Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2035316 original size:13 final size:13
Alignment explanation
Indices: 2035294--2035329 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2035284 AAGATCCTAA
2035294 TAGA-GATGAAGG
1 TAGAGGATGAAGG
2035306 TAGAGGATGAAGG
1 TAGAGGATGAAGG
*
2035319 TGGAGGATGAA
1 TAGAGGATGAA
2035330 CGGGATTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.39, C:0.00, G:0.44, T:0.17
Consensus pattern (13 bp):
TAGAGGATGAAGG
Found at i:2036078 original size:23 final size:22
Alignment explanation
Indices: 2036046--2036122 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
2036036 TGACCCTGTA
2036046 CATCGATGCACATTCAAGGCATG
1 CATCGATGCACATTCAAGG-ATG
* *
2036069 CATC-ACTGCACCTTC-ATGATG
1 CATCGA-TGCACATTCAAGGATG
*
2036090 TATCGATGCACATTCAAGGATG
1 CATCGATGCACATTCAAGGATG
*
2036112 AATCGATGCAC
1 CATCGATGCAC
2036123 TGTTAGGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 14 0.31
22 19 0.42
23 12 0.27
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATG
Found at i:2041985 original size:64 final size:63
Alignment explanation
Indices: 2041913--2042109 Score: 220
Period size: 65 Copynumber: 3.0 Consensus size: 63
2041903 CTAAGAGTGT
* *
2041913 ATCGATGCATCAAGTGCATTTGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TGGTGC
** *
2041977 ATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTATGTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-GGTG
2042041 C
63 C
* ** *
2042042 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--TGGT
2042105 GC
62 GC
2042107 ATC
1 ATC
2042110 ACTTCTGAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 43 0.38
65 61 0.54
66 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTGGTGC
Found at i:2042416 original size:16 final size:17
Alignment explanation
Indices: 2042397--2042428 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2042387 TAAAGGTACC
2042397 GGTC-TCTAAAATAATT
1 GGTCATCTAAAATAATT
2042413 GGTCATCTAAAATAAT
1 GGTCATCTAAAATAAT
2042429 GTATAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (17 bp):
GGTCATCTAAAATAATT
Found at i:2044466 original size:2 final size:2
Alignment explanation
Indices: 2044455--2044491 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2044445 TGAATCATTG
2044455 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2044492 GAACATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2045575 original size:23 final size:23
Alignment explanation
Indices: 2045518--2045576 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2045508 ACCTTATATA
*
2045518 GCACTTCGGTGCAATTTTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* *
2045541 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTCTACGCG
*
2045564 GCACTTCAGTGCA
1 GCACTTCGGTGCA
2045577 TTTATACGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:2045584 original size:23 final size:22
Alignment explanation
Indices: 2045518--2045584 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
2045508 ACCTTATATA
2045518 GCACTTCGGTGCAATTTTACGCG
1 GCACTTCGGTGC-ATTTTACGCG
* * *
2045541 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGC-ATTTTACGCG
*
2045564 GCACTTCAGTGCATTTATACG
1 GCACTTCGGTGCATTT-TACG
2045585 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 3 0.08
23 34 0.92
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (22 bp):
GCACTTCGGTGCATTTTACGCG
Found at i:2045959 original size:24 final size:26
Alignment explanation
Indices: 2045923--2045970 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
2045913 TGATTACATG
* *
2045923 TATGTGAACAAGTATGT-AATTGTTA
1 TATGTGAAAAAGTATATGAATTGTTA
2045948 TATG-GAAAAAGTATATGAATTGT
1 TATGTGAAAAAGTATATGAATTGT
2045971 ATGATTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.38
Consensus pattern (26 bp):
TATGTGAAAAAGTATATGAATTGTTA
Found at i:2047043 original size:25 final size:21
Alignment explanation
Indices: 2046987--2047035 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2046977 CAAAAGGCTA
2046987 TTTTTCAATCACTGGTAACCC
1 TTTTTCAATCACTGGTAACCC
2047008 TTTTTCAATCACTGGTAACCC
1 TTTTTCAATCACTGGTAACCC
2047029 TTTTTCA
1 TTTTTCA
2047036 TTCCATCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (21 bp):
TTTTTCAATCACTGGTAACCC
Found at i:2053239 original size:35 final size:35
Alignment explanation
Indices: 2053188--2053282 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
2053178 ATTTCATTCC
* *
2053188 CAAATTCCAAAGTAATTCAATTTCATTCTAAA-CT
1 CAAATTCCAAAATAATTCAATTTAATTCTAAACCT
*
2053222 CTAAATTCCAAAATAATTCAATTAAATTCTAAACCT
1 C-AAATTCCAAAATAATTCAATTTAATTCTAAACCT
* *
2053258 CAAATTCTAAAATACTTCAATTTAA
1 CAAATTCCAAAATAATTCAATTTAA
2053283 GGTTTATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.02
35 49 0.92
36 3 0.06
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (35 bp):
CAAATTCCAAAATAATTCAATTTAATTCTAAACCT
Found at i:2053322 original size:35 final size:35
Alignment explanation
Indices: 2053276--2053350 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2053266 AAAATACTTC
* * * *
2053276 AATTTAAGGTTTATAATGTAATTGAA-TTGTTTTGG
1 AATTTAAGGTTTAGAATGAAATT-AAGGTGTTTTGA
*
2053311 AATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTAAGGTGTTTTGA
2053346 AATTT
1 AATTT
2053351 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.45
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTAAGGTGTTTTGA
Found at i:2055390 original size:35 final size:35
Alignment explanation
Indices: 2055340--2055461 Score: 163
Period size: 35 Copynumber: 3.4 Consensus size: 35
2055330 TCTAAACCTT
* *
2055340 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATG
* * * *
2055375 TAATTGAATTGTTTTAGAATTTAGGGTTTAGAGTG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATG
*
2055410 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAGAATG
2055445 AAATTGAGGATTATTTT
1 AAATTGA--ATTATTTT
2055462 GCAAGTTTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 66 0.89
37 8 0.11
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAGAATG
Found at i:2057624 original size:20 final size:21
Alignment explanation
Indices: 2057587--2057646 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
2057577 ACAGTTAAAA
2057587 AAATTAATTTAAAAAAAA-TT
1 AAATTAATTTAAAAAAAAGTT
*
2057607 AAATT-ATTTAATATAAAAGTT
1 AAATTAATTTAA-AAAAAAGTT
*
2057628 -AATATCATTGTAAAAAAAA
1 AAAT-TAATT-TAAAAAAAA
2057647 TAGATAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 6 0.18
20 13 0.39
21 3 0.09
22 8 0.24
23 3 0.09
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (21 bp):
AAATTAATTTAAAAAAAAGTT
Found at i:2060429 original size:71 final size:71
Alignment explanation
Indices: 2060313--2060455 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
2060303 TAATGGAGCT
*
2060313 ACATCAAGTACTCCAAATGAATCACTTGAAAATCCTCTTGTTTCACTTGAATGTTTCATCTTTCT
1 ACATCAAGTACTCCAAATGAATCACTTGAAAATCCTCTTGTTTCACTTGAATGATTCATCTTTCT
2060378 CTAGAG
66 CTAGAG
2060384 ACATCAAGTACTCCAAATGAATCACTTGAAAATCCTCTTGTTTCACTTGAATGATTCATCTTTCT
1 ACATCAAGTACTCCAAATGAATCACTTGAAAATCCTCTTGTTTCACTTGAATGATTCATCTTTCT
2060449 CTAGAG
66 CTAGAG
2060455 A
1 A
2060456 TTAAGAATGT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (71 bp):
ACATCAAGTACTCCAAATGAATCACTTGAAAATCCTCTTGTTTCACTTGAATGATTCATCTTTCT
CTAGAG
Found at i:2066033 original size:31 final size:31
Alignment explanation
Indices: 2065988--2066064 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
2065978 AAATTTTTAA
*
2065988 AAAATATATATATAAATATTTTCCAACTTGTT
1 AAAA-ATATATATAAATATTTTCCAAATTGTT
*
2066020 AATAAA-ATATATAAATATTTTTCAAATTGTT
1 AA-AAATATATATAAATATTTTCCAAATTGTT
2066051 AAAAATATATATAA
1 AAAAATATATATAA
2066065 TAAGGACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
30 3 0.07
31 33 0.80
32 3 0.07
33 2 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAAATATATATAAATATTTTCCAAATTGTT
Found at i:2066993 original size:21 final size:21
Alignment explanation
Indices: 2066969--2067008 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2066959 AATCAGAATA
2066969 TAATCATTT-AAAAATAATATT
1 TAAT-ATTTAAAAAATAATATT
*
2066990 TAATTTTTAAAAAATAATA
1 TAATATTTAAAAAATAATA
2067009 ATTTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATATTTAAAAAATAATATT
Found at i:2067003 original size:22 final size:22
Alignment explanation
Indices: 2066978--2067019 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2066968 ATAATCATTT
2066978 AAAAATAAT-ATTTAATTTTTA
1 AAAAATAATAATTTAATTTTTA
*
2066999 AAAAATAATAATTTTATTTTT
1 AAAAATAATAATTTAATTTTT
2067020 TTTAATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAAATAATAATTTAATTTTTA
Found at i:2068262 original size:166 final size:166
Alignment explanation
Indices: 2067939--2068269 Score: 614
Period size: 167 Copynumber: 2.0 Consensus size: 166
2067929 AACTGTAAAC
2067939 AGCTACATTAGTATAAATAAAAATAAATTCTCTTAATGTAAAAGTTATACAAAAAATTAGAATAT
1 AGCTACATTAGTATAAATAAAAATAAATTCTCTTAATGTAAAAGTTATACAAAAAATTAGAATAT
2068004 TTAATGCATATCTACCGGAGAAATTGATCATTATTCATATTAATTTTCGTTGCACCTAACTATTT
66 TTAATGCATATCTACCGGAGAAATTGATCATTATTCATATTAATTTTCGTTGCACCTAACTATTT
2068069 TGTATTAGTAATCTTATGTCGTCATCTAAACAACAA
131 TGTATTAGTAATCTTATGTCGTCATCTAAACAACAA
2068105 AGCTACATTAGTATATAATAAAAATAAATTCTCTTAATGTAAAAGTTATACAAAAAATTAGAATA
1 AGCTACATTAGTATA-AATAAAAATAAATTCTCTTAATGTAAAAGTTATACAAAAAATTAGAATA
2068170 TTTAATGCATATCTACCGGAGAAATTGATCATTATTCATACATTAATTTTC-TTGCACCT-ACTA
65 TTTAATGCATATCTACCGGAGAAATTGATCATTATTCAT--ATTAATTTTCGTTGCACCTAACTA
2068233 -TTTGTATTAGTAATCTTATGTCGTCATCTAAACAACA
128 TTTTGTATTAGTAATCTTATGTCGTCATCTAAACAACA
2068270 TAATAAATAC
Statistics
Matches: 162, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
166 52 0.32
167 92 0.57
168 8 0.05
169 10 0.06
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (166 bp):
AGCTACATTAGTATAAATAAAAATAAATTCTCTTAATGTAAAAGTTATACAAAAAATTAGAATAT
TTAATGCATATCTACCGGAGAAATTGATCATTATTCATATTAATTTTCGTTGCACCTAACTATTT
TGTATTAGTAATCTTATGTCGTCATCTAAACAACAA
Found at i:2070482 original size:50 final size:49
Alignment explanation
Indices: 2070407--2070510 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 49
2070397 GATAGATTTT
** * *
2070407 AATAAAAAAATATTTTATTGGAACTCATCATCTTGGCGTGATGA-TTCG
1 AATAAAAAAATATTTTATTAAAACTCATAATCTTGACGTGATGAGTTCG
* *
2070455 AATAAAAAAATATTTTTTATTAAAACTCGTAATCTTGACGTGATGAGTTCT
1 AATAAAAAAATA--TTTTATTAAAACTCATAATCTTGACGTGATGAGTTCG
2070506 AATAA
1 AATAA
2070511 CACAATAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 12 0.26
50 27 0.57
51 8 0.17
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (49 bp):
AATAAAAAAATATTTTATTAAAACTCATAATCTTGACGTGATGAGTTCG
Found at i:2072034 original size:185 final size:184
Alignment explanation
Indices: 2071781--2072152 Score: 581
Period size: 185 Copynumber: 2.0 Consensus size: 184
2071771 AATTGAAATT
* *
2071781 AAATTTTAAATATATTATATATATAACATATGAGCTCAACCCAAACCATTTAAAACTCAATTAAT
1 AAATATTAAATATATTATATATATAACATATGAACTCAACCCAAACCATTTAAAACTCAATTAAT
2071846 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAAATTATATAAAA
66 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAAAATTATATAAAA
* *
2071911 TTTTTATTGTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTT-AATTAAA
130 TTTTTATTGTATAATTATATATTAATTAAATTAATTAT-AA-T-TTTTTTGAATTAAA
*
2071968 AAATATTAAATATA-T-TATATATAACATATGAACT-AAGTCCAAACCATTTAAAACTCAATTAA
1 AAATATTAAATATATTATATATATAACATATGAACTCAA-CCCAAACCATTTAAAACTCAATTAA
* * * *
2072030 TAATTTAATATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA
65 TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAA
*
2072095 TTTTTATTTTATAATTATATATTAATTAAATTAATTATAATTTTTTTGAATTAAA
130 TTTTTATTGTATAATTATATATTAATTAAATTAATTATAATTTTTTTGAATTAAA
2072150 AAA
1 AAA
2072153 CATTTAATTT
Statistics
Matches: 173, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
181 6 0.03
182 11 0.06
183 2 0.01
184 51 0.29
185 89 0.51
186 1 0.01
187 13 0.08
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (184 bp):
AAATATTAAATATATTATATATATAACATATGAACTCAACCCAAACCATTTAAAACTCAATTAAT
AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAAT
TTTTATTGTATAATTATATATTAATTAAATTAATTATAATTTTTTTGAATTAAA
Found at i:2072184 original size:26 final size:24
Alignment explanation
Indices: 2072118--2072185 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
2072108 ATTATATATT
* *
2072118 AATTAAATTAATTATAATTTTTTTG
1 AATTAAA-AAATTTTAATTTTTTTG
*
2072143 AATTAAAAAACATTTAATTTTTTTG
1 AATTAAAAAA-TTTTAATTTTTTTG
*
2072168 TAAATTAGAAAATTTTAA
1 --AATTAAAAAATTTTAA
2072186 AAAATTTCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.06
25 19 0.54
26 5 0.14
27 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (24 bp):
AATTAAAAAATTTTAATTTTTTTG
Found at i:2075011 original size:37 final size:37
Alignment explanation
Indices: 2074970--2075090 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 37
2074960 TTTTAAGAAA
2074970 TAAAATATTATATGAAATGTATTTCAAGTATATTTTT
1 TAAAATATTATATGAAATGTATTTCAAGTATATTTTT
* * * ****
2075007 TAAAATATTA-AT--AAT-TTTTTAACAAAAGGAAATGAAA
1 TAAAATATTATATGAAATGTATTT--C--AAGTATATTTTT
2075044 TAAAATATTATATGAAATGTATTTCAAGTATATTTTT
1 TAAAATATTATATGAAATGTATTTCAAGTATATTTTT
2075081 TAAAATATTA
1 TAAAATATTA
2075091 ATAATTTTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 16
0.67 0.15 0.17
Matches are distributed among these distances:
33 4 0.06
34 3 0.05
35 1 0.02
36 2 0.03
37 42 0.68
38 2 0.03
39 1 0.02
40 3 0.05
41 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.43
Consensus pattern (37 bp):
TAAAATATTATATGAAATGTATTTCAAGTATATTTTT
Found at i:2075051 original size:74 final size:74
Alignment explanation
Indices: 2074966--2075114 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
2074956 CAAATTTTAA
*
2074966 GAAATAAAATATTATATGAAATGTATTTCAAGTATATTTTTTAAAATATTAATAATTTTTTAACA
1 GAAATAAAATATTATATGAAATGTATTTCAAGTATATTTTTTAAAATATTAATAATTTTGTAACA
2075031 AAAGGAAAT
66 AAAGGAAAT
2075040 GAAATAAAATATTATATGAAATGTATTTCAAGTATATTTTTTAAAATATTAATAATTTTGTAACA
1 GAAATAAAATATTATATGAAATGTATTTCAAGTATATTTTTTAAAATATTAATAATTTTGTAACA
2075105 AAAGGAAAT
66 AAAGGAAAT
2075114 G
1 G
2075115 TTCTTCTCCA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.40
Consensus pattern (74 bp):
GAAATAAAATATTATATGAAATGTATTTCAAGTATATTTTTTAAAATATTAATAATTTTGTAACA
AAAGGAAAT
Found at i:2076064 original size:23 final size:22
Alignment explanation
Indices: 2076024--2076091 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
2076014 CTCGTATAAA
2076024 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2076046 TGCACCGAAGTTGCCCGTAGAAT
1 TGCACCGAAG-TGCCCGTAGAAT
2076069 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2076091 T
1 T
2076092 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
22 23 0.51
23 22 0.49
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2076348 original size:30 final size:31
Alignment explanation
Indices: 2076309--2076368 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2076299 TAGACATAGT
*
2076309 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2076339 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2076369 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2076412 original size:26 final size:26
Alignment explanation
Indices: 2076383--2076460 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 26
2076373 TTTTCTGCAT
2076383 ATTCATGTCATGTATACATTAATATA
1 ATTCATGTCATGTATACATTAATATA
*
2076409 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGT-ATACA-TTAATA-TA
2076438 ATTCATGTCATGTAT-CA-TAATAT
1 ATTCATGTCATGTATACATTAATAT
2076461 GGAATGTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 5 0.11
26 13 0.28
27 7 0.15
28 8 0.17
29 14 0.30
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (26 bp):
ATTCATGTCATGTATACATTAATATA
Found at i:2076755 original size:21 final size:21
Alignment explanation
Indices: 2076725--2076767 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2076715 AATCATTTCG
* *
2076725 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2076746 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2076767 T
1 T
2076768 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2082746 original size:22 final size:22
Alignment explanation
Indices: 2082712--2082786 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
2082702 TGTCACCACG
*
2082712 CCGTA-AAATGCACCGAAGTGC
1 CCGTAGAATTGCACCGAAGTGC
2082733 CCGTAGAATTGCACCGAAGTGC
1 CCGTAGAATTGCACCGAAGTGC
2082755 CCGTAGAATTGCACCGAAGTGC
1 CCGTAGAATTGCACCGAAGTGC
2082777 CCGTAGAATT
1 CCGTAGAATT
2082787 ATGTCCATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 5 0.10
22 47 0.90
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
CCGTAGAATTGCACCGAAGTGC
Found at i:2083046 original size:30 final size:31
Alignment explanation
Indices: 2083005--2083064 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
2082995 TAGACATAGT
*
2083005 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
2083035 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
2083065 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:2083121 original size:29 final size:29
Alignment explanation
Indices: 2083079--2083150 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
2083069 TTTTCTGCAT
**
2083079 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
2083108 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
2083137 ATTCATGTCATGTA
1 ATTCATGTCATGTA
2083151 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:2083572 original size:67 final size:67
Alignment explanation
Indices: 2083448--2083596 Score: 164
Period size: 67 Copynumber: 2.3 Consensus size: 67
2083438 CTTTTCTCAT
* * *
2083448 GGGGGAATCGGTT-CCCCCTTAGGGGTATCGATTCCCCTCAAGCAATCTGAAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGAAATTTCAT-TACGA
2083512 TGA
65 TGA
* * *
2083515 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGA-TCCCCTCTAA-CATTCTGGAAA-TTCATTTCG
1 GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTC-AAGCAATCT-GAAATTTCATTACG
*
2083577 TTGA
64 ATGA
*
2083581 AGGGGTATC-GTTCCCC
1 GGGGGTATCGGTTCCCC
2083597 TTGAATGGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
65 7 0.10
66 14 0.20
67 29 0.41
68 21 0.30
ACGTcount: A:0.20, C:0.27, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTAGGGGTACCGATTCCCCTCAAGCAATCTGAAATTTCATTACGAT
GA
Found at i:2083606 original size:20 final size:21
Alignment explanation
Indices: 2083577--2083618 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2083567 ATTCATTTCG
*
2083577 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2083597 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2083618 T
1 T
2083619 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2084599 original size:7 final size:7
Alignment explanation
Indices: 2084556--2084648 Score: 55
Period size: 7 Copynumber: 13.3 Consensus size: 7
2084546 TCACATAATC
2084556 GGATTTA
1 GGATTTA
*
2084563 GGGTTTA
1 GGATTTA
* *
2084570 GCACTTA
1 GGATTTA
*
2084577 GGATTAAA
1 GGATT-TA
2084585 GG-TTTA
1 GGATTTA
2084591 GGATTTA
1 GGATTTA
**
2084598 GGATTCG
1 GGATTTA
*
2084605 GGGTTTA
1 GGATTTA
*
2084612 GGGTTTA
1 GGATTTA
*
2084619 GGGTTTA
1 GGATTTA
*
2084626 TGATTTA
1 GGATTTA
2084633 -GATTTTA
1 GGA-TTTA
*
2084640 GGGTTTA
1 GGATTTA
2084647 GG
1 GG
2084649 CCTTAGGGTT
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
6 5 0.08
7 57 0.86
8 4 0.06
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (7 bp):
GGATTTA
Found at i:2084616 original size:28 final size:28
Alignment explanation
Indices: 2084585--2084648 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
2084575 TAGGATTAAA
* *
2084585 GGTTTAGGATTTAGGATTCGGGGTTTAG
1 GGTTTAGGATTTAGGATTCAGAGTTTAG
* * * *
2084613 GGTTTAGGGTTTATGATTTAGATTTTAG
1 GGTTTAGGATTTAGGATTCAGAGTTTAG
2084641 GGTTTAGG
1 GGTTTAGG
2084649 CCTTAGGGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.44
Consensus pattern (28 bp):
GGTTTAGGATTTAGGATTCAGAGTTTAG
Found at i:2084622 original size:14 final size:14
Alignment explanation
Indices: 2084585--2084658 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
2084575 TAGGATTAAA
*
2084585 GGTTTAGGATTTAG
1 GGTTTAGGGTTTAG
* **
2084599 GATTCGGGGTTTAG
1 GGTTTAGGGTTTAG
*
2084613 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAG
* **
2084627 GATTTAGATTTTAG
1 GGTTTAGGGTTTAG
**
2084641 GGTTTAGGCCTTAG
1 GGTTTAGGGTTTAG
2084655 GGTT
1 GGTT
2084659 CATTACAAAT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.43
Consensus pattern (14 bp):
GGTTTAGGGTTTAG
Found at i:2084654 original size:21 final size:21
Alignment explanation
Indices: 2084615--2084654 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2084605 GGGTTTAGGG
* *
2084615 TTTAGGGTTTATGATTTAGAT
1 TTTAGGGTTTAGGACTTAGAT
*
2084636 TTTAGGGTTTAGGCCTTAG
1 TTTAGGGTTTAGGACTTAG
2084655 GGTTCATTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.05, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAGGACTTAGAT
Found at i:2087302 original size:32 final size:32
Alignment explanation
Indices: 2087266--2087331 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
2087256 ATATATAAAA
2087266 AGTATATAATAATATAAATA-TATAAACTATAT
1 AGTATATAA-AATATAAATATTATAAACTATAT
* * *
2087298 AGTATGTAAACTATATATATTATAAACTATAT
1 AGTATATAAAATATAAATATTATAAACTATAT
2087330 AG
1 AG
2087332 AAAACTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.38
Consensus pattern (32 bp):
AGTATATAAAATATAAATATTATAAACTATAT
Found at i:2087307 original size:16 final size:17
Alignment explanation
Indices: 2087286--2087331 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
2087276 AATATAAATA
2087286 TATAAACTATATAGTA-
1 TATAAACTATATAGTAT
*
2087302 TGTAAACTATATA-TAT
1 TATAAACTATATAGTAT
2087318 TATAAACTATATAG
1 TATAAACTATATAG
2087332 AAAACTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 2 0.08
16 24 0.92
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (17 bp):
TATAAACTATATAGTAT
Found at i:2087471 original size:2 final size:2
Alignment explanation
Indices: 2087460--2087821 Score: 65
Period size: 2 Copynumber: 174.5 Consensus size: 2
2087450 TTATATAGTT
* * *
2087460 TA TA TT TA TA TA CTA TA TA AA T- TA TA TA GTG TA TA TGA -A CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA T-A TA -TA
* * *
2087502 TA TA AA CTA TA TA TA AA CTA TA GTT TA TA TGA -A TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA -TA TA -TA TA TA T-A TA TA TA TA TA TA
* * * * *
2087545 CTA TA TA AA CTA TA TA GTT TA TA TT TA TA TA CA -A TG TA TA -A
1 -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2087586 CT- TA -A T- TA TA TA CTA T- TA TA TA TA TA TA CTA TA TA TA AA
1 -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
2087625 TCA -A TA CTA TA TA TA TA TA AA CTA TA TA TG TA TA AA CTA TA -A
1 T-A TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA
* * * * * *
2087667 TT TA TA TA AA CTA TA TG TA -A TA TA TA CA CTA TA TA GTT TA CA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * *
2087709 TA TGA -A CCA TA TA -A TC TA TA TA TA CTA TA TA AA CTA TA -A AA
1 TA T-A TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
* * * *
2087750 TA TG TA -A AA CTA TG TA TA TA CTA TA TA TA TA -A TC 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
*
2087792 TA TA CTA TA TA TA AA CTA TA TA TA CTA TA T
1 TA TA -TA TA TA TA TA -TA TA TA TA -TA TA T
2087822 GGTTTACATA
Statistics
Matches: 257, Mismatches: 56, Indels: 94
0.63 0.14 0.23
Matches are distributed among these distances:
1 17 0.07
2 202 0.79
3 38 0.15
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:2087478 original size:9 final size:9
Alignment explanation
Indices: 2087466--2087821 Score: 106
Period size: 9 Copynumber: 40.3 Consensus size: 9
2087456 AGTTTATATT
2087466 TATATACTA
1 TATATACTA
*
2087475 TATA-AAT-
1 TATATACTA
* *
2087482 TATATAGTG
1 TATATACTA
2087491 TATATGAACTA
1 TATAT--ACTA
*
2087502 TATAAACTA
1 TATATACTA
2087511 TATATAAACTA
1 TATAT--ACTA
*
2087522 TAGTTTA-TA
1 TA-TATACTA
2087531 TGA-ATA-TA
1 T-ATATACTA
2087539 TATATACTA
1 TATATACTA
*
2087548 TATAAACTA
1 TATATACTA
2087557 TATAGT--T-
1 TATA-TACTA
2087564 TATAT--T-
1 TATATACTA
*
2087570 TATATACAA
1 TATATACTA
*
2087579 TGTATAACTTAA
1 TATAT-AC-T-A
2087591 TTATATACTA
1 -TATATACTA
2087601 T-TATA-TA
1 TATATACTA
2087608 TATATACTA
1 TATATACTA
*
2087617 TATATA-AA
1 TATATACTA
2087625 TCA-ATACTA
1 T-ATATACTA
2087634 TATATA-TA
1 TATATACTA
2087642 TA-A-ACTA
1 TATATACTA
*
2087649 TATAT-GTA
1 TATATACTA
2087657 TA-A-ACTA
1 TATATACTA
*
2087664 TA-AT-TTA
1 TATATACTA
*
2087671 TATAAACTA
1 TATATACTA
* *
2087680 TATGTAATA
1 TATATACTA
*
2087689 TATACACTA
1 TATATACTA
2087698 TATAGTTTAC-A
1 TATA---TACTA
*
2087709 TATGA-ACCA
1 TAT-ATACTA
2087718 TATA-ATCTA
1 TATATA-CTA
2087727 TATATACTA
1 TATATACTA
*
2087736 TATAAACTA
1 TATATACTA
*
2087745 TA-A-AATA
1 TATATACTA
* *
2087752 TGTAAAACTA
1 TAT-ATACTA
2087762 TGTATATACTA
1 --TATATACTA
2087773 TATATA-TAA
1 TATATACT-A
*
2087782 TCTATA-TA
1 TATATACTA
2087790 TATATACTA
1 TATATACTA
2087799 TATATAAACTA
1 TATAT--ACTA
2087810 TATATACTA
1 TATATACTA
2087819 TAT
1 TAT
2087822 GGTTTACATA
Statistics
Matches: 264, Mismatches: 37, Indels: 92
0.67 0.09 0.23
Matches are distributed among these distances:
6 8 0.03
7 31 0.12
8 49 0.19
9 122 0.46
10 9 0.03
11 31 0.12
12 10 0.04
13 4 0.02
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:2087505 original size:11 final size:10
Alignment explanation
Indices: 2087491--2087821 Score: 61
Period size: 11 Copynumber: 33.3 Consensus size: 10
2087481 TTATATAGTG
2087491 TATATGAACTA
1 TATAT-AACTA
2087502 TATA-AACTA
1 TATATAACTA
2087511 TATATAAACTA
1 TATAT-AACTA
*
2087522 TAGTTTATATGAATA
1 TA---TATA--ACTA
2087537 TATATATACTA
1 TATATA-ACTA
2087548 TATA-AACTA
1 TATATAACTA
*
2087557 TATAGTTTA-TA
1 TATA--TAACTA
* *
2087568 TTTATATACAA
1 TATATA-ACTA
*
2087579 TGTATAACT-
1 TATATAACTA
2087588 TAATTATATACTA
1 T-A-TATA-ACTA
2087601 T-TAT-A-TA
1 TATATAACTA
2087608 TATAT-ACTA
1 TATATAACTA
*
2087617 TATATAAATCA
1 TATATAACT-A
2087628 -ATACTATA-TA
1 TATA-TA-ACTA
2087638 TATATAAACTA
1 TATAT-AACTA
*
2087649 TATATGTA-TA
1 TATAT-AACTA
* *
2087659 AACTATAA-TT
1 TA-TATAACTA
2087669 TATATAAACTA
1 TATAT-AACTA
*
2087680 TATGTAA-TA
1 TATATAACTA
*
2087689 TATA-CACTA
1 TATATAACTA
*
2087698 TATAGTTTAC-A
1 TATA--TAACTA
* *
2087709 TAT-GAACCA
1 TATATAACTA
*
2087718 TATA-ATCTA
1 TATATAACTA
2087727 TATAT-ACTA
1 TATATAACTA
2087736 TATA-AACTA
1 TATATAACTA
2087745 TA-A-AA-TA
1 TATATAACTA
* *
2087752 TGTAAAACTA
1 TATATAACTA
*
2087762 TGTATATACTA
1 TATATA-ACTA
2087773 TATAT-A-TA
1 TATATAACTA
*
2087781 -ATCT-A-TA
1 TATATAACTA
2087788 TATATATACTA
1 TATATA-ACTA
2087799 TATATAAACTA
1 TATAT-AACTA
2087810 TATAT-ACTA
1 TATATAACTA
2087819 TAT
1 TAT
2087822 GGTTTACATA
Statistics
Matches: 243, Mismatches: 32, Indels: 92
0.66 0.09 0.25
Matches are distributed among these distances:
7 12 0.05
8 17 0.07
9 74 0.30
10 33 0.14
11 85 0.35
12 12 0.05
13 2 0.01
14 3 0.01
15 5 0.02
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (10 bp):
TATATAACTA
Found at i:2087791 original size:24 final size:24
Alignment explanation
Indices: 2087756--2087820 Score: 87
Period size: 24 Copynumber: 2.7 Consensus size: 24
2087746 AAAATATGTA
*
2087756 AAACTATGTATATACTA-TATATAT
1 AAACTATATATATA-TACTATATAT
*
2087780 AATCTATATATATATACTATATAT
1 AAACTATATATATATACTATATAT
2087804 AAACTATATATACTATA
1 AAACTATATATA-TATA
2087821 TGGTTTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.06
24 30 0.83
25 4 0.11
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.42
Consensus pattern (24 bp):
AAACTATATATATATACTATATAT
Found at i:2087979 original size:23 final size:23
Alignment explanation
Indices: 2087930--2087981 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2087920 CACACATATA
***
2087930 TATATATATAGATATATATAGTT
1 TATATATATAGATATATATAAAC
*
2087953 TATATATATATATATATATAAAC
1 TATATATATAGATATATATAAAC
2087976 TATATA
1 TATATA
2087982 GTTTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (23 bp):
TATATATATAGATATATATAAAC
Found at i:2087981 original size:2 final size:2
Alignment explanation
Indices: 2087925--2087972 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
2087915 ACACACACAC
* *
2087925 AT AT AT AT AT AT AT AG AT AT AT AT AGT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
2087968 AT AT A
1 AT AT A
2087973 AACTATATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 40 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2088004 original size:30 final size:30
Alignment explanation
Indices: 2087944--2088070 Score: 177
Period size: 30 Copynumber: 4.2 Consensus size: 30
2087934 TATATAGATA
*
2087944 TATATAGTTTATATA-TATATATATATATAAAC
1 TATATAGTTTAT-TACTATATAT-GA-ATAAAC
* *
2087976 TATATAGTTTATTATTATATTTGAATAAAC
1 TATATAGTTTATTACTATATATGAATAAAC
2088006 TATATAGTTTATTACTATATATGAATAAAC
1 TATATAGTTTATTACTATATATGAATAAAC
*
2088036 TATATAGTTTATTACTATATATGAACAAA-
1 TATATAGTTTATTACTATATATGAATAAAC
2088065 TATATA
1 TATATA
2088071 TGAACTAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
29 6 0.07
30 62 0.70
31 3 0.03
32 18 0.20
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (30 bp):
TATATAGTTTATTACTATATATGAATAAAC
Found at i:2088070 original size:14 final size:15
Alignment explanation
Indices: 2088051--2088087 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2088041 AGTTTATTAC
2088051 TATATATGAAC-AAA
1 TATATATGAACTAAA
2088065 TATATATGAACTAAA
1 TATATATGAACTAAA
2088080 TATTATAT
1 TA-TATAT
2088088 ATAAATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (15 bp):
TATATATGAACTAAA
Found at i:2088087 original size:60 final size:58
Alignment explanation
Indices: 2087962--2088099 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 58
2087952 TTATATATAT
* * * ** *
2087962 ATATATATATAAACTATATAGTTTATTATTATATTTGAATAAACTATATAGTTTATTA
1 ATATATATATAAACTATATAGTTTATTACTATATATGAACAAACTATATAGTGAATAA
*
2088020 CTATATATGAATAAACTATATAGTTTATTACTATATATGAACAAA-TATATA-TGAACTAA
1 ATATATAT--ATAAACTATATAGTTTATTACTATATATGAACAAACTATATAGTGAA-TAA
*
2088079 ATATTATATATAAATTATATA
1 ATA-TATATATAAACTATATA
2088100 TTATATAGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
58 20 0.30
59 10 0.15
60 37 0.55
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (58 bp):
ATATATATATAAACTATATAGTTTATTACTATATATGAACAAACTATATAGTGAATAA
Found at i:2088152 original size:125 final size:122
Alignment explanation
Indices: 2088034--2088280 Score: 363
Period size: 125 Copynumber: 2.0 Consensus size: 122
2088024 ATATGAATAA
* *
2088034 ACTATATAGTTTATTACTAT-A-TATGAACAAATATATATGAACTAAATATTATATATAAATTAT
1 ACTATATAGTTCATTAATATAATTATGAAC-AATATATATGAACTAAATATTATATATAAATTAT
*
2088097 ATATTATATAGTTCATTAATATAAACTATATATTAATTTATTAATATAAACTATATAT
65 ATATTATATAGTTCATTAATATAAACAATATATTAATTTATTAATATAAACTATATAT
* * *
2088155 ATTATATAGTTCATTAATATAAACTTTATGAACTATATATATGAACTATATATTATATATAAATT
1 ACTATATAGTTCATTAATAT-AA--TTATGAACAATATATATGAACTAAATATTATATATAAATT
* * *
2088220 ATATATTATATAGTTTATTAATATAAACAATGTATTAATTTCTTAATATAAACTATATAT
63 ATATATTATATAGTTCATTAATATAAACAATATATTAATTTATTAATATAAACTATATAT
2088280 A
1 A
2088281 GTCCATTAGT
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
121 17 0.15
123 1 0.01
125 87 0.78
126 7 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (122 bp):
ACTATATAGTTCATTAATATAATTATGAACAATATATATGAACTAAATATTATATATAAATTATA
TATTATATAGTTCATTAATATAAACAATATATTAATTTATTAATATAAACTATATAT
Found at i:2088154 original size:56 final size:53
Alignment explanation
Indices: 2088080--2088375 Score: 204
Period size: 54 Copynumber: 5.7 Consensus size: 53
2088070 ATGAACTAAA
*
2088080 TATTATATATAAA-T-TATATATTATATAGTTCATTAATATAAACTATATATTAATT
1 TATTA-ATATAAACTATATATATTATATA-TTCATTAATATAAACT-TATA-TAGTT
**
2088135 TATTAATATAAACTATATATATTATATAGTTCATTAATATAAACTT-TAT-GAAC
1 TATTAATATAAACTATATATATTATATA-TTCATTAATATAAACTTATATAG-TT
* **
2088188 TA-TATATATGAAC--TATATATTATATATAAATT-ATAT--A-TTATATAGTT
1 TATTA-ATATAAACTATATATATTATATATTCATTAATATAAACTTATATAGTT
* *
2088235 TATTAATATAAAC-A-ATGTATTA-AT-TTC-TTAATATAAACTATATATAGTC
1 TATTAATATAAACTATATATATTATATATTCATTAATATAAACT-TATATAGTT
* * * *
2088284 CATTAGTATAAACTATGAACTATATTATATA-T-ACTATGTATAAAC-TATATAGTT
1 TATTAATATAAACTAT--A-TATATTATATATTCATTA-ATATAAACTTATATAGTT
2088338 TATTAATATAAACTATATGA-ATTATAGT-TT-ATTAATAT
1 TATTAATATAAACTATAT-ATATTATA-TATTCATTAATAT
2088376 TAAATTTCAT
Statistics
Matches: 193, Mismatches: 23, Indels: 54
0.71 0.09 0.20
Matches are distributed among these distances:
44 2 0.01
45 5 0.03
46 4 0.02
47 21 0.11
48 4 0.02
49 23 0.12
50 5 0.03
51 23 0.12
52 9 0.05
53 11 0.06
54 37 0.19
55 12 0.06
56 37 0.19
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (53 bp):
TATTAATATAAACTATATATATTATATATTCATTAATATAAACTTATATAGTT
Found at i:2088199 original size:13 final size:13
Alignment explanation
Indices: 2088181--2088207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2088171 ATATAAACTT
2088181 TATGAACTATATA
1 TATGAACTATATA
2088194 TATGAACTATATA
1 TATGAACTATATA
2088207 T
1 T
2088208 TATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TATGAACTATATA
Found at i:2088243 original size:18 final size:18
Alignment explanation
Indices: 2088065--2088231 Score: 73
Period size: 18 Copynumber: 9.3 Consensus size: 18
2088055 TATGAACAAA
* * *
2088065 TATATATGAACTAAATAT
1 TATATATAAATTATATAT
2088083 TATATATAAATTATATAT
1 TATATATAAATTATATAT
**
2088101 TATATAGTTCATTA-ATA-
1 TATATA-TAAATTATATAT
* * *
2088118 TAAACTATATATTAATTTAT
1 TATA-TATAAATT-ATATAT
*
2088138 TA-ATATAAACTATATA-
1 TATATATAAATTATATAT
* * *
2088154 TAT-TATATAGT-T-CAT
1 TATATATAAATTATATAT
2088169 TA-ATATAAACTT-TATGAACT
1 TATATATAAA-TTATAT--A-T
* *
2088189 ATATATATGAACTATATAT
1 -TATATATAAATTATATAT
2088208 TATATATAAATTATATAT
1 TATATATAAATTATATAT
2088226 TATATA
1 TATATA
2088232 GTTTATTAAT
Statistics
Matches: 111, Mismatches: 22, Indels: 32
0.67 0.13 0.19
Matches are distributed among these distances:
14 1 0.01
15 8 0.07
16 10 0.09
17 11 0.10
18 55 0.50
19 10 0.09
20 4 0.04
21 3 0.03
22 9 0.08
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (18 bp):
TATATATAAATTATATAT
Found at i:2088355 original size:125 final size:125
Alignment explanation
Indices: 2088053--2088355 Score: 316
Period size: 125 Copynumber: 2.4 Consensus size: 125
2088043 TTTATTACTA
* * * * *
2088053 TATATGAACAAATATATATGAACTAAATATTATATATAAATTATATATTATATAGTTCATTAATA
1 TATATGAAC-TATATATATAAACTATATATTATATATAAATTATAAACTATATAGTTCATTAATA
* * *
2088118 TAAACTATATATTAATTTATTAATATAAACTATATATATTATATAGTTCATTAATATAAAC
65 TAAACAATATATTAATTTATTAATATAAACTATATATATCATATAGTTCATAAATATAAAC
* * * * *
2088179 TTTATGAACTATATATATGAACTATATATTATATATAAATTATATATTATATAGTTTATTAATAT
1 TATATGAACTATATATATAAACTATATATTATATATAAATTATAAACTATATAGTTCATTAATAT
* * *
2088244 AAACAATGTATTAATTTCTTAATATAAACTATATATAGTCCAT-TAG-T-ATAAACTATGAAC
66 AAACAATATATTAATTTATTAATATAAACTATATATA-T-CATATAGTTCATAAA-TATAAAC
*
2088304 TATATTATA-TATACTATGTATAAACTATATAGTT-TAT-T-AA-TATAAACTATAT
1 TATATGA-ACTATA-TA--TATAAACTATATA-TTATATATAAATTATAAACTATAT
2088356 GAATTATAGT
Statistics
Matches: 154, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
124 4 0.03
125 113 0.73
126 17 0.11
127 3 0.02
128 15 0.10
129 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (125 bp):
TATATGAACTATATATATAAACTATATATTATATATAAATTATAAACTATATAGTTCATTAATAT
AAACAATATATTAATTTATTAATATAAACTATATATATCATATAGTTCATAAATATAAAC
Found at i:2088920 original size:100 final size:100
Alignment explanation
Indices: 2088712--2088931 Score: 277
Period size: 101 Copynumber: 2.2 Consensus size: 100
2088702 TGATCTTCAC
* * *
2088712 ACAAACACCAAAACTCAAACCTATCCTATTTTTTCGATCAAAACACCCAAAATTAAACCCTTGTT
1 ACAAACACTAAAAC-CAAACCTATCCTATTTTTTCGATCAAAACACCCAAAATTAAACCATTATT
* * * *
2088777 TTTCTATGTTATCCCCAACCTTATTCTTTGATCTTT
65 TATCTATGTTATCCCCAACCTTATTCTTTAACCCTT
* *
2088813 ACAAACACTAAAACCAAACTCTATCCTATTTTTTCGATC-AAACACCCCAAATTCAACCATTATT
1 ACAAACACTAAAACCAAAC-CTATCCTATTTTTTCGATCAAAACACCCAAAATTAAACCATTATT
2088877 TAT-TAGTGTTCATCCCCAAACC-T-TTCTTTAACCCTT
65 TATCTA-TGTT-ATCCCC-AACCTTATTCTTTAACCCTT
2088913 ACAAACACCTAAAACCAAA
1 ACAAACA-CTAAAACCAAA
2088932 ACCCAACCCA
Statistics
Matches: 105, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
99 2 0.02
100 49 0.47
101 50 0.48
102 4 0.04
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (100 bp):
ACAAACACTAAAACCAAACCTATCCTATTTTTTCGATCAAAACACCCAAAATTAAACCATTATTT
ATCTATGTTATCCCCAACCTTATTCTTTAACCCTT
Found at i:2088975 original size:106 final size:106
Alignment explanation
Indices: 2088837--2089043 Score: 251
Period size: 106 Copynumber: 2.0 Consensus size: 106
2088827 CAAACTCTAT
* * * * * *
2088837 CCTATTTTTTCGATCAAACACCCCAAATTCAAC-CATTATTTAT-TAGTGTTCATCCCCAAACCT
1 CCTATTTTTTCAATCAAACACCCCAAACTCAACAC-TTATTCATCCA-TATTCATCCCCAAACCC
*
2088900 TTCTTTAACCCTTACAAACACCTAAAACCAAAACCCAACCCAA
64 TTCTTTAACCCTTACAAACACCCAAAACCAAAACCCAACCCAA
2088943 CCTATTTTTTCAATC-AA-ACCCCAAACCCTCAACACTTATTCATCCATATTCATCCCCAAACCC
1 CCTATTTTTTCAATCAAACACCCCAAA--CTCAACACTTATTCATCCATATTCATCCCCAAACCC
* * * *
2089006 TTGTTTGATCCTTACAAACACCCAAAAGCAAAACCCAA
64 TTCTTTAACCCTTACAAACACCCAAAACCAAAACCCAA
2089044 ACTATTTTTA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
104 8 0.09
105 2 0.02
106 74 0.86
107 2 0.02
ACGTcount: A:0.36, C:0.34, G:0.03, T:0.27
Consensus pattern (106 bp):
CCTATTTTTTCAATCAAACACCCCAAACTCAACACTTATTCATCCATATTCATCCCCAAACCCTT
CTTTAACCCTTACAAACACCCAAAACCAAAACCCAACCCAA
Found at i:2089202 original size:52 final size:52
Alignment explanation
Indices: 2089086--2089257 Score: 168
Period size: 52 Copynumber: 3.2 Consensus size: 52
2089076 TTCTAACTTT
* * *
2089086 TTCTCTAACCTTAAACCCTAACCAAA-CATTTTTTTATTCTTTT-TATCTGTTCATC
1 TTCTCTAACCTTAAACCCTAA-CAAAGC--CTATTTA-TCTTTTGT-TTTGTTCATC
* * *
2089141 TTCTTTAACCTTAAACCCTAACTAAGCCTATTTATCTTTTGTTTTGTTCATA
1 TTCTCTAACCTTAAACCCTAACAAAGCCTATTTATCTTTTGTTTTGTTCATC
* ** * *
2089193 TTCTCTAACCCTAAATTCTAACCAAAGCCTATTCATCTTTTGTTTCTATTCATC
1 TTCTCTAACCTTAAACCCTAA-CAAAGCCTATTTATCTTTTGTTT-TGTTCATC
2089247 TTCTCTAACCT
1 TTCTCTAACCT
2089258 AATCGATAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
52 31 0.32
53 27 0.28
54 19 0.19
55 21 0.21
ACGTcount: A:0.25, C:0.26, G:0.03, T:0.46
Consensus pattern (52 bp):
TTCTCTAACCTTAAACCCTAACAAAGCCTATTTATCTTTTGTTTTGTTCATC
Found at i:2089259 original size:53 final size:51
Alignment explanation
Indices: 2089135--2089259 Score: 151
Period size: 53 Copynumber: 2.4 Consensus size: 51
2089125 TTTTTATCTG
* * * *
2089135 TTCATCTTCTTTAACCTTAAACCCTAACTAAGCCTATTTATCTTTTGTTTTG
1 TTCATCTTCTCTAACC-TAAACCCTAACAAAGCCTATTCATCTTTTGTTTTA
* **
2089187 TTCATATTCTCTAACCCTAAATTCTAACCAAAGCCTATTCATCTTTTGTTTCTA
1 TTCATCTTCTCTAA-CCTAAACCCTAA-CAAAGCCTATTCATCTTTTGTTT-TA
2089241 TTCATCTTCTCTAACCTAA
1 TTCATCTTCTCTAACCTAA
2089260 TCGATAATTC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
52 20 0.32
53 28 0.45
54 14 0.23
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.45
Consensus pattern (51 bp):
TTCATCTTCTCTAACCTAAACCCTAACAAAGCCTATTCATCTTTTGTTTTA
Found at i:2092599 original size:30 final size:31
Alignment explanation
Indices: 2092558--2092615 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
2092548 GTAACTTTTG
2092558 TTTATTTATGTTTATTAAATTAAATTTTATA
1 TTTATTTATGTTTATTAAATTAAATTTTATA
*
2092589 TTTA-TTATGTTTATTAAATTAATTTTT
1 TTTATTTATGTTTATTAAATTAAATTTT
2092616 CGATAAGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTATTTATGTTTATTAAATTAAATTTTATA
Found at i:2093653 original size:16 final size:16
Alignment explanation
Indices: 2093617--2093672 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
2093607 TTTCATCAAT
*
2093617 GGTAATATAT-AATTCA
1 GGTAA-ATATCAAATCA
2093633 GGTAAATATCAAATCA
1 GGTAAATATCAAATCA
* *
2093649 TGTAAATATCATATCA
1 GGTAAATATCAAATCA
2093665 GGTAAATA
1 GGTAAATA
2093673 ACAAGTCGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
GGTAAATATCAAATCA
Found at i:2094242 original size:27 final size:27
Alignment explanation
Indices: 2094204--2094287 Score: 159
Period size: 27 Copynumber: 3.1 Consensus size: 27
2094194 GTGGTGGCCG
*
2094204 GGTAAAACGGAGTGTTTTGAGCTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
2094231 GGTAAAACGGAGTGTTTTGAGGTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
2094258 GGTAAAACGGAGTGTTTTGAGGTAGCT
1 GGTAAAACGGAGTGTTTTGAGGTAGCT
2094285 GGT
1 GGT
2094288 TGAGCGAAGA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.25, C:0.08, G:0.37, T:0.30
Consensus pattern (27 bp):
GGTAAAACGGAGTGTTTTGAGGTAGCT
Found at i:2103918 original size:19 final size:20
Alignment explanation
Indices: 2103894--2103952 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 20
2103884 TTTGGTGCAG
*
2103894 AGGGAATCGA-TCCCCCTTC
1 AGGGAACCGATTCCCCCTTC
*
2103913 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCC-TT-C
2103935 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
2103953 CCACAGGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.26
20 6 0.18
21 2 0.06
22 1 0.03
23 16 0.47
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.19
Consensus pattern (20 bp):
AGGGAACCGATTCCCCCTTC
Found at i:2115072 original size:40 final size:40
Alignment explanation
Indices: 2114960--2115072 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 40
2114950 TTGGGTAAAC
*
2114960 AGTACCGATATTGTTCTTACAGGATCGATACCTCCTGAAT
1 AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
*
2115000 TGTACACGATATTGTTCTTACAGGATCGATACCGCCTGAAT
1 AGTAC-CGATATTGTTCTTACAGGATCGATACCGCCTGAAT
* * * *
2115041 AGTACCGATACTGTTCTTGCAGTATCAATACC
1 AGTACCGATATTGTTCTTACAGGATCGATACC
2115073 AAAGGTAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 27 0.42
41 38 0.58
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (40 bp):
AGTACCGATATTGTTCTTACAGGATCGATACCGCCTGAAT
Found at i:2117982 original size:39 final size:39
Alignment explanation
Indices: 2117923--2118024 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 39
2117913 TAGATTTTTT
* ** **
2117923 ATTCTTAA-TTCCTAAATTATTTCACTCTAGCATTATAA
1 ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
* * *
2117961 TTTCTTAATTTCTTAAATTATTTAACAATAAAATTCTAA
1 ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
*
2118000 ATTATTAATTTCTT-AATTATTTCAC
1 ATTCTTAATTTCTTAAATTATTTCAC
2118025 CCTAAAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 17 0.33
39 35 0.67
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (39 bp):
ATTCTTAATTTCTTAAATTATTTCACAATAAAATTATAA
Found at i:2118031 original size:38 final size:38
Alignment explanation
Indices: 2117927--2118043 Score: 117
Period size: 38 Copynumber: 3.1 Consensus size: 38
2117917 TTTTTTATTC
* * * ** * * *
2117927 TTAATTCCTAAATTATTTCACTCTAGCATTATAATTTC
1 TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
* *
2117965 TTAATTTCTTAAATTATTTAACAATAAAATTCTAAATTA
1 TTAATTTCTT-AATTATTTCACACTAAAATTCTAAATTA
* *
2118004 TTAATTTCTTAATTATTTCACCCTAAAAATCTAAATTA
1 TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
2118042 TT
1 TT
2118044 CCTCAAATTA
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 34 0.53
39 30 0.47
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (38 bp):
TTAATTTCTTAATTATTTCACACTAAAATTCTAAATTA
Found at i:2120307 original size:31 final size:31
Alignment explanation
Indices: 2120230--2120300 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
2120220 GTTTTAAAAA
* *
2120230 TAACAAATTAGTCATTAACATTAACGATTTG
1 TAACAAAATAGTCACTAACATTAACGATTTG
* * *
2120261 TAATAAAATAGTCACTAACGTTATCGATTTG
1 TAACAAAATAGTCACTAACATTAACGATTTG
2120292 TAACAAAAT
1 TAACAAAAT
2120301 GATCACTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
TAACAAAATAGTCACTAACATTAACGATTTG
Found at i:2120933 original size:31 final size:31
Alignment explanation
Indices: 2120898--2120956 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2120888 ATAAAGGTGA
*
2120898 AGTGACCA-TTTTGTTACAAATTGATAACTGT
1 AGTGA-CAGTTTTGTTACAAATCGATAACTGT
2120929 AGTGACAGTTTTGTTACAAATCGATAAC
1 AGTGACAGTTTTGTTACAAATCGATAAC
2120957 GTTAGTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (31 bp):
AGTGACAGTTTTGTTACAAATCGATAACTGT
Found at i:2122841 original size:92 final size:92
Alignment explanation
Indices: 2122684--2122856 Score: 285
Period size: 92 Copynumber: 1.9 Consensus size: 92
2122674 ATTTTCTTGA
2122684 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
1 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
2122749 AACTCGATTCGAGATCGTTTGCATATT
66 AACTCGATTCGAGATCGTTTGCATATT
* * * * *
2122776 GATAGATTTTTGGCGACTCCTTAGGTGTTCAAGATCTTTTGGTTATCTGTCTCC-TAAGATACAA
1 GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAA-ATACAA
2122840 CAACTCGATTCGAGATC
65 CAACTCGATTCGAGATC
2122857 ACAAACTATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
91 3 0.04
92 72 0.96
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (92 bp):
GATAGATTTTCGGAGACTCCTTACGTGTTCAAGATCTTTTGGTCACCTGTCTCCTTAAATACAAC
AACTCGATTCGAGATCGTTTGCATATT
Found at i:2123061 original size:34 final size:34
Alignment explanation
Indices: 2123016--2123080 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2123006 AGTCAAACAT
*
2123016 ATATTTTTTAATATTCAAAT-TTAAAAAGATAATA
1 ATATCTTTTAAT-TTCAAATATTAAAAAGATAATA
* *
2123050 ATATCTTTTAATTTGAAATATTCAAAAGATA
1 ATATCTTTTAATTTCAAATATTAAAAAGATA
2123081 TAAACAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 6 0.22
34 21 0.78
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (34 bp):
ATATCTTTTAATTTCAAATATTAAAAAGATAATA
Found at i:2123157 original size:64 final size:64
Alignment explanation
Indices: 2123055--2123175 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
2123045 TAATAATATC
* *
2123055 TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTATTATTTAAACTTAAATAAATATTA
1 TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTAATATTTAAAATTAAATAAATATTA
* * **
2123119 TTTTAA-TTGAAAATATTTAATAGTATATAATTAA-TTTTTAATATTTAAAATTAAATA
1 TTTTAATTTG-AAATATTCAAAAG-ATATAAACAATTTTTTAATATTTAAAATTAAATA
2123176 GATAGCAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.06
64 38 0.78
65 8 0.16
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (64 bp):
TTTTAATTTGAAATATTCAAAAGATATAAACAATTTTTTAATATTTAAAATTAAATAAATATTA
Found at i:2125125 original size:36 final size:36
Alignment explanation
Indices: 2125083--2125158 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
2125073 TTATAGCTAA
*
2125083 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2125119 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
2125155 AAAA
1 AAAA
2125159 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Done.