Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000091.1 Hibiscus syriacus cultivar Beakdansim tig00000170_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: 340608
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:664 original size:12 final size:11
Alignment explanation
Indices: 649--687 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
639 ACACAAAATA
649 TAAATATAGTAT
1 TAAATATA-TAT
661 TAAATATATAT
1 TAAATATATAT
*
672 ATATATATATAT
1 -TAAATATATAT
684 TAAA
1 TAAA
688 ACTAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TAAATATATAT
Found at i:907 original size:2 final size:2
Alignment explanation
Indices: 900--924 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
890 AATTTTTATG
900 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
925 AATGAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23041 original size:36 final size:36
Alignment explanation
Indices: 22994--23076 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
22984 GGCACAAAAT
*
22994 TCAAATTATTGACGTGATGAGGAAATGGAATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
* *
23030 TCAAATTATTGAGGTGATAAGGAAATGGGATTTTGA
1 TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
23066 TCAAATTATTG
1 TCAAATTATTG
23077 GCTAACTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (36 bp):
TCAAATTATTGACGTGATAAGGAAATGGAATTTTGA
Found at i:28915 original size:20 final size:20
Alignment explanation
Indices: 28890--28947 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
28880 TTTGGTTCAC
*
28890 GGAATGTAAGATTATTAGTG
1 GGAATGTAAGATTATCAGTG
*
28910 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTATCAGTG
*
28930 GGAATATAAGATTATCAG
1 GGAATGTAAGATTATCAG
28948 AGAATAGGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:29820 original size:3 final size:3
Alignment explanation
Indices: 29812--29899 Score: 58
Period size: 3 Copynumber: 28.0 Consensus size: 3
29802 AAATTGAAAT
*
29812 TAA TAA TAAA TAAA TAA -ATA TAA TAA TAA TAA TAA TAA TTAA TAA TAT
1 TAA TAA T-AA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA
*
29860 TAAA TAT TAA -ATA TAA TAAA TAA TTAA -AA T-A TAA TAA TAA
1 T-AA TAA TAA TA-A TAA T-AA TAA -TAA TAA TAA TAA TAA TAA
29900 ATAAATATAT
Statistics
Matches: 70, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
2 6 0.09
3 44 0.63
4 20 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29854 original size:16 final size:16
Alignment explanation
Indices: 29812--29920 Score: 72
Period size: 16 Copynumber: 6.9 Consensus size: 16
29802 AAATTGAAAT
*
29812 TAATAATAAATAAATAA
1 TAATAATTAAT-AATAA
29829 -ATATAA-TAATAATAA
1 TA-ATAATTAATAATAA
*
29844 TAATAATTAATAATAT
1 TAATAATTAATAATAA
29860 TAA-ATATTAA-ATATAA
1 TAATA-ATTAATA-ATAA
29876 TAAATAATTAA-AAT-A
1 T-AATAATTAATAATAA
*
29891 TAATAATAAATAA-ATA
1 TAATAATTAATAATA-A
*
29907 TATTAATTAA-AATA
1 TAATAATTAATAATA
29921 GACATTTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
14 8 0.11
15 17 0.23
16 37 0.49
17 12 0.16
18 1 0.01
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAATTAATAATAA
Found at i:29856 original size:7 final size:7
Alignment explanation
Indices: 29809--29903 Score: 51
Period size: 7 Copynumber: 14.3 Consensus size: 7
29799 TTCAAATTGA
29809 AATTAAT
1 AATTAAT
*
29816 AATAAAT
1 AATTAAT
*
29823 AAAT-A-
1 AATTAAT
29828 AATATAAT
1 AAT-TAAT
29836 AA-TAAT
1 AATTAAT
29842 AA-TAAT
1 AATTAAT
29848 AATTAAT
1 AATTAAT
*
29855 AA-TATT
1 AATTAAT
* *
29861 AAATATT
1 AATTAAT
*
29868 AAAT-AT
1 AATTAAT
*
29874 AATAAAT
1 AATTAAT
29881 AATTAA-
1 AATTAAT
29887 AATATAAT
1 AAT-TAAT
*
29895 AATAAAT
1 AATTAAT
29902 AA
1 AA
29904 ATATATTAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 2 0.03
6 25 0.36
7 38 0.54
8 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AATTAAT
Found at i:29865 original size:29 final size:28
Alignment explanation
Indices: 29812--29912 Score: 92
Period size: 25 Copynumber: 3.8 Consensus size: 28
29802 AAATTGAAAT
29812 TAATAATAAATAAATAA-A-TATAATAATAA
1 TAATAAT-AATAAATAATATTA-AAT-ATAA
* *
29841 TAATAATAATTAATAATATTAAATATTA
1 TAATAATAATAAATAATATTAAATATAA
*
29869 -AAT-ATAATAAATAAT-TAAAATATAA
1 TAATAATAATAAATAATATTAAATATAA
29894 TAAT-A-AATAAAT-ATATTAA
1 TAATAATAATAAATAATATTAA
29913 TTAAAATAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
24 2 0.03
25 18 0.29
26 15 0.24
27 3 0.05
28 11 0.18
29 11 0.18
30 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAATAATAATAAATAATATTAAATATAA
Found at i:29894 original size:50 final size:49
Alignment explanation
Indices: 29813--29912 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 49
29803 AATTGAAATT
*
29813 AATAATAAATAAATAAATATAATAATAATAATAAT-AATTAATAATATTA
1 AATAATAAATAAATAAATATAATAATAATAATAATAAATAAAT-ATATTA
*
29862 AATATTAAATATAATAAATAATTAA-AAT-ATAATAATAAATAAATATATTA
1 AATAATAAATA-AATAAAT-A-TAATAATAATAATAATAAATAAATATATTA
29912 A
1 A
29913 TTAAAATAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
49 10 0.22
50 22 0.49
51 10 0.22
52 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (49 bp):
AATAATAAATAAATAAATATAATAATAATAATAATAAATAAATATATTA
Found at i:30030 original size:14 final size:13
Alignment explanation
Indices: 29984--30035 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
29974 AAATTATATG
*
29984 TATAATATATTAAA
1 TATAATATA-TAAT
*
29998 TATAATAAATAAT
1 TATAATATATAAT
30011 TAATAATATTATAAT
1 T-ATAATA-TATAAT
*
30026 TATAAAATAT
1 TATAATATAT
30036 TTTGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 7 0.22
14 19 0.59
15 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAATATATAAT
Found at i:32341 original size:16 final size:16
Alignment explanation
Indices: 32317--32412 Score: 77
Period size: 17 Copynumber: 5.8 Consensus size: 16
32307 ATTAATTTTA
*
32317 ATTACTATATTTATTT
1 ATTATTATATTTATTT
*
32333 ATTATTATATTTTAATT
1 ATTATTATA-TTTATTT
* *
32350 AGTTATTATATTTAATA
1 A-TTATTATATTTATTT
* *
32367 ATTAATATTATTATATCT
1 ATTATTA-TATT-TATTT
32385 ATTTATTATATTTATTT
1 A-TTATTATATTTATTT
*
32402 GTTATTA-ATTT
1 ATTATTATATTT
32413 CAATTTGAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
15 4 0.06
16 19 0.29
17 22 0.34
18 15 0.23
19 5 0.08
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:32370 original size:20 final size:18
Alignment explanation
Indices: 32322--32362 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
32312 TTTTAATTAC
*
32322 TATA-TTTATTTA-TTAT
1 TATATTTTAATTAGTTAT
32338 TATATTTTAATTAGTTAT
1 TATATTTTAATTAGTTAT
32356 TATATTT
1 TATATTT
32363 AATAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TATATTTTAATTAGTTAT
Found at i:32392 original size:22 final size:21
Alignment explanation
Indices: 32332--32396 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 21
32322 TATATTTATT
*
32332 TATTATTATAT-T-TTAATTA
1 TATTATTATATCTAATAATTA
* *
32351 -GTTATTATATTTAATAATTAA
1 TATTATTATATCTAATAATT-A
* *
32372 TATTATTATATCTATTTATTA
1 TATTATTATATCTAATAATTA
32393 TATT
1 TATT
32397 TATTTGTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 9 0.25
19 1 0.03
20 5 0.14
21 6 0.17
22 15 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATTATATCTAATAATTA
Found at i:66006 original size:11 final size:11
Alignment explanation
Indices: 65986--66015 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
65976 CTGTGTTTCG
65986 TTTG-TTTTGT
1 TTTGTTTTTGT
65996 TTTGTTTTTGT
1 TTTGTTTTTGT
66007 TTTGTTTTT
1 TTTGTTTTT
66016 TGTAGCAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (11 bp):
TTTGTTTTTGT
Found at i:74879 original size:65 final size:65
Alignment explanation
Indices: 74804--75194 Score: 549
Period size: 65 Copynumber: 6.1 Consensus size: 65
74794 GTCTTTGCAA
* *
74804 TATTCAATTATCACTCCACCTCATGCACCACAAAAGTACACGAGTCATATGAGTGATCTGTACTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
* * * *
74869 TATTCAATTATCACTCCACCTTATGCACTACAAAGGTACATGAGTCATATGAGTGATATGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
* * ** *
74934 TATACAATTATCACTCTACCTCATGCACCACAAAGGTACAACAGTCATATGAGTGATCAGTACTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
** * *
74999 TATTCAATTATCACTCCATATCATGCACCACAAAGGTACATAAGTCATATGAGTGAT-T-TATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
*
75062 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATTG
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
* * * * * *
75127 TATTCAATTATCAATCTACCTCATTCACCACAAATGTGCATGAGTC--ATGAGTGATTTGTACT-
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
75189 TATTCA
1 TATTCA
75195 CTCTACCTTT
Statistics
Matches: 291, Mismatches: 33, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
62 6 0.02
63 72 0.25
64 1 0.00
65 212 0.73
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (65 bp):
TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTACTG
Found at i:75137 original size:193 final size:195
Alignment explanation
Indices: 74804--75160 Score: 592
Period size: 193 Copynumber: 1.8 Consensus size: 195
74794 GTCTTTGCAA
* *
74804 TATTCAATTATCACTCCACCTCATGCACCACAAAAGTACACGAGTCATATGAGTGATCTGTACTG
1 TATTCAATTATCACTCCACATCATGCACCACAAAAGTACACAAGTCATATGAGTGATCTGTACTG
* *
74869 TATTCAATTATCACTCCACCTTATGCACTACAAAGGTACATGAGTCATATGAGTGATATGTATTG
66 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
*
74934 TATACAATTATCACTCTACCTCATGCACCACAAAGGTACAACAGTCATATGAGTGATCAGTACTG
131 TATACAATTATCAATCTACCTCATGCACCACAAAGGTACAACAGTCATATGAGTGATCAGTACTG
* * * *
74999 TATTCAATTATCACTCCATATCATGCACCACAAAGGTACATAAGTCATATGAGTGAT-T-TATTG
1 TATTCAATTATCACTCCACATCATGCACCACAAAAGTACACAAGTCATATGAGTGATCTGTACTG
*
75062 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATCTGTATTG
66 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
* *
75127 TATTCAATTATCAATCTACCTCATTCACCACAAA
131 TATACAATTATCAATCTACCTCATGCACCACAAA
75161 TGTGCATGAG
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
193 97 0.65
194 1 0.01
195 52 0.35
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (195 bp):
TATTCAATTATCACTCCACATCATGCACCACAAAAGTACACAAGTCATATGAGTGATCTGTACTG
TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATTG
TATACAATTATCAATCTACCTCATGCACCACAAAGGTACAACAGTCATATGAGTGATCAGTACTG
Found at i:82608 original size:28 final size:28
Alignment explanation
Indices: 82568--82632 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
82558 TCGATTACAT
*
82568 TAGTAATCTTATATAATACTAATGAGAA
1 TAGTAATCCTATATAATACTAATGAGAA
82596 TAGTAATCCTATATAATACTAATGAGAA
1 TAGTAATCCTATATAATACTAATGAGAA
82624 TAGTAATCC
1 TAGTAATCC
82633 CGACAATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (28 bp):
TAGTAATCCTATATAATACTAATGAGAA
Found at i:84179 original size:20 final size:20
Alignment explanation
Indices: 84114--84220 Score: 123
Period size: 20 Copynumber: 5.4 Consensus size: 20
84104 GTCAAAAGAA
84114 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
*
84136 AATCGCAACGCGATT-GAA-
1 AATCGCAACGCGATTCCAAG
*
84154 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* *
84174 AATCGCAATGCGATT--GAG
1 AATCGCAACGCGATTCCAAG
84192 AAATCGCAACGCGATTCCAAG
1 -AATCGCAACGCGATTCCAAG
84213 AATCGCAA
1 AATCGCAA
84221 AACGGCAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
18 16 0.22
19 17 0.24
20 24 0.33
21 2 0.03
22 13 0.18
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:84207 original size:39 final size:38
Alignment explanation
Indices: 84111--84220 Score: 175
Period size: 39 Copynumber: 2.8 Consensus size: 38
84101 ACGGTCAAAA
84111 GAAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 GAAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT
* *
84151 GAAAATCGCAACGCGATTCCAGGAATCGCAATGCGATT
1 GAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
84189 GAGAAATCGCAACGCGATTCCAAGAATCGCAA
1 GA-AAATCGCAACGCGATTCCAAGAATCGCAA
84221 AACGGCAAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
38 22 0.33
39 28 0.42
40 16 0.24
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (38 bp):
GAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATT
Found at i:84319 original size:6 final size:6
Alignment explanation
Indices: 84308--84346 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
84298 GACACGTATT
84308 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
84347 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:85093 original size:5 final size:5
Alignment explanation
Indices: 85083--85114 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
85073 CCGCCGCCGC
85083 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
85115 GGTCGTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:85120 original size:15 final size:15
Alignment explanation
Indices: 85086--85120 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
85076 CCGCCGCCGT
*
85086 CTCGTCTCGTCTCGT
1 CTCGTCTCGTCTCGG
85101 CTCGTCTCGTCTCGG
1 CTCGTCTCGTCTCGG
*
85116 GTCGT
1 CTCGT
85121 GGTCGTGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.37, G:0.26, T:0.37
Consensus pattern (15 bp):
CTCGTCTCGTCTCGG
Found at i:87217 original size:2 final size:2
Alignment explanation
Indices: 87210--87239 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
87200 TAGCTTAATA
87210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87240 TATGTTACCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101115 original size:9 final size:9
Alignment explanation
Indices: 101101--101172 Score: 56
Period size: 9 Copynumber: 7.6 Consensus size: 9
101091 TGGCTGCTGG
101101 AACCGGTTT
1 AACCGGTTT
101110 AACCGGTTTT
1 AACCGG-TTT
101120 CAACCGGTTCT
1 -AACCGGTT-T
*
101131 GACCGGTTT
1 AACCGGTTT
*
101140 GACCGGTTT
1 AACCGGTTT
*
101149 CAA-CGGTTCG
1 -AACCGGTT-T
101159 AACCGGTTT
1 AACCGGTTT
*
101168 GACCG
1 AACCG
101173 TCTGAATCGG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
9 27 0.52
10 18 0.35
11 7 0.13
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:101126 original size:20 final size:21
Alignment explanation
Indices: 101101--101139 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
101091 TGGCTGCTGG
101101 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
101121 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
101140 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:101164 original size:28 final size:31
Alignment explanation
Indices: 101100--101172 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 31
101090 GTGGCTGCTG
*
101100 GAACCGGTTTAACCGGTTTTCAACCGGTTCT
1 GAACCGGTTTGACCGGTTTTCAACCGGTTCT
101131 G-ACCGGTTTGACCGG-TTTCAA-CGGTTC-
1 GAACCGGTTTGACCGGTTTTCAACCGGTTCT
101158 GAACCGGTTTGACCG
1 GAACCGGTTTGACCG
101173 TCTGAATCGG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 1 0.03
28 19 0.47
29 6 0.15
30 13 0.32
31 1 0.03
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (31 bp):
GAACCGGTTTGACCGGTTTTCAACCGGTTCT
Found at i:101183 original size:28 final size:27
Alignment explanation
Indices: 101102--101192 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 27
101092 GGCTGCTGGA
* *
101102 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAA-CGGTTC-G
*
101132 ACCGGTTTGACCGGTTTCAACGGTTCG
1 ACCGGTTTGACCGGTCTCAACGGTTCG
* *
101159 AACCGGTTTGACC-GTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTCTCAA-CGGTTCG
101187 ACCGGT
1 ACCGGT
101193 CCGACCCGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.22
28 24 0.44
29 6 0.11
30 13 0.24
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (27 bp):
ACCGGTTTGACCGGTCTCAACGGTTCG
Found at i:101203 original size:5 final size:5
Alignment explanation
Indices: 101193--101252 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
101183 TTTGACCGGT
* *
101193 CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC
1 CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC CCGAC
101242 CCGAC CCGAC C
1 CCGAC CCGAC C
101253 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
5 39 0.83
7 8 0.17
ACGTcount: A:0.18, C:0.53, G:0.22, T:0.07
Consensus pattern (5 bp):
CCGAC
Found at i:101219 original size:22 final size:22
Alignment explanation
Indices: 101193--101259 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
101183 TTTGACCGGT
101193 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
101215 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
101237 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
101259 C
1 C
101260 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:101261 original size:7 final size:7
Alignment explanation
Indices: 101249--101279 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
101239 GACCCGACCC
101249 GACCGTT
1 GACCGTT
101256 GACCGTT
1 GACCGTT
101263 GACCGTT
1 GACCGTT
101270 GACCGTT
1 GACCGTT
101277 GAC
1 GAC
101280 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:108415 original size:10 final size:9
Alignment explanation
Indices: 108380--108472 Score: 78
Period size: 10 Copynumber: 9.7 Consensus size: 9
108370 GCTGCTGGAA
*
108380 ACCGGTTTA
1 ACCGGTTTG
*
108389 ACCGGTTTTCA
1 ACCGG-TTT-G
108400 ACCGGTTCTG
1 ACCGGTT-TG
108410 ACCGGTTTG
1 ACCGGTTTG
*
108419 ACCGGTTTCA
1 ACCGGTTT-G
*
108429 ACCGGTTCG
1 ACCGGTTTG
108438 AACCGGTTTG
1 -ACCGGTTTG
*
108448 ACCGGTCTG
1 ACCGGTTTG
*
108457 AATCGGTTTG
1 -ACCGGTTTG
108467 ACCGGT
1 ACCGGT
108473 CCGACCCGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
9 28 0.41
10 34 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:108424 original size:19 final size:20
Alignment explanation
Indices: 108380--108472 Score: 95
Period size: 19 Copynumber: 4.8 Consensus size: 20
108370 GCTGCTGGAA
* * *
108380 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
108400 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
108419 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
108439 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
*
108458 ATCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
108473 CCGACCCGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:108442 original size:29 final size:30
Alignment explanation
Indices: 108379--108453 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
108369 GGCTGCTGGA
*
108379 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
108410 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
108438 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
108454 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:108463 original size:29 final size:28
Alignment explanation
Indices: 108380--108472 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
108370 GCTGCTGGAA
* *
108380 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
108410 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* * *
108438 AACCGGTTTGACCGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTCTCAACCGGTTCG
108467 ACCGGT
1 ACCGGT
108473 CCGACCCGAC
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 7 0.12
29 37 0.65
30 13 0.23
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:108483 original size:5 final size:5
Alignment explanation
Indices: 108473--108532 Score: 66
Period size: 5 Copynumber: 11.2 Consensus size: 5
108463 TTTGACCGGT
* *
108473 CCGAC CCGAC CCGAC CGTTGAC CCGAC CCGAC CCGAC CGTTGAC CCGAC
1 CCGAC CCGAC CCGAC C--CGAC CCGAC CCGAC CCGAC C--CGAC CCGAC
108522 CCGAC CCGAC C
1 CCGAC CCGAC C
108533 GTTGACCGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
5 39 0.83
7 8 0.17
ACGTcount: A:0.18, C:0.53, G:0.22, T:0.07
Consensus pattern (5 bp):
CCGAC
Found at i:108499 original size:22 final size:22
Alignment explanation
Indices: 108473--108539 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
108463 TTTGACCGGT
108473 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
108495 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
108517 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
108539 C
1 C
108540 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:108541 original size:7 final size:7
Alignment explanation
Indices: 108529--108559 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
108519 GACCCGACCC
108529 GACCGTT
1 GACCGTT
108536 GACCGTT
1 GACCGTT
108543 GACCGTT
1 GACCGTT
108550 GACCGTT
1 GACCGTT
108557 GAC
1 GAC
108560 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:121322 original size:12 final size:12
Alignment explanation
Indices: 121307--121344 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
121297 GTTATTTAAA
121307 CGGGTATTGGGC
1 CGGGTATTGGGC
*
121319 CGGGTATTGGGT
1 CGGGTATTGGGC
121331 CGGGTATTGGGC
1 CGGGTATTGGGC
121343 CG
1 CG
121345 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:121334 original size:24 final size:24
Alignment explanation
Indices: 121307--121361 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
121297 GTTATTTAAA
* * *
121307 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
121331 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
121355 CGGGTAT
1 CGGGTAT
121362 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:121447 original size:32 final size:32
Alignment explanation
Indices: 121362--121463 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 32
121352 GGTCGGGTAT
* *
121362 ATATATATATATATATTTAAATTAAATATATAA
1 ATAT-TATATATATATTTAAATTAAATTTATTA
* *
121395 ATA-TATATTTTTTATTTAAATTAAATTTATTA
1 ATATTATA-TATATATTTAAATTAAATTTATTA
*
121427 ATATTATATATATATATAAA-TAATTATTT-TTA
1 ATATTATATATATATTTAAATTAA--ATTTATTA
121459 ATATT
1 ATATT
121464 TATCGGGTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
31 7 0.12
32 40 0.69
33 11 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
ATATTATATATATATTTAAATTAAATTTATTA
Found at i:123061 original size:6 final size:6
Alignment explanation
Indices: 123050--123087 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
123040 AGCGGCTCAT
* *
123050 TCCGCC TCCGCC TCCGCC TCCGCC TCTGCC TCTGCC TC
1 TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC TCCGCC TC
123088 ATTGACCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.61, G:0.16, T:0.24
Consensus pattern (6 bp):
TCCGCC
Found at i:141352 original size:21 final size:21
Alignment explanation
Indices: 141326--141379 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
141316 ACGGTTGGTT
*
141326 TGTTTATTCCATCATTAAATA
1 TGTTTATTCCATCATTAAAAA
141347 TGTTTATTCCATCATTAAAAA
1 TGTTTATTCCATCATTAAAAA
141368 TGTTTATTCCAT
1 TGTTTATTCCAT
141380 TGGCGGCGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (21 bp):
TGTTTATTCCATCATTAAAAA
Found at i:154994 original size:2 final size:2
Alignment explanation
Indices: 154987--155012 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
154977 GAATCCAAAC
154987 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
155013 TATCTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:156321 original size:22 final size:22
Alignment explanation
Indices: 156296--156343 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
156286 CAAAATTTAA
*
156296 CGAAATCGAAATCAACCCAAAC
1 CGAAACCGAAATCAACCCAAAC
* * *
156318 CGAAACCGAAATTAACTCGAAC
1 CGAAACCGAAATCAACCCAAAC
156340 CGAA
1 CGAA
156344 TGAAACCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.29, G:0.12, T:0.10
Consensus pattern (22 bp):
CGAAACCGAAATCAACCCAAAC
Found at i:156366 original size:33 final size:32
Alignment explanation
Indices: 156314--156376 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
156304 AAATCAACCC
* *
156314 AAACCGAAACCGAAATTAACTCGAACCGAATG
1 AAACCCAAACCGAAATTAACCCGAACCGAATG
* *
156346 AAACCCAAACCGAATTTTAACCCGATCCGAA
1 AAACCCAAACCGAA-ATTAACCCGAACCGAA
156377 AGTAACCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.44, C:0.29, G:0.13, T:0.14
Consensus pattern (32 bp):
AAACCCAAACCGAAATTAACCCGAACCGAATG
Found at i:156384 original size:33 final size:32
Alignment explanation
Indices: 156314--156384 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
156304 AAATCAACCC
* * *
156314 AAACCGAAACCGAAATTAACTCGAACCGAATG
1 AAACCCAAACCGAAATTAACCCGAACCGAAAG
* *
156346 AAACCCAAACCGAATTTTAACCCGATCCGAAAG
1 AAACCCAAACCGAA-ATTAACCCGAACCGAAAG
*
156379 TAACCC
1 AAACCC
156385 GAATAGAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.44, C:0.30, G:0.13, T:0.14
Consensus pattern (32 bp):
AAACCCAAACCGAAATTAACCCGAACCGAAAG
Found at i:156496 original size:18 final size:18
Alignment explanation
Indices: 156473--156527 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
156463 TTAATAATAA
156473 ATTAATTTAAATAAAATT
1 ATTAATTTAAATAAAATT
**
156491 GA-TAATTTATTTAAAATT
1 -ATTAATTTAAATAAAATT
156509 ATTATATTTATAATAAAAT
1 ATTA-ATTTA-AATAAAAT
156528 AATAGAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 6 0.21
20 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTAATTTAAATAAAATT
Found at i:157189 original size:32 final size:31
Alignment explanation
Indices: 157110--157199 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
157100 GGTTGACATA
* * * *
157110 AACCGAAAATCAATCGATCTGATATTGATCC
1 AACCAAAAATCAATCGATCCGATATTAAACC
**
157141 AACCTGAAATCTAATCGATCCGATATTAAACC
1 AACCAAAAATC-AATCGATCCGATATTAAACC
* *
157173 GACCCAAAAATCAATCGATCCGGTATT
1 -AACCAAAAATCAATCGATCCGATATT
157200 GACCCACCCG
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 9 0.19
32 31 0.65
33 8 0.17
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (31 bp):
AACCAAAAATCAATCGATCCGATATTAAACC
Found at i:158394 original size:14 final size:14
Alignment explanation
Indices: 158360--158386 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
158350 TTCCTAATTC
158360 CTAAACCTTAAACA
1 CTAAACCTTAAACA
158374 CTAAACCTTAAAC
1 CTAAACCTTAAAC
158387 TGTAAACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
CTAAACCTTAAACA
Found at i:158427 original size:21 final size:21
Alignment explanation
Indices: 158389--158428 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
158379 CCTTAAACTG
158389 TAAACCCTAAGTCATAAATAC
1 TAAACCCTAAGTCATAAATAC
158410 TAAACCCTAAGCTC-TAAAT
1 TAAACCCTAAG-TCATAAAT
158429 CATAATCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAGTCATAAATAC
Found at i:160005 original size:17 final size:16
Alignment explanation
Indices: 159984--160014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
159974 TCTTGATTTT
159984 TTTTTTGAATTCGAGC
1 TTTTTTGAATTCGAGC
*
160000 TTTTTTGAGTTCGAG
1 TTTTTTGAATTCGAG
160015 TTGAGTTTCA
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:0.16, C:0.10, G:0.23, T:0.52
Consensus pattern (16 bp):
TTTTTTGAATTCGAGC
Found at i:161560 original size:15 final size:15
Alignment explanation
Indices: 161542--161580 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
161532 GATTAAATTG
161542 CTTTCGATTCGATTA
1 CTTTCGATTCGATTA
*
161557 CTTTCGATTCGGTTA
1 CTTTCGATTCGATTA
*
161572 ATTTCGATT
1 CTTTCGATT
161581 AAACTATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (15 bp):
CTTTCGATTCGATTA
Found at i:165413 original size:2 final size:2
Alignment explanation
Indices: 165401--165457 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
165391 TTTCACAGCT
*
165401 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
165443 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
165458 TGAATGATGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:170618 original size:22 final size:22
Alignment explanation
Indices: 170593--170636 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
170583 TTAAACCAAA
170593 TAAAAT-TTATTGTTCTAAAAAT
1 TAAAATATT-TTGTTCTAAAAAT
170615 TAAAATATTTTGTTCTAAAAAT
1 TAAAATATTTTGTTCTAAAAAT
170637 CATGTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TAAAATATTTTGTTCTAAAAAT
Found at i:172891 original size:18 final size:19
Alignment explanation
Indices: 172856--172892 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
172846 CACGGAATGT
172856 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
172876 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
172893 GAATTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:173081 original size:36 final size:38
Alignment explanation
Indices: 173032--173108 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 38
173022 ATAATATTAC
173032 AAATTGCAAAATATTTATAT-ATTTTCTTTAAAAAATT
1 AAATTGCAAAATATTTATATAATTTTCTTTAAAAAATT
* * *
173069 AAATT-CATAATATTTATATAATTTTTTTTACAAAATT
1 AAATTGCAAAATATTTATATAATTTTCTTTAAAAAATT
173106 AAA
1 AAA
173109 AATATAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 13 0.36
37 23 0.64
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (38 bp):
AAATTGCAAAATATTTATATAATTTTCTTTAAAAAATT
Found at i:193047 original size:2 final size:2
Alignment explanation
Indices: 193040--193066 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193030 CTGCTGAATT
193040 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
193067 TTTTCTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:194045 original size:16 final size:17
Alignment explanation
Indices: 194024--194061 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
194014 TAAATTAAAA
194024 ATTTTAATTTTA-ACTT
1 ATTTTAATTTTACACTT
* *
194040 ATTTTAGTTTTACTCTT
1 ATTTTAATTTTACACTT
194057 ATTTT
1 ATTTT
194062 TTTATGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTTTAATTTTACACTT
Found at i:209000 original size:2 final size:2
Alignment explanation
Indices: 208993--209024 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
208983 AAAATAAAAT
208993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
209025 ATTTAGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:210382 original size:63 final size:64
Alignment explanation
Indices: 210309--210470 Score: 150
Period size: 63 Copynumber: 2.5 Consensus size: 64
210299 ATCCCTTGAC
* * * *
210309 GGGTTCATCGATGCACTA-TCTATGCATCGGTGCA-TAAATCCCATTCGATGTTTGTA-TTTAAG
1 GGGTGCATCGATGCACTACT-TATGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAA
210371 G
64 G
* * * ** *
210372 GGGTGCATCGATGCAGTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTACTTATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
* * * * *
210436 GAGTGCATCGATGCACTTCATGTGCATCAATACAC
1 GGGTGCATCGATGCACTACTTATGCATCGATACAC
210471 CTTGAACCAT
Statistics
Matches: 81, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
63 43 0.53
64 38 0.47
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:210461 original size:64 final size:63
Alignment explanation
Indices: 210350--210470 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
210340 GCATAAATCC
* * * * *
210350 CATTCGATGTTTGTATTTAAGGGGGTGCATCGATGCAGTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTAAAGGAGTGCATCGATGCACTACATGTGCATCAATACACTGATGG
* *
210413 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATGCACTTCATGTGCATCAATACAC
1 CATTCGATGTTTGTA-TTTAAAGGAGTGCATCGATGCACTACATGTGCATCAATACAC
210471 CTTGAACCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 14 0.28
64 36 0.72
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (63 bp):
CATTCGATGTTTGTATTTAAAGGAGTGCATCGATGCACTACATGTGCATCAATACACTGATGG
Found at i:229048 original size:2 final size:2
Alignment explanation
Indices: 229041--229067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
229031 ATAAATATGG
229041 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 A
229068 GTCAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:229483 original size:11 final size:11
Alignment explanation
Indices: 229467--229491 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
229457 GATTTTATTC
229467 ACATAATGTAA
1 ACATAATGTAA
229478 ACATAATGTAA
1 ACATAATGTAA
229489 ACA
1 ACA
229492 AGTGGACCAA
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
ACATAATGTAA
Found at i:243324 original size:77 final size:78
Alignment explanation
Indices: 243228--243397 Score: 211
Period size: 78 Copynumber: 2.2 Consensus size: 78
243218 GGATGCGTAT
* * *
243228 AAAAATATCATGGTTCACT-AGAAA-ATAGGTTGCGATATGGAATATTAATA-TTTTTATTAATA
1 AAAAATGTCATGGTTCACTAAGAAATATA--TTGCGATATGAAATACTAATATTTTTTATTAATA
* *
243290 AAATGGGTTGCGCCC
64 AAATGGGTTGCACAC
* * *
243305 AAAAATGTCATGGTTCACTAAGAAATATATTGCGATCTGAAATGCTAATATTTTTTGTTAATAAA
1 AAAAATGTCATGGTTCACTAAGAAATATATTGCGATATGAAATACTAATATTTTTTATTAATAAA
243370 ATGGGTTGCACAC
66 ATGGGTTGCACAC
* *
243383 AAGAATGTTATGGTT
1 AAAAATGTCATGGTT
243398 AATTTTTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
77 35 0.44
78 42 0.52
79 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (78 bp):
AAAAATGTCATGGTTCACTAAGAAATATATTGCGATATGAAATACTAATATTTTTTATTAATAAA
ATGGGTTGCACAC
Found at i:245037 original size:39 final size:36
Alignment explanation
Indices: 244982--245074 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 36
244972 GAGATGAGTT
* *
244982 TAATGTTAAGGATAACAAATTATAACAGTTGACCTCATA
1 TAATGTTAAGGTTAACAAATTATAACAGTCGA--TC-TA
*
245021 TAATGTTAAGGTTAACAAATTATAATAGTCGATCTA
1 TAATGTTAAGGTTAACAAATTATAACAGTCGATCTA
*
245057 GAATGTTAAAGGTTAACA
1 TAATGTT-AAGGTTAACA
245075 TTCTTCTGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 8 0.16
37 12 0.24
39 29 0.59
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (36 bp):
TAATGTTAAGGTTAACAAATTATAACAGTCGATCTA
Found at i:248330 original size:16 final size:17
Alignment explanation
Indices: 248309--248343 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
248299 TTACTATTCA
248309 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
248325 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
248342 CG
1 CG
248344 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:249111 original size:15 final size:16
Alignment explanation
Indices: 249093--249125 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
249083 GTGGCAGATC
249093 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
249108 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
249124 AA
1 AA
249126 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:265311 original size:225 final size:226
Alignment explanation
Indices: 265011--265682 Score: 1010
Period size: 225 Copynumber: 3.0 Consensus size: 226
265001 ATAGAGTCAT
* * *
265011 GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
265075 ATTACGAACTTTCTCTGGCAATGATGATCCATTGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGCAATGATGATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
*
265140 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCT-TCTG
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTCTCTG
* * *
265204 GCAATGCTGATCCATCAAGTGATGGATTTGAA
196 GCAATGCTAATCCATCAAGTGAT-GAATTAAA
* * *
265236 -CAAAAGGTTGAACAAGTTCTTATTATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
265300 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAGG
66 ATTATGAACTTTCTCTGGCAATGATGATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
* * **
265365 TTCTTCTCATTATGAACTTCTTATTCCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTCTCTG
**
265430 GCAATGCTAATCCATCGGGTGATGAATTAAA
196 GCAATGCTAATCCATCAAGTGATGAATTAAA
265461 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * **
265526 ATTATGAACGCT-TCTGGAAATGTTGATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGCAATGATGATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
** *
265590 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
131 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTCTCTG
* **
265655 GCAATGGTAATCCATTGAGTGATGAATT
196 GCAATGCTAATCCATCAAGTGATGAATT
265683 CAAATCTTTG
Statistics
Matches: 406, Mismatches: 38, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
224 38 0.09
225 273 0.67
226 95 0.23
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (226 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGCAATGATGATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTCTCTG
GCAATGCTAATCCATCAAGTGATGAATTAAA
Found at i:265377 original size:113 final size:113
Alignment explanation
Indices: 265011--265682 Score: 1019
Period size: 113 Copynumber: 6.0 Consensus size: 113
265001 ATAGAGTCAT
* * *
265011 GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
265075 ATTACGAACTTTCTCTGGCAATGATGATCCATTGGGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATTAAA
*
265123 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * *
265188 ATTATGAACGCT-TCTGGCAATGCTGATCCATCAAGTGATGGATTTGAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGAT-GAATTAAA
* * *
265236 -CAAAAGGTTGAACAAGTTCTTATTATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
265300 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATTAAA
* * *
265348 GCAAAAGGTTGAACAGGTTCTTCTCATTATGAACTTCTTATTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
265413 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATTAAA
265461 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * *
265526 ATTATGAACGCT-TCTGGAAATGTTGATCCATCAAGTGATGAATTAAA
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATTAAA
265573 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
265638 ATTATGAACTTTCTCTAGCAATGGTAATCCATTGAGTGATGAATT
66 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATT
265683 CAAATCTTTG
Statistics
Matches: 509, Mismatches: 46, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
112 247 0.49
113 262 0.51
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGCAATGCTAATCCATCGAGTGATGAATTAAA
Found at i:265456 original size:338 final size:337
Alignment explanation
Indices: 265011--265682 Score: 1121
Period size: 338 Copynumber: 2.0 Consensus size: 337
265001 ATAGAGTCAT
* *
265011 GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTATTCCTATTCAGATAAGTTCTTCTCA
* *
265076 TTACGAACTTTCTCTGGCAATGATGATCCATTGGGTGATGAATTAAAGCAAAAGGTTGAACAAGT
66 TTACGAACTTTCTCTGGCAATGATAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAGT
* *
265141 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGC
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGA
* * *
265206 AATGCTGATCCATCAAGTGATGGATTTGAA-CAAAAGGTTGAACAAGTTCTTATTATTATGAACT
196 AATGCTGATCCATCAAGTGAT-GAATTAAAGCAAAAGGTTGAACAAGTTCTTATCATTATGAACT
* *
265270 TCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCGG
260 TCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGCAATGCTAATCCATCGA
265335 GTGATGAATTAAA
325 GTGATGAATTAAA
* * * *
265348 GCAAAAGGTTGAACAGGTTCTTCTCATTATGAACTTCTTATTCCTTATTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTATTCC-TATTCAGATAAGTTCTTCTC
* *
265413 ATTATGAACTTTCTCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
65 ATTACGAACTTTCTCTGGCAATGATAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAG
265478 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGG
130 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGG
* *
265543 AAATGTTGATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
195 AAATGCTGATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTATCATTATGAACT
* * *
265608 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGCAATGGTAATCCATTGA
260 TCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGCAATGCTAATCCATCGA
265673 GTGATGAATT
325 GTGATGAATT
265683 CAAATCTTTG
Statistics
Matches: 311, Mismatches: 22, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
337 46 0.15
338 265 0.85
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (337 bp):
GCAAAAGGTTGAACAAGCTCTGCTCATTATGAACTTCTTATTCCTATTCAGATAAGTTCTTCTCA
TTACGAACTTTCTCTGGCAATGATAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACGCTTCTGGA
AATGCTGATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAACAAGTTCTTATCATTATGAACTT
CCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGCAATGCTAATCCATCGAG
TGATGAATTAAA
Found at i:266828 original size:18 final size:18
Alignment explanation
Indices: 266805--266845 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
266795 AAAATAAAAG
* *
266805 AATAAATTGAATTTCAAA
1 AATAAATTAAATCTCAAA
266823 AATAAATTAAATCTCAAA
1 AATAAATTAAATCTCAAA
266841 AATAA
1 AATAA
266846 TAAATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAATTAAATCTCAAA
Found at i:267244 original size:22 final size:20
Alignment explanation
Indices: 267219--267268 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
267209 CTTTTTTTTA
* *
267219 TTTTCTTCTTTTTTTCTTTTCT
1 TTTTCTTCTTTATTTC-ATT-T
*
267241 TTTTTTTCTTTATTTCATTT
1 TTTTCTTCTTTATTTCATTT
267261 TTTTCTTC
1 TTTTCTTC
267269 AAGCATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTCTTTATTTCATTT
Found at i:267244 original size:30 final size:31
Alignment explanation
Indices: 267208--267267 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
267198 ATCTTGACCC
267208 TCTTTTTTTTATTT-TCTTC-TTTTTTTCTTT
1 TCTTTTTTTTATTTAT-TTCATTTTTTTCTTT
*
267238 TCTTTTTTTTCTTTATTTCATTTTTTTCTT
1 TCTTTTTTTTATTTATTTCATTTTTTTCTT
267268 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (31 bp):
TCTTTTTTTTATTTATTTCATTTTTTTCTTT
Found at i:267245 original size:14 final size:14
Alignment explanation
Indices: 267208--267251 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
267198 ATCTTGACCC
*
267208 TCTTTTTTTTATTT
1 TCTTTTTTTTCTTT
267222 TCTTCTTTTTTTCTTT
1 TC-T-TTTTTTTCTTT
267238 TCTTTTTTTTCTTT
1 TCTTTTTTTTCTTT
267252 ATTTCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 13 0.48
15 2 0.07
16 12 0.44
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (14 bp):
TCTTTTTTTTCTTT
Found at i:267256 original size:17 final size:16
Alignment explanation
Indices: 267210--267264 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
267200 CTTGACCCTC
267210 TTTTTTTTATTTTCTTCT
1 TTTTTTTTA-TTTCTT-T
*
267228 TTTTTTCT-TTTCTTT
1 TTTTTTTTATTTCTTT
267243 TTTTTCTTTATTTCATTT
1 TTTTT-TTTATTTC-TTT
267261 TTTT
1 TTTT
267265 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 8 0.25
17 4 0.12
18 14 0.44
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTATTTCTTT
Found at i:267265 original size:9 final size:8
Alignment explanation
Indices: 267211--267267 Score: 55
Period size: 8 Copynumber: 7.2 Consensus size: 8
267201 TTGACCCTCT
*
267211 TTTTTTTA
1 TTTTTTTC
*
267219 TTTTCTTC
1 TTTTTTTC
267227 TTTTTTTC
1 TTTTTTTC
*
267235 -TTTTCT-
1 TTTTTTTC
267241 TTTTTTTC
1 TTTTTTTC
*
267249 TTTATTTC
1 TTTTTTTC
267257 ATTTTTTTC
1 -TTTTTTTC
267266 TT
1 TT
267268 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
7 10 0.26
8 22 0.56
9 7 0.18
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:270791 original size:9 final size:9
Alignment explanation
Indices: 270776--270807 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
270766 GAAAAATAAT
270776 GAATGTAAA
1 GAATGTAAA
*
270785 AAATGTAAA
1 GAATGTAAA
270794 GAATGTAAA
1 GAATGTAAA
270803 GAATG
1 GAATG
270808 ATTGCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
GAATGTAAA
Found at i:277945 original size:22 final size:22
Alignment explanation
Indices: 277920--277961 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
277910 ATTATGAAAA
277920 TAATAAATATATAT-AATTTTTT
1 TAATAAA-ATATATGAATTTTTT
277942 TAATAAAATATATGAATTTT
1 TAATAAAATATATGAATTTT
277962 AAATTTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TAATAAAATATATGAATTTTTT
Found at i:278448 original size:23 final size:23
Alignment explanation
Indices: 278403--278449 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
278393 ATTTTATGAA
*
278403 AATATATTAATTTAAATATAAAT
1 AATATATTAATTTAAATAGAAAT
* **
278426 AATATATTTATTTATTTAGAAAT
1 AATATATTAATTTAAATAGAAAT
278449 A
1 A
278450 TCAGAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATATTAATTTAAATAGAAAT
Found at i:280097 original size:3 final size:3
Alignment explanation
Indices: 280091--280151 Score: 104
Period size: 3 Copynumber: 19.7 Consensus size: 3
280081 ATTTATTATT
280091 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
280139 TATA TAAA TAA TA
1 TA-A T-AA TAA TA
280152 TTCAAAATGA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 51 0.91
4 4 0.07
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:282255 original size:17 final size:18
Alignment explanation
Indices: 282219--282260 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
282209 TTTCGTCTTT
*
282219 TATTAT-TAATATTATTA
1 TATTATATAATATTATCA
282236 TATTATATAATATTA-CA
1 TATTATATAATATTATCA
282253 TATTATAT
1 TATTATAT
282261 TGTATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATATAATATTATCA
Found at i:283465 original size:17 final size:16
Alignment explanation
Indices: 283430--283474 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
283420 TTATAATTTC
283430 TTTTATTTTTACTTCT
1 TTTTATTTTTACTTCT
283446 TTTTATTATTTACTAT-T
1 TTTTATT-TTTACT-TCT
283463 TTTTCATTTTTA
1 TTTT-ATTTTTA
283475 TACTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.27
17 15 0.58
18 4 0.15
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTTTACTTCT
Found at i:295292 original size:95 final size:95
Alignment explanation
Indices: 295117--295293 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 95
295107 ATTTCAGAGC
* * *
295117 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACAAAGGATATTAGACCCAAGAAAACACAAGCTCAACTTCACGACGAAG
* * *
295182 GGGCGGCTGATTGTCAAATTCATTCAAAGT
66 AGGCGACTGACTGTCAAATTCATTCAAAGT
*** * *
295212 CAATTTCAACTTCACGGTAAAGGATATTATACTCAAGAAAACACAAGCTCAACTTCAC-AGCGAA
1 CAATTTCAACTTCACAACAAAGGATATTAGACCCAAGAAAACACAAGCTCAACTTCACGA-CGAA
295276 GAGGCGACTGACTGTCAA
65 GAGGCGACTGACTGTCAA
295294 CAAAAAATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
94 1 0.01
95 69 0.99
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (95 bp):
CAATTTCAACTTCACAACAAAGGATATTAGACCCAAGAAAACACAAGCTCAACTTCACGACGAAG
AGGCGACTGACTGTCAAATTCATTCAAAGT
Found at i:296122 original size:22 final size:22
Alignment explanation
Indices: 296087--296151 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 22
296077 TGTCTTTTAT
296087 TATTAATATTATTATATTATATAA
1 TATT-ATA-TATTATATTATATAA
*
296111 TATTATATATTATATTGTAT-A
1 TATTATATATTATATTATATAA
*
296132 -ATTATATATAATATTA-ATAA
1 TATTATATATTATATTATATAA
296152 CTGTATTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.05
20 15 0.41
21 1 0.03
22 12 0.32
23 3 0.08
24 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTATATATTATATTATATAA
Found at i:296124 original size:15 final size:16
Alignment explanation
Indices: 296084--296147 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 16
296074 TTCTGTCTTT
296084 TATTATTAATATTATTA
1 TATTA-TAATATTATTA
296101 TATTATATAATATTA-TA
1 TA-T-TATAATATTATTA
* *
296118 TATTATATTGTATAATTA
1 TATTATA--ATATTATTA
296136 TA-TATAATATTA
1 TATTATAATATTA
296148 ATAACTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 14 0.37
18 13 0.34
19 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTATAATATTATTA
Found at i:297678 original size:13 final size:15
Alignment explanation
Indices: 297649--297680 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
297639 TCTTGTTCAT
297649 TTTTACTTTTACTTA
1 TTTTACTTTTACTTA
297664 TTTTA-TTTT-CTTA
1 TTTTACTTTTACTTA
297677 TTTT
1 TTTT
297681 TATCTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTACTTTTACTTA
Found at i:316479 original size:9 final size:9
Alignment explanation
Indices: 316467--316500 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
316457 GAATTCAGTT
316467 AATTAACCG
1 AATTAACCG
316476 AATTAACCG
1 AATTAACCG
316485 AATTAACCG
1 AATTAACCG
316494 AAATTAA
1 -AATTAA
316501 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:316818 original size:184 final size:184
Alignment explanation
Indices: 316506--316893 Score: 656
Period size: 184 Copynumber: 2.1 Consensus size: 184
316496 ATTAAATTTT
** *
316506 AAATATTAAATATATTATATATAACATATGGGTTTAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGACTAACCCAAACCATTTAAAACCCAATTAATAA
316571 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
* *
316636 TTATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
316690 AAATATTAAATATATTATATATAACATAT-GGACTAAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGACTAA-CCCAAACCATTTAAAACCCAATTAATA
* *
316754 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAATTT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAATTT
316819 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
316874 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
316894 AATTAGAAAA
Statistics
Matches: 193, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
183 19 0.10
184 174 0.90
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGACTAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:317929 original size:19 final size:19
Alignment explanation
Indices: 317874--317936 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
317864 TTATAATATT
317874 TTTTTCAATTTAGTCCATTAA
1 TTTTTCAATTTA-TCCATT-A
317895 TTTTTCATATTT-TCC-TTA
1 TTTTTCA-ATTTATCCATTA
*
317913 TTTCTTCAATTTATCCTTTA
1 TTT-TTCAATTTATCCATTA
317933 TTTT
1 TTTT
317937 AAGTATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 8 0.21
19 10 0.26
20 9 0.24
21 7 0.18
22 4 0.11
ACGTcount: A:0.21, C:0.16, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTCAATTTATCCATTA
Found at i:321724 original size:28 final size:28
Alignment explanation
Indices: 321678--321733 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
321668 CATCGTCGTT
* *
321678 GCTTTCAAGCACTGGCTCGATGCCATAA
1 GCTTTCAAGCACTGACTCGATGACATAA
*
321706 GCTTTCAAGCATTGACTCGATGACATAA
1 GCTTTCAAGCACTGACTCGATGACATAA
321734 TGTAAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (28 bp):
GCTTTCAAGCACTGACTCGATGACATAA
Found at i:329277 original size:2 final size:2
Alignment explanation
Indices: 329272--329303 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
329262 TATATGTGCA
329272 TG TG TG TG TG TG T- TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
329304 TAAAAAACGT
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:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Done.