Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 12
Found at i:31728 original size:38 final size:36
Alignment explanation
Indices: 31692--31761 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
31682 TTACAATTTG
31692 TAAAATATTTATAT-ATTTTCTTTAAAAAATTAAATT
1 TAAAATATTTATATAATTTT-TTTAAAAAATTAAATT
* *
31728 TATAATATTTATATAATTTTTTTACAAAATTAAA
1 TAAAATATTTATATAATTTTTTTAAAAAATTAAA
31762 AATATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 26 0.84
37 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (36 bp):
TAAAATATTTATATAATTTTTTTAAAAAATTAAATT
Found at i:33245 original size:16 final size:16
Alignment explanation
Indices: 33215--33245 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33205 TAATATTGAA
*
33215 ACTTGAACTCGAAAAT
1 ACTTGAACTCAAAAAT
33231 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
33246 AAAATTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (16 bp):
ACTTGAACTCAAAAAT
Found at i:33660 original size:22 final size:21
Alignment explanation
Indices: 33632--33672 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
33622 TATATAAAAT
33632 TATTTTTATTAAATATTTTTGA
1 TATTTTTATTAAAT-TTTTTGA
*
33654 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
33673 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGA
Found at i:34368 original size:36 final size:39
Alignment explanation
Indices: 34324--34399 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 39
34314 ATTTAGATAA
*
34324 AAAATAAAT-AAAAC-ATTCATAA-AATATTACGAAAAT
1 AAAATAAATAAAAACAATTCATAATAATAATACGAAAAT
34360 AAAATAAATAAAAAAACAATTCATAATAATAATACGAAAA
1 AAAATAAAT--AAAAACAATTCATAATAATAATACGAAAA
34400 ATATAAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 9 0.26
39 5 0.15
40 8 0.24
41 12 0.35
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (39 bp):
AAAATAAATAAAAACAATTCATAATAATAATACGAAAAT
Found at i:34473 original size:25 final size:27
Alignment explanation
Indices: 34439--34496 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
34429 TAAAAAATTA
34439 ATATTTTTAT-T-TA-TCTAATTTTAAT
1 ATATTTTTATCTATATTCTAA-TTTAAT
*
34464 ATATTTTTATCTATATTTTAATTTAAT
1 ATATTTTTATCTATATTCTAATTTAAT
34491 ATATTT
1 ATATTT
34497 GAATTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 10 0.34
26 1 0.03
27 14 0.48
28 4 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATTTTTATCTATATTCTAATTTAAT
Found at i:36128 original size:2 final size:2
Alignment explanation
Indices: 36121--36148 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
36111 CATCCGCCAC
36121 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
36149 ACCTAATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38587 original size:11 final size:11
Alignment explanation
Indices: 38564--38595 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
38554 TGTAATTTAT
38564 TATTTATATATA
1 TATTTA-ATATA
38576 TATTTAATATA
1 TATTTAATATA
38587 TATTTAATA
1 TATTTAATA
38596 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:38599 original size:3 final size:3
Alignment explanation
Indices: 38591--38667 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
38581 AATATATATT
*
38591 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38639 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
38668 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39116 original size:113 final size:113
Alignment explanation
Indices: 38978--39535 Score: 971
Period size: 113 Copynumber: 5.0 Consensus size: 113
38968 TGTGATAGTA
*
38978 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
39042 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
39090 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
39155 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
*
39203 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
39268 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
39316 TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
39380 TCTCATTATGAACTTTTTCTGG-AAAAATGATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
*** *
39427 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
39492 TCTCATTATGAACTTTCTCT-TCAAAAAATAATCCATCAATTGAT
66 TCTCATTATGAACCTTCTCTGGC-AAAAATAATCCATCAAGTGAT
39536 AGATTTGAAT
Statistics
Matches: 428, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
111 27 0.06
112 159 0.37
113 242 0.57
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
Found at i:40272 original size:14 final size:14
Alignment explanation
Indices: 40253--40280 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40243 GGTTCTGTAG
40253 TTCCTACTAAACCA
1 TTCCTACTAAACCA
40267 TTCCTACTAAACCA
1 TTCCTACTAAACCA
40281 AATCAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCCTACTAAACCA
Found at i:40357 original size:52 final size:52
Alignment explanation
Indices: 40276--40420 Score: 272
Period size: 52 Copynumber: 2.8 Consensus size: 52
40266 ATTCCTACTA
* *
40276 AACCAAATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTTGGTTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGGTTCTGTCT
40328 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGGTTCTGTCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGGTTCTGTCT
40380 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
40421 ATTGGCAAAT
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 91 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (52 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTTGGTTCTGTCT
Found at i:40507 original size:83 final size:83
Alignment explanation
Indices: 40368--40703 Score: 595
Period size: 83 Copynumber: 4.0 Consensus size: 83
40358 CAGAAGATGC
*
40368 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
40433 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
40451 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
40516 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
* * *
40534 TTGGTTTTG-CCAAACCAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACAT
1 TTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAAT
40597 TCATCTTCTAAATTCAATGA
64 TCATCTTCTAAATTCAATGA
*
40617 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
40682 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
40700 TTGG
1 TTGG
40704 ACTAAGATAT
Statistics
Matches: 241, Mismatches: 8, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
82 4 0.02
83 234 0.97
84 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (83 bp):
TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTCAATGA
Found at i:54616 original size:3 final size:3
Alignment explanation
Indices: 54608--54684 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
54598 TTAATATATT
* *
54608 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54656 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
54685 TGGATAAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:57246 original size:23 final size:22
Alignment explanation
Indices: 57204--57275 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
57194 GCCACTCAAG
*
57204 TAAAA-AATTAAATAAAAAACAT
1 TAAAACAAATAAAT-AAAAACAT
*
57226 TACAAACTAAAT-AGTAAAAACAAT
1 TA-AAAC-AAATAAATAAAAAC-AT
*
57250 TAAAACAATTAAATAAAAACAT
1 TAAAACAAATAAATAAAAACAT
57272 TAAA
1 TAAA
57276 TATAAATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 11 0.27
23 21 0.51
24 6 0.15
25 3 0.07
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.22
Consensus pattern (22 bp):
TAAAACAAATAAATAAAAACAT
Found at i:62553 original size:16 final size:16
Alignment explanation
Indices: 62529--62559 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62519 TGCTTCATTT
*
62529 AGAGGAGAAAAATGAG
1 AGAGAAGAAAAATGAG
62545 AGAGAAGAAAAATGA
1 AGAGAAGAAAAATGA
62560 AAAATAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.06
Consensus pattern (16 bp):
AGAGAAGAAAAATGAG
Found at i:65629 original size:15 final size:16
Alignment explanation
Indices: 65609--65643 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
65599 CTAATGAAAA
65609 TAAAATATT-AACTCT
1 TAAAATATTAAACTCT
65624 TAAAATATTCAAACTCT
1 TAAAATATT-AAACTCT
65641 TAA
1 TAA
65644 TTCTAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATATTAAACTCT
Found at i:65683 original size:38 final size:37
Alignment explanation
Indices: 65640--65718 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 37
65630 ATTCAAACTC
* *
65640 TTAATTCTAATAAACTAAAAATCCTAATTAATAAATTA
1 TTAATTCTAACAAACCAAAAATCCTAATTAATAAA-TA
65678 TTAATTCTAACAAACCAAAAATCCTAATTAATAAATA
1 TTAATTCTAACAAACCAAAAATCCTAATTAATAAATA
65715 TTAA
1 TTAA
65719 AAATCTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 6 0.15
38 33 0.85
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (37 bp):
TTAATTCTAACAAACCAAAAATCCTAATTAATAAATA
Found at i:66191 original size:42 final size:42
Alignment explanation
Indices: 66105--66191 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
66095 TATTGCCTTT
* * * *
66105 AATCACTAAAACCATTTTATGAATAGATAAATTTAATTCTTA
1 AATCACTAAAACCACTTTATGAATAGAGAAATTTAATGCATA
* *
66147 AATCACTAAAACCACTTTATGGATAGAGAATTTTAATGCATA
1 AATCACTAAAACCACTTTATGAATAGAGAAATTTAATGCATA
66189 AAT
1 AAT
66192 AAAATAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (42 bp):
AATCACTAAAACCACTTTATGAATAGAGAAATTTAATGCATA
Found at i:68408 original size:20 final size:19
Alignment explanation
Indices: 68362--68408 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 19
68352 AACTTGGGAT
68362 CCAAATTAAAA-TACATGA
1 CCAAATTAAAATTACATGA
68380 --AAATT--AATTACAGTGA
1 CCAAATTAAAATTACA-TGA
68396 CCAAATTAAAATT
1 CCAAATTAAAATT
68409 TTACAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
14 2 0.09
15 4 0.17
16 8 0.35
18 5 0.22
20 4 0.17
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (19 bp):
CCAAATTAAAATTACATGA
Found at i:70513 original size:31 final size:31
Alignment explanation
Indices: 70488--70551 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
70478 AAAATTGAAG
70488 TTTCATGTGTACAATTAAATTAAAATCAAAA
1 TTTCATGTGTACAATTAAATTAAAATCAAAA
* * * *
70519 TTTTATGTGTATAATTACATT-AAGTCAAAA
1 TTTCATGTGTACAATTAAATTAAAATCAAAA
70549 TTT
1 TTT
70552 ATATATCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (31 bp):
TTTCATGTGTACAATTAAATTAAAATCAAAA
Found at i:79027 original size:21 final size:20
Alignment explanation
Indices: 79003--79060 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
78993 CTCATATATT
79003 TAAAATTCAATAAAAATACAA
1 TAAAATTCAATAAAAAT-CAA
*** * *
79024 TAAAAAAGAATTAAAAGTGAA
1 TAAAATTCAA-TAAAAATCAA
79045 TAAAATTCAATAAAAA
1 TAAAATTCAATAAAAA
79061 AAAGAAGGTA
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (20 bp):
TAAAATTCAATAAAAATCAA
Found at i:85690 original size:29 final size:30
Alignment explanation
Indices: 85634--85692 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
85624 TTGGATCCAA
* *
85634 AATTTAATTAAAATTTCACTTTGGTCCTCG
1 AATTTAATTAAAATTTCAATTTAGTCCTCG
85664 AATTTAATTAAAA-TTCAATTTAGTCCTCG
1 AATTTAATTAAAATTTCAATTTAGTCCTCG
85693 TGAAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (30 bp):
AATTTAATTAAAATTTCAATTTAGTCCTCG
Found at i:95526 original size:13 final size:13
Alignment explanation
Indices: 95491--95518 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
95481 AATAAAATAA
95491 TTATTATTATTTT
1 TTATTATTATTTT
95504 TTATTATTATTTT
1 TTATTATTATTTT
95517 TT
1 TT
95519 GATATTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:95969 original size:24 final size:25
Alignment explanation
Indices: 95910--95969 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 25
95900 AAGAAGTTAT
* *
95910 ATTAAAAAAATTTAAGGAATGTGAA
1 ATTAAAAAATTTTAAGGAATGAGAA
* * *
95935 GTTATACAATTTTAAGG-ATGAGAA
1 ATTAAAAAATTTTAAGGAATGAGAA
*
95959 ATTAAATAATT
1 ATTAAAAAATT
95970 AATAAAAATA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.33
Consensus pattern (25 bp):
ATTAAAAAATTTTAAGGAATGAGAA
Found at i:95982 original size:22 final size:22
Alignment explanation
Indices: 95957--96012 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
95947 TAAGGATGAG
95957 AAATTAAATAATTAATA-AAAA
1 AAATTAAATAATTAATATAAAA
* *
95978 TAAATAAAAT-ATAAAATATAAAA
1 -AAATTAAATAAT-TAATATAAAA
96001 AAATTAAA-AATT
1 AAATTAAATAATT
96013 CCAAGAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
21 2 0.07
22 21 0.78
23 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATTAAATAATTAATATAAAA
Found at i:95991 original size:17 final size:16
Alignment explanation
Indices: 95971--96011 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
95961 TAAATAATTA
95971 ATAAAAATAAATAAAAT
1 ATAAAAATAAA-AAAAT
95988 ATAAAATATAAAAAAAT
1 ATAAAA-ATAAAAAAAT
96005 -TAAAAAT
1 ATAAAAAT
96012 TCCAAGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 2 0.09
16 5 0.22
17 11 0.48
18 5 0.22
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
ATAAAAATAAAAAAAT
Found at i:96933 original size:23 final size:24
Alignment explanation
Indices: 96888--96933 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
96878 CATACGATAG
*
96888 TCAAATCAGAGCAAAACATTCATT
1 TCAAATCAGAGCAAAACAATCATT
* *
96912 TCAAATTAGAG-AAAATAATCAT
1 TCAAATCAGAGCAAAACAATCAT
96934 GTGCATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (24 bp):
TCAAATCAGAGCAAAACAATCATT
Found at i:97496 original size:32 final size:32
Alignment explanation
Indices: 97405--97503 Score: 93
Period size: 32 Copynumber: 3.2 Consensus size: 32
97395 TATGACTTTG
*
97405 GGTCAAAGTTAACAGTCAA-C-A-CTGGTCAAA
1 GGTCAAAGATAA-AGTCAATCGATCTGGTCAAA
* *
97435 GGTCAAAGTTAAAGTCAATGGATCTGGTCAAA
1 GGTCAAAGATAAAGTCAATCGATCTGGTCAAA
*
97467 GGTCAACAGAT-AAGTCAA-CGATTTGGGTC-AA
1 GGTCAA-AGATAAAGTCAATCGATCT-GGTCAAA
97498 GGTCAA
1 GGTCAA
97504 TGGGTCAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
29 6 0.10
30 12 0.20
31 13 0.22
32 26 0.43
33 3 0.05
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (32 bp):
GGTCAAAGATAAAGTCAATCGATCTGGTCAAA
Found at i:98405 original size:23 final size:23
Alignment explanation
Indices: 98379--98429 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
98369 TAGCCTAGTG
98379 TCTAGGGCACGGGAAGCCATAAC
1 TCTAGGGCACGGGAAGCCATAAC
* * *
98402 TCTAAGGTCATGGGTAGCCATAAC
1 TCT-AGGGCACGGGAAGCCATAAC
98426 TCTA
1 TCTA
98430 AGGTCATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
TCTAGGGCACGGGAAGCCATAAC
Found at i:98420 original size:24 final size:24
Alignment explanation
Indices: 98393--98440 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
98383 GGGCACGGGA
98393 AGCCATAACTCTAAGGTCATGGGT
1 AGCCATAACTCTAAGGTCATGGGT
98417 AGCCATAACTCTAAGGTCATGGGT
1 AGCCATAACTCTAAGGTCATGGGT
98441 TCATGCCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
AGCCATAACTCTAAGGTCATGGGT
Found at i:98768 original size:18 final size:18
Alignment explanation
Indices: 98741--98779 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
98731 CCAAACAAAT
*
98741 AAATAAATGATTACATGA
1 AAATAAATGATCACATGA
* *
98759 AAATATATGATCATATGA
1 AAATAAATGATCACATGA
98777 AAA
1 AAA
98780 GATAAAGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.28
Consensus pattern (18 bp):
AAATAAATGATCACATGA
Found at i:99269 original size:23 final size:24
Alignment explanation
Indices: 99224--99269 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
99214 AGATTCAGGT
* *
99224 TCGAGTTTGAGTTTAAGGCTTCAA
1 TCGAGTTTAAGTTTAAGACTTCAA
*
99248 TCGAG-TTAAGTTTAAGATTTCA
1 TCGAGTTTAAGTTTAAGACTTCA
99270 TTTTTTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (24 bp):
TCGAGTTTAAGTTTAAGACTTCAA
Found at i:107756 original size:63 final size:63
Alignment explanation
Indices: 107661--107782 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
107651 TTCTACATTG
* * * * *
107661 ATTTCACCGCCGTTGGATAAACCCTTCCCTTCTATTTCCACTATTCCG-TCGTCGTTTTCATCA
1 ATTTCACCGCCGGTGGACAAACCATTACCTTCTACTTCCACTATT-CGATCGTCGTTTTCATCA
* * *
107724 ATTTCACCGCTGGTGGACAAATCATTACCTTCTACTTCCACTATTTGATCGTCGTTTTC
1 ATTTCACCGCCGGTGGACAAACCATTACCTTCTACTTCCACTATTCGATCGTCGTTTTC
107783 TTCATCGGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
62 1 0.02
63 49 0.98
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (63 bp):
ATTTCACCGCCGGTGGACAAACCATTACCTTCTACTTCCACTATTCGATCGTCGTTTTCATCA
Found at i:116398 original size:16 final size:16
Alignment explanation
Indices: 116377--116407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
116367 TGTATAGATC
*
116377 TTTTAATTAGTTATAA
1 TTTTAATTAATTATAA
116393 TTTTAATTAATTATA
1 TTTTAATTAATTATA
116408 TAATTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTTTAATTAATTATAA
Found at i:116422 original size:20 final size:20
Alignment explanation
Indices: 116378--116423 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
116368 GTATAGATCT
116378 TTTAATTAGTTATAATTTTAA
1 TTTAATTAG-TATAATTTTAA
116399 -TTAATTA-TATAATTTTATA
1 TTTAATTAGTATAATTTTA-A
116418 TTTAAT
1 TTTAAT
116424 ATTATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.43
19 1 0.04
20 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAATTAGTATAATTTTAA
Found at i:123139 original size:21 final size:21
Alignment explanation
Indices: 123110--123163 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
123100 GATGCATGTA
*
123110 GTTCTCAGGGGCTGGAGCAAAT
1 GTTC-CAGGCGCTGGAGCAAAT
123132 GTTCCAGGCGCTGGAGCAAAT
1 GTTCCAGGCGCTGGAGCAAAT
123153 GTTCCAGGCGC
1 GTTCCAGGCGC
123164 CGATGGATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (21 bp):
GTTCCAGGCGCTGGAGCAAAT
Found at i:134863 original size:19 final size:18
Alignment explanation
Indices: 134835--134870 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
134825 ATTTTATAAA
134835 TTTTTATTAAAAATTTAC
1 TTTTTATTAAAAATTTAC
*
134853 TTTTATATTAAAATTTTA
1 TTTT-TATTAAAAATTTA
134871 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTATTAAAAATTTAC
Found at i:136228 original size:25 final size:26
Alignment explanation
Indices: 136187--136235 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
136177 TTTTATAATA
*
136187 ATAAATTTTTATAATTTT-AAAAATT
1 ATAAATTTATATAATTTTGAAAAATT
136212 ATAAATTTCATAT-ATTTTGAAAAA
1 ATAAATTT-ATATAATTTTGAAAAA
136236 ATTAGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (26 bp):
ATAAATTTATATAATTTTGAAAAATT
Found at i:139134 original size:184 final size:185
Alignment explanation
Indices: 138830--139216 Score: 633
Period size: 184 Copynumber: 2.1 Consensus size: 185
138820 TTTTCTAATT
* *
138830 TATATAA-A-ATTAAATA-TTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAA
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAA
*
138892 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* *
138957 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
*
139012 TATATAATATATTTAATATTTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATA
*
139076 ATTATAAAATAAAAAATTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
65 ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
*
139140 TTGGATCTTAAATTATTAATTGAGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
130 TTGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
139196 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
139217 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
182 7 0.04
183 3 0.02
184 124 0.65
185 57 0.30
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAA
TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGAGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:139367 original size:27 final size:30
Alignment explanation
Indices: 139309--139380 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 30
139299 CCATTAATCG
139309 ACCGAACTAATTCGATAATCGAACCGAATTA
1 ACCGAACTAATTCGAT-ATCGAACCGAATTA
* *
139340 ACCGAACTAATTCGAT-TCG-ATCG-GTTA
1 ACCGAACTAATTCGATATCGAACCGAATTA
*
139367 ACCGAATTAATTCG
1 ACCGAACTAATTCG
139381 GTTATTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 16 0.42
28 3 0.08
29 3 0.08
31 16 0.42
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (30 bp):
ACCGAACTAATTCGATATCGAACCGAATTA
Found at i:142350 original size:31 final size:31
Alignment explanation
Indices: 142258--142361 Score: 163
Period size: 31 Copynumber: 3.4 Consensus size: 31
142248 AAAACATGAT
* *
142258 ATTTGGTCACTTTTATTTTTATTTAATTAAA
1 ATTTGATCACTTTTATTTTTATTTAATTAAG
* *
142289 ATTTGGTCACTTTCATTTTTATTTAATTAAG
1 ATTTGATCACTTTTATTTTTATTTAATTAAG
142320 ATTTGATCACTTTTATTTTTATTTAATTAAG
1 ATTTGATCACTTTTATTTTTATTTAATTAAG
*
142351 ATGTGATCACT
1 ATTTGATCACT
142362 AAGAGTTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (31 bp):
ATTTGATCACTTTTATTTTTATTTAATTAAG
Found at i:142951 original size:17 final size:18
Alignment explanation
Indices: 142929--142977 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
142919 TGTCACATAC
142929 ATATTTTTAAAAAATA-T
1 ATATTTTTAAAAAATATT
*
142946 ATATTTTTAAATAATATT
1 ATATTTTTAAAAAATATT
*
142964 TTATTTTTAAAAAA
1 ATATTTTTAAAAAA
142978 ATTGGACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTTTAAAAAATATT
Found at i:144315 original size:6 final size:7
Alignment explanation
Indices: 144290--144314 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
144280 TTCTGCAAAA
144290 AAAAACT
1 AAAAACT
144297 AAAAACT
1 AAAAACT
144304 AAAAACT
1 AAAAACT
144311 AAAA
1 AAAA
144315 CCAAAGGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAACT
Found at i:147589 original size:74 final size:73
Alignment explanation
Indices: 147443--147858 Score: 486
Period size: 74 Copynumber: 5.7 Consensus size: 73
147433 CCGTATGTAG
* * * * * *
147443 TTTAATGTAATAGGTAGTGTCTA-TTTTTTTACGGTTTACATTATTAGCAACTTTCAAAAAATCA
1 TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT-AAAAAAACA
*
147507 -GTAGGTAT
65 TGTAAGTAT
147515 TTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACA
1 TTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACA
147580 TGTAAGTAT
65 TGTAAGTAT
* ** * *
147589 TTTAATGTAATAGGTAGCGCCTATTTTATTTTATCGTTTACATTATTTGCAATCTTTAAACAAAC
1 TTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAACAA-CCTTAAA-AAAA
*
147654 CA-GTAGGTAT
63 CATGTAAGTAT
* * *
147664 TTTAATGTAATAGGTAGCACATATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAA-AT
1 TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACAT
* **
147728 CAGTATGTGG
66 --GTAAGTAT
* *
147738 TTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTCAAAAAA-A
1 TTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACA
* *
147802 TGATAAATAA
65 TG-TAAGTAT
*
147812 TTTAATGTAATAGGTAGCG-CTA-TTTTTTTACTGTTTACATTATTAAC
1 TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAAC
147859 CATTTTTACT
Statistics
Matches: 300, Mismatches: 33, Indels: 23
0.84 0.09 0.06
Matches are distributed among these distances:
71 25 0.08
72 24 0.08
73 22 0.07
74 147 0.49
75 77 0.26
76 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (73 bp):
TTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAACAT
GTAAGTAT
Found at i:147678 original size:149 final size:144
Alignment explanation
Indices: 147439--147858 Score: 526
Period size: 149 Copynumber: 2.9 Consensus size: 144
147429 ATATCCGTAT
* *
147439 GTAGTTTAATGTAATAGGTAGTGTCTA-TTTTTTTACGGTTTACATTATTAGCAACTTTCAAAAA
1 GTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTAC-GTTTACATTATTAGCAACTTT-AAAAA
147503 ATCAGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAAC
64 ATCAGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTACCGTTTACATTATTAACAAC
147568 CTTAAAAAAACAT-GTAA
128 CTTAAAAAAA-ATAGTAA
* *
147585 GTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTATCGTTTACATTATTTGCAATCTTTAAAC
1 GTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTA-CGTTTACATTATTAGCAA-CTTTAAA-
* * * *
147650 AAACCAGTAGGTATTTTAATGTAATAGGTAGCACATATTTTTTTTACCGTTTACATTATTAGCAA
62 AAATCAGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAA
*
147715 CCTTAAAAAAAATCAGTAT
127 CCTTAAAAAAAAT-AGTAA
* * * *
147734 GTGGTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTCAAAA
1 GTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTA-CGTTTACATTATTAGCAA-CTT-TAAA
* ** * *
147799 AAATGA-TAAATAATTTAATGTAATAGGTAGCG-CTA-TTTTTTTACTGTTTACATTATTAAC
62 AAATCAGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAAC
147859 CATTTTTACT
Statistics
Matches: 239, Mismatches: 26, Indels: 18
0.84 0.09 0.06
Matches are distributed among these distances:
146 47 0.20
147 7 0.03
148 84 0.35
149 94 0.39
150 7 0.03
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (144 bp):
GTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACGTTTACATTATTAGCAACTTTAAAAAAT
CAGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT
AAAAAAAATAGTAA
Found at i:147829 original size:223 final size:218
Alignment explanation
Indices: 147443--147855 Score: 625
Period size: 223 Copynumber: 1.9 Consensus size: 218
147433 CCGTATGTAG
** * **
147443 TTTAATGTAATAGGTAGTGTCTATTTTTTTACGGTTTACATTATTAGCAACTTTCAAAAAATCAG
1 TTTAATGTAATAGGTAGTCACTATTTTTTTACCGTTTACATTATTAGCAACTTAAAAAAAATCAG
* *
147508 TAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTAA
66 TAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTAA
* *
147573 AAAAACATGTAAGTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTA-TCGTTTACATTATTT
131 AAAAACATGTAAATAATTTAATGTAATAGGTAGCG-CTA-TTT-TTTTACT-GTTTACATTATTT
147637 GCAATCTTTAAACAAACCAGTAGGTAT
192 GCAATCTTTAAACAAACCAGTAGGTAT
147664 TTTAATGTAATAGGTAG-CACATATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAAT
1 TTTAATGTAATAGGTAGTCAC-TA-TTTTTTTACCGTTTACATTATTAGCAA-CTTAAAAAAAAT
* *
147728 CAGTATGTGGTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCT
63 CAGTAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCT
*
147793 TCAAAAAA-ATGATAAATAATTTAATGTAATAGGTAGCGCTATTTTTTTACTGTTTACATTATT
128 TAAAAAAACATG-TAAATAATTTAATGTAATAGGTAGCGCTATTTTTTTACTGTTTACATTATT
147856 AACCATTTTT
Statistics
Matches: 175, Mismatches: 12, Indels: 11
0.88 0.06 0.06
Matches are distributed among these distances:
220 18 0.10
221 23 0.13
222 32 0.18
223 102 0.58
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (218 bp):
TTTAATGTAATAGGTAGTCACTATTTTTTTACCGTTTACATTATTAGCAACTTAAAAAAAATCAG
TAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAACAACCTTAA
AAAAACATGTAAATAATTTAATGTAATAGGTAGCGCTATTTTTTTACTGTTTACATTATTTGCAA
TCTTTAAACAAACCAGTAGGTAT
Found at i:149497 original size:16 final size:16
Alignment explanation
Indices: 149473--149517 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
149463 AGACAATATC
149473 TTTTAAAAATCAAT-TTT
1 TTTTAAAAA--AATATTT
149490 TTTTAAAAAAATATTT
1 TTTTAAAAAAATATTT
149506 TTTTAAAGAAAA
1 TTTTAAA-AAAA
149518 ATCATTTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTTAAAAAAATATTT
Found at i:151268 original size:39 final size:38
Alignment explanation
Indices: 151225--151302 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
151215 TCAGATGCAA
*
151225 ATCTTCTTCGTAACATTTTAGGTTGCAACAAAAAATGTT
1 ATCTTCTTCATAACATTTTAGGTTG-AACAAAAAATGTT
* * * *
151264 ATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTT
1 ATCTTCTTCATAACATTTTAGGTTGAACAAAAAATGTT
151302 A
1 A
151303 AAATATTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
38 14 0.41
39 20 0.59
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (38 bp):
ATCTTCTTCATAACATTTTAGGTTGAACAAAAAATGTT
Found at i:151291 original size:167 final size:167
Alignment explanation
Indices: 151015--151346 Score: 646
Period size: 167 Copynumber: 2.0 Consensus size: 167
151005 AGGTTGTGTG
151015 CAACCTAAAATGTTAATTTTTTCTTAATATTTTTCAGATGCAAATCTTCTTCGTAACATTTTAGG
1 CAACCTAAAATGTTAATTTTTTCTTAATATTTTTCAGATGCAAATCTTCTTCGTAACATTTTAGG
*
151080 TTGCAATAAAAAATATTATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTTAAAATATTAT
66 TTGCAACAAAAAATATTATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTTAAAATATTAT
151145 GTTGTTTATAACATTTCGATAGCTCTTGTCCTTAGCA
131 GTTGTTTATAACATTTCGATAGCTCTTGTCCTTAGCA
151182 CAACCTAAAATGTTAATTTTTTCTTAATATTTTTCAGATGCAAATCTTCTTCGTAACATTTTAGG
1 CAACCTAAAATGTTAATTTTTTCTTAATATTTTTCAGATGCAAATCTTCTTCGTAACATTTTAGG
*
151247 TTGCAACAAAAAATGTTATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTTAAAATATTAT
66 TTGCAACAAAAAATATTATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTTAAAATATTAT
151312 GTTGTTTATAACATTTCGATAGCTCTTGTCCTTAG
131 GTTGTTTATAACATTTCGATAGCTCTTGTCCTTAG
151347 TCTTATATTA
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 163 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (167 bp):
CAACCTAAAATGTTAATTTTTTCTTAATATTTTTCAGATGCAAATCTTCTTCGTAACATTTTAGG
TTGCAACAAAAAATATTATCTTTTTCATTATATTTTTGGTTGAACAAAAAATGTTAAAATATTAT
GTTGTTTATAACATTTCGATAGCTCTTGTCCTTAGCA
Found at i:151372 original size:32 final size:32
Alignment explanation
Indices: 151336--151431 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
151326 TTCGATAGCT
*
151336 CTTGTCCTTAGTCTTATATTAAGTTGCTATAC
1 CTTGTCCTTTGTCTTATATTAAGTTGCTATAC
*
151368 CTTGTCCTTTGTCTTATATTAAATTGCTATAC
1 CTTGTCCTTTGTCTTATATTAAGTTGCTATAC
* *
151400 CTTGACCTTTGTCTTATATTAAGTTGTTATAC
1 CTTGTCCTTTGTCTTATATTAAGTTGCTATAC
151432 GGTTGAACTA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (32 bp):
CTTGTCCTTTGTCTTATATTAAGTTGCTATAC
Found at i:152964 original size:33 final size:33
Alignment explanation
Indices: 152920--153149 Score: 327
Period size: 33 Copynumber: 7.0 Consensus size: 33
152910 AGGAGGACCA
* * * *
152920 CCTCTTGCTCCTCTAGGCGAGTAGTCTTCCCTG
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
*
152953 CCTCTTCCTCCTCTGGGAAAGTAGTCGTCCCTG
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
* *
152986 CCTCTTCCTCCTCTGGGAGAGTAGTCTTCCCCG
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
* *
153019 CCTCTTCCTCCTCTGGAAGTGTAGTCGTCCCTG
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
*
153052 CCTCTTCCTCCTCTGGGAGAGTAGTCTTCCCAT-
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCC-TG
*
153085 CCTCTTCCTCCTCTGGAAGAGTAGTCGTCCCTG
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
**
153118 CCTCTTCCTCCTCTGGGAGAAAAGTCGTCCCT
1 CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCT
153150 ACGAGGAGGA
Statistics
Matches: 175, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
32 1 0.01
33 173 0.99
34 1 0.01
ACGTcount: A:0.11, C:0.37, G:0.20, T:0.31
Consensus pattern (33 bp):
CCTCTTCCTCCTCTGGGAGAGTAGTCGTCCCTG
Found at i:156340 original size:203 final size:203
Alignment explanation
Indices: 155990--156394 Score: 765
Period size: 203 Copynumber: 2.0 Consensus size: 203
155980 TGGTGAAGAT
155990 TAATAATTTAAATTTTTTAAAAATAACTAAAATTCCACGTCAGCTTAAAAATTAAAAAATATGTC
1 TAATAATTTAAATTTTTTAAAAATAACTAAAATTCCACGTCAGCTTAAAAATTAAAAAATATGTC
156055 TCAATAATCGATTGACACATGAGACATCTTGATTGGAGTATTAATTTTTAATTAAATTAAAATTA
66 TCAATAATCGATTGACACATGAGACATCTTGATTGGAGTATTAATTTTTAATTAAATTAAAATTA
*
156120 AGACTAAATTAATAAAATATACAAGTATTGAAGATCAAATGTGTAATTATATAAATTTTTGTTAA
131 AGACTAAATTAATAAAATATACAAATATTGAAGATCAAATGTGTAATTATATAAATTTTTGTTAA
156185 CTCCACAA
196 CTCCACAA
*
156193 TAATAATTTAAATTTTTTAAAAATAACTAAAATTCCACTTCAGCTTAAAAATTAAAAAATATGTC
1 TAATAATTTAAATTTTTTAAAAATAACTAAAATTCCACGTCAGCTTAAAAATTAAAAAATATGTC
**
156258 TCAATAATCGATTGACTTATGAGACATCTTGATTGGAGTATTAATTTTTAATTAAATTAAAATTA
66 TCAATAATCGATTGACACATGAGACATCTTGATTGGAGTATTAATTTTTAATTAAATTAAAATTA
*
156323 AGACTAAATTGATAAAATATACAAATATTGAAGATCAAATGTGTAATTATATAAATTTTTGTTAA
131 AGACTAAATTAATAAAATATACAAATATTGAAGATCAAATGTGTAATTATATAAATTTTTGTTAA
156388 CTCCACA
196 CTCCACA
156395 TCACCCTCCG
Statistics
Matches: 197, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
203 197 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (203 bp):
TAATAATTTAAATTTTTTAAAAATAACTAAAATTCCACGTCAGCTTAAAAATTAAAAAATATGTC
TCAATAATCGATTGACACATGAGACATCTTGATTGGAGTATTAATTTTTAATTAAATTAAAATTA
AGACTAAATTAATAAAATATACAAATATTGAAGATCAAATGTGTAATTATATAAATTTTTGTTAA
CTCCACAA
Found at i:159174 original size:24 final size:24
Alignment explanation
Indices: 159147--159198 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
159137 GTTTAAATGA
*
159147 TAAACGAACACAAATAAACGAACG
1 TAAACGAACACAAACAAACGAACG
*
159171 TAAACGAACATAAACAAACGAACG
1 TAAACGAACACAAACAAACGAACG
159195 TAAA
1 TAAA
159199 ATTAATTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.10
Consensus pattern (24 bp):
TAAACGAACACAAACAAACGAACG
Found at i:159426 original size:26 final size:27
Alignment explanation
Indices: 159387--159443 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
159377 ACTACATTAT
159387 ATATTATATATTA-TTATTATT-CTAAA
1 ATATTATATATTATTTATTATTAC-AAA
159413 ATATTAT-TATTTATTTATTATTACAAA
1 ATATTATATA-TTATTTATTATTACAAA
159440 ATAT
1 ATAT
159444 CCAAACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.07
26 10 0.36
27 15 0.54
28 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATTATATATTATTTATTATTACAAA
Found at i:159461 original size:20 final size:20
Alignment explanation
Indices: 159436--159478 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
159426 TTTATTATTA
159436 CAAAATATCC-AAACCAAACC
1 CAAAATA-CCTAAACCAAACC
159456 CAAAATACCTAAACCAAACC
1 CAAAATACCTAAACCAAACC
159476 CAA
1 CAA
159479 GCCCATTACC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (20 bp):
CAAAATACCTAAACCAAACC
Found at i:159904 original size:3 final size:3
Alignment explanation
Indices: 159898--159929 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
159888 GAAAATAATC
159898 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
159930 AAGGAGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:164621 original size:56 final size:57
Alignment explanation
Indices: 164554--164688 Score: 157
Period size: 56 Copynumber: 2.4 Consensus size: 57
164544 TATATATTTG
* * * *
164554 TATTTAAATTTAATTTTACAGTACACTTTAGTGTTTATTTTTTGT-ATCTAATTAGA
1 TATTTAAATTTAATTTTAAAGTACAATTTAGTGCTTATTTTTTGTAATCCAATTAGA
* * * * *
164610 TATTTAAATTTAGTTTTAAATTATAATTTGGTGCTTATTTTTTTTAATCCAATTAGA
1 TATTTAAATTTAATTTTAAAGTACAATTTAGTGCTTATTTTTTGTAATCCAATTAGA
*
164667 TATTTGAAA-TTAATTTTTAAGT
1 TATTT-AAATTTAATTTTAAAGT
164689 TAAAATTAGT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
56 37 0.57
57 25 0.38
58 3 0.05
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (57 bp):
TATTTAAATTTAATTTTAAAGTACAATTTAGTGCTTATTTTTTGTAATCCAATTAGA
Found at i:168180 original size:18 final size:18
Alignment explanation
Indices: 168157--168193 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
168147 TTCGACTATA
168157 TGGTACTACTT-TTTTTAG
1 TGGTACTA-TTATTTTTAG
168175 TGGTACTATTATTTTTAG
1 TGGTACTATTATTTTTAG
168193 T
1 T
168194 TCTCTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.19, C:0.08, G:0.16, T:0.57
Consensus pattern (18 bp):
TGGTACTATTATTTTTAG
Found at i:178484 original size:15 final size:14
Alignment explanation
Indices: 178464--178545 Score: 73
Period size: 13 Copynumber: 5.9 Consensus size: 14
178454 TGTCGTACTG
178464 GTTTATACATATATA
1 GTTTATA-ATATATA
*
178479 GTTTAT-ATACATA
1 GTTTATAATATATA
178492 GTTTATATATATATA
1 GTTTATA-ATATATA
*
178507 ATTCGTATAA-ATATA
1 GTT--TATAATATATA
178522 GTTTAT-ATATATA
1 GTTTATAATATATA
*
178535 GCTTAT-ATATA
1 GTTTATAATATA
178546 AACTTATATT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.02
13 30 0.53
15 21 0.37
16 1 0.02
17 4 0.07
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (14 bp):
GTTTATAATATATA
Found at i:178504 original size:28 final size:29
Alignment explanation
Indices: 178464--178534 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
178454 TGTCGTACTG
* * *
178464 GTTTATACATATATAGTT-TATATACATA
1 GTTTATATATATATAATTCTATAAACATA
*
178492 GTTTATATATATATAATTCGTATAAATATA
1 GTTTATATATATATAATTC-TATAAACATA
178522 GTTTATATATATA
1 GTTTATATATATA
178535 GCTTATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 16 0.43
30 21 0.57
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (29 bp):
GTTTATATATATATAATTCTATAAACATA
Found at i:178542 original size:13 final size:13
Alignment explanation
Indices: 178512--178558 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
178502 ATATAATTCG
* *
178512 TATAAATATAGTT
1 TATATATATAGCT
178525 TATATATATAGCT
1 TATATATATAGCT
*
178538 TATATATA-AACT
1 TATATATATAGCT
178550 TATAT-TATA
1 TATATATATA
178559 TTAATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 19 0.63
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (13 bp):
TATATATATAGCT
Found at i:178543 original size:28 final size:26
Alignment explanation
Indices: 178472--178541 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 26
178462 TGGTTTATAC
*
178472 ATATATAGTTTATATACATAGTTTATAT
1 ATATATAGTTTATAAACATAG-TT-TAT
* *
178500 ATATATAATTCGTATAAATATAGTTTAT
1 ATATATAGTT--TATAAACATAGTTTAT
*
178528 ATATATAGCTTATA
1 ATATATAGTTTATA
178542 TATAAACTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.11
28 20 0.57
29 2 0.06
30 9 0.26
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (26 bp):
ATATATAGTTTATAAACATAGTTTAT
Found at i:178599 original size:9 final size:9
Alignment explanation
Indices: 178569--178601 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
178559 TTAATATAAA
178569 TTATATACT
1 TTATATACT
178578 TTA-ATACT
1 TTATATACT
*
178586 TTATATAGT
1 TTATATACT
178595 TTATATA
1 TTATATA
178602 TTGTTTACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (9 bp):
TTATATACT
Found at i:178706 original size:15 final size:15
Alignment explanation
Indices: 178688--178746 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
178678 TACTTAATAT
178688 ACTATATATATATAA
1 ACTATATATATATAA
*
178703 ACTATATACATA-AA
1 ACTATATATATATAA
* *
178717 TCT-TATATATTATAT
1 ACTATATATA-TATAA
*
178732 A-TTTATATATATAA
1 ACTATATATATATAA
178746 A
1 A
178747 TTACATAGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
13 5 0.14
14 12 0.34
15 18 0.51
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (15 bp):
ACTATATATATATAA
Found at i:180445 original size:2 final size:2
Alignment explanation
Indices: 180433--180479 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
180423 GTGTTGTCTT
180433 TA TA TA CTA TA TA TA TA TA TA TA TA TA TA -A 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
180475 T- TA TA
1 TA TA TA
180480 AGTGTTTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:180459 original size:21 final size:19
Alignment explanation
Indices: 180433--180480 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
180423 GTGTTGTCTT
180433 TATATACTAT-ATATATATA
1 TATATA-TATAATATATATA
180452 TATATATATAATATATATA
1 TATATATATAATATATATA
180471 TATAT-TATAA
1 TATATATATAA
180481 GTGTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATATAATATATATA
Found at i:180613 original size:15 final size:16
Alignment explanation
Indices: 180579--180628 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
180569 CCTTTTGTGT
180579 TTTTAATTTATTTCAA
1 TTTTAATTTATTTCAA
* *
180595 TTTTAA-TTCTTTCAC
1 TTTTAATTTATTTCAA
180610 TTTTATATTTA-TTCAA
1 TTTTA-ATTTATTTCAA
180626 TTT
1 TTT
180629 AGTCCTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 14 0.50
17 2 0.07
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTAATTTATTTCAA
Found at i:182627 original size:16 final size:16
Alignment explanation
Indices: 182602--182644 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
182592 AACGTCTTTT
182602 AAAAACAATTTT-TAAG
1 AAAAA-AATTTTATAAG
182618 AAAAATAATTTTATAAG
1 AAAAA-AATTTTATAAG
*
182635 ACAAAAATTT
1 AAAAAAATTT
182645 GGTCTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAAAAATTTTATAAG
Found at i:185025 original size:25 final size:25
Alignment explanation
Indices: 184974--185047 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
184964 GAGTAGGGGA
* *
184974 TTAGGGTTTGAAA-CCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
184998 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
185023 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
185048 GGGTTGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 13 0.28
25 34 0.72
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:185170 original size:3 final size:3
Alignment explanation
Indices: 185162--185199 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
185152 AATGTAAAAT
185162 TAA TAA TAA TAA TAA TTAA TAA TAA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
185200 AAAATAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:185198 original size:13 final size:15
Alignment explanation
Indices: 185156--185209 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
185146 AAATGTAATG
185156 TAAAATTAATAATAA
1 TAAAATTAATAATAA
185171 TAATAATTAATAATAA
1 TAA-AATTAATAATAA
185187 TAAAA-TAA-AATAA
1 TAAAATTAATAATAA
*
185200 -AAAATAAATA
1 TAAAATTAATA
185210 TAAAAGACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 4 0.11
13 7 0.20
14 4 0.11
15 5 0.14
16 15 0.43
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATTAATAATAA
Found at i:185198 original size:16 final size:16
Alignment explanation
Indices: 185156--185214 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 16
185146 AAATGTAATG
185156 TAAAATTAATAATAATAA
1 TAAAA-TAATAATAA-AA
185174 TAATTAATAATAATAAAA
1 TAA--AATAATAATAAAA
*
185192 TAAAATAAAAAATAAATA
1 TAAAAT-AATAATAAA-A
185210 TAAAA
1 TAAAA
185215 GACCCGGACA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 3 0.08
17 8 0.22
18 14 0.39
19 9 0.25
20 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAATAATAATAAAA
Found at i:185212 original size:13 final size:12
Alignment explanation
Indices: 185163--185214 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
185153 ATGTAAAATT
*
185163 AATAATAATAATA
1 AATAA-AATAAAA
*
185176 ATTAATAATAATAA
1 AATAA-AATAA-AA
185190 AATAAAATAAAA
1 AATAAAATAAAA
185202 AATAAATATAAAA
1 AATAAA-ATAAAA
185215 GACCCGGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.24
13 21 0.62
14 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:197588 original size:16 final size:17
Alignment explanation
Indices: 197563--197602 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
197553 AACGTCTTTT
*
197563 AAAAACAATTTT-TAAG
1 AAAAATAATTTTATAAG
197579 AAAAATAATTTTATAAG
1 AAAAATAATTTTATAAG
197596 ACAAAAT
1 A-AAAAT
197603 TTGGTCTACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 5 0.24
18 5 0.24
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAAATAATTTTATAAG
Found at i:200174 original size:25 final size:25
Alignment explanation
Indices: 200140--200214 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
200130 GAGTAGGGGA
* *
200140 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
200165 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
200190 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
200215 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:200340 original size:3 final size:3
Alignment explanation
Indices: 200332--200364 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
200322 TATGTAAAAT
200332 TAA TAA TAA TAA TTAA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
200365 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:200345 original size:13 final size:13
Alignment explanation
Indices: 200329--200364 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
200319 TAATATGTAA
200329 AATTAATAATAAT
1 AATTAATAATAAT
200342 AATTAATAATAAT
1 AATTAATAATAAT
200355 AA--AATAATAA
1 AATTAATAATAA
200365 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.35
13 15 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:200371 original size:16 final size:18
Alignment explanation
Indices: 200333--200378 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
200323 ATGTAAAATT
*
200333 AATAATAATAATTAATAAT
1 AATAA-AATAATTAATAAA
200352 AATAAAATAA-TAA-AAA
1 AATAAAATAATTAATAAA
200368 AATAAATATAA
1 AATAAA-ATAA
200379 AAGACCCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 5 0.20
19 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AATAAAATAATTAATAAA
Found at i:200380 original size:11 final size:11
Alignment explanation
Indices: 200333--200372 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
200323 ATGTAAAATT
200333 AATAATAATAA
1 AATAATAATAA
200344 TTAATAATAATAA
1 --AATAATAATAA
*
200357 AATAATAAAAA
1 AATAATAATAA
200368 AATAA
1 AATAA
200373 ATATAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:208984 original size:24 final size:24
Alignment explanation
Indices: 208957--209007 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
208947 AAAATATAAC
208957 TAAAAAATATTAGACACATATTTT
1 TAAAAAATATTAGACACATATTTT
208981 TAAAAAATATTAGACACATATTTT
1 TAAAAAATATTAGACACATATTTT
209005 TAA
1 TAA
209008 CGAAAATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAAAATATTAGACACATATTTT
Found at i:210500 original size:4 final size:4
Alignment explanation
Indices: 210491--210529 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
210481 ATGTTAGAGA
* *
210491 AAAT AAAT AAAT AAAT AAAT AAAT AGAT -ACT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
210530 CAAAAGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 1 0.03
4 29 0.97
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:210843 original size:18 final size:18
Alignment explanation
Indices: 210757--210858 Score: 55
Period size: 19 Copynumber: 5.4 Consensus size: 18
210747 TCAAAAAAGA
*
210757 AAAAAAAGTCAAAAAGTTT
1 AAAAAAAGT-AAAAAGGTT
*
210776 GAAAAAAAGTAAATA-GTT
1 -AAAAAAAGTAAAAAGGTT
* * *
210794 ATAAAAGAG-GAAAATGTT
1 A-AAAAAAGTAAAAAGGTT
* * *
210812 GAAAATATTGAAAAAGGTT
1 AAAAAAAGT-AAAAAGGTT
*
210831 AAAAAAAGTAAAAAAGTT
1 AAAAAAAGTAAAAAGGTT
210849 GAAAAGAAAG
1 -AAAA-AAAG
210859 GTTGAAAAAC
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
17 9 0.15
18 19 0.31
19 21 0.34
20 13 0.21
ACGTcount: A:0.62, C:0.01, G:0.18, T:0.20
Consensus pattern (18 bp):
AAAAAAAGTAAAAAGGTT
Found at i:210912 original size:20 final size:19
Alignment explanation
Indices: 210884--210945 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 19
210874 GAAAAAATGT
*
210884 TAATGATAATAAAATACATA
1 TAATAATAATAAAATA-ATA
210904 TAATAATAATAATAA-AGATA
1 TAATAATAATAA-AATA-ATA
* *
210924 AAAGAATAATGAAAATAATA
1 TAATAATAAT-AAAATAATA
210944 TA
1 TA
210946 GTAAAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (19 bp):
TAATAATAATAAAATAATA
Found at i:210932 original size:26 final size:25
Alignment explanation
Indices: 210903--210951 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
210893 TAAAATACAT
210903 ATAAT-AATAATAATAAAGATAAAAGA
1 ATAATGAA-AATAATAAAG-TAAAAGA
*
210929 ATAATGAAAATAATATAGTAAAA
1 ATAATGAAAATAATAAAGTAAAA
210952 AATTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 14 0.67
27 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (25 bp):
ATAATGAAAATAATAAAGTAAAAGA
Found at i:211069 original size:12 final size:12
Alignment explanation
Indices: 211051--211083 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
211041 TATTAGGTAA
211051 AAATAATAAT-C
1 AAATAATAATAC
211062 ATAATAATAATAC
1 A-AATAATAATAC
211075 AAATAATAA
1 AAATAATAA
211084 AAAAGGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.05
12 17 0.85
13 2 0.10
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATAATAATAC
Found at i:212899 original size:84 final size:84
Alignment explanation
Indices: 212811--213793 Score: 1046
Period size: 84 Copynumber: 11.8 Consensus size: 84
212801 GCTTGCCTCT
* * * *
212811 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
212876 CTACAAATGATGTACCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
212895 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
212959 GCTGTAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* * * * * * *
212980 AAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTTGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
213041 ATGCAAATGATGTGCGTTG
66 CTGCAAATGATGTGCCTTG
*
213060 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
213125 CTACAAATGATATGCCTTA
66 CTGCAAATGATGTGCCTTG
* * * * *
213144 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCATTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
213208 GCTGTAAATGATGTGCCCTCG
65 GCTGCAAATGATGTG-CCTTG
* ** * * * * * *
213229 AAATTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGCAGATAGCCCTTCTCAACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
213294 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * *
213313 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGG-TGACATATAACCCTTCTAGCCTTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *
213377 GTTGTAAATGATGTGCCCTTG
65 GCTGCAAATGATGTG-CCTTG
* * * * * * * * * *
213398 AAGCTGAGTGTAATCGAAATCG-AGG-GTTT--TTGGTAGATAGCTCTTCTCAACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
213459 CTGCAAATGATATGCCTTG
66 CTGCAAATGATGTGCCTTG
* * *
213478 AAGCTGAGCGAAGTCGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
213543 CTGCAAATGATGTACCTTA
66 CTGCAAATGATGTGCCTTG
* * * *
213562 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAAATAACCCTTCTAG-CATTGAGTTAT
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGTTAT
* *
213625 GCTGTAAATGATATGCCTTG
65 GCTGCAAATGATGTGCCTTG
* * *
213645 GAGCTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAGCCATTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
213706 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * * * *
213725 GAGCTGAGCGGAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
213790 CTGC
66 CTGC
213794 GAATAGTTTC
Statistics
Matches: 732, Mismatches: 143, Indels: 48
0.79 0.15 0.05
Matches are distributed among these distances:
80 115 0.16
81 74 0.10
82 10 0.01
83 67 0.09
84 340 0.46
85 126 0.17
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:213089 original size:249 final size:247
Alignment explanation
Indices: 212811--213721 Score: 1063
Period size: 249 Copynumber: 3.7 Consensus size: 247
212801 GCTTGCCTCT
* * * * * *
212811 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATG
* *
212876 CTACAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACC
65 CTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTG-CAGATAACC
* * * * *
212941 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGG
129 ATTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGG
* * * *
213006 TCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGATGCAAATGATGTGCGTTG
194 TCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* *
213060 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GACAGATAACCCTTCTAGACTTAAGTTATG
* *
213125 CTACAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACC
65 CTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTG-CAGATAACC
* * * * ** *
213190 ATTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAATTGAGTGTAATCAAACTCGAGGG
129 ATTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGG
*
213255 TCTTTGGTTGGCAGATAGCCCTTCTCAACTTAAGTTATGCTGCAAATGATGTGCCTTG
194 TC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* * * *
213313 GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGTGACATATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAGTTATG
* ** * * * * * *
213378 TTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAAA-TCGAGGGT-TTTTGGT--AGATAGC
65 CTACAAATGATATG-CCTTGGAGCTGAGCGTAGTC-AAACTCGAAGGTCTTTTGGTGCAGATAAC
* * *
213439 TC-TTCTCA-ACTTAAGCTATGCTGCAAATGATATG-CCTTGAAGCTGAGCG-AAGTCGAACTCG
128 -CATTCT-AGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA-TCGAACTCG
* * * *
213500 AAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCTTA
190 AGGGTCTTT-G---GCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
* *
213562 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAG-CATTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGAC-TTAAGTTATG
** * *
213626 CTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT-G-GCAGATAGCCA
65 CTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGCAGATAACCA
*
213688 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
130 TTCTAGACTTAAGCTATGCTGCAAATGATGTGCC
213722 TTGGAGCTGA
Statistics
Matches: 579, Mismatches: 60, Indels: 47
0.84 0.09 0.07
Matches are distributed among these distances:
245 2 0.00
246 5 0.01
247 65 0.11
248 49 0.08
249 278 0.48
250 31 0.05
251 3 0.01
253 115 0.20
254 29 0.05
255 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (247 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGC
TACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGCAGATAACCAT
TCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC
TTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
Found at i:213592 original size:418 final size:416
Alignment explanation
Indices: 212814--213792 Score: 1516
Period size: 418 Copynumber: 2.4 Consensus size: 416
212804 TGCCTCTGAG
* * *
212814 CTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTA
1 CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
*
212879 CAAATGATGTACCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
*
212944 CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
131 CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAATCGAGGGTCT
** * * * *
213009 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGATGCAAATGATGTGCGTTGGAGCTGAGCGTAGT
196 TTGGCAGATAGCCCTTCTCAACTTAAGCTATGATGCAAATGATATGCCTTGAAGCTGAGCGAAGT
* *
213074 CGAACTCGAAGGTCTTTGGTCGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATG
261 CGAACTCGAAGGTCTTTGGTCAGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATA
* *
213139 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCATTCTAGCCTTGAG
326 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAAATAACCATTCTAGCATTGAG
*
213204 TTATGCTGTAAATGATGTGCCCTCGAAA
390 TTATGCTGTAAATGATATG-CCTCGAAA
* * * * *
213232 TTGAGTGTAATCAAACTCGAGGGTCTTTGGTTGGCAGATAGCCCTTCTCAACTTAAGTTATGCTG
1 CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* * *
213297 CAAATGATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGTGACATATAACCCTT
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
* * *
213362 CTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAAATCGAGGGTTT
131 CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAATCGAGGGTCT
* * *
213427 TTGGTAGATAGCTCTTCTCAACTTAAGCTATGCTGCAAATGATATGCCTTGAAGCTGAGCGAAGT
196 TTGGCAGATAGCCCTTCTCAACTTAAGCTATGATGCAAATGATATGCCTTGAAGCTGAGCGAAGT
* * *
213492 CGAACTCGAAGGTCTTTGGTTAGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTA
261 CGAACTCGAAGGTCTTTGGTCAGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATA
*
213557 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCATTGAGT
326 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCATTCTAGCATTGAGT
* * *
213622 TATGCTGTAAATGATATGCCTTGGAG
391 TATGCTGTAAATGATATGCCTCGAAA
* * *
213648 CTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGATAGCCATTCTCGACTTAAGCTATGCTG
1 CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
* * *
213709 CAAATGATGTGCCTTGGAGCTGAGCGGAGTCAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTT
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
*
213774 ATAGCCTTGAGTTATGCTG
131 CTAGCCTTGAGTTATGCTG
213793 CGAATAGTTT
Statistics
Matches: 508, Mismatches: 53, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
412 108 0.21
414 1 0.00
416 25 0.05
417 46 0.09
418 328 0.65
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (416 bp):
CTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTG
CAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGACAGATAACCCTT
CTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAATCGAGGGTCT
TTGGCAGATAGCCCTTCTCAACTTAAGCTATGATGCAAATGATATGCCTTGAAGCTGAGCGAAGT
CGAACTCGAAGGTCTTTGGTCAGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATA
CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAAATAACCATTCTAGCATTGAGT
TATGCTGTAAATGATATGCCTCGAAA
Found at i:215075 original size:95 final size:95
Alignment explanation
Indices: 214886--215148 Score: 348
Period size: 95 Copynumber: 2.7 Consensus size: 95
214876 GGCTAGCTGA
* * * * * * *
214886 ATCCATAAAGCCGGGACATTTAACCAATTTCTCTAGAGGGACATCTTAATATCATTGTATAG-AT
1 ATCCATAAAGCCGGGACGTTTAACCAATTGCTTTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
214950 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* *
214984 ATCCCTAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGACGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
* * *
215049 TAATCATCTTTATCAGGTTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
215079 ATCCATAAAGCCGTGACGTTTAACCAATTGCTTTAGAGGTACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGACGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAT-T
215144 ATAAT
65 ATAAT
215149 TATAATTTGG
Statistics
Matches: 147, Mismatches: 16, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
94 4 0.03
95 94 0.64
96 8 0.05
97 2 0.01
98 39 0.27
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCCGGGACGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:216881 original size:21 final size:21
Alignment explanation
Indices: 216855--216899 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
216845 GATTTCTGGG
* *
216855 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
216876 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
216897 CAA
1 CAA
216900 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:217454 original size:24 final size:23
Alignment explanation
Indices: 217427--217473 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
217417 ATATGGCATG
* *
217427 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAA-TATATATATGAAA
217451 TGATATGAAATATATATATGAAA
1 TGATATGAAATATATATATGAAA
217474 ACAAGTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (23 bp):
TGATATGAAATATATATATGAAA
Found at i:217727 original size:31 final size:31
Alignment explanation
Indices: 217689--217829 Score: 203
Period size: 31 Copynumber: 4.5 Consensus size: 31
217679 GGGTCGAGGG
217689 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
*
217720 TTTACCTATGTTCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* * *
217751 TTTACCTATGTTCTTCGGAACATACGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
217782 TTTACCTATGTCCTTCGGGACATATGGATTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
217814 -TTACCTAGGTTCTTCG
1 TTTACCTATGTTCTTCG
217830 AAATCTATGG
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:220826 original size:21 final size:21
Alignment explanation
Indices: 220800--220844 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
220790 GATTTCTGGG
* *
220800 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
220821 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
220842 CAA
1 CAA
220845 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:221414 original size:23 final size:24
Alignment explanation
Indices: 221371--221417 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
221361 ATATGGCATG
*
221371 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
221395 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
221418 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:221671 original size:31 final size:31
Alignment explanation
Indices: 221633--221788 Score: 224
Period size: 31 Copynumber: 5.0 Consensus size: 31
221623 AGGGTCGAGG
*
221633 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
221664 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
221695 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
221726 GTTTACCTATGTCCTTCGGTACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
221757 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
221788 G
1 G
221789 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:224781 original size:65 final size:65
Alignment explanation
Indices: 224674--224823 Score: 246
Period size: 65 Copynumber: 2.3 Consensus size: 65
224664 TCCCCATCTA
* * * *
224674 GAGAATAAATTCACACGAAGACATAAGGTATATGAATCCCGAAGGTTACTTGCTAGGCTCATACG
1 GAGAATAAATTCACACGAAGACATAAGGTATATAAATACCGAAGGTTACTTACTAGGCCCATACG
*
224739 GAGAATAAATTCACACGAAGACATAAGGTATATAAATACCGAATGTTACTTACTAGGCCCATACG
1 GAGAATAAATTCACACGAAGACATAAGGTATATAAATACCGAAGGTTACTTACTAGGCCCATACG
*
224804 GAAAATAAATTCACACGAAG
1 GAGAATAAATTCACACGAAG
224824 GTGTCACTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 79 1.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (65 bp):
GAGAATAAATTCACACGAAGACATAAGGTATATAAATACCGAAGGTTACTTACTAGGCCCATACG
Found at i:225318 original size:12 final size:13
Alignment explanation
Indices: 225301--225329 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
225291 TTTAATTGCG
225301 AAAATTAAAA-TT
1 AAAATTAAAATTT
225313 AAAATTAAAATTT
1 AAAATTAAAATTT
225326 AAAA
1 AAAA
225330 GCATTCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:225456 original size:15 final size:15
Alignment explanation
Indices: 225418--225459 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
225408 TAAATAAATC
225418 AAAAGAAAAATTAAA
1 AAAAGAAAAATTAAA
* *
225433 GAAA-TAAAATTAAA
1 AAAAGAAAAATTAAA
225447 AAAAGAAAAATTA
1 AAAAGAAAAATTA
225460 TCATAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAGAAAAATTAAA
Found at i:225544 original size:26 final size:25
Alignment explanation
Indices: 225515--225569 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
225505 AAATCAAAGG
*
225515 ACAAAAGATAATTTTAAAAATAAAAA
1 ACAAAAGATAAATTTAAAAA-AAAAA
* *
225541 AC--AATATAAATTTAAAAAAATAA
1 ACAAAAGATAAATTTAAAAAAAAAA
225564 ACAAAA
1 ACAAAA
225570 TATTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
23 6 0.25
24 14 0.58
25 2 0.08
26 2 0.08
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (25 bp):
ACAAAAGATAAATTTAAAAAAAAAA
Found at i:225554 original size:24 final size:23
Alignment explanation
Indices: 225522--225567 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
225512 AGGACAAAAG
*
225522 ATAATTTTAAAAATAAAAAACAAT
1 ATAAATTTAAAAA-AAAAAACAAT
*
225546 ATAAATTTAAAAAAATAAACAA
1 ATAAATTTAAAAAAAAAAACAA
225568 AATATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAATTTAAAAAAAAAAACAAT
Found at i:225585 original size:26 final size:26
Alignment explanation
Indices: 225530--225612 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
225520 AGATAATTTT
*
225530 AAAAATAAAAAACAATATAAATTTAA
1 AAAAATAAAAAACAATATAAATTAAA
* *
225556 AAAAATAAACAA-AATATTAAATAAACA
1 AAAAATAAAAAACAATA-TAAATTAA-A
** *
225583 AAAAATATAAAATGAA-ATAAAATAAA
1 AAAAATA-AAAAACAATATAAATTAAA
225609 AAAA
1 AAAA
225613 TGTTTAGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
25 4 0.09
26 22 0.48
27 14 0.30
28 4 0.09
29 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (26 bp):
AAAAATAAAAAACAATATAAATTAAA
Found at i:225589 original size:18 final size:16
Alignment explanation
Indices: 225557--225610 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
225547 TAAATTTAAA
225557 AAAATAAACAAAATAT
1 AAAATAAACAAAATAT
*
225573 TAAATAAACAAAAAATAT
1 AAAATAAAC--AAAATAT
*
225591 AAAATGAAATAAAATA-
1 AAAAT-AAACAAAATAT
225607 AAAA
1 AAAA
225611 AATGTTTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 12 0.38
17 6 0.19
18 11 0.34
19 3 0.09
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATAAACAAAATAT
Found at i:225609 original size:23 final size:22
Alignment explanation
Indices: 225532--225610 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 22
225522 ATAATTTTAA
* *
225532 AAATAAAAAACAATATAAATTT
1 AAATAAAAAAAAATATAAAATT
* *
225554 AAA-AAAATAAACA-A-AATATT
1 AAATAAAA-AAAAATATAAAATT
*
225574 AAATAAACAAAAAATATAAAATG
1 AAATAAA-AAAAAATATAAAATT
225597 AAATAAAATAAAAA
1 AAATAAAA-AAAAA
225611 AATGTTTAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
20 7 0.16
21 12 0.27
22 9 0.20
23 16 0.36
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (22 bp):
AAATAAAAAAAAATATAAAATT
Found at i:225613 original size:43 final size:42
Alignment explanation
Indices: 225532--225613 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 42
225522 ATAATTTTAA
* * *
225532 AAATAAAAAACAATATAAATTTAAAAAAATAAACAAAATATT
1 AAATAAAAAAAAATATAAAATGAAAAAAATAAACAAAATATT
225574 AAATAAACAAAAAATATAAAATGAAATAAAATAAA-AAAAT
1 AAATAAA-AAAAAATATAAAATGAAA-AAAATAAACAAAAT
225614 GTTTAGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 7 0.20
43 20 0.57
44 8 0.23
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (42 bp):
AAATAAAAAAAAATATAAAATGAAAAAAATAAACAAAATATT
Found at i:225907 original size:9 final size:9
Alignment explanation
Indices: 225892--225943 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
225882 AATAAAAAAG
225892 AAATAATAA
1 AAATAATAA
* *
225901 TAATAATAG
1 AAATAATAA
**
225910 TTATAATAA
1 AAATAATAA
225919 AAATAAATAA
1 AAAT-AATAA
225929 AAATAATAA
1 AAATAATAA
*
225938 CAATAA
1 AAATAA
225944 AGAATAGTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
9 26 0.74
10 9 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (9 bp):
AAATAATAA
Found at i:233762 original size:13 final size:13
Alignment explanation
Indices: 233746--233773 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
233736 TTCTTTTCAC
233746 TTTCACTTTTACT
1 TTTCACTTTTACT
233759 TTTCACTTTTACT
1 TTTCACTTTTACT
233772 TT
1 TT
233774 CTTTCATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTCACTTTTACT
Found at i:241174 original size:21 final size:20
Alignment explanation
Indices: 241150--241297 Score: 91
Period size: 21 Copynumber: 7.0 Consensus size: 20
241140 TCGAGGGTTC
241150 TATGTGGTCCTTCGAGACATA
1 TATGTGGTCCTTCG-GACATA
* * *
241171 TATGTGATCATTTGGA-ATA
1 TATGTGGTCCTTCGGACATA
* *
241190 TTTATGTGGTTCTTCAGGATATA
1 --TATGTGGTCCTTC-GGACATA
* * *
241213 TATTTGGTCATTTGGAACATA
1 TATGTGGTCCTTCGG-ACATA
* *
241234 TATGTGGTCCTTAGGAACAATTC
1 TATGTGGTCCTTCGG-AC-A-TA
*
241257 TATGTGGTCATTCGGGACATA
1 TATGTGGTCCTTC-GGACATA
*
241278 TATGTGGTCCCTTGGGACAT
1 TATGTGGT-CCTTCGGACAT
241298 TTCTACGTGG
Statistics
Matches: 97, Mismatches: 21, Indels: 18
0.71 0.15 0.13
Matches are distributed among these distances:
19 3 0.03
20 4 0.04
21 63 0.65
22 8 0.08
23 17 0.18
24 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (20 bp):
TATGTGGTCCTTCGGACATA
Found at i:241214 original size:42 final size:42
Alignment explanation
Indices: 241150--241287 Score: 136
Period size: 42 Copynumber: 3.2 Consensus size: 42
241140 TCGAGGGTTC
* *
241150 TATGTGGTCCTTC-GAGACATATATGTGATCATTTGGAATATT
1 TATGTGGTCCTTCAG-GACATATATGTGATCATTTGGAACATA
* * * *
241192 TATGTGGTTCTTCAGGATATATATTTGGTCATTTGGAACATA
1 TATGTGGTCCTTCAGGACATATATGTGATCATTTGGAACATA
* * * *
241234 TATGTGGTCCTT-AGGAACAATTCTATGTGGTCATTCGGGACATA
1 TATGTGGTCCTTCAGG-AC-A-TATATGTGATCATTTGGAACATA
241278 TATGTGGTCC
1 TATGTGGTCC
241288 CTTGGGACAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.04
42 46 0.57
43 2 0.03
44 29 0.36
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (42 bp):
TATGTGGTCCTTCAGGACATATATGTGATCATTTGGAACATA
Found at i:241263 original size:23 final size:23
Alignment explanation
Indices: 241234--241322 Score: 94
Period size: 23 Copynumber: 4.0 Consensus size: 23
241224 TTGGAACATA
*
241234 TATGTGGTCCTTAGGAACAATTC
1 TATGTGGTCCTTAGGGACAATTC
* * *
241257 TATGTGGTCATTCGGGAC-A-TA
1 TATGTGGTCCTTAGGGACAATTC
*
241278 TATGTGGTCCCTT-GGGACATTTC
1 TATGTGGT-CCTTAGGGACAATTC
*
241301 TACGTGGTCCTTAGGGACAATT
1 TATGTGGTCCTTAGGGACAATT
241323 TTATATGGCA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
21 14 0.26
22 8 0.15
23 31 0.58
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (23 bp):
TATGTGGTCCTTAGGGACAATTC
Found at i:241277 original size:44 final size:44
Alignment explanation
Indices: 241217--241319 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
241207 GATATATATT
* * *
241217 TGGTCATTTGGAACATATATGTGGT-CCTTAGGAACAATTCTATG
1 TGGTCATTAGGGACATATATGTGGTCCCTT-GGAACAATTCTACG
* * *
241261 TGGTCATTCGGGACATATATGTGGTCCCTTGGGACATTTCTACG
1 TGGTCATTAGGGACATATATGTGGTCCCTTGGAACAATTCTACG
*
241305 TGGTCCTTAGGGACA
1 TGGTCATTAGGGACA
241320 ATTTTATATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 47 0.92
45 4 0.08
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (44 bp):
TGGTCATTAGGGACATATATGTGGTCCCTTGGAACAATTCTACG
Found at i:248946 original size:197 final size:198
Alignment explanation
Indices: 248603--249001 Score: 674
Period size: 197 Copynumber: 2.0 Consensus size: 198
248593 TCCCTTTAAC
*
248603 TCATTCGCAATATTCATTCTCTAAGTTAAAGAGACAAGAAGTTGAAATCACGTCAAGATGGCATC
1 TCATTCACAATATTCATTCTCTAAGTTAAAGAGACAAGAAGTTGAAATCACGTCAAGATGGCATC
*
248668 CAACGTCCTAAAGAAAATATATTGATCTCCTACAGGTACTCCAGAAGGTATATGTTCTTCACATT
66 CAACCTCCTAAAGAAAATATATTGATCTCCTACAGGTACTCCAGAAGGTATATGTTCTTCACATT
* *
248733 GCCTGGCCAGGGTAGGTAAATTACTACTCTTGGATGACCTATCTTCTCTTGCTTTACTTCGACAG
131 GCCTGGCCAGGGTAGGTAAATTACTACTCTTGGATGACCTATCTTCTCTCGCTGTACTTCGACAG
248798 CTA
196 CTA
* * * *
248801 TCATTCACAATATTCATTCTTTAAGTTGAAGAGACAAGAAGTTGAAATCGCGTCAAGATGGCGTC
1 TCATTCACAATATTCATTCTCTAAGTTAAAGAGACAAGAAGTTGAAATCACGTCAAGATGGCATC
* * *
248866 CAACCTCCTAAA-AAAATATCTTGATCTCCTACAGGTACTCCAGAAGGTGTATGTTCTTCACCTT
66 CAACCTCCTAAAGAAAATATATTGATCTCCTACAGGTACTCCAGAAGGTATATGTTCTTCACATT
* *
248930 GCCTGGCCAGGGTAGGTAAATTACTACTCTTGGCTGACCTATCTTCTCTCGCTGTACTTCGGCAG
131 GCCTGGCCAGGGTAGGTAAATTACTACTCTTGGATGACCTATCTTCTCTCGCTGTACTTCGACAG
248995 CTA
196 CTA
248998 TCAT
1 TCAT
249002 GTCTAGACAT
Statistics
Matches: 188, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
197 117 0.62
198 71 0.38
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (198 bp):
TCATTCACAATATTCATTCTCTAAGTTAAAGAGACAAGAAGTTGAAATCACGTCAAGATGGCATC
CAACCTCCTAAAGAAAATATATTGATCTCCTACAGGTACTCCAGAAGGTATATGTTCTTCACATT
GCCTGGCCAGGGTAGGTAAATTACTACTCTTGGATGACCTATCTTCTCTCGCTGTACTTCGACAG
CTA
Found at i:252858 original size:24 final size:27
Alignment explanation
Indices: 252817--252870 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
252807 ATATAAATTT
* *
252817 TATAAATTTAAATTTAATA-AA-AATA
1 TATAAATTGAAATATAATACAATAATA
252842 TATAAATTGAAA-ATAATACAATAATA
1 TATAAATTGAAATATAATACAATAATA
252868 TAT
1 TAT
252871 TTTCTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 13 0.52
26 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TATAAATTGAAATATAATACAATAATA
Found at i:253008 original size:13 final size:13
Alignment explanation
Indices: 252990--253023 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
252980 TTCTTATAAC
252990 CAAACATTGTAAT
1 CAAACATTGTAAT
*
253003 CAAACACTGTAAT
1 CAAACATTGTAAT
*
253016 CATACATT
1 CAAACATT
253024 AATATTAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (13 bp):
CAAACATTGTAAT
Found at i:260822 original size:16 final size:15
Alignment explanation
Indices: 260787--260836 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
260777 GGAAAGGTTT
**
260787 GATTTTTTTTAATAA
1 GATTTTTTTTTTTAA
* *
260802 TATTTTTATTTTTTAT
1 GATTTTT-TTTTTTAA
260818 GATTTTTTTTTTTAA
1 GATTTTTTTTTTTAA
260833 GATT
1 GATT
260837 ATGACACGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (15 bp):
GATTTTTTTTTTTAA
Found at i:261770 original size:6 final size:6
Alignment explanation
Indices: 261759--261783 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
261749 GATTTAAGTC
261759 CGGTGG CGGTGG CGGTGG CGGTGG C
1 CGGTGG CGGTGG CGGTGG CGGTGG C
261784 CACCTCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.64, T:0.16
Consensus pattern (6 bp):
CGGTGG
Found at i:282812 original size:21 final size:21
Alignment explanation
Indices: 282788--282848 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
282778 AACTTTGAAA
282788 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
282809 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
282823 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
282844 AAATG
1 AAATG
282849 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:282895 original size:36 final size:36
Alignment explanation
Indices: 282780--282888 Score: 184
Period size: 35 Copynumber: 3.0 Consensus size: 36
282770 TTGCAACCAA
282780 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
282817 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
282852 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
282889 GTTGAAATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
35 35 0.51
36 7 0.10
37 27 0.39
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:283927 original size:15 final size:15
Alignment explanation
Indices: 283907--283937 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
283897 TTGGAATGCT
283907 ACTGTTACAGCAGTC
1 ACTGTTACAGCAGTC
283922 ACTGTTACAGCAGTC
1 ACTGTTACAGCAGTC
283937 A
1 A
283938 GCATCTCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (15 bp):
ACTGTTACAGCAGTC
Found at i:287463 original size:21 final size:21
Alignment explanation
Indices: 287439--287499 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
287429 AACTTTGAAA
287439 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
287460 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
287474 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
287495 AAATG
1 AAATG
287500 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:287530 original size:37 final size:36
Alignment explanation
Indices: 287431--287539 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
287421 TGGCAACCAA
287431 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
287468 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
287503 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
287540 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 6 0.09
37 27 0.40
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Done.