Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009629.1 Hibiscus syriacus cultivar Beakdansim tig00117022_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: 453070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:253959 original size:29 final size:28
Alignment explanation
Indices: 253878--253962 Score: 107
Period size: 29 Copynumber: 3.0 Consensus size: 28
253868 CTCAAAGTTT
* * *
253878 TTCAAAAGAAACGACTCAAAGATATTTA
1 TTCAAAAGGAACAACTCAAAGATTTTTA
* *
253906 TTCAAAAAGAACCAACTCCAAGATTTTTA
1 TTCAAAAGGAA-CAACTCAAAGATTTTTA
253935 TTCAAAAGGAACAAACTCAAAGATTTTT
1 TTCAAAAGGAAC-AACTCAAAGATTTTT
253963 TAAGAGAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
28 10 0.21
29 38 0.79
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.27
Consensus pattern (28 bp):
TTCAAAAGGAACAACTCAAAGATTTTTA
Found at i:253961 original size:28 final size:27
Alignment explanation
Indices: 253867--253961 Score: 97
Period size: 29 Copynumber: 3.5 Consensus size: 27
253857 AAATAAATAG
* *
253867 ACTCAAAG--TTT-TTCAAAAGAAACG
1 ACTCAAAGATTTTATTCAAAAGGAACA
*
253891 ACTCAAAGATATTTATTCAAAAAGAACCA
1 ACTCAAAGAT-TTTATTCAAAAGGAA-CA
*
253920 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTTATTCAAAAGGAAC-A
253949 ACTCAAAGATTTT
1 ACTCAAAGATTTT
253962 TTAAGAGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.14
27 3 0.05
28 14 0.24
29 32 0.55
30 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.27
Consensus pattern (27 bp):
ACTCAAAGATTTTATTCAAAAGGAACA
Found at i:254293 original size:36 final size:36
Alignment explanation
Indices: 254209--254312 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
254199 GAGAAAATGA
* * * *
254209 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
* **
254243 AGTCTCAAATGAGACAAAATTTGTTTTTAGAAAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
*
254279 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AGAAA
254313 CGATTTCAAG
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 19 0.34
35 4 0.07
36 28 0.50
37 5 0.09
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAAAAT
Found at i:254987 original size:4 final size:4
Alignment explanation
Indices: 254978--255027 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
254968 TTTATGTATC
* *
254978 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT AAGT TTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
255024 ATGT
1 ATGT
255028 GTATACTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
4 38 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:256232 original size:12 final size:11
Alignment explanation
Indices: 256204--256241 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
256194 CCTCTTTTTG
*
256204 TTCTTTGCTTT
1 TTCTTTGATTT
256215 TTCTTTGATTT
1 TTCTTTGATTT
256226 TTGCTTTGATTT
1 TT-CTTTGATTT
256238 TTCT
1 TTCT
256242 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:256245 original size:13 final size:12
Alignment explanation
Indices: 256199--256246 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
256189 TTTGTCCTCT
256199 TTTTGTTCTTTG-
1 TTTT-TTCTTTGA
*
256211 CTTTTTCTTTGA
1 TTTTTTCTTTGA
*
256223 TTTTTGCTTTGA
1 TTTTTTCTTTGA
256235 TTTTTCTCTTTG
1 TTTTT-TCTTTG
256247 CTCTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 7 0.23
12 18 0.60
13 5 0.17
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTTTCTTTGA
Found at i:256246 original size:18 final size:17
Alignment explanation
Indices: 256225--256271 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
256215 TTCTTTGATT
256225 TTTGCTTTGATTTTTCTC
1 TTTGCTTTGATTTTT-TC
256243 TTTGCTCTTTG-TTTTTTC
1 TTTG--CTTTGATTTTTTC
*
256261 TTTGGTTTGAT
1 TTTGCTTTGAT
256272 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTGCTTTGATTTTTTC
Found at i:256925 original size:20 final size:20
Alignment explanation
Indices: 256844--256918 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
256834 AAATACAGTG
*
256844 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
256863 TTTCAAGGTCACAAAGAGAGGGAATG
1 TTTCAAGGT--CGAA-A-A--GAATA
256889 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
256909 TTTCAAGGTC
1 TTTCAAGGTC
256919 TCAAAGAGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
22 2 0.05
23 2 0.05
24 4 0.09
26 13 0.30
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:256932 original size:26 final size:26
Alignment explanation
Indices: 256854--256933 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
256844 TTTCAAGGTG
*
256854 GAAAGAATATTTCAAGGTCACAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
256880 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
256901 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
256926 GATAGAAT
1 GAAAGAAT
256934 GTCAAAAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 1 0.03
25 2 0.05
26 20 0.50
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.23
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:256934 original size:46 final size:45
Alignment explanation
Indices: 256842--256935 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
256832 ATAAATACAG
* *
256842 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCACAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
* *
256887 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
256933 TGT
1 TGT
256936 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCACAAAGAGAGAGAA
Found at i:260473 original size:59 final size:59
Alignment explanation
Indices: 260406--260529 Score: 248
Period size: 59 Copynumber: 2.1 Consensus size: 59
260396 TTGAACATCA
260406 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
1 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
260465 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
1 GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
260524 GCCAAA
1 GCCAAA
260530 GTAAAATATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.54, C:0.18, G:0.09, T:0.19
Consensus pattern (59 bp):
GCCAAAACATACAACATATAAAAATCAATGACTAAAATGAAACTAATACAAACATTGTG
Found at i:262018 original size:25 final size:25
Alignment explanation
Indices: 261987--262046 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
261977 ATTTAGGGGA
261987 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
262012 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
262037 TTAGGGTTTG
1 TTAGGGTTTG
262047 TTGGGCTCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:262112 original size:3 final size:3
Alignment explanation
Indices: 262104--262143 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
262094 ATTAATAAAC
262104 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
262144 CGATAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:262129 original size:22 final size:22
Alignment explanation
Indices: 262096--262139 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
262086 AATATGTAAT
262096 TAATAAACATAATAATAATAAA
1 TAATAAACATAATAATAATAAA
262118 TAATAATA-ATAATAATAATAAA
1 TAATAA-ACATAATAATAATAAA
262140 ATAACGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAATAAACATAATAATAATAAA
Found at i:269423 original size:31 final size:31
Alignment explanation
Indices: 269383--269445 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
269373 AAAATATAAT
* * *
269383 ATTTGGTCACTTTCGTTTCATTTTAATTAAG
1 ATTTAGTCACTTTCATTTCACTTTAATTAAG
269414 ATTTAGTCACTTTCATTTCACTTTAATTAAG
1 ATTTAGTCACTTTCATTTCACTTTAATTAAG
269445 A
1 A
269446 CGTAATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTAGTCACTTTCATTTCACTTTAATTAAG
Found at i:269455 original size:31 final size:31
Alignment explanation
Indices: 269389--269455 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
269379 TAATATTTGG
* * ** *
269389 TCACTTTCGTTTCATTTTAATTAAGATTTAG
1 TCACTTTCATTTCACTTTAATTAAGACGTAA
269420 TCACTTTCATTTCACTTTAATTAAGACGTAA
1 TCACTTTCATTTCACTTTAATTAAGACGTAA
269451 TCACT
1 TCACT
269456 AAAGATTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.46
Consensus pattern (31 bp):
TCACTTTCATTTCACTTTAATTAAGACGTAA
Found at i:270781 original size:16 final size:16
Alignment explanation
Indices: 270760--270798 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
270750 AGAAATCTTT
270760 CATTATTCTTGAAATG
1 CATTATTCTTGAAATG
270776 CATTATTCTTGAAATG
1 CATTATTCTTGAAATG
270792 CATTATT
1 CATTATT
270799 AGTCTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (16 bp):
CATTATTCTTGAAATG
Found at i:270804 original size:19 final size:18
Alignment explanation
Indices: 270761--270809 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 18
270751 GAAATCTTTC
270761 ATTATTCTTGAAATGCATT
1 ATTA-TCTTGAAATGCATT
270780 A-T-TCTTGAAATGCATT
1 ATTATCTTGAAATGCATT
270796 ATTAGTCTTTGAAA
1 ATTA-TC-TTGAAA
270810 GAAGACAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 1 0.04
19 3 0.12
20 6 0.23
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (18 bp):
ATTATCTTGAAATGCATT
Found at i:271083 original size:31 final size:31
Alignment explanation
Indices: 271048--271125 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
271038 TTCAACGTCA
*
271048 AAGTGACCAAAACTTAATAAAACGATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
*
271079 AAGTGACCAAAACTTAATAAAACGATAGCAT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
271110 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
271126 TGCTTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACAT
Found at i:272389 original size:11 final size:11
Alignment explanation
Indices: 272373--272400 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
272363 GGGTCTAGCT
272373 AGATCCAATCC
1 AGATCCAATCC
272384 AGATCCAATCC
1 AGATCCAATCC
272395 AGATCC
1 AGATCC
272401 GACCCATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.18
Consensus pattern (11 bp):
AGATCCAATCC
Found at i:273122 original size:24 final size:24
Alignment explanation
Indices: 273090--273150 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
273080 TTTGGAAATT
* *
273090 GAGTCAACTTAGATCGAGTCAATC
1 GAGTCAACTCAGAACGAGTCAATC
*
273114 GAGTCAACTCAGAACGAGTCAGTC
1 GAGTCAACTCAGAACGAGTCAATC
*
273138 AAGTCAACTCAGA
1 GAGTCAACTCAGA
273151 CCTGACCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (24 bp):
GAGTCAACTCAGAACGAGTCAATC
Found at i:273243 original size:20 final size:20
Alignment explanation
Indices: 273218--273266 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
273208 GACTTTGACG
* *
273218 AAAAAATTAATTTTTTCAGA
1 AAAAAATCAACTTTTTCAGA
*
273238 AAAAAATCAACTTTTTCGGA
1 AAAAAATCAACTTTTTCAGA
273258 AAAAAATCA
1 AAAAAATCA
273267 TATTTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (20 bp):
AAAAAATCAACTTTTTCAGA
Found at i:275229 original size:30 final size:30
Alignment explanation
Indices: 275183--275248 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
275173 TTAACTTGTG
*
275183 GTGATCACATCTTAATTAAATAAAAACGAAA
1 GTGA-CACAACTTAATTAAATAAAAACGAAA
275214 GTGACACAACTTAATTAAATAAAAACGAAA
1 GTGACACAACTTAATTAAATAAAAACGAAA
275244 GTGAC
1 GTGAC
275249 CATATATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.52, C:0.14, G:0.12, T:0.23
Consensus pattern (30 bp):
GTGACACAACTTAATTAAATAAAAACGAAA
Found at i:275445 original size:60 final size:59
Alignment explanation
Indices: 275380--275545 Score: 181
Period size: 60 Copynumber: 2.8 Consensus size: 59
275370 AACCCTTATT
* *
275380 TTAAATTAGTCTTTAAACTTTTGAATATTCCAATTTTATCCCCAAACTATG-ACTCTCATC
1 TTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAACTATGAAC-CTC-TC
* * * ** * *
275440 TTAAATTAGTCCTTAAAATTTTGAGTGTTATAATTTCATCCCTAAACTATGAACCTCTT
1 TTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAACTATGAACCTCTC
* ** *
275499 TCTAAATTAATCCCCAAACTTTTGAATATTCCAATATCATCCCCAAA
1 T-TAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAA
275546 TTCATCCAAA
Statistics
Matches: 85, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
59 2 0.02
60 81 0.95
61 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
TTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCCCAAACTATGAACCTCTC
Found at i:275858 original size:60 final size:60
Alignment explanation
Indices: 275736--275858 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
275726 CATAGTTTAG
* * * * ** *
275736 GGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATTGTTTGA
1 GGATGAAATTAGAAGATTCAAAAATTTAAAGACCAATTTAAAATGAGAGTCATACTTCGA
* *
275796 GGATGAAATTGGAAGATTCAAAAATTTAAAGACCAATTTAAAATGA-AGGTTATACTTCGA
1 GGATGAAATTAGAAGATTCAAAAATTTAAAGACCAATTTAAAATGAGA-GTCATACTTCGA
275856 GGA
1 GGA
275859 CATGTGATGC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (60 bp):
GGATGAAATTAGAAGATTCAAAAATTTAAAGACCAATTTAAAATGAGAGTCATACTTCGA
Found at i:276220 original size:19 final size:19
Alignment explanation
Indices: 276168--276231 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
276158 TTATTTTCAT
* *
276168 ATTATAATAT-TATTTAAT
1 ATTATAAAATATATTTAAA
* *
276186 A-TATCAAATACAATTTAAA
1 ATTATAAAATA-TATTTAAA
276205 ATTATAAAATATATTTACAA
1 ATTATAAAATATATTTA-AA
276225 CATTATA
1 -ATTATA
276232 TTTTAAAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 12 0.34
20 10 0.29
21 6 0.17
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAAATATATTTAAA
Found at i:280502 original size:20 final size:20
Alignment explanation
Indices: 280474--280526 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
280464 GACCAACAAA
*
280474 TTCGCAACG-TAATCTCCAAT
1 TTCGCAACGCGAA-CTCCAAT
*
280494 TTTGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
280514 TTCGCAACGCGAA
1 TTCGCAACGCGAA
280527 TTTCCTAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:280638 original size:20 final size:20
Alignment explanation
Indices: 280615--280659 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
280605 GCGAATATGT
*
280615 AATTCATAACACAGAAGTCA
1 AATTCACAACACAGAAGTCA
*
280635 AATTCGCAACACAGAAGTCA
1 AATTCACAACACAGAAGTCA
280655 AATTC
1 AATTC
280660 GAAAAGCACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (20 bp):
AATTCACAACACAGAAGTCA
Found at i:280660 original size:20 final size:20
Alignment explanation
Indices: 280622--280660 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
280612 TGTAATTCAT
280622 AACACAGAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGC
280642 AACACAGAAGTCAAATTCG
1 AACACAGAAGTCAAATTCG
280661 AAAAGCACGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGC
Found at i:280859 original size:20 final size:20
Alignment explanation
Indices: 280814--280859 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
280804 GCGAACATGT
*
280814 AATTCACAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
280834 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
280854 AATTCG
1 AATTCG
280860 AAAAGCGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.13, T:0.17
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:280921 original size:199 final size:199
Alignment explanation
Indices: 280581--280974 Score: 682
Period size: 199 Copynumber: 2.0 Consensus size: 199
280571 TCTTTTCCGC
* *
280581 AACGCGATTTTCCAAATTCGCAACGCGAATATGTAATTCATAACACAGAAGTCAAATTCGCAACA
1 AACGCGATTTTCCAAATTCGCAACGCGAACATGTAATTCACAACACAGAAGTCAAATTCGCAACA
*
280646 CAGAAGTCAAATTCGAAAAGCACGTTTATTTTCACAATGCGAATTTTATTTTCGAATTCAAAACA
66 CAGAAGTCAAATTCGAAAAGCACGTTTATTTTCACAACGCGAATTTTATTTTCGAATTCAAAACA
* *
280711 CAATGTTAATTTCGCAACACAAATGTAAACAATATAATTGCAACTCATAACCTAAAACTCTAAAT
131 CAATATTAATTTCGCAACACAAATATAAACAATATAATTGCAACTCATAACCTAAAACTCTAAAT
280776 TCGT
196 TCGT
280780 AACGCGATTTTCCAAATTCGCAGA-GCGAACATGTAATTCACAACACAGAAGTCAAATTCGCAAC
1 AACGCGATTTTCCAAATTCGCA-ACGCGAACATGTAATTCACAACACAGAAGTCAAATTCGCAAC
** * * *
280844 ACAGAAGTCAAATTCGAAAAGCGTGTTTATTTTCGCAACGTGAATTTTATTTTCGAATTCGAAAC
65 ACAGAAGTCAAATTCGAAAAGCACGTTTATTTTCACAACGCGAATTTTATTTTCGAATTCAAAAC
280909 ACAATATTAATTTCGCAACACAAATATAAACAATATAATTGCAACTCATAACCTAAAACTCTAAA
130 ACAATATTAATTTCGCAACACAAATATAAACAATATAATTGCAACTCATAACCTAAAACTCTAAA
280974 T
195 T
280975 CACAACTTAG
Statistics
Matches: 184, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
199 183 0.99
200 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (199 bp):
AACGCGATTTTCCAAATTCGCAACGCGAACATGTAATTCACAACACAGAAGTCAAATTCGCAACA
CAGAAGTCAAATTCGAAAAGCACGTTTATTTTCACAACGCGAATTTTATTTTCGAATTCAAAACA
CAATATTAATTTCGCAACACAAATATAAACAATATAATTGCAACTCATAACCTAAAACTCTAAAT
TCGT
Found at i:281392 original size:20 final size:20
Alignment explanation
Indices: 281369--281423 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
281359 TTTGAAACTT
*
281369 AAATTTGCAACACGAAAATG
1 AAATTAGCAACACGAAAATG
*
281389 AAATTCGCAACACGAAAATG
1 AAATTAGCAACACGAAAATG
*
281409 AAAATAGCAACACGA
1 AAATTAGCAACACGA
281424 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAATTAGCAACACGAAAATG
Found at i:281448 original size:20 final size:20
Alignment explanation
Indices: 281423--281466 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
281413 TAGCAACACG
281423 ATTTTAGTTTCGCGTTGCAA
1 ATTTTAGTTTCGCGTTGCAA
* *
281443 ATTTTATTTTCGTGTTGCAA
1 ATTTTAGTTTCGCGTTGCAA
281463 ATTT
1 ATTT
281467 CATTTTCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.16, T:0.52
Consensus pattern (20 bp):
ATTTTAGTTTCGCGTTGCAA
Found at i:281471 original size:20 final size:20
Alignment explanation
Indices: 281430--281486 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
281420 ACGATTTTAG
* *
281430 TTTCGCGTTGCAAATTTTAT
1 TTTCGTGTTGCAAATTTCAT
281450 TTTCGTGTTGCAAATTTCAT
1 TTTCGTGTTGCAAATTTCAT
* *
281470 TTTCATGTTGCGAATTT
1 TTTCGTGTTGCAAATTT
281487 AAGTTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCAAATTTCAT
Found at i:281493 original size:20 final size:20
Alignment explanation
Indices: 281436--281494 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
281426 TTAGTTTCGC
* *
281436 GTTGCAAATTTTATTTTCGT
1 GTTGCAAATTTAATTTTCAT
*
281456 GTTGCAAATTTCATTTTCAT
1 GTTGCAAATTTAATTTTCAT
* *
281476 GTTGCGAATTTAAGTTTCA
1 GTTGCAAATTTAATTTTCA
281495 AAATCTACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (20 bp):
GTTGCAAATTTAATTTTCAT
Found at i:283190 original size:21 final size:21
Alignment explanation
Indices: 283142--283191 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
283132 GTTAGGGGAG
* *
283142 TTACGTGATGAGGTTAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * *
283163 TTGCGTGATGAGGTCGGTATT
1 TTACGTGATGAGGTCAGTACT
283184 TTACGTGA
1 TTACGTGA
283192 CGACAATGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.10, G:0.34, T:0.38
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:283232 original size:21 final size:22
Alignment explanation
Indices: 283208--283303 Score: 76
Period size: 21 Copynumber: 4.5 Consensus size: 22
283198 TGGTGGATGG
283208 CGTGATGAGGTACGGT-CTTTA
1 CGTGATGAGGTACGGTACTTTA
* * *
283229 CGTGGTGAGGTA-GCTATTTTA
1 CGTGATGAGGTACGGTACTTTA
* * * *
283250 CGCGATGACG-ATGGTGCTTTA
1 CGTGATGAGGTACGGTACTTTA
*
283271 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
283292 CGTGATGAGGTA
1 CGTGATGAGGTA
283304 GCCGCTCTAC
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 3 0.05
21 52 0.93
22 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.33, T:0.33
Consensus pattern (22 bp):
CGTGATGAGGTACGGTACTTTA
Found at i:283247 original size:63 final size:63
Alignment explanation
Indices: 283145--283305 Score: 148
Period size: 63 Copynumber: 2.6 Consensus size: 63
283135 AGGGGAGTTA
* * * *
283145 CGTGATGAGGTTAGTGCTTTGCGTGATGAGGTCGGTATTTTACGTGACGACAATGGTGGATGG
1 CGTGATGAGGTTAGTGCTTTACGTGATGAGGTAGCTATTTTACGCGACGACAATGGTGGATGG
* * * ** **
283208 CGTGATGAGG-TACG-GTCTTTACGTGGTGAGGTAGCTATTTTACGCGATGACGATGGTGCTTTA
1 CGTGATGAGGTTA-GTG-CTTTACGTGATGAGGTAGCTATTTTACGCGACGACAATGGTGGATGG
* * *
283271 CGTGGTGAGG-TATCTACTTTACGTGATGAGGTAGC
1 CGTGATGAGGTTA-GTGCTTTACGTGATGAGGTAGC
283306 CGCTCTACGT
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
62 3 0.04
63 76 0.96
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.32
Consensus pattern (63 bp):
CGTGATGAGGTTAGTGCTTTACGTGATGAGGTAGCTATTTTACGCGACGACAATGGTGGATGG
Found at i:283257 original size:42 final size:43
Alignment explanation
Indices: 283211--283303 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 43
283201 TGGATGGCGT
*
283211 GATGAGGTACGGT-CTTTACGTGGTGAGGTAGCTATTTTACGC
1 GATGAGGTACGGTGCTTTACGTGGTGAGGTAGCTACTTTACGC
* * * *
283253 GATGACG-ATGGTGCTTTACGTGGTGAGGTATCTACTTTACGT
1 GATGAGGTACGGTGCTTTACGTGGTGAGGTAGCTACTTTACGC
283295 GATGAGGTA
1 GATGAGGTA
283304 GCCGCTCTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
41 4 0.09
42 38 0.88
43 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.33, T:0.33
Consensus pattern (43 bp):
GATGAGGTACGGTGCTTTACGTGGTGAGGTAGCTACTTTACGC
Found at i:283315 original size:42 final size:42
Alignment explanation
Indices: 283208--283316 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
283198 TGGTGGATGG
* *
283208 CGTGATGAGGTA-CGGTCTTTACGTGGTGAGGTAGCTATTTTA
1 CGTGATGAGGTAGCCG-CTTTACGTGGTGAGGTAGCTACTTTA
* * ** *
283250 CGCGATGACG-ATGGTGCTTTACGTGGTGAGGTATCTACTTTA
1 CGTGATGAGGTA-GCCGCTTTACGTGGTGAGGTAGCTACTTTA
*
283292 CGTGATGAGGTAGCCGCTCTACGTG
1 CGTGATGAGGTAGCCGCTTTACGTG
283317 AGATTGTTTC
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
41 1 0.02
42 50 0.94
43 2 0.04
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.32
Consensus pattern (42 bp):
CGTGATGAGGTAGCCGCTTTACGTGGTGAGGTAGCTACTTTA
Found at i:283631 original size:21 final size:21
Alignment explanation
Indices: 283605--283652 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
283595 CATGTCATCA
* *
283605 TTCAAGAGGCCCCTCCTATCG
1 TTCAAGAGGCCCCTCCCACCG
*
283626 TTCAAGAGGCCCTTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
283647 TTCAAG
1 TTCAAG
283653 TGCCCGATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:285163 original size:20 final size:20
Alignment explanation
Indices: 285138--285190 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
285128 AAGGTACACT
285138 TTCGCAACACGAAAATCAAA
1 TTCGCAACACGAAAATCAAA
** *
285158 TTCGCAATGCGAAAGTCAAA
1 TTCGCAACACGAAAATCAAA
*
285178 TTTGCAACACGAA
1 TTCGCAACACGAA
285191 TTTTACTTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
TTCGCAACACGAAAATCAAA
Found at i:287972 original size:12 final size:12
Alignment explanation
Indices: 287951--287984 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
287941 TGTTGTGGGT
*
287951 TTTGAGATTGTG
1 TTTGATATTGTG
287963 TTTGATATTGTG
1 TTTGATATTGTG
*
287975 TTTGGTATTG
1 TTTGATATTG
287985 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:288804 original size:20 final size:20
Alignment explanation
Indices: 288781--288929 Score: 56
Period size: 20 Copynumber: 7.5 Consensus size: 20
288771 AAAATTTGTA
288781 TTGCGAATTCGAAAATCGAG
1 TTGCGAATTCGAAAATCGAG
** *
288801 TTGCGAAAAC-AAAATTCGTG
1 TTGCGAATTCGAAAA-TCGAG
* **
288821 TTGCGATTTAC-AAAATCTTG
1 TTGCGAATT-CGAAAATCGAG
*** * * *
288841 TTGCGAAAAGGAAACTTGTG
1 TTGCGAATTCGAAAATCGAG
*** * *
288861 TTGCGAAAAAGAAATTCGCG
1 TTGCGAATTCGAAAATCGAG
288881 TTGCGAATTC-AGAAATCGAG
1 TTGCGAATTCGA-AAATCGAG
*
288901 TTGCG-ATTGCAGAAACT-GAG
1 TTGCGAATT-C-GAAAATCGAG
288921 TTGCGAATT
1 TTGCGAATT
288930 TGGAAACTGT
Statistics
Matches: 97, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
19 8 0.08
20 77 0.79
21 11 0.11
22 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (20 bp):
TTGCGAATTCGAAAATCGAG
Found at i:288806 original size:40 final size:40
Alignment explanation
Indices: 288760--288849 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
288750 AATAAAAGCT
** *
288760 GTTGCGAAATTAAAATTTGTATTGCGAATT-CGAAAATCGA
1 GTTGCGAAAACAAAATTCGTATTGCGAATTAC-AAAATCGA
* * **
288800 GTTGCGAAAACAAAATTCGTGTTGCGATTTACAAAATCTT
1 GTTGCGAAAACAAAATTCGTATTGCGAATTACAAAATCGA
288840 GTTGCGAAAA
1 GTTGCGAAAA
288850 GGAAACTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 41 0.98
41 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTATTGCGAATTACAAAATCGA
Found at i:288935 original size:20 final size:20
Alignment explanation
Indices: 288912--288951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
288902 TGCGATTGCA
288912 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAATTTG
* *
288932 GAAACTGTGTTGTGAATTTG
1 GAAACTGAGTTGCGAATTTG
288952 TTGGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (20 bp):
GAAACTGAGTTGCGAATTTG
Found at i:290904 original size:31 final size:31
Alignment explanation
Indices: 290866--291021 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
290856 CCCGAAGGAC
* *
290866 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
290897 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
290928 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
290959 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
290990 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
291021 C
1 C
291022 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:291875 original size:21 final size:21
Alignment explanation
Indices: 291845--291889 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
291835 ATTCTGTCGT
* *
291845 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
291866 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
291887 TTG
1 TTG
291890 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:294772 original size:31 final size:31
Alignment explanation
Indices: 294734--294889 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
294724 CCCGAAGGAC
* *
294734 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
294765 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
294796 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
294827 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
294858 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
294889 C
1 C
294890 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:295094 original size:23 final size:24
Alignment explanation
Indices: 295068--295114 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
295058 ATATACTTGT
*
295068 TTTCACATATATA-TTTCATATCA
1 TTTCACATATAAACTTTCATATCA
295091 TTTCACATATAAACTTTCATATCA
1 TTTCACATATAAACTTTCATATCA
295115 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATAAACTTTCATATCA
Found at i:295747 original size:21 final size:21
Alignment explanation
Indices: 295717--295761 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
295707 ATTCTGTCGT
* *
295717 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
295738 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
295759 TTG
1 TTG
295762 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:296747 original size:69 final size:69
Alignment explanation
Indices: 296626--296763 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
296616 TGCCTCTCTA
* *
296626 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATTAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
296691 TCAT
66 TCAT
* * * *
296695 TTGATGCTCTATGATCTTTGAGTGAAGTGGTTCAGTGATTCAGAAATTATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
296760 TCAT
66 TCAT
296764 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:296866 original size:20 final size:19
Alignment explanation
Indices: 296837--296887 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
296827 TTTCTTCAAC
296837 TTTCCTTTTTTTTATTTTCTA
1 TTTCC-TTTTTTTATTTT-TA
* *
296858 TTTCCTTTTTTTCTTTTTT
1 TTTCCTTTTTTTATTTTTA
296877 TTTCTCTTTTT
1 TTTC-CTTTTT
296888 GTTCTGATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 5 0.19
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCCTTTTTTTATTTTTA
Found at i:296875 original size:21 final size:20
Alignment explanation
Indices: 296837--296892 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
296827 TTTCTTCAAC
296837 TTTCCTTTTTTT-TATTTTCT
1 TTTCCTTTTTTTCTATTTT-T
296857 ATTTCCTTTTTTTCT-TTTTT
1 -TTTCCTTTTTTTCTATTTTT
296877 TTTCTCTTTTTGTTCT
1 TTTC-CTTTTT-TTCT
296893 GATTGAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.12
20 7 0.22
21 20 0.62
22 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTCCTTTTTTTCTATTTTT
Found at i:300056 original size:9 final size:9
Alignment explanation
Indices: 300037--300108 Score: 56
Period size: 9 Copynumber: 7.7 Consensus size: 9
300027 AACGAAAAGA
300037 AAAATAAAT
1 AAAATAAAT
300046 -AAATAAAAT
1 AAAAT-AAAT
*
300055 AAAATACATAA
1 AAAATA-A-AT
300066 AAAATAAAT
1 AAAATAAAT
**
300075 AAAATTCAT
1 AAAATAAAT
*
300084 AAAAGCAAAT
1 AAAA-TAAAT
*
300094 GAAATAAAT
1 AAAATAAAT
300103 AAAATA
1 AAAATA
300109 CTAGAAAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
8 4 0.08
9 26 0.54
10 11 0.23
11 7 0.15
ACGTcount: A:0.72, C:0.04, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:300076 original size:20 final size:21
Alignment explanation
Indices: 300040--300087 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
300030 GAAAAGAAAA
300040 ATAAATAAATAAAATAAAATAC
1 ATAAA-AAATAAAATAAAATAC
*
300062 ATAAAAAAT-AAATAAAATTC
1 ATAAAAAATAAAATAAAATAC
300082 ATAAAA
1 ATAAAA
300088 GCAAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 16 0.64
21 4 0.16
22 5 0.20
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAAAAATAAAATAAAATAC
Found at i:300093 original size:19 final size:20
Alignment explanation
Indices: 300051--300106 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
300041 TAAATAAATA
*
300051 AAATAAAATACATAAAAAAT
1 AAATAAAATACATAAAAAAC
* *
300071 AAATAAAATTCAT-AAAAGC
1 AAATAAAATACATAAAAAAC
* *
300090 AAATGAAATAAATAAAA
1 AAATAAAATACATAAAA
300107 TACTAGAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.20
Consensus pattern (20 bp):
AAATAAAATACATAAAAAAC
Found at i:300400 original size:23 final size:22
Alignment explanation
Indices: 300341--300406 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
300331 GTGTGTAATC
*
300341 TAAAAAATATATATAC-T-AAAG
1 TAAAAAAAATAT-TACATAAAAG
*
300362 TAAAAAAGAA-AATACATAAAATG
1 TAAAAAA-AATATTACATAAAA-G
300385 TAAAAAAAATATTACATGAAAA
1 TAAAAAAAATATTACAT-AAAA
300407 AAAAGAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 3 0.08
21 9 0.25
22 6 0.17
23 14 0.39
24 4 0.11
ACGTcount: A:0.67, C:0.05, G:0.06, T:0.23
Consensus pattern (22 bp):
TAAAAAAAATATTACATAAAAG
Found at i:301118 original size:42 final size:42
Alignment explanation
Indices: 301059--301155 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
301049 CCCCACTTTG
* * * * *
301059 AGAGCCATCACCTGATCGAGTCGATTCTACAGCTAGACACCC
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
* *
301101 AGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAACT
1 AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
301143 AGAGCCATCACCT
1 AGAGCCATCACCT
301156 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGAGCCGATTATACACCTACACAACC
Found at i:301319 original size:21 final size:21
Alignment explanation
Indices: 301270--301319 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
301260 GTTAGGGGAG
*
301270 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
** *
301291 TTGTGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
301312 TTACGTGA
1 TTACGTGA
301320 CAACAATGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:301442 original size:21 final size:21
Alignment explanation
Indices: 301397--301445 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
301387 AATGGTGCTT
* * *
301397 TACGTGGTGAGGTATCCACTT
1 TACGTGATGAGGTAGCCACTC
*
301418 TACGTGATGAGGTAGCCGCTC
1 TACGTGATGAGGTAGCCACTC
301439 TACGTGA
1 TACGTGA
301446 GATTGTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (21 bp):
TACGTGATGAGGTAGCCACTC
Found at i:301748 original size:21 final size:21
Alignment explanation
Indices: 301720--301817 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
301710 GATTCACCTT
301720 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
301741 -CTATCGTTCAAGAGGCCTCTC
1 TC-ATCGTTCAAGAGGCCCCTC
301762 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
301783 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
301804 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
301818 CCCGATTCAC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
20 1 0.01
21 69 0.97
22 1 0.01
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:304611 original size:24 final size:24
Alignment explanation
Indices: 304577--304630 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
304567 CTGAAACATC
* *
304577 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* *
304601 ATCAAAGTCCGGGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
304625 ATCAAA
1 ATCAAA
304631 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:305569 original size:20 final size:20
Alignment explanation
Indices: 305544--305634 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
305534 CAAAACATTT
305544 GTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
305564 GTGTTGCG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
* **
305584 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAATTC
* *
305604 GTGTTGCG-ATTTAGAAAATC
1 GTGTTGCGAAATTA-AAATTC
*
305624 TTGTTGCGAAA
1 GTGTTGCGAAA
305635 AGGAAACTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
19 10 0.18
20 38 0.69
21 7 0.13
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:305601 original size:40 final size:40
Alignment explanation
Indices: 305546--305713 Score: 137
Period size: 40 Copynumber: 4.2 Consensus size: 40
305536 AAACATTTGT
** *
305546 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* **
305586 GTTGCGAAAACAAAATTCGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
* * ** * *
305626 GTTGCGAAAAGGAAACTT-GTGTTGCGAAAAAGAAAGTCGC
1 GTTGCGAAAA-CAAAATTCGTGTTGCGAATTAGAAAATCGA
** *
305666 GTTGCGAATTCAGAAA-TCGCGTTGCG-ATT-GCAGAAATCGA
1 GTTGCGAAAACA-AAATTCGTGTTGCGAATTAG-A-AAATCGA
305706 GTTGCGAA
1 GTTGCGAA
305714 TTTAGAAACT
Statistics
Matches: 100, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 90 0.90
41 5 0.05
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (40 bp):
GTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:305640 original size:20 final size:20
Alignment explanation
Indices: 305542--305660 Score: 73
Period size: 20 Copynumber: 6.0 Consensus size: 20
305532 CCCAAAACAT
**
305542 TTGTGTTGCG-AAATTAAAA
1 TTGTGTTGCGAAAAAGAAAA
***
305561 TTCGTGTTGCGAATTCGAAAA
1 TT-GTGTTGCGAAAAAGAAAA
* * *
305582 TCGAGTTGCG-AAAACAAAA
1 TTGTGTTGCGAAAAAGAAAA
***
305601 TTCGTGTTGCGATTTAGAAAA
1 TT-GTGTTGCGAAAAAGAAAA
* *
305622 TCT-TGTTGCGAAAAGGAAAC
1 T-TGTGTTGCGAAAAAGAAAA
305642 TTGTGTTGCGAAAAAGAAA
1 TTGTGTTGCGAAAAAGAAA
305661 GTCGCGTTGC
Statistics
Matches: 72, Mismatches: 22, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
19 9 0.12
20 50 0.69
21 12 0.17
22 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (20 bp):
TTGTGTTGCGAAAAAGAAAA
Found at i:305669 original size:20 final size:19
Alignment explanation
Indices: 305626--305692 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
305616 AGAAAATCTT
* * *
305626 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAAAGAAA-TCGC
305646 GTTGCGAAAAAGAAAGTCGC
1 GTTGCGAAAAAGAAA-TCGC
**
305666 GTTGCGAATTCAGAAATCGC
1 GTTGCGAA-AAAGAAATCGC
305686 GTTGCGA
1 GTTGCGA
305693 TTGCAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 35 0.88
21 5 0.12
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (19 bp):
GTTGCGAAAAAGAAATCGC
Found at i:305699 original size:20 final size:19
Alignment explanation
Indices: 305656--305751 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 19
305646 GTTGCGAAAA
305656 AGAAAGTCGCGTTGCGAATTC
1 AGAAA-TCGCGTTGCG-ATTC
305677 AGAAATCGCGTTGCGATTGC
1 AGAAATCGCGTTGCGATT-C
* *
305697 AGAAATCGAGTTGCGAATTT
1 AGAAATCGCGTTGCG-ATTC
*
305717 AGAAA-CTGTGTTGCGAATT-
1 AGAAATC-GCGTTGCG-ATTC
* *
305736 TGAGATCGCGTTGCGA
1 AGAAATCGCGTTGCGA
305752 ATTTGTTGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 14 0.22
20 42 0.65
21 8 0.12
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (19 bp):
AGAAATCGCGTTGCGATTC
Found at i:313414 original size:66 final size:66
Alignment explanation
Indices: 313323--313463 Score: 187
Period size: 66 Copynumber: 2.1 Consensus size: 66
313313 ACACTAGGGC
* * * *
313323 AGATGTGGAACATATTGATGAAAAGAATTCC-AGCTCGTTATCT-TCCTCTGCTGTTGAGACTAA
1 AGATGTAGAACATATCGATGAAAAGAATTCCGA-CGCATTATCTGT-CTCTGCTGTTGAGACTAA
313386 CAG
64 CAG
* * *
313389 AGATGTAGATCATATCGGTGAAAAGAATTCCGACGCATTATCTGTCTCTGCTGTTGAGAGTAACA
1 AGATGTAGAACATATCGATGAAAAGAATTCCGACGCATTATCTGTCTCTGCTGTTGAGACTAACA
313454 G
66 G
313455 AGATGTAGA
1 AGATGTAGA
313464 GCATGCTGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 64 0.97
67 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (66 bp):
AGATGTAGAACATATCGATGAAAAGAATTCCGACGCATTATCTGTCTCTGCTGTTGAGACTAACA
G
Found at i:321975 original size:32 final size:32
Alignment explanation
Indices: 321934--322030 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
321924 GAGTCGAGGG
321934 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
321966 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
321997 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
322029 TT
1 TT
322031 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:322006 original size:31 final size:31
Alignment explanation
Indices: 321933--322033 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
321923 AGAGTCGAGG
321933 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
321964 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
321996 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
322027 GTTTACC
1 GTTTACC
322034 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:322065 original size:30 final size:30
Alignment explanation
Indices: 322021--322114 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
322011 AAGGAACATA
322021 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
322052 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
322082 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
322111 TGGA
1 TGGA
322115 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:324233 original size:25 final size:25
Alignment explanation
Indices: 324205--324266 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
324195 GTTTGAAACT
* *
324205 ACCTCTCGAGTATAATGGGTCCGTC
1 ACCTCTCGAGTACAACGGGTCCGTC
* *
324230 ACCTTCTCGGGTACAACGGGTCGGTC
1 ACC-TCTCGAGTACAACGGGTCCGTC
324256 ACCTCATCGAG
1 ACCTC-TCGAG
324267 CGACCTGATG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.19, C:0.31, G:0.26, T:0.24
Consensus pattern (25 bp):
ACCTCTCGAGTACAACGGGTCCGTC
Found at i:328830 original size:26 final size:27
Alignment explanation
Indices: 328780--328830 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
328770 AAATTTTCAA
* *
328780 ATTAAAATAATATAAAGATTCAATTCC
1 ATTAAAATAATAAAAAGATTAAATTCC
328807 ATTAAAATAA-AAAAAGATTAAATT
1 ATTAAAATAATAAAAAGATTAAATT
328831 TTCAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (27 bp):
ATTAAAATAATAAAAAGATTAAATTCC
Found at i:348044 original size:18 final size:19
Alignment explanation
Indices: 347999--348045 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
347989 ATAATGTTAT
347999 ATTTAAAAAACACACAAAA
1 ATTTAAAAAACACACAAAA
348018 ATTTCAAAATAAC-C-CAAAA
1 ATTT-AAAA-AACACACAAAA
*
348037 CTTTAAAAA
1 ATTTAAAAA
348046 CTTTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 4 0.16
19 12 0.48
20 5 0.20
21 3 0.12
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (19 bp):
ATTTAAAAAACACACAAAA
Found at i:352298 original size:27 final size:27
Alignment explanation
Indices: 352260--352319 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
352250 AATAAGGACG
352260 GGCAGCAACGTAAAGGAGAAAGCTCAT
1 GGCAGCAACGTAAAGGAGAAAGCTCAT
*
352287 GGCAGCAACGTAAAGGAGAAAGCTTAT
1 GGCAGCAACGTAAAGGAGAAAGCTCAT
352314 GGCAGC
1 GGCAGC
352320 GCAAACTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (27 bp):
GGCAGCAACGTAAAGGAGAAAGCTCAT
Found at i:352479 original size:24 final size:24
Alignment explanation
Indices: 352447--352529 Score: 166
Period size: 24 Copynumber: 3.5 Consensus size: 24
352437 AAAAGGCGCA
352447 CCTAGGCGCAAAAGGTCCCTGGAG
1 CCTAGGCGCAAAAGGTCCCTGGAG
352471 CCTAGGCGCAAAAGGTCCCTGGAG
1 CCTAGGCGCAAAAGGTCCCTGGAG
352495 CCTAGGCGCAAAAGGTCCCTGGAG
1 CCTAGGCGCAAAAGGTCCCTGGAG
352519 CCTAGGCGCAA
1 CCTAGGCGCAA
352530 GGCGCACTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (24 bp):
CCTAGGCGCAAAAGGTCCCTGGAG
Found at i:353381 original size:10 final size:10
Alignment explanation
Indices: 353366--353394 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
353356 GCCATCTTCA
353366 GTGCCTGGCT
1 GTGCCTGGCT
353376 GTGCCTGGCT
1 GTGCCTGGCT
353386 GTGCCTGGC
1 GTGCCTGGC
353395 GCGCCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (10 bp):
GTGCCTGGCT
Found at i:356352 original size:12 final size:12
Alignment explanation
Indices: 356335--356362 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
356325 CAAGTAATTG
356335 TTGTTATAACTC
1 TTGTTATAACTC
356347 TTGTTATAACTC
1 TTGTTATAACTC
356359 TTGT
1 TTGT
356363 AACTGACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (12 bp):
TTGTTATAACTC
Found at i:357444 original size:27 final size:27
Alignment explanation
Indices: 357414--357467 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
357404 AAAAGAATCA
357414 GTTGATTTGGGACTGAATTAAAATTAC
1 GTTGATTTGGGACTGAATTAAAATTAC
*
357441 GTTGATTTGGGACTGAATTACAATTAC
1 GTTGATTTGGGACTGAATTAAAATTAC
357468 ACTGCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.37
Consensus pattern (27 bp):
GTTGATTTGGGACTGAATTAAAATTAC
Found at i:359358 original size:60 final size:60
Alignment explanation
Indices: 359285--359412 Score: 247
Period size: 60 Copynumber: 2.1 Consensus size: 60
359275 CACCAAACAT
359285 ATCCATTTATCAAGGTATTCCTGAAAACTCAAGGGTGGAGAAAGAACCACATACCAGGTG
1 ATCCATTTATCAAGGTATTCCTGAAAACTCAAGGGTGGAGAAAGAACCACATACCAGGTG
*
359345 ATCCATTTATCAAGGTATTCCTGAAAACTCAATGGTGGAGAAAGAACCACATACCAGGTG
1 ATCCATTTATCAAGGTATTCCTGAAAACTCAAGGGTGGAGAAAGAACCACATACCAGGTG
359405 ATCCATTT
1 ATCCATTT
359413 TTGGATGGAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (60 bp):
ATCCATTTATCAAGGTATTCCTGAAAACTCAAGGGTGGAGAAAGAACCACATACCAGGTG
Found at i:364587 original size:57 final size:59
Alignment explanation
Indices: 364511--364630 Score: 217
Period size: 58 Copynumber: 2.1 Consensus size: 59
364501 TATTTTAATT
364511 AAAATGCTGGCGTAAATTTTCCTTCTTTATGTTTAGTTG-AAAAGGGTTTTATTAAGAG
1 AAAATGCTGGCGTAAATTTTCCTTCTTTATGTTTAGTTGAAAAAGGGTTTTATTAAGAG
*
364569 AAAATGCT-GCGTAGATTTTCCTTCTTTATGTTTAGTTGAAAAAGGGTTTTATTAAGAG
1 AAAATGCTGGCGTAAATTTTCCTTCTTTATGTTTAGTTGAAAAAGGGTTTTATTAAGAG
364627 AAAA
1 AAAA
364631 GAAATCCAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 29 0.48
58 31 0.52
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (59 bp):
AAAATGCTGGCGTAAATTTTCCTTCTTTATGTTTAGTTGAAAAAGGGTTTTATTAAGAG
Found at i:366969 original size:2 final size:2
Alignment explanation
Indices: 366962--366993 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
366952 GAAAGGTCGT
366962 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
366994 ATGAGAGATT
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:368143 original size:142 final size:139
Alignment explanation
Indices: 367882--368163 Score: 451
Period size: 142 Copynumber: 2.0 Consensus size: 139
367872 CTATTGTTAT
*
367882 TCTTGAGGACCCGGTTCGAGCACCATAAATGCTAGGGATGTGAGCGTTCAATATTGAAAGGTTGA
1 TCTTGAGGACCCGGTTCGAGCACCATAAATGCTAGGGATGTGAGCGTTCAATATTAAAAGGTTGA
*
367947 GAGTTATCTTCGAACATATACTACCTTATACTTACCCCAGATTATTCCAAAAAAAAAGAGTTCAA
66 GAGTTATCTTCGAACATATACTACCTTATACTTACCCCAAATTATT--AAAAAAAAAGAGTTCAA
368012 GAATAGTTGAC
129 GAATAGTTGAC
* *
368023 TCTTGAGGACCCGAGTTCGAGCACCATAGATGAC-AGGGGTGTGAGCGTTCAATATTAAAAGGTT
1 TCTTGAGGACCCG-GTTCGAGCACCATAAATG-CTAGGGATGTGAGCGTTCAATATTAAAAGGTT
* *
368087 GAGAGTTATCTTCTAACGA-ATACTACCTTGTACTTACCCCAAATTATTAAAAAAAAAGAGTTCA
64 GAGAGTTATCTTCGAAC-ATATACTACCTTATACTTACCCCAAATTATTAAAAAAAAAGAGTTCA
368151 AGAATAGTTGAC
128 AGAATAGTTGAC
368163 T
1 T
368164 ATAACTTCAT
Statistics
Matches: 132, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
140 29 0.22
141 13 0.10
142 88 0.67
143 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (139 bp):
TCTTGAGGACCCGGTTCGAGCACCATAAATGCTAGGGATGTGAGCGTTCAATATTAAAAGGTTGA
GAGTTATCTTCGAACATATACTACCTTATACTTACCCCAAATTATTAAAAAAAAAGAGTTCAAGA
ATAGTTGAC
Found at i:369931 original size:2 final size:2
Alignment explanation
Indices: 369924--370004 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
369914 TAATTAACTT
369924 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
369966 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
370005 GTACACACAC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:372727 original size:2 final size:2
Alignment explanation
Indices: 372720--372750 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
372710 GTACAATGAG
372720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
372751 ACGTATAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:374458 original size:214 final size:213
Alignment explanation
Indices: 373790--375058 Score: 1370
Period size: 214 Copynumber: 6.0 Consensus size: 213
373780 ACGGAGAGTG
*
373790 CAAGGTTCATAAAAAG-AGTTC-ATGGATAACCAC-AAACTCCTAAATCCTCCCTAGCCAAATAA
1 CAAGGTTCATAAAAAGCA-TTCGA-GGATAATCACAAAAC-CCTAAATCCTCCCTAGCCAAATAA
* * * * * * ** *
373852 CTCTATTCACATTAATAAAACTAAAGCTCTAGTTCTACT-AAGGTATCCTTAAACGGTAACCCTT
63 ATCTATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTC
* * * * * *
373916 TCTATCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAGGTAATCGAAATGGTTAG
128 ACTCTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAA-CTAAACGCTTAG
* *
373981 AATCAATCAAACACGGGGTGCA
192 AATCAATCAAACACAGAGTGCA
* * * * ** * *
374003 CAAGGTTCATGAAAAGTATTCGATGATACTCATGAAACCCTAAATCCT-CCAAGCCAAATAACTC
1 CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
* * * * *
374067 TATTCACATTAACAAAGCTACATCTCAGGTTTTACTAAAGGTATTCTTAAACCATTACCCTCCTC
66 TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCT-CAC
* * * * * *
374132 GTTCTCAACAATCACCATAACAACTATAATTCTGAAA-CATTCGATAAAGTAATTGAAACACTTA
130 --TCTCATCAAACACCATAACAACTACAATTC-CAAACCATTCGATAAAGTAACT-AAACGCTTA
*
374196 GAATCAATCAAACACAAAGTGCA
191 GAATCAATCAAACACAGAGTGCA
* *
374219 AAAGGTTCATAAAAAACATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
1 CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
*
374284 TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTGTCCTTAAACCATAACCCTCACT
66 TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACT
* * * * *
374349 CTCGTCAAACACCATAACAACTACAACTCCAAACCACTGGATAAAGTACCCTAAACGCTTAGAAT
131 CTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTA-ACTAAACGCTTAGAAT
* *
374414 CAATTAAACACAGAATGCA
195 CAATCAAACACAGAGTGCA
** * * * *
374433 TGAGGTTCACAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTACCTAGCCAAATAACTT
1 CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
* * * * * *
374498 TATTCTCATTAACAAAGCTACAACTCTGGTTTCACTAAAAGTATCCTTAAACCATAGCCCTCGCT
66 TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACT
* * * * * *
374563 CTCATCAAACACCATAACAGCTACAATTCCGAACCACTCGATAAAGTAACCGAAAAGCCTAGAAT
131 CTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAA-CTAAACGCTTAGAAT
* *
374628 CAATCAAACACAGGGTTCA
195 CAATCAAACACAGAGTGCA
* *
374647 CAGGGTTCATAAAAAGCATTTGAGGATAATCACAAAACCCTAAATCCTCCCTAGCC----AAA--
1 CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
* * *
374706 -A---ACATTAACAAAGTTACATCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCGCT
66 TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACT
* * * * *
374767 TTCATCAAACACCATAACAACTATAATTCCAAACCATTCAATAATGTAATTGAAACGCTTAGAAT
131 CTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAACT-AAACGCTTAGAAT
* **
374832 CAAACAAACATGGAGTGCA
195 CAATCAAACACAGAGTGCA
* * *
374851 CGAGTTTCATAAAAAGCATTCGAGGATAATAACAAAACCCTAAATCCTCCCTAG-CAAGAT--AT
1 CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAA-ATAAAT
* * * * *
374913 CTACTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAAGTATCCTTTAACCATGACCGTCAC
65 CTATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCAC
** * ** * * * * *
374978 TCGAATCAAACACCGTATTAACTATAATTCCGAACCATTTGATAAAGTAATTGAAACACTTAGAA
130 TCTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAACT-AAACGCTTAGAA
* *
375043 TTAATCAAACAAAGAG
194 TCAATCAAACACAGAG
375059 CGTGCGAGGC
Statistics
Matches: 886, Mismatches: 145, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
203 1 0.00
204 170 0.19
206 1 0.00
207 1 0.00
209 1 0.00
210 2 0.00
212 162 0.18
213 57 0.06
214 309 0.35
215 1 0.00
216 108 0.12
217 73 0.08
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (213 bp):
CAAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATC
TATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACT
CTCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAACTAAACGCTTAGAATC
AATCAAACACAGAGTGCA
Found at i:374830 original size:418 final size:420
Alignment explanation
Indices: 373791--375053 Score: 1427
Period size: 418 Copynumber: 3.0 Consensus size: 420
373781 CGGAGAGTGC
* *
373791 AAGGTTCATAAAAAGA-GTTC-ATGGATAACCAC-AAACTCCTAAATCCTCCCTAGCCAAATAAC
1 AAGGTTCATAAAAA-ACATTCGA-GGATAATCACAAAAC-CCTAAATCCTCCCTAGCC-AA-AA-
* * * * * ** **
373853 TCTATTCACATTAATAAAACTAAAGCTCTAGTTCTACT-AAGGTATCCTTAAACGGTAACCCTTT
60 --TA-T-ACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCA
* * * *
373917 CTATCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAGGTAATCGAAATGGTTAGA
121 CTATCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAATTGAAACGCTTAGA
* * * * * * **
373982 ATCAATCAAACACGGGGTGCACAAGGTTCATGAAAAGTATTCGATGATACTCATGAAACCCTAAA
186 ATCAATCAAACACGGAGTGCACGAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAA
* * * * *
374047 TCCTCCAAGCCAAATAACTCTATTCACATTAACAAAGCTACATCTCAGGTTTTACTAAAGGTATT
251 TCCTCCTAGCCAAATAACTCTATTCACATTAACAAAGCTACAACTCTGGTTTTACTAAAAGTATC
* * * * * *
374112 CTTAAACCATTACCCTCCTCGTTCTCAACAATCACCATAACAACTATAATTCTGAAACATTCGAT
316 CTTAAACCA-TA-GC-CCTCGCTCTCATCAAACACCATAACAACTATAATTCCGAACCATTCGAT
374177 AAAGTAATTGAAACACTTAGAATCAATCAAACACAAAGTGCAA
378 AAAGTAATTGAAACACTTAGAATCAATCAAACACAAAGTGCAA
374220 AAGGTTCATAAAAAACATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAATAAATCT
1 AAGGTTCATAAAAAACATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCC--A-AAA--T
* *
374285 ATTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTGTCCTTAAACCATAACCCTCACTC
61 A-T-ACATTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACTA
* * * * **
374350 TCGTCAAACACCATAACAACTACAACTCCAAACCACTGGATAAAGTACCCT-AAACGCTTAGAAT
124 TCATCAAACACCATAACAACTACAATTCCAAACCATTCGATAAAGTA-ATTGAAACGCTTAGAAT
* * * * *
374414 CAATTAAACACAGAATGCATGAGGTTCACAAAAAGCATTCGAGGATAATCACAAAACCCTAAATC
188 CAATCAAACACGGAGTGCACGAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATC
* * *
374479 CTACCTAGCCAAATAACTTTATTCTCATTAACAAAGCTACAACTCTGGTTTCACTAAAAGTATCC
253 CT-CCTAGCCAAATAACTCTATTCACATTAACAAAGCTACAACTCTGGTTTTACTAAAAGTATCC
* * *
374544 TTAAACCATAGCCCTCGCTCTCATCAAACACCATAACAGCTACAATTCCGAACCACTCGATAAAG
317 TTAAACCATAGCCCTCGCTCTCATCAAACACCATAACAACTATAATTCCGAACCATTCGATAAAG
** * ** * *
374609 TAACCGAAA-AGCCTAGAATCAATCAAACACAGGGTTCAC
382 TAATTGAAACA-CTTAGAATCAATCAAACACAAAGTGCAA
* * *
374648 AGGGTTCATAAAAAGCATTTGAGGATAATCACAAAACCCTAAATCCTCCCTAGCC-AAA-A-ACA
1 AAGGTTCATAAAAAACATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAAATATACA
* * * *
374710 TTAACAAAGTTACATCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCGCTTTCATCAA
66 TTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACTATCATCAA
* * * *
374775 ACACCATAACAACTATAATTCCAAACCATTCAATAATGTAATTGAAACGCTTAGAATCAAACAAA
131 ACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAATTGAAACGCTTAGAATCAATCAAA
* * *
374840 CATGGAGTGCACGAGTTTCATAAAAAGCATTCGAGGATAATAACAAAACCCTAAATCCTCCCTAG
196 CACGGAGTGCACGAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCT-CCTAG
* * *
374905 -CAAGAT-A-TCTACTCACATTAACAAAGCTACAGCTCTGGTTTTACTAAAAGTATCCTTTAACC
260 CCAA-ATAACTCTATTCACATTAACAAAGCTACAACTCTGGTTTTACTAAAAGTATCCTTAAACC
* * ** * ** *
374967 AT-GACCGTCACTCGAATCAAACACCGTATTAACTATAATTCCGAACCATTTGATAAAGTAATTG
324 ATAG-CCCTCGCTCTCATCAAACACCATAACAACTATAATTCCGAACCATTCGATAAAGTAATTG
*
375031 AAACACTTAGAATTAATCAAACA
388 AAACACTTAGAATCAATCAAACA
375054 AAGAGCGTGC
Statistics
Matches: 713, Mismatches: 108, Indels: 39
0.83 0.13 0.05
Matches are distributed among these distances:
415 1 0.00
416 117 0.16
417 6 0.01
418 174 0.24
421 1 0.00
424 3 0.00
427 1 0.00
428 128 0.18
429 78 0.11
430 141 0.20
431 63 0.09
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.25
Consensus pattern (420 bp):
AAGGTTCATAAAAAACATTCGAGGATAATCACAAAACCCTAAATCCTCCCTAGCCAAAATATACA
TTAACAAAGCTACAGCTCTGGTTTTACTAAAGGTATCCTTAAACCATAACCCTCACTATCATCAA
ACACCATAACAACTACAATTCCAAACCATTCGATAAAGTAATTGAAACGCTTAGAATCAATCAAA
CACGGAGTGCACGAGGTTCATAAAAAGCATTCGAGGATAATCACAAAACCCTAAATCCTCCTAGC
CAAATAACTCTATTCACATTAACAAAGCTACAACTCTGGTTTTACTAAAAGTATCCTTAAACCAT
AGCCCTCGCTCTCATCAAACACCATAACAACTATAATTCCGAACCATTCGATAAAGTAATTGAAA
CACTTAGAATCAATCAAACACAAAGTGCAA
Found at i:377141 original size:25 final size:25
Alignment explanation
Indices: 377088--377141 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
377078 TGTTTCTTCT
* *
377088 TCTTCATTGTATTCAATATCCGTCT
1 TCTTCATTGTATTCAATATCCGACA
*
377113 TCTTCATTGTATTCAATATCCGAGA
1 TCTTCATTGTATTCAATATCCGACA
377138 TCTT
1 TCTT
377142 GAACAAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (25 bp):
TCTTCATTGTATTCAATATCCGACA
Found at i:377141 original size:28 final size:25
Alignment explanation
Indices: 377085--377134 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
377075 GCTTGTTTCT
377085 TCTTCTTCATTGTATTCAATATCCG
1 TCTTCTTCATTGTATTCAATATCCG
377110 TCTTCTTCATTGTATTCAATATCCG
1 TCTTCTTCATTGTATTCAATATCCG
377135 AGATCTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (25 bp):
TCTTCTTCATTGTATTCAATATCCG
Found at i:380907 original size:7 final size:7
Alignment explanation
Indices: 380895--380942 Score: 96
Period size: 7 Copynumber: 6.9 Consensus size: 7
380885 GTTTCTTTGT
380895 TGCTTCA
1 TGCTTCA
380902 TGCTTCA
1 TGCTTCA
380909 TGCTTCA
1 TGCTTCA
380916 TGCTTCA
1 TGCTTCA
380923 TGCTTCA
1 TGCTTCA
380930 TGCTTCA
1 TGCTTCA
380937 TGCTTC
1 TGCTTC
380943 CTCCCTTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (7 bp):
TGCTTCA
Found at i:381908 original size:20 final size:20
Alignment explanation
Indices: 381814--382182 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
381804 GATTTTCCAT
* ** *
381814 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
381834 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
381854 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
381874 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
381894 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
381914 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
381934 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
381954 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
381974 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
381994 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
382014 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
382034 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
382054 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
382074 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
382094 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
382114 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
382134 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
382154 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
382174 AATCACAAC
1 AATCGCAAC
382183 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:382895 original size:24 final size:24
Alignment explanation
Indices: 382856--382902 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
382846 AAATTTGGTC
382856 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
382880 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
382903 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:383094 original size:12 final size:12
Alignment explanation
Indices: 383077--383101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
383067 ATATAATCCT
383077 GAAGAAGAAAAA
1 GAAGAAGAAAAA
383089 GAAGAAGAAAAA
1 GAAGAAGAAAAA
383101 G
1 G
383102 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:385429 original size:19 final size:19
Alignment explanation
Indices: 385407--385712 Score: 338
Period size: 19 Copynumber: 17.4 Consensus size: 19
385397 CGGAAAATAC
*
385407 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
385426 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
* *
385440 AATCGTAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
385459 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
385473 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
385492 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
385511 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
385525 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
385544 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
385563 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
385577 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
385596 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
385615 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
385634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
385653 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
*
385667 AATCGCAATGCGATATGAA
1 AATCGCAATGCGAAATGAA
385686 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
385705 AATCGCAA
1 AATCGCAA
385713 CGAGATAATC
Statistics
Matches: 245, Mismatches: 17, Indels: 50
0.79 0.05 0.16
Matches are distributed among these distances:
14 44 0.18
15 4 0.02
16 15 0.06
17 16 0.07
18 4 0.02
19 162 0.66
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:385450 original size:33 final size:33
Alignment explanation
Indices: 385407--385734 Score: 154
Period size: 33 Copynumber: 9.5 Consensus size: 33
385397 CGGAAAATAC
385407 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAACGCGAAATGAAAATCCCAACGA-GAA
* * *
385440 AATCGTAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCCCAACGAGAA
* *
385473 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCCCAA--CG--A-GAA
* * * *
385511 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAACGCGA-AAT-GAAAATCCCAACGA-GAA
* * * *
385544 AATCGCAATGCGAAATGAAAAT-CGAACCGACAT
1 AATCGCAACGCGAAATGAAAATCCCAA-CGAGAA
* * *
385577 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACGCGAAATGAAAATC-CCA-ACG--A-GAA
* *
385615 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCCCAA--CG--A-GAA
*
385653 AATCGCAA--CGAAA-G--AATCGCAATGCGATATGAA
1 AATCGCAACGCGAAATGAAAATCCCAA--CG--A-GAA
* * *
385686 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCCCAACGAGAA
*
385719 AATCGCAATGCGAAAT
1 AATCGCAACGCGAAAT
385735 TATAAACGCA
Statistics
Matches: 244, Mismatches: 26, Indels: 50
0.76 0.08 0.16
Matches are distributed among these distances:
31 5 0.02
32 6 0.02
33 135 0.55
34 3 0.01
35 12 0.05
36 10 0.04
37 3 0.01
38 61 0.25
39 8 0.03
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCCCAACGAGAA
Found at i:385491 original size:52 final size:53
Alignment explanation
Indices: 385435--385712 Score: 347
Period size: 52 Copynumber: 5.2 Consensus size: 53
385425 AAATCCCAAC
* * *
385435 ATGAAAATCGTAACGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
385487 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
385539 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
385591 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
385648 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGATATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
385700 ATGAAAATCGCAA
1 ATGAAAATCGCAA
385713 CGAGATAATC
Statistics
Matches: 209, Mismatches: 11, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
51 2 0.01
52 169 0.81
53 2 0.01
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:385555 original size:71 final size:71
Alignment explanation
Indices: 385473--385712 Score: 346
Period size: 71 Copynumber: 3.4 Consensus size: 71
385463 GCAACGAGAG
*
385473 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
385538 AATGAA
66 AATGAA
* * *
385544 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
385604 TACGAAATGAA
61 TGCGAAATGAA
385615 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
*
385680 TATGAA
66 AATGAA
385686 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
385713 CGAGATAATC
Statistics
Matches: 149, Mismatches: 10, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 112 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:385751 original size:71 final size:71
Alignment explanation
Indices: 385407--385750 Score: 281
Period size: 71 Copynumber: 4.9 Consensus size: 71
385397 CGGAAAATAC
* * * * * *
385407 AATCGCAACGCGAAATGAAAATCCCAA-C-ATGAAAATCGTAACGCGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACCGA-GATAATCGCAATGCGAAATTAAAA-CGCAATGC
*
385468 G--A-GAG
64 GAAATGAA
* * * * *
385473 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
385534 GCGAAATGAA
62 GCGAAATGAA
* *
385544 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAA-CGCAATGCG
385608 AAATGAA
65 AAATGAA
* * * *
385615 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
*
385676 GCGATATGAA
62 GCGAAATGAA
*
385686 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAACGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTA-AAACGCAATGCG
385750 A
65 A
385751 TTTTCATTTC
Statistics
Matches: 228, Mismatches: 25, Indels: 45
0.77 0.08 0.15
Matches are distributed among these distances:
66 49 0.21
67 4 0.02
68 12 0.05
69 8 0.04
70 5 0.02
71 129 0.57
72 4 0.02
73 2 0.01
74 5 0.02
75 1 0.00
76 9 0.04
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAACGCAATGCGA
AATGAA
Found at i:385850 original size:19 final size:19
Alignment explanation
Indices: 385741--385842 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
385731 AAATTATAAA
385741 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
385760 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
385780 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
385796 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
385813 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
385832 CGCATTGCGAT
1 CGCATTGCGAT
385843 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:385968 original size:14 final size:14
Alignment explanation
Indices: 385949--385985 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
385939 CATCAATTAC
385949 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
385963 ACAAATCATCTTTT
1 ACAAATCAACTTTT
385977 ACAAATCAA
1 ACAAATCAA
385986 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:387963 original size:14 final size:14
Alignment explanation
Indices: 387944--388000 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
387934 GCGAAATGAA
*
387944 AATCGCAACGACAG
1 AATCGCAACGAAAG
387958 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
387975 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
387991 AATCGCAACG
1 AATCGCAACG
388001 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:387971 original size:33 final size:33
Alignment explanation
Indices: 387925--388017 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
387915 GCGAAACCAA
*
387925 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
387958 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
387991 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
388018 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:387982 original size:19 final size:19
Alignment explanation
Indices: 387888--388022 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
387878 TAGTTTACTT
* *
387888 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
387908 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
387927 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
387946 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
387960 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
387979 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
387993 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
388012 TCGCAATGCGA
1 TCGCAACGCGA
388023 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:388040 original size:19 final size:19
Alignment explanation
Indices: 388018--388146 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
388008 AAAATCGCAA
388018 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
388037 TGCGATCTT-G--T--AGT
1 TGCGATTTTGGTTTCGCGT
388051 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
388070 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
388084 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
388103 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
388122 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
388142 TGCGA
1 TGCGA
388147 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:388060 original size:33 final size:33
Alignment explanation
Indices: 388018--388109 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
388008 AAAATCGCAA
388018 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTAGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTAGT
*
388051 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTAGT
**
388084 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
388110 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTAGT
Found at i:388461 original size:93 final size:93
Alignment explanation
Indices: 388188--388657 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
388178 TTGAATGGAT
388188 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-ACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388251 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
388279 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388343 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
388371 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388436 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
388464 AAATTTACTTTCAACCAAAAGACAAAACAACGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388528 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
388556 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388621 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
388649 AAATTTACT
1 AAATTTACT
388658 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
90 10 0.03
91 25 0.07
92 169 0.45
93 169 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:388509 original size:185 final size:185
Alignment explanation
Indices: 388188--388657 Score: 901
Period size: 185 Copynumber: 2.6 Consensus size: 185
388178 TTGAATGGAT
388188 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-ACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388251 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
388316 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
388371 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
388436 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAACGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
388501 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
388556 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
388621 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
388658 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
183 34 0.12
184 2 0.01
185 233 0.82
186 14 0.05
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:390383 original size:14 final size:14
Alignment explanation
Indices: 390364--390439 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
390354 TTGAAATGAA
390364 AATCGCAACGAGAG
1 AATCGCAACGAGAG
390378 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
390395 ACAATCGCAACGCGAAATGAA
1 --AATCGCAA--CG--A-GAG
390416 AATCGCAACGAGAG
1 AATCGCAACGAGAG
390430 AATCGCAACG
1 AATCGCAACG
390440 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.38
15 1 0.02
16 5 0.10
17 3 0.06
19 20 0.38
21 1 0.02
22 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:390402 original size:19 final size:19
Alignment explanation
Indices: 390378--390461 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
390368 GCAACGAGAG
* *
390378 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
390397 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
390416 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
390430 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
390449 AATCGCAATGCGA
1 AATCGCAACGCGA
390462 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:390418 original size:52 final size:52
Alignment explanation
Indices: 390356--390461 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
390346 TCTTTTGGTT
* *
390356 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
390408 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
390460 GA
1 GA
390462 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:390492 original size:14 final size:14
Alignment explanation
Indices: 390473--390527 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
390463 TTTGGTTTCG
390473 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
390487 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
390506 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
390520 CGTTGCGA
1 CGTTGCGA
390528 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:390690 original size:33 final size:33
Alignment explanation
Indices: 390648--390718 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
390638 AATACTAACT
*
390648 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
390681 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
390714 TGAAA
1 TGAAA
390719 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:390952 original size:22 final size:22
Alignment explanation
Indices: 390900--390954 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
390890 TGGTTGTGAG
**
390900 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
390922 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
390944 GGATTTCTTCG
1 GGATTTCTTCG
390955 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:391124 original size:20 final size:20
Alignment explanation
Indices: 391099--391292 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
391089 CTTTAAATAT
391099 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
391119 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
391141 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
391160 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
391180 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
391200 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
391220 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
391240 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
391260 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
391280 CGCGTTGCGATTT
1 CGCGTTGCGATTT
391293 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:391286 original size:60 final size:60
Alignment explanation
Indices: 391099--391292 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
391089 CTTTAAATAT
**
391099 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
391160 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
391220 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
391280 CGCGTTGCGATTT
1 CGCGTTGCGATTT
391293 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:391309 original size:21 final size:20
Alignment explanation
Indices: 391285--391361 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
391275 ATATTCGCGT
391285 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
391306 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
391326 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
391348 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
391362 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:391372 original size:20 final size:20
Alignment explanation
Indices: 391347--391398 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
391337 AAGAATCGCG
*
391347 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
391367 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
391387 TTGCGATTCTGG
1 TTGCGATTCTGG
391399 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:392834 original size:20 final size:21
Alignment explanation
Indices: 392797--392840 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
392787 AAAGATTTTT
*
392797 AATATATTTTTATAATATTAA
1 AATATATTATTATAATATTAA
392818 AATATATTATT-TAATATTAA
1 AATATATTATTATAATATTAA
392838 AAT
1 AAT
392841 TATAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATTATTATAATATTAA
Found at i:392934 original size:43 final size:44
Alignment explanation
Indices: 392815--392926 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 44
392805 TTTATAATAT
* *
392815 TAAAATATATTA-TTTAA-TA-TTA-AAATTATAATAAATTATTA
1 TAAAATATATTATTTTAATTATTTATAAA-AATAATAAATAATTA
*
392856 TAAAATTTATTATTTTAATTATTTATAAAAATAATAAATAATTA
1 TAAAATATATTATTTTAATTATTTATAAAAATAATAAATAATTA
*
392900 T-AAATATATTATTTTAATTGTTT-TAAA
1 TAAAATATATTATTTTAATTATTTATAAA
392927 TATTAATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 11 0.18
42 9 0.15
43 22 0.35
44 17 0.27
45 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (44 bp):
TAAAATATATTATTTTAATTATTTATAAAAATAATAAATAATTA
Done.