation
Indices: 244163--244220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
244153 AATGACCACC
* * *
244163 ATAGGTCTTCAGGAGCACATGGCGACCTCT
1 ATAGGTCTCCAGAAGCACACGGCGACCTCT
*
244193 ATAGGTCTCCATAAGCACACGGCGACCT
1 ATAGGTCTCCAGAAGCACACGGCGACCT
244221 ATGGAACTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (30 bp):
ATAGGTCTCCAGAAGCACACGGCGACCTCT
Found at i:253188 original size:24 final size:24
Alignment explanation
Indices: 253152--253202 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
253142 AGGATTGTAC
** *
253152 CACAAGAGTAGAGAAAACACATGT
1 CACAAGAACAGAGAAAAAACATGT
*
253176 CACAAGAACAGAGAAAAAACGTGT
1 CACAAGAACAGAGAAAAAACATGT
253200 CAC
1 CAC
253203 GAGGACATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.10
Consensus pattern (24 bp):
CACAAGAACAGAGAAAAAACATGT
Found at i:253428 original size:2 final size:2
Alignment explanation
Indices: 253423--253477 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
253413 TATGCAAAGA
253423 AT AT AT AT AT AT AT AT AT AT AT A- 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
253464 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
253478 GTTGAGTTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:256265 original size:2 final size:2
Alignment explanation
Indices: 256260--256295 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
256250 TATGCAAAGA
256260 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
256296 TGTTGAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257391 original size:2 final size:2
Alignment explanation
Indices: 257349--257374 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
257339 TGTTTTCAAC
257349 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
257375 TATTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258691 original size:26 final size:27
Alignment explanation
Indices: 258661--258711 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
258651 ATTTCCCCTC
*
258661 CCCTTCGCCAGTGCTCT-CCCATCATT
1 CCCTTCGCCAGAGCTCTCCCCATCATT
*
258687 CCCTTCGCCCGAGCTCTCCCCATCA
1 CCCTTCGCCAGAGCTCTCCCCATCA
258712 ACCTCATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.12, C:0.51, G:0.12, T:0.25
Consensus pattern (27 bp):
CCCTTCGCCAGAGCTCTCCCCATCATT
Found at i:259650 original size:4 final size:4
Alignment explanation
Indices: 259641--259670 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
259631 TAATATTTTG
259641 ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
259671 GATCTCGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:263305 original size:41 final size:43
Alignment explanation
Indices: 263233--263316 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 43
263223 ATATCATAAT
* *
263233 ATTATATAAATAAGTTCAATTAAATTTTTTTAAA-AATTAAAATTA
1 ATTAAATAAATAAGTTCAAATAAA--TTTTTAAATAA-TAAAATTA
263278 ATTAAATAAA-AAGTTCAAATAAA-TTTTAAATAATAAAAT
1 ATTAAATAAATAAGTTCAAATAAATTTTTAAATAATAAAAT
263317 AATACACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
41 13 0.36
42 2 0.06
44 12 0.33
45 9 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (43 bp):
ATTAAATAAATAAGTTCAAATAAATTTTTAAATAATAAAATTA
Found at i:263791 original size:20 final size:21
Alignment explanation
Indices: 263752--263794 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
263742 CAAACTGAAT
263752 GCTGAACGGTTCAACATTAAGA
1 GCTGAACGGTTC-ACATTAAGA
*
263774 GCTGAATGGTTC-CATTAAGA
1 GCTGAACGGTTCACATTAAGA
263794 G
1 G
263795 GCAAACAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
GCTGAACGGTTCACATTAAGA
Found at i:266602 original size:24 final size:24
Alignment explanation
Indices: 266575--266620 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
266565 TTTATAATTA
266575 TCCTTTATTTAAATTAATTCATAC
1 TCCTTTATTTAAATTAATTCATAC
266599 TCCTTTATTTAAATTAATTCAT
1 TCCTTTATTTAAATTAATTCAT
266621 TCTTGTACCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (24 bp):
TCCTTTATTTAAATTAATTCATAC
Found at i:270439 original size:20 final size:20
Alignment explanation
Indices: 270414--270454 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
270404 TATGCTACAT
270414 GTGATGATTGTAGATAATGG
1 GTGATGATTGTAGATAATGG
270434 GTGATGATTGTAGATAATGG
1 GTGATGATTGTAGATAATGG
270454 G
1 G
270455 CTTTCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (20 bp):
GTGATGATTGTAGATAATGG
Found at i:271511 original size:2 final size:2
Alignment explanation
Indices: 271506--271534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
271496 GATTAAAATA
271506 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 A
271535 CACCCACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:274320 original size:50 final size:51
Alignment explanation
Indices: 274243--274376 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 51
274233 TGTAGCACTT
* * *
274243 AACACATACTTACACTGATGTAAGTGAATAAAATAAACAATTATAACACAG
1 AACATATACTTACACTGATGTAAGTGAATAAAATAAACAAGTATAACACAC
* * * *
274294 AACATATACTTACAC-CATGTAAGTGAATAAAATAAACAAGTGTAGCACTC
1 AACATATACTTACACTGATGTAAGTGAATAAAATAAACAAGTATAACACAC
*
274344 AACATATACTTACACTGGTGTAAGTGAATAAAA
1 AACATATACTTACACTGATGTAAGTGAATAAAA
274377 AAAATGTAGC
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 44 0.60
51 29 0.40
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25
Consensus pattern (51 bp):
AACATATACTTACACTGATGTAAGTGAATAAAATAAACAAGTATAACACAC
Found at i:274420 original size:54 final size:57
Alignment explanation
Indices: 274344--274452 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 57
274334 TGTAGCACTC
* * *
274344 AACATATACTTACACTGGTGTAAGTGAAT-AA-AAAAAA-TGTAGCACTTAACAGTT
1 AACACATACTTACAATGGTGTAAGTAAATAAATAAAAAAGTGTAGCACTTAACAGTT
*
274398 AACACATACTTATAATGGTGTAAGTAAATAAAATAAAAAAGTGTAGCACTTAACA
1 AACACATACTTACAATGGTGTAAGTAAAT-AAATAAAAAAGTGTAGCACTTAACA
274453 CATATTACAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
54 25 0.53
56 2 0.04
57 6 0.13
58 14 0.30
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.27
Consensus pattern (57 bp):
AACACATACTTACAATGGTGTAAGTAAATAAATAAAAAAGTGTAGCACTTAACAGTT
Found at i:275268 original size:30 final size:29
Alignment explanation
Indices: 275200--275267 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 29
275190 TGACCATACG
275200 TTTATTTTTGTTAAGTTTAGTACATAAAC
1 TTTATTTTTGTTAAGTTTAGTACATAAAC
*
275229 TATTATTTTTGTTAAGTTTGGTACATAAAC
1 T-TTATTTTTGTTAAGTTTAGTACATAAAC
275259 TTTATTTTT
1 TTTATTTTT
275268 TTTTTCAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 9 0.24
30 28 0.76
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTATTTTTGTTAAGTTTAGTACATAAAC
Found at i:277045 original size:23 final size:20
Alignment explanation
Indices: 277001--277052 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
276991 GAGAGTAAAA
277001 TAAAAGAAAATAAAGAAGAT
1 TAAAAGAAAATAAAGAAGAT
*
277021 TAAAGAGAAAAGTAAAAGAATAT
1 TAAA-AGAAAA-T-AAAGAAGAT
277044 TAAGAAGAA
1 TAA-AAGAA
277053 GATTTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 6 0.22
22 1 0.04
23 15 0.56
24 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (20 bp):
TAAAAGAAAATAAAGAAGAT
Found at i:277063 original size:12 final size:11
Alignment explanation
Indices: 277012--277064 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
277002 AAAAGAAAAT
277012 AAAGAAGATTA
1 AAAGAAGATTA
* *
277023 AAGAGAAAAGTA
1 AA-AGAAGATTA
*
277035 AAAGAATATTA
1 AAAGAAGATTA
277046 AGAAGAAGATTTA
1 A-AAGAAGA-TTA
277059 AAAGAA
1 AAAGAA
277065 ATAAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 10 0.29
12 20 0.59
13 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (11 bp):
AAAGAAGATTA
Found at i:278254 original size:4 final size:4
Alignment explanation
Indices: 278240--278273 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
278230 AATTTTTAAG
*
278240 ATAA ATAAA ATAA ATAA ATAA ATAA TTAA ATAA A
1 ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA A
278274 ATTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:279493 original size:24 final size:24
Alignment explanation
Indices: 279460--279520 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
279450 TAGATAGATC
279460 ACTTTTGTTTATTTTGTCTTCTCT
1 ACTTTTGTTTATTTTGTCTTCTCT
* *
279484 ATTTTTGTTTATTTTGTCTTGTCT
1 ACTTTTGTTTATTTTGTCTTCTCT
*
279508 ACTTTTGATTATT
1 ACTTTTGTTTATT
279521 AGTTTTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.11, C:0.11, G:0.10, T:0.67
Consensus pattern (24 bp):
ACTTTTGTTTATTTTGTCTTCTCT
Found at i:279671 original size:20 final size:21
Alignment explanation
Indices: 279638--279681 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
279628 TTTAGATCTT
*
279638 TTTATTTACCCATTATCTTAG
1 TTTATTTACACATTATCTTAG
279659 TTTA-TTACACATTATCTTAG
1 TTTATTTACACATTATCTTAG
279679 TTT
1 TTT
279682 TATCTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTATTTACACATTATCTTAG
Found at i:279686 original size:11 final size:11
Alignment explanation
Indices: 279670--279696 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
279660 TTATTACACA
279670 TTATCTTAGTT
1 TTATCTTAGTT
279681 TTATCTTAGTT
1 TTATCTTAGTT
279692 TTATC
1 TTATC
279697 ACATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (11 bp):
TTATCTTAGTT
Found at i:282918 original size:19 final size:19
Alignment explanation
Indices: 282894--282942 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
282884 TAAAAGGTGT
282894 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
282913 ATCGATGCACTCCCTATGC
1 ATCGATGCACTCCCTATGC
282932 ATCGATGCACT
1 ATCGATGCACT
282943 TATTAAATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCCCTATGC
Found at i:284372 original size:18 final size:18
Alignment explanation
Indices: 284346--284384 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
284336 CCAAGTTAGC
284346 ATTACTTGCATAAAT-CTT
1 ATTACTTGCA-AAATACTT
*
284364 ATTATTTGCAAAATACTT
1 ATTACTTGCAAAATACTT
284382 ATT
1 ATT
284385 CGAATCACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTACTTGCAAAATACTT
Found at i:286934 original size:31 final size:30
Alignment explanation
Indices: 286862--286952 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 30
286852 GAAGGACCTA
* *
286862 TCCATATGTTCTGAAGAACAAAGGTAACATTG
1 TCCATATG-TCTGAAG-ACATAGGTAACACTG
*
286894 TTCATATGTCCTGAATGACATAGGTAA-ACTG
1 TCCATATGT-CTGAA-GACATAGGTAACACTG
286925 TCCATATGTCTCGAAAGACATAGGTAAC
1 TCCATATGTCT-G-AAGACATAGGTAAC
286953 CCTCGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
30 2 0.04
31 24 0.48
32 23 0.46
33 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (30 bp):
TCCATATGTCTGAAGACATAGGTAACACTG
Found at i:291752 original size:244 final size:243
Alignment explanation
Indices: 291298--291999 Score: 736
Period size: 244 Copynumber: 2.9 Consensus size: 243
291288 TGTTAACTGG
* * * * * * * ** *
291298 ACCTTCTAGTAGTTGTTAACTCACAGCCACATCAACATTTCATACCTAAATTCATGTTCACTATT
1 ACCTTCTAGAAGGTGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATACTCACTGTT
* * *
291363 CCAACTTTGATTCCAGAACAAAAAGTGTC-A-TTTTA---A-GTT-----CATTTTTCAGAAGTC
66 CCAACCTCGATTCCAGAACAAAAAGT-ACAATTTTTAGTCATGTTAAGCACATTTTTCAGAAGTC
* * * * *
291417 ATTTCCCTGCACAGAAATCACATAAATAGTCCAAAATCAGCAATAATAATGAACAAACGAGGAGT
130 ATTGCCCTACACAGAAATCACGTAAAAAG-CCAAAATCAGTAATAATAATGAACAAACGAGGAGT
* * * *
291482 ATTTAATCATAAAATGTTGTCCAAAATAAACATTGAACGCTACTGAGTGG
194 ATTTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAGCGA
** ** * * * *
291532 AGTTTCTAGAATTTGTTGACTCACTGTCACGTCAACATTTCATGCCCAAATTCATGC-CTACTGT
1 ACCTTCTAGAAGGTGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATACTC-ACTGT
* * **
291596 TCCAACCTTGATTCGAGAACAAAAAGTGTAATTTTTAGTCATGTTAAGCACATTTTTCAGAAGTC
65 TCCAACCTCGATTCCAGAACAAAAAGTACAATTTTTAGTCATGTTAAGCACATTTTTCAGAAGTC
* * *
291661 ATTGCCCTACACAGAAATCACGTAAAAAGACCCAAATCAGTAATAATAATTAACAACCGAGGAGT
130 ATTGCCCTACACAGAAATCACGTAAAAAG-CCAAAATCAGTAATAATAATGAACAAACGAGGAGT
* *
291726 ATTTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTGCTGTGCGA
194 ATTTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAGCGA
291776 ACCTTCTAGAAGGTGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATACTCACTGTT
1 ACCTTCTAGAAGGTGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATACTCACTGTT
* * * * *
291841 CCAGCCTCGATTCCAGAACAAAAAGTACAATTTTTAGTCTTTTTAAGCATATTTCT-AGAAGTCA
66 CCAACCTCGATTCCAGAACAAAAAGTACAATTTTTAGTCATGTTAAGCACATTTTTCAGAAGTCA
* * ** ** * *
291905 TTGCCTTGA-A-ATAATATCTTGTAAAAAGGTAAAATCAATAATAATAATGAACAAACGATGA-T
131 TTGCCCT-ACACAGAA-ATCACGTAAAAAGCCAAAATCAGTAATAATAATGAACAAACGAGGAGT
*
291967 CATTTAATCATAAAATATT-GCATAAAATAAACA
194 -ATTTAATCATAAAATATTGGC-CAAAATAAACA
292000 CTAGTTAATT
Statistics
Matches: 391, Mismatches: 60, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
233 1 0.00
234 76 0.19
235 5 0.01
238 1 0.00
239 3 0.01
241 3 0.01
242 57 0.15
243 26 0.07
244 218 0.56
245 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.30
Consensus pattern (243 bp):
ACCTTCTAGAAGGTGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATACTCACTGTT
CCAACCTCGATTCCAGAACAAAAAGTACAATTTTTAGTCATGTTAAGCACATTTTTCAGAAGTCA
TTGCCCTACACAGAAATCACGTAAAAAGCCAAAATCAGTAATAATAATGAACAAACGAGGAGTAT
TTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAGCGA
Found at i:293792 original size:22 final size:21
Alignment explanation
Indices: 293764--293819 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
293754 TAATATCATC
293764 ACACATTTAGATCTT-TTTATTT
1 ACACATTT--ATCTTATTTATTT
293786 ACACA-TTATCTTAGTTTATTT
1 ACACATTTATCTTA-TTTATTT
293807 ACACA-TTATCTTA
1 ACACATTTATCTTA
293820 GTTTTATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
21 22 0.69
22 5 0.16
ACGTcount: A:0.30, C:0.16, G:0.04, T:0.50
Consensus pattern (21 bp):
ACACATTTATCTTATTTATTT
Found at i:293805 original size:21 final size:21
Alignment explanation
Indices: 293779--293823 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
293769 TTTAGATCTT
293779 TTTATTTACACATTATCTTAG
1 TTTATTTACACATTATCTTAG
293800 TTTATTTACACATTATCTTAG
1 TTTATTTACACATTATCTTAG
293821 TTT
1 TTT
293824 TATCTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.13, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTATTTACACATTATCTTAG
Found at i:293826 original size:11 final size:11
Alignment explanation
Indices: 293812--293838 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
293802 TATTTACACA
293812 TTATCTTAGTT
1 TTATCTTAGTT
293823 TTATCTTAGTT
1 TTATCTTAGTT
293834 TTATC
1 TTATC
293839 ACACTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (11 bp):
TTATCTTAGTT
Found at i:300388 original size:31 final size:32
Alignment explanation
Indices: 300316--300406 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 32
300306 GAAGGACCTA
* *
300316 TCCATATGTTTCG-AAGAACATAGGTAACATTG
1 TCCATATGTCTCGAAAG-ACATAGGTAACACTG
* *
300348 TTCATATGTC-CTGAATGACATAGGTAA-ACTG
1 TCCATATGTCTC-GAAAGACATAGGTAACACTG
300379 TCCATATGTCTCGAAAGACATAGGTAAC
1 TCCATATGTCTCGAAAGACATAGGTAAC
300407 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
31 27 0.55
32 20 0.41
33 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (32 bp):
TCCATATGTCTCGAAAGACATAGGTAACACTG
Found at i:301197 original size:24 final size:24
Alignment explanation
Indices: 301165--301224 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
301155 CACACTATAA
301165 TGTATCGATGCATTCCTGAACGTG
1 TGTATCGATGCATTCCTGAACGTG
301189 TGTATCGATGCATTCCTGAACGTG
1 TGTATCGATGCATTCCTGAACGTG
301213 TGTATCGATGCA
1 TGTATCGATGCA
301225 CTACCTATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (24 bp):
TGTATCGATGCATTCCTGAACGTG
Found at i:305348 original size:244 final size:242
Alignment explanation
Indices: 304891--305595 Score: 765
Period size: 244 Copynumber: 2.9 Consensus size: 242
304881 CGCTGCTAAC
* * * *
304891 TGGATCTTCTAGTAGTTGTTGACTCACTGCCACATCAACATTTCATACCTAAATTCATGTCC-AC
1 TGGACCTTCTAGAAGTTGTTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATG-CCTAC
* * *
304955 TATTCCAACTTTGATTCGAGAACAAAAAGTGTCATTTTA---A-GTT----CATTTTTCAGAAGT
65 TGTTCCAACCTTGATTCGAGAACAAAAAGTGTAATTTTAGTCATGTTAACACATTTTTCAGAAGT
* * * *
305012 CATTTCCCTGCACAGAAATCACATAAATAGGCCAAAATCAGCAATAATAATGAACAAACGAGGAG
130 CATTGCCCTACACAGAAATCACATAAAAAGACCAAAATCAGCAATAATAATGAACAAACGAGGAG
*
305077 TATCTAATCATAAAATATTGTCCAAAATAAACATTGAACGCTACTGAG
195 TATCTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAG
* *
305125 TGGAGCTTCTAGAAGTTGTTGACTCACTGCCACGTCAACATTTCATGCCCAAATTCATGCCTACT
1 TGGACCTTCTAGAAGTTGTTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATGCCTACT
305190 GTTCCAACCTTGATTCGAGAACAAAAAGTGTAATTTTTAGTCATGTTAAGCACATTTTTCAGAAG
66 GTTCCAACCTTGATTCGAGAACAAAAAGTGTAA-TTTTAGTCATGTTAA-CACATTTTTCAGAAG
* * * * *
305255 TCATTGCCCTACACAGAAATCACGTAAAAAGACCCAAATCAGTAATAATAATTAACAACCGAGGA
129 TCATTGCCCTACACAGAAATCACATAAAAAGACCAAAATCAGCAATAATAATGAACAAACGAGGA
* * *
305320 GTATTTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTGCTGTG
194 GTATCTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAG
* * * * * *
305369 CGAACCTTCTAAAAGATGCTGACTCACTGCCACATCAACATTTCATGCCCAAATTCAT-ACTCAC
1 TGGACCTTCTAGAAGTTGTTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATGCCT-AC
** * * * ** * * *
305433 TGTTCCAGTCTCGATTCCAGAATAAAAAGTACAAATTTTAGTCTTTTTAAACACATTTCT-AGAA
65 TGTTCCAACCTTGATTCGAGAACAAAAAGT-GTAATTTTAGTCATGTT-AACACATTTTTCAGAA
* * *** ** * *
305497 GTCATTGCCTTGA-A-ATAATATCTTGTAAAAAG-GTAAAATCAACAATAATAATAAACAAACGA
128 GTCATTGCCCT-ACACAGAA-ATCACATAAAAAGACCAAAATCAGCAATAATAATGAACAAACGA
* * * *
305559 TGAGCATTTAATCATAAAATGTT-GCACAAAATAAACA
191 GGAGTATCTAATCATAAAATATTGGC-CAAAATAAACA
305596 CTAGTTAATT
Statistics
Matches: 401, Mismatches: 53, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
233 2 0.00
234 87 0.22
235 5 0.01
238 1 0.00
239 3 0.01
241 2 0.00
242 57 0.14
243 28 0.07
244 212 0.53
245 4 0.01
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (242 bp):
TGGACCTTCTAGAAGTTGTTGACTCACTGCCACATCAACATTTCATGCCCAAATTCATGCCTACT
GTTCCAACCTTGATTCGAGAACAAAAAGTGTAATTTTAGTCATGTTAACACATTTTTCAGAAGTC
ATTGCCCTACACAGAAATCACATAAAAAGACCAAAATCAGCAATAATAATGAACAAACGAGGAGT
ATCTAATCATAAAATATTGGCCAAAATAAACATTGAACGCTACTGAG
Found at i:311902 original size:17 final size:17
Alignment explanation
Indices: 311880--311936 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
311870 GAAACCATAT
*
311880 AGCTTCACAGTTGAATA
1 AGCTTCACAGTTGAATG
311897 AGCTTCACAGTTGAATG
1 AGCTTCACAGTTGAATG
311914 AGCTTCACAGTTGAATG
1 AGCTTCACAGTTGAATG
311931 AGCTTC
1 AGCTTC
311937 CTTGTTCCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (17 bp):
AGCTTCACAGTTGAATG
Found at i:314659 original size:22 final size:23
Alignment explanation
Indices: 314622--314668 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
314612 AACCCTAAAT
314622 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
314645 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
314667 AA
1 AA
314669 CTCGCGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:316294 original size:28 final size:29
Alignment explanation
Indices: 316223--316294 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
316213 TAAACCCATT
* ***
316223 TCTTATTCTCTGCTCATTTAATCACTGTT
1 TCTTATTCTCTGCTCATTCAATCACTCCA
316252 TCTCT-TTCTCT-CTCATTCAATCAC-CCA
1 TCT-TATTCTCTGCTCATTCAATCACTCCA
316279 TCTTATTCTCTGCTCA
1 TCTTATTCTCTGCTCA
316295 CAACCAGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 1 0.03
27 9 0.25
28 16 0.44
29 9 0.25
30 1 0.03
ACGTcount: A:0.17, C:0.32, G:0.04, T:0.47
Consensus pattern (29 bp):
TCTTATTCTCTGCTCATTCAATCACTCCA
Found at i:317386 original size:227 final size:227
Alignment explanation
Indices: 316981--317402 Score: 674
Period size: 227 Copynumber: 1.9 Consensus size: 227
316971 ACACGACACA
*
316981 AAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTGAAAAAATTATATATATA
1 AAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATATA
*
317046 AGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTATCGGGTCGGTCCGG
66 AGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTATCGAGTCGG--CGG
* * *
317111 TTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATTACACTTAAAAAACCCGACCCGAC
129 TATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCGAC
317176 CCGACCCGAACAAAATAAAATTTCACTCGACCCG
194 CCGACCCGAACAAAATAAAATTTCACTCGACCCG
* *
317210 AAATAATAAAAAAA-TATTTTTATTCAATAAAAATAGTGACTTAATTG-AAATATATATATATAT
1 AAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAT-TATATATAT
317273 ATAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT-TCGAGTC-G
65 A-AGG-G-ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTATCGAGTCGG
*
317336 -GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACCGACCC
126 CGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACCC
317400 GAC
191 GAC
317403 TCGGCCAAAA
Statistics
Matches: 180, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
227 68 0.38
228 41 0.23
229 17 0.09
230 2 0.01
231 49 0.27
232 3 0.02
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.31
Consensus pattern (227 bp):
AAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATTATATATATA
AGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTATCGAGTCGGCGGTA
TTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAACCGACCCGACCC
GACCCGAACAAAATAAAATTTCACTCGACCCG
Found at i:317436 original size:227 final size:228
Alignment explanation
Indices: 316966--317438 Score: 635
Period size: 227 Copynumber: 2.1 Consensus size: 228
316956 TAGAAATCCA
* * *
316966 ACCCGACACGACACAAAATAATAAAAAAATTATTTTTATTCAATAAAAACATTGACTTAATTGAA
1 ACCCGACACGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
317031 AAAATTATATATATAAGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTT
66 AAAATTATATATATAAGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTT
* * *
317096 ATCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATTACACTTAA
131 ATCGAGTCGG--CGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
317161 AAAACCCGACCCGACCCGACCCGAACAAAATAAAATTT
194 AAAA--C-ACCCGACCCGACCCGAACAAAATAAAATTT
* *
317199 ---C-ACTCGACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAATAGTGACTTAATTG-A
1 ACCCGACACGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
*
317258 AATATATATATATATATAGGAGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
66 AAAAT-TATATATATA-AGG-G-ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
*
317323 TATTT-TCGAGTC-G-GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACT
127 T-TTTATCGAGTCGGCGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACT
* ** *
317385 TAAAAAA-A-CCGACCCGACTCGGCCAAAATAAAGTTT
191 TAAAAAACACCCGACCCGACCCGAACAAAATAAAATTT
*
317421 CACCCGACCCGACCCGAA
1 -ACCCGACACGACCCGAA
317439 TATATGAATT
Statistics
Matches: 215, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
222 24 0.11
223 1 0.00
226 1 0.00
227 69 0.32
228 41 0.19
229 24 0.11
230 3 0.01
231 49 0.23
232 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (228 bp):
ACCCGACACGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAA
AAAATTATATATATAAGGGATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTT
ATCGAGTCGGCGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
AACACCCGACCCGACCCGAACAAAATAAAATTT
Found at i:319726 original size:31 final size:30
Alignment explanation
Indices: 319659--319735 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
319649 CACATCTTAA
* * *
319659 TAATTAAATACAAACGAACATTACCACATT
1 TAATTAAATACAAATGAACATGAACACATT
**
319689 TCAATTAAATACAAATGAACATGAACGTATCT
1 T-AATTAAATACAAATGAACATGAACACAT-T
*
319721 TAATTAAATAAAAAT
1 TAATTAAATACAAAT
319736 AAAAATGATC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 1 0.03
31 36 0.92
32 2 0.05
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (30 bp):
TAATTAAATACAAATGAACATGAACACATT
Found at i:320959 original size:19 final size:20
Alignment explanation
Indices: 320916--320982 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
320906 GCTGCTGGAA
*
320916 ACCGGTT-T-AACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
*
320935 AACGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
320954 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
320973 ACCGG-TCTGA
1 ACCGGTTCTGA
320983 CCCGACCCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 2 0.05
19 30 0.73
20 9 0.22
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:320969 original size:29 final size:29
Alignment explanation
Indices: 320915--320984 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
320905 GGCTGCTGGA
* *
320915 AACCGGTTTAACCGGTTTCAAACGGTTCG
1 AACCGGTTTGACCGGTCTCAAACGGTTCG
* * *
320944 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 AACCGGTTTGACCGGTCTCAAACGGTTCG
*
320973 -ACCGGTCTGACC
1 AACCGGTTTGACC
320985 CGACCCGACC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.27
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTCAAACGGTTCG
Found at i:321007 original size:22 final size:22
Alignment explanation
Indices: 320981--321106 Score: 190
Period size: 22 Copynumber: 6.0 Consensus size: 22
320971 TGACCGGTCT
320981 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
321003 GACCCGAACCGACCGTTGACCT
1 GACCCGACCCGACCGTTGACCC
321025 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
321047 GACCCGAACCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
321069 GACCCG----G-CCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
321086 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
321107 GTTGACCATT
Statistics
Matches: 94, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.17
18 1 0.01
21 1 0.01
22 76 0.81
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:321023 original size:39 final size:39
Alignment explanation
Indices: 320980--321106 Score: 191
Period size: 39 Copynumber: 3.1 Consensus size: 39
320970 TTGACCGGTC
320980 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGTT
1 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCG-T
321020 GACCTGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
1 ----TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
* *
321063 TGACCCGACCCGGCCGTTGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
321102 TGACC
1 TGACC
321107 GTTGACCATT
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
39 42 0.52
43 1 0.01
44 38 0.47
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (39 bp):
TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
Found at i:321106 original size:17 final size:17
Alignment explanation
Indices: 320980--321094 Score: 93
Period size: 17 Copynumber: 6.9 Consensus size: 17
320970 TTGACCGGTC
320980 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
320997 TGACCCGACCCGAACC--
1 TGACCCGACCCG-ACCGT
**
321013 -GA-CCG--TTGACC--
1 TGACCCGACCCGACCGT
321024 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
321041 TGACCCGACCCGAACCGACCGT
1 TGACCCGA--C---CCGACCGT
*
321063 TGACCCGACCCGGCCGT
1 TGACCCGACCCGACCGT
321080 TGACCCGACCCGACC
1 TGACCCGACCCGACC
321095 CGACCGTTGA
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 3 0.04
14 3 0.04
15 6 0.08
17 41 0.51
18 3 0.04
19 1 0.01
20 1 0.01
22 16 0.20
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:328291 original size:9 final size:9
Alignment explanation
Indices: 328277--328370 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
328267 GGCTGCTGGA
328277 AACCGGTTT
1 AACCGGTTT
328286 AACCGGTTTT
1 AACCGG-TTT
328296 CAACCGGTTCT
1 -AACCGGTT-T
*
328307 GACCGGTTT
1 AACCGGTTT
*
328316 GACCGGTTT
1 AACCGGTTT
* *
328325 CAAACGGTTCG
1 -AACCGGTT-T
328336 AACCGGTTT
1 AACCGGTTT
* *
328345 GACCGGTCTG
1 AACCGGT-TT
*
328355 AATCGGTTT
1 AACCGGTTT
*
328364 GACCGGT
1 AACCGGT
328371 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 28 0.42
10 31 0.47
11 7 0.11
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:328302 original size:20 final size:21
Alignment explanation
Indices: 328277--328315 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
328267 GGCTGCTGGA
328277 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
328297 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
328316 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:328322 original size:19 final size:19
Alignment explanation
Indices: 328279--328376 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
328269 CTGCTGGAAA
* * *
328279 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
328299 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
* *
328318 CCGGTTTCAAACGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
328338 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
328357 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
328375 CC
1 CC
328377 CGACCCGACC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.08
19 37 0.57
20 15 0.23
21 8 0.12
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:328340 original size:29 final size:30
Alignment explanation
Indices: 328277--328376 Score: 109
Period size: 29 Copynumber: 3.4 Consensus size: 30
328267 GGCTGCTGGA
* *
328277 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAAACGGTTCTG
328308 -ACCGGTTTGACCGGTTTCAAACGGTTC-G
1 AACCGGTTTGACCGGTTTCAAACGGTTCTG
* * *
328336 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAAACGGTTCTG
*
328365 -ACCGGTCTGACC
1 AACCGGTTTGACC
328377 CGACCCGACC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
28 12 0.20
29 36 0.59
30 13 0.21
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAAACGGTTCTG
Found at i:328399 original size:22 final size:22
Alignment explanation
Indices: 328373--328498 Score: 190
Period size: 22 Copynumber: 6.0 Consensus size: 22
328363 TGACCGGTCT
328373 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
* *
328395 GACCCGAACCGACCGTTGACCT
1 GACCCGACCCGACCGTTGACCC
328417 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
328439 GACCCGAACCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
328461 GACCCG----G-CCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
328478 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
328499 GTTGACCATT
Statistics
Matches: 94, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
17 16 0.17
18 1 0.01
21 1 0.01
22 76 0.81
ACGTcount: A:0.19, C:0.47, G:0.24, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:328415 original size:39 final size:39
Alignment explanation
Indices: 328372--328498 Score: 191
Period size: 39 Copynumber: 3.1 Consensus size: 39
328362 TTGACCGGTC
328372 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGTT
1 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCG-T
328412 GACCTGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
1 ----TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
* *
328455 TGACCCGACCCGGCCGTTGACCCGACCCGACCCGACCGT
1 TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
328494 TGACC
1 TGACC
328499 GTTGACCATT
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
39 42 0.52
43 1 0.01
44 38 0.47
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (39 bp):
TGACCCGACCCGACCGTTGACCCGACCCGAACCGACCGT
Found at i:328498 original size:17 final size:17
Alignment explanation
Indices: 328372--328486 Score: 93
Period size: 17 Copynumber: 6.9 Consensus size: 17
328362 TTGACCGGTC
328372 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
328389 TGACCCGACCCGAACC--
1 TGACCCGACCCG-ACCGT
**
328405 -GA-CCG--TTGACC--
1 TGACCCGACCCGACCGT
328416 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
328433 TGACCCGACCCGAACCGACCGT
1 TGACCCGA--C---CCGACCGT
*
328455 TGACCCGACCCGGCCGT
1 TGACCCGACCCGACCGT
328472 TGACCCGACCCGACC
1 TGACCCGACCCGACC
328487 CGACCGTTGA
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
11 3 0.04
12 3 0.04
13 3 0.04
14 3 0.04
15 6 0.08
17 41 0.51
18 3 0.04
19 1 0.01
20 1 0.01
22 16 0.20
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.10
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:340538 original size:6 final size:6
Alignment explanation
Indices: 340522--340555 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
340512 GACTTTCCAG
340522 GCCGAAA GCCGAA GCCGAA GCCGAA GCCGAA GCC
1 GCCG-AA GCCGAA GCCGAA GCCGAA GCCGAA GCC
340556 AAAACCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (6 bp):
GCCGAA
Found at i:340566 original size:18 final size:18
Alignment explanation
Indices: 340526--340567 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
340516 TTCCAGGCCG
* *
340526 AAAGCCGAAGCCGAAGCC
1 AAAGCCGAAGCCAAAACC
*
340544 GAAGCCGAAGCCAAAACC
1 AAAGCCGAAGCCAAAACC
340562 AAAGCC
1 AAAGCC
340568 TTTCTCTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.43, C:0.33, G:0.24, T:0.00
Consensus pattern (18 bp):
AAAGCCGAAGCCAAAACC
Found at i:354000 original size:21 final size:22
Alignment explanation
Indices: 353948--354005 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
353938 CAATTTAATC
*
353948 ATATTTTTAATAAATTAAAATAAA
1 ATATTTTT--TAAATAAAAATAAA
353972 ATATTTTTTAAATAAAAATAAA
1 ATATTTTTTAAATAAAAATAAA
*
353994 GTA-TTTTTAAAT
1 ATATTTTTTAAAT
354006 TAATTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
24 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTTTTTAAATAAAAATAAA
Found at i:354054 original size:19 final size:20
Alignment explanation
Indices: 354005--354063 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
353995 TATTTTTAAA
*
354005 TTAATTTAATAGTAAAATAAT
1 TTAAGTTAATA-TAAAATAAT
354026 TTAAAAGTTAATATAAAAT-AT
1 TT--AAGTTAATATAAAATAAT
354047 TTAAGTTAATATAAAAT
1 TTAAGTTAATATAAAAT
354064 TATATATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 15 0.43
21 6 0.17
22 6 0.17
23 8 0.23
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
TTAAGTTAATATAAAATAAT
Found at i:358586 original size:21 final size:20
Alignment explanation
Indices: 358560--358598 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
358550 ATATAAAAAT
358560 TATTTTTATTAAAATTTTTTG
1 TATTTTTATT-AAATTTTTTG
*
358581 TATTTTTATTTAATTTTT
1 TATTTTTATTAAATTTTT
358599 AAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTTTATTAAATTTTTTG
Found at i:362295 original size:14 final size:14
Alignment explanation
Indices: 362278--362304 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
362268 AACGGACATA
362278 AACGAACGTAAACG
1 AACGAACGTAAACG
362292 AACGAACGTAAAC
1 AACGAACGTAAAC
362305 AAACAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.22, G:0.19, T:0.07
Consensus pattern (14 bp):
AACGAACGTAAACG
Done.