Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 27 of 30
Found at i:5192251 original size:108 final size:108
Alignment explanation
Indices: 5192132--5192362 Score: 426
Period size: 108 Copynumber: 2.1 Consensus size: 108
5192122 CGAAATTTTC
* *
5192132 TCAAGAGAGACAAAATTTTGTTTCAAAATAAATAGACTCAAAAAACTTTTTCCTCACAATAAACA
1 TCAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAAAACTTTTTCCTCACAATAAACA
5192197 ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTGTT
66 ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTGTT
*
5192240 TCAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAAAACTTTTTTCTCACAATAAACA
1 TCAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAAAACTTTTTCCTCACAATAAACA
5192305 ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTGTT
66 ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTGTT
*
5192348 TCAAGAGAGAAAAAA
1 TCAAGAGAGACAAAA
5192363 ATCGTTTTAA
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 119 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (108 bp):
TCAAGAGAGACAAAACTTTGTTTCAAAAGAAATAGACTCAAAAAACTTTTTCCTCACAATAAACA
ACTCAAAGATTTTTATTCAAAAGGAACAGACTCAAAGATTGTT
Found at i:5192661 original size:105 final size:104
Alignment explanation
Indices: 5192480--5192673 Score: 302
Period size: 105 Copynumber: 1.9 Consensus size: 104
5192470 TTTTGAAAAG
* *
5192480 CTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTCAGAGAAGAAATGT
1 CTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTGAAATTTGTATCTCAAAGAAGAAATGT
5192545 CTCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAAT
66 CTCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAAT
* *
5192584 CTCAAGTGAGATTAATTTTGTTTCATGTGA-AGCAAATTCGAAATTTGTATCTCAAAGGAA-AAA
1 CTCAAGTGAGATTAATTTTGTTTCAAGT-ACAACAAATT-GAAATTTGTATCTCAAA-GAAGAAA
*
5192647 TGTCTCAAGTGAGACGAAATTTGTTTT
63 TGTCTCAAGCGAGACGAAATTTGTTTT
5192674 AAGAGAAATT
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
104 34 0.41
105 45 0.55
106 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (104 bp):
CTCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTGAAATTTGTATCTCAAAGAAGAAATGT
CTCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAAT
Found at i:5192732 original size:35 final size:35
Alignment explanation
Indices: 5192641--5192752 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
5192631 TATCTCAAAG
*
5192641 GAAAAATGTCTCAAGTGAGACGAAATTTGTTTTAA
1 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTAA
* * *
5192676 GAGAAATTGTCTTAAGTGAGACAAAATTTGTTTTTA
1 GA-AAAATGTCTCAAGTGAGACAAAATTTGTTTTAA
* * * *
5192712 TAAAACTGTCTCAAGCGAGACAAAATTTGTTTCAA
1 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTAA
5192747 GAAAAA
1 GAAAAA
5192753 CACCCTCAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 34 0.53
36 30 0.47
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (35 bp):
GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTAA
Found at i:5193060 original size:4 final size:4
Alignment explanation
Indices: 5193051--5193096 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
5193041 CTCATGTAAC
*
5193051 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATAT AT-T GATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT
5193097 CTTCTCGATC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
2 2 0.05
3 1 0.03
4 33 0.89
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:5194313 original size:12 final size:11
Alignment explanation
Indices: 5194296--5194359 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
5194286 TATCTTTTTG
5194296 TTCTTTGCTCTT
1 TTCTTTG-TCTT
5194308 TTCTTTGT-TT
1 TTCTTTGTCTT
*
5194318 TTGCTTT-TGTT
1 TT-CTTTGTCTT
*
5194329 TTCTTTGTTTT
1 TTCTTTGTCTT
*
5194340 TTCTTTGTTTT
1 TTCTTTGTCTT
5194351 TCTCTTTGT
1 T-TCTTTGT
5194360 TTCTTTCTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.19
11 24 0.51
12 14 0.30
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (11 bp):
TTCTTTGTCTT
Found at i:5194330 original size:21 final size:22
Alignment explanation
Indices: 5194306--5194361 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
5194296 TTCTTTGCTC
5194306 TTTTCTTTGTTTTTGCTTT-TG
1 TTTTCTTTGTTTTTGCTTTGTG
* *
5194327 TTTTCTTTGTTTTTTCTTTGTT
1 TTTTCTTTGTTTTTGCTTTGTG
5194349 TTTCTCTTTGTTT
1 TTT-TCTTTGTTT
5194362 CTTTCTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 18 0.58
22 4 0.13
23 9 0.29
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (22 bp):
TTTTCTTTGTTTTTGCTTTGTG
Found at i:5194342 original size:32 final size:32
Alignment explanation
Indices: 5194279--5194371 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
5194269 TTGTTTGTGC
* *
5194279 TCTTTG-TTATCTTTTTG-TTCTTTGCTCTTT
1 TCTTTGTTTTTCTCTTTGTTTCTTTGCTCTTT
*
5194309 TCTTTGTTTTTGCT-TTTGTTTTCTTTG-TTTTT
1 TCTTTGTTTTT-CTCTTTG-TTTCTTTGCTCTTT
5194341 TCTTTGTTTTTCTCTTTGTTTCTTT-CTCTTT
1 TCTTTGTTTTTCTCTTTGTTTCTTTGCTCTTT
5194372 GCTTCTTTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
30 6 0.11
31 20 0.37
32 21 0.39
33 7 0.13
ACGTcount: A:0.01, C:0.15, G:0.10, T:0.74
Consensus pattern (32 bp):
TCTTTGTTTTTCTCTTTGTTTCTTTGCTCTTT
Found at i:5194379 original size:14 final size:12
Alignment explanation
Indices: 5194309--5194372 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 12
5194299 TTTGCTCTTT
5194309 TCTTTGTTTTTGC
1 TCTTTGTTTTT-C
5194322 T-TTTG--TTT-
1 TCTTTGTTTTTC
5194330 TCTTTGTTTTT-
1 TCTTTGTTTTTC
5194341 TCTTTGTTTTTC
1 TCTTTGTTTTTC
5194353 TCTTTGTTTCTTTC
1 TCTTTG-TT-TTTC
5194367 TCTTTG
1 TCTTTG
5194373 CTTCTTTGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 3 0.07
11 14 0.31
12 10 0.22
13 3 0.07
14 10 0.22
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (12 bp):
TCTTTGTTTTTC
Found at i:5196421 original size:31 final size:30
Alignment explanation
Indices: 5196386--5196448 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
5196376 TGATGAAAAA
*
5196386 TAACACAAGCA-AATGAGAAAAAATGAGTTAG
1 TAACACAAACACAA-GAG-AAAAATGAGTTAG
*
5196417 TAACACAAACACCAGAGAAAAATGAGTTAG
1 TAACACAAACACAAGAGAAAAATGAGTTAG
5196447 TA
1 TA
5196449 CAAATGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 15 0.52
31 13 0.45
32 1 0.03
ACGTcount: A:0.54, C:0.13, G:0.17, T:0.16
Consensus pattern (30 bp):
TAACACAAACACAAGAGAAAAATGAGTTAG
Found at i:5197410 original size:11 final size:11
Alignment explanation
Indices: 5197394--5197418 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5197384 AAAATTTTTG
5197394 TAATTTGGAAT
1 TAATTTGGAAT
5197405 TAATTTGGAAT
1 TAATTTGGAAT
5197416 TAA
1 TAA
5197419 ATCGAATGAG
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
TAATTTGGAAT
Found at i:5199442 original size:3 final size:3
Alignment explanation
Indices: 5199429--5199458 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5199419 GTAAAAATGC
*
5199429 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5199459 TAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:5199909 original size:134 final size:134
Alignment explanation
Indices: 5199655--5199909 Score: 361
Period size: 134 Copynumber: 1.9 Consensus size: 134
5199645 GTTCGGGTCG
* *
5199655 TCTTTAGGAAGGGTGATAACTCGGTTCTTACACGATGAGGACGACTGGTTATCTATGGGTGACAC
1 TCTTTAGGAAGGCTGATAACTCGGTTCTTACACGATGAGGACGACTGGTTATCTAAGGGTGACAC
* * *
5199720 GGCTCCTACATGATGAGGAGGTCTGGTCGAGGGATGAAACTGCTCATACGCGATGAATAGTTCTA
66 GGCTCCTACATGATGAGGAGATCTGGTCGAGGGATGAAACGGCTCATACACGATGAATAGTTCTA
5199785 GCTA
131 GCTA
* * *
5199789 TCTTTAGGAAGGCTGATAACTCGGTT-TCTACATGATGAGGACGACTGGTTATCTAAGGTTGACG
1 TCTTTAGGAAGGCTGATAACTCGGTTCT-TACACGATGAGGACGACTGGTTATCTAAGGGTGACA
* * * * *
5199853 CGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGGATGATACGGTTCCTACATGATGA
65 CGGCTCCTACATGATGAGGAGATCTGGTCGA-GGGATGAAACGGCTCATACACGATGA
5199910 GGATGACTGG
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
133 2 0.02
134 104 0.98
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (134 bp):
TCTTTAGGAAGGCTGATAACTCGGTTCTTACACGATGAGGACGACTGGTTATCTAAGGGTGACAC
GGCTCCTACATGATGAGGAGATCTGGTCGAGGGATGAAACGGCTCATACACGATGAATAGTTCTA
GCTA
Found at i:5200406 original size:92 final size:92
Alignment explanation
Indices: 5200230--5200559 Score: 262
Period size: 92 Copynumber: 3.6 Consensus size: 92
5200220 TTTTTCAAAG
* ** * * * *
5200230 GAAACAATCTCAAAGGTTGTTTTTCATTAGAAATTGTCT-TA-AGAGACAATA-TTTACTTT-TA
1 GAAACAA-CTCAAAGATT-TTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTT-GTTTCAA
* * **
5200291 AAGAAATAAACTCAAAGATGATTTTGTTAGTA
63 AAGAAACAGACTCAAA-A-GATTTTGTTAAAA
* *
5200323 GAAACAACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCCAAA
1 GAAACAACTCAAAGATTTTTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
* *
5200388 TAAACATACTC-AAAGATTTTTGTTTCAAAA
65 GAAACAGACTCAAAAGA-TTTTG-TT-AAAA
** * *
5200418 GAAATTACTCGAATATTTTTTTTC--AAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
1 GAAACAACTCAAAGA-TTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
* * * * * *
5200481 GAAATAGACTCAAAAAAAATTTCTCACAA
65 GAAACAGACTC-AAAAGATTTTGTTAAAA
* *
5200510 GAAACAACTCAAAGA-TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 GAAACAACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAA
5200560 ATCGTTTTAA
Statistics
Matches: 192, Mismatches: 32, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
90 7 0.04
91 4 0.02
92 63 0.33
93 60 0.31
94 19 0.10
95 33 0.17
96 6 0.03
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (92 bp):
GAAACAACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAG
AAACAGACTCAAAAGATTTTGTTAAAA
Found at i:5200426 original size:29 final size:30
Alignment explanation
Indices: 5200375--5200443 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
5200365 AGAGACAAAA
* *
5200375 TTTTGTTTCCAAATAAACATACTCAAAGAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
* * *
5200405 TTTTGTTTCAAAAGAAA-TTACTCGAATAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
5200434 TTTT-TTTCAA
1 TTTTGTTTCAA
5200444 GAAATTGTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 6 0.18
29 13 0.38
30 15 0.44
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACATACTCAAAGAT
Found at i:5200530 original size:93 final size:94
Alignment explanation
Indices: 5200322--5200559 Score: 277
Period size: 93 Copynumber: 2.6 Consensus size: 94
5200312 TTTTGTTAGT
* * *
5200322 AGAAACAACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCCAA
1 AGAAACAACTCAAAGATTTTTTTTC-AAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAA
* * * *** *
5200387 ATAAACATACTCAAAGATTTTTGTTTCAAA
65 AGAAACAGACTCAAAAAAAATTGTCTCAAA
** * *
5200417 AGAAATTACTCGAATATTTTTTTTC-AAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
1 AGAAACAACTCAAAGATTTTTTTTCAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
* *
5200481 GAAATAGACTCAAAAAAAATT-TCTCACA
66 GAAACAGACTCAAAAAAAATTGTCTCAAA
*
5200509 AGAAACAACTCAAAGA--TTTTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 AGAAACAACTCAAAGATTTTTTTTCAA-AGAAATTGTCTCAAGAGAGACAAAA
5200560 ATCGTTTTAA
Statistics
Matches: 120, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
90 7 0.06
91 1 0.01
92 41 0.34
93 51 0.43
95 20 0.17
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.29
Consensus pattern (94 bp):
AGAAACAACTCAAAGATTTTTTTTCAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
GAAACAGACTCAAAAAAAATTGTCTCAAA
Found at i:5200860 original size:105 final size:104
Alignment explanation
Indices: 5200675--5200867 Score: 280
Period size: 105 Copynumber: 1.8 Consensus size: 104
5200665 TTTGAAAATA
* * *
5200675 TCAAGTGAGGTTAATTTTGTTTCAAGTACAACAAATTTAAATTTGTATCTCATAGAAAAAATGTC
1 TCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAAAGAAAAAATGTC
* *
5200740 TCAATCGAGATGAAATTTGTTTTGAAATAAACAACAATC
66 TCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAATC
* * * *
5200779 TCAAGTGATATTAATTTTGTTTCATGTGA-AGCAAATTCAAAATTTGTATCTCAAAGGAAAAATG
1 TCAAGTGAGATTAATTTTGTTTCAAGT-ACAACAAATT-AAAATTTGTATCTCAAAGAAAAAATG
5200843 TCTCAAGCGAGACGAAATTTGTTTT
64 TCTCAAGCGAGACGAAATTTGTTTT
5200868 AAGAGAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
104 31 0.40
105 47 0.60
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (104 bp):
TCAAGTGAGATTAATTTTGTTTCAAGTACAACAAATTAAAATTTGTATCTCAAAGAAAAAATGTC
TCAAGCGAGACGAAATTTGTTTTGAAATAAACAACAATC
Found at i:5200926 original size:35 final size:35
Alignment explanation
Indices: 5200835--5200946 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
5200825 TATCTCAAAG
*
5200835 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
* * * *
5200870 GAGAAATTGTCTTAAGTGAGACAAAATTTGTTTTTA
1 GA-AAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
* * *
5200906 TAAAACTGTCTCAAGCGAGACAAAATTTGTTTCAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
5200941 GAAAAA
1 GAAAAA
5200947 CACCCTCAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 34 0.54
36 29 0.46
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (35 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTAA
Found at i:5201277 original size:12 final size:14
Alignment explanation
Indices: 5201244--5201281 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5201234 CTCATGTAAC
*
5201244 ATGTATGTATGTGT
1 ATGTATGTATGTAT
5201258 ATGTATGTATGTAT
1 ATGTATGTATGTAT
5201272 -TG-ATGTATGT
1 ATGTATGTATGT
5201282 CTTCTCGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 2 0.09
14 13 0.57
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTAT
Found at i:5203016 original size:23 final size:23
Alignment explanation
Indices: 5202986--5203034 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
5202976 TGGTGGTTGG
*
5202986 TTTAATGG-ATGTTCTAACTTTAT
1 TTTAATGGTATATT-TAACTTTAT
*
5203009 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
5203032 TTT
1 TTT
5203035 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:5206278 original size:23 final size:22
Alignment explanation
Indices: 5206248--5206303 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
5206238 TGTTTGGTTG
* *
5206248 TTTATTTTTATTTGTTATATTTC
1 TTTATTTTTATTT-TAATATTAC
5206271 TTTATTTTTAATTTTAATATTAC
1 TTTATTTTT-ATTTTAATATTAC
*
5206294 TTTTTTTTTA
1 TTTATTTTTA
5206304 GGACAAAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 24 0.83
24 4 0.14
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTATTTTTATTTTAATATTAC
Found at i:5209753 original size:12 final size:10
Alignment explanation
Indices: 5209721--5209791 Score: 67
Period size: 11 Copynumber: 6.9 Consensus size: 10
5209711 TTGTCTGTGC
*
5209721 TCTTTG-TTA
1 TCTTTGTTTT
5209730 TCTTT-TTTT
1 TCTTTGTTTT
5209739 TCTTTGCTATTT
1 TCTTTG-T-TTT
5209751 TCTTTGTTTT
1 TCTTTGTTTT
5209761 TGCTTT-TGTTT
1 T-CTTTGT-TTT
5209772 TCTTTGTTTTT
1 TCTTTG-TTTT
5209783 TCTTTGTTT
1 TCTTTGTTT
5209792 CTTTCTCTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 15
0.77 0.01 0.22
Matches are distributed among these distances:
9 12 0.23
10 12 0.23
11 19 0.36
12 10 0.19
ACGTcount: A:0.03, C:0.11, G:0.10, T:0.76
Consensus pattern (10 bp):
TCTTTGTTTT
Found at i:5209782 original size:21 final size:21
Alignment explanation
Indices: 5209718--5209805 Score: 76
Period size: 21 Copynumber: 4.2 Consensus size: 21
5209708 TCATTGTCTG
*
5209718 TGCTCTTTGTTATCTTT-TTTT
1 TGCT-TTTGTTTTCTTTGTTTT
*
5209739 T-CTTTGCTATTTTCTTTGTTTT
1 TGCTTT--TGTTTTCTTTGTTTT
5209761 TGCTTTTGTTTTCTTTGTTTT
1 TGCTTTTGTTTTCTTTGTTTT
* * *
5209782 TTC-TTTG-TTTCTTTCTCTT
1 TGCTTTTGTTTTCTTTGTTTT
5209801 TGCTT
1 TGCTT
5209806 CTTTGATTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
19 14 0.25
20 7 0.13
21 25 0.45
22 5 0.09
23 4 0.07
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (21 bp):
TGCTTTTGTTTTCTTTGTTTT
Found at i:5209783 original size:11 final size:11
Alignment explanation
Indices: 5209734--5209797 Score: 76
Period size: 11 Copynumber: 5.7 Consensus size: 11
5209724 TTGTTATCTT
5209734 TTTTTTCTTTG
1 TTTTTTCTTTG
*
5209745 CTATTTTCTTTG
1 -TTTTTTCTTTG
*
5209757 TTTTTGCTTT-
1 TTTTTTCTTTG
*
5209767 TGTTTTCTTTG
1 TTTTTTCTTTG
5209778 TTTTTTCTTTG
1 TTTTTTCTTTG
5209789 TTTCTTTCT
1 TTT-TTTCT
5209798 CTTTGCTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
10 8 0.18
11 21 0.48
12 15 0.34
ACGTcount: A:0.02, C:0.12, G:0.09, T:0.77
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:5209784 original size:32 final size:32
Alignment explanation
Indices: 5209731--5209791 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5209721 TCTTTGTTAT
5209731 CTTTTTTTTCTTTGCTATTTTCTTTGTTTTTG
1 CTTTTTTTTCTTTGCTATTTTCTTTGTTTTTG
*
5209763 CTTTTGTTTTCTTTG-TTTTTTCTTTGTTT
1 CTTTT-TTTTCTTTGCTATTTTCTTTGTTT
5209792 CTTTCTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.02, C:0.11, G:0.10, T:0.77
Consensus pattern (32 bp):
CTTTTTTTTCTTTGCTATTTTCTTTGTTTTTG
Found at i:5209800 original size:14 final size:12
Alignment explanation
Indices: 5209736--5209809 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 12
5209726 GTTATCTTTT
* *
5209736 TTTTCTTTGCTA
1 TTTTCTTTGTTC
5209748 TTTTCTTTGTT-
1 TTTTCTTTGTTC
* *
5209759 TTTGC-TT-TTG
1 TTTTCTTTGTTC
5209769 TTTTCTTTGTT-
1 TTTTCTTTGTTC
5209780 TTTTCTTTGTTTC
1 TTTTCTTTG-TTC
5209793 TTTCTCTTTGCTTC
1 TTT-TCTTTG-TTC
5209807 TTT
1 TTT
5209810 GATTAGATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
9 2 0.04
10 6 0.12
11 15 0.29
12 14 0.27
13 3 0.06
14 12 0.23
ACGTcount: A:0.01, C:0.15, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTCTTTGTTC
Found at i:5209808 original size:33 final size:33
Alignment explanation
Indices: 5209738--5209810 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
5209728 TATCTTTTTT
*
5209738 TTCTTTGCTATTTTCTTTGTTTTTGCTTTTGTT
1 TTCTTTGCTATTTTCTTTGTTTTTGCTTTTGTC
* *
5209771 TTCTTTG-TTTTTTCTTTGTTTCTTTCTCTTTG-C
1 TTCTTTGCTATTTTCTTTGTTT-TTGCT-TTTGTC
5209804 TTCTTTG
1 TTCTTTG
5209811 ATTAGATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 13 0.37
33 18 0.51
34 4 0.11
ACGTcount: A:0.01, C:0.15, G:0.11, T:0.73
Consensus pattern (33 bp):
TTCTTTGCTATTTTCTTTGTTTTTGCTTTTGTC
Found at i:5214823 original size:19 final size:20
Alignment explanation
Indices: 5214799--5214843 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
5214789 TCGATTCCTC
5214799 TCTTTTTCTC-TTTTGTTTT
1 TCTTTTTCTCTTTTTGTTTT
5214818 TCTTTTTCTCTTTTTGTTTT
1 TCTTTTTCTCTTTTTGTTTT
5214838 T-TTTTT
1 TCTTTTT
5214844 GTTCTTCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (20 bp):
TCTTTTTCTCTTTTTGTTTT
Found at i:5214849 original size:20 final size:20
Alignment explanation
Indices: 5214801--5214849 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5214791 GATTCCTCTC
5214801 TTTTTCTCTTTTGTTTTTCTT
1 TTTTTCT-TTTTGTTTTTCTT
*
5214822 TTTCTCTTTTTGTTTTT-TT
1 TTTTTCTTTTTGTTTTTCTT
5214841 TTTGTTCTT
1 TTT-TTCTT
5214850 CCCCAGTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (20 bp):
TTTTTCTTTTTGTTTTTCTT
Found at i:5216952 original size:129 final size:129
Alignment explanation
Indices: 5216720--5217024 Score: 477
Period size: 129 Copynumber: 2.4 Consensus size: 129
5216710 TACTTCTCTA
* * *
5216720 AAGATCCGTGAAAACTGAAAACTAGTGCCGGCTCGGGTGGTTATTACTTTCGTGTTCTGAGTTCC
1 AAGATTCGTGACAACTCAAAACTAGTGCCGGCTCGGGTGGTTATTACTTTCGTGTTCTGAGTTCC
* *
5216785 AAATCATGACGTTAGTTAACGAACTTTCTTTTTCCATTATCTCAATACCGCACCAACGGGGATC
66 AAATCATGACGTTAGTTAACGAACTTTCTTTTTCCATTATCTCAATACCACAACAACGGGGATC
* *
5216849 AAGATTCGTGACAACTCAAAACTAGTGCCGGCTCGGGTGGTTATTGCTTTTGTGTTCTGAGTTCC
1 AAGATTCGTGACAACTCAAAACTAGTGCCGGCTCGGGTGGTTATTACTTTCGTGTTCTGAGTTCC
* * * * *
5216914 GAATCTTGACGTTAGTTACCTAACTTTCTTTGTT-CATTATCTCGATACCACAACAACGGGGATC
66 AAATCATGACGTTAGTTAACGAACTTTCTTT-TTCCATTATCTCAATACCACAACAACGGGGATC
*
5216978 AAGATTCGTGACAACTCAAAACTAGTGCTGGCTCGGGTGGTTATTAC
1 AAGATTCGTGACAACTCAAAACTAGTGCCGGCTCGGGTGGTTATTAC
5217025 AGAGTTCAGA
Statistics
Matches: 161, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 159 0.99
130 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (129 bp):
AAGATTCGTGACAACTCAAAACTAGTGCCGGCTCGGGTGGTTATTACTTTCGTGTTCTGAGTTCC
AAATCATGACGTTAGTTAACGAACTTTCTTTTTCCATTATCTCAATACCACAACAACGGGGATC
Found at i:5228192 original size:3 final size:3
Alignment explanation
Indices: 5228184--5228221 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5228174 CACGAATCTA
5228184 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5228222 AGCTTACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5229083 original size:9 final size:9
Alignment explanation
Indices: 5229033--5229084 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
5229023 TTAGACTATT
5229033 TAAAA-AAA
1 TAAAATAAA
*
5229041 TAAAA-AAG
1 TAAAATAAA
*
5229049 TATAATTAATA
1 TA-AAATAA-A
5229060 TAAAATAAA
1 TAAAATAAA
5229069 TAAAATAAA
1 TAAAATAAA
5229078 TAAAATA
1 TAAAATA
5229085 GATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 9 0.24
9 19 0.51
10 7 0.19
11 2 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (9 bp):
TAAAATAAA
Found at i:5230419 original size:78 final size:79
Alignment explanation
Indices: 5230324--5230479 Score: 224
Period size: 79 Copynumber: 2.0 Consensus size: 79
5230314 ATTAATATTT
* * * *
5230324 TTTAACATTTCCGGTAAAGTGCTACCTAAAATATTA-TTTTTCTACTGAAAATGTTAATATTAGG
1 TTTAACATTTCCGGTAAAGTGCTAACTAAAACATTATTTTTTCTACCGAAAATATTAATATTAGG
5230388 CGCTACCTAAAATG
66 CGCTACCTAAAATG
* * **
5230402 TTTAACATTTTCGGTAAAGTGCTAACTAAAACATTATTTTTTTTACCGGTAATATTAATATTAGG
1 TTTAACATTTCCGGTAAAGTGCTAACTAAAACATTATTTTTTCTACCGAAAATATTAATATTAGG
*
5230467 CGCTACTTAAAAT
66 CGCTACCTAAAAT
5230480 ATTATTTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 33 0.49
79 35 0.51
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (79 bp):
TTTAACATTTCCGGTAAAGTGCTAACTAAAACATTATTTTTTCTACCGAAAATATTAATATTAGG
CGCTACCTAAAATG
Found at i:5231370 original size:21 final size:21
Alignment explanation
Indices: 5231319--5231371 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5231309 ATTATGACTA
5231319 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
5231340 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
5231361 TCGCAATGCGA
1 TCGCAATGCGA
5231372 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:5231386 original size:20 final size:21
Alignment explanation
Indices: 5231361--5231412 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5231351 TTTTCCCAAT
*
5231361 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
5231381 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5231402 TCGCAATGCGA
1 TCGCAATGCGA
5231413 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:5231426 original size:20 final size:20
Alignment explanation
Indices: 5231401--5231495 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
5231391 AATTTGGAAA
*
5231401 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5231421 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
5231442 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5231462 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
5231482 TTCGCAACGAGATA
1 ATCGCAACGCGATA
5231496 ATACATAATC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.71
21 15 0.23
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5231474 original size:41 final size:41
Alignment explanation
Indices: 5231398--5231475 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
5231388 GCGAATTTGG
*
5231398 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
5231439 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
5231476 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:5231509 original size:21 final size:20
Alignment explanation
Indices: 5231401--5231515 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
5231391 AATTTGGAAA
* *
5231401 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
5231421 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
5231442 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
5231462 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
5231482 TTCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
5231502 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
5231516 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.05
20 48 0.61
21 25 0.32
22 2 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:5231710 original size:22 final size:22
Alignment explanation
Indices: 5231682--5231725 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5231672 CACTCTCTCA
5231682 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
5231704 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
5231726 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:5232037 original size:20 final size:20
Alignment explanation
Indices: 5231988--5232046 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
5231978 TTTATTCTCT
* **
5231988 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
5232008 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
5232028 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
5232047 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:5233388 original size:18 final size:18
Alignment explanation
Indices: 5233367--5233414 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
5233357 TCCACTTCGG
*
5233367 GAGCCATCAGCTCACCCA
1 GAGCCATCACCTCACCCA
*
5233385 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5233403 GAGCCATCACCT
1 GAGCCATCACCT
5233415 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.15, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5234001 original size:19 final size:20
Alignment explanation
Indices: 5233947--5234013 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5233937 TAGTTTACTT
* *
5233947 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
5233967 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
5233987 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
5234006 TCGCAACG
1 TCGCAACG
5234014 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:5234021 original size:14 final size:14
Alignment explanation
Indices: 5234002--5234060 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
5233992 ATGCGAAATG
5234002 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5234016 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
5234035 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
5234049 CAAATCGCAACG
1 AAAATCGCAACG
5234061 CGAAGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 21 0.57
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.27
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5234028 original size:33 final size:33
Alignment explanation
Indices: 5233986--5234077 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
5233976 GGAAATGGCT
5233986 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
5234019 ATCGCAATGCGAAATGAAAATCGCAACGACCAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
5234052 ATCGCAACGCGAAGTGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
5234078 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:5234040 original size:19 final size:19
Alignment explanation
Indices: 5233986--5234082 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
5233976 GGAAATGGCT
5233986 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5234005 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
5234019 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
5234038 ATCGCAA--CG--A-CCAA
1 ATCGCAATGCGAAATGAAA
* *
5234052 ATCGCAACGCGAAGTGAAA
1 ATCGCAATGCGAAATGAAA
5234071 ATCGCAATGCGA
1 ATCGCAATGCGA
5234083 TTTGTGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 1 0.02
19 30 0.50
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5234113 original size:14 final size:14
Alignment explanation
Indices: 5234094--5234152 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
5234084 TTGTGTTTCG
5234094 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5234108 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
5234125 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
5234141 CGTTGTGATTTT
1 CGTTGCGATTTT
5234153 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5234126 original size:33 final size:33
Alignment explanation
Indices: 5234089--5234168 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
5234079 GCGATTTGTG
*
5234089 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
5234122 TTTCGCATTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
5234155 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
5234169 AGCCATTTCG
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:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:5234134 original size:19 final size:19
Alignment explanation
Indices: 5234110--5234187 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 19
5234100 GATTTTGTCG
5234110 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
5234129 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
5234143 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
5234162 TTGCGATAGCCATTTCGCG
1 TTGCGATTTTCATTTCGCA
5234181 TTGCGAT
1 TTGCGAT
5234188 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
14 5 0.11
15 3 0.07
16 4 0.09
17 4 0.09
18 3 0.07
19 27 0.59
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:5234202 original size:20 final size:19
Alignment explanation
Indices: 5234153--5234226 Score: 112
Period size: 20 Copynumber: 3.8 Consensus size: 19
5234143 TTGTGATTTT
*
5234153 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
5234172 CATTTCGCGTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5234191 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
5234211 CATTTTCGCGTTGCGA
1 CA-TTTCGCGTTGCGA
5234227 AAGTAAGTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
19 23 0.45
20 25 0.49
21 3 0.06
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5234237 original size:20 final size:19
Alignment explanation
Indices: 5234154--5234252 Score: 81
Period size: 20 Copynumber: 5.1 Consensus size: 19
5234144 TGTGATTTTC
* * **
5234154 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* **
5234173 ATTTCGCGTTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
*
5234192 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
5234213 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
5234232 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
5234252 A
1 A
5234253 ACTATTCTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
19 23 0.33
20 44 0.63
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:5234244 original size:40 final size:39
Alignment explanation
Indices: 5234154--5234246 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 39
5234144 TGTGATTTTC
* * *
5234154 ATTT-CGCATTGCGATAGCCATTTCGCGTTGCGATAGCC
1 ATTTCCGCGTTGCGATAGCCATTTCGCGTTGCGAAAGCA
* *
5234192 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCA-TTTCGCGTTGCGAAAGCA
*
5234232 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
5234247 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 4 0.09
39 14 0.30
40 25 0.54
41 3 0.07
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (39 bp):
ATTTCCGCGTTGCGATAGCCATTTCGCGTTGCGAAAGCA
Found at i:5235978 original size:14 final size:14
Alignment explanation
Indices: 5235936--5235972 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5235926 TATTGTTTAA
*
5235936 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
5235950 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
5235964 TTGATTTGT
1 TTGATTTGT
5235973 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:5236154 original size:19 final size:19
Alignment explanation
Indices: 5236079--5236144 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
5236069 AAAAATGACT
*
5236079 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
5236098 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
5236112 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
5236131 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
5236145 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:5236172 original size:19 final size:19
Alignment explanation
Indices: 5236150--5236300 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
5236140 CGAAACTAAA
5236150 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5236169 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5236184 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5236202 TTCGCATTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
* *
5236217 -TCTCATTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5236235 TTCACGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5236250 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
5236268 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
5236287 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
5236301 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 29 0.28
16 9 0.09
17 9 0.09
19 45 0.44
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5236194 original size:14 final size:14
Alignment explanation
Indices: 5236175--5236262 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
5236165 TCATTTCGCT
5236175 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
5236189 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
* *
5236206 CATTGCGATTATCTCA
1 --TTGCGATTCTCTCG
*
5236222 TTGCGATTTTCATTTCACG
1 TTGCGA--TTC---TCTCG
5236241 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
5236255 TTGCGATT
1 TTGCGATT
5236263 TTCATTTCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
14 24 0.43
16 8 0.14
17 9 0.16
19 15 0.27
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:5236196 original size:33 final size:33
Alignment explanation
Indices: 5236154--5236280 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
5236144 ACTAAATTCG
*
5236154 CGTTGCGATTTTCATTTCGCTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
5236187 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * *
5236220 CATTGCGATTTTCATTTCACGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
5236253 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5236281 AGTCATTTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:5236245 original size:66 final size:66
Alignment explanation
Indices: 5236156--5236280 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
5236146 TAAATTCGCG
* *
5236156 TTGCGATTTTCATTTCGCTTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
5236221 A
66 A
5236222 TTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
5236281 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (66 bp):
TTGCGATTTTCATTTCACGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTATCTC
A
Found at i:5236299 original size:20 final size:19
Alignment explanation
Indices: 5236253--5236307 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5236243 GCGATTCTCT
**
5236253 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
5236272 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
5236292 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
5236308 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:5236346 original size:20 final size:20
Alignment explanation
Indices: 5236274--5236346 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
5236264 TCATTTCGCA
**
5236274 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
5236294 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
5236314 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
5236335 TTGCGATAGTCA
1 TTGCGATAGTCA
5236347 AATGATTGCC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:5239684 original size:41 final size:41
Alignment explanation
Indices: 5239571--5239708 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
5239561 AACTTTGAAA
* * *
5239571 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
* * *** ** *
5239612 ATCTCGTTGC-A-AAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGATAGTCAGT
*
5239652 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
5239693 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
5239709 CCAAGTTCGC
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
39 2 0.03
40 28 0.37
41 44 0.58
42 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
Found at i:5239697 original size:20 final size:20
Alignment explanation
Indices: 5239591--5239705 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
5239581 GATTCTGTAT
*
5239591 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
5239611 AATCTCGTTGCAAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
5239631 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
5239651 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
5239672 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
5239692 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
5239706 TTTCCAAGTT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.76
21 14 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:5239724 original size:41 final size:41
Alignment explanation
Indices: 5239632--5239726 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
5239622 AAAAGTCAGA
* * ** *
5239632 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAGT
5239673 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAGT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAGT
*
5239715 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
5239727 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAGT
Found at i:5239787 original size:21 final size:22
Alignment explanation
Indices: 5239738--5239787 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
5239728 TACTTATTCA
5239738 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
**
5239759 CAACGCGAAATT-GGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
5239780 CATTGCGA
1 CATTGCGA
5239788 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCG
Found at i:5240615 original size:28 final size:27
Alignment explanation
Indices: 5240535--5240625 Score: 102
Period size: 28 Copynumber: 3.4 Consensus size: 27
5240525 TATCACATAA
5240535 AATTAAATATTTATTTTAACTAAAAAT
1 AATTAAATATTTATTTTAACTAAAAAT
* *
5240562 AATTAAA-A--TA-TTAAAC-AATATAT
1 AATTAAATATTTATTTTAACTAA-AAAT
5240585 AATTTAAATATTTATTTTAACTAAAAAT
1 AA-TTAAATATTTATTTTAACTAAAAAT
5240613 AATTAAAGTATTT
1 AATTAAA-TATTT
5240626 GAAGTGGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
22 2 0.04
23 10 0.19
24 7 0.13
25 1 0.02
26 1 0.02
27 14 0.27
28 15 0.29
29 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (27 bp):
AATTAAATATTTATTTTAACTAAAAAT
Found at i:5245142 original size:16 final size:16
Alignment explanation
Indices: 5245123--5245156 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5245113 CAATATACGA
5245123 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
5245139 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
5245155 AT
1 AT
5245157 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:5245230 original size:16 final size:18
Alignment explanation
Indices: 5245198--5245231 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5245188 TATTAATGTA
5245198 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
5245216 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
5245232 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:5245903 original size:130 final size:130
Alignment explanation
Indices: 5245699--5245946 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
5245689 AATTTTCTTC
* *
5245699 TAATTAGGTGGTGACACGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
5245764 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
5245829 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
5245894 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
5245947 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:5246392 original size:35 final size:35
Alignment explanation
Indices: 5246342--5246417 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
5246332 AATTGAATTT
* *
5246342 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
5246377 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
5246412 AATTGA
1 AATTGA
5246418 TGATTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:5247822 original size:39 final size:39
Alignment explanation
Indices: 5247775--5247886 Score: 188
Period size: 39 Copynumber: 2.8 Consensus size: 39
5247765 GCAGTCATGA
5247775 CTTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAG
1 CTTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAG
* *
5247814 CTTTATATATATTGTTCAATTTTGAATGAAATTGGTCAG
1 CTTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAG
*
5247853 CTTTATATATTTTCTTCAATCTTGAATGGAAATT
1 CTTTATATATTTTGTTCAATCTTGAAT-GAAATT
5247887 TTGGTCAACT
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 61 0.91
40 6 0.09
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.47
Consensus pattern (39 bp):
CTTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAG
Found at i:5248175 original size:54 final size:54
Alignment explanation
Indices: 5248079--5248193 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
5248069 ACATACTTAA
* * * * * * *
5248079 TTACATCGGTGTAAATATGTATATCTCCCAGAACGTGTAGCACTTAATATATAC
1 TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGCACTTAAGACATAC
* *
5248133 TTACACCGGCGTAAGTATGTATATCTCTCAAAAAGTGCAGCACTTAAGACATAC
1 TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGCACTTAAGACATAC
5248187 TTACACC
1 TTACACC
5248194 AGTACAAGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (54 bp):
TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGCACTTAAGACATAC
Found at i:5248203 original size:54 final size:54
Alignment explanation
Indices: 5248094--5248316 Score: 183
Period size: 54 Copynumber: 4.2 Consensus size: 54
5248084 TCGGTGTAAA
* * * * * * **
5248094 TATGTATATCTCCCAGAACGTGTAGCACTTAATATATACTTACACCGGCGTAAG
1 TATGTATATCTCTCAAAAAGTGTAGCACTTAAGACATACTTACACCAGTATAAG
* *
5248148 TATGTATATCTCTCAAAAAGTGCAGCACTTAAGACATACTTACACCAGTACAAG
1 TATGTATATCTCTCAAAAAGTGTAGCACTTAAGACATACTTACACCAGTATAAG
* * * * * *
5248202 TA--AATA-ATATAAAAAAGTGTAGCACTTAAGACATACTTACA-CATGTGTAGG
1 TATGTATATCTCTCAAAAAGTGTAGCACTTAAGACATACTTACACCA-GTATAAG
* * * *
5248253 TA--TATATCTAC-CAAAAAAGTGTAACACTTAACATATACTTACATCAGTATAAG
1 TATGTATATCT-CTC-AAAAAGTGTAGCACTTAAGACATACTTACACCAGTATAAG
5248306 TATGTA-ATCTC
1 TATGTATATCTC
5248317 CTAATATTAT
Statistics
Matches: 135, Mismatches: 27, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
50 2 0.01
51 40 0.30
52 4 0.03
53 35 0.26
54 52 0.39
55 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (54 bp):
TATGTATATCTCTCAAAAAGTGTAGCACTTAAGACATACTTACACCAGTATAAG
Found at i:5250806 original size:39 final size:39
Alignment explanation
Indices: 5250763--5250887 Score: 196
Period size: 39 Copynumber: 3.1 Consensus size: 39
5250753 CAGTCATGAT
5250763 TTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAGC
1 TTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAGC
*
5250802 TTTATATATATTGTTCAATCTTGAATGAAATTGGTCAGC
1 TTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAGC
* *
5250841 TTTATATATTTTCTTCAATCTTGAATGGAAATTTTGGTCAAC
1 TTTATATATTTTGTTCAATCTTGAAT-GAAA--TTGGTCAGC
5250883 TTTAT
1 TTTAT
5250888 TGAAGGTTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 62 0.78
40 4 0.05
42 13 0.16
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (39 bp):
TTTATATATTTTGTTCAATCTTGAATGAAATTGGTCAGC
Found at i:5251173 original size:54 final size:54
Alignment explanation
Indices: 5251065--5251179 Score: 140
Period size: 54 Copynumber: 2.1 Consensus size: 54
5251055 ACATACTTAA
* * ** * * * *
5251065 TTACACCGGTGTAAATATGTATATCTCCCAGATCGTGTAGAACTTAATATATAC
1 TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGAACTAAAGACATAC
* *
5251119 TTACACCGGCGTAAATATGTATATCTCTCAAAAAGTGCAGCACTAAAGACATAC
1 TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGAACTAAAGACATAC
5251173 TTACACC
1 TTACACC
5251180 AGTACAAGTA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (54 bp):
TTACACCGGCGTAAATATGTATATCTCCCAAAAAGTGCAGAACTAAAGACATAC
Found at i:5266120 original size:18 final size:18
Alignment explanation
Indices: 5266090--5266139 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5266080 ATGCTATAAT
* *
5266090 TTTTGTAAT-TTTTTTTA
1 TTTTATAATATTTTTTCA
*
5266107 TTTT-TAAATATTTTATCA
1 TTTTAT-AATATTTTTTCA
5266125 TTTTATAATATTTTT
1 TTTTATAATATTTTT
5266140 AATAAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 18 0.67
19 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTTATAATATTTTTTCA
Found at i:5269034 original size:64 final size:64
Alignment explanation
Indices: 5268933--5269098 Score: 160
Period size: 64 Copynumber: 2.6 Consensus size: 64
5268923 ATCGATTTTG
* * * * * *
5268933 ATGCATAACGGTGCATTATCAGCATAAAAATGTCACT-ATTAAAAAAATCAATCGATTTTGATTA
1 ATGCATAACAGTGCATTATCGGCTTAAAATTGCCACTAATGAAAAAAAT-AATCGATTTTGATTA
** * *
5268997 ATGCATAACAGTGC-TTATCGGCTTAAAAGTTGCCACTAATGAAATTAATGATCGATTTTGTTTA
1 ATGCATAACAGTGCATTATCGGCTTAAAA-TTGCCACTAATGAAAAAAATAATCGATTTTGATTA
*
5269061 A-GCATAAACAATGCATTATCGG-TATAAAATGTGCCACT
1 ATGCAT-AACAGTGCATTATCGGCT-TAAAAT-TGCCACT
5269099 CATGGTATTC
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
63 16 0.19
64 42 0.49
65 27 0.32
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (64 bp):
ATGCATAACAGTGCATTATCGGCTTAAAATTGCCACTAATGAAAAAAATAATCGATTTTGATTA
Found at i:5272509 original size:18 final size:18
Alignment explanation
Indices: 5272486--5272520 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5272476 TTCCATCCGG
*
5272486 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
5272504 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
5272521 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:5284280 original size:21 final size:21
Alignment explanation
Indices: 5284250--5284299 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
5284240 GTTAATCGTT
*
5284250 AACT-TTGATTGTTGACTTTTG
1 AACTGTTGATTGTTAAC-TTTG
5284271 -ACTGTTGATTGTTAACTTTG
1 AACTGTTGATTGTTAACTTTG
5284291 AACTGTTGA
1 AACTGTTGA
5284300 CGTTTTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (21 bp):
AACTGTTGATTGTTAACTTTG
Found at i:5284285 original size:34 final size:35
Alignment explanation
Indices: 5284228--5284305 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
5284218 CCAGTGATCA
*
5284228 TTGAC-TTTGACCGTTAATCGTTAACTTTG-ATTG
1 TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
* * *
5284261 TTGACTTTTGACTGTTGATTGTTAACTTTGAACTG
1 TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
5284296 TTGACGTTTT
1 TTGAC-TTTT
5284306 CTAAAGACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 5 0.13
34 21 0.55
35 8 0.21
36 4 0.11
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (35 bp):
TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
Found at i:5284959 original size:28 final size:29
Alignment explanation
Indices: 5284895--5284959 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
5284885 CCTGATTTTG
* *
5284895 CATGGGATTATATCTATGTCTTTGTTCTT
1 CATGGGATTATATCTACGTCTTTGTTCTA
* *
5284924 TATTGGATTATATC-ACGTC-TTGTTTCTA
1 CATGGGATTATATCTACGTCTTTG-TTCTA
5284952 CATGGGAT
1 CATGGGAT
5284960 CCTCTACAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 3 0.10
28 14 0.48
29 12 0.41
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (29 bp):
CATGGGATTATATCTACGTCTTTGTTCTA
Found at i:5289510 original size:2 final size:2
Alignment explanation
Indices: 5289499--5289530 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5289489 GAATTTAAGA
5289499 AT AT -T 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 A
5289531 GTATTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5292010 original size:9 final size:10
Alignment explanation
Indices: 5291995--5292049 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 10
5291985 ACAAAAGTTT
5291995 TTTTAAAAAA
1 TTTTAAAAAA
5292005 TTTAAATAAAAAA
1 TTT---TAAAAAA
5292018 TTTTAAAAAA
1 TTTTAAAAAA
5292028 TTTAAATAAAAAA
1 TTT---TAAAAAA
5292041 TTTTAAAAA
1 TTTTAAAAA
5292050 TATTAGAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
10 19 0.49
13 20 0.51
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:5292014 original size:13 final size:13
Alignment explanation
Indices: 5291998--5292043 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
5291988 AAAGTTTTTT
5291998 TAAAAAATTTAAA
1 TAAAAAATTTAAA
5292011 TAAAAAATTT---
1 TAAAAAATTTAAA
5292021 TAAAAAATTTAAA
1 TAAAAAATTTAAA
5292034 TAAAAAATTT
1 TAAAAAATTT
5292044 TAAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
13 20 0.67
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAAATTTAAA
Found at i:5292021 original size:23 final size:23
Alignment explanation
Indices: 5291995--5292049 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
5291985 ACAAAAGTTT
5291995 TTTTAAAAAATTTAAATAAAAAA
1 TTTTAAAAAATTTAAATAAAAAA
5292018 TTTTAAAAAATTTAAATAAAAAA
1 TTTTAAAAAATTTAAATAAAAAA
5292041 TTTTAAAAA
1 TTTTAAAAA
5292050 TATTAGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
TTTTAAAAAATTTAAATAAAAAA
Found at i:5297975 original size:13 final size:13
Alignment explanation
Indices: 5297957--5297983 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5297947 ACTGAAATTA
5297957 ACGATTCACGACG
1 ACGATTCACGACG
5297970 ACGATTCACGACG
1 ACGATTCACGACG
5297983 A
1 A
5297984 AAGGTTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.22, T:0.15
Consensus pattern (13 bp):
ACGATTCACGACG
Found at i:5299416 original size:18 final size:18
Alignment explanation
Indices: 5299395--5299444 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
5299385 TAAATTATTA
*
5299395 AAAATATTATAAAATGAT
1 AAAATATTATAAAATAAT
5299413 AAAATATTCA-AAAATAAT
1 AAAATATT-ATAAAATAAT
* *
5299431 AAAAAACTATAAAA
1 AAAATATTATAAAA
5299445 CTTATAGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAATATTATAAAATAAT
Found at i:5299436 original size:28 final size:27
Alignment explanation
Indices: 5299385--5299444 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
5299375 CGAAAAATTT
* * *
5299385 TAAATTATTAAAAATATTATAAAA-TGA
1 TAAAATATTAAAAATAATAAAAAACT-A
5299412 TAAAATATTCAAAAATAATAAAAAACTA
1 TAAAATATT-AAAAATAATAAAAAACTA
5299440 TAAAA
1 TAAAA
5299445 CTTATAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 19 0.68
29 1 0.04
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (27 bp):
TAAAATATTAAAAATAATAAAAAACTA
Found at i:5299535 original size:2 final size:2
Alignment explanation
Indices: 5299524--5299555 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5299514 TGATTTAAGA
5299524 AT AT -T 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 A
5299556 GTATTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5301758 original size:2 final size:2
Alignment explanation
Indices: 5301747--5301778 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5301737 GAATTTAAGA
5301747 AT AT -T 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 A
5301779 GTATTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5302647 original size:21 final size:21
Alignment explanation
Indices: 5302621--5302669 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
5302611 ACTCTTCAAG
5302621 AAATAAATTATTTTAAAAAAT
1 AAATAAATTATTTTAAAAAAT
5302642 AAATAAATTATTTTAAAAAAT
1 AAATAAATTATTTTAAAAAAT
5302663 AAATAAA
1 AAATAAA
5302670 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATAAATTATTTTAAAAAAT
Found at i:5304562 original size:16 final size:18
Alignment explanation
Indices: 5304541--5304574 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
5304531 TTATAAAATG
5304541 ATAAATT-ATT-CAAAAA
1 ATAAATTAATTACAAAAA
5304557 ATAAATTAATTACAAAAA
1 ATAAATTAATTACAAAAA
5304575 TTATAGCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATTAATTACAAAAA
Found at i:5311267 original size:16 final size:16
Alignment explanation
Indices: 5311256--5311302 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5311246 TTATTAAAAT
*
5311256 ATTATAAAATTATAAA
1 ATTATAAAATAATAAA
*
5311272 ATAATAAAA-AATAAA
1 ATTATAAAATAATAAA
5311287 ATTACTAGAAATAATA
1 ATTA-TA-AAATAATA
5311303 GCAACAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 8 0.32
16 10 0.40
17 3 0.12
18 4 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTATAAAATAATAAA
Found at i:5311282 original size:18 final size:19
Alignment explanation
Indices: 5311243--5311283 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5311233 GAAAAATTTC
* *
5311243 AAATTATTAAAATATTATA
1 AAATTATTAAAATAATAAA
5311262 AAATTA-TAAAATAATAAA
1 AAATTATTAAAATAATAAA
5311280 AAAT
1 AAAT
5311284 AAAATTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTATTAAAATAATAAA
Found at i:5313627 original size:20 final size:21
Alignment explanation
Indices: 5313602--5313640 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5313592 TGATCATTCA
5313602 CACATG-ACAACCATGTAAAT
1 CACATGAACAACCATGTAAAT
*
5313622 CACATGAACTACCATGTAA
1 CACATGAACAACCATGTAA
5313641 CAATTGTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (21 bp):
CACATGAACAACCATGTAAAT
Found at i:5317090 original size:2 final size:2
Alignment explanation
Indices: 5317080--5317119 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5317070 ACATATATGC
*
5317080 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5317120 TTTGTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5317170 original size:19 final size:18
Alignment explanation
Indices: 5317133--5317207 Score: 57
Period size: 18 Copynumber: 4.1 Consensus size: 18
5317123 GTATTTTATC
*
5317133 TTATTATTTCTTTACTTTT
1 TTATTATTTATTTA-TTTT
5317152 TTATTATTATATTTA-TTT
1 TTATTATT-TATTTATTTT
* *
5317170 TCATTATTTAGTTT-TTCTA
1 TTATTATTTA-TTTATT-TT
*
5317189 TTATTA-TTATATATTTT
1 TTATTATTTATTTATTTT
5317206 TT
1 TT
5317208 TCCTCTCTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 7 0.16
18 19 0.42
19 14 0.31
20 5 0.11
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:5319307 original size:19 final size:19
Alignment explanation
Indices: 5319283--5319324 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5319273 ACAAGAATTG
*
5319283 GTTGGTAGAAAACCTTGTT
1 GTTGGTAGAAAACCTTGGT
5319302 GTTGGTAGAAAACCTTGGT
1 GTTGGTAGAAAACCTTGGT
5319321 GTTG
1 GTTG
5319325 CTGCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.36
Consensus pattern (19 bp):
GTTGGTAGAAAACCTTGGT
Found at i:5319933 original size:18 final size:19
Alignment explanation
Indices: 5319912--5319954 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5319902 CAAATTATTA
* *
5319912 AAAATATTATAAAATGAT-
1 AAAATATTAAAAAATAATC
5319930 AAAATATTAAAAAATAATC
1 AAAATATTAAAAAATAATC
5319949 AAAATA
1 AAAATA
5319955 AAAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATTAAAAAATAATC
Found at i:5319952 original size:27 final size:25
Alignment explanation
Indices: 5319903--5319971 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
5319893 GAAAATTTTC
*
5319903 AAATTATTAAAAATATTATAAAATGATA
1 AAATTATTAAAAA-ATAATAAAAT-A-A
5319931 AAA-TATTAAAAAATAATCAAAATAA
1 AAATTATTAAAAAATAAT-AAAATAA
5319956 AAATTAATTAAAAAAT
1 AAATT-ATTAAAAAAT
5319972 TTTAGCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 4 0.11
26 6 0.16
27 24 0.65
28 3 0.08
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
AAATTATTAAAAAATAATAAAATAA
Found at i:5324185 original size:13 final size:13
Alignment explanation
Indices: 5324169--5324222 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 13
5324159 CATAATGAAA
*
5324169 ATAAATAAATAGT
1 ATAAATAAATAAT
5324182 ATAAATAAAATAAT
1 ATAAAT-AAATAAT
5324196 A-AAATAAA-AA-
1 ATAAATAAATAAT
*
5324206 ATATATAAA-AAT
1 ATAAATAAATAAT
5324218 ATAAA
1 ATAAA
5324223 AATGTATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 10 0.29
12 7 0.20
13 10 0.29
14 7 0.20
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
ATAAATAAATAAT
Found at i:5324216 original size:17 final size:16
Alignment explanation
Indices: 5324188--5324225 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 16
5324178 TAGTATAAAT
5324188 AAAATAATAAAATA-A
1 AAAATAATAAAATATA
5324203 AAAATATATAAAAATATA
1 AAAATA-AT-AAAATATA
5324221 AAAAT
1 AAAAT
5324226 GTATGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 6 0.30
18 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATAAAATATA
Found at i:5324983 original size:37 final size:37
Alignment explanation
Indices: 5324942--5325041 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
5324932 GGATCATATC
* **
5324942 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
* *
5324979 TTTAGGAGTTTGAATCCTAGCA-ACATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGA-ACTCTATCCTATT
5325016 TTTAGGAGTTTGAATCCTAGTAGAAC
1 TTTAGGAGTTTGAATCCTAGTAGAAC
5325042 GAAAAAGTGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.02
37 52 0.96
38 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTATT
Found at i:5325972 original size:106 final size:106
Alignment explanation
Indices: 5325788--5326626 Score: 1331
Period size: 106 Copynumber: 7.9 Consensus size: 106
5325778 GCATTGTTCC
* * * * *
5325788 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
5325853 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
5325894 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
5325959 CCATCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5326000 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5326065 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5326106 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
5326170 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5326212 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
5326277 CCAGCGGTCCCTTCGTCGTTAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
5326318 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5326383 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
5326424 GAGTCTAATATCATTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
5326489 CCAGCGG-CCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
5326530 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGATCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
5326595 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
5326627 TGTTATCTTG
Statistics
Matches: 678, Mismatches: 51, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
105 3 0.00
106 672 0.99
107 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:5327469 original size:22 final size:22
Alignment explanation
Indices: 5327443--5327519 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
5327433 TTATGTTTGG
5327443 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
5327465 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGGCATTTGATGC
*
5327487 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
5327509 TCAACGGTTTG
1 TCAAAGGTTTG
5327520 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:5328244 original size:172 final size:165
Alignment explanation
Indices: 5327915--5328245 Score: 488
Period size: 167 Copynumber: 2.0 Consensus size: 165
5327905 TAAATAGGCC
*
5327915 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
5327980 CTCAAAATGTCTCTCTCTTAATACTCTATGATCTTTGAGTAAAGTGATTCGAGAATGATTGTGCT
64 CTCAAAATGTCTCTCTCTTAATACTCTATGATCTTTGAGTAAAGTGATTCGAGAATGATTGTGCT
5328045 TGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 TGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
5328082 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
* * *
5328144 CAAAATGTTTCTCTCTCTTAATGCTCTATGATCTTCTAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTAATACTCTATGATC-T-T--TG-AGT-A--AAGTGATTCGAGAATG
5328209 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATG
121 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATG
5328246 CACCATTTGT
Statistics
Matches: 149, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
162 14 0.09
164 24 0.16
165 1 0.01
166 2 0.01
167 51 0.34
168 2 0.01
169 3 0.02
170 1 0.01
172 51 0.34
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (165 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTAATACTCTATGATCTTTGAGTAAAGTGATTCGAGAATGATTGTGCTTG
ATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:5328328 original size:32 final size:29
Alignment explanation
Indices: 5328289--5328361 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 29
5328279 TTTTTGTCCA
5328289 TTTTTCTTTTTGATTTTTGTTCTTGTTT-CTCT
1 TTTTTCTTTTT-ATTTTTGTT-TT-TTTGCT-T
*
5328321 TTTTTCTTTATTTTTTTTGTTTTTTTGCTT
1 TTTTTCTTT-TTATTTTTGTTTTTTTGCTT
*
5328351 CTTTTCTTTTT
1 TTTTTCTTTTT
5328362 TGTTCTTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 2 0.05
30 12 0.32
31 4 0.11
32 17 0.46
33 2 0.05
ACGTcount: A:0.03, C:0.11, G:0.07, T:0.79
Consensus pattern (29 bp):
TTTTTCTTTTTATTTTTGTTTTTTTGCTT
Found at i:5328346 original size:21 final size:24
Alignment explanation
Indices: 5328320--5328365 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5328310 CTTGTTTCTC
5328320 TTTTTT-CTT-TATT-TTTTTTGT
1 TTTTTTGCTTCTATTCTTTTTTGT
*
5328341 TTTTTTGCTTCTTTTCTTTTTTGT
1 TTTTTTGCTTCTATTCTTTTTTGT
5328365 T
1 T
5328366 CTTGATTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 3 0.14
24 9 0.43
ACGTcount: A:0.02, C:0.09, G:0.07, T:0.83
Consensus pattern (24 bp):
TTTTTTGCTTCTATTCTTTTTTGT
Found at i:5332979 original size:18 final size:17
Alignment explanation
Indices: 5332953--5333003 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
5332943 GGATGAAACA
5332953 AATATAAAAAAATGAAAATG
1 AATA-AAAAAAAT--AAATG
5332973 AATAAAATAAAATAAATG
1 AATAAAA-AAAATAAATG
*
5332991 AAGAAAAAAAATA
1 AATAAAAAAAATA
5333004 TATATACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
19 3 0.10
20 9 0.31
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.18
Consensus pattern (17 bp):
AATAAAAAAAATAAATG
Found at i:5333108 original size:22 final size:20
Alignment explanation
Indices: 5333083--5333145 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
5333073 AACTAAAAAC
5333083 ATAATGAAAATAAATAAATAGT
1 ATAAT-AAAATAAATAAATA-T
5333105 ATAAATAAAAT-AA-AAATAT
1 AT-AATAAAATAAATAAATAT
*
5333124 AT-ATAAAAATATATAAATAT
1 ATAAT-AAAATAAATAAATAT
5333144 AT
1 AT
5333146 GTATAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 2 0.06
18 5 0.14
19 4 0.11
20 13 0.36
21 2 0.06
22 7 0.19
23 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (20 bp):
ATAATAAAATAAATAAATAT
Found at i:5333131 original size:12 final size:12
Alignment explanation
Indices: 5333114--5333138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5333104 TATAAATAAA
5333114 ATAAAAATATAT
1 ATAAAAATATAT
5333126 ATAAAAATATAT
1 ATAAAAATATAT
5333138 A
1 A
5333139 AATATATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAATATAT
Found at i:5333150 original size:12 final size:12
Alignment explanation
Indices: 5333092--5333163 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 12
5333082 CATAATGAAA
*
5333092 ATAAATAAATAGT
1 ATAAATATATA-T
5333105 ATAAATA-A-A-
1 ATAAATATATAT
*
5333114 ATAAAAATATAT
1 ATAAATATATAT
5333126 ATAAA-A-ATAT
1 ATAAATATATAT
*
5333136 ATAAATATATGT
1 ATAAATATATAT
5333148 AT-AATATA-AT
1 ATAAATATATAT
5333158 A-AAATA
1 ATAAATA
5333164 CTAAATAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
9 6 0.12
10 16 0.32
11 10 0.20
12 11 0.22
13 7 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:5333159 original size:20 final size:21
Alignment explanation
Indices: 5333091--5333160 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
5333081 ACATAATGAA
* *
5333091 AATAAATAAATAGTATAAATAA
1 AATAAATATAT-GTATAAATAT
* * *
5333113 AATAAAAATATATATAAAAAT
1 AATAAATATATGTATAAATAT
5333134 ATATAAATATATGTAT-AATAT
1 A-ATAAATATATGTATAAATAT
5333155 AATAAA
1 AATAAA
5333161 ATACTAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.13
21 13 0.33
22 21 0.54
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AATAAATATATGTATAAATAT
Found at i:5333275 original size:28 final size:28
Alignment explanation
Indices: 5333221--5333283 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
5333211 ATATTAACTA
*
5333221 AAAAAAATAGTAATCATAGAAATATAG-T
1 AAAAAAATAGTAA-CATAGAAACATAGAT
5333249 AAAAAAATAGTAA-ATAGGTAAACATAGAT
1 AAAAAAATAGTAACATA-G-AAACATAGAT
5333278 AAAAAA
1 AAAAAA
5333284 TAATAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 3 0.10
27 1 0.03
28 20 0.65
29 7 0.23
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.21
Consensus pattern (28 bp):
AAAAAAATAGTAACATAGAAACATAGAT
Found at i:5333357 original size:10 final size:9
Alignment explanation
Indices: 5333344--5333381 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
5333334 AAATGAAAAA
5333344 AAATTATAAT
1 AAATTA-AAT
5333354 AAA-TAAAT
1 AAATTAAAT
5333362 AAATTAAAT
1 AAATTAAAT
5333371 ATAATTAAAT
1 A-AATTAAAT
5333381 A
1 A
5333382 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:5333379 original size:19 final size:18
Alignment explanation
Indices: 5333344--5333381 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5333334 AAATGAAAAA
5333344 AAATTATAATAAATAAAT
1 AAATTATAATAAATAAAT
5333362 AAATTA-AATATAATTAAAT
1 AAATTATAATA-AA-TAAAT
5333381 A
1 A
5333382 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTATAATAAATAAAT
Found at i:5333386 original size:2 final size:2
Alignment explanation
Indices: 5333379--5333408 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5333369 ATATAATTAA
*
5333379 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5333409 TAATAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5333857 original size:37 final size:37
Alignment explanation
Indices: 5333816--5333900 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
5333806 GGATCATATC
* *
5333816 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
** *
5333853 TTTAGGAGTTTAAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
5333890 TTTAGGAGTTT
1 TTTAGGAGTTT
5333901 GAATCCTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:5336721 original size:67 final size:71
Alignment explanation
Indices: 5336559--5336758 Score: 223
Period size: 67 Copynumber: 2.8 Consensus size: 71
5336549 ATTTTAAACA
* * ***
5336559 TTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAACTTTTAGAATATT
1 TTATCTTTATCTTGGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAG-A-A--
*
5336624 TTTTTTATATT
61 TTTATTATATT
*
5336635 TTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAG-A-TTAT
1 TTATCTTTATCTTGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATTTAT
5336698 TATATT
66 TATATT
*
5336704 ATTAT-TTT-T-TTGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 -TTATCTTTATCTTGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
5336759 AGATGTTTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
66 5 0.04
67 38 0.33
68 1 0.01
69 12 0.10
70 4 0.03
72 1 0.01
75 22 0.19
76 32 0.28
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (71 bp):
TTATCTTTATCTTGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATTTAT
TATATT
Found at i:5355015 original size:6 final size:6
Alignment explanation
Indices: 5355004--5355055 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
5354994 ATTAACACCT
* *
5355004 TTTGCA TTTGCA TTTAGCA TTGGCA TTTTCA TTTAGCA TTTGCA TTTGCA
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA
5355054 TT
1 TT
5355056 ACATGTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 30 0.75
7 10 0.25
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (6 bp):
TTTGCA
Found at i:5355031 original size:19 final size:19
Alignment explanation
Indices: 5355007--5355055 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5354997 AACACCTTTT
5355007 GCATTTGCATTTAGCATTG
1 GCATTTGCATTTAGCATTG
* *
5355026 GCATTTTCATTTAGCATTT
1 GCATTTGCATTTAGCATTG
5355045 GCATTTGCATT
1 GCATTTGCATT
5355056 ACATGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
GCATTTGCATTTAGCATTG
Found at i:5355042 original size:13 final size:12
Alignment explanation
Indices: 5355004--5355055 Score: 68
Period size: 13 Copynumber: 4.2 Consensus size: 12
5354994 ATTAACACCT
5355004 TTTGCATTTGCA
1 TTTGCATTTGCA
*
5355016 TTTAGCATTGGCA
1 TTT-GCATTTGCA
*
5355029 TTTTCATTTAGCA
1 TTTGCATTT-GCA
5355042 TTTGCATTTGCA
1 TTTGCATTTGCA
5355054 TT
1 TT
5355056 ACATGTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 12 0.35
13 22 0.65
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:5359963 original size:42 final size:41
Alignment explanation
Indices: 5359902--5359998 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 41
5359892 GATTTGTAAG
* * *
5359902 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATG-ATAAA
* * *
5359944 TCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
5359985 TCCTTCGGGCCATC
1 TCCTTCGGGCCATC
5359999 CATAAGACCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 16 0.33
42 32 0.67
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGTCTTTAGAGCAAGATGATAAA
Done.